diff --git a/example_workflows/arithmetic/aiida.ipynb b/example_workflows/arithmetic/aiida.ipynb index 3e7dcd9..c95e15e 100644 --- a/example_workflows/arithmetic/aiida.ipynb +++ b/example_workflows/arithmetic/aiida.ipynb @@ -1,26 +1,38 @@ { + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat_minor": 4, + "nbformat": 4, "cells": [ { "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Aiida" - ] + "source": "# Aiida", + "metadata": {} }, { "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Define workflow with aiida" - ] + "source": "## Define workflow with aiida", + "metadata": {} }, { "cell_type": "code", - "execution_count": 1, - "metadata": { - "trusted": true - }, - "outputs": [], "source": [ "from python_workflow_definition.aiida import write_workflow_json\n", "\n", @@ -29,104 +41,76 @@ "load_profile()\n", "\n", "workflow_json_filename = \"aiida_simple.json\"" - ] + ], + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 1 }, { "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], "source": [ "from workflow import (\n", " get_sum as _get_sum,\n", " get_prod_and_div as _get_prod_and_div,\n", " get_square as _get_square,\n", ")" - ] + ], + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 2 }, { "cell_type": "code", - "execution_count": null, - "metadata": {}, + "source": "wg = WorkGraph(\"arithmetic\")", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "wg = WorkGraph(\"arithmetic\")" - ] + "execution_count": 3 }, { "cell_type": "code", - "execution_count": 4, + "source": "get_prod_and_div_task = wg.add_task(\n task(outputs=['prod', 'div'])(_get_prod_and_div),\n x=orm.Float(1),\n y=orm.Float(2),\n)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "get_prod_and_div_task = wg.add_task(\n", - " task(outputs=['prod', 'div'])(_get_prod_and_div),\n", - " x=orm.Float(1),\n", - " y=orm.Float(2),\n", - ")" - ] + "execution_count": 4 }, { "cell_type": "code", - "execution_count": null, + "source": "get_sum_task = wg.add_task(\n _get_sum,\n x=get_prod_and_div_task.outputs.prod,\n y=get_prod_and_div_task.outputs.div,\n)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "get_sum_task = wg.add_task(\n", - " _get_sum,\n", - " x=get_prod_and_div_task.outputs.prod,\n", - " y=get_prod_and_div_task.outputs.div,\n", - ")" - ] + "execution_count": 5 }, { "cell_type": "code", - "execution_count": null, - "metadata": {}, + "source": "get_square_task = wg.add_task(\n _get_square,\n x=get_sum_task.outputs.result,\n)", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "get_square_task = wg.add_task(\n", - " _get_square,\n", - " x=get_sum_task.outputs.result,\n", - ")" - ] + "execution_count": 6 }, { "cell_type": "code", - "execution_count": 6, + "source": "write_workflow_json(wg=wg, file_name=workflow_json_filename)", "metadata": { "trusted": true }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'nodes': [{'id': 0, 'function': 'arithmetic_workflow.get_prod_and_div'},\n", - " {'id': 1, 'function': 'arithmetic_workflow.get_sum'},\n", - " {'id': 2, 'value': 1.0},\n", - " {'id': 3, 'value': 2.0}],\n", - " 'edges': [{'target': 1, 'targetPort': 'x', 'source': 0, 'sourcePort': 'prod'},\n", - " {'target': 1, 'targetPort': 'y', 'source': 0, 'sourcePort': 'div'},\n", - " {'target': 0, 'targetPort': 'x', 'source': 2, 'sourcePort': None},\n", - " {'target': 0, 'targetPort': 'y', 'source': 3, 'sourcePort': None}]}" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "write_workflow_json(wg=wg, file_name=workflow_json_filename)" - ] + "outputs": [], + "execution_count": 7 }, { "cell_type": "code", - "execution_count": 7, + "source": "!cat {workflow_json_filename}", "metadata": { "trusted": true }, @@ -134,114 +118,46 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "{\n", - " \"nodes\": [\n", - " {\n", - " \"id\": 0,\n", - " \"function\": \"arithmetic_workflow.get_prod_and_div\"\n", - " },\n", - " {\n", - " \"id\": 1,\n", - " \"function\": \"arithmetic_workflow.get_sum\"\n", - " },\n", - " {\n", - " \"id\": 2,\n", - " \"value\": 1.0\n", - " },\n", - " {\n", - " \"id\": 3,\n", - " \"value\": 2.0\n", - " }\n", - " ],\n", - " \"edges\": [\n", - " {\n", - " \"target\": 1,\n", - " \"targetPort\": \"x\",\n", - " \"source\": 0,\n", - " \"sourcePort\": \"prod\"\n", - " },\n", - " {\n", - " \"target\": 1,\n", - " \"targetPort\": \"y\",\n", - " \"source\": 0,\n", - " \"sourcePort\": \"div\"\n", - " },\n", - " {\n", - " \"target\": 0,\n", - " \"targetPort\": \"x\",\n", - " \"source\": 2,\n", - " \"sourcePort\": null\n", - " },\n", - " {\n", - " \"target\": 0,\n", - " \"targetPort\": \"y\",\n", - " \"source\": 3,\n", - " \"sourcePort\": null\n", - " }\n", - " ]\n", - "}" - ] + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.get_prod_and_div\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.get_sum\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.get_square\"\n },\n {\n \"id\": 3,\n \"type\": \"input\",\n \"name\": \"x\",\n \"value\": 1.0\n },\n {\n \"id\": 4,\n \"type\": \"input\",\n \"name\": \"y\",\n \"value\": 2.0\n },\n {\n \"id\": 5,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 1,\n \"targetPort\": \"x\",\n \"source\": 0,\n \"sourcePort\": \"prod\"\n },\n {\n \"target\": 1,\n \"targetPort\": \"y\",\n \"source\": 0,\n \"sourcePort\": \"div\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"x\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"x\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"y\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": null,\n \"source\": 2,\n \"sourcePort\": null\n }\n ]\n}" } ], - "source": [ - "!cat {workflow_json_filename}" - ] + "execution_count": 8 }, { "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Load Workflow with jobflow" - ] + "source": "## Load Workflow with jobflow", + "metadata": {} }, { "cell_type": "code", - "execution_count": 8, + "source": "from python_workflow_definition.jobflow import load_workflow_json", "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"cipher\": algorithms.TripleDES,\n", - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"class\": algorithms.TripleDES,\n" - ] - } - ], - "source": [ - "from python_workflow_definition.jobflow import load_workflow_json" - ] + "outputs": [], + "execution_count": 9 }, { "cell_type": "code", - "execution_count": 9, + "source": "from jobflow.managers.local import run_locally", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from jobflow.managers.local import run_locally" - ] + "execution_count": 10 }, { "cell_type": "code", - "execution_count": 10, + "source": "flow = load_workflow_json(file_name=workflow_json_filename)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "flow = load_workflow_json(file_name=workflow_json_filename)" - ] + "execution_count": 11 }, { "cell_type": "code", - "execution_count": 11, + "source": "result = run_locally(flow)\nresult", "metadata": { "trusted": true }, @@ -249,148 +165,54 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "2025-04-23 09:27:52,129 INFO Started executing jobs locally\n", - "2025-04-23 09:27:52,561 INFO Starting job - get_prod_and_div (6eae194f-04a4-4c7c-b0d9-baf624bac375)\n", - "2025-04-23 09:27:52,564 INFO Finished job - get_prod_and_div (6eae194f-04a4-4c7c-b0d9-baf624bac375)\n", - "2025-04-23 09:27:52,564 INFO Starting job - get_sum (21fda98d-7701-45c7-a30a-816e9a91ab75)\n", - "2025-04-23 09:27:52,566 INFO Finished job - get_sum (21fda98d-7701-45c7-a30a-816e9a91ab75)\n", - "2025-04-23 09:27:52,566 INFO Finished executing jobs locally\n" - ] + "text": "2025-05-24 05:37:36,950 INFO Started executing jobs locally\n2025-05-24 05:37:37,216 INFO Starting job - get_prod_and_div (3ea26df7-3e4f-4541-a399-52684f0d763e)\n2025-05-24 05:37:37,218 INFO Finished job - get_prod_and_div (3ea26df7-3e4f-4541-a399-52684f0d763e)\n2025-05-24 05:37:37,219 INFO Starting job - get_sum (8d0957e4-21b1-433e-8e9a-b2af7b2d9b6d)\n2025-05-24 05:37:37,220 INFO Finished job - get_sum (8d0957e4-21b1-433e-8e9a-b2af7b2d9b6d)\n2025-05-24 05:37:37,221 INFO Starting job - get_square (af8ae958-4ce4-4b1f-a5df-eb7768a9aa86)\n2025-05-24 05:37:37,223 INFO Finished job - get_square (af8ae958-4ce4-4b1f-a5df-eb7768a9aa86)\n2025-05-24 05:37:37,223 INFO Finished executing jobs locally\n" }, { + "execution_count": 12, + "output_type": "execute_result", "data": { - "text/plain": [ - "{'6eae194f-04a4-4c7c-b0d9-baf624bac375': {1: Response(output={'prod': 2.0, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n", - " '21fda98d-7701-45c7-a30a-816e9a91ab75': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" - ] + "text/plain": "{'3ea26df7-3e4f-4541-a399-52684f0d763e': {1: Response(output={'prod': 2.0, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n '8d0957e4-21b1-433e-8e9a-b2af7b2d9b6d': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n 'af8ae958-4ce4-4b1f-a5df-eb7768a9aa86': {1: Response(output=6.25, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))}}" }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "result = run_locally(flow)\n", - "result" - ] + "execution_count": 12 }, { "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Load Workflow with pyiron_base" - ] + "source": "## Load Workflow with pyiron_base", + "metadata": {} }, { "cell_type": "code", - "execution_count": 12, + "source": "from python_workflow_definition.pyiron_base import load_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.pyiron_base import load_workflow_json" - ] + "execution_count": 13 }, { "cell_type": "code", - "execution_count": 13, + "source": "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, "outputs": [ { + "output_type": "display_data", "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "create_function_job_92b349b68e1d28facd2c0cc67fea0894\n", - "\n", - "create_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7407d4c7d100>\n", - "\n", - "\n", - "\n", - "x_c8e04d7c4ce41e51517caabdd70267c4\n", - "\n", - "x=<pyiron_base.project.delayed.DelayedObject object at 0x7407ca519a90>\n", - "\n", - "\n", - "\n", - "x_c8e04d7c4ce41e51517caabdd70267c4->create_function_job_92b349b68e1d28facd2c0cc67fea0894\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "x_974924ff998969b91bfc8b2db5f854a1\n", - "\n", - "x=1.0\n", - "\n", - "\n", - "\n", - "x_974924ff998969b91bfc8b2db5f854a1->x_c8e04d7c4ce41e51517caabdd70267c4\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_6c83c1caef87634071eb9102b68e73cf\n", - "\n", - "y=<pyiron_base.project.delayed.DelayedObject object at 0x7407bf835610>\n", - "\n", - "\n", - "\n", - "x_974924ff998969b91bfc8b2db5f854a1->y_6c83c1caef87634071eb9102b68e73cf\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_6c83c1caef87634071eb9102b68e73cf->create_function_job_92b349b68e1d28facd2c0cc67fea0894\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_f12a7f1986b9dd058dfc666dbe230b20\n", - "\n", - "y=2.0\n", - "\n", - "\n", - "\n", - "y_f12a7f1986b9dd058dfc666dbe230b20->x_c8e04d7c4ce41e51517caabdd70267c4\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_f12a7f1986b9dd058dfc666dbe230b20->y_6c83c1caef87634071eb9102b68e73cf\n", - "\n", - "\n", - "\n", - "\n", - "" - ], - "text/plain": [ - "" - ] + "text/plain": "", + "image/svg+xml": "\n\n\n\n\ncreate_function_job_9e748c1c8cdef9464869503612dbb8dd\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7960e32575c0>\n\n\n\nx_a067a96e1de754e11581b419c5c1d4dd\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x7960e3257350>\n\n\n\nx_a067a96e1de754e11581b419c5c1d4dd->create_function_job_9e748c1c8cdef9464869503612dbb8dd\n\n\n\n\n\nx_e71e72d9c42ba1008579078b6c079655\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x7960ec8cc9b0>\n\n\n\nx_e71e72d9c42ba1008579078b6c079655->x_a067a96e1de754e11581b419c5c1d4dd\n\n\n\n\n\nx_974924ff998969b91bfc8b2db5f854a1\n\nx=1.0\n\n\n\nx_974924ff998969b91bfc8b2db5f854a1->x_e71e72d9c42ba1008579078b6c079655\n\n\n\n\n\ny_49c159de63f318f02b04278442feee05\n\ny=<pyiron_base.project.delayed.DelayedObject object at 0x7960e3257020>\n\n\n\nx_974924ff998969b91bfc8b2db5f854a1->y_49c159de63f318f02b04278442feee05\n\n\n\n\n\ny_49c159de63f318f02b04278442feee05->x_a067a96e1de754e11581b419c5c1d4dd\n\n\n\n\n\ny_f12a7f1986b9dd058dfc666dbe230b20\n\ny=2.0\n\n\n\ny_f12a7f1986b9dd058dfc666dbe230b20->x_e71e72d9c42ba1008579078b6c079655\n\n\n\n\n\ny_f12a7f1986b9dd058dfc666dbe230b20->y_49c159de63f318f02b04278442feee05\n\n\n\n\n" }, - "metadata": {}, - "output_type": "display_data" + "metadata": {} } ], - "source": [ - "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n", - "delayed_object_lst[-1].draw()" - ] + "execution_count": 14 }, { "cell_type": "code", - "execution_count": 14, + "source": "delayed_object_lst[-1].pull()", "metadata": { "trusted": true }, @@ -398,46 +220,18 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "The job get_prod_and_div_7c19c6233dddb02781fc331f609558a1 was saved and received the ID: 1\n", - "The job get_sum_92b8e0a2d45fff6b04940562a8d7d8f7 was saved and received the ID: 2\n" - ] + "text": "The job get_prod_and_div_4729edf2c689ca4cf512acd163c98b28 was saved and received the ID: 1\nThe job get_sum_25f72a559657d0b1549593792391953e was saved and received the ID: 2\nThe job get_square_9cc2f0545498916d7720c59c1120a66d was saved and received the ID: 3\n" }, { + "execution_count": 15, + "output_type": "execute_result", "data": { - "text/plain": [ - "2.5" - ] + "text/plain": "6.25" }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "delayed_object_lst[-1].pull()" - ] + "execution_count": 15 } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.8" - } - }, - "nbformat": 4, - "nbformat_minor": 4 + ] } diff --git a/example_workflows/arithmetic/cwl.ipynb b/example_workflows/arithmetic/cwl.ipynb index b83e6a0..9912fa9 100644 --- a/example_workflows/arithmetic/cwl.ipynb +++ b/example_workflows/arithmetic/cwl.ipynb @@ -62,7 +62,7 @@ { "name": "stdout", "output_type": "stream", - "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/0xeme5n4/stgba321752-0a06-41dd-95c0-f5890f1dfaae/workflow.py \\\n --function=workflow.get_prod_and_div \\\n --arg_y=/tmp/0xeme5n4/stg9f21530f-2f98-44e6-80b6-afa2aac5a083/y.pickle \\\n --arg_x=/tmp/0xeme5n4/stg2e35a78a-a776-48de-b82f-8075d3284a3c/x.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/u07nctrs$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/sa53wz5h/stg686b1324-0030-4bfd-bdab-64fc9ee4d491/workflow.py \\\n --function=workflow.get_sum \\\n --arg_y=/tmp/sa53wz5h/stg1679a702-ac89-4c84-8cb5-7a57ae9e1834/div.pickle \\\n --arg_x=/tmp/sa53wz5h/stg6ab588fe-2723-416e-a7b8-648b1a63406e/prod.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" + "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/_1apt559$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/dyuxg6ka/stgf337bac5-2f8e-4489-bd51-83491b1d5f0e/workflow.py \\\n --function=workflow.get_prod_and_div \\\n --arg_x=/tmp/dyuxg6ka/stgd87c2fe4-ca8e-4031-9af0-751d6944cbe7/x.pickle \\\n --arg_y=/tmp/dyuxg6ka/stg7bcb8ced-0e5b-442e-a0e0-2b3117afe2d8/y.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/ysau_yra$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/rm6c9qek/stgfef68b90-5d69-4da9-a952-b9c2f2a1eb76/workflow.py \\\n --function=workflow.get_sum \\\n --arg_x=/tmp/rm6c9qek/stg35728be7-5a6d-487b-bd02-345581007663/prod.pickle \\\n --arg_y=/tmp/rm6c9qek/stgc0992786-237e-4308-9d9e-814ebbfb0319/div.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_square_2\n\u001B[1;30mINFO\u001B[0m [step get_square_2] start\n\u001B[1;30mINFO\u001B[0m [job get_square_2] /tmp/o3gzya8t$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/6a3sltnz/stg58ccf048-a5c3-4ba3-a24f-c64adfff84cd/workflow.py \\\n --function=workflow.get_square \\\n --arg_x=/tmp/6a3sltnz/stg70203cec-cbd4-4fea-a3de-70e9373d9c9d/result.pickle\n\u001B[1;30mINFO\u001B[0m [job get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [step get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$1fd8f217331336b1226b84e351c56fb9a8d93685\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" } ], "execution_count": 4 @@ -78,7 +78,7 @@ { "name": "stdout", "output_type": "stream", - "text": "2.5\n" + "text": "6.25\n" } ], "execution_count": 5 diff --git a/example_workflows/arithmetic/jobflow.ipynb b/example_workflows/arithmetic/jobflow.ipynb index 58c782d..afe56ae 100644 --- a/example_workflows/arithmetic/jobflow.ipynb +++ b/example_workflows/arithmetic/jobflow.ipynb @@ -1,42 +1,53 @@ { + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat_minor": 5, + "nbformat": 4, "cells": [ { - "cell_type": "markdown", "id": "982a4fbe-7cf9-45dd-84ae-9854149db0b9", - "metadata": {}, - "source": [ - "# jobflow" - ] + "cell_type": "markdown", + "source": "# jobflow", + "metadata": {} }, { - "cell_type": "markdown", "id": "e6180712-d081-45c7-ba41-fc5191f10427", - "metadata": {}, - "source": [ - "## Define workflow with jobflow\n", - "\n", - "This tutorial will demonstrate how to use the PWD with `jobflow` and load the workflow with `aiida` and `pyiron`.\n", - "\n", - "[`jobflow`](https://joss.theoj.org/papers/10.21105/joss.05995) was developed to simplify the development of high-throughput workflows. It uses a decorator-based approach to define the “Job“s that can be connected to form complex workflows (“Flow“s). `jobflow` is the workflow language of the workflow library [`atomate2`](https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9), designed to replace [atomate](https://www.sciencedirect.com/science/article/pii/S0927025617303919), which was central to the development of the [Materials Project](https://pubs.aip.org/aip/apm/article/1/1/011002/119685/Commentary-The-Materials-Project-A-materials) database." - ] + "cell_type": "markdown", + "source": "## Define workflow with jobflow\n\nThis tutorial will demonstrate how to use the PWD with `jobflow` and load the workflow with `aiida` and `pyiron`.\n\n[`jobflow`](https://joss.theoj.org/papers/10.21105/joss.05995) was developed to simplify the development of high-throughput workflows. It uses a decorator-based approach to define the “Job“s that can be connected to form complex workflows (“Flow“s). `jobflow` is the workflow language of the workflow library [`atomate2`](https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9), designed to replace [atomate](https://www.sciencedirect.com/science/article/pii/S0927025617303919), which was central to the development of the [Materials Project](https://pubs.aip.org/aip/apm/article/1/1/011002/119685/Commentary-The-Materials-Project-A-materials) database.", + "metadata": {} }, { - "cell_type": "markdown", "id": "69bedfb9ec12c092", + "cell_type": "markdown", + "source": "First, we start by importing the job decorator and the Flow class from jobflow, as welll as the necessary modules from the python workflow definition and the example arithmetic workflow.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "First, we start by importing the job decorator and the Flow class from jobflow, as welll as the necessary modules from the python workflow definition and the example arithmetic workflow." - ] + } }, { - "cell_type": "code", - "execution_count": 1, "id": "000bbd4a-f53c-4eea-9d85-76f0aa2ca10b", + "cell_type": "code", + "source": "from jobflow import job, Flow", "metadata": { "ExecuteTime": { "end_time": "2025-04-24T12:51:34.747117656Z", @@ -44,67 +55,44 @@ }, "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"cipher\": algorithms.TripleDES,\n", - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"class\": algorithms.TripleDES,\n" - ] - } - ], - "source": [ - "from jobflow import job, Flow" - ] + "outputs": [], + "execution_count": 1 }, { - "cell_type": "code", - "execution_count": 2, "id": "06c2bd9e-b2ac-4b88-9158-fa37331c3418", + "cell_type": "code", + "source": "from python_workflow_definition.jobflow import write_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.jobflow import write_workflow_json" - ] + "execution_count": 2 }, { - "cell_type": "code", - "execution_count": null, "id": "f9217ce7b093b5fc", + "cell_type": "code", + "source": "from workflow import (\n get_sum as _get_sum,\n get_prod_and_div as _get_prod_and_div,\n get_square as _get_square,\n)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from workflow import (\n", - " get_sum as _get_sum,\n", - " get_prod_and_div as _get_prod_and_div,\n", - " get_square as _get_square,\n", - ")" - ] + "execution_count": 3 }, { - "cell_type": "markdown", "id": "2639deadfae9c591", + "cell_type": "markdown", + "source": "Using the job object decorator, the imported functions from the arithmetic workflow are transformed into jobflow “Job”s. These “Job”s can delay the execution of Python functions and can be chained into workflows (“Flow”s). A “Job” can return serializable outputs (e.g., a number, a dictionary, or a Pydantic model) or a so-called “Response” object, which enables the execution of dynamic workflows where the number of nodes is not known prior to the workflow’s execution. ", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "Using the job object decorator, the imported functions from the arithmetic workflow are transformed into jobflow “Job”s. These “Job”s can delay the execution of Python functions and can be chained into workflows (“Flow”s). A “Job” can return serializable outputs (e.g., a number, a dictionary, or a Pydantic model) or a so-called “Response” object, which enables the execution of dynamic workflows where the number of nodes is not known prior to the workflow’s execution. " - ] + } }, { - "cell_type": "code", - "execution_count": 4, "id": "1feba0898ee4e361", + "cell_type": "code", + "source": "workflow_json_filename = \"jobflow_simple.json\"", "metadata": { "ExecuteTime": { "end_time": "2025-04-24T10:30:04.751088Z", @@ -113,101 +101,83 @@ "trusted": true }, "outputs": [], - "source": [ - "workflow_json_filename = \"jobflow_simple.json\"" - ] + "execution_count": 4 }, { - "cell_type": "code", - "execution_count": null, "id": "07598344-0f75-433b-8902-bea21a42088c", + "cell_type": "code", + "source": "get_sum = job(_get_sum)\n# Note: one could also transfer the outputs to the datastore as well: get_prod_and_div = job(_get_prod_and_div, data=[\"prod\", \"div\"])\n# On the way from the general definition to the jobflow definition, we do this automatically to avoid overflow databases.\nget_prod_and_div = job(_get_prod_and_div)\nget_square = job(_get_square)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "get_sum = job(_get_sum)\n", - "# Note: one could also transfer the outputs to the datastore as well: get_prod_and_div = job(_get_prod_and_div, data=[\"prod\", \"div\"])\n", - "# On the way from the general definition to the jobflow definition, we do this automatically to avoid overflow databases.\n", - "get_prod_and_div = job(_get_prod_and_div)\n", - "get_square = job(_get_square)" - ] + "execution_count": 5 }, { - "cell_type": "code", - "execution_count": null, "id": "ecef1ed5-a8d3-48c3-9e01-4a40e55c1153", + "cell_type": "code", + "source": "prod_and_div = get_prod_and_div(x=1, y=2)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "prod_and_div = get_prod_and_div(x=1, y=2)" - ] + "execution_count": 6 }, { - "cell_type": "code", - "execution_count": null, "id": "2b88a30a-e26b-4802-89b7-79ca08cc0af9", + "cell_type": "code", + "source": "tmp_sum = get_sum(x=prod_and_div.output.prod, y=prod_and_div.output.div)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "tmp_sum = get_sum(x=prod_and_div.output.prod, y=prod_and_div.output.div)" - ] + "execution_count": 7 }, { - "cell_type": "code", - "execution_count": null, "id": "8d95c3aa", - "metadata": {}, + "cell_type": "code", + "source": "result = get_square(x=tmp_sum.output)", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "result = get_square(x=tmp_sum.output)" - ] + "execution_count": 8 }, { - "cell_type": "code", - "execution_count": null, "id": "a5e5ca63-2906-47c9-bac6-adebf8643cba", + "cell_type": "code", + "source": "flow = Flow([prod_and_div, tmp_sum, result])", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "flow = Flow([prod_and_div, tmp_sum, result])" - ] + "execution_count": 9 }, { - "cell_type": "markdown", "id": "27688edd256f1420", + "cell_type": "markdown", + "source": "As jobflow itself is only a workflow language, the workflows are typically executed on high-performance computers with a workflow manager such as [Fireworks](https://onlinelibrary.wiley.com/doi/full/10.1002/cpe.3505) or [jobflow-remote](https://github.com/Matgenix/jobflow-remote). For smaller and test workflows, simple linear, non-parallel execution of the workflow graph can be performed with jobflow itself. All outputs of individual jobs are saved in a database. For high-throughput applications typically, a MongoDB database is used. For testing and smaller workflows, a memory database can be used instead.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "As jobflow itself is only a workflow language, the workflows are typically executed on high-performance computers with a workflow manager such as [Fireworks](https://onlinelibrary.wiley.com/doi/full/10.1002/cpe.3505) or [jobflow-remote](https://github.com/Matgenix/jobflow-remote). For smaller and test workflows, simple linear, non-parallel execution of the workflow graph can be performed with jobflow itself. All outputs of individual jobs are saved in a database. For high-throughput applications typically, a MongoDB database is used. For testing and smaller workflows, a memory database can be used instead." - ] + } }, { - "cell_type": "code", - "execution_count": 9, "id": "e464da97-16a1-4772-9a07-0a47f152781d", + "cell_type": "code", + "source": "write_workflow_json(flow=flow, file_name=workflow_json_filename)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "write_workflow_json(flow=flow, file_name=workflow_json_filename)" - ] + "execution_count": 10 }, { - "cell_type": "code", - "execution_count": 10, "id": "bca646b2-0a9a-4271-966a-e5903a8c9031", + "cell_type": "code", + "source": "!cat {workflow_json_filename}", "metadata": { "trusted": true }, @@ -215,134 +185,107 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "{\"nodes\": [{\"id\": 0, \"function\": \"workflow.get_prod_and_div\"}, {\"id\": 1, \"function\": \"workflow.get_sum\"}, {\"id\": 2, \"value\": 1}, {\"id\": 3, \"value\": 2}], \"edges\": [{\"target\": 0, \"targetPort\": \"x\", \"source\": 2, \"sourcePort\": null}, {\"target\": 0, \"targetPort\": \"y\", \"source\": 3, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"x\", \"source\": 0, \"sourcePort\": \"prod\"}, {\"target\": 1, \"targetPort\": \"y\", \"source\": 0, \"sourcePort\": \"div\"}]}" - ] + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.get_prod_and_div\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.get_sum\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.get_square\"\n },\n {\n \"id\": 3,\n \"type\": \"input\",\n \"name\": \"x\",\n \"value\": 1\n },\n {\n \"id\": 4,\n \"type\": \"input\",\n \"name\": \"y\",\n \"value\": 2\n },\n {\n \"id\": 5,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 0,\n \"targetPort\": \"x\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"y\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"x\",\n \"source\": 0,\n \"sourcePort\": \"prod\"\n },\n {\n \"target\": 1,\n \"targetPort\": \"y\",\n \"source\": 0,\n \"sourcePort\": \"div\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"x\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": null,\n \"source\": 2,\n \"sourcePort\": null\n }\n ]\n}" } ], - "source": [ - "!cat {workflow_json_filename}" - ] + "execution_count": 11 }, { - "cell_type": "markdown", "id": "65389ef27c38fdec", + "cell_type": "markdown", + "source": "Finally, you can write the workflow data into a JSON file to be imported later.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "Finally, you can write the workflow data into a JSON file to be imported later." - ] + } }, { - "cell_type": "markdown", "id": "87a27540-c390-4d34-ae75-4739bfc4c1b7", - "metadata": {}, - "source": [ - "## Load Workflow with aiida\n", - "\n", - "In this part, we will demonstrate how to import the `jobflow` workflow into `aiida` via the PWD." - ] + "cell_type": "markdown", + "source": "## Load Workflow with aiida\n\nIn this part, we will demonstrate how to import the `jobflow` workflow into `aiida` via the PWD.", + "metadata": {} }, { - "cell_type": "code", - "execution_count": 11, "id": "66a1b3a6-3d3b-4caa-b58f-d8bc089b1074", + "cell_type": "code", + "source": "from aiida import load_profile\n\nload_profile()", "metadata": { "trusted": true }, "outputs": [ { + "execution_count": 12, + "output_type": "execute_result", "data": { - "text/plain": [ - "Profile" - ] + "text/plain": "Profile" }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "from aiida import load_profile\n", - "\n", - "load_profile()" - ] + "execution_count": 12 }, { - "cell_type": "code", - "execution_count": 12, "id": "4679693b-039b-45cf-8c67-5b2b3d705a83", + "cell_type": "code", + "source": "from python_workflow_definition.aiida import load_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.aiida import load_workflow_json" - ] + "execution_count": 13 }, { - "cell_type": "markdown", "id": "cc7127193d31d8ef", + "cell_type": "markdown", + "source": "We import the necessary modules from `aiida` and the PWD, as well as the workflow JSON file.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "We import the necessary modules from `aiida` and the PWD, as well as the workflow JSON file." - ] + } }, { - "cell_type": "code", - "execution_count": 13, "id": "68c41a61-d185-47e8-ba31-eeff71d8b2c6", + "cell_type": "code", + "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg", "metadata": { "trusted": true }, "outputs": [ { + "execution_count": 14, + "output_type": "execute_result", "data": { + "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…", "application/vnd.jupyter.widget-view+json": { - "model_id": "2bbe8584e19148d79f7be020abafa3eb", "version_major": 2, - "version_minor": 1 - }, - "text/plain": [ - "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…" - ] + "version_minor": 1, + "model_id": "9f822f7ac5ca4cb9960374af471f79cf" + } }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "wg = load_workflow_json(file_name=workflow_json_filename)\n", - "wg" - ] + "execution_count": 14 }, { - "cell_type": "markdown", "id": "4816325767559bbe", + "cell_type": "markdown", + "source": "Finally, we are now able to run the workflow with `aiida`.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "Finally, we are now able to run the workflow with `aiida`." - ] + } }, { - "cell_type": "code", - "execution_count": 14, "id": "05228ece-643c-420c-8df8-4ce3df379515", + "cell_type": "code", + "source": "wg.run()", "metadata": { "trusted": true }, @@ -350,142 +293,50 @@ { "name": "stderr", "output_type": "stream", - "text": [ - "04/24/2025 02:55:50 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div1\n", - "04/24/2025 02:55:50 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: get_prod_and_div1, type: PyFunction, finished.\n", - "04/24/2025 02:55:50 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum2\n", - "04/24/2025 02:55:51 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: get_sum2, type: PyFunction, finished.\n", - "04/24/2025 02:55:51 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n", - "04/24/2025 02:55:51 PM <99> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|finalize]: Finalize workgraph.\n" - ] + "text": "05/24/2025 05:38:40 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div1\n05/24/2025 05:38:41 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: get_prod_and_div1, type: PyFunction, finished.\n05/24/2025 05:38:41 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum2\n05/24/2025 05:38:41 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: get_sum2, type: PyFunction, finished.\n05/24/2025 05:38:41 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_square3\n05/24/2025 05:38:42 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: get_square3, type: PyFunction, finished.\n05/24/2025 05:38:42 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:38:42 AM <306> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|finalize]: Finalize workgraph.\n" } ], - "source": [ - "wg.run()" - ] + "execution_count": 15 }, { - "cell_type": "markdown", "id": "2c942094-61b4-4e94-859a-64f87b5bec64", - "metadata": {}, - "source": [ - "## Load Workflow with pyiron_base\n", - "\n", - "In this part, we will demonstrate how to import the `jobflow` workflow into `pyiron` via the PWD." - ] + "cell_type": "markdown", + "source": "## Load Workflow with pyiron_base\n\nIn this part, we will demonstrate how to import the `jobflow` workflow into `pyiron` via the PWD.", + "metadata": {} }, { - "cell_type": "code", - "execution_count": 15, "id": "ea102341-84f7-4156-a7d1-c3ab1ea613a5", + "cell_type": "code", + "source": "from python_workflow_definition.pyiron_base import load_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.pyiron_base import load_workflow_json" - ] + "execution_count": 16 }, { - "cell_type": "code", - "execution_count": 16, "id": "8f2a621d-b533-4ddd-8bcd-c22db2f922ec", + "cell_type": "code", + "source": "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, "outputs": [ { + "output_type": "display_data", "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "create_function_job_c942e1812492f8750b853ea68445d43f\n", - "\n", - "create_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x719ee1a6ee70>\n", - "\n", - "\n", - "\n", - "x_5a41f1a01c281872a92d14b5bf806b3c\n", - "\n", - "x=<pyiron_base.project.delayed.DelayedObject object at 0x719ee39de8d0>\n", - "\n", - "\n", - "\n", - "x_5a41f1a01c281872a92d14b5bf806b3c->create_function_job_c942e1812492f8750b853ea68445d43f\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "x_1d847da32ecaabf6731c38f798c3d4ce\n", - "\n", - "x=1\n", - "\n", - "\n", - "\n", - "x_1d847da32ecaabf6731c38f798c3d4ce->x_5a41f1a01c281872a92d14b5bf806b3c\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_2f79d27085d95c7ddb45d9566ae33dfb\n", - "\n", - "y=<pyiron_base.project.delayed.DelayedObject object at 0x719ee1d5d940>\n", - "\n", - "\n", - "\n", - "x_1d847da32ecaabf6731c38f798c3d4ce->y_2f79d27085d95c7ddb45d9566ae33dfb\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_2f79d27085d95c7ddb45d9566ae33dfb->create_function_job_c942e1812492f8750b853ea68445d43f\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_a9ec4f5f33f0d64e74ed5d9900bceac6\n", - "\n", - "y=2\n", - "\n", - "\n", - "\n", - "y_a9ec4f5f33f0d64e74ed5d9900bceac6->x_5a41f1a01c281872a92d14b5bf806b3c\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "y_a9ec4f5f33f0d64e74ed5d9900bceac6->y_2f79d27085d95c7ddb45d9566ae33dfb\n", - "\n", - "\n", - "\n", - "\n", - "" - ], - "text/plain": [ - "" - ] + "text/plain": "", + "image/svg+xml": "\n\n\n\n\ncreate_function_job_25906340bd0c28c44fd73d69e7a3d8bc\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x733f400d1310>\n\n\n\nx_1a7fff02f6473a13e5e8742988186611\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x733f40ddb0e0>\n\n\n\nx_1a7fff02f6473a13e5e8742988186611->create_function_job_25906340bd0c28c44fd73d69e7a3d8bc\n\n\n\n\n\nx_e4655695917c433de56d1c64232473f9\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x733f4db8caa0>\n\n\n\nx_e4655695917c433de56d1c64232473f9->x_1a7fff02f6473a13e5e8742988186611\n\n\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce\n\nx=1\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->x_e4655695917c433de56d1c64232473f9\n\n\n\n\n\ny_3b83397feef07a74d9a046a1b7f57749\n\ny=<pyiron_base.project.delayed.DelayedObject object at 0x733f4ed91130>\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->y_3b83397feef07a74d9a046a1b7f57749\n\n\n\n\n\ny_3b83397feef07a74d9a046a1b7f57749->x_1a7fff02f6473a13e5e8742988186611\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6\n\ny=2\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->x_e4655695917c433de56d1c64232473f9\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->y_3b83397feef07a74d9a046a1b7f57749\n\n\n\n\n" }, - "metadata": {}, - "output_type": "display_data" + "metadata": {} } ], - "source": [ - "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n", - "delayed_object_lst[-1].draw()" - ] + "execution_count": 17 }, { - "cell_type": "code", - "execution_count": 17, "id": "cf80267d-c2b0-4236-bf1d-a57596985fc1", + "cell_type": "code", + "source": "delayed_object_lst[-1].pull()", "metadata": { "trusted": true }, @@ -493,43 +344,34 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "The job get_prod_and_div_00cf2c787390eacfbc4a51e9a0c38ec7 was saved and received the ID: 1\n", - "The job get_sum_4b5b9d16b259a13b6a32798ce2779af8 was saved and received the ID: 2\n" - ] + "text": "The job get_prod_and_div_00cf2c787390eacfbc4a51e9a0c38ec7 was saved and received the ID: 1\nThe job get_sum_4b5b9d16b259a13b6a32798ce2779af8 was saved and received the ID: 2\nThe job get_square_9cc2f0545498916d7720c59c1120a66d was saved and received the ID: 3\n" }, { + "execution_count": 18, + "output_type": "execute_result", "data": { - "text/plain": [ - "2.5" - ] + "text/plain": "6.25" }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "delayed_object_lst[-1].pull()" - ] + "execution_count": 18 }, { - "cell_type": "markdown", "id": "9414680d1cbc3b2e", + "cell_type": "markdown", + "source": "Here, the procedure is the same as before: Import the necessary `pyiron_base` module from the PWD, import the workflow JSON file and run the workflow with pyiron.", "metadata": { "collapsed": false, "jupyter": { "outputs_hidden": false } - }, - "source": [ - "Here, the procedure is the same as before: Import the necessary `pyiron_base` module from the PWD, import the workflow JSON file and run the workflow with pyiron." - ] + } }, { - "cell_type": "code", - "execution_count": null, "id": "c199b28f3c0399cc", + "cell_type": "code", + "source": "", "metadata": { "collapsed": false, "jupyter": { @@ -538,28 +380,7 @@ "trusted": true }, "outputs": [], - "source": [] + "execution_count": null } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.8" - } - }, - "nbformat": 4, - "nbformat_minor": 5 + ] } diff --git a/example_workflows/arithmetic/pyiron_base.ipynb b/example_workflows/arithmetic/pyiron_base.ipynb index b355109..1fea0cd 100644 --- a/example_workflows/arithmetic/pyiron_base.ipynb +++ b/example_workflows/arithmetic/pyiron_base.ipynb @@ -1,133 +1,132 @@ { + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat_minor": 5, + "nbformat": 4, "cells": [ { - "cell_type": "markdown", "id": "c39b76fb-259f-4e16-a44d-02a295c82386", - "metadata": {}, - "source": [ - "# pyiron" - ] + "cell_type": "markdown", + "source": "# pyiron", + "metadata": {} }, { - "cell_type": "markdown", "id": "3638419b-a0cb-49e2-b157-7fbb1acde90f", - "metadata": {}, - "source": [ - "## Define workflow with pyiron_base" - ] + "cell_type": "markdown", + "source": "## Define workflow with pyiron_base", + "metadata": {} }, { - "cell_type": "code", - "execution_count": 1, "id": "b4a78447-e87c-4fb4-8d17-d9a280eb7254", + "cell_type": "code", + "source": "from pyiron_base import job", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from pyiron_base import job" - ] + "execution_count": 1 }, { - "cell_type": "code", - "execution_count": 2, "id": "06c2bd9e-b2ac-4b88-9158-fa37331c3418", + "cell_type": "code", + "source": "from python_workflow_definition.pyiron_base import write_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.pyiron_base import write_workflow_json" - ] + "execution_count": 2 }, { - "cell_type": "code", - "execution_count": null, "id": "6d859dfff0c2df5c", - "metadata": {}, + "cell_type": "code", + "source": "from workflow import (\n get_sum as _get_sum,\n get_prod_and_div as _get_prod_and_div,\n get_square as _get_square,\n)", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "from workflow import (\n", - " get_sum as _get_sum,\n", - " get_prod_and_div as _get_prod_and_div,\n", - " get_square as _get_square,\n", - ")" - ] + "execution_count": 3 }, { - "cell_type": "code", - "execution_count": null, "id": "77135b0c61898507", - "metadata": {}, + "cell_type": "code", + "source": "workflow_json_filename = \"pyiron_arithmetic.json\"", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "workflow_json_filename = \"pyiron_arithmetic.json\"" - ] + "execution_count": 4 }, { - "cell_type": "code", - "execution_count": null, "id": "07598344-0f75-433b-8902-bea21a42088c", + "cell_type": "code", + "source": "get_sum = job(_get_sum)\nget_prod_and_div = job(_get_prod_and_div, output_key_lst=[\"prod\", \"div\"])\nget_square = job(_get_square)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "get_sum = job(_get_sum)\n", - "get_prod_and_div = job(_get_prod_and_div, output_key_lst=[\"prod\", \"div\"])\n", - "get_square = job(_get_square)" - ] + "execution_count": 5 }, { - "cell_type": "code", - "execution_count": null, "id": "2b88a30a-e26b-4802-89b7-79ca08cc0af9", + "cell_type": "code", + "source": "prod_and_div = get_prod_and_div(x=1, y=2)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "prod_and_div = get_prod_and_div(x=1, y=2)" - ] + "execution_count": 6 }, { - "cell_type": "code", - "execution_count": null, "id": "a5e5ca63-2906-47c9-bac6-adebf8643cba", + "cell_type": "code", + "source": "tmp_sum = get_sum(x=prod_and_div.output.prod, y=prod_and_div.output.div)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "tmp_sum = get_sum(x=prod_and_div.output.prod, y=prod_and_div.output.div)" - ] + "execution_count": 7 }, { - "cell_type": "code", - "execution_count": null, "id": "eae321f1", - "metadata": {}, + "cell_type": "code", + "source": "result = get_square(x=tmp_sum)", + "metadata": { + "trusted": true + }, "outputs": [], - "source": [ - "result = get_square(x=tmp_sum)" - ] + "execution_count": 8 }, { - "cell_type": "code", - "execution_count": null, "id": "e464da97-16a1-4772-9a07-0a47f152781d", + "cell_type": "code", + "source": "write_workflow_json(delayed_object=result, file_name=workflow_json_filename)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "write_workflow_json(delayed_object=result, file_name=workflow_json_filename)" - ] + "execution_count": 9 }, { - "cell_type": "code", - "execution_count": 9, "id": "bca646b2-0a9a-4271-966a-e5903a8c9031", + "cell_type": "code", + "source": "!cat {workflow_json_filename}", "metadata": { "trusted": true }, @@ -135,93 +134,74 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "{\"nodes\": [{\"id\": 0, \"function\": \"arithmetic_workflow.get_sum\"}, {\"id\": 1, \"function\": \"arithmetic_workflow.get_prod_and_div\"}, {\"id\": 2, \"value\": 1}, {\"id\": 3, \"value\": 2}], \"edges\": [{\"target\": 0, \"targetPort\": \"x\", \"source\": 1, \"sourcePort\": \"prod\"}, {\"target\": 1, \"targetPort\": \"x\", \"source\": 2, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"y\", \"source\": 3, \"sourcePort\": null}, {\"target\": 0, \"targetPort\": \"y\", \"source\": 1, \"sourcePort\": \"div\"}]}" - ] + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.get_square\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.get_sum\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.get_prod_and_div\"\n },\n {\n \"id\": 3,\n \"type\": \"input\",\n \"name\": \"x\",\n \"value\": 1\n },\n {\n \"id\": 4,\n \"type\": \"input\",\n \"name\": \"y\",\n \"value\": 2\n },\n {\n \"id\": 5,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 0,\n \"targetPort\": \"x\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"x\",\n \"source\": 2,\n \"sourcePort\": \"prod\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"x\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"y\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"y\",\n \"source\": 2,\n \"sourcePort\": \"div\"\n },\n {\n \"target\": 5,\n \"targetPort\": null,\n \"source\": 0,\n \"sourcePort\": null\n }\n ]\n}" } ], - "source": [ - "!cat {workflow_json_filename}" - ] + "execution_count": 10 }, { - "cell_type": "markdown", "id": "a4c0faaf-e30d-4ded-8e9f-57f97f51b14c", - "metadata": {}, - "source": [ - "## Load Workflow with aiida" - ] + "cell_type": "markdown", + "source": "## Load Workflow with aiida", + "metadata": {} }, { - "cell_type": "code", - "execution_count": 10, "id": "2ecc229f-daa1-49b9-9279-a6b5ae1aa4f2", + "cell_type": "code", + "source": "from aiida import load_profile\n\nload_profile()", "metadata": { "trusted": true }, "outputs": [ { + "execution_count": 11, + "output_type": "execute_result", "data": { - "text/plain": [ - "Profile" - ] + "text/plain": "Profile" }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "from aiida import load_profile\n", - "\n", - "load_profile()" - ] + "execution_count": 11 }, { - "cell_type": "code", - "execution_count": 11, "id": "68a56b32-9f99-43d7-aaee-0c1cd9522681", + "cell_type": "code", + "source": "from python_workflow_definition.aiida import load_workflow_json", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from python_workflow_definition.aiida import load_workflow_json" - ] + "execution_count": 12 }, { - "cell_type": "code", - "execution_count": 12, "id": "8f2a621d-b533-4ddd-8bcd-c22db2f922ec", + "cell_type": "code", + "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg", "metadata": { "trusted": true }, "outputs": [ { + "execution_count": 13, + "output_type": "execute_result", "data": { + "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…", "application/vnd.jupyter.widget-view+json": { - "model_id": "cb6aafce370b43bb9904c64f03c93cc0", "version_major": 2, - "version_minor": 1 - }, - "text/plain": [ - "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…" - ] + "version_minor": 1, + "model_id": "f52e57854d6e4d07b6a2c11a75873efe" + } }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "wg = load_workflow_json(file_name=workflow_json_filename)\n", - "wg" - ] + "execution_count": 13 }, { - "cell_type": "code", - "execution_count": 13, "id": "cf80267d-c2b0-4236-bf1d-a57596985fc1", + "cell_type": "code", + "source": "\nwg.run()", "metadata": { "trusted": true }, @@ -229,80 +209,51 @@ { "name": "stderr", "output_type": "stream", - "text": [ - "04/23/2025 09:45:47 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div2\n", - "04/23/2025 09:45:48 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|update_task_state]: Task: get_prod_and_div2, type: PyFunction, finished.\n", - "04/23/2025 09:45:48 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum1\n", - "04/23/2025 09:45:48 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|update_task_state]: Task: get_sum1, type: PyFunction, finished.\n", - "04/23/2025 09:45:48 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n", - "04/23/2025 09:45:48 AM <4032> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [138|WorkGraphEngine|finalize]: Finalize workgraph.\n" - ] + "text": "05/24/2025 05:39:21 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div3\n05/24/2025 05:39:21 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|update_task_state]: Task: get_prod_and_div3, type: PyFunction, finished.\n05/24/2025 05:39:21 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum2\n05/24/2025 05:39:21 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|update_task_state]: Task: get_sum2, type: PyFunction, finished.\n05/24/2025 05:39:21 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_square1\n05/24/2025 05:39:22 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|update_task_state]: Task: get_square1, type: PyFunction, finished.\n05/24/2025 05:39:22 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:39:22 AM <524> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [19|WorkGraphEngine|finalize]: Finalize workgraph.\n" } ], - "source": [ - "\n", - "wg.run()" - ] + "execution_count": 14 }, { - "cell_type": "markdown", "id": "0c3503e1-0a32-40e1-845d-3fd9ec3c4c19", - "metadata": {}, - "source": [ - "## Load Workflow with jobflow" - ] + "cell_type": "markdown", + "source": "## Load Workflow with jobflow", + "metadata": {} }, { - "cell_type": "code", - "execution_count": 14, "id": "4abb0481-8e38-479d-ae61-6c46d091653e", + "cell_type": "code", + "source": "from python_workflow_definition.jobflow import load_workflow_json", "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"cipher\": algorithms.TripleDES,\n", - "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n", - " \"class\": algorithms.TripleDES,\n" - ] - } - ], - "source": [ - "from python_workflow_definition.jobflow import load_workflow_json" - ] + "outputs": [], + "execution_count": 15 }, { - "cell_type": "code", - "execution_count": 15, "id": "8253dd7c283bf3f7", + "cell_type": "code", + "source": "from jobflow.managers.local import run_locally", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "from jobflow.managers.local import run_locally" - ] + "execution_count": 16 }, { - "cell_type": "code", - "execution_count": 16, "id": "4b45e83b-945f-48c5-8e20-9df0ce0a14a1", + "cell_type": "code", + "source": "flow = load_workflow_json(file_name=workflow_json_filename)", "metadata": { "trusted": true }, "outputs": [], - "source": [ - "flow = load_workflow_json(file_name=workflow_json_filename)" - ] + "execution_count": 17 }, { - "cell_type": "code", - "execution_count": 17, "id": "8665c39c-220c-4982-b738-c31f6460530f", + "cell_type": "code", + "source": "result = run_locally(flow)\nresult", "metadata": { "trusted": true }, @@ -310,62 +261,28 @@ { "name": "stdout", "output_type": "stream", - "text": [ - "2025-04-23 09:45:49,174 INFO Started executing jobs locally\n", - "2025-04-23 09:45:49,540 INFO Starting job - get_prod_and_div (77d76447-21f8-4ad8-b2b5-bef7263ef5b9)\n", - "2025-04-23 09:45:49,543 INFO Finished job - get_prod_and_div (77d76447-21f8-4ad8-b2b5-bef7263ef5b9)\n", - "2025-04-23 09:45:49,544 INFO Starting job - get_sum (e61e0bc0-bddd-4ac9-93f0-cf5f064e17b0)\n", - "2025-04-23 09:45:49,546 INFO Finished job - get_sum (e61e0bc0-bddd-4ac9-93f0-cf5f064e17b0)\n", - "2025-04-23 09:45:49,546 INFO Finished executing jobs locally\n" - ] + "text": "2025-05-24 05:39:22,893 INFO Started executing jobs locally\n2025-05-24 05:39:23,184 INFO Starting job - get_prod_and_div (82cb13d7-d7c8-4bd1-84d1-c301d4ee2422)\n2025-05-24 05:39:23,187 INFO Finished job - get_prod_and_div (82cb13d7-d7c8-4bd1-84d1-c301d4ee2422)\n2025-05-24 05:39:23,187 INFO Starting job - get_sum (19c0830c-e918-44d2-82f1-b9418463c057)\n2025-05-24 05:39:23,189 INFO Finished job - get_sum (19c0830c-e918-44d2-82f1-b9418463c057)\n2025-05-24 05:39:23,189 INFO Starting job - get_square (78fc4e6e-2a99-490e-b829-fae9704296c2)\n2025-05-24 05:39:23,190 INFO Finished job - get_square (78fc4e6e-2a99-490e-b829-fae9704296c2)\n2025-05-24 05:39:23,191 INFO Finished executing jobs locally\n" }, { + "execution_count": 18, + "output_type": "execute_result", "data": { - "text/plain": [ - "{'77d76447-21f8-4ad8-b2b5-bef7263ef5b9': {1: Response(output={'prod': 2, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n", - " 'e61e0bc0-bddd-4ac9-93f0-cf5f064e17b0': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" - ] + "text/plain": "{'82cb13d7-d7c8-4bd1-84d1-c301d4ee2422': {1: Response(output={'prod': 2, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n '19c0830c-e918-44d2-82f1-b9418463c057': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n '78fc4e6e-2a99-490e-b829-fae9704296c2': {1: Response(output=6.25, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))}}" }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" + "metadata": {} } ], - "source": [ - "result = run_locally(flow)\n", - "result" - ] + "execution_count": 18 }, { - "cell_type": "code", - "execution_count": null, "id": "cf76f305-24de-45a7-be8e-cfe45cd6458e", + "cell_type": "code", + "source": "", "metadata": { "trusted": true }, "outputs": [], - "source": [] + "execution_count": null } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.8" - } - }, - "nbformat": 4, - "nbformat_minor": 5 + ] } diff --git a/example_workflows/arithmetic/universal_workflow.ipynb b/example_workflows/arithmetic/universal_workflow.ipynb index e1775b2..60d0ab2 100644 --- a/example_workflows/arithmetic/universal_workflow.ipynb +++ b/example_workflows/arithmetic/universal_workflow.ipynb @@ -51,7 +51,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\n0\n\narithmetic_workflow.get_prod_and_div\n\n\n\n1\n\narithmetic_workflow.get_sum\n\n\n\n0->1\n\n\nx=result[prod], y=result[div]\n\n\n\n2\n\n1\n\n\n\n2->0\n\n\nx\n\n\n\n3\n\n2\n\n\n\n3->0\n\n\ny\n\n\n" + "image/svg+xml": "\n\n\n\n\n0\n\nworkflow.get_prod_and_div\n\n\n\n1\n\nworkflow.get_sum\n\n\n\n0->1\n\n\n\n\n\n2\n\nworkflow.get_square\n\n\n\n1->2\n\n\nx\n\n\n\n5\n\nresult\n\n\n\n2->5\n\n\n\n\n\n3\n\n1\n\n\n\n3->0\n\n\nx\n\n\n\n4\n\n2\n\n\n\n4->0\n\n\ny\n\n\n" }, "metadata": {} } @@ -74,7 +74,7 @@ "execution_count": 3, "output_type": "execute_result", "data": { - "text/plain": "Profile" + "text/plain": "Profile" }, "metadata": {} } @@ -105,7 +105,7 @@ "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 1, - "model_id": "10427ed751dc4ec8853025eebb109925" + "model_id": "fc63f59e75a74fbcab9e44a06ecb6d18" } }, "metadata": {} @@ -123,7 +123,7 @@ { "name": "stderr", "output_type": "stream", - "text": "04/23/2025 09:51:40 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div1\n04/23/2025 09:51:40 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|update_task_state]: Task: get_prod_and_div1, type: PyFunction, finished.\n04/23/2025 09:51:40 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum2\n04/23/2025 09:51:41 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|update_task_state]: Task: get_sum2, type: PyFunction, finished.\n04/23/2025 09:51:41 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/23/2025 09:51:41 AM <5717> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [273|WorkGraphEngine|finalize]: Finalize workgraph.\n" + "text": "05/24/2025 05:39:46 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_prod_and_div1\n05/24/2025 05:39:46 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|update_task_state]: Task: get_prod_and_div1, type: PyFunction, finished.\n05/24/2025 05:39:46 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_sum2\n05/24/2025 05:39:47 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|update_task_state]: Task: get_sum2, type: PyFunction, finished.\n05/24/2025 05:39:47 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_square3\n05/24/2025 05:39:47 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|update_task_state]: Task: get_square3, type: PyFunction, finished.\n05/24/2025 05:39:47 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:39:47 AM <644> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [35|WorkGraphEngine|finalize]: Finalize workgraph.\n" } ], "execution_count": 6 @@ -153,10 +153,7 @@ }, { "cell_type": "code", - "source": [ - "with SingleNodeExecutor(max_workers=1) as exe:\n", - " result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()" - ], + "source": "with SingleNodeExecutor(max_workers=1) as exe:\n result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()", "metadata": { "trusted": true }, @@ -174,7 +171,7 @@ "execution_count": 10, "output_type": "execute_result", "data": { - "text/plain": "2.5" + "text/plain": "6.25" }, "metadata": {} } @@ -192,13 +189,7 @@ "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 11 }, { @@ -229,13 +220,13 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:51:44,679 INFO Started executing jobs locally\n2025-04-23 09:51:44,779 INFO Starting job - get_prod_and_div (51955f11-032f-4a6d-b643-c4fc87967298)\n2025-04-23 09:51:44,782 INFO Finished job - get_prod_and_div (51955f11-032f-4a6d-b643-c4fc87967298)\n2025-04-23 09:51:44,782 INFO Starting job - get_sum (3ed0bbc7-babb-475a-be16-2cdfe4c0c583)\n2025-04-23 09:51:44,784 INFO Finished job - get_sum (3ed0bbc7-babb-475a-be16-2cdfe4c0c583)\n2025-04-23 09:51:44,784 INFO Finished executing jobs locally\n" + "text": "2025-05-24 05:39:49,427 INFO Started executing jobs locally\n2025-05-24 05:39:49,510 INFO Starting job - get_prod_and_div (f82f13df-44cc-4bce-8712-ab5a1408c551)\n2025-05-24 05:39:49,512 INFO Finished job - get_prod_and_div (f82f13df-44cc-4bce-8712-ab5a1408c551)\n2025-05-24 05:39:49,513 INFO Starting job - get_sum (bb1c3b6d-986a-4e5d-b2f4-6611940ba4c6)\n2025-05-24 05:39:49,514 INFO Finished job - get_sum (bb1c3b6d-986a-4e5d-b2f4-6611940ba4c6)\n2025-05-24 05:39:49,515 INFO Starting job - get_square (5c60ac07-39fd-4511-93d8-3bd65c6bd7ca)\n2025-05-24 05:39:49,516 INFO Finished job - get_square (5c60ac07-39fd-4511-93d8-3bd65c6bd7ca)\n2025-05-24 05:39:49,516 INFO Finished executing jobs locally\n" }, { "execution_count": 14, "output_type": "execute_result", "data": { - "text/plain": "{'51955f11-032f-4a6d-b643-c4fc87967298': {1: Response(output={'prod': 2, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '3ed0bbc7-babb-475a-be16-2cdfe4c0c583': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" + "text/plain": "{'f82f13df-44cc-4bce-8712-ab5a1408c551': {1: Response(output={'prod': 2, 'div': 0.5}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n 'bb1c3b6d-986a-4e5d-b2f4-6611940ba4c6': {1: Response(output=2.5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))},\n '5c60ac07-39fd-4511-93d8-3bd65c6bd7ca': {1: Response(output=6.25, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/arithmetic'))}}" }, "metadata": {} } @@ -258,10 +249,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\n", - "delayed_object_lst[-1].draw()" - ], + "source": "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, @@ -270,7 +258,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\ncreate_function_job_a30133cc7a07a2e64b505497250df84d\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x72b84012a420>\n\n\n\nx_03371e8bbb210fff8c1beb07977c6fca\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x72b8402f8fb0>\n\n\n\nx_03371e8bbb210fff8c1beb07977c6fca->create_function_job_a30133cc7a07a2e64b505497250df84d\n\n\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce\n\nx=1\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->x_03371e8bbb210fff8c1beb07977c6fca\n\n\n\n\n\ny_69de87ef8d8a066b8926b02e01e9f7f8\n\ny=<pyiron_base.project.delayed.DelayedObject object at 0x72b84012a150>\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->y_69de87ef8d8a066b8926b02e01e9f7f8\n\n\n\n\n\ny_69de87ef8d8a066b8926b02e01e9f7f8->create_function_job_a30133cc7a07a2e64b505497250df84d\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6\n\ny=2\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->x_03371e8bbb210fff8c1beb07977c6fca\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->y_69de87ef8d8a066b8926b02e01e9f7f8\n\n\n\n\n" + "image/svg+xml": "\n\n\n\n\ncreate_function_job_25906340bd0c28c44fd73d69e7a3d8bc\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x749611736a50>\n\n\n\nx_1a7fff02f6473a13e5e8742988186611\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x7496117367e0>\n\n\n\nx_1a7fff02f6473a13e5e8742988186611->create_function_job_25906340bd0c28c44fd73d69e7a3d8bc\n\n\n\n\n\nx_e4655695917c433de56d1c64232473f9\n\nx=<pyiron_base.project.delayed.DelayedObject object at 0x74961213ea50>\n\n\n\nx_e4655695917c433de56d1c64232473f9->x_1a7fff02f6473a13e5e8742988186611\n\n\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce\n\nx=1\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->x_e4655695917c433de56d1c64232473f9\n\n\n\n\n\ny_3b83397feef07a74d9a046a1b7f57749\n\ny=<pyiron_base.project.delayed.DelayedObject object at 0x74961eca0a10>\n\n\n\nx_1d847da32ecaabf6731c38f798c3d4ce->y_3b83397feef07a74d9a046a1b7f57749\n\n\n\n\n\ny_3b83397feef07a74d9a046a1b7f57749->x_1a7fff02f6473a13e5e8742988186611\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6\n\ny=2\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->x_e4655695917c433de56d1c64232473f9\n\n\n\n\n\ny_a9ec4f5f33f0d64e74ed5d9900bceac6->y_3b83397feef07a74d9a046a1b7f57749\n\n\n\n\n" }, "metadata": {} } @@ -287,13 +275,13 @@ { "name": "stdout", "output_type": "stream", - "text": "The job get_prod_and_div_955f44280fa0072653e4d910a57d7b92 was saved and received the ID: 1\nThe job get_sum_55b699570ac3c74e1e8078a45b657240 was saved and received the ID: 2\n" + "text": "The job get_prod_and_div_00cf2c787390eacfbc4a51e9a0c38ec7 was saved and received the ID: 1\nThe job get_sum_4b5b9d16b259a13b6a32798ce2779af8 was saved and received the ID: 2\nThe job get_square_9cc2f0545498916d7720c59c1120a66d was saved and received the ID: 3\n" }, { "execution_count": 17, "output_type": "execute_result", "data": { - "text/plain": "2.5" + "text/plain": "6.25" }, "metadata": {} } @@ -325,7 +313,7 @@ "execution_count": 19, "output_type": "execute_result", "data": { - "text/plain": "2.5" + "text/plain": "6.25" }, "metadata": {} } diff --git a/example_workflows/nfdi/aiida.ipynb b/example_workflows/nfdi/aiida.ipynb index f6d55f0..8b25fa2 100644 --- a/example_workflows/nfdi/aiida.ipynb +++ b/example_workflows/nfdi/aiida.ipynb @@ -1 +1,360 @@ -{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"106ded66-d202-46ac-82b0-2755ca309bdd","cell_type":"markdown","source":"# Aiida\n\nhttps://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements","metadata":{}},{"id":"11e09b78-cb72-465f-9c8b-5b77f0aa729c","cell_type":"markdown","source":"## Define workflow with aiida","metadata":{}},{"id":"17173d54-dc76-4052-ab39-d44771ac903d","cell_type":"code","source":"import os","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"89c02460-b543-442c-a27e-f1757dc2262e","cell_type":"code","source":"from python_workflow_definition.aiida import write_workflow_json\n\nfrom aiida_workgraph import WorkGraph, task\nfrom aiida import orm, load_profile\nload_profile()","metadata":{"trusted":true},"outputs":[{"execution_count":2,"output_type":"execute_result","data":{"text/plain":"Profile"},"metadata":{}}],"execution_count":2},{"id":"6dac225a1ce86b25","cell_type":"code","source":"from workflow import (\n generate_mesh,\n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line,\n substitute_macros,\n compile_paper,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"c47205d289499756","cell_type":"code","source":"convert_to_xdmf = task(outputs=[\"xdmf_file\", \"h5_file\"])(_convert_to_xdmf)\npoisson = task(outputs=[\"numdofs\", \"pvd_file\", \"vtu_file\"])(_poisson)","metadata":{"trusted":true},"outputs":[],"execution_count":4},{"id":"37c9d988-1755-446c-9f7b-c32f99e280d4","cell_type":"code","source":"source_directory = orm.Str(os.path.abspath(os.path.join(os.curdir, \"source\")))","metadata":{"trusted":true},"outputs":[],"execution_count":5},{"id":"8d911f98-3b80-457f-a0f4-3cb37ebf1691","cell_type":"code","source":"domain_size = orm.Float(2.0)","metadata":{"trusted":true},"outputs":[],"execution_count":6},{"id":"1e7e14ba-c4a7-485f-9bd8-44625830cca0","cell_type":"code","source":"wg = WorkGraph(\"wg-nfdi\")","metadata":{"trusted":true},"outputs":[],"execution_count":7},{"id":"71d411b6-cbec-489e-99e3-ba71680bcb5b","cell_type":"code","source":"gmsh_output_file = wg.add_task(\n generate_mesh,\n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":8},{"id":"1d0d9804-f250-48b3-a5d0-a546d520f79b","cell_type":"code","source":"meshio_output_dict = wg.add_task(\n convert_to_xdmf,\n gmsh_output_file=gmsh_output_file.outputs.result,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":9},{"id":"7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590","cell_type":"code","source":"poisson_dict = wg.add_task(\n poisson,\n meshio_output_xdmf=meshio_output_dict.outputs.xdmf_file, \n meshio_output_h5=meshio_output_dict.outputs.h5_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":10},{"id":"3c4a29b0-eb1e-490a-8be0-e03cfff15e0a","cell_type":"code","source":"pvbatch_output_file = wg.add_task(\n plot_over_line,\n poisson_output_pvd_file=poisson_dict.outputs.pvd_file, \n poisson_output_vtu_file=poisson_dict.outputs.vtu_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":11},{"id":"a0a4c233-322d-4723-9627-62ca2487bfa9","cell_type":"code","source":"macros_tex_file = wg.add_task(\n substitute_macros,\n pvbatch_output_file=pvbatch_output_file.outputs.result, \n ndofs=poisson_dict.outputs.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":12},{"id":"c281408f-e63d-4380-a7e6-c595d49fbb8f","cell_type":"code","source":"paper_output = wg.add_task(\n compile_paper,\n macros_tex=macros_tex_file.outputs.result, \n plot_file=pvbatch_output_file.outputs.result,\n source_directory=source_directory,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":13},{"id":"a384d70a-8ef5-4fdd-880c-56ac7eaf87b9","cell_type":"code","source":"wg","metadata":{"trusted":true},"outputs":[{"execution_count":14,"output_type":"execute_result","data":{"text/plain":"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'wg-nfdi…","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":1,"model_id":"146d8dc7dfb641ca8d2e9d74c21dd397"}},"metadata":{}}],"execution_count":14},{"id":"fb23ad9c-76fd-4c0b-b546-e305d6c49796","cell_type":"code","source":"workflow_json_filename = \"aiida_nfdi.json\"","metadata":{"trusted":true},"outputs":[],"execution_count":15},{"id":"4139547a-9717-4708-b1a5-8202a0382d77","cell_type":"code","source":"write_workflow_json(wg=wg, file_name=workflow_json_filename)","metadata":{"trusted":true},"outputs":[],"execution_count":16},{"id":"490df6a3-e402-4620-acf2-dbcfa0c5d537","cell_type":"code","source":"!cat {workflow_json_filename}","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"{\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.generate_mesh\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.convert_to_xdmf\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.poisson\"\n },\n {\n \"id\": 3,\n \"type\": \"function\",\n \"value\": \"workflow.plot_over_line\"\n },\n {\n \"id\": 4,\n \"type\": \"function\",\n \"value\": \"workflow.substitute_macros\"\n },\n {\n \"id\": 5,\n \"type\": \"function\",\n \"value\": \"workflow.compile_paper\"\n },\n {\n \"id\": 6,\n \"type\": \"input\",\n \"name\": \"domain_size\",\n \"value\": 2.0\n },\n {\n \"id\": 7,\n \"type\": \"input\",\n \"name\": \"source_directory\",\n \"value\": \"/home/jovyan/example_workflows/nfdi/source\"\n },\n {\n \"id\": 8,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 1,\n \"targetPort\": \"gmsh_output_file\",\n \"source\": 0,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"meshio_output_xdmf\",\n \"source\": 1,\n \"sourcePort\": \"xdmf_file\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"meshio_output_h5\",\n \"source\": 1,\n \"sourcePort\": \"h5_file\"\n },\n {\n \"target\": 3,\n \"targetPort\": \"poisson_output_pvd_file\",\n \"source\": 2,\n \"sourcePort\": \"pvd_file\"\n },\n {\n \"target\": 3,\n \"targetPort\": \"poisson_output_vtu_file\",\n \"source\": 2,\n \"sourcePort\": \"vtu_file\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"pvbatch_output_file\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"ndofs\",\n \"source\": 2,\n \"sourcePort\": \"numdofs\"\n },\n {\n \"target\": 5,\n \"targetPort\": \"macros_tex\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"plot_file\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"domain_size\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"domain_size\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": null,\n \"source\": 5,\n \"sourcePort\": null\n }\n ]\n}"}],"execution_count":17},{"id":"11a829e2-face-469f-b343-2c95763b1f13","cell_type":"markdown","source":"## Load Workflow with jobflow","metadata":{}},{"id":"4f3acabe-55df-479a-af4d-a23a80c4660d","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":18},{"id":"b6ba9444-a2c8-451b-b74c-19b0f69ba369","cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":true},"outputs":[],"execution_count":19},{"id":"c3528d55-6bf7-47ed-a110-65c47446ba92","cell_type":"code","source":"flow = load_workflow_json(file_name=workflow_json_filename)","metadata":{"trusted":true},"outputs":[],"execution_count":20},{"id":"5ef48778-4209-425f-8c6b-85a4cd2f92ec","cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-05-14 08:19:05,840 INFO Started executing jobs locally\n2025-05-14 08:19:06,092 INFO Starting job - generate_mesh (2b5d3769-0843-43a0-b074-2b307413b932)\n2025-05-14 08:19:07,248 INFO Finished job - generate_mesh (2b5d3769-0843-43a0-b074-2b307413b932)\n2025-05-14 08:19:07,249 INFO Starting job - convert_to_xdmf (60d93a50-60c8-4ebc-9822-fae5e9f6bf4b)\n2025-05-14 08:19:08,519 INFO Finished job - convert_to_xdmf (60d93a50-60c8-4ebc-9822-fae5e9f6bf4b)\n2025-05-14 08:19:08,521 INFO Starting job - poisson (06a30fcc-b3e5-4223-aa6e-1090166cd9c7)\n2025-05-14 08:19:11,239 INFO Finished job - poisson (06a30fcc-b3e5-4223-aa6e-1090166cd9c7)\n2025-05-14 08:19:11,240 INFO Starting job - plot_over_line (f899080b-495a-401e-a71c-3abba9e81a5b)\n2025-05-14 08:19:12,690 INFO Finished job - plot_over_line (f899080b-495a-401e-a71c-3abba9e81a5b)\n2025-05-14 08:19:12,691 INFO Starting job - substitute_macros (b1612cb4-0027-4140-95c2-8cb7581109ca)\n2025-05-14 08:19:13,570 INFO Finished job - substitute_macros (b1612cb4-0027-4140-95c2-8cb7581109ca)\n2025-05-14 08:19:13,571 INFO Starting job - compile_paper (c5e6caaa-9766-4079-a235-a774a6d5c7fa)\n2025-05-14 08:19:15,636 INFO Finished job - compile_paper (c5e6caaa-9766-4079-a235-a774a6d5c7fa)\n2025-05-14 08:19:15,637 INFO Finished executing jobs locally\n"},{"execution_count":21,"output_type":"execute_result","data":{"text/plain":"{'2b5d3769-0843-43a0-b074-2b307413b932': {1: Response(output='/home/jovyan/example_workflows/nfdi/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '60d93a50-60c8-4ebc-9822-fae5e9f6bf4b': {1: Response(output={'xdmf_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '06a30fcc-b3e5-4223-aa6e-1090166cd9c7': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/example_workflows/nfdi/processing/poisson.pvd', 'vtu_file': '/home/jovyan/example_workflows/nfdi/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'f899080b-495a-401e-a71c-3abba9e81a5b': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'b1612cb4-0027-4140-95c2-8cb7581109ca': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'c5e6caaa-9766-4079-a235-a774a6d5c7fa': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))}}"},"metadata":{}}],"execution_count":21},{"id":"397b16a2-e1ec-4eec-8562-1c84f585c347","cell_type":"markdown","source":"## Load Workflow with pyiron_base","metadata":{}},{"id":"be4d5d93-e9f6-4072-a6be-0ee5dc93590f","cell_type":"code","source":"from python_workflow_definition.pyiron_base import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":22},{"id":"4452a648-d4c3-4f5f-8678-ffb54bef17dc","cell_type":"code","source":"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()","metadata":{"trusted":true},"outputs":[{"output_type":"display_data","data":{"text/plain":"","image/svg+xml":"\n\n\n\n\ncreate_function_job_9564f1c400f389023de93231c8a62a65\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7e2106518c20>\n\n\n\nmacros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x7e21065189b0>\n\n\n\nmacros_tex_4fdd7c93c52394e1a5aed103adf6dba4->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\npvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7e2106518680>\n\n\n\npvbatch_output_file_e4a68dc408161a17988f364b0337f341->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x7e21065183e0>\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nplot_file_e4a68dc408161a17988f364b0337f341\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x7e2106518680>\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nplot_file_e4a68dc408161a17988f364b0337f341->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x7e21064e7d40>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x7e21065183b0>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x7e2106518710>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nndofs_8b9741bf01bd3f1fc0fe9a772777a903->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7e21064e7dd0>\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1->meshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x7e21064e7e90>\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1->meshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696\n\nsource_directory=/home/jovyan/example_workflows/nfdi/source\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->gmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\n\n\n\n"},"metadata":{}}],"execution_count":23},{"id":"1c2760b6-96b4-4f44-ac49-a229d4a0cf67","cell_type":"code","source":"delayed_object_lst[-1].pull()","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"The job generate_mesh_47725c16637f799ac042e47468005db3 was saved and received the ID: 1\nThe job convert_to_xdmf_d6a46eb9a4ec352aa996e783ec3c785f was saved and received the ID: 2\nThe job poisson_3c147fc86db87cf0c0f94bda333f8cd8 was saved and received the ID: 3\nThe job plot_over_line_ef50933291910dadcc8311924971e127 was saved and received the ID: 4\nThe job substitute_macros_63766eafd6b1980c7832dd8c9a97c96e was saved and received the ID: 5\nThe job compile_paper_128d1d58374953c00e95b8de62cbb10b was saved and received the ID: 6\n"},{"execution_count":24,"output_type":"execute_result","data":{"text/plain":"'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'"},"metadata":{}}],"execution_count":24}]} +{ + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12.8", + "mimetype": "text/x-python", + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "pygments_lexer": "ipython3", + "nbconvert_exporter": "python", + "file_extension": ".py" + } + }, + "nbformat_minor": 5, + "nbformat": 4, + "cells": [ + { + "id": "106ded66-d202-46ac-82b0-2755ca309bdd", + "cell_type": "markdown", + "source": "# Aiida\n\nhttps://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements", + "metadata": {} + }, + { + "id": "11e09b78-cb72-465f-9c8b-5b77f0aa729c", + "cell_type": "markdown", + "source": "## Define workflow with aiida", + "metadata": {} + }, + { + "id": "17173d54-dc76-4052-ab39-d44771ac903d", + "cell_type": "code", + "source": "import os", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 1 + }, + { + "id": "89c02460-b543-442c-a27e-f1757dc2262e", + "cell_type": "code", + "source": "from python_workflow_definition.aiida import write_workflow_json\n\nfrom aiida_workgraph import WorkGraph, task\nfrom aiida import orm, load_profile\nload_profile()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 2, + "output_type": "execute_result", + "data": { + "text/plain": "Profile" + }, + "metadata": {} + } + ], + "execution_count": 2 + }, + { + "id": "6dac225a1ce86b25", + "cell_type": "code", + "source": "from workflow import (\n generate_mesh,\n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line,\n substitute_macros,\n compile_paper,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 3 + }, + { + "id": "c47205d289499756", + "cell_type": "code", + "source": "convert_to_xdmf = task(outputs=[\"xdmf_file\", \"h5_file\"])(_convert_to_xdmf)\npoisson = task(outputs=[\"numdofs\", \"pvd_file\", \"vtu_file\"])(_poisson)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 4 + }, + { + "id": "37c9d988-1755-446c-9f7b-c32f99e280d4", + "cell_type": "code", + "source": "source_directory = orm.Str(os.path.abspath(os.path.join(os.curdir, \"source\")))", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 5 + }, + { + "id": "8d911f98-3b80-457f-a0f4-3cb37ebf1691", + "cell_type": "code", + "source": "domain_size = orm.Float(2.0)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 6 + }, + { + "id": "1e7e14ba-c4a7-485f-9bd8-44625830cca0", + "cell_type": "code", + "source": "wg = WorkGraph(\"wg-nfdi\")", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 7 + }, + { + "id": "71d411b6-cbec-489e-99e3-ba71680bcb5b", + "cell_type": "code", + "source": "gmsh_output_file = wg.add_task(\n generate_mesh,\n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 8 + }, + { + "id": "1d0d9804-f250-48b3-a5d0-a546d520f79b", + "cell_type": "code", + "source": "meshio_output_dict = wg.add_task(\n convert_to_xdmf,\n gmsh_output_file=gmsh_output_file.outputs.result,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 9 + }, + { + "id": "7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590", + "cell_type": "code", + "source": "poisson_dict = wg.add_task(\n poisson,\n meshio_output_xdmf=meshio_output_dict.outputs.xdmf_file, \n meshio_output_h5=meshio_output_dict.outputs.h5_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 10 + }, + { + "id": "3c4a29b0-eb1e-490a-8be0-e03cfff15e0a", + "cell_type": "code", + "source": "pvbatch_output_file = wg.add_task(\n plot_over_line,\n poisson_output_pvd_file=poisson_dict.outputs.pvd_file, \n poisson_output_vtu_file=poisson_dict.outputs.vtu_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 11 + }, + { + "id": "a0a4c233-322d-4723-9627-62ca2487bfa9", + "cell_type": "code", + "source": "macros_tex_file = wg.add_task(\n substitute_macros,\n pvbatch_output_file=pvbatch_output_file.outputs.result, \n ndofs=poisson_dict.outputs.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 12 + }, + { + "id": "c281408f-e63d-4380-a7e6-c595d49fbb8f", + "cell_type": "code", + "source": "paper_output = wg.add_task(\n compile_paper,\n macros_tex=macros_tex_file.outputs.result, \n plot_file=pvbatch_output_file.outputs.result,\n source_directory=source_directory,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 13 + }, + { + "id": "a384d70a-8ef5-4fdd-880c-56ac7eaf87b9", + "cell_type": "code", + "source": "wg", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 14, + "output_type": "execute_result", + "data": { + "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'wg-nfdi…", + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 1, + "model_id": "17520c019e5c413fb7a119ecc997c3ea" + } + }, + "metadata": {} + } + ], + "execution_count": 14 + }, + { + "id": "fb23ad9c-76fd-4c0b-b546-e305d6c49796", + "cell_type": "code", + "source": "workflow_json_filename = \"aiida_nfdi.json\"", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 15 + }, + { + "id": "4139547a-9717-4708-b1a5-8202a0382d77", + "cell_type": "code", + "source": "write_workflow_json(wg=wg, file_name=workflow_json_filename)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 16 + }, + { + "id": "490df6a3-e402-4620-acf2-dbcfa0c5d537", + "cell_type": "code", + "source": "!cat {workflow_json_filename}", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.generate_mesh\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.convert_to_xdmf\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.poisson\"\n },\n {\n \"id\": 3,\n \"type\": \"function\",\n \"value\": \"workflow.plot_over_line\"\n },\n {\n \"id\": 4,\n \"type\": \"function\",\n \"value\": \"workflow.substitute_macros\"\n },\n {\n \"id\": 5,\n \"type\": \"function\",\n \"value\": \"workflow.compile_paper\"\n },\n {\n \"id\": 6,\n \"type\": \"input\",\n \"name\": \"domain_size\",\n \"value\": 2.0\n },\n {\n \"id\": 7,\n \"type\": \"input\",\n \"name\": \"source_directory\",\n \"value\": \"/home/jovyan/example_workflows/nfdi/source\"\n },\n {\n \"id\": 8,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 1,\n \"targetPort\": \"gmsh_output_file\",\n \"source\": 0,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"meshio_output_xdmf\",\n \"source\": 1,\n \"sourcePort\": \"xdmf_file\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"meshio_output_h5\",\n \"source\": 1,\n \"sourcePort\": \"h5_file\"\n },\n {\n \"target\": 3,\n \"targetPort\": \"poisson_output_pvd_file\",\n \"source\": 2,\n \"sourcePort\": \"pvd_file\"\n },\n {\n \"target\": 3,\n \"targetPort\": \"poisson_output_vtu_file\",\n \"source\": 2,\n \"sourcePort\": \"vtu_file\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"pvbatch_output_file\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"ndofs\",\n \"source\": 2,\n \"sourcePort\": \"numdofs\"\n },\n {\n \"target\": 5,\n \"targetPort\": \"macros_tex\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"plot_file\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"domain_size\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"domain_size\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"source_directory\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": null,\n \"source\": 5,\n \"sourcePort\": null\n }\n ]\n}" + } + ], + "execution_count": 17 + }, + { + "id": "11a829e2-face-469f-b343-2c95763b1f13", + "cell_type": "markdown", + "source": "## Load Workflow with jobflow", + "metadata": {} + }, + { + "id": "4f3acabe-55df-479a-af4d-a23a80c4660d", + "cell_type": "code", + "source": "from python_workflow_definition.jobflow import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 18 + }, + { + "id": "b6ba9444-a2c8-451b-b74c-19b0f69ba369", + "cell_type": "code", + "source": "from jobflow.managers.local import run_locally", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 19 + }, + { + "id": "c3528d55-6bf7-47ed-a110-65c47446ba92", + "cell_type": "code", + "source": "flow = load_workflow_json(file_name=workflow_json_filename)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 20 + }, + { + "id": "5ef48778-4209-425f-8c6b-85a4cd2f92ec", + "cell_type": "code", + "source": "result = run_locally(flow)\nresult", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": "2025-05-24 05:41:02,340 INFO Started executing jobs locally\n2025-05-24 05:41:02,615 INFO Starting job - generate_mesh (1c3eab15-7639-4f4e-9ca7-7523ba640ca5)\n2025-05-24 05:41:03,800 INFO Finished job - generate_mesh (1c3eab15-7639-4f4e-9ca7-7523ba640ca5)\n2025-05-24 05:41:03,801 INFO Starting job - convert_to_xdmf (07acbed1-2abb-4141-896d-170b58aba7c2)\n2025-05-24 05:41:05,099 INFO Finished job - convert_to_xdmf (07acbed1-2abb-4141-896d-170b58aba7c2)\n2025-05-24 05:41:05,100 INFO Starting job - poisson (b212b743-f36d-4f7b-a64a-79060469f34b)\n2025-05-24 05:41:12,945 INFO Finished job - poisson (b212b743-f36d-4f7b-a64a-79060469f34b)\n2025-05-24 05:41:12,946 INFO Starting job - plot_over_line (af5a3a54-b7fa-45f8-a70f-7f95d23c32c4)\n2025-05-24 05:41:14,360 INFO Finished job - plot_over_line (af5a3a54-b7fa-45f8-a70f-7f95d23c32c4)\n2025-05-24 05:41:14,360 INFO Starting job - substitute_macros (ec55c04a-a5cb-4d8f-9981-961f7297532e)\n2025-05-24 05:41:15,171 INFO Finished job - substitute_macros (ec55c04a-a5cb-4d8f-9981-961f7297532e)\n2025-05-24 05:41:15,172 INFO Starting job - compile_paper (629539b7-2541-4ba7-9546-b7adb0cc312e)\n2025-05-24 05:42:14,698 INFO Finished job - compile_paper (629539b7-2541-4ba7-9546-b7adb0cc312e)\n2025-05-24 05:42:14,699 INFO Finished executing jobs locally\n" + }, + { + "execution_count": 21, + "output_type": "execute_result", + "data": { + "text/plain": "{'1c3eab15-7639-4f4e-9ca7-7523ba640ca5': {1: Response(output='/home/jovyan/example_workflows/nfdi/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '07acbed1-2abb-4141-896d-170b58aba7c2': {1: Response(output={'xdmf_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'b212b743-f36d-4f7b-a64a-79060469f34b': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/example_workflows/nfdi/processing/poisson.pvd', 'vtu_file': '/home/jovyan/example_workflows/nfdi/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'af5a3a54-b7fa-45f8-a70f-7f95d23c32c4': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'ec55c04a-a5cb-4d8f-9981-961f7297532e': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '629539b7-2541-4ba7-9546-b7adb0cc312e': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))}}" + }, + "metadata": {} + } + ], + "execution_count": 21 + }, + { + "id": "397b16a2-e1ec-4eec-8562-1c84f585c347", + "cell_type": "markdown", + "source": "## Load Workflow with pyiron_base", + "metadata": {} + }, + { + "id": "be4d5d93-e9f6-4072-a6be-0ee5dc93590f", + "cell_type": "code", + "source": "from python_workflow_definition.pyiron_base import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 22 + }, + { + "id": "4452a648-d4c3-4f5f-8678-ffb54bef17dc", + "cell_type": "code", + "source": "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "output_type": "display_data", + "data": { + "text/plain": "", + "image/svg+xml": "\n\n\n\n\ncreate_function_job_724cfd00ffeb70f8b463a938195e0447\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf38aa0>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf38830>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf38500>\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf07a10>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf38500>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf07da0>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf381a0>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf38590>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf07b00>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x74ee3cf07d70>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696\n\nsource_directory=/home/jovyan/example_workflows/nfdi/source\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n" + }, + "metadata": {} + } + ], + "execution_count": 23 + }, + { + "id": "1c2760b6-96b4-4f44-ac49-a229d4a0cf67", + "cell_type": "code", + "source": "delayed_object_lst[-1].pull()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": "The job generate_mesh_47725c16637f799ac042e47468005db3 was saved and received the ID: 1\nThe job convert_to_xdmf_d6a46eb9a4ec352aa996e783ec3c785f was saved and received the ID: 2\nThe job poisson_3c147fc86db87cf0c0f94bda333f8cd8 was saved and received the ID: 3\nThe job plot_over_line_ef50933291910dadcc8311924971e127 was saved and received the ID: 4\nThe job substitute_macros_63766eafd6b1980c7832dd8c9a97c96e was saved and received the ID: 5\nThe job compile_paper_128d1d58374953c00e95b8de62cbb10b was saved and received the ID: 6\n" + }, + { + "execution_count": 24, + "output_type": "execute_result", + "data": { + "text/plain": "'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'" + }, + "metadata": {} + } + ], + "execution_count": 24 + } + ] +} diff --git a/example_workflows/nfdi/cwl.ipynb b/example_workflows/nfdi/cwl.ipynb index 0906490..fc40e63 100644 --- a/example_workflows/nfdi/cwl.ipynb +++ b/example_workflows/nfdi/cwl.ipynb @@ -124,7 +124,7 @@ { "name": "stdout", "output_type": "stream", - "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/nfdi/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step generate_mesh_0\n\u001B[1;30mINFO\u001B[0m [step generate_mesh_0] start\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] /tmp/2zy1qyud$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/3kq1m6dv/stgfdd0e5fa-ab2c-4ee5-a621-421e0f130c2d/workflow.py \\\n --function=workflow.generate_mesh \\\n --arg_source_directory=/tmp/3kq1m6dv/stgb3cb8d7a-2fd4-4bed-bddd-a53347db76d4/source_directory.pickle \\\n --arg_domain_size=/tmp/3kq1m6dv/stgf88b878d-cda3-46dc-b95b-1a5866fc79df/domain_size.pickle\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] Max memory used: 51MiB\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] completed success\n\u001B[1;30mINFO\u001B[0m [step generate_mesh_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step convert_to_xdmf_1\n\u001B[1;30mINFO\u001B[0m [step convert_to_xdmf_1] start\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] /tmp/wtfrae9y$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/mnez84gw/stg3b3a2c97-dc53-4fa4-8b26-1c0ef725455a/workflow.py \\\n --function=workflow.convert_to_xdmf \\\n --arg_gmsh_output_file=/tmp/mnez84gw/stg7cb20c0e-e3a4-40c7-b347-90b3861ac948/result.pickle\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] Max memory used: 62MiB\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] completed success\n\u001B[1;30mINFO\u001B[0m [step convert_to_xdmf_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step poisson_2\n\u001B[1;30mINFO\u001B[0m [step poisson_2] start\n\u001B[1;30mINFO\u001B[0m [job poisson_2] /tmp/c25cseik$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/mdjrrwsb/stg9fc40fe1-ad74-4530-9b90-3f25cda3228b/workflow.py \\\n --function=workflow.poisson \\\n --arg_source_directory=/tmp/mdjrrwsb/stg95c5865b-b3b7-41a3-9f91-8c0d4e64e2cc/source_directory.pickle \\\n --arg_meshio_output_xdmf=/tmp/mdjrrwsb/stg3f852952-6283-4843-8a5a-799885c3a16f/xdmf_file.pickle \\\n --arg_meshio_output_h5=/tmp/mdjrrwsb/stg4c12ec47-0d6d-4749-afb0-b44bcfdae15c/h5_file.pickle\n\u001B[1;30mINFO\u001B[0m [job poisson_2] Max memory used: 71MiB\n\u001B[1;30mINFO\u001B[0m [job poisson_2] completed success\n\u001B[1;30mINFO\u001B[0m [step poisson_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step plot_over_line_3\n\u001B[1;30mINFO\u001B[0m [step plot_over_line_3] start\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] /tmp/6taq1l9y$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/fr8grips/stgcc344580-aae9-480d-915b-b011888e11a9/workflow.py \\\n --function=workflow.plot_over_line \\\n --arg_poisson_output_pvd_file=/tmp/fr8grips/stg7c2c93df-069a-4d33-8ebc-402be33d67d0/pvd_file.pickle \\\n --arg_poisson_output_vtu_file=/tmp/fr8grips/stg481f6c15-8e7c-4198-9f1b-d61aa097b829/vtu_file.pickle \\\n --arg_source_directory=/tmp/fr8grips/stge25af463-7689-43d8-b783-165f68b907bd/source_directory.pickle\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] Max memory used: 71MiB\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] completed success\n\u001B[1;30mINFO\u001B[0m [step plot_over_line_3] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step substitute_macros_4\n\u001B[1;30mINFO\u001B[0m [step substitute_macros_4] start\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] /tmp/ry44k1po$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/_yac4p7u/stge908c7b1-0d4d-44a4-a2d4-62c97b75d25f/workflow.py \\\n --function=workflow.substitute_macros \\\n --arg_ndofs=/tmp/_yac4p7u/stgd19106a7-26ec-4159-87e5-c55df4e05b3e/numdofs.pickle \\\n --arg_source_directory=/tmp/_yac4p7u/stgea87bc3d-5042-4044-b2bb-58a83646f704/source_directory.pickle \\\n --arg_pvbatch_output_file=/tmp/_yac4p7u/stga426ce18-a7c0-4941-9b4c-988615fb6dd6/result.pickle \\\n --arg_domain_size=/tmp/_yac4p7u/stg75e4cce3-e411-4ffe-b1df-e5d40daa8d61/domain_size.pickle\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] Max memory used: 92MiB\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] completed success\n\u001B[1;30mINFO\u001B[0m [step substitute_macros_4] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step compile_paper_5\n\u001B[1;30mINFO\u001B[0m [step compile_paper_5] start\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] /tmp/u4tewx74$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/c_jbp86a/stge99c916c-dabe-474c-b5f1-947214d3f9ed/workflow.py \\\n --function=workflow.compile_paper \\\n --arg_source_directory=/tmp/c_jbp86a/stg09ed111f-9743-4670-a6e6-182b1b32360d/source_directory.pickle \\\n --arg_plot_file=/tmp/c_jbp86a/stg5649e17e-4a2b-416c-8107-31df66b6e769/result.pickle \\\n --arg_macros_tex=/tmp/c_jbp86a/stg26421152-a968-4c63-97a0-8ed741b07f1a/result.pickle\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] Max memory used: 260MiB\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] completed success\n\u001B[1;30mINFO\u001B[0m [step compile_paper_5] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/nfdi/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$1be622d292821508f2a41ec4bc8a04d06dfbdbaf\",\n \"size\": 53,\n \"path\": \"/home/jovyan/example_workflows/nfdi/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" + "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/nfdi/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step generate_mesh_0\n\u001B[1;30mINFO\u001B[0m [step generate_mesh_0] start\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] /tmp/xjzxjjxg$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/lint8hha/stgaa9fa1cf-dae6-4402-aa25-3da9289e3937/workflow.py \\\n --function=workflow.generate_mesh \\\n --arg_domain_size=/tmp/lint8hha/stg94834a09-0454-4ad4-bc93-b8f3a1dc72f4/domain_size.pickle \\\n --arg_source_directory=/tmp/lint8hha/stg03fa6508-a0ea-4379-97b1-e3815dfe7395/source_directory.pickle\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] Max memory used: 60MiB\n\u001B[1;30mINFO\u001B[0m [job generate_mesh_0] completed success\n\u001B[1;30mINFO\u001B[0m [step generate_mesh_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step convert_to_xdmf_1\n\u001B[1;30mINFO\u001B[0m [step convert_to_xdmf_1] start\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] /tmp/q47niux0$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/pd0inpeh/stg928009b1-efc5-45d7-9746-e1af8d96f0c5/workflow.py \\\n --function=workflow.convert_to_xdmf \\\n --arg_gmsh_output_file=/tmp/pd0inpeh/stg03750262-f7c4-4bb9-b558-0b7ea0a54cf3/result.pickle\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] Max memory used: 69MiB\n\u001B[1;30mINFO\u001B[0m [job convert_to_xdmf_1] completed success\n\u001B[1;30mINFO\u001B[0m [step convert_to_xdmf_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step poisson_2\n\u001B[1;30mINFO\u001B[0m [step poisson_2] start\n\u001B[1;30mINFO\u001B[0m [job poisson_2] /tmp/e045_wvq$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/rsa0i3o4/stgfd3d067f-0d0e-46b6-8b1c-e63a936cca99/workflow.py \\\n --function=workflow.poisson \\\n --arg_meshio_output_xdmf=/tmp/rsa0i3o4/stgebd53ba4-dbbc-4769-b359-f1f95611d02d/xdmf_file.pickle \\\n --arg_meshio_output_h5=/tmp/rsa0i3o4/stga4bcfd98-5bf0-4da3-b1e6-a4d55a00cc30/h5_file.pickle \\\n --arg_source_directory=/tmp/rsa0i3o4/stg003e0d81-81e0-4138-9e97-103a910c925e/source_directory.pickle\n\u001B[1;30mINFO\u001B[0m [job poisson_2] Max memory used: 81MiB\n\u001B[1;30mINFO\u001B[0m [job poisson_2] completed success\n\u001B[1;30mINFO\u001B[0m [step poisson_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step plot_over_line_3\n\u001B[1;30mINFO\u001B[0m [step plot_over_line_3] start\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] /tmp/0tov09ih$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/z9a5oiuc/stgcde66eb7-274f-4ae3-833b-c8d99fe3bbb1/workflow.py \\\n --function=workflow.plot_over_line \\\n --arg_poisson_output_vtu_file=/tmp/z9a5oiuc/stg144f313e-e286-4800-a3d2-86a6cae36a98/vtu_file.pickle \\\n --arg_source_directory=/tmp/z9a5oiuc/stg224c0c40-7cb8-4f1c-921c-013809fb5cbf/source_directory.pickle \\\n --arg_poisson_output_pvd_file=/tmp/z9a5oiuc/stgc4c75ca6-aab0-40be-bfbd-f432d3523d2b/pvd_file.pickle\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] Max memory used: 68MiB\n\u001B[1;30mINFO\u001B[0m [job plot_over_line_3] completed success\n\u001B[1;30mINFO\u001B[0m [step plot_over_line_3] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step substitute_macros_4\n\u001B[1;30mINFO\u001B[0m [step substitute_macros_4] start\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] /tmp/08mfe8f0$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/5valbs4a/stg15353150-ebc3-49de-93a8-564a25f33270/workflow.py \\\n --function=workflow.substitute_macros \\\n --arg_domain_size=/tmp/5valbs4a/stg0734ab21-1efd-480b-ba2b-cea9ed24012e/domain_size.pickle \\\n --arg_source_directory=/tmp/5valbs4a/stg0c79cde6-159f-4b82-bdb9-aabef8678f9f/source_directory.pickle \\\n --arg_ndofs=/tmp/5valbs4a/stg770f9cb7-d2c3-4ce5-bc00-7a9cdb11d64d/numdofs.pickle \\\n --arg_pvbatch_output_file=/tmp/5valbs4a/stgdd978452-6c84-4308-abf6-7ae2609fc91d/result.pickle\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] Max memory used: 60MiB\n\u001B[1;30mINFO\u001B[0m [job substitute_macros_4] completed success\n\u001B[1;30mINFO\u001B[0m [step substitute_macros_4] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step compile_paper_5\n\u001B[1;30mINFO\u001B[0m [step compile_paper_5] start\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] /tmp/hjjeng16$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/3bq2mxdl/stg34a5d902-97c3-43f1-95eb-5e14d0c68386/workflow.py \\\n --function=workflow.compile_paper \\\n --arg_macros_tex=/tmp/3bq2mxdl/stg184e0acf-5138-4b37-97f0-ba406ed71433/result.pickle \\\n --arg_plot_file=/tmp/3bq2mxdl/stg2360c6e9-26ec-43f5-99a2-26c05668b2fa/result.pickle \\\n --arg_source_directory=/tmp/3bq2mxdl/stg7194b36e-38db-4ef7-af5d-368e9575f15f/source_directory.pickle\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] Max memory used: 265MiB\n\u001B[1;30mINFO\u001B[0m [job compile_paper_5] completed success\n\u001B[1;30mINFO\u001B[0m [step compile_paper_5] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/nfdi/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$a23617d3f4b4e6970b7f4fb9eb4d2148f9888e58\",\n \"size\": 53,\n \"path\": \"/home/jovyan/example_workflows/nfdi/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" } ], "execution_count": 9 @@ -140,7 +140,7 @@ { "name": "stdout", "output_type": "stream", - "text": "/tmp/u4tewx74/postprocessing/paper.pdf\n" + "text": "/tmp/hjjeng16/postprocessing/paper.pdf\n" } ], "execution_count": 10 diff --git a/example_workflows/nfdi/jobflow.ipynb b/example_workflows/nfdi/jobflow.ipynb index f5df278..69c8916 100644 --- a/example_workflows/nfdi/jobflow.ipynb +++ b/example_workflows/nfdi/jobflow.ipynb @@ -1 +1,332 @@ -{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"048b53d1-db08-44ff-84cc-a4ff50032944","cell_type":"markdown","source":"# jobflow","metadata":{}},{"id":"106ded66-d202-46ac-82b0-2755ca309bdd","cell_type":"markdown","source":"https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements","metadata":{}},{"id":"856b2ba2-93d5-4516-93e1-a1eac49c48f2","cell_type":"markdown","source":"## Define workflow with jobflow","metadata":{}},{"id":"43d5c810-a701-4971-8534-56dcbd112716","cell_type":"code","source":"import os","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"89c02460-b543-442c-a27e-f1757dc2262e","cell_type":"code","source":"from jobflow import job, Flow\n\nfrom python_workflow_definition.jobflow import write_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":2},{"id":"864f048d78ea3f08","cell_type":"code","source":"from workflow import (\n generate_mesh as _generate_mesh, \n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line as _plot_over_line,\n substitute_macros as _substitute_macros,\n compile_paper as _compile_paper,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"147b81b7b494ceda","cell_type":"code","source":"generate_mesh = job(_generate_mesh)\nconvert_to_xdmf = job(_convert_to_xdmf)\npoisson = job(_poisson)\nplot_over_line = job(_plot_over_line)\nsubstitute_macros = job(_substitute_macros)\ncompile_paper = job(_compile_paper)","metadata":{"trusted":true},"outputs":[],"execution_count":4},{"id":"981e548b-a3b4-49a3-9653-85e90f05c60e","cell_type":"code","source":"source_directory = os.path.abspath(os.path.join(os.curdir, \"source\"))","metadata":{"trusted":true},"outputs":[],"execution_count":5},{"id":"8d911f98-3b80-457f-a0f4-3cb37ebf1691","cell_type":"code","source":"domain_size = 2.0","metadata":{"trusted":true},"outputs":[],"execution_count":6},{"id":"71d411b6-cbec-489e-99e3-ba71680bcb5b","cell_type":"code","source":"gmsh_output_file = generate_mesh(\n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":7},{"id":"1d0d9804-f250-48b3-a5d0-a546d520f79b","cell_type":"code","source":"meshio_output_dict = convert_to_xdmf(\n gmsh_output_file=gmsh_output_file.output,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":8},{"id":"7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590","cell_type":"code","source":"poisson_dict = poisson(\n meshio_output_xdmf=meshio_output_dict.output.xdmf_file, \n meshio_output_h5=meshio_output_dict.output.h5_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":9},{"id":"3c4a29b0-eb1e-490a-8be0-e03cfff15e0a","cell_type":"code","source":"pvbatch_output_file = plot_over_line(\n poisson_output_pvd_file=poisson_dict.output.pvd_file, \n poisson_output_vtu_file=poisson_dict.output.vtu_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":10},{"id":"a0a4c233-322d-4723-9627-62ca2487bfa9","cell_type":"code","source":"macros_tex_file = substitute_macros( \n pvbatch_output_file=pvbatch_output_file.output, \n ndofs=poisson_dict.output.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":11},{"id":"c281408f-e63d-4380-a7e6-c595d49fbb8f","cell_type":"code","source":"paper_output = compile_paper(\n macros_tex=macros_tex_file.output, \n plot_file=pvbatch_output_file.output,\n source_directory=source_directory,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":12},{"id":"a384d70a-8ef5-4fdd-880c-56ac7eaf87b9","cell_type":"code","source":"flow = Flow([gmsh_output_file, meshio_output_dict, poisson_dict, pvbatch_output_file, macros_tex_file, paper_output])","metadata":{"trusted":true},"outputs":[],"execution_count":13},{"id":"fb23ad9c-76fd-4c0b-b546-e305d6c49796","cell_type":"code","source":"workflow_json_filename = \"jobflow_nfdi.json\"","metadata":{"trusted":true},"outputs":[],"execution_count":14},{"id":"4139547a-9717-4708-b1a5-8202a0382d77","cell_type":"code","source":"write_workflow_json(flow=flow, file_name=workflow_json_filename)","metadata":{"trusted":true},"outputs":[],"execution_count":15},{"id":"11a829e2-face-469f-b343-2c95763b1f13","cell_type":"markdown","source":"## Load Workflow with aiida","metadata":{}},{"id":"4f3acabe-55df-479a-af4d-a23a80c4660d","cell_type":"code","source":"from aiida import load_profile\n\nload_profile()","metadata":{"trusted":true},"outputs":[{"execution_count":16,"output_type":"execute_result","data":{"text/plain":"Profile"},"metadata":{}}],"execution_count":16},{"id":"b6ba9444-a2c8-451b-b74c-19b0f69ba369","cell_type":"code","source":"from python_workflow_definition.aiida import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":17},{"id":"c3528d55-6bf7-47ed-a110-65c47446ba92","cell_type":"code","source":"wg = load_workflow_json(file_name=workflow_json_filename)\nwg","metadata":{"trusted":true},"outputs":[{"execution_count":18,"output_type":"execute_result","data":{"text/plain":"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":1,"model_id":"fd19d63f68234bebaa4e1db7d6dcfc99"}},"metadata":{}}],"execution_count":18},{"id":"5ef48778-4209-425f-8c6b-85a4cd2f92ec","cell_type":"code","source":"wg.run()","metadata":{"trusted":true},"outputs":[{"name":"stderr","output_type":"stream","text":"05/14/2025 08:21:04 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh1\n05/14/2025 08:21:06 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: generate_mesh1, type: PyFunction, finished.\n05/14/2025 08:21:06 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf2\n05/14/2025 08:21:08 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf2, type: PyFunction, finished.\n05/14/2025 08:21:08 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson3\n05/14/2025 08:21:11 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: poisson3, type: PyFunction, finished.\n05/14/2025 08:21:11 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line4\n05/14/2025 08:21:13 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: plot_over_line4, type: PyFunction, finished.\n05/14/2025 08:21:13 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros5\n05/14/2025 08:21:14 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: substitute_macros5, type: PyFunction, finished.\n05/14/2025 08:21:14 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper6\n05/14/2025 08:21:17 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: compile_paper6, type: PyFunction, finished.\n05/14/2025 08:21:17 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/14/2025 08:21:17 AM <3280> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|finalize]: Finalize workgraph.\n"}],"execution_count":19},{"id":"397b16a2-e1ec-4eec-8562-1c84f585c347","cell_type":"markdown","source":"## Load Workflow with pyiron_base","metadata":{}},{"id":"be4d5d93-e9f6-4072-a6be-0ee5dc93590f","cell_type":"code","source":"from python_workflow_definition.pyiron_base import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":20},{"id":"4452a648-d4c3-4f5f-8678-ffb54bef17dc","cell_type":"code","source":"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()","metadata":{"trusted":true},"outputs":[{"output_type":"display_data","data":{"text/plain":"","image/svg+xml":"\n\n\n\n\ncreate_function_job_9564f1c400f389023de93231c8a62a65\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a77d0>\n\n\n\nmacros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a75f0>\n\n\n\nmacros_tex_4fdd7c93c52394e1a5aed103adf6dba4->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\npvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a7320>\n\n\n\npvbatch_output_file_e4a68dc408161a17988f364b0337f341->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a7020>\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nplot_file_e4a68dc408161a17988f364b0337f341\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a7320>\n\n\n\npoisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nplot_file_e4a68dc408161a17988f364b0337f341->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x7efce8178620>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a6ff0>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a73b0>\n\n\n\nmeshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\npoisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nndofs_8b9741bf01bd3f1fc0fe9a772777a903->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7efce8ba3e90>\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1->meshio_output_xdmf_6ee525037bdcb254ca562ddfe379237e\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x7efce81a6d20>\n\n\n\ngmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1->meshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nmeshio_output_h5_f154dadcde14b5da6730af6d0a4c9df7->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696\n\nsource_directory=/home/jovyan/example_workflows/nfdi/source\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->create_function_job_9564f1c400f389023de93231c8a62a65\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->macros_tex_4fdd7c93c52394e1a5aed103adf6dba4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->pvbatch_output_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_pvd_file_7da70c04cc70bbdbd26f7da8deeaca29\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->plot_file_e4a68dc408161a17988f364b0337f341\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_vtu_file_fa01b3a624ada2dba805b7518365a6a4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->ndofs_8b9741bf01bd3f1fc0fe9a772777a903\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->gmsh_output_file_4b409dc4c5063e64794e38b2cd0b37e1\n\n\n\n\n"},"metadata":{}}],"execution_count":21},{"id":"1c2760b6-96b4-4f44-ac49-a229d4a0cf67","cell_type":"code","source":"delayed_object_lst[-1].pull()","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"The job generate_mesh_47725c16637f799ac042e47468005db3 was saved and received the ID: 1\nThe job convert_to_xdmf_d6a46eb9a4ec352aa996e783ec3c785f was saved and received the ID: 2\nThe job poisson_3c147fc86db87cf0c0f94bda333f8cd8 was saved and received the ID: 3\nThe job plot_over_line_ef50933291910dadcc8311924971e127 was saved and received the ID: 4\nThe job substitute_macros_63766eafd6b1980c7832dd8c9a97c96e was saved and received the ID: 5\nThe job compile_paper_128d1d58374953c00e95b8de62cbb10b was saved and received the ID: 6\n"},{"execution_count":22,"output_type":"execute_result","data":{"text/plain":"'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'"},"metadata":{}}],"execution_count":22}]} \ No newline at end of file +{ + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12.8", + "mimetype": "text/x-python", + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "pygments_lexer": "ipython3", + "nbconvert_exporter": "python", + "file_extension": ".py" + } + }, + "nbformat_minor": 5, + "nbformat": 4, + "cells": [ + { + "id": "048b53d1-db08-44ff-84cc-a4ff50032944", + "cell_type": "markdown", + "source": "# jobflow", + "metadata": {} + }, + { + "id": "106ded66-d202-46ac-82b0-2755ca309bdd", + "cell_type": "markdown", + "source": "https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements", + "metadata": {} + }, + { + "id": "856b2ba2-93d5-4516-93e1-a1eac49c48f2", + "cell_type": "markdown", + "source": "## Define workflow with jobflow", + "metadata": {} + }, + { + "id": "43d5c810-a701-4971-8534-56dcbd112716", + "cell_type": "code", + "source": "import os", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 1 + }, + { + "id": "89c02460-b543-442c-a27e-f1757dc2262e", + "cell_type": "code", + "source": "from jobflow import job, Flow\n\nfrom python_workflow_definition.jobflow import write_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 2 + }, + { + "id": "864f048d78ea3f08", + "cell_type": "code", + "source": "from workflow import (\n generate_mesh as _generate_mesh, \n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line as _plot_over_line,\n substitute_macros as _substitute_macros,\n compile_paper as _compile_paper,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 3 + }, + { + "id": "147b81b7b494ceda", + "cell_type": "code", + "source": "generate_mesh = job(_generate_mesh)\nconvert_to_xdmf = job(_convert_to_xdmf)\npoisson = job(_poisson)\nplot_over_line = job(_plot_over_line)\nsubstitute_macros = job(_substitute_macros)\ncompile_paper = job(_compile_paper)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 4 + }, + { + "id": "981e548b-a3b4-49a3-9653-85e90f05c60e", + "cell_type": "code", + "source": "source_directory = os.path.abspath(os.path.join(os.curdir, \"source\"))", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 5 + }, + { + "id": "8d911f98-3b80-457f-a0f4-3cb37ebf1691", + "cell_type": "code", + "source": "domain_size = 2.0", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 6 + }, + { + "id": "71d411b6-cbec-489e-99e3-ba71680bcb5b", + "cell_type": "code", + "source": "gmsh_output_file = generate_mesh(\n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 7 + }, + { + "id": "1d0d9804-f250-48b3-a5d0-a546d520f79b", + "cell_type": "code", + "source": "meshio_output_dict = convert_to_xdmf(\n gmsh_output_file=gmsh_output_file.output,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 8 + }, + { + "id": "7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590", + "cell_type": "code", + "source": "poisson_dict = poisson(\n meshio_output_xdmf=meshio_output_dict.output.xdmf_file, \n meshio_output_h5=meshio_output_dict.output.h5_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 9 + }, + { + "id": "3c4a29b0-eb1e-490a-8be0-e03cfff15e0a", + "cell_type": "code", + "source": "pvbatch_output_file = plot_over_line(\n poisson_output_pvd_file=poisson_dict.output.pvd_file, \n poisson_output_vtu_file=poisson_dict.output.vtu_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 10 + }, + { + "id": "a0a4c233-322d-4723-9627-62ca2487bfa9", + "cell_type": "code", + "source": "macros_tex_file = substitute_macros( \n pvbatch_output_file=pvbatch_output_file.output, \n ndofs=poisson_dict.output.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 11 + }, + { + "id": "c281408f-e63d-4380-a7e6-c595d49fbb8f", + "cell_type": "code", + "source": "paper_output = compile_paper(\n macros_tex=macros_tex_file.output, \n plot_file=pvbatch_output_file.output,\n source_directory=source_directory,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 12 + }, + { + "id": "a384d70a-8ef5-4fdd-880c-56ac7eaf87b9", + "cell_type": "code", + "source": "flow = Flow([gmsh_output_file, meshio_output_dict, poisson_dict, pvbatch_output_file, macros_tex_file, paper_output])", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 13 + }, + { + "id": "fb23ad9c-76fd-4c0b-b546-e305d6c49796", + "cell_type": "code", + "source": "workflow_json_filename = \"jobflow_nfdi.json\"", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 14 + }, + { + "id": "4139547a-9717-4708-b1a5-8202a0382d77", + "cell_type": "code", + "source": "write_workflow_json(flow=flow, file_name=workflow_json_filename)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 15 + }, + { + "id": "11a829e2-face-469f-b343-2c95763b1f13", + "cell_type": "markdown", + "source": "## Load Workflow with aiida", + "metadata": {} + }, + { + "id": "4f3acabe-55df-479a-af4d-a23a80c4660d", + "cell_type": "code", + "source": "from aiida import load_profile\n\nload_profile()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 16, + "output_type": "execute_result", + "data": { + "text/plain": "Profile" + }, + "metadata": {} + } + ], + "execution_count": 16 + }, + { + "id": "b6ba9444-a2c8-451b-b74c-19b0f69ba369", + "cell_type": "code", + "source": "from python_workflow_definition.aiida import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 17 + }, + { + "id": "c3528d55-6bf7-47ed-a110-65c47446ba92", + "cell_type": "code", + "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 18, + "output_type": "execute_result", + "data": { + "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…", + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 1, + "model_id": "47a0a80d777f424aa98a551c4cbe7e1e" + } + }, + "metadata": {} + } + ], + "execution_count": 18 + }, + { + "id": "5ef48778-4209-425f-8c6b-85a4cd2f92ec", + "cell_type": "code", + "source": "wg.run()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": "05/24/2025 05:44:19 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh1\n05/24/2025 05:44:21 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: generate_mesh1, type: PyFunction, finished.\n05/24/2025 05:44:21 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf2\n05/24/2025 05:44:22 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf2, type: PyFunction, finished.\n05/24/2025 05:44:22 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson3\n05/24/2025 05:44:25 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: poisson3, type: PyFunction, finished.\n05/24/2025 05:44:25 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line4\n05/24/2025 05:44:27 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: plot_over_line4, type: PyFunction, finished.\n05/24/2025 05:44:27 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros5\n05/24/2025 05:44:29 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: substitute_macros5, type: PyFunction, finished.\n05/24/2025 05:44:29 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper6\n05/24/2025 05:44:31 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|update_task_state]: Task: compile_paper6, type: PyFunction, finished.\n05/24/2025 05:44:31 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:44:31 AM <3034> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [51|WorkGraphEngine|finalize]: Finalize workgraph.\n" + } + ], + "execution_count": 19 + }, + { + "id": "397b16a2-e1ec-4eec-8562-1c84f585c347", + "cell_type": "markdown", + "source": "## Load Workflow with pyiron_base", + "metadata": {} + }, + { + "id": "be4d5d93-e9f6-4072-a6be-0ee5dc93590f", + "cell_type": "code", + "source": "from python_workflow_definition.pyiron_base import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 20 + }, + { + "id": "4452a648-d4c3-4f5f-8678-ffb54bef17dc", + "cell_type": "code", + "source": "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "output_type": "display_data", + "data": { + "text/plain": "", + "image/svg+xml": "\n\n\n\n\ncreate_function_job_724cfd00ffeb70f8b463a938195e0447\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b9b80>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b9910>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b95e0>\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b9280>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b95e0>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b8e90>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b9250>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b9670>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b8b90>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x7da7483b8e60>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696\n\nsource_directory=/home/jovyan/example_workflows/nfdi/source\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n" + }, + "metadata": {} + } + ], + "execution_count": 21 + }, + { + "id": "1c2760b6-96b4-4f44-ac49-a229d4a0cf67", + "cell_type": "code", + "source": "delayed_object_lst[-1].pull()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": "The job generate_mesh_47725c16637f799ac042e47468005db3 was saved and received the ID: 1\nThe job convert_to_xdmf_d6a46eb9a4ec352aa996e783ec3c785f was saved and received the ID: 2\nThe job poisson_3c147fc86db87cf0c0f94bda333f8cd8 was saved and received the ID: 3\nThe job plot_over_line_ef50933291910dadcc8311924971e127 was saved and received the ID: 4\nThe job substitute_macros_63766eafd6b1980c7832dd8c9a97c96e was saved and received the ID: 5\nThe job compile_paper_128d1d58374953c00e95b8de62cbb10b was saved and received the ID: 6\n" + }, + { + "execution_count": 22, + "output_type": "execute_result", + "data": { + "text/plain": "'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'" + }, + "metadata": {} + } + ], + "execution_count": 22 + } + ] +} diff --git a/example_workflows/nfdi/pyiron_base.ipynb b/example_workflows/nfdi/pyiron_base.ipynb index 0c91dd0..99c9a1c 100644 --- a/example_workflows/nfdi/pyiron_base.ipynb +++ b/example_workflows/nfdi/pyiron_base.ipynb @@ -1 +1,317 @@ -{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"106ded66-d202-46ac-82b0-2755ca309bdd","cell_type":"markdown","source":"# pyiron\n\nhttps://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements","metadata":{}},{"id":"91dd48ea-aa7e-4937-a68e-59fc5017eb1e","cell_type":"markdown","source":"## Define workflow with pyiron_base","metadata":{}},{"id":"2c9622f5-ab7e-460e-b8e4-8d21413eda77","cell_type":"code","source":"import os ","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"d265bb5aa6af79d6","cell_type":"code","source":"from workflow import (\n generate_mesh as _generate_mesh, \n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line as _plot_over_line,\n substitute_macros as _substitute_macros,\n compile_paper as _compile_paper,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":2},{"id":"2dced28725813fc1","cell_type":"code","source":"from pyiron_base import job\n\nfrom python_workflow_definition.pyiron_base import write_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"549ecf27-88ef-4e77-8bd4-b616cfdda2e4","cell_type":"code","source":"generate_mesh = job(_generate_mesh)\nconvert_to_xdmf = job(_convert_to_xdmf, output_key_lst=[\"xdmf_file\", \"h5_file\"])\npoisson = job(_poisson, output_key_lst=[\"numdofs\", \"pvd_file\", \"vtu_file\"])\nplot_over_line = job(_plot_over_line)\nsubstitute_macros = job(_substitute_macros)\ncompile_paper = job(_compile_paper)","metadata":{"trusted":true},"outputs":[],"execution_count":4},{"id":"8d911f98-3b80-457f-a0f4-3cb37ebf1691","cell_type":"code","source":"domain_size = 2.0","metadata":{"trusted":true},"outputs":[],"execution_count":5},{"id":"c6ea980b-6761-4191-8407-7b1f78a4c3ea","cell_type":"code","source":"source_directory = os.path.abspath(os.path.join(os.curdir, \"source\"))","metadata":{"trusted":true},"outputs":[],"execution_count":6},{"id":"71d411b6-cbec-489e-99e3-ba71680bcb5b","cell_type":"code","source":"gmsh_output_file = generate_mesh(\n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":7},{"id":"1d0d9804-f250-48b3-a5d0-a546d520f79b","cell_type":"code","source":"meshio_output_dict = convert_to_xdmf(\n gmsh_output_file=gmsh_output_file,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":8},{"id":"7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590","cell_type":"code","source":"poisson_dict = poisson(\n meshio_output_xdmf=meshio_output_dict.output.xdmf_file, \n meshio_output_h5=meshio_output_dict.output.h5_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":9},{"id":"3c4a29b0-eb1e-490a-8be0-e03cfff15e0a","cell_type":"code","source":"pvbatch_output_file = plot_over_line(\n poisson_output_pvd_file=poisson_dict.output.pvd_file, \n poisson_output_vtu_file=poisson_dict.output.vtu_file,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":10},{"id":"a0a4c233-322d-4723-9627-62ca2487bfa9","cell_type":"code","source":"macros_tex_file = substitute_macros( \n pvbatch_output_file=pvbatch_output_file, \n ndofs=poisson_dict.output.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)","metadata":{"tags":[],"trusted":true},"outputs":[],"execution_count":11},{"id":"c281408f-e63d-4380-a7e6-c595d49fbb8f","cell_type":"code","source":"paper_output = compile_paper(\n macros_tex=macros_tex_file, \n plot_file=pvbatch_output_file,\n source_directory=source_directory,\n)","metadata":{"trusted":true},"outputs":[],"execution_count":12},{"id":"63f29646-3846-4a97-a033-20e9df0ac214","cell_type":"code","source":"workflow_json_filename = \"pyiron_base_nfdi.json\"","metadata":{"trusted":true},"outputs":[],"execution_count":13},{"id":"f62111ba-9271-4987-9c7e-3b1c9f9eae7a","cell_type":"code","source":"write_workflow_json(delayed_object=paper_output, file_name=workflow_json_filename)","metadata":{"trusted":true},"outputs":[],"execution_count":14},{"id":"d789971e-8f41-45fa-832a-11fd72dea96e","cell_type":"markdown","source":"## Load Workflow with aiida","metadata":{}},{"id":"a6e85e89-5d7a-40eb-809c-ac44974e3fd7","cell_type":"code","source":"from aiida import load_profile\n\nload_profile()","metadata":{"trusted":true},"outputs":[{"execution_count":15,"output_type":"execute_result","data":{"text/plain":"Profile"},"metadata":{}}],"execution_count":15},{"id":"3de84fb7-b01b-4541-868a-92e881eb6e77","cell_type":"code","source":"from python_workflow_definition.aiida import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":16},{"id":"b33f5528-10cd-47c8-8723-622902978859","cell_type":"code","source":"wg = load_workflow_json(file_name=workflow_json_filename)\nwg","metadata":{"trusted":true},"outputs":[{"execution_count":17,"output_type":"execute_result","data":{"text/plain":"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":1,"model_id":"ab6acab36bbd42c9860072a9faa50796"}},"metadata":{}}],"execution_count":17},{"id":"15282ca1-d339-40e7-ad68-8a7613ed08da","cell_type":"code","source":"wg.run()","metadata":{"trusted":true},"outputs":[{"name":"stderr","output_type":"stream","text":"05/14/2025 08:13:58 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh6\n05/14/2025 08:14:00 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: generate_mesh6, type: PyFunction, finished.\n05/14/2025 08:14:00 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf5\n05/14/2025 08:14:02 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf5, type: PyFunction, finished.\n05/14/2025 08:14:02 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson4\n05/14/2025 08:14:10 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: poisson4, type: PyFunction, finished.\n05/14/2025 08:14:10 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line3\n05/14/2025 08:14:12 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: plot_over_line3, type: PyFunction, finished.\n05/14/2025 08:14:12 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros2\n05/14/2025 08:14:13 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: substitute_macros2, type: PyFunction, finished.\n05/14/2025 08:14:13 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper1\n05/14/2025 08:15:13 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|update_task_state]: Task: compile_paper1, type: PyFunction, finished.\n05/14/2025 08:15:13 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/14/2025 08:15:13 AM <465> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21|WorkGraphEngine|finalize]: Finalize workgraph.\n"}],"execution_count":18},{"id":"55dc8d12-dfe6-4465-a368-b7e590ae6800","cell_type":"markdown","source":"## Load Workflow with jobflow","metadata":{}},{"id":"dff46eb8-e0e7-49bb-8c40-0db2df133124","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":19},{"id":"6a189459-84e4-4738-ada1-37ee8c65b2ab","cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":true},"outputs":[],"execution_count":20},{"id":"6e7f3614-c971-4e2d-83f0-96f0d0fc04de","cell_type":"code","source":"flow = load_workflow_json(file_name=workflow_json_filename)","metadata":{"trusted":true},"outputs":[],"execution_count":21},{"id":"2d87ed45-f5d9-403f-a03a-26be4a47a3ef","cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-05-14 08:15:14,382 INFO Started executing jobs locally\n2025-05-14 08:15:14,545 INFO Starting job - generate_mesh (e5f18781-922f-446c-961b-3acdf00c5688)\n2025-05-14 08:15:15,654 INFO Finished job - generate_mesh (e5f18781-922f-446c-961b-3acdf00c5688)\n2025-05-14 08:15:15,655 INFO Starting job - convert_to_xdmf (2ee6c9fd-3a29-4f2a-bf4b-dd588ce58b79)\n2025-05-14 08:15:16,962 INFO Finished job - convert_to_xdmf (2ee6c9fd-3a29-4f2a-bf4b-dd588ce58b79)\n2025-05-14 08:15:16,963 INFO Starting job - poisson (ff73ebf0-2704-4c65-ab6d-a1a880634a1f)\n2025-05-14 08:15:19,635 INFO Finished job - poisson (ff73ebf0-2704-4c65-ab6d-a1a880634a1f)\n2025-05-14 08:15:19,636 INFO Starting job - plot_over_line (7225c5f3-ad66-425c-98b5-786d2a2da40d)\n2025-05-14 08:15:21,057 INFO Finished job - plot_over_line (7225c5f3-ad66-425c-98b5-786d2a2da40d)\n2025-05-14 08:15:21,059 INFO Starting job - substitute_macros (c1ae26db-a52a-491d-b5ea-52060b5fe0a7)\n2025-05-14 08:15:21,885 INFO Finished job - substitute_macros (c1ae26db-a52a-491d-b5ea-52060b5fe0a7)\n2025-05-14 08:15:21,886 INFO Starting job - compile_paper (36f03213-4816-4c5b-aa1a-a643e317e9e9)\n2025-05-14 08:15:24,020 INFO Finished job - compile_paper (36f03213-4816-4c5b-aa1a-a643e317e9e9)\n2025-05-14 08:15:24,021 INFO Finished executing jobs locally\n"},{"execution_count":22,"output_type":"execute_result","data":{"text/plain":"{'e5f18781-922f-446c-961b-3acdf00c5688': {1: Response(output='/home/jovyan/example_workflows/nfdi/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '2ee6c9fd-3a29-4f2a-bf4b-dd588ce58b79': {1: Response(output={'xdmf_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'ff73ebf0-2704-4c65-ab6d-a1a880634a1f': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/example_workflows/nfdi/processing/poisson.pvd', 'vtu_file': '/home/jovyan/example_workflows/nfdi/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '7225c5f3-ad66-425c-98b5-786d2a2da40d': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'c1ae26db-a52a-491d-b5ea-52060b5fe0a7': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '36f03213-4816-4c5b-aa1a-a643e317e9e9': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))}}"},"metadata":{}}],"execution_count":22}]} \ No newline at end of file +{ + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12.8", + "mimetype": "text/x-python", + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "pygments_lexer": "ipython3", + "nbconvert_exporter": "python", + "file_extension": ".py" + } + }, + "nbformat_minor": 5, + "nbformat": 4, + "cells": [ + { + "id": "106ded66-d202-46ac-82b0-2755ca309bdd", + "cell_type": "markdown", + "source": "# pyiron\n\nhttps://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements", + "metadata": {} + }, + { + "id": "91dd48ea-aa7e-4937-a68e-59fc5017eb1e", + "cell_type": "markdown", + "source": "## Define workflow with pyiron_base", + "metadata": {} + }, + { + "id": "2c9622f5-ab7e-460e-b8e4-8d21413eda77", + "cell_type": "code", + "source": "import os", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 1 + }, + { + "id": "d265bb5aa6af79d6", + "cell_type": "code", + "source": "from workflow import (\n generate_mesh as _generate_mesh, \n convert_to_xdmf as _convert_to_xdmf,\n poisson as _poisson,\n plot_over_line as _plot_over_line,\n substitute_macros as _substitute_macros,\n compile_paper as _compile_paper,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 2 + }, + { + "id": "2dced28725813fc1", + "cell_type": "code", + "source": "from pyiron_base import job\n\nfrom python_workflow_definition.pyiron_base import write_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 3 + }, + { + "id": "549ecf27-88ef-4e77-8bd4-b616cfdda2e4", + "cell_type": "code", + "source": "generate_mesh = job(_generate_mesh)\nconvert_to_xdmf = job(_convert_to_xdmf, output_key_lst=[\"xdmf_file\", \"h5_file\"])\npoisson = job(_poisson, output_key_lst=[\"numdofs\", \"pvd_file\", \"vtu_file\"])\nplot_over_line = job(_plot_over_line)\nsubstitute_macros = job(_substitute_macros)\ncompile_paper = job(_compile_paper)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 4 + }, + { + "id": "8d911f98-3b80-457f-a0f4-3cb37ebf1691", + "cell_type": "code", + "source": "domain_size = 2.0", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 5 + }, + { + "id": "c6ea980b-6761-4191-8407-7b1f78a4c3ea", + "cell_type": "code", + "source": "source_directory = os.path.abspath(os.path.join(os.curdir, \"source\"))", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 6 + }, + { + "id": "71d411b6-cbec-489e-99e3-ba71680bcb5b", + "cell_type": "code", + "source": "gmsh_output_file = generate_mesh(\n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 7 + }, + { + "id": "1d0d9804-f250-48b3-a5d0-a546d520f79b", + "cell_type": "code", + "source": "meshio_output_dict = convert_to_xdmf(\n gmsh_output_file=gmsh_output_file,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 8 + }, + { + "id": "7b69bcff-e2b1-4d4a-b62c-6a1c86eeb590", + "cell_type": "code", + "source": "poisson_dict = poisson(\n meshio_output_xdmf=meshio_output_dict.output.xdmf_file, \n meshio_output_h5=meshio_output_dict.output.h5_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 9 + }, + { + "id": "3c4a29b0-eb1e-490a-8be0-e03cfff15e0a", + "cell_type": "code", + "source": "pvbatch_output_file = plot_over_line(\n poisson_output_pvd_file=poisson_dict.output.pvd_file, \n poisson_output_vtu_file=poisson_dict.output.vtu_file,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 10 + }, + { + "id": "a0a4c233-322d-4723-9627-62ca2487bfa9", + "cell_type": "code", + "source": "macros_tex_file = substitute_macros( \n pvbatch_output_file=pvbatch_output_file, \n ndofs=poisson_dict.output.numdofs, \n domain_size=domain_size,\n source_directory=source_directory,\n)", + "metadata": { + "tags": [], + "trusted": true + }, + "outputs": [], + "execution_count": 11 + }, + { + "id": "c281408f-e63d-4380-a7e6-c595d49fbb8f", + "cell_type": "code", + "source": "paper_output = compile_paper(\n macros_tex=macros_tex_file, \n plot_file=pvbatch_output_file,\n source_directory=source_directory,\n)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 12 + }, + { + "id": "63f29646-3846-4a97-a033-20e9df0ac214", + "cell_type": "code", + "source": "workflow_json_filename = \"pyiron_base_nfdi.json\"", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 13 + }, + { + "id": "f62111ba-9271-4987-9c7e-3b1c9f9eae7a", + "cell_type": "code", + "source": "write_workflow_json(delayed_object=paper_output, file_name=workflow_json_filename)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 14 + }, + { + "id": "d789971e-8f41-45fa-832a-11fd72dea96e", + "cell_type": "markdown", + "source": "## Load Workflow with aiida", + "metadata": {} + }, + { + "id": "a6e85e89-5d7a-40eb-809c-ac44974e3fd7", + "cell_type": "code", + "source": "from aiida import load_profile\n\nload_profile()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 15, + "output_type": "execute_result", + "data": { + "text/plain": "Profile" + }, + "metadata": {} + } + ], + "execution_count": 15 + }, + { + "id": "3de84fb7-b01b-4541-868a-92e881eb6e77", + "cell_type": "code", + "source": "from python_workflow_definition.aiida import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 16 + }, + { + "id": "b33f5528-10cd-47c8-8723-622902978859", + "cell_type": "code", + "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "execution_count": 17, + "output_type": "execute_result", + "data": { + "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…", + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 1, + "model_id": "ecd2de75aecb4dc7b8db86590fff92bb" + } + }, + "metadata": {} + } + ], + "execution_count": 17 + }, + { + "id": "15282ca1-d339-40e7-ad68-8a7613ed08da", + "cell_type": "code", + "source": "wg.run()", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": "05/24/2025 05:45:10 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh6\n05/24/2025 05:45:12 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: generate_mesh6, type: PyFunction, finished.\n05/24/2025 05:45:12 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf5\n05/24/2025 05:45:13 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf5, type: PyFunction, finished.\n05/24/2025 05:45:13 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson4\n05/24/2025 05:45:16 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: poisson4, type: PyFunction, finished.\n05/24/2025 05:45:16 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line3\n05/24/2025 05:45:18 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: plot_over_line3, type: PyFunction, finished.\n05/24/2025 05:45:18 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros2\n05/24/2025 05:45:20 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: substitute_macros2, type: PyFunction, finished.\n05/24/2025 05:45:20 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper1\n05/24/2025 05:45:22 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|update_task_state]: Task: compile_paper1, type: PyFunction, finished.\n05/24/2025 05:45:22 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:45:22 AM <4326> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [81|WorkGraphEngine|finalize]: Finalize workgraph.\n" + } + ], + "execution_count": 18 + }, + { + "id": "55dc8d12-dfe6-4465-a368-b7e590ae6800", + "cell_type": "markdown", + "source": "## Load Workflow with jobflow", + "metadata": {} + }, + { + "id": "dff46eb8-e0e7-49bb-8c40-0db2df133124", + "cell_type": "code", + "source": "from python_workflow_definition.jobflow import load_workflow_json", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 19 + }, + { + "id": "6a189459-84e4-4738-ada1-37ee8c65b2ab", + "cell_type": "code", + "source": "from jobflow.managers.local import run_locally", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 20 + }, + { + "id": "6e7f3614-c971-4e2d-83f0-96f0d0fc04de", + "cell_type": "code", + "source": "flow = load_workflow_json(file_name=workflow_json_filename)", + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 21 + }, + { + "id": "2d87ed45-f5d9-403f-a03a-26be4a47a3ef", + "cell_type": "code", + "source": "result = run_locally(flow)\nresult", + "metadata": { + "trusted": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": "2025-05-24 05:45:23,211 INFO Started executing jobs locally\n2025-05-24 05:45:23,487 INFO Starting job - generate_mesh (afd8b83e-2283-40e8-9a75-4553a7ca72d0)\n2025-05-24 05:45:24,604 INFO Finished job - generate_mesh (afd8b83e-2283-40e8-9a75-4553a7ca72d0)\n2025-05-24 05:45:24,605 INFO Starting job - convert_to_xdmf (6723daca-18b6-4f38-8b3e-a92c2a227dc3)\n2025-05-24 05:45:26,001 INFO Finished job - convert_to_xdmf (6723daca-18b6-4f38-8b3e-a92c2a227dc3)\n2025-05-24 05:45:26,002 INFO Starting job - poisson (db43f907-45eb-4596-ac6b-ab5978cc5e17)\n2025-05-24 05:45:28,507 INFO Finished job - poisson (db43f907-45eb-4596-ac6b-ab5978cc5e17)\n2025-05-24 05:45:28,509 INFO Starting job - plot_over_line (b6493a73-f134-4067-ba0d-d6e2cd246afe)\n2025-05-24 05:45:29,933 INFO Finished job - plot_over_line (b6493a73-f134-4067-ba0d-d6e2cd246afe)\n2025-05-24 05:45:29,934 INFO Starting job - substitute_macros (65c3db44-dcc1-44ca-a1bb-374e8f5c771e)\n2025-05-24 05:45:30,774 INFO Finished job - substitute_macros (65c3db44-dcc1-44ca-a1bb-374e8f5c771e)\n2025-05-24 05:45:30,775 INFO Starting job - compile_paper (84277487-0e26-444b-92dc-4516ae8a4eba)\n2025-05-24 05:45:32,790 INFO Finished job - compile_paper (84277487-0e26-444b-92dc-4516ae8a4eba)\n2025-05-24 05:45:32,791 INFO Finished executing jobs locally\n" + }, + { + "execution_count": 22, + "output_type": "execute_result", + "data": { + "text/plain": "{'afd8b83e-2283-40e8-9a75-4553a7ca72d0': {1: Response(output='/home/jovyan/example_workflows/nfdi/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '6723daca-18b6-4f38-8b3e-a92c2a227dc3': {1: Response(output={'xdmf_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'db43f907-45eb-4596-ac6b-ab5978cc5e17': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/example_workflows/nfdi/processing/poisson.pvd', 'vtu_file': '/home/jovyan/example_workflows/nfdi/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'b6493a73-f134-4067-ba0d-d6e2cd246afe': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '65c3db44-dcc1-44ca-a1bb-374e8f5c771e': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '84277487-0e26-444b-92dc-4516ae8a4eba': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))}}" + }, + "metadata": {} + } + ], + "execution_count": 22 + } + ] +} diff --git a/example_workflows/nfdi/universal_workflow.ipynb b/example_workflows/nfdi/universal_workflow.ipynb index e04294b..1efe4fe 100644 --- a/example_workflows/nfdi/universal_workflow.ipynb +++ b/example_workflows/nfdi/universal_workflow.ipynb @@ -51,7 +51,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\n0\n\nnfdi_ing_workflow.generate_mesh\n\n\n\n1\n\nnfdi_ing_workflow.convert_to_xdmf\n\n\n\n0->1\n\n\ngmsh_output_file\n\n\n\n2\n\nnfdi_ing_workflow.poisson\n\n\n\n1->2\n\n\nmeshio_output_xdmf=result[xdmf_file], meshio_output_h5=result[h5_file]\n\n\n\n3\n\nnfdi_ing_workflow.plot_over_line\n\n\n\n2->3\n\n\npoisson_output_pvd_file=result[pvd_file], poisson_output_vtu_file=result[vtu_file]\n\n\n\n4\n\nnfdi_ing_workflow.substitute_macros\n\n\n\n2->4\n\n\nndofs=result[numdofs]\n\n\n\n3->4\n\n\npvbatch_output_file\n\n\n\n5\n\nnfdi_ing_workflow.compile_paper\n\n\n\n3->5\n\n\nplot_file\n\n\n\n4->5\n\n\nmacros_tex\n\n\n\n6\n\n2.0\n\n\n\n6->0\n\n\ndomain_size\n\n\n\n6->4\n\n\ndomain_size\n\n\n" + "image/svg+xml": "\n\n\n\n\n0\n\nworkflow.generate_mesh\n\n\n\n1\n\nworkflow.convert_to_xdmf\n\n\n\n0->1\n\n\ngmsh_output_file\n\n\n\n2\n\nworkflow.poisson\n\n\n\n1->2\n\n\n\n\n\n3\n\nworkflow.plot_over_line\n\n\n\n2->3\n\n\n\n\n\n4\n\nworkflow.substitute_macros\n\n\n\n2->4\n\n\nndofs=result[numdofs]\n\n\n\n3->4\n\n\npvbatch_output_file\n\n\n\n5\n\nworkflow.compile_paper\n\n\n\n3->5\n\n\nplot_file\n\n\n\n4->5\n\n\nmacros_tex\n\n\n\n8\n\nresult\n\n\n\n5->8\n\n\n\n\n\n6\n\n2.0\n\n\n\n6->0\n\n\ndomain_size\n\n\n\n6->4\n\n\ndomain_size\n\n\n\n7\n\n/home/jovyan/example_workflows/nfdi/source\n\n\n\n7->0\n\n\nsource_directory\n\n\n\n7->2\n\n\nsource_directory\n\n\n\n7->3\n\n\nsource_directory\n\n\n\n7->4\n\n\nsource_directory\n\n\n\n7->5\n\n\nsource_directory\n\n\n" }, "metadata": {} } @@ -74,7 +74,7 @@ "execution_count": 3, "output_type": "execute_result", "data": { - "text/plain": "Profile" + "text/plain": "Profile" }, "metadata": {} } @@ -105,7 +105,7 @@ "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 1, - "model_id": "492cc805bc524eaa96137a512b2616fb" + "model_id": "b9f711f3af4b4f9c9f6260d595667b1d" } }, "metadata": {} @@ -123,7 +123,7 @@ { "name": "stderr", "output_type": "stream", - "text": "04/23/2025 09:52:22 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh1\n04/23/2025 09:52:24 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: generate_mesh1, type: PyFunction, finished.\n04/23/2025 09:52:24 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf2\n04/23/2025 09:52:26 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf2, type: PyFunction, finished.\n04/23/2025 09:52:26 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson3\n04/23/2025 09:52:30 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: poisson3, type: PyFunction, finished.\n04/23/2025 09:52:30 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line4\n04/23/2025 09:52:33 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: plot_over_line4, type: PyFunction, finished.\n04/23/2025 09:52:33 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros5\n04/23/2025 09:52:35 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: substitute_macros5, type: PyFunction, finished.\n04/23/2025 09:52:35 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper6\n04/23/2025 09:52:38 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|update_task_state]: Task: compile_paper6, type: PyFunction, finished.\n04/23/2025 09:52:38 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/23/2025 09:52:38 AM <6139> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [284|WorkGraphEngine|finalize]: Finalize workgraph.\n" + "text": "05/24/2025 05:45:59 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_mesh1\n05/24/2025 05:46:01 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: generate_mesh1, type: PyFunction, finished.\n05/24/2025 05:46:01 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: convert_to_xdmf2\n05/24/2025 05:46:03 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: convert_to_xdmf2, type: PyFunction, finished.\n05/24/2025 05:46:03 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: poisson3\n05/24/2025 05:46:06 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: poisson3, type: PyFunction, finished.\n05/24/2025 05:46:06 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_over_line4\n05/24/2025 05:46:08 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: plot_over_line4, type: PyFunction, finished.\n05/24/2025 05:46:08 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: substitute_macros5\n05/24/2025 05:46:09 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: substitute_macros5, type: PyFunction, finished.\n05/24/2025 05:46:09 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: compile_paper6\n05/24/2025 05:46:12 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|update_task_state]: Task: compile_paper6, type: PyFunction, finished.\n05/24/2025 05:46:12 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:46:12 AM <5606> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [111|WorkGraphEngine|finalize]: Finalize workgraph.\n" } ], "execution_count": 6 @@ -153,10 +153,7 @@ }, { "cell_type": "code", - "source": [ - "with SingleNodeExecutor(max_workers=1) as exe:\n", - " result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()" - ], + "source": "with SingleNodeExecutor(max_workers=1) as exe:\n result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()", "metadata": { "trusted": true }, @@ -174,7 +171,7 @@ "execution_count": 10, "output_type": "execute_result", "data": { - "text/plain": "'/home/jovyan/postprocessing/paper.pdf'" + "text/plain": "'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'" }, "metadata": {} } @@ -192,13 +189,7 @@ "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 11 }, { @@ -229,13 +220,13 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:52:59,822 INFO Started executing jobs locally\n2025-04-23 09:52:59,957 INFO Starting job - generate_mesh (3dfb7e61-0ac4-48e8-90b9-5dc1c8e9cc3a)\n2025-04-23 09:53:01,321 INFO Finished job - generate_mesh (3dfb7e61-0ac4-48e8-90b9-5dc1c8e9cc3a)\n2025-04-23 09:53:01,325 INFO Starting job - convert_to_xdmf (2457090f-84ec-40dc-87dc-16e1ecd5c5ef)\n2025-04-23 09:53:03,102 INFO Finished job - convert_to_xdmf (2457090f-84ec-40dc-87dc-16e1ecd5c5ef)\n2025-04-23 09:53:03,103 INFO Starting job - poisson (ddd8574c-2717-4d3c-a638-2e55670ae679)\n2025-04-23 09:53:06,212 INFO Finished job - poisson (ddd8574c-2717-4d3c-a638-2e55670ae679)\n2025-04-23 09:53:06,213 INFO Starting job - plot_over_line (669dc5b4-0fe1-41fa-8861-305009122991)\n2025-04-23 09:53:08,100 INFO Finished job - plot_over_line (669dc5b4-0fe1-41fa-8861-305009122991)\n2025-04-23 09:53:08,101 INFO Starting job - substitute_macros (bb6ad245-506d-4524-ae3e-e54bc4fcea61)\n2025-04-23 09:53:09,122 INFO Finished job - substitute_macros (bb6ad245-506d-4524-ae3e-e54bc4fcea61)\n2025-04-23 09:53:09,123 INFO Starting job - compile_paper (034ed702-2349-4e6b-b3e5-c5f83772b5aa)\n2025-04-23 09:53:11,397 INFO Finished job - compile_paper (034ed702-2349-4e6b-b3e5-c5f83772b5aa)\n2025-04-23 09:53:11,398 INFO Finished executing jobs locally\n" + "text": "2025-05-24 05:46:27,374 INFO Started executing jobs locally\n2025-05-24 05:46:27,453 INFO Starting job - generate_mesh (e65df967-702e-4def-9172-6be0b3b95604)\n2025-05-24 05:46:28,600 INFO Finished job - generate_mesh (e65df967-702e-4def-9172-6be0b3b95604)\n2025-05-24 05:46:28,601 INFO Starting job - convert_to_xdmf (173b17f6-c6d6-4002-81f3-fdc267be7837)\n2025-05-24 05:46:29,943 INFO Finished job - convert_to_xdmf (173b17f6-c6d6-4002-81f3-fdc267be7837)\n2025-05-24 05:46:29,944 INFO Starting job - poisson (91e67802-de2e-462d-a076-536c2e874b0b)\n2025-05-24 05:46:32,711 INFO Finished job - poisson (91e67802-de2e-462d-a076-536c2e874b0b)\n2025-05-24 05:46:32,712 INFO Starting job - plot_over_line (5094148b-2ae8-4f88-bbf3-73b68fe02fb1)\n2025-05-24 05:46:34,138 INFO Finished job - plot_over_line (5094148b-2ae8-4f88-bbf3-73b68fe02fb1)\n2025-05-24 05:46:34,139 INFO Starting job - substitute_macros (8badd91e-4495-491e-b978-0b1abac4c680)\n2025-05-24 05:46:34,939 INFO Finished job - substitute_macros (8badd91e-4495-491e-b978-0b1abac4c680)\n2025-05-24 05:46:34,940 INFO Starting job - compile_paper (ae640287-0fda-4682-8bd9-da3251f2cd30)\n2025-05-24 05:46:37,022 INFO Finished job - compile_paper (ae640287-0fda-4682-8bd9-da3251f2cd30)\n2025-05-24 05:46:37,024 INFO Finished executing jobs locally\n" }, { "execution_count": 14, "output_type": "execute_result", "data": { - "text/plain": "{'3dfb7e61-0ac4-48e8-90b9-5dc1c8e9cc3a': {1: Response(output='/home/jovyan/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '2457090f-84ec-40dc-87dc-16e1ecd5c5ef': {1: Response(output={'xdmf_file': '/home/jovyan/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'ddd8574c-2717-4d3c-a638-2e55670ae679': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/processing/poisson.pvd', 'vtu_file': '/home/jovyan/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '669dc5b4-0fe1-41fa-8861-305009122991': {1: Response(output='/home/jovyan/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'bb6ad245-506d-4524-ae3e-e54bc4fcea61': {1: Response(output='/home/jovyan/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '034ed702-2349-4e6b-b3e5-c5f83772b5aa': {1: Response(output='/home/jovyan/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" + "text/plain": "{'e65df967-702e-4def-9172-6be0b3b95604': {1: Response(output='/home/jovyan/example_workflows/nfdi/preprocessing/square.msh', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '173b17f6-c6d6-4002-81f3-fdc267be7837': {1: Response(output={'xdmf_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.xdmf', 'h5_file': '/home/jovyan/example_workflows/nfdi/preprocessing/square.h5'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '91e67802-de2e-462d-a076-536c2e874b0b': {1: Response(output={'numdofs': 357, 'pvd_file': '/home/jovyan/example_workflows/nfdi/processing/poisson.pvd', 'vtu_file': '/home/jovyan/example_workflows/nfdi/processing/poisson000000.vtu'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '5094148b-2ae8-4f88-bbf3-73b68fe02fb1': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/plotoverline.csv', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n '8badd91e-4495-491e-b978-0b1abac4c680': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/macros.tex', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))},\n 'ae640287-0fda-4682-8bd9-da3251f2cd30': {1: Response(output='/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/nfdi'))}}" }, "metadata": {} } @@ -258,10 +249,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\n", - "delayed_object_lst[-1].draw()" - ], + "source": "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, @@ -270,7 +258,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\ncreate_function_job_69b38eef29d5c9aba4c6de512da1bb24\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d2c0e0>\n\n\n\nmacros_tex_c5f640fc7b11414962941f82a40a8b04\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07dd0>\n\n\n\nmacros_tex_c5f640fc7b11414962941f82a40a8b04->create_function_job_69b38eef29d5c9aba4c6de512da1bb24\n\n\n\n\n\npvbatch_output_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07d70>\n\n\n\npvbatch_output_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78->macros_tex_c5f640fc7b11414962941f82a40a8b04\n\n\n\n\n\npoisson_output_pvd_file_08c5d21e2c998fd513709b7a059c6649\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07bc0>\n\n\n\npoisson_output_pvd_file_08c5d21e2c998fd513709b7a059c6649->pvbatch_output_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\n\n\n\n\nplot_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07d70>\n\n\n\npoisson_output_pvd_file_08c5d21e2c998fd513709b7a059c6649->plot_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\n\n\n\n\nplot_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78->create_function_job_69b38eef29d5c9aba4c6de512da1bb24\n\n\n\n\n\nmeshio_output_xdmf_fc75e768124c1b73ca0efc70a5765dea\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d078c0>\n\n\n\nmeshio_output_xdmf_fc75e768124c1b73ca0efc70a5765dea->poisson_output_pvd_file_08c5d21e2c998fd513709b7a059c6649\n\n\n\n\n\npoisson_output_vtu_file_62144723b416cb6b52989d18b3dec55b\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07b90>\n\n\n\nmeshio_output_xdmf_fc75e768124c1b73ca0efc70a5765dea->poisson_output_vtu_file_62144723b416cb6b52989d18b3dec55b\n\n\n\n\n\nndofs_c3811e53ce75b5460d97029d314439b5\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d07e00>\n\n\n\nmeshio_output_xdmf_fc75e768124c1b73ca0efc70a5765dea->ndofs_c3811e53ce75b5460d97029d314439b5\n\n\n\n\n\npoisson_output_vtu_file_62144723b416cb6b52989d18b3dec55b->pvbatch_output_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\n\n\n\n\npoisson_output_vtu_file_62144723b416cb6b52989d18b3dec55b->plot_file_5f8f87a5c4f1bd1a4b6cca85a1fc2b78\n\n\n\n\n\nndofs_c3811e53ce75b5460d97029d314439b5->macros_tex_c5f640fc7b11414962941f82a40a8b04\n\n\n\n\n\ngmsh_output_file_950b49ac6562a70cf11f14756f9831ea\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d076b0>\n\n\n\ngmsh_output_file_950b49ac6562a70cf11f14756f9831ea->meshio_output_xdmf_fc75e768124c1b73ca0efc70a5765dea\n\n\n\n\n\nmeshio_output_h5_efe999f964b5fb7603bd642abcd8905d\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x7c1a34d078f0>\n\n\n\ngmsh_output_file_950b49ac6562a70cf11f14756f9831ea->meshio_output_h5_efe999f964b5fb7603bd642abcd8905d\n\n\n\n\n\nmeshio_output_h5_efe999f964b5fb7603bd642abcd8905d->poisson_output_pvd_file_08c5d21e2c998fd513709b7a059c6649\n\n\n\n\n\nmeshio_output_h5_efe999f964b5fb7603bd642abcd8905d->poisson_output_vtu_file_62144723b416cb6b52989d18b3dec55b\n\n\n\n\n\nmeshio_output_h5_efe999f964b5fb7603bd642abcd8905d->ndofs_c3811e53ce75b5460d97029d314439b5\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_c5f640fc7b11414962941f82a40a8b04\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_950b49ac6562a70cf11f14756f9831ea\n\n\n\n\n" + "image/svg+xml": "\n\n\n\n\ncreate_function_job_724cfd00ffeb70f8b463a938195e0447\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7cace97128d0>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7\n\nmacros_tex=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9712660>\n\n\n\nmacros_tex_b52804e5fa845b3657fa99b738e02cf7->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\npvbatch_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9712330>\n\n\n\npvbatch_output_file_554a54a50a86b23416c0daf6ab0938df->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\npoisson_output_pvd_file=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9711fd0>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df\n\nplot_file=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9712330>\n\n\n\npoisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nplot_file_554a54a50a86b23416c0daf6ab0938df->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\nmeshio_output_xdmf=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9711d60>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\npoisson_output_vtu_file=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9711fa0>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26\n\nndofs=<pyiron_base.project.delayed.DelayedObject object at 0x7cace97123c0>\n\n\n\nmeshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\npoisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nndofs_e826761b60042b070e0c0a24b472ee26->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\ngmsh_output_file=<pyiron_base.project.delayed.DelayedObject object at 0x7cace97119a0>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_xdmf_52103bbf2f92608bdb3c6bedb045e0e1\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\nmeshio_output_h5=<pyiron_base.project.delayed.DelayedObject object at 0x7cace9711d30>\n\n\n\ngmsh_output_file_553a0d07e32ca83a3640e955a7b868a4->meshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nmeshio_output_h5_0e11ecf3d5834e399bb91f99309bf3fe->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20\n\ndomain_size=2.0\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\ndomain_size_f12a7f1986b9dd058dfc666dbe230b20->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696\n\nsource_directory=/home/jovyan/example_workflows/nfdi/source\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->create_function_job_724cfd00ffeb70f8b463a938195e0447\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->macros_tex_b52804e5fa845b3657fa99b738e02cf7\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->pvbatch_output_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_pvd_file_50ce5e5ed091c2b7a77b69e1c1750ad9\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->plot_file_554a54a50a86b23416c0daf6ab0938df\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->poisson_output_vtu_file_fdcc35c5e09c1b2a481c5350749d9810\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->ndofs_e826761b60042b070e0c0a24b472ee26\n\n\n\n\n\nsource_directory_053958014e7cd4a4df22cfa51c9fc696->gmsh_output_file_553a0d07e32ca83a3640e955a7b868a4\n\n\n\n\n" }, "metadata": {} } @@ -287,13 +275,13 @@ { "name": "stdout", "output_type": "stream", - "text": "The job generate_mesh_0b48cf5155cd6802c17d20bb58104132 was saved and received the ID: 1\nThe job convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43 was saved and received the ID: 2\nThe job poisson_a0224b23ceb2119d105a5d98ef37f93e was saved and received the ID: 3\nThe job plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b was saved and received the ID: 4\nThe job substitute_macros_874fc185ecec04b4cb9537c58b7efb7b was saved and received the ID: 5\nThe job compile_paper_3cee534ffe692833d37faf1fd2170cb6 was saved and received the ID: 6\n" + "text": "The job generate_mesh_47725c16637f799ac042e47468005db3 was saved and received the ID: 1\nThe job convert_to_xdmf_d6a46eb9a4ec352aa996e783ec3c785f was saved and received the ID: 2\nThe job poisson_3c147fc86db87cf0c0f94bda333f8cd8 was saved and received the ID: 3\nThe job plot_over_line_ef50933291910dadcc8311924971e127 was saved and received the ID: 4\nThe job substitute_macros_63766eafd6b1980c7832dd8c9a97c96e was saved and received the ID: 5\nThe job compile_paper_128d1d58374953c00e95b8de62cbb10b was saved and received the ID: 6\n" }, { "execution_count": 17, "output_type": "execute_result", "data": { - "text/plain": "'/home/jovyan/postprocessing/paper.pdf'" + "text/plain": "'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'" }, "metadata": {} } @@ -325,7 +313,7 @@ "execution_count": 19, "output_type": "execute_result", "data": { - "text/plain": "'/home/jovyan/postprocessing/paper.pdf'" + "text/plain": "'/home/jovyan/example_workflows/nfdi/postprocessing/paper.pdf'" }, "metadata": {} } diff --git a/example_workflows/quantum_espresso/aiida.ipynb b/example_workflows/quantum_espresso/aiida.ipynb index 49698dd..6504617 100644 --- a/example_workflows/quantum_espresso/aiida.ipynb +++ b/example_workflows/quantum_espresso/aiida.ipynb @@ -50,32 +50,31 @@ "execution_count": 2 }, { - "metadata": {}, "cell_type": "code", + "source": "from workflow import (\n generate_structures,\n get_bulk_structure,\n calculate_qe as _calculate_qe,\n plot_energy_volume_curve,\n)", + "metadata": { + "trusted": true + }, "outputs": [], - "execution_count": null, - "source": [ - "from workflow import (\n", - " generate_structures,\n", - " get_bulk_structure,\n", - " calculate_qe as _calculate_qe,\n", - " plot_energy_volume_curve,\n", - ")" - ] - }, - { - "metadata": {}, + "execution_count": 3 + }, + { "cell_type": "code", + "source": "calculate_qe = task(outputs=[\"energy\", \"volume\", \"structure\"])(_calculate_qe)", + "metadata": { + "trusted": true + }, "outputs": [], - "execution_count": null, - "source": "calculate_qe = task(outputs=[\"energy\", \"volume\", \"structure\"])(_calculate_qe)" + "execution_count": 4 }, { - "metadata": {}, "cell_type": "code", + "source": "wg = WorkGraph(\"wg-qe\")", + "metadata": { + "trusted": true + }, "outputs": [], - "execution_count": null, - "source": "wg = WorkGraph(\"wg-qe\")" + "execution_count": 5 }, { "cell_type": "markdown", @@ -174,7 +173,7 @@ "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 1, - "model_id": "a44258c4d19f490bb7e35a61d721b97c" + "model_id": "5e2142f5189b4350bb20fb6f6fa3ceb4" } }, "metadata": {} @@ -201,7 +200,7 @@ { "name": "stdout", "output_type": "stream", - "text": "{\n \"nodes\": [\n {\n \"id\": 0,\n \"function\": \"quantum_espresso_workflow.get_bulk_structure\"\n },\n {\n \"id\": 1,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 2,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 3,\n \"function\": \"quantum_espresso_workflow.generate_structures\"\n },\n {\n \"id\": 4,\n \"function\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 5,\n \"function\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 6,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 7,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 8,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 9,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 10,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 11,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 12,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 13,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 14,\n \"function\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 15,\n \"function\": \"quantum_espresso_workflow.calculate_qe\"\n },\n {\n \"id\": 16,\n \"function\": \"quantum_espresso_workflow.plot_energy_volume_curve\"\n },\n {\n \"id\": 17,\n \"value\": \"Al\"\n },\n {\n \"id\": 18,\n \"value\": 4.04\n },\n {\n \"id\": 19,\n \"value\": true\n },\n {\n \"id\": 20,\n \"value\": \"vc-relax\"\n },\n {\n \"id\": 21,\n \"value\": [\n 3,\n 3,\n 3\n ]\n },\n {\n \"id\": 22,\n \"value\": {\n \"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"\n }\n },\n {\n \"id\": 23,\n \"value\": 0.02\n },\n {\n \"id\": 24,\n \"value\": \"mini\"\n },\n {\n \"id\": 25,\n \"value\": [\n 0.9,\n 0.95,\n 1.0,\n 1.05,\n 1.1\n ]\n },\n {\n \"id\": 26,\n \"value\": \"scf\"\n },\n {\n \"id\": 27,\n \"value\": \"strain_0\"\n },\n {\n \"id\": 28,\n \"value\": \"strain_1\"\n },\n {\n \"id\": 29,\n \"value\": \"strain_2\"\n },\n {\n \"id\": 30,\n \"value\": \"strain_3\"\n },\n {\n \"id\": 31,\n \"value\": \"strain_4\"\n }\n ],\n \"edges\": [\n {\n \"target\": 1,\n \"targetPort\": \"structure\",\n \"source\": 0,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"input_dict\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"structure\"\n },\n {\n \"target\": 6,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_0\"\n },\n {\n \"target\": 7,\n \"targetPort\": \"input_dict\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"0\",\n \"source\": 7,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"0\",\n \"source\": 7,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 8,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_1\"\n },\n {\n \"target\": 9,\n \"targetPort\": \"input_dict\",\n \"source\": 8,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"1\",\n \"source\": 9,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"1\",\n \"source\": 9,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 10,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_2\"\n },\n {\n \"target\": 11,\n \"targetPort\": \"input_dict\",\n \"source\": 10,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"2\",\n \"source\": 11,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"2\",\n \"source\": 11,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 12,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_3\"\n },\n {\n \"target\": 13,\n \"targetPort\": \"input_dict\",\n \"source\": 12,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"3\",\n \"source\": 13,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"3\",\n \"source\": 13,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 14,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_4\"\n },\n {\n \"target\": 15,\n \"targetPort\": \"input_dict\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"4\",\n \"source\": 15,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"4\",\n \"source\": 15,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"volume_lst\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 16,\n \"targetPort\": \"energy_lst\",\n \"source\": 5,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"element\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"a\",\n \"source\": 18,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"cubic\",\n \"source\": 19,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"calculation\",\n \"source\": 20,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"working_directory\",\n \"source\": 24,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"strain_lst\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"working_directory\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"working_directory\",\n \"source\": 28,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"working_directory\",\n \"source\": 29,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"working_directory\",\n \"source\": 30,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"working_directory\",\n \"source\": 31,\n \"sourcePort\": null\n }\n ]\n}" + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.get_bulk_structure\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 3,\n \"type\": \"function\",\n \"value\": \"workflow.generate_structures\"\n },\n {\n \"id\": 4,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 5,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 6,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 7,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 8,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 9,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 10,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 11,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 12,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 13,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 14,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 15,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 16,\n \"type\": \"function\",\n \"value\": \"workflow.plot_energy_volume_curve\"\n },\n {\n \"id\": 17,\n \"type\": \"input\",\n \"name\": \"element\",\n \"value\": \"Al\"\n },\n {\n \"id\": 18,\n \"type\": \"input\",\n \"name\": \"a\",\n \"value\": 4.04\n },\n {\n \"id\": 19,\n \"type\": \"input\",\n \"name\": \"cubic\",\n \"value\": true\n },\n {\n \"id\": 20,\n \"type\": \"input\",\n \"name\": \"calculation_0\",\n \"value\": \"vc-relax\"\n },\n {\n \"id\": 21,\n \"type\": \"input\",\n \"name\": \"kpts\",\n \"value\": [\n 3,\n 3,\n 3\n ]\n },\n {\n \"id\": 22,\n \"type\": \"input\",\n \"name\": \"pseudopotentials\",\n \"value\": {\n \"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"\n }\n },\n {\n \"id\": 23,\n \"type\": \"input\",\n \"name\": \"smearing\",\n \"value\": 0.02\n },\n {\n \"id\": 24,\n \"type\": \"input\",\n \"name\": \"working_directory_0\",\n \"value\": \"mini\"\n },\n {\n \"id\": 25,\n \"type\": \"input\",\n \"name\": \"strain_lst\",\n \"value\": [\n 0.9,\n 0.95,\n 1.0,\n 1.05,\n 1.1\n ]\n },\n {\n \"id\": 26,\n \"type\": \"input\",\n \"name\": \"calculation_1\",\n \"value\": \"scf\"\n },\n {\n \"id\": 27,\n \"type\": \"input\",\n \"name\": \"working_directory_1\",\n \"value\": \"strain_0\"\n },\n {\n \"id\": 28,\n \"type\": \"input\",\n \"name\": \"working_directory_2\",\n \"value\": \"strain_1\"\n },\n {\n \"id\": 29,\n \"type\": \"input\",\n \"name\": \"working_directory_3\",\n \"value\": \"strain_2\"\n },\n {\n \"id\": 30,\n \"type\": \"input\",\n \"name\": \"working_directory_4\",\n \"value\": \"strain_3\"\n },\n {\n \"id\": 31,\n \"type\": \"input\",\n \"name\": \"working_directory_5\",\n \"value\": \"strain_4\"\n },\n {\n \"id\": 32,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 1,\n \"targetPort\": \"structure\",\n \"source\": 0,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"input_dict\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"structure\"\n },\n {\n \"target\": 6,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_0\"\n },\n {\n \"target\": 7,\n \"targetPort\": \"input_dict\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"0\",\n \"source\": 7,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"0\",\n \"source\": 7,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 8,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_1\"\n },\n {\n \"target\": 9,\n \"targetPort\": \"input_dict\",\n \"source\": 8,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"1\",\n \"source\": 9,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"1\",\n \"source\": 9,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 10,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_2\"\n },\n {\n \"target\": 11,\n \"targetPort\": \"input_dict\",\n \"source\": 10,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"2\",\n \"source\": 11,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"2\",\n \"source\": 11,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 12,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_3\"\n },\n {\n \"target\": 13,\n \"targetPort\": \"input_dict\",\n \"source\": 12,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"3\",\n \"source\": 13,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"3\",\n \"source\": 13,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 14,\n \"targetPort\": \"structure\",\n \"source\": 3,\n \"sourcePort\": \"s_4\"\n },\n {\n \"target\": 15,\n \"targetPort\": \"input_dict\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"4\",\n \"source\": 15,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"4\",\n \"source\": 15,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"volume_lst\",\n \"source\": 4,\n \"sourcePort\": null\n },\n {\n \"target\": 16,\n \"targetPort\": \"energy_lst\",\n \"source\": 5,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"element\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"a\",\n \"source\": 18,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"cubic\",\n \"source\": 19,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"calculation\",\n \"source\": 20,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"working_directory\",\n \"source\": 24,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"strain_lst\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"working_directory\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"working_directory\",\n \"source\": 28,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"working_directory\",\n \"source\": 29,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"working_directory\",\n \"source\": 30,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"calculation\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"kpts\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"smearing\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"working_directory\",\n \"source\": 31,\n \"sourcePort\": null\n },\n {\n \"target\": 32,\n \"targetPort\": null,\n \"source\": 16,\n \"sourcePort\": null\n }\n ]\n}" } ], "execution_count": 16 @@ -217,13 +216,7 @@ "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 17 }, { @@ -263,83 +256,73 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:31:18,763 INFO Started executing jobs locally\n2025-04-23 09:31:19,023 INFO Starting job - get_bulk_structure (ceb203d4-4b50-4fbf-bd60-36680543382b)\n2025-04-23 09:31:19,030 INFO Finished job - get_bulk_structure (ceb203d4-4b50-4fbf-bd60-36680543382b)\n2025-04-23 09:31:19,031 INFO Starting job - get_dict (27f28719-6394-4a85-b93f-c8ece2feceaf)\n2025-04-23 09:31:19,034 INFO Finished job - get_dict (27f28719-6394-4a85-b93f-c8ece2feceaf)\n2025-04-23 09:31:19,035 INFO Starting job - calculate_qe (ae0b4b06-5734-41ea-a7cc-e8393ef01e55)\n" - }, - { - "name": "stderr", - "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01795] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" - }, - { - "name": "stdout", - "output_type": "stream", - "text": "2025-04-23 09:32:12,183 INFO Finished job - calculate_qe (ae0b4b06-5734-41ea-a7cc-e8393ef01e55)\n2025-04-23 09:32:12,184 INFO Starting job - generate_structures (e9deb2a2-2e2a-4077-a221-a6afc9701377)\n2025-04-23 09:32:12,189 INFO Finished job - generate_structures (e9deb2a2-2e2a-4077-a221-a6afc9701377)\n2025-04-23 09:32:12,189 INFO Starting job - get_dict (9f4a0c82-798c-4178-9a46-c5430a2853c1)\n2025-04-23 09:32:12,190 INFO Finished job - get_dict (9f4a0c82-798c-4178-9a46-c5430a2853c1)\n2025-04-23 09:32:12,191 INFO Starting job - get_dict (8e10ca3a-91ba-4647-bca8-3c905020fb39)\n2025-04-23 09:32:12,192 INFO Finished job - get_dict (8e10ca3a-91ba-4647-bca8-3c905020fb39)\n2025-04-23 09:32:12,193 INFO Starting job - get_dict (765da827-3180-44d3-940e-e9d5a7e2ae45)\n2025-04-23 09:32:12,194 INFO Finished job - get_dict (765da827-3180-44d3-940e-e9d5a7e2ae45)\n2025-04-23 09:32:12,195 INFO Starting job - get_dict (5f8ce3d7-f65e-481d-8cb0-291d204df659)\n2025-04-23 09:32:12,196 INFO Finished job - get_dict (5f8ce3d7-f65e-481d-8cb0-291d204df659)\n2025-04-23 09:32:12,196 INFO Starting job - get_dict (12912688-d0c2-4053-80b2-a758b50ce86a)\n2025-04-23 09:32:12,208 INFO Finished job - get_dict (12912688-d0c2-4053-80b2-a758b50ce86a)\n2025-04-23 09:32:12,209 INFO Starting job - calculate_qe (282ce127-dc4e-4e2d-9769-c22bdcdf2e3f)\n" + "text": "2025-05-24 05:48:01,786 INFO Started executing jobs locally\n2025-05-24 05:48:02,013 INFO Starting job - get_bulk_structure (28c24969-efdd-4239-a6bd-af123fff4298)\n2025-05-24 05:48:02,017 INFO Finished job - get_bulk_structure (28c24969-efdd-4239-a6bd-af123fff4298)\n2025-05-24 05:48:02,018 INFO Starting job - get_dict (ffd8792f-e232-4cd7-8a66-15d61be9e29f)\n2025-05-24 05:48:02,019 INFO Finished job - get_dict (ffd8792f-e232-4cd7-8a66-15d61be9e29f)\n2025-05-24 05:48:02,020 INFO Starting job - calculate_qe (69b4c8f3-8419-4df1-b569-dd1c7fefd764)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01814] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08863] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:32:23,091 INFO Finished job - calculate_qe (282ce127-dc4e-4e2d-9769-c22bdcdf2e3f)\n2025-04-23 09:32:23,092 INFO Starting job - calculate_qe (76b1d287-fd0f-4fed-a0b7-cc817dffe2d8)\n" + "text": "2025-05-24 05:48:54,204 INFO Finished job - calculate_qe (69b4c8f3-8419-4df1-b569-dd1c7fefd764)\n2025-05-24 05:48:54,205 INFO Starting job - generate_structures (2d24374c-9473-456d-98ff-1be0c02c2bb7)\n2025-05-24 05:48:54,208 INFO Finished job - generate_structures (2d24374c-9473-456d-98ff-1be0c02c2bb7)\n2025-05-24 05:48:54,209 INFO Starting job - get_dict (56abaa34-f9a4-4d28-bf90-2897fe970beb)\n2025-05-24 05:48:54,210 INFO Finished job - get_dict (56abaa34-f9a4-4d28-bf90-2897fe970beb)\n2025-05-24 05:48:54,210 INFO Starting job - get_dict (2dd35376-658a-46ff-a277-a9b8e88ddac5)\n2025-05-24 05:48:54,211 INFO Finished job - get_dict (2dd35376-658a-46ff-a277-a9b8e88ddac5)\n2025-05-24 05:48:54,211 INFO Starting job - get_dict (33527acb-a9e4-4422-8198-08f80992ac9e)\n2025-05-24 05:48:54,212 INFO Finished job - get_dict (33527acb-a9e4-4422-8198-08f80992ac9e)\n2025-05-24 05:48:54,213 INFO Starting job - get_dict (75067890-ee04-48e4-81e3-d8bf8072b673)\n2025-05-24 05:48:54,214 INFO Finished job - get_dict (75067890-ee04-48e4-81e3-d8bf8072b673)\n2025-05-24 05:48:54,214 INFO Starting job - get_dict (10b85da2-e05d-4de0-85bd-a572aab2a34f)\n2025-05-24 05:48:54,215 INFO Finished job - get_dict (10b85da2-e05d-4de0-85bd-a572aab2a34f)\n2025-05-24 05:48:54,216 INFO Starting job - calculate_qe (254a56bb-69a7-478c-a5bc-162d183e0454)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01825] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08876] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:32:34,038 INFO Finished job - calculate_qe (76b1d287-fd0f-4fed-a0b7-cc817dffe2d8)\n2025-04-23 09:32:34,038 INFO Starting job - calculate_qe (2c6bfb73-15c3-4be7-95ab-f9afbeaf53bc)\n" + "text": "2025-05-24 05:49:04,619 INFO Finished job - calculate_qe (254a56bb-69a7-478c-a5bc-162d183e0454)\n2025-05-24 05:49:04,620 INFO Starting job - calculate_qe (6f1b1b10-81d7-4f4a-95a9-c37697b4ff22)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01836] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:08887] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:32:46,472 INFO Finished job - calculate_qe (2c6bfb73-15c3-4be7-95ab-f9afbeaf53bc)\n2025-04-23 09:32:46,473 INFO Starting job - calculate_qe (4f947882-06db-4296-8456-b12cff2e66e3)\n" + "text": "2025-05-24 05:49:15,345 INFO Finished job - calculate_qe (6f1b1b10-81d7-4f4a-95a9-c37697b4ff22)\n2025-05-24 05:49:15,346 INFO Starting job - calculate_qe (adfa9cb1-8d89-4943-832b-9e21782861cd)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01847] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:08897] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:33:00,409 INFO Finished job - calculate_qe (4f947882-06db-4296-8456-b12cff2e66e3)\n2025-04-23 09:33:00,410 INFO Starting job - calculate_qe (d7bd31df-d3a7-49a1-9ae8-7766d4c519ec)\n" + "text": "2025-05-24 05:49:26,680 INFO Finished job - calculate_qe (adfa9cb1-8d89-4943-832b-9e21782861cd)\n2025-05-24 05:49:26,681 INFO Starting job - calculate_qe (c8bd32cf-c431-4189-9f09-708a86fa8aa0)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01858] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:08908] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:33:14,798 INFO Finished job - calculate_qe (d7bd31df-d3a7-49a1-9ae8-7766d4c519ec)\n2025-04-23 09:33:14,800 INFO Starting job - get_list (daa806da-16e9-4733-afe1-2ae60dc6292f)\n2025-04-23 09:33:14,804 INFO Finished job - get_list (daa806da-16e9-4733-afe1-2ae60dc6292f)\n2025-04-23 09:33:14,805 INFO Starting job - get_list (407d4cb0-b4f3-41f5-ba66-077754af69eb)\n2025-04-23 09:33:14,808 INFO Finished job - get_list (407d4cb0-b4f3-41f5-ba66-077754af69eb)\n2025-04-23 09:33:14,810 INFO Starting job - plot_energy_volume_curve (e363e583-bcc3-4cd8-b943-f6e4487b11f0)\n" + "text": "2025-05-24 05:49:40,830 INFO Finished job - calculate_qe (c8bd32cf-c431-4189-9f09-708a86fa8aa0)\n2025-05-24 05:49:40,831 INFO Starting job - calculate_qe (140c1cae-54ed-492f-8589-d9c0490142c6)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:08919] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:33:14,912 INFO Finished job - plot_energy_volume_curve (e363e583-bcc3-4cd8-b943-f6e4487b11f0)\n2025-04-23 09:33:14,913 INFO Finished executing jobs locally\n" + "text": "2025-05-24 05:49:54,690 INFO Finished job - calculate_qe (140c1cae-54ed-492f-8589-d9c0490142c6)\n2025-05-24 05:49:54,691 INFO Starting job - get_list (1eade2dd-772e-4e49-8264-2ff6ee8ff6ff)\n2025-05-24 05:49:54,694 INFO Finished job - get_list (1eade2dd-772e-4e49-8264-2ff6ee8ff6ff)\n2025-05-24 05:49:54,694 INFO Starting job - get_list (0b1cb308-c310-4995-b18b-1441b1ff1a22)\n2025-05-24 05:49:54,697 INFO Finished job - get_list (0b1cb308-c310-4995-b18b-1441b1ff1a22)\n2025-05-24 05:49:54,698 INFO Starting job - plot_energy_volume_curve (2fd7c54d-8f3d-437c-a59f-8236978defdc)\n2025-05-24 05:49:54,794 INFO Finished job - plot_energy_volume_curve (2fd7c54d-8f3d-437c-a59f-8236978defdc)\n2025-05-24 05:49:54,795 INFO Finished executing jobs locally\n" }, { "execution_count": 21, "output_type": "execute_result", "data": { - "text/plain": "{'ceb203d4-4b50-4fbf-bd60-36680543382b': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '27f28719-6394-4a85-b93f-c8ece2feceaf': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'vc-relax', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'ae0b4b06-5734-41ea-a7cc-e8393ef01e55': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946818, 0.0, 0.0], [0.0, 4.045637215946818, 0.0], [0.0, 0.0, 4.045637215946818]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973409, 2.022818607973409], [2.022818607973409, 0.0, 2.022818607973409], [2.022818607973409, 2.022818607973409, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.93652622536, 'volume': 66.21567448236135}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'e9deb2a2-2e2a-4077-a221-a6afc9701377': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019785962126, 0.0, 0.0], [0.0, 3.906019785962126, 0.0], [0.0, 0.0, 3.906019785962126]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981063, 1.953009892981063], [1.953009892981063, 0.0, 1.953009892981063], [1.953009892981063, 1.953009892981063, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443180263, 0.0, 0.0], [0.0, 3.9770538443180263, 0.0], [0.0, 0.0, 3.9770538443180263]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590132, 1.9885269221590132], [1.9885269221590132, 0.0, 1.9885269221590132], [1.9885269221590132, 1.9885269221590132, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946818, 0.0, 0.0], [0.0, 4.045637215946818, 0.0], [0.0, 0.0, 4.045637215946818]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973409, 2.022818607973409], [2.022818607973409, 0.0, 2.022818607973409], [2.022818607973409, 2.022818607973409, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282933, 0.0, 0.0], [0.0, 4.111970927282933, 0.0], [0.0, 0.0, 4.111970927282933]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414663, 2.0559854636414663], [2.0559854636414663, 0.0, 2.0559854636414663], [2.0559854636414663, 2.0559854636414663, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372157, 0.0, 0.0], [0.0, 4.176230852372157, 0.0], [0.0, 0.0, 4.176230852372157]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860786, 2.0881154261860786], [2.0881154261860786, 0.0, 2.0881154261860786], [2.0881154261860786, 2.0881154261860786, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '9f4a0c82-798c-4178-9a46-c5430a2853c1': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019785962126, 0.0, 0.0], [0.0, 3.906019785962126, 0.0], [0.0, 0.0, 3.906019785962126]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981063, 1.953009892981063], [1.953009892981063, 0.0, 1.953009892981063], [1.953009892981063, 1.953009892981063, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '8e10ca3a-91ba-4647-bca8-3c905020fb39': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443180263, 0.0, 0.0], [0.0, 3.9770538443180263, 0.0], [0.0, 0.0, 3.9770538443180263]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590132, 1.9885269221590132], [1.9885269221590132, 0.0, 1.9885269221590132], [1.9885269221590132, 1.9885269221590132, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '765da827-3180-44d3-940e-e9d5a7e2ae45': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946818, 0.0, 0.0], [0.0, 4.045637215946818, 0.0], [0.0, 0.0, 4.045637215946818]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973409, 2.022818607973409], [2.022818607973409, 0.0, 2.022818607973409], [2.022818607973409, 2.022818607973409, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '5f8ce3d7-f65e-481d-8cb0-291d204df659': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282933, 0.0, 0.0], [0.0, 4.111970927282933, 0.0], [0.0, 0.0, 4.111970927282933]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414663, 2.0559854636414663], [2.0559854636414663, 0.0, 2.0559854636414663], [2.0559854636414663, 2.0559854636414663, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '12912688-d0c2-4053-80b2-a758b50ce86a': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372157, 0.0, 0.0], [0.0, 4.176230852372157, 0.0], [0.0, 0.0, 4.176230852372157]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860786, 2.0881154261860786], [2.0881154261860786, 0.0, 2.0881154261860786], [2.0881154261860786, 2.0881154261860786, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '282ce127-dc4e-4e2d-9769-c22bdcdf2e3f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019768889166, 0.0, 0.0], [0.0, 3.906019768889166, 0.0], [0.0, 0.0, 3.906019768889166]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8457446150626, 'volume': 59.594106252679225}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '76b1d287-fd0f-4fed-a0b7-cc817dffe2d8': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538269345797, 0.0, 0.0], [0.0, 3.9770538269345797, 0.0], [0.0, 0.0, 3.9770538269345797]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082753, 1.9885269135082753], [1.9885269135082753, 0.0, 1.9885269135082753], [1.9885269135082753, 1.9885269135082753, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9161488594607, 'volume': 62.90488993338357}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '2c6bfb73-15c3-4be7-95ab-f9afbeaf53bc': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263596, 0.0, 0.0], [0.0, 4.045637198263596, 0.0], [0.0, 0.0, 4.045637198263596]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583882, 2.0228185991583882], [2.0228185991583882, 0.0, 2.0228185991583882], [2.0228185991583882, 2.0228185991583882, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365241668372, 'volume': 66.21567361408789}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '4f947882-06db-4296-8456-b12cff2e66e3': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309766, 0.0, 0.0], [0.0, 4.111970909309766, 0.0], [0.0, 0.0, 4.111970909309766]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025842, 'volume': 69.52645729479204}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'd7bd31df-d3a7-49a1-9ae8-7766d4c519ec': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411812, 0.0, 0.0], [0.0, 4.17623083411812, 0.0], [0.0, 0.0, 4.17623083411812]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.08811541707298, 2.08811541707298], [2.08811541707298, 0.0, 2.08811541707298], [2.08811541707298, 2.08811541707298, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.87379046934, 'volume': 72.83724097549673}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'daa806da-16e9-4733-afe1-2ae60dc6292f': {1: Response(output=[59.594106252679225, 62.90488993338357, 66.21567361408789, 69.52645729479204, 72.83724097549673], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '407d4cb0-b4f3-41f5-ba66-077754af69eb': {1: Response(output=[-1074.8457446150626, -1074.9161488594607, -1074.9365241668372, -1074.9192860025842, -1074.87379046934], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'e363e583-bcc3-4cd8-b943-f6e4487b11f0': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" + "text/plain": "{'28c24969-efdd-4239-a6bd-af123fff4298': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'ffd8792f-e232-4cd7-8a66-15d61be9e29f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'vc-relax', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '69b4c8f3-8419-4df1-b569-dd1c7fefd764': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946848, 0.0, 0.0], [0.0, 4.045637215946848, 0.0], [0.0, 0.0, 4.045637215946848]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734236, 2.0228186079734236], [2.0228186079734236, 0.0, 2.0228186079734236], [2.0228186079734236, 2.0228186079734236, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.936526225353, 'volume': 66.21567448236287}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '2d24374c-9473-456d-98ff-1be0c02c2bb7': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859621555, 0.0, 0.0], [0.0, 3.9060197859621555, 0.0], [0.0, 0.0, 3.9060197859621555]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810773, 1.9530098929810773], [1.9530098929810773, 0.0, 1.9530098929810773], [1.9530098929810773, 1.9530098929810773, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844318056, 0.0, 0.0], [0.0, 3.977053844318056, 0.0], [0.0, 0.0, 3.977053844318056]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590276, 1.9885269221590276], [1.9885269221590276, 0.0, 1.9885269221590276], [1.9885269221590276, 1.9885269221590276, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946848, 0.0, 0.0], [0.0, 4.045637215946848, 0.0], [0.0, 0.0, 4.045637215946848]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734236, 2.0228186079734236], [2.0228186079734236, 0.0, 2.0228186079734236], [2.0228186079734236, 2.0228186079734236, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282964, 0.0, 0.0], [0.0, 4.111970927282964, 0.0], [0.0, 0.0, 4.111970927282964]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414814, 2.0559854636414814], [2.0559854636414814, 0.0, 2.0559854636414814], [2.0559854636414814, 2.0559854636414814, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372188, 0.0, 0.0], [0.0, 4.176230852372188, 0.0], [0.0, 0.0, 4.176230852372188]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860937, 2.0881154261860937], [2.0881154261860937, 0.0, 2.0881154261860937], [2.0881154261860937, 2.0881154261860937, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '56abaa34-f9a4-4d28-bf90-2897fe970beb': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859621555, 0.0, 0.0], [0.0, 3.9060197859621555, 0.0], [0.0, 0.0, 3.9060197859621555]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810773, 1.9530098929810773], [1.9530098929810773, 0.0, 1.9530098929810773], [1.9530098929810773, 1.9530098929810773, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '2dd35376-658a-46ff-a277-a9b8e88ddac5': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844318056, 0.0, 0.0], [0.0, 3.977053844318056, 0.0], [0.0, 0.0, 3.977053844318056]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590276, 1.9885269221590276], [1.9885269221590276, 0.0, 1.9885269221590276], [1.9885269221590276, 1.9885269221590276, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '33527acb-a9e4-4422-8198-08f80992ac9e': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946848, 0.0, 0.0], [0.0, 4.045637215946848, 0.0], [0.0, 0.0, 4.045637215946848]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734236, 2.0228186079734236], [2.0228186079734236, 0.0, 2.0228186079734236], [2.0228186079734236, 2.0228186079734236, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '75067890-ee04-48e4-81e3-d8bf8072b673': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282964, 0.0, 0.0], [0.0, 4.111970927282964, 0.0], [0.0, 0.0, 4.111970927282964]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414814, 2.0559854636414814], [2.0559854636414814, 0.0, 2.0559854636414814], [2.0559854636414814, 2.0559854636414814, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '10b85da2-e05d-4de0-85bd-a572aab2a34f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372188, 0.0, 0.0], [0.0, 4.176230852372188, 0.0], [0.0, 0.0, 4.176230852372188]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860937, 2.0881154261860937], [2.0881154261860937, 0.0, 2.0881154261860937], [2.0881154261860937, 2.0881154261860937, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'calculation': 'scf', 'kpts': [3, 3, 3], 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '254a56bb-69a7-478c-a5bc-162d183e0454': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019768889195, 0.0, 0.0], [0.0, 3.906019768889195, 0.0], [0.0, 0.0, 3.906019768889195]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8457446150612, 'volume': 59.59410625268055}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '6f1b1b10-81d7-4f4a-95a9-c37697b4ff22': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.97705382693461, 0.0, 0.0], [0.0, 3.97705382693461, 0.0], [0.0, 0.0, 3.97705382693461]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082753, 1.9885269135082753], [1.9885269135082753, 0.0, 1.9885269135082753], [1.9885269135082753, 1.9885269135082753, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9161488594598, 'volume': 62.90488993338502}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'adfa9cb1-8d89-4943-832b-9e21782861cd': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263626, 0.0, 0.0], [0.0, 4.045637198263626, 0.0], [0.0, 0.0, 4.045637198263626]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583882, 2.0228185991583882], [2.0228185991583882, 0.0, 2.0228185991583882], [2.0228185991583882, 2.0228185991583882, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365241668352, 'volume': 66.21567361408935}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'c8bd32cf-c431-4189-9f09-708a86fa8aa0': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309796, 0.0, 0.0], [0.0, 4.111970909309796, 0.0], [0.0, 0.0, 4.111970909309796]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025823, 'volume': 69.52645729479359}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '140c1cae-54ed-492f-8589-d9c0490142c6': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411815, 0.0, 0.0], [0.0, 4.17623083411815, 0.0], [0.0, 0.0, 4.17623083411815]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154170729803, 2.0881154170729803], [2.0881154170729803, 0.0, 2.0881154170729803], [2.0881154170729803, 2.0881154170729803, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8737904693437, 'volume': 72.83724097549829}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '1eade2dd-772e-4e49-8264-2ff6ee8ff6ff': {1: Response(output=[59.59410625268055, 62.90488993338502, 66.21567361408935, 69.52645729479359, 72.83724097549829], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '0b1cb308-c310-4995-b18b-1441b1ff1a22': {1: Response(output=[-1074.8457446150612, -1074.9161488594598, -1074.9365241668352, -1074.9192860025823, -1074.8737904693437], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '2fd7c54d-8f3d-437c-a59f-8236978defdc': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))}}" }, "metadata": {} }, @@ -379,7 +362,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\ncreate_function_job_81ad14ceddd174cc2129a2d071b8dfeb\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def64e90>\n\n\n\nvolume_lst_7877f4496713e91ee9569a3d39477944\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def64320>\n\n\n\nvolume_lst_7877f4496713e91ee9569a3d39477944->create_function_job_81ad14ceddd174cc2129a2d071b8dfeb\n\n\n\n\n\n0_e81e45d48628cffd23c97591d4742381\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def46db0>\n\n\n\n0_e81e45d48628cffd23c97591d4742381->volume_lst_7877f4496713e91ee9569a3d39477944\n\n\n\n\n\ninput_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47f80>\n\n\n\ninput_dict_2104e1cd318f16e37db9c8fc50b44bf7->0_e81e45d48628cffd23c97591d4742381\n\n\n\n\n\n0_79d0e65e922efc9f26386930f67b4593\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47a70>\n\n\n\ninput_dict_2104e1cd318f16e37db9c8fc50b44bf7->0_79d0e65e922efc9f26386930f67b4593\n\n\n\n\n\nenergy_lst_c39c096e088c6198246309199a06e31a\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def46c00>\n\n\n\n0_79d0e65e922efc9f26386930f67b4593->energy_lst_c39c096e088c6198246309199a06e31a\n\n\n\n\n\nstructure_8ec2a7af77e9d22260dc56b435bba70b\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47cb0>\n\n\n\nstructure_8ec2a7af77e9d22260dc56b435bba70b->input_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\n\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def46cf0>\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3->structure_8ec2a7af77e9d22260dc56b435bba70b\n\n\n\n\n\nstructure_c401a7118deb546adf8cacc894a995d4\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47980>\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3->structure_c401a7118deb546adf8cacc894a995d4\n\n\n\n\n\nstructure_503093210fb645799cb9c53a6111f31d\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47650>\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3->structure_503093210fb645799cb9c53a6111f31d\n\n\n\n\n\nstructure_feae982cf556b8d382334d6cbdf1cd8d\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47320>\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3->structure_feae982cf556b8d382334d6cbdf1cd8d\n\n\n\n\n\nstructure_d63e04359ed4866d6c7b37b920475e13\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def46ff0>\n\n\n\nstructure_a2e153ee6a338726bca4488fd55e61d3->structure_d63e04359ed4866d6c7b37b920475e13\n\n\n\n\n\ninput_dict_b90e408f5e84971a0acbe801ef8e7167\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47c20>\n\n\n\nstructure_c401a7118deb546adf8cacc894a995d4->input_dict_b90e408f5e84971a0acbe801ef8e7167\n\n\n\n\n\ninput_dict_09a5f6ff4398ee33f2c690b496ea0142\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def478f0>\n\n\n\nstructure_503093210fb645799cb9c53a6111f31d->input_dict_09a5f6ff4398ee33f2c690b496ea0142\n\n\n\n\n\ninput_dict_b75fbdc25556c6a295e00bd54557cdf3\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def475c0>\n\n\n\nstructure_feae982cf556b8d382334d6cbdf1cd8d->input_dict_b75fbdc25556c6a295e00bd54557cdf3\n\n\n\n\n\ninput_dict_dff830eead42379c139eeb9148710ae8\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47290>\n\n\n\nstructure_d63e04359ed4866d6c7b37b920475e13->input_dict_dff830eead42379c139eeb9148710ae8\n\n\n\n\n\ninput_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def46660>\n\n\n\ninput_dict_2f4bdfa637c1310ad67c1dbef51e42fc->structure_a2e153ee6a338726bca4488fd55e61d3\n\n\n\n\n\nstructure_8a946279df78421b8c6c2efb8df18e00\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def467b0>\n\n\n\nstructure_8a946279df78421b8c6c2efb8df18e00->input_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_8a946279df78421b8c6c2efb8df18e00\n\n\n\n\n\na_457b6d376c6fce696df148a385afa46d\n\na=4.04\n\n\n\na_457b6d376c6fce696df148a385afa46d->structure_8a946279df78421b8c6c2efb8df18e00\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_8a946279df78421b8c6c2efb8df18e00\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_b90e408f5e84971a0acbe801ef8e7167\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_09a5f6ff4398ee33f2c690b496ea0142\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_b75fbdc25556c6a295e00bd54557cdf3\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_dff830eead42379c139eeb9148710ae8\n\n\n\n\n\n1_6ad77da55455ab9aa590aedabc104f68\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def648f0>\n\n\n\ninput_dict_b90e408f5e84971a0acbe801ef8e7167->1_6ad77da55455ab9aa590aedabc104f68\n\n\n\n\n\n1_f7ad5955f13722bf930d81c2b9e742e9\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47a40>\n\n\n\ninput_dict_b90e408f5e84971a0acbe801ef8e7167->1_f7ad5955f13722bf930d81c2b9e742e9\n\n\n\n\n\n2_e195a45cae0bfce238475e97d9a58cd5\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def64c20>\n\n\n\ninput_dict_09a5f6ff4398ee33f2c690b496ea0142->2_e195a45cae0bfce238475e97d9a58cd5\n\n\n\n\n\n2_112c792629e86543b9cea4a872270624\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47350>\n\n\n\ninput_dict_09a5f6ff4398ee33f2c690b496ea0142->2_112c792629e86543b9cea4a872270624\n\n\n\n\n\n3_a983b77487f6859f18062f31bb895319\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def647a0>\n\n\n\ninput_dict_b75fbdc25556c6a295e00bd54557cdf3->3_a983b77487f6859f18062f31bb895319\n\n\n\n\n\n3_f629cc0dcbd5dc353789776418f3701f\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def473b0>\n\n\n\ninput_dict_b75fbdc25556c6a295e00bd54557cdf3->3_f629cc0dcbd5dc353789776418f3701f\n\n\n\n\n\n4_c9c83b9132566cff0bc7068536ede7ca\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def64da0>\n\n\n\ninput_dict_dff830eead42379c139eeb9148710ae8->4_c9c83b9132566cff0bc7068536ede7ca\n\n\n\n\n\n4_4d455a4b322d423d9821fbd74191eb62\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x7b15def47050>\n\n\n\ninput_dict_dff830eead42379c139eeb9148710ae8->4_4d455a4b322d423d9821fbd74191eb62\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_b90e408f5e84971a0acbe801ef8e7167\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_09a5f6ff4398ee33f2c690b496ea0142\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_b75fbdc25556c6a295e00bd54557cdf3\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_dff830eead42379c139eeb9148710ae8\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_2f4bdfa637c1310ad67c1dbef51e42fc\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_b90e408f5e84971a0acbe801ef8e7167\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_09a5f6ff4398ee33f2c690b496ea0142\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_b75fbdc25556c6a295e00bd54557cdf3\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_dff830eead42379c139eeb9148710ae8\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_a2e153ee6a338726bca4488fd55e61d3\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781\n\nstrain_lst=[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_8ec2a7af77e9d22260dc56b435bba70b\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_c401a7118deb546adf8cacc894a995d4\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_503093210fb645799cb9c53a6111f31d\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_feae982cf556b8d382334d6cbdf1cd8d\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_d63e04359ed4866d6c7b37b920475e13\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_2104e1cd318f16e37db9c8fc50b44bf7\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_b90e408f5e84971a0acbe801ef8e7167\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_09a5f6ff4398ee33f2c690b496ea0142\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_b75fbdc25556c6a295e00bd54557cdf3\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_dff830eead42379c139eeb9148710ae8\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_e81e45d48628cffd23c97591d4742381\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_79d0e65e922efc9f26386930f67b4593\n\n\n\n\n\n1_6ad77da55455ab9aa590aedabc104f68->volume_lst_7877f4496713e91ee9569a3d39477944\n\n\n\n\n\n1_f7ad5955f13722bf930d81c2b9e742e9->energy_lst_c39c096e088c6198246309199a06e31a\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_6ad77da55455ab9aa590aedabc104f68\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_f7ad5955f13722bf930d81c2b9e742e9\n\n\n\n\n\n2_e195a45cae0bfce238475e97d9a58cd5->volume_lst_7877f4496713e91ee9569a3d39477944\n\n\n\n\n\n2_112c792629e86543b9cea4a872270624->energy_lst_c39c096e088c6198246309199a06e31a\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_e195a45cae0bfce238475e97d9a58cd5\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_112c792629e86543b9cea4a872270624\n\n\n\n\n\n3_a983b77487f6859f18062f31bb895319->volume_lst_7877f4496713e91ee9569a3d39477944\n\n\n\n\n\n3_f629cc0dcbd5dc353789776418f3701f->energy_lst_c39c096e088c6198246309199a06e31a\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_a983b77487f6859f18062f31bb895319\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_f629cc0dcbd5dc353789776418f3701f\n\n\n\n\n\n4_c9c83b9132566cff0bc7068536ede7ca->volume_lst_7877f4496713e91ee9569a3d39477944\n\n\n\n\n\n4_4d455a4b322d423d9821fbd74191eb62->energy_lst_c39c096e088c6198246309199a06e31a\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_c9c83b9132566cff0bc7068536ede7ca\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_4d455a4b322d423d9821fbd74191eb62\n\n\n\n\n\nenergy_lst_c39c096e088c6198246309199a06e31a->create_function_job_81ad14ceddd174cc2129a2d071b8dfeb\n\n\n\n\n" + "image/svg+xml": "\n\n\n\n\ncreate_function_job_ce91e09311e572ee896f354746ffdb52\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed8a120>\n\n\n\nvolume_lst_4362c8494e9d76136a3dc40484677c25\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89ca0>\n\n\n\nvolume_lst_4362c8494e9d76136a3dc40484677c25->create_function_job_ce91e09311e572ee896f354746ffdb52\n\n\n\n\n\n0_48d1c0a308a7f85ce736e70fdee35d55\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88fe0>\n\n\n\n0_48d1c0a308a7f85ce736e70fdee35d55->volume_lst_4362c8494e9d76136a3dc40484677c25\n\n\n\n\n\ninput_dict_8627e51bf0fa1c75dee291b4340323c2\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89250>\n\n\n\ninput_dict_8627e51bf0fa1c75dee291b4340323c2->0_48d1c0a308a7f85ce736e70fdee35d55\n\n\n\n\n\n0_1721b1c587d3246df560cbea90be3167\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed5bd70>\n\n\n\ninput_dict_8627e51bf0fa1c75dee291b4340323c2->0_1721b1c587d3246df560cbea90be3167\n\n\n\n\n\nenergy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89340>\n\n\n\n0_1721b1c587d3246df560cbea90be3167->energy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\n\n\n\n\nstructure_af012e13faed0d05917b623737d05e8b\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88fb0>\n\n\n\nstructure_af012e13faed0d05917b623737d05e8b->input_dict_8627e51bf0fa1c75dee291b4340323c2\n\n\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed5bf80>\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf->structure_af012e13faed0d05917b623737d05e8b\n\n\n\n\n\nstructure_b3473c8aec01409cf59d1ab8ae13b0e4\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88c80>\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf->structure_b3473c8aec01409cf59d1ab8ae13b0e4\n\n\n\n\n\nstructure_1b95020855b9511547e4b9d147627ef3\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88950>\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf->structure_1b95020855b9511547e4b9d147627ef3\n\n\n\n\n\nstructure_dc5cfe2671bba250d930134be90215e3\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88620>\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf->structure_dc5cfe2671bba250d930134be90215e3\n\n\n\n\n\nstructure_0c3f6812beb497f64d4c870867ff8b01\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed882f0>\n\n\n\nstructure_bc5fd42ff40265090f1e99574d8705cf->structure_0c3f6812beb497f64d4c870867ff8b01\n\n\n\n\n\ninput_dict_7994b289405d0aa8bda047d28839ddbf\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88f20>\n\n\n\nstructure_b3473c8aec01409cf59d1ab8ae13b0e4->input_dict_7994b289405d0aa8bda047d28839ddbf\n\n\n\n\n\ninput_dict_319e78e342e67e35a419f59eef3a5dd8\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88bf0>\n\n\n\nstructure_1b95020855b9511547e4b9d147627ef3->input_dict_319e78e342e67e35a419f59eef3a5dd8\n\n\n\n\n\ninput_dict_155901cdf9fd0dbb07cd9ae061d26936\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed888c0>\n\n\n\nstructure_dc5cfe2671bba250d930134be90215e3->input_dict_155901cdf9fd0dbb07cd9ae061d26936\n\n\n\n\n\ninput_dict_8e1b79be7495dee3b8ab20b53ae70673\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88590>\n\n\n\nstructure_0c3f6812beb497f64d4c870867ff8b01->input_dict_8e1b79be7495dee3b8ab20b53ae70673\n\n\n\n\n\ninput_dict_e87d51228d04b598ed01c576c04974d3\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed5b710>\n\n\n\ninput_dict_e87d51228d04b598ed01c576c04974d3->structure_bc5fd42ff40265090f1e99574d8705cf\n\n\n\n\n\nstructure_dfe10bce77b4e5e0e99fc065e50a75a8\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed5b950>\n\n\n\nstructure_dfe10bce77b4e5e0e99fc065e50a75a8->input_dict_e87d51228d04b598ed01c576c04974d3\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\na_457b6d376c6fce696df148a385afa46d\n\na=4.04\n\n\n\na_457b6d376c6fce696df148a385afa46d->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_e87d51228d04b598ed01c576c04974d3\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_8627e51bf0fa1c75dee291b4340323c2\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_e87d51228d04b598ed01c576c04974d3\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_7994b289405d0aa8bda047d28839ddbf\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_319e78e342e67e35a419f59eef3a5dd8\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_155901cdf9fd0dbb07cd9ae061d26936\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_8e1b79be7495dee3b8ab20b53ae70673\n\n\n\n\n\n1_eca78ff83d64c5f761b971a2ed89c46d\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89370>\n\n\n\ninput_dict_7994b289405d0aa8bda047d28839ddbf->1_eca78ff83d64c5f761b971a2ed89c46d\n\n\n\n\n\n1_1dda55804b8c5fad99178011f9e02a31\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed5bdd0>\n\n\n\ninput_dict_7994b289405d0aa8bda047d28839ddbf->1_1dda55804b8c5fad99178011f9e02a31\n\n\n\n\n\n2_3d421c4b25f966d418b487e9bcc07050\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89850>\n\n\n\ninput_dict_319e78e342e67e35a419f59eef3a5dd8->2_3d421c4b25f966d418b487e9bcc07050\n\n\n\n\n\n2_8214b14dfa8739686a7b35b9991651ec\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89eb0>\n\n\n\ninput_dict_319e78e342e67e35a419f59eef3a5dd8->2_8214b14dfa8739686a7b35b9991651ec\n\n\n\n\n\n3_b116ea1b52d0f5cba9218547d9878e49\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed88d40>\n\n\n\ninput_dict_155901cdf9fd0dbb07cd9ae061d26936->3_b116ea1b52d0f5cba9218547d9878e49\n\n\n\n\n\n3_23d597151f325f654ab132719a58a92c\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89e50>\n\n\n\ninput_dict_155901cdf9fd0dbb07cd9ae061d26936->3_23d597151f325f654ab132719a58a92c\n\n\n\n\n\n4_46b58af9c8d7d6e1055921a1c97893c0\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed889b0>\n\n\n\ninput_dict_8e1b79be7495dee3b8ab20b53ae70673->4_46b58af9c8d7d6e1055921a1c97893c0\n\n\n\n\n\n4_8a2a2119bba392d8d14dc78b7b1f750b\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x72f36ed89d60>\n\n\n\ninput_dict_8e1b79be7495dee3b8ab20b53ae70673->4_8a2a2119bba392d8d14dc78b7b1f750b\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_8627e51bf0fa1c75dee291b4340323c2\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_e87d51228d04b598ed01c576c04974d3\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_7994b289405d0aa8bda047d28839ddbf\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_319e78e342e67e35a419f59eef3a5dd8\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_155901cdf9fd0dbb07cd9ae061d26936\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_8e1b79be7495dee3b8ab20b53ae70673\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_8627e51bf0fa1c75dee291b4340323c2\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_e87d51228d04b598ed01c576c04974d3\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_7994b289405d0aa8bda047d28839ddbf\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_319e78e342e67e35a419f59eef3a5dd8\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_155901cdf9fd0dbb07cd9ae061d26936\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_8e1b79be7495dee3b8ab20b53ae70673\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_bc5fd42ff40265090f1e99574d8705cf\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781\n\nstrain_lst=[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_af012e13faed0d05917b623737d05e8b\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_b3473c8aec01409cf59d1ab8ae13b0e4\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_1b95020855b9511547e4b9d147627ef3\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_dc5cfe2671bba250d930134be90215e3\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_0c3f6812beb497f64d4c870867ff8b01\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_8627e51bf0fa1c75dee291b4340323c2\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_7994b289405d0aa8bda047d28839ddbf\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_319e78e342e67e35a419f59eef3a5dd8\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_155901cdf9fd0dbb07cd9ae061d26936\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_8e1b79be7495dee3b8ab20b53ae70673\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_48d1c0a308a7f85ce736e70fdee35d55\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_1721b1c587d3246df560cbea90be3167\n\n\n\n\n\n1_eca78ff83d64c5f761b971a2ed89c46d->volume_lst_4362c8494e9d76136a3dc40484677c25\n\n\n\n\n\n1_1dda55804b8c5fad99178011f9e02a31->energy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_eca78ff83d64c5f761b971a2ed89c46d\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_1dda55804b8c5fad99178011f9e02a31\n\n\n\n\n\n2_3d421c4b25f966d418b487e9bcc07050->volume_lst_4362c8494e9d76136a3dc40484677c25\n\n\n\n\n\n2_8214b14dfa8739686a7b35b9991651ec->energy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_3d421c4b25f966d418b487e9bcc07050\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_8214b14dfa8739686a7b35b9991651ec\n\n\n\n\n\n3_b116ea1b52d0f5cba9218547d9878e49->volume_lst_4362c8494e9d76136a3dc40484677c25\n\n\n\n\n\n3_23d597151f325f654ab132719a58a92c->energy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_b116ea1b52d0f5cba9218547d9878e49\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_23d597151f325f654ab132719a58a92c\n\n\n\n\n\n4_46b58af9c8d7d6e1055921a1c97893c0->volume_lst_4362c8494e9d76136a3dc40484677c25\n\n\n\n\n\n4_8a2a2119bba392d8d14dc78b7b1f750b->energy_lst_b57492ae1fc39dfaf2681d3af8243aa4\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_46b58af9c8d7d6e1055921a1c97893c0\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_8a2a2119bba392d8d14dc78b7b1f750b\n\n\n\n\n\nenergy_lst_b57492ae1fc39dfaf2681d3af8243aa4->create_function_job_ce91e09311e572ee896f354746ffdb52\n\n\n\n\n" }, "metadata": {} } @@ -405,67 +388,67 @@ { "name": "stdout", "output_type": "stream", - "text": "The job get_bulk_structure_f1e730ed97e30e5439e855d2ac41396f was saved and received the ID: 1\nThe job get_dict_20400c1655d51731f9f5ffb50c2b401f was saved and received the ID: 2\nThe job calculate_qe_22b5d0934d89d8f08761e744e4612c30 was saved and received the ID: 3\n" + "text": "The job get_bulk_structure_2ca4aeae204ceaa28593c93054b07908 was saved and received the ID: 1\nThe job get_dict_20400c1655d51731f9f5ffb50c2b401f was saved and received the ID: 2\nThe job calculate_qe_b261e97e2e1714bf57ce6e5016ae4632 was saved and received the ID: 3\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01892] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08955] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job generate_structures_6bbb6b6ae566b035388bec7f6f658394 was saved and received the ID: 4\nThe job get_dict_7fbef1423a72155d480420469f6f0f78 was saved and received the ID: 5\nThe job calculate_qe_35d4282b6beff7c2fc7a850e02ff3f07 was saved and received the ID: 6\n" + "text": "The job generate_structures_fcb3884e78b15be7a9a6069869171c61 was saved and received the ID: 4\nThe job get_dict_9d50dca89ce2c8f1319206888212f261 was saved and received the ID: 5\nThe job calculate_qe_495edf27cca1893fd71d860b009fde57 was saved and received the ID: 6\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01908] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08970] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_bcd13fb93bbd4d7a7a99c460c0591b51 was saved and received the ID: 7\nThe job calculate_qe_3159d3281f1fccbf1a91388144a7957f was saved and received the ID: 8\n" + "text": "The job get_dict_c6f3d017cbf308a2712facb53625f0ca was saved and received the ID: 7\nThe job calculate_qe_7dc568c59eb166c911415fcb78d508b6 was saved and received the ID: 8\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01919] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08982] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_5b1eeb4af2f8eb4018b7326f4af63eca was saved and received the ID: 9\nThe job calculate_qe_4d1c131dceca1e8897f7cda47cb24f9e was saved and received the ID: 10\n" + "text": "The job get_dict_df08484509ac6c4b41f32ea3fb5035cf was saved and received the ID: 9\nThe job calculate_qe_923ca5c6b53423773a8c74e3340d3471 was saved and received the ID: 10\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01930] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:08993] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_566acb6c9830b82fd09efc4e8227e6e6 was saved and received the ID: 11\nThe job calculate_qe_e463d009aee35caa551669d8efc7c8cd was saved and received the ID: 12\n" + "text": "The job get_dict_04da5d650a8c957b7325cc9188f1cd07 was saved and received the ID: 11\nThe job calculate_qe_49ab6c2d99e5462024081421d2c1b7a7 was saved and received the ID: 12\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01941] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:09004] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_75499df774616aa1b379a3fa72da90fb was saved and received the ID: 13\nThe job calculate_qe_6ef5649cee1f8db43ecd79d266f477b5 was saved and received the ID: 14\n" + "text": "The job get_dict_9d21f3f8e376847d495acc88b24aa2bd was saved and received the ID: 13\nThe job calculate_qe_4ca4360fd423b8cef4abf77502fef1ca was saved and received the ID: 14\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:01953] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:09015] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_list_5d2e404624b12c3bb1f93528d1b1dddb was saved and received the ID: 15\nThe job get_list_8628ae553e40ba9aab5dde25ea2d7ba2 was saved and received the ID: 16\nThe job plot_energy_volume_curve_d715578098aa2e6221fb76f20377b5cf was saved and received the ID: 17\n" + "text": "The job get_list_b7d643bf967628f7c04f17614baa0c5f was saved and received the ID: 15\nThe job get_list_1980b54721033684c33ad75357848857 was saved and received the ID: 16\nThe job plot_energy_volume_curve_9ba5af92db6796aafb006576962dec7c was saved and received the ID: 17\n" }, { "output_type": "display_data", diff --git a/example_workflows/quantum_espresso/cwl.ipynb b/example_workflows/quantum_espresso/cwl.ipynb index 5dae00c..5dc1979 100644 --- a/example_workflows/quantum_espresso/cwl.ipynb +++ b/example_workflows/quantum_espresso/cwl.ipynb @@ -82,7 +82,7 @@ { "name": "stdout", "output_type": "stream", - "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/quantum_espresso/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_bulk_structure_0\n\u001B[1;30mINFO\u001B[0m [step get_bulk_structure_0] start\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] /tmp/o5wvbmxj$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/3uzk268a/stgc8824dc9-f08d-44b9-9d9c-518dc0415f4d/workflow.py \\\n --function=workflow.get_bulk_structure \\\n --arg_a=/tmp/3uzk268a/stgbcb5cab3-e9ef-46e5-8f20-1a73f5b242e9/a.pickle \\\n --arg_element=/tmp/3uzk268a/stgb2678406-1178-4bf6-ba96-2b623c74f408/element.pickle \\\n --arg_cubic=/tmp/3uzk268a/stg7d836c8f-b499-4ea6-a341-97ff1a366b8f/cubic.pickle\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] Max memory used: 100MiB\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_bulk_structure_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_13\n\u001B[1;30mINFO\u001B[0m [step get_dict_13] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_13] /tmp/que74c90$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/k_sm4nc9/stg029d45cb-9d3e-4d26-a4f6-95cb0fb162d5/kpts.pickle \\\n --arg_structure=/tmp/k_sm4nc9/stgbde5b9c0-6926-4c08-886c-a7425fdf5571/result.pickle \\\n --arg_pseudopotentials=/tmp/k_sm4nc9/stg6717dca8-3880-4d1b-bed2-4078dca65fdb/pseudopotentials.pickle \\\n --arg_calculation=/tmp/k_sm4nc9/stg0e219c86-340f-4f1a-bc25-e366286137ea/calculation_0.pickle \\\n --arg_smearing=/tmp/k_sm4nc9/stg299bfaba-cb42-4aa5-b372-3101efa15660/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_13] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_13] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_1\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_1] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] /tmp/9ew4474v$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/3hzmn68a/stgf58c4a14-7b0f-4efc-bedd-3561b9fdb227/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/3hzmn68a/stg41392280-cfd6-4e67-ab11-915bfcbd0304/result.pickle \\\n --arg_working_directory=/tmp/3hzmn68a/stg6aa2aff2-eca4-41b7-bef5-a917188e0853/working_directory_0.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:01664] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] Max memory used: 250MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step generate_structures_2\n\u001B[1;30mINFO\u001B[0m [step generate_structures_2] start\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] /tmp/l8wkgfu9$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/aibj9rr4/stgb715e49b-e705-4371-8c63-5bc9f8addb97/workflow.py \\\n --function=workflow.generate_structures \\\n --arg_structure=/tmp/aibj9rr4/stg88fe1a91-5cb6-4f9c-9fff-a63e477a0ccb/structure.pickle \\\n --arg_strain_lst=/tmp/aibj9rr4/stg3489de05-cdc1-4f7f-af63-cb8612cefe10/strain_lst.pickle\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] Max memory used: 108MiB\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] completed success\n\u001B[1;30mINFO\u001B[0m [step generate_structures_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_20\n\u001B[1;30mINFO\u001B[0m [step get_dict_20] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_20] /tmp/0ls08hbo$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/yb9nqwe7/stg475a5983-0e88-40ee-b3a4-0c9b916f08f1/kpts.pickle \\\n --arg_structure=/tmp/yb9nqwe7/stg4f27a44f-d76c-4278-855d-ab654ebe6e32/s_0.pickle \\\n --arg_pseudopotentials=/tmp/yb9nqwe7/stgbfcb2c02-776a-4101-b906-06a8ef758140/pseudopotentials.pickle \\\n --arg_calculation=/tmp/yb9nqwe7/stgd91d742a-82f8-459e-939b-2cd0876f41ee/calculation_1.pickle \\\n --arg_smearing=/tmp/yb9nqwe7/stga65643a5-b1bb-416e-bc6c-ee7b52c28bd8/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_20] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_20] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_3\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_3] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] /tmp/nzsw1xr6$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/gjwsgfmj/stg3069d789-517f-41bf-8d4b-07e51f9e924d/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/gjwsgfmj/stg9575b9dd-3336-4e26-a106-7c52c1e41f91/result.pickle \\\n --arg_working_directory=/tmp/gjwsgfmj/stg28ff68ea-caa6-47bf-be5e-67394ab72f64/working_directory_1.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:01846] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] Max memory used: 239MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_3] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_25\n\u001B[1;30mINFO\u001B[0m [step get_dict_25] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_25] /tmp/zrs68r3d$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/jj2_r82j/stg13ba3696-061f-46f7-b012-bb7ab8a40796/kpts.pickle \\\n --arg_structure=/tmp/jj2_r82j/stg5ca9e71a-98fe-44df-8ca5-550908525a4e/s_2.pickle \\\n --arg_pseudopotentials=/tmp/jj2_r82j/stg9e1fe3f0-1192-4cde-9772-6be8dfa314fe/pseudopotentials.pickle \\\n --arg_calculation=/tmp/jj2_r82j/stgde664722-b13c-4ae9-9562-aec2063d548a/calculation_1.pickle \\\n --arg_smearing=/tmp/jj2_r82j/stg799e1f26-f08e-40bf-a7a9-c58e907674c8/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_25] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_25] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_23\n\u001B[1;30mINFO\u001B[0m [step get_dict_23] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_23] /tmp/7qgifyu_$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/ojouuynn/stg7b99ab8b-9235-4007-b6b7-dd4170bd1760/kpts.pickle \\\n --arg_structure=/tmp/ojouuynn/stg8bfd87ff-e83d-4918-9a0d-71b958c46154/s_1.pickle \\\n --arg_pseudopotentials=/tmp/ojouuynn/stg0bcc3451-1700-46e0-9a5e-fca9968c8521/pseudopotentials.pickle \\\n --arg_calculation=/tmp/ojouuynn/stgb9d8de26-7d88-4119-ad13-8374ff498f72/calculation_1.pickle \\\n --arg_smearing=/tmp/ojouuynn/stg01fe91f8-b588-4adc-b207-9d9d4e0956e3/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_23] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_23] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_27\n\u001B[1;30mINFO\u001B[0m [step get_dict_27] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_27] /tmp/v83aah99$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/_wg2md43/stgee67f0e5-87a9-4768-82ed-cb6c6cf74b6d/kpts.pickle \\\n --arg_structure=/tmp/_wg2md43/stgb39aa4d9-0909-4ffb-bfe8-c448a3d77669/s_3.pickle \\\n --arg_pseudopotentials=/tmp/_wg2md43/stgc7b618ee-6e90-4b93-a079-785fab087237/pseudopotentials.pickle \\\n --arg_calculation=/tmp/_wg2md43/stg738933fd-9a31-4c0e-ac99-984d1002fd0a/calculation_1.pickle \\\n --arg_smearing=/tmp/_wg2md43/stg174b61ec-1446-4c63-a433-49a940e48f39/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_27] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_27] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_4\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_4] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] /tmp/abio0491$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/pltanpun/stg312b10e4-f5f2-4770-b776-12c659453bef/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/pltanpun/stgceefbf38-ae57-4369-872d-4ea0895a6976/result.pickle \\\n --arg_working_directory=/tmp/pltanpun/stg6abc0b8b-ed0d-4692-b100-b510fe7de457/working_directory_2.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:01928] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] Max memory used: 244MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_4] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_29\n\u001B[1;30mINFO\u001B[0m [step get_dict_29] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_29] /tmp/li__ygke$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_kpts=/tmp/20wxb6mt/stg4f9c6f04-e0da-4f1d-9b91-17867111fcec/kpts.pickle \\\n --arg_structure=/tmp/20wxb6mt/stg27aeb042-5dba-406d-ad3f-c1a15414d462/s_4.pickle \\\n --arg_pseudopotentials=/tmp/20wxb6mt/stg00a521b7-0d6f-44fa-849f-611e82b816d2/pseudopotentials.pickle \\\n --arg_calculation=/tmp/20wxb6mt/stg51a4e465-9a6d-465e-a329-ec65c9631dca/calculation_1.pickle \\\n --arg_smearing=/tmp/20wxb6mt/stg72f4b40d-8647-441e-94ce-b4d60eb84837/smearing.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_29] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_29] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_7\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_7] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] /tmp/26ontyw1$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/3e7bw8e2/stg86169764-ce4e-40f6-9b63-ef5e11208258/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/3e7bw8e2/stge349561c-3f24-48da-94fa-2d16e4df4779/result.pickle \\\n --arg_working_directory=/tmp/3e7bw8e2/stg30622d6d-1c64-4440-9d76-7a70e081ff5e/working_directory_5.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:02006] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] Max memory used: 243MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_7] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_5\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_5] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] /tmp/nwlrltkk$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/q_jjx0ja/stgb8b85eae-791f-4e34-9696-ceb277f72155/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/q_jjx0ja/stg2efa8335-1138-47c3-b9e9-d8ea2d8754c0/result.pickle \\\n --arg_working_directory=/tmp/q_jjx0ja/stg4f726c25-7adb-4ce0-970e-bd9ddc5191cc/working_directory_3.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:02086] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] Max memory used: 246MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_5] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_6\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_6] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] /tmp/9yp55i6u$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/1c_enl4x/stg2aeb7a80-3364-48a0-810d-955e246aa33b/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/1c_enl4x/stg19bec723-020c-4d0e-bca0-8124f6962c7e/result.pickle \\\n --arg_working_directory=/tmp/1c_enl4x/stgc36f93b3-f6f6-4fec-8eb2-0de1ca22f3cd/working_directory_4.pickle\n[jupyter-pythonworkflow-fl--x---ff79c5c6:02164] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] Max memory used: 243MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_6] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_list_31\n\u001B[1;30mINFO\u001B[0m [step get_list_31] start\n\u001B[1;30mINFO\u001B[0m [job get_list_31] /tmp/xgme48c0$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_list \\\n --arg_2=/tmp/u2adengu/stg036d73c4-50fd-4b84-9054-ef00e66e0ea8/energy.pickle \\\n --arg_4=/tmp/u2adengu/stg8736d42d-b110-43b3-8e1d-da22b9883ff5/energy.pickle \\\n --arg_1=/tmp/u2adengu/stg8cac7eb7-6132-4085-865d-673027e26baa/energy.pickle \\\n --arg_3=/tmp/u2adengu/stg55b370b4-c852-4493-bb7b-4acaa0588aa8/energy.pickle \\\n --arg_0=/tmp/u2adengu/stg5d319d67-b4fc-4c4d-886a-529b9bfd2458/energy.pickle\n\u001B[1;30mINFO\u001B[0m [job get_list_31] completed success\n\u001B[1;30mINFO\u001B[0m [step get_list_31] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_list_30\n\u001B[1;30mINFO\u001B[0m [step get_list_30] start\n\u001B[1;30mINFO\u001B[0m [job get_list_30] /tmp/1xbu0rii$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_list \\\n --arg_2=/tmp/0ads3xzd/stg24fc8770-2739-45d1-b535-89924a6234ed/volume.pickle \\\n --arg_4=/tmp/0ads3xzd/stgfb79ea5f-6109-4f2e-a1d6-0817648a5350/volume.pickle \\\n --arg_1=/tmp/0ads3xzd/stg0b1e9637-dba2-4e42-9dbe-c605e7469714/volume.pickle \\\n --arg_3=/tmp/0ads3xzd/stgdf4991ae-4266-4ab6-82be-8f87d46fa7f6/volume.pickle \\\n --arg_0=/tmp/0ads3xzd/stg623a06b5-d2a0-44fd-9473-833452ad5762/volume.pickle\n\u001B[1;30mINFO\u001B[0m [job get_list_30] completed success\n\u001B[1;30mINFO\u001B[0m [step get_list_30] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step plot_energy_volume_curve_8\n\u001B[1;30mINFO\u001B[0m [step plot_energy_volume_curve_8] start\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] /tmp/vcffw_nr$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/6s32h5zf/stg79d5980d-139d-4481-9277-3f58bb27d49f/workflow.py \\\n --function=workflow.plot_energy_volume_curve \\\n --arg_volume_lst=/tmp/6s32h5zf/stg67eb8ed0-f498-4181-a5a5-c7e74ecd3276/result.pickle \\\n --arg_energy_lst=/tmp/6s32h5zf/stg3ebdb224-bd9a-4ae7-ad4e-03489dcfb661/result.pickle\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] Max memory used: 110MiB\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] completed success\n\u001B[1;30mINFO\u001B[0m [step plot_energy_volume_curve_8] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/quantum_espresso/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$dbc1aaddc8b7343d6d33b34edcf608b8f8801918\",\n \"size\": 4,\n \"path\": \"/home/jovyan/example_workflows/quantum_espresso/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" + "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/quantum_espresso/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_bulk_structure_0\n\u001B[1;30mINFO\u001B[0m [step get_bulk_structure_0] start\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] /tmp/9sant4h9$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/va137af6/stga19aac01-d6f9-48d3-ba6b-d8a6e460f525/workflow.py \\\n --function=workflow.get_bulk_structure \\\n --arg_cubic=/tmp/va137af6/stgd2861bb7-939d-449d-9600-71f380ee058d/cubic.pickle \\\n --arg_element=/tmp/va137af6/stg93f5775e-477a-4b2e-87ac-822ff4097346/element.pickle \\\n --arg_a=/tmp/va137af6/stgcfd0bd7b-a186-4b46-80a6-663aeb5d0fa9/a.pickle\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] Max memory used: 110MiB\n\u001B[1;30mINFO\u001B[0m [job get_bulk_structure_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_bulk_structure_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_13\n\u001B[1;30mINFO\u001B[0m [step get_dict_13] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_13] /tmp/_o8rxcyc$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/1h2uwpt9/stg17e865b8-f1f4-406f-a9c7-b8deddc5695d/smearing.pickle \\\n --arg_calculation=/tmp/1h2uwpt9/stgf1d25320-f3de-48f7-8087-5cdb5531765c/calculation_0.pickle \\\n --arg_kpts=/tmp/1h2uwpt9/stgc9e37196-83cf-49d9-88e1-b5acb7c53e7f/kpts.pickle \\\n --arg_pseudopotentials=/tmp/1h2uwpt9/stgcfb6bfd1-3ae7-4600-b07d-ca107c1a275c/pseudopotentials.pickle \\\n --arg_structure=/tmp/1h2uwpt9/stg0da627e7-f19e-4948-b23e-4552aa692862/result.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_13] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_13] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_1\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_1] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] /tmp/q56p65x4$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/5hwlsb8q/stga00637b3-d27a-4b67-b4b2-5857ffc8f94a/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/5hwlsb8q/stgea0d773c-cef9-49b7-9895-09c22db6f52d/result.pickle \\\n --arg_working_directory=/tmp/5hwlsb8q/stg541840e1-d4a6-4a2c-a220-ab09e72c869d/working_directory_0.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09273] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] Max memory used: 273MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_1] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step generate_structures_2\n\u001B[1;30mINFO\u001B[0m [step generate_structures_2] start\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] /tmp/81vwps2h$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/0d6xih7u/stg8da9bfd1-34a7-4282-8446-97a728d4747b/workflow.py \\\n --function=workflow.generate_structures \\\n --arg_structure=/tmp/0d6xih7u/stg89eb15f9-014d-4c20-8197-87c6c7345ffe/structure.pickle \\\n --arg_strain_lst=/tmp/0d6xih7u/stg80ec088c-9b6a-45bd-8565-e68fd3c76210/strain_lst.pickle\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] Max memory used: 96MiB\n\u001B[1;30mINFO\u001B[0m [job generate_structures_2] completed success\n\u001B[1;30mINFO\u001B[0m [step generate_structures_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_25\n\u001B[1;30mINFO\u001B[0m [step get_dict_25] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_25] /tmp/hj3teyvh$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/ky497mud/stgf2ab029c-fd78-4490-a4aa-2ee352fa40a2/smearing.pickle \\\n --arg_calculation=/tmp/ky497mud/stg12f82711-28cb-42e6-80c5-59e7fa946ea8/calculation_1.pickle \\\n --arg_kpts=/tmp/ky497mud/stgd35fecc6-83e5-493e-85ad-caf6acd301cb/kpts.pickle \\\n --arg_pseudopotentials=/tmp/ky497mud/stg9b98aba6-11a6-4718-bd3a-23f160518077/pseudopotentials.pickle \\\n --arg_structure=/tmp/ky497mud/stg00376f4a-a991-469a-b494-27c160e6c15d/s_2.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_25] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_25] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_20\n\u001B[1;30mINFO\u001B[0m [step get_dict_20] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_20] /tmp/y9drdoe7$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/dsu142t1/stgcba59359-36e1-4bf9-9e6f-e7cf99a23077/smearing.pickle \\\n --arg_calculation=/tmp/dsu142t1/stg56a2646f-2057-4670-bb4e-f55af62c5858/calculation_1.pickle \\\n --arg_kpts=/tmp/dsu142t1/stgc443e9a8-c9b6-4c5e-8321-6a70d347706b/kpts.pickle \\\n --arg_pseudopotentials=/tmp/dsu142t1/stg47b4b44d-c69c-4629-aaed-0e15bf14426e/pseudopotentials.pickle \\\n --arg_structure=/tmp/dsu142t1/stg0e5b3c6e-a315-4eaf-9a66-dbf5669eaada/s_0.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_20] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_20] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_23\n\u001B[1;30mINFO\u001B[0m [step get_dict_23] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_23] /tmp/9v59c4vd$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/2mc_byfs/stgace4b178-c0ff-406e-95ac-754318766886/smearing.pickle \\\n --arg_calculation=/tmp/2mc_byfs/stg793df1d8-8f8d-4bb3-9c7c-243a48dc494b/calculation_1.pickle \\\n --arg_kpts=/tmp/2mc_byfs/stga852e76a-885f-4e39-8ab4-ecebf95c656f/kpts.pickle \\\n --arg_pseudopotentials=/tmp/2mc_byfs/stgd06acdff-6e0c-476c-be57-1f21b2d03711/pseudopotentials.pickle \\\n --arg_structure=/tmp/2mc_byfs/stg02210df5-d3e2-42b8-a75e-47e2f2c9f274/s_1.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_23] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_23] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_29\n\u001B[1;30mINFO\u001B[0m [step get_dict_29] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_29] /tmp/q_svsf9g$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/8u8e7db4/stgbba611dc-3b23-4653-a293-f71d492a42af/smearing.pickle \\\n --arg_calculation=/tmp/8u8e7db4/stge9a32972-6649-4eb5-abd7-9db61d929d2d/calculation_1.pickle \\\n --arg_kpts=/tmp/8u8e7db4/stg02098ea5-7487-4a66-bb77-99a6336d7b71/kpts.pickle \\\n --arg_pseudopotentials=/tmp/8u8e7db4/stg571b6259-4599-4c39-8cb2-79a70feb78b8/pseudopotentials.pickle \\\n --arg_structure=/tmp/8u8e7db4/stg64c55a4d-8af6-40bf-abfd-3ec8a690b90b/s_4.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_29] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_29] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_dict_27\n\u001B[1;30mINFO\u001B[0m [step get_dict_27] start\n\u001B[1;30mINFO\u001B[0m [job get_dict_27] /tmp/vgcwzb84$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_dict \\\n --arg_smearing=/tmp/xf32x1ld/stg3cbb6408-2383-49d0-9476-ef3fbee7c165/smearing.pickle \\\n --arg_calculation=/tmp/xf32x1ld/stgeb36ed3b-b442-43ea-b14d-1397875e8839/calculation_1.pickle \\\n --arg_kpts=/tmp/xf32x1ld/stge8854d32-32f3-4a90-8e66-8ce7b1160d8d/kpts.pickle \\\n --arg_pseudopotentials=/tmp/xf32x1ld/stg0dba3c44-e6af-46a9-9f00-c08969392ede/pseudopotentials.pickle \\\n --arg_structure=/tmp/xf32x1ld/stg4223a500-1f85-4651-9130-bd1629008770/s_3.pickle\n\u001B[1;30mINFO\u001B[0m [job get_dict_27] completed success\n\u001B[1;30mINFO\u001B[0m [step get_dict_27] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_3\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_3] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] /tmp/v2e_84tz$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/n81xp6_a/stgf98a9803-3329-400e-a03c-02b51d3f3c97/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/n81xp6_a/stgd93a737b-2598-4fb8-bdcb-bb1d2048116f/result.pickle \\\n --arg_working_directory=/tmp/n81xp6_a/stg5ad2a52b-2844-45e4-b227-3d835efa01f6/working_directory_1.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09459] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] Max memory used: 240MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_3] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_3] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_4\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_4] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] /tmp/tgwdkhxx$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/l5mihx97/stgf73a20aa-bd97-46af-a923-b8d776da2b98/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/l5mihx97/stgb8c3fcbe-9277-46c4-b8a2-a1171a292580/result.pickle \\\n --arg_working_directory=/tmp/l5mihx97/stg3ae0b93a-2e0b-4f1b-b079-985ea6bbaa72/working_directory_2.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09533] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] Max memory used: 213MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_4] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_4] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_5\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_5] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] /tmp/d36x49f6$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/nvm7fsf5/stg384bab04-833c-43f2-bd00-f4b5a5c93eec/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/nvm7fsf5/stg9aa51e21-01b0-4157-b73f-a3feee8a917a/result.pickle \\\n --arg_working_directory=/tmp/nvm7fsf5/stg02ef6345-c598-4127-95c7-e92d0a977c40/working_directory_3.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09611] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] Max memory used: 243MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_5] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_5] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_6\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_6] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] /tmp/eiyg8it6$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/708xmf3f/stg791b1717-cfb1-4569-ba75-d648a84e0a72/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/708xmf3f/stg9ebf7054-080c-4173-a8b9-2247d01a0068/result.pickle \\\n --arg_working_directory=/tmp/708xmf3f/stg1afccee5-d9b6-46ed-bc2c-fa36bdb8013d/working_directory_4.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09688] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] Max memory used: 245MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_6] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_6] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step calculate_qe_7\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_7] start\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] /tmp/qjgxwxnd$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/g3sp392q/stg0a51a8da-c7a7-4d90-a49c-1817002a62a6/workflow.py \\\n --function=workflow.calculate_qe \\\n --arg_input_dict=/tmp/g3sp392q/stg67e73a60-3cc6-46dd-b009-cfc0034aec2c/result.pickle \\\n --arg_working_directory=/tmp/g3sp392q/stgf3d265db-820b-4af3-8975-0a6faa0d7a67/working_directory_5.pickle\n[jupyter-pythonworkflow-fl--x---d7231032:09770] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] Max memory used: 244MiB\n\u001B[1;30mINFO\u001B[0m [job calculate_qe_7] completed success\n\u001B[1;30mINFO\u001B[0m [step calculate_qe_7] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_list_31\n\u001B[1;30mINFO\u001B[0m [step get_list_31] start\n\u001B[1;30mINFO\u001B[0m [job get_list_31] /tmp/mnovytq_$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_list \\\n --arg_0=/tmp/bz0ntajx/stgdab2f59b-b118-44c4-96ef-b4639edaee4e/energy.pickle \\\n --arg_2=/tmp/bz0ntajx/stg2e9bec4d-1824-4152-b003-aab0eac204cd/energy.pickle \\\n --arg_1=/tmp/bz0ntajx/stg9511563e-9784-48a9-8d81-74ade3a084c1/energy.pickle \\\n --arg_4=/tmp/bz0ntajx/stg17845efd-e335-421e-9891-6e627254edb4/energy.pickle \\\n --arg_3=/tmp/bz0ntajx/stg051fa3bc-832a-4d70-b9fb-b9948f51904d/energy.pickle\n\u001B[1;30mINFO\u001B[0m [job get_list_31] completed success\n\u001B[1;30mINFO\u001B[0m [step get_list_31] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_list_30\n\u001B[1;30mINFO\u001B[0m [step get_list_30] start\n\u001B[1;30mINFO\u001B[0m [job get_list_30] /tmp/vc0dzppy$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --function=python_workflow_definition.shared.get_list \\\n --arg_0=/tmp/mejux8b1/stg71e3a6a9-c56b-4be8-8720-0ca90ac40513/volume.pickle \\\n --arg_2=/tmp/mejux8b1/stg429d498d-cf56-4561-a653-8048c1213851/volume.pickle \\\n --arg_1=/tmp/mejux8b1/stgee1a0001-20f2-45de-ac4e-77b0d0c59957/volume.pickle \\\n --arg_4=/tmp/mejux8b1/stg0de2a6dc-57cd-4a0c-9637-ef2e63e96fce/volume.pickle \\\n --arg_3=/tmp/mejux8b1/stga4551f25-d5f6-47c6-92ea-452cf694a286/volume.pickle\n\u001B[1;30mINFO\u001B[0m [job get_list_30] completed success\n\u001B[1;30mINFO\u001B[0m [step get_list_30] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step plot_energy_volume_curve_8\n\u001B[1;30mINFO\u001B[0m [step plot_energy_volume_curve_8] start\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] /tmp/j4v3j3mt$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/_67k4bu3/stg5be48d76-8a92-4b02-b3d6-7bdb4c35c9ce/workflow.py \\\n --function=workflow.plot_energy_volume_curve \\\n --arg_volume_lst=/tmp/_67k4bu3/stgd43e71b0-d16b-4eb2-8d14-83924dafd7d6/result.pickle \\\n --arg_energy_lst=/tmp/_67k4bu3/stg43eeacdd-5042-4f2d-8efc-d8e0d5fe1c14/result.pickle\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] Max memory used: 112MiB\n\u001B[1;30mINFO\u001B[0m [job plot_energy_volume_curve_8] completed success\n\u001B[1;30mINFO\u001B[0m [step plot_energy_volume_curve_8] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/quantum_espresso/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$dbc1aaddc8b7343d6d33b34edcf608b8f8801918\",\n \"size\": 4,\n \"path\": \"/home/jovyan/example_workflows/quantum_espresso/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n" } ], "execution_count": 6 diff --git a/example_workflows/quantum_espresso/jobflow.ipynb b/example_workflows/quantum_espresso/jobflow.ipynb index 901abda..442b711 100644 --- a/example_workflows/quantum_espresso/jobflow.ipynb +++ b/example_workflows/quantum_espresso/jobflow.ipynb @@ -23,34 +23,27 @@ "cells": [ { "cell_type": "markdown", - "source": [ - "# jobflow" - ], + "source": "# jobflow", "metadata": {} }, { "cell_type": "markdown", - "source": [ - "[`jobflow`](https://materialsproject.github.io/jobflow/index.html) and [`atomate2`](https://materialsproject.github.io/atomate2/index.html) are key packages of the [Materials Project](https://materialsproject.org/) . `jobflow` was especially designed to simplify the execution of dynamic workflows -- when the actual number of jobs is dynamically determined upon runtime instead of being statically fixed before running the workflow(s). `jobflow`'s overall flexibility allows for building workflows that go beyond the usage in materials science. `jobflow` serves as the basis of `atomate2`, which implements data generation workflows in the context of materials science and will be used for data generation in the Materials Project in the future." - ], + "source": "[`jobflow`](https://materialsproject.github.io/jobflow/index.html) and [`atomate2`](https://materialsproject.github.io/atomate2/index.html) are key packages of the [Materials Project](https://materialsproject.org/) . `jobflow` was especially designed to simplify the execution of dynamic workflows -- when the actual number of jobs is dynamically determined upon runtime instead of being statically fixed before running the workflow(s). `jobflow`'s overall flexibility allows for building workflows that go beyond the usage in materials science. `jobflow` serves as the basis of `atomate2`, which implements data generation workflows in the context of materials science and will be used for data generation in the Materials Project in the future.", "metadata": { - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } } }, { "cell_type": "markdown", - "source": [ - "## Define workflow with jobflow\n", - "\n", - "We start by importing the job decorator and Flow class from `jobflow` and the respective PWD tools." - ], + "source": "## Define workflow with jobflow\n\nWe start by importing the job decorator and Flow class from `jobflow` and the respective PWD tools.", "metadata": {} }, { "cell_type": "code", - "source": [ - "import numpy as np" - ], + "source": "import numpy as np", "metadata": { "trusted": true }, @@ -59,26 +52,16 @@ }, { "cell_type": "code", - "source": [ - "from jobflow import job, Flow" - ], + "source": "from jobflow import job, Flow", "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 2 }, { "cell_type": "code", - "source": [ - "from python_workflow_definition.jobflow import write_workflow_json" - ], + "source": "from python_workflow_definition.jobflow import write_workflow_json", "metadata": { "trusted": true }, @@ -87,24 +70,17 @@ }, { "cell_type": "markdown", - "source": [ - "## Quantum Espresso Workflow\n", - "We will use the knowledge from the previous arithmetic workflow example to create the Quantum Espresso-related tasks for calculating an \"Energy vs. Volume\" curve. It’s important to note that this is only a basic implementation, and further extensions towards data validation or for a simplified user experience can be added. For example, one can typically configure run commands for quantum-chemical programs via configuration files in atomate2." - ], + "source": "## Quantum Espresso Workflow\nWe will use the knowledge from the previous arithmetic workflow example to create the Quantum Espresso-related tasks for calculating an \"Energy vs. Volume\" curve. It’s important to note that this is only a basic implementation, and further extensions towards data validation or for a simplified user experience can be added. For example, one can typically configure run commands for quantum-chemical programs via configuration files in atomate2.", "metadata": { - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } } }, { "cell_type": "code", - "source": [ - "from workflow import (\n", - " calculate_qe as _calculate_qe, \n", - " generate_structures as _generate_structures, \n", - " get_bulk_structure as _get_bulk_structure, \n", - " plot_energy_volume_curve as _plot_energy_volume_curve,\n", - ")" - ], + "source": "from workflow import (\n calculate_qe as _calculate_qe, \n generate_structures as _generate_structures, \n get_bulk_structure as _get_bulk_structure, \n plot_energy_volume_curve as _plot_energy_volume_curve,\n)", "metadata": { "trusted": true }, @@ -113,9 +89,7 @@ }, { "cell_type": "code", - "source": [ - "workflow_json_filename = \"jobflow_qe.json\"" - ], + "source": "workflow_json_filename = \"jobflow_qe.json\"", "metadata": { "trusted": true }, @@ -124,12 +98,7 @@ }, { "cell_type": "code", - "source": [ - "calculate_qe = job(_calculate_qe)\n", - "generate_structures = job(_generate_structures)\n", - "plot_energy_volume_curve = job(_plot_energy_volume_curve)\n", - "get_bulk_structure = job(_get_bulk_structure)" - ], + "source": "calculate_qe = job(_calculate_qe)\ngenerate_structures = job(_generate_structures)\nplot_energy_volume_curve = job(_plot_energy_volume_curve)\nget_bulk_structure = job(_get_bulk_structure)", "metadata": { "trusted": true }, @@ -138,18 +107,17 @@ }, { "cell_type": "markdown", - "source": [ - "We need to specify the typical QE input like pseudopotential(s) and structure model." - ], + "source": "We need to specify the typical QE input like pseudopotential(s) and structure model.", "metadata": { - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } } }, { "cell_type": "code", - "source": [ - "pseudopotentials = {\"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"}" - ], + "source": "pseudopotentials = {\"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"}", "metadata": { "trusted": true }, @@ -158,13 +126,7 @@ }, { "cell_type": "code", - "source": [ - "structure = get_bulk_structure(\n", - " element=\"Al\",\n", - " a=4.04,\n", - " cubic=True,\n", - ")" - ], + "source": "structure = get_bulk_structure(\n element=\"Al\",\n a=4.04,\n cubic=True,\n)", "metadata": { "trusted": true }, @@ -173,18 +135,7 @@ }, { "cell_type": "code", - "source": [ - "calc_mini = calculate_qe(\n", - " working_directory=\"mini\",\n", - " input_dict={\n", - " \"structure\": structure.output,\n", - " \"pseudopotentials\": pseudopotentials,\n", - " \"kpts\": (3, 3, 3),\n", - " \"calculation\": \"vc-relax\",\n", - " \"smearing\": 0.02,\n", - " },\n", - ")" - ], + "source": "calc_mini = calculate_qe(\n working_directory=\"mini\",\n input_dict={\n \"structure\": structure.output,\n \"pseudopotentials\": pseudopotentials,\n \"kpts\": (3, 3, 3),\n \"calculation\": \"vc-relax\",\n \"smearing\": 0.02,\n },\n)", "metadata": { "trusted": true }, @@ -193,22 +144,17 @@ }, { "cell_type": "markdown", - "source": [ - "Next, for the \"Energy vs. Volume\" curve, we meed to specify the number of strained structures and save them into a list object. For each of the strained structures, we will carry out a QE calculation." - ], + "source": "Next, for the \"Energy vs. Volume\" curve, we meed to specify the number of strained structures and save them into a list object. For each of the strained structures, we will carry out a QE calculation.", "metadata": { - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } } }, { "cell_type": "code", - "source": [ - "number_of_strains = 5\n", - "structure_lst = generate_structures(\n", - " structure=calc_mini.output.structure,\n", - " strain_lst=np.linspace(0.9, 1.1, number_of_strains),\n", - ")" - ], + "source": "number_of_strains = 5\nstructure_lst = generate_structures(\n structure=calc_mini.output.structure,\n strain_lst=np.linspace(0.9, 1.1, number_of_strains),\n)", "metadata": { "trusted": true }, @@ -217,21 +163,7 @@ }, { "cell_type": "code", - "source": [ - "job_strain_lst = []\n", - "for i in range(number_of_strains):\n", - " calc_strain = calculate_qe(\n", - " working_directory=\"strain_\" + str(i),\n", - " input_dict={\n", - " \"structure\": getattr(structure_lst.output, f\"s_{i}\"),\n", - " \"pseudopotentials\": pseudopotentials,\n", - " \"kpts\": (3, 3, 3),\n", - " \"calculation\": \"scf\",\n", - " \"smearing\": 0.02,\n", - " },\n", - " )\n", - " job_strain_lst.append(calc_strain)" - ], + "source": "job_strain_lst = []\nfor i in range(number_of_strains):\n calc_strain = calculate_qe(\n working_directory=\"strain_\" + str(i),\n input_dict={\n \"structure\": getattr(structure_lst.output, f\"s_{i}\"),\n \"pseudopotentials\": pseudopotentials,\n \"kpts\": (3, 3, 3),\n \"calculation\": \"scf\",\n \"smearing\": 0.02,\n },\n )\n job_strain_lst.append(calc_strain)", "metadata": { "trusted": true }, @@ -240,21 +172,17 @@ }, { "cell_type": "markdown", - "source": [ - "Finally, we specify a plotter for the \"Energy vs. Volume\" curve and can export the workflow." - ], + "source": "Finally, we specify a plotter for the \"Energy vs. Volume\" curve and can export the workflow.", "metadata": { - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } } }, { "cell_type": "code", - "source": [ - "plot = plot_energy_volume_curve(\n", - " volume_lst=[job.output.volume for job in job_strain_lst],\n", - " energy_lst=[job.output.energy for job in job_strain_lst],\n", - ")" - ], + "source": "plot = plot_energy_volume_curve(\n volume_lst=[job.output.volume for job in job_strain_lst],\n energy_lst=[job.output.energy for job in job_strain_lst],\n)", "metadata": { "trusted": true }, @@ -263,9 +191,7 @@ }, { "cell_type": "code", - "source": [ - "flow = Flow([structure, calc_mini, structure_lst] + job_strain_lst + [plot])" - ], + "source": "flow = Flow([structure, calc_mini, structure_lst] + job_strain_lst + [plot])", "metadata": { "trusted": true }, @@ -274,9 +200,7 @@ }, { "cell_type": "code", - "source": [ - "write_workflow_json(flow=flow, file_name=workflow_json_filename)" - ], + "source": "write_workflow_json(flow=flow, file_name=workflow_json_filename)", "metadata": { "trusted": true }, @@ -285,9 +209,7 @@ }, { "cell_type": "code", - "source": [ - "!cat {workflow_json_filename}" - ], + "source": "!cat {workflow_json_filename}", "metadata": { "trusted": true }, @@ -295,27 +217,19 @@ { "name": "stdout", "output_type": "stream", - "text": "{\"nodes\": [{\"id\": 0, \"function\": \"workflow.get_bulk_structure\"}, {\"id\": 1, \"function\": \"workflow.calculate_qe\"}, {\"id\": 2, \"function\": \"workflow.generate_structures\"}, {\"id\": 3, \"function\": \"workflow.calculate_qe\"}, {\"id\": 4, \"function\": \"workflow.calculate_qe\"}, {\"id\": 5, \"function\": \"workflow.calculate_qe\"}, {\"id\": 6, \"function\": \"workflow.calculate_qe\"}, {\"id\": 7, \"function\": \"workflow.calculate_qe\"}, {\"id\": 8, \"function\": \"workflow.plot_energy_volume_curve\"}, {\"id\": 9, \"value\": \"Al\"}, {\"id\": 10, \"value\": 4.04}, {\"id\": 11, \"value\": true}, {\"id\": 12, \"value\": \"mini\"}, {\"id\": 13, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 14, \"value\": {\"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"}}, {\"id\": 15, \"value\": [3, 3, 3]}, {\"id\": 16, \"value\": \"vc-relax\"}, {\"id\": 17, \"value\": 0.02}, {\"id\": 18, \"value\": [0.9, 0.9500000000000001, 1.0, 1.05, 1.1]}, {\"id\": 19, \"value\": \"strain_0\"}, {\"id\": 20, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 21, \"value\": \"scf\"}, {\"id\": 22, \"value\": \"strain_1\"}, {\"id\": 23, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 24, \"value\": \"strain_2\"}, {\"id\": 25, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 26, \"value\": \"strain_3\"}, {\"id\": 27, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 28, \"value\": \"strain_4\"}, {\"id\": 29, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 30, \"function\": \"python_workflow_definition.shared.get_list\"}, {\"id\": 31, \"function\": \"python_workflow_definition.shared.get_list\"}], \"edges\": [{\"target\": 0, \"targetPort\": \"element\", \"source\": 9, \"sourcePort\": null}, {\"target\": 0, \"targetPort\": \"a\", \"source\": 10, \"sourcePort\": null}, {\"target\": 0, \"targetPort\": \"cubic\", \"source\": 11, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"working_directory\", \"source\": 12, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"structure\", \"source\": 0, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"calculation\", \"source\": 16, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"input_dict\", \"source\": 13, \"sourcePort\": null}, {\"target\": 2, \"targetPort\": \"structure\", \"source\": 1, \"sourcePort\": \"structure\"}, {\"target\": 2, \"targetPort\": \"strain_lst\", \"source\": 18, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"working_directory\", \"source\": 19, \"sourcePort\": null}, {\"target\": 20, \"targetPort\": \"structure\", \"source\": 2, \"sourcePort\": \"s_0\"}, {\"target\": 20, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 20, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 20, \"targetPort\": \"calculation\", \"source\": 21, \"sourcePort\": null}, {\"target\": 20, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"input_dict\", \"source\": 20, \"sourcePort\": null}, {\"target\": 4, \"targetPort\": \"working_directory\", \"source\": 22, \"sourcePort\": null}, {\"target\": 23, \"targetPort\": \"structure\", \"source\": 2, \"sourcePort\": \"s_1\"}, {\"target\": 23, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 23, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 23, \"targetPort\": \"calculation\", \"source\": 21, \"sourcePort\": null}, {\"target\": 23, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 4, \"targetPort\": \"input_dict\", \"source\": 23, \"sourcePort\": null}, {\"target\": 5, \"targetPort\": \"working_directory\", \"source\": 24, \"sourcePort\": null}, {\"target\": 25, \"targetPort\": \"structure\", \"source\": 2, \"sourcePort\": \"s_2\"}, {\"target\": 25, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 25, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 25, \"targetPort\": \"calculation\", \"source\": 21, \"sourcePort\": null}, {\"target\": 25, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 5, \"targetPort\": \"input_dict\", \"source\": 25, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"working_directory\", \"source\": 26, \"sourcePort\": null}, {\"target\": 27, \"targetPort\": \"structure\", \"source\": 2, \"sourcePort\": \"s_3\"}, {\"target\": 27, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 27, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 27, \"targetPort\": \"calculation\", \"source\": 21, \"sourcePort\": null}, {\"target\": 27, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"input_dict\", \"source\": 27, \"sourcePort\": null}, {\"target\": 7, \"targetPort\": \"working_directory\", \"source\": 28, \"sourcePort\": null}, {\"target\": 29, \"targetPort\": \"structure\", \"source\": 2, \"sourcePort\": \"s_4\"}, {\"target\": 29, \"targetPort\": \"pseudopotentials\", \"source\": 14, \"sourcePort\": null}, {\"target\": 29, \"targetPort\": \"kpts\", \"source\": 15, \"sourcePort\": null}, {\"target\": 29, \"targetPort\": \"calculation\", \"source\": 21, \"sourcePort\": null}, {\"target\": 29, \"targetPort\": \"smearing\", \"source\": 17, \"sourcePort\": null}, {\"target\": 7, \"targetPort\": \"input_dict\", \"source\": 29, \"sourcePort\": null}, {\"target\": 30, \"targetPort\": \"0\", \"source\": 3, \"sourcePort\": \"volume\"}, {\"target\": 30, \"targetPort\": \"1\", \"source\": 4, \"sourcePort\": \"volume\"}, {\"target\": 30, \"targetPort\": \"2\", \"source\": 5, \"sourcePort\": \"volume\"}, {\"target\": 30, \"targetPort\": \"3\", \"source\": 6, \"sourcePort\": \"volume\"}, {\"target\": 30, \"targetPort\": \"4\", \"source\": 7, \"sourcePort\": \"volume\"}, {\"target\": 8, \"targetPort\": \"volume_lst\", \"source\": 30, \"sourcePort\": null}, {\"target\": 31, \"targetPort\": \"0\", \"source\": 3, \"sourcePort\": \"energy\"}, {\"target\": 31, \"targetPort\": \"1\", \"source\": 4, \"sourcePort\": \"energy\"}, {\"target\": 31, \"targetPort\": \"2\", \"source\": 5, \"sourcePort\": \"energy\"}, {\"target\": 31, \"targetPort\": \"3\", \"source\": 6, \"sourcePort\": \"energy\"}, {\"target\": 31, \"targetPort\": \"4\", \"source\": 7, \"sourcePort\": \"energy\"}, {\"target\": 8, \"targetPort\": \"energy_lst\", \"source\": 31, \"sourcePort\": null}]}" + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.get_bulk_structure\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.generate_structures\"\n },\n {\n \"id\": 3,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 4,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 5,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 6,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 7,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 8,\n \"type\": \"function\",\n \"value\": \"workflow.plot_energy_volume_curve\"\n },\n {\n \"id\": 9,\n \"type\": \"input\",\n \"name\": \"element\",\n \"value\": \"Al\"\n },\n {\n \"id\": 10,\n \"type\": \"input\",\n \"name\": \"a\",\n \"value\": 4.04\n },\n {\n \"id\": 11,\n \"type\": \"input\",\n \"name\": \"cubic\",\n \"value\": true\n },\n {\n \"id\": 12,\n \"type\": \"input\",\n \"name\": \"working_directory_0\",\n \"value\": \"mini\"\n },\n {\n \"id\": 13,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 14,\n \"type\": \"input\",\n \"name\": \"pseudopotentials\",\n \"value\": {\n \"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"\n }\n },\n {\n \"id\": 15,\n \"type\": \"input\",\n \"name\": \"kpts\",\n \"value\": [\n 3,\n 3,\n 3\n ]\n },\n {\n \"id\": 16,\n \"type\": \"input\",\n \"name\": \"calculation_0\",\n \"value\": \"vc-relax\"\n },\n {\n \"id\": 17,\n \"type\": \"input\",\n \"name\": \"smearing\",\n \"value\": 0.02\n },\n {\n \"id\": 18,\n \"type\": \"input\",\n \"name\": \"strain_lst\",\n \"value\": [\n 0.9,\n 0.9500000000000001,\n 1.0,\n 1.05,\n 1.1\n ]\n },\n {\n \"id\": 19,\n \"type\": \"input\",\n \"name\": \"working_directory_1\",\n \"value\": \"strain_0\"\n },\n {\n \"id\": 20,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 21,\n \"type\": \"input\",\n \"name\": \"calculation_1\",\n \"value\": \"scf\"\n },\n {\n \"id\": 22,\n \"type\": \"input\",\n \"name\": \"working_directory_2\",\n \"value\": \"strain_1\"\n },\n {\n \"id\": 23,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 24,\n \"type\": \"input\",\n \"name\": \"working_directory_3\",\n \"value\": \"strain_2\"\n },\n {\n \"id\": 25,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 26,\n \"type\": \"input\",\n \"name\": \"working_directory_4\",\n \"value\": \"strain_3\"\n },\n {\n \"id\": 27,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 28,\n \"type\": \"input\",\n \"name\": \"working_directory_5\",\n \"value\": \"strain_4\"\n },\n {\n \"id\": 29,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 30,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 31,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 32,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 0,\n \"targetPort\": \"element\",\n \"source\": 9,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"a\",\n \"source\": 10,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"cubic\",\n \"source\": 11,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"working_directory\",\n \"source\": 12,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"structure\",\n \"source\": 0,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"calculation\",\n \"source\": 16,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"input_dict\",\n \"source\": 13,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"structure\",\n \"source\": 1,\n \"sourcePort\": \"structure\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"strain_lst\",\n \"source\": 18,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"working_directory\",\n \"source\": 19,\n \"sourcePort\": null\n },\n {\n \"target\": 20,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"s_0\"\n },\n {\n \"target\": 20,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 20,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 20,\n \"targetPort\": \"calculation\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 20,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"input_dict\",\n \"source\": 20,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"working_directory\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 23,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"s_1\"\n },\n {\n \"target\": 23,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 23,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 23,\n \"targetPort\": \"calculation\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 23,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"input_dict\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"working_directory\",\n \"source\": 24,\n \"sourcePort\": null\n },\n {\n \"target\": 25,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"s_2\"\n },\n {\n \"target\": 25,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 25,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 25,\n \"targetPort\": \"calculation\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 25,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"input_dict\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"working_directory\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 27,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"s_3\"\n },\n {\n \"target\": 27,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 27,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 27,\n \"targetPort\": \"calculation\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 27,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"input_dict\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"working_directory\",\n \"source\": 28,\n \"sourcePort\": null\n },\n {\n \"target\": 29,\n \"targetPort\": \"structure\",\n \"source\": 2,\n \"sourcePort\": \"s_4\"\n },\n {\n \"target\": 29,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 14,\n \"sourcePort\": null\n },\n {\n \"target\": 29,\n \"targetPort\": \"kpts\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 29,\n \"targetPort\": \"calculation\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 29,\n \"targetPort\": \"smearing\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"input_dict\",\n \"source\": 29,\n \"sourcePort\": null\n },\n {\n \"target\": 30,\n \"targetPort\": \"0\",\n \"source\": 3,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 30,\n \"targetPort\": \"1\",\n \"source\": 4,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 30,\n \"targetPort\": \"2\",\n \"source\": 5,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 30,\n \"targetPort\": \"3\",\n \"source\": 6,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 30,\n \"targetPort\": \"4\",\n \"source\": 7,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 8,\n \"targetPort\": \"volume_lst\",\n \"source\": 30,\n \"sourcePort\": null\n },\n {\n \"target\": 31,\n \"targetPort\": \"0\",\n \"source\": 3,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 31,\n \"targetPort\": \"1\",\n \"source\": 4,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 31,\n \"targetPort\": \"2\",\n \"source\": 5,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 31,\n \"targetPort\": \"3\",\n \"source\": 6,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 31,\n \"targetPort\": \"4\",\n \"source\": 7,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 8,\n \"targetPort\": \"energy_lst\",\n \"source\": 31,\n \"sourcePort\": null\n },\n {\n \"target\": 32,\n \"targetPort\": null,\n \"source\": 8,\n \"sourcePort\": null\n }\n ]\n}" } ], "execution_count": 15 }, { "cell_type": "markdown", - "source": [ - "## Load Workflow with aiida\n", - "\n", - "Now, we can import the workflow, run it with `aiida` and plot the \"Energy vs. Volume\" curve." - ], + "source": "## Load Workflow with aiida\n\nNow, we can import the workflow, run it with `aiida` and plot the \"Energy vs. Volume\" curve.", "metadata": {} }, { "cell_type": "code", - "source": [ - "from aiida import orm, load_profile\n", - "\n", - "load_profile()" - ], + "source": "from aiida import orm, load_profile\n\nload_profile()", "metadata": { "trusted": true }, @@ -324,7 +238,7 @@ "execution_count": 16, "output_type": "execute_result", "data": { - "text/plain": "Profile" + "text/plain": "Profile" }, "metadata": {} } @@ -333,9 +247,7 @@ }, { "cell_type": "code", - "source": [ - "from python_workflow_definition.aiida import load_workflow_json" - ], + "source": "from python_workflow_definition.aiida import load_workflow_json", "metadata": { "trusted": true }, @@ -344,9 +256,7 @@ }, { "cell_type": "code", - "source": [ - "wg = load_workflow_json(workflow_json_filename)" - ], + "source": "wg = load_workflow_json(workflow_json_filename)", "metadata": { "trusted": true }, @@ -355,9 +265,7 @@ }, { "cell_type": "code", - "source": [ - "wg.nodes.get_bulk_structure1.inputs.a.value = orm.Float(4.05)" - ], + "source": "wg.nodes.get_bulk_structure1.inputs.a.value = orm.Float(4.05)", "metadata": { "scrolled": true, "trusted": true @@ -367,9 +275,7 @@ }, { "cell_type": "code", - "source": [ - "wg" - ], + "source": "wg", "metadata": { "trusted": true }, @@ -382,7 +288,7 @@ "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 1, - "model_id": "adc64841c31f40c68e2f9cdd4652e3ab" + "model_id": "39e130485f144a8abbf5c63c4812a3e3" } }, "metadata": {} @@ -392,9 +298,7 @@ }, { "cell_type": "code", - "source": [ - "wg.run()" - ], + "source": "wg.run()", "metadata": { "trusted": true }, @@ -402,7 +306,7 @@ { "name": "stderr", "output_type": "stream", - "text": "04/24/2025 02:18:49 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure1\n04/24/2025 02:18:49 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_bulk_structure1, type: PyFunction, finished.\n04/24/2025 02:18:49 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10\n04/24/2025 02:18:50 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n04/24/2025 02:18:50 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe2\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01816] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:19:40 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n04/24/2025 02:19:40 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe2, type: PyFunction, finished.\n04/24/2025 02:19:40 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures3\n04/24/2025 02:19:41 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: generate_structures3, type: PyFunction, finished.\n04/24/2025 02:19:42 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict11,get_dict12,get_dict13,get_dict14,get_dict15\n04/24/2025 02:19:42 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict11, type: PyFunction, finished.\n04/24/2025 02:19:42 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe4,get_dict12,get_dict13,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01832] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:19:53 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/24/2025 02:19:53 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe4, type: PyFunction, finished.\n04/24/2025 02:19:53 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict13,get_dict14,get_dict15\n04/24/2025 02:19:54 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n04/24/2025 02:19:54 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe5,get_dict13,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01842] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:20:05 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/24/2025 02:20:06 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe5, type: PyFunction, finished.\n04/24/2025 02:20:06 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict13,get_dict14,get_dict15\n04/24/2025 02:20:07 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict13, type: PyFunction, finished.\n04/24/2025 02:20:07 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01852] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:20:19 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/24/2025 02:20:19 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n04/24/2025 02:20:19 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict15\n04/24/2025 02:20:20 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n04/24/2025 02:20:20 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe7,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01862] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:20:34 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/24/2025 02:20:34 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe7, type: PyFunction, finished.\n04/24/2025 02:20:35 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict15\n04/24/2025 02:20:35 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_dict15, type: PyFunction, finished.\n04/24/2025 02:20:35 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe8\n[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01876] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/24/2025 02:20:51 PM <1741> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/24/2025 02:20:51 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: calculate_qe8, type: PyFunction, finished.\n04/24/2025 02:20:51 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list16,get_list17\n04/24/2025 02:20:52 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_list16, type: PyFunction, finished.\n04/24/2025 02:20:52 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n04/24/2025 02:20:52 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n04/24/2025 02:20:52 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve9\n04/24/2025 02:20:53 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve9, type: PyFunction, finished.\n04/24/2025 02:20:53 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/24/2025 02:20:54 PM <1741> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [58|WorkGraphEngine|finalize]: Finalize workgraph.\n" + "text": "05/24/2025 05:55:37 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure1\n05/24/2025 05:55:38 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_bulk_structure1, type: PyFunction, finished.\n05/24/2025 05:55:38 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10\n05/24/2025 05:55:38 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n05/24/2025 05:55:38 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe2\n[jupyter-pythonworkflow-fl--x---d7231032:10078] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:56:29 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n05/24/2025 05:56:29 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe2, type: PyFunction, finished.\n05/24/2025 05:56:30 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures3\n05/24/2025 05:56:30 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: generate_structures3, type: PyFunction, finished.\n05/24/2025 05:56:30 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict11,get_dict12,get_dict13,get_dict14,get_dict15\n05/24/2025 05:56:31 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict11, type: PyFunction, finished.\n05/24/2025 05:56:31 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe4,get_dict12,get_dict13,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10097] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:56:42 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 05:56:42 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe4, type: PyFunction, finished.\n05/24/2025 05:56:42 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict13,get_dict14,get_dict15\n05/24/2025 05:56:43 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n05/24/2025 05:56:43 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe5,get_dict13,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10108] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:56:54 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 05:56:55 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe5, type: PyFunction, finished.\n05/24/2025 05:56:55 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict13,get_dict14,get_dict15\n05/24/2025 05:56:55 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict13, type: PyFunction, finished.\n05/24/2025 05:56:55 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10120] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:57:07 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 05:57:08 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n05/24/2025 05:57:08 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict15\n05/24/2025 05:57:08 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n05/24/2025 05:57:08 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe7,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10131] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:57:22 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 05:57:22 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe7, type: PyFunction, finished.\n05/24/2025 05:57:22 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict15\n05/24/2025 05:57:23 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_dict15, type: PyFunction, finished.\n05/24/2025 05:57:23 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe8\n[jupyter-pythonworkflow-fl--x---d7231032:10146] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 05:57:40 AM <10006> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 05:57:40 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: calculate_qe8, type: PyFunction, finished.\n05/24/2025 05:57:40 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list16,get_list17\n05/24/2025 05:57:41 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_list16, type: PyFunction, finished.\n05/24/2025 05:57:41 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n05/24/2025 05:57:41 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n05/24/2025 05:57:41 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve9\n05/24/2025 05:57:41 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve9, type: PyFunction, finished.\n05/24/2025 05:57:42 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 05:57:42 AM <10006> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [155|WorkGraphEngine|finalize]: Finalize workgraph.\n" }, { "output_type": "display_data", @@ -417,18 +321,12 @@ }, { "cell_type": "markdown", - "source": [ - "## Load Workflow with pyiron_base\n", - "\n", - "And we can repeat the same process using `pyiron`." - ], + "source": "## Load Workflow with pyiron_base\n\nAnd we can repeat the same process using `pyiron`.", "metadata": {} }, { "cell_type": "code", - "source": [ - "from python_workflow_definition.pyiron_base import load_workflow_json" - ], + "source": "from python_workflow_definition.pyiron_base import load_workflow_json", "metadata": { "trusted": true }, @@ -437,10 +335,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n", - "delayed_object_lst[-1].draw()" - ], + "source": "delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, @@ -449,7 +344,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\ncreate_function_job_4d3ed4e7c563ae330e22f930d0400ed1\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a2ab0>\n\n\n\nvolume_lst_8f481a1c2032fb2664763537b0da7fe5\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a2840>\n\n\n\nvolume_lst_8f481a1c2032fb2664763537b0da7fe5->create_function_job_4d3ed4e7c563ae330e22f930d0400ed1\n\n\n\n\n\n0_ef19beb41624e4e0008e53d9d5b9d119\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a22a0>\n\n\n\n0_ef19beb41624e4e0008e53d9d5b9d119->volume_lst_8f481a1c2032fb2664763537b0da7fe5\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_ef19beb41624e4e0008e53d9d5b9d119\n\n\n\n\n\n0_d1d8d77a711438827afcb0ca2a429507\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1c70>\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_d1d8d77a711438827afcb0ca2a429507\n\n\n\n\n\nenergy_lst_291d449ffe6031374863f6c90014edea\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a2210>\n\n\n\n0_d1d8d77a711438827afcb0ca2a429507->energy_lst_291d449ffe6031374863f6c90014edea\n\n\n\n\n\ninput_dict_adcb8214845c6f8ca7a9f217ca605d92\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1130>\n\n\n\ninput_dict_adcb8214845c6f8ca7a9f217ca605d92->0_ef19beb41624e4e0008e53d9d5b9d119\n\n\n\n\n\ninput_dict_adcb8214845c6f8ca7a9f217ca605d92->0_d1d8d77a711438827afcb0ca2a429507\n\n\n\n\n\nstructure_6d41e0eac8dfd18f09880d77216e7f15\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0e60>\n\n\n\nstructure_6d41e0eac8dfd18f09880d77216e7f15->input_dict_adcb8214845c6f8ca7a9f217ca605d92\n\n\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb83973ef0>\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5->structure_6d41e0eac8dfd18f09880d77216e7f15\n\n\n\n\n\nstructure_6cccbc8c9e2e8a9c676ebd7f81495653\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0b30>\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5->structure_6cccbc8c9e2e8a9c676ebd7f81495653\n\n\n\n\n\nstructure_b319381aa5a2e4aac9814b7285e411f2\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0800>\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5->structure_b319381aa5a2e4aac9814b7285e411f2\n\n\n\n\n\nstructure_707d1bdbbecf3410f0a6bbde3d033846\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a04d0>\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5->structure_707d1bdbbecf3410f0a6bbde3d033846\n\n\n\n\n\nstructure_f09b1d6b22659890eabfbd87ea7a04c9\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb83973da0>\n\n\n\nstructure_f8bc49b8d2c99821a1af955c22172dc5->structure_f09b1d6b22659890eabfbd87ea7a04c9\n\n\n\n\n\ninput_dict_52e847aed32e0c3b8d5cce4046119fea\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0dd0>\n\n\n\nstructure_6cccbc8c9e2e8a9c676ebd7f81495653->input_dict_52e847aed32e0c3b8d5cce4046119fea\n\n\n\n\n\ninput_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0aa0>\n\n\n\nstructure_b319381aa5a2e4aac9814b7285e411f2->input_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\n\n\n\n\ninput_dict_a8652fe185a1b8add35aa55273a41532\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0770>\n\n\n\nstructure_707d1bdbbecf3410f0a6bbde3d033846->input_dict_a8652fe185a1b8add35aa55273a41532\n\n\n\n\n\ninput_dict_e6ce1da5514cd71e266fc2718ca86f14\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a0440>\n\n\n\nstructure_f09b1d6b22659890eabfbd87ea7a04c9->input_dict_e6ce1da5514cd71e266fc2718ca86f14\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_f8bc49b8d2c99821a1af955c22172dc5\n\n\n\n\n\ninput_dict_6788a3e86aac081f9530a587e4e014f1\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x75fb83973620>\n\n\n\ninput_dict_6788a3e86aac081f9530a587e4e014f1->structure_f8bc49b8d2c99821a1af955c22172dc5\n\n\n\n\n\nstructure_e9df848813fc62a9f6779fd8d4b62535\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x75fb83973830>\n\n\n\nstructure_e9df848813fc62a9f6779fd8d4b62535->input_dict_6788a3e86aac081f9530a587e4e014f1\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_e9df848813fc62a9f6779fd8d4b62535\n\n\n\n\n\na_457b6d376c6fce696df148a385afa46d\n\na=4.04\n\n\n\na_457b6d376c6fce696df148a385afa46d->structure_e9df848813fc62a9f6779fd8d4b62535\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_e9df848813fc62a9f6779fd8d4b62535\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_adcb8214845c6f8ca7a9f217ca605d92\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_6788a3e86aac081f9530a587e4e014f1\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_52e847aed32e0c3b8d5cce4046119fea\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_a8652fe185a1b8add35aa55273a41532\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_e6ce1da5514cd71e266fc2718ca86f14\n\n\n\n\n\n1_51d5b1ef225b81dcb707362e767ddf31\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a2270>\n\n\n\ninput_dict_52e847aed32e0c3b8d5cce4046119fea->1_51d5b1ef225b81dcb707362e767ddf31\n\n\n\n\n\n1_e84622c341e50289fd3d7396cf64aaa9\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1c40>\n\n\n\ninput_dict_52e847aed32e0c3b8d5cce4046119fea->1_e84622c341e50289fd3d7396cf64aaa9\n\n\n\n\n\n2_7a05249df5ced08ddddf5c3d6bf864a3\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a2090>\n\n\n\ninput_dict_484844f6c9f4804aeb0ebb63b8fa3096->2_7a05249df5ced08ddddf5c3d6bf864a3\n\n\n\n\n\n2_f81d5b2784ff607e4830e3fcae0a7566\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1850>\n\n\n\ninput_dict_484844f6c9f4804aeb0ebb63b8fa3096->2_f81d5b2784ff607e4830e3fcae0a7566\n\n\n\n\n\n3_eeed557abcafc052c1b7626ab00a4b2b\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a23f0>\n\n\n\ninput_dict_a8652fe185a1b8add35aa55273a41532->3_eeed557abcafc052c1b7626ab00a4b2b\n\n\n\n\n\n3_7f66b5d1a8afda658d25152ca5ce852c\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1dc0>\n\n\n\ninput_dict_a8652fe185a1b8add35aa55273a41532->3_7f66b5d1a8afda658d25152ca5ce852c\n\n\n\n\n\n4_12b2d8e6d7e2e61d2a5708f6ba633ae1\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a24b0>\n\n\n\ninput_dict_e6ce1da5514cd71e266fc2718ca86f14->4_12b2d8e6d7e2e61d2a5708f6ba633ae1\n\n\n\n\n\n4_2dc46d83cd73aa36387c694fededf8d1\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x75fb837a1e80>\n\n\n\ninput_dict_e6ce1da5514cd71e266fc2718ca86f14->4_2dc46d83cd73aa36387c694fededf8d1\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_adcb8214845c6f8ca7a9f217ca605d92\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_6788a3e86aac081f9530a587e4e014f1\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_52e847aed32e0c3b8d5cce4046119fea\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_a8652fe185a1b8add35aa55273a41532\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_e6ce1da5514cd71e266fc2718ca86f14\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_6788a3e86aac081f9530a587e4e014f1\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_adcb8214845c6f8ca7a9f217ca605d92\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_6788a3e86aac081f9530a587e4e014f1\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_52e847aed32e0c3b8d5cce4046119fea\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_a8652fe185a1b8add35aa55273a41532\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_e6ce1da5514cd71e266fc2718ca86f14\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86\n\nstrain_lst=[0.9, 0.9500000000000001, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_6d41e0eac8dfd18f09880d77216e7f15\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_6cccbc8c9e2e8a9c676ebd7f81495653\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_b319381aa5a2e4aac9814b7285e411f2\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_707d1bdbbecf3410f0a6bbde3d033846\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_f09b1d6b22659890eabfbd87ea7a04c9\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_adcb8214845c6f8ca7a9f217ca605d92\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_52e847aed32e0c3b8d5cce4046119fea\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_484844f6c9f4804aeb0ebb63b8fa3096\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_a8652fe185a1b8add35aa55273a41532\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_e6ce1da5514cd71e266fc2718ca86f14\n\n\n\n\n\n1_51d5b1ef225b81dcb707362e767ddf31->volume_lst_8f481a1c2032fb2664763537b0da7fe5\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_51d5b1ef225b81dcb707362e767ddf31\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_e84622c341e50289fd3d7396cf64aaa9\n\n\n\n\n\n1_e84622c341e50289fd3d7396cf64aaa9->energy_lst_291d449ffe6031374863f6c90014edea\n\n\n\n\n\n2_7a05249df5ced08ddddf5c3d6bf864a3->volume_lst_8f481a1c2032fb2664763537b0da7fe5\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_7a05249df5ced08ddddf5c3d6bf864a3\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_f81d5b2784ff607e4830e3fcae0a7566\n\n\n\n\n\n2_f81d5b2784ff607e4830e3fcae0a7566->energy_lst_291d449ffe6031374863f6c90014edea\n\n\n\n\n\n3_eeed557abcafc052c1b7626ab00a4b2b->volume_lst_8f481a1c2032fb2664763537b0da7fe5\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_eeed557abcafc052c1b7626ab00a4b2b\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_7f66b5d1a8afda658d25152ca5ce852c\n\n\n\n\n\n3_7f66b5d1a8afda658d25152ca5ce852c->energy_lst_291d449ffe6031374863f6c90014edea\n\n\n\n\n\n4_12b2d8e6d7e2e61d2a5708f6ba633ae1->volume_lst_8f481a1c2032fb2664763537b0da7fe5\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_12b2d8e6d7e2e61d2a5708f6ba633ae1\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_2dc46d83cd73aa36387c694fededf8d1\n\n\n\n\n\n4_2dc46d83cd73aa36387c694fededf8d1->energy_lst_291d449ffe6031374863f6c90014edea\n\n\n\n\n\nenergy_lst_291d449ffe6031374863f6c90014edea->create_function_job_4d3ed4e7c563ae330e22f930d0400ed1\n\n\n\n\n" + "image/svg+xml": "\n\n\n\n\ncreate_function_job_c1bd4fa8a953503eb91dd3a4c0e050c1\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faaa5a0>\n\n\n\nvolume_lst_3bbc92d0a53d92db965d7d7300f35662\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faaa120>\n\n\n\nvolume_lst_3bbc92d0a53d92db965d7d7300f35662->create_function_job_c1bd4fa8a953503eb91dd3a4c0e050c1\n\n\n\n\n\n0_1486065434a8893d86e82aa18a53c13f\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9190>\n\n\n\n0_1486065434a8893d86e82aa18a53c13f->volume_lst_3bbc92d0a53d92db965d7d7300f35662\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_1486065434a8893d86e82aa18a53c13f\n\n\n\n\n\n0_10cddf24f3df2b8e55717b9765166f6d\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faaa390>\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_10cddf24f3df2b8e55717b9765166f6d\n\n\n\n\n\nenergy_lst_0a36f26513e729da8bf6203d51de85ce\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa91f0>\n\n\n\n0_10cddf24f3df2b8e55717b9765166f6d->energy_lst_0a36f26513e729da8bf6203d51de85ce\n\n\n\n\n\ninput_dict_de0231a2cb57ae7c5f270591e461e498\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9700>\n\n\n\ninput_dict_de0231a2cb57ae7c5f270591e461e498->0_1486065434a8893d86e82aa18a53c13f\n\n\n\n\n\ninput_dict_de0231a2cb57ae7c5f270591e461e498->0_10cddf24f3df2b8e55717b9765166f6d\n\n\n\n\n\nstructure_ebabdb4e3893711b0b0b9bde48219a29\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9430>\n\n\n\nstructure_ebabdb4e3893711b0b0b9bde48219a29->input_dict_de0231a2cb57ae7c5f270591e461e498\n\n\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa84a0>\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c->structure_ebabdb4e3893711b0b0b9bde48219a29\n\n\n\n\n\nstructure_42401d269bf34371c3019bdc4bfb75a2\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9100>\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c->structure_42401d269bf34371c3019bdc4bfb75a2\n\n\n\n\n\nstructure_c78a04df8e59a6ea69048b21d98d8f35\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8dd0>\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c->structure_c78a04df8e59a6ea69048b21d98d8f35\n\n\n\n\n\nstructure_035363b78ccad8fa3d1ed5663631f443\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8b00>\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c->structure_035363b78ccad8fa3d1ed5663631f443\n\n\n\n\n\nstructure_082651b60d0775f1e4fd226180d32ccd\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa87d0>\n\n\n\nstructure_fa711d84fccf4b52119bc24d6a7d148c->structure_082651b60d0775f1e4fd226180d32ccd\n\n\n\n\n\ninput_dict_244ae7db7309f48a16fb16f358edb739\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa93a0>\n\n\n\nstructure_42401d269bf34371c3019bdc4bfb75a2->input_dict_244ae7db7309f48a16fb16f358edb739\n\n\n\n\n\ninput_dict_811eb58a852081af57d9d8db9199be2e\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9070>\n\n\n\nstructure_c78a04df8e59a6ea69048b21d98d8f35->input_dict_811eb58a852081af57d9d8db9199be2e\n\n\n\n\n\ninput_dict_524ee86f5c443ec91b3b7be26ca077a8\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8d40>\n\n\n\nstructure_035363b78ccad8fa3d1ed5663631f443->input_dict_524ee86f5c443ec91b3b7be26ca077a8\n\n\n\n\n\ninput_dict_d68a1483bcccf569bef4e76ffedd1551\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8a70>\n\n\n\nstructure_082651b60d0775f1e4fd226180d32ccd->input_dict_d68a1483bcccf569bef4e76ffedd1551\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_fa711d84fccf4b52119bc24d6a7d148c\n\n\n\n\n\ninput_dict_f6f21f5be91964bd92bb0715985756ac\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x761e9fa6fbc0>\n\n\n\ninput_dict_f6f21f5be91964bd92bb0715985756ac->structure_fa711d84fccf4b52119bc24d6a7d148c\n\n\n\n\n\nstructure_dfe10bce77b4e5e0e99fc065e50a75a8\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x761e9fa6fc50>\n\n\n\nstructure_dfe10bce77b4e5e0e99fc065e50a75a8->input_dict_f6f21f5be91964bd92bb0715985756ac\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\na_457b6d376c6fce696df148a385afa46d\n\na=4.04\n\n\n\na_457b6d376c6fce696df148a385afa46d->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_dfe10bce77b4e5e0e99fc065e50a75a8\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_de0231a2cb57ae7c5f270591e461e498\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_f6f21f5be91964bd92bb0715985756ac\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_244ae7db7309f48a16fb16f358edb739\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_811eb58a852081af57d9d8db9199be2e\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_524ee86f5c443ec91b3b7be26ca077a8\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_d68a1483bcccf569bef4e76ffedd1551\n\n\n\n\n\n1_8f0b6b80405de7055941d933f333b118\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa91c0>\n\n\n\ninput_dict_244ae7db7309f48a16fb16f358edb739->1_8f0b6b80405de7055941d933f333b118\n\n\n\n\n\n1_85e2b119e56f47d946031fd8b36e0cd8\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faaa360>\n\n\n\ninput_dict_244ae7db7309f48a16fb16f358edb739->1_85e2b119e56f47d946031fd8b36e0cd8\n\n\n\n\n\n2_78df7e08d41d7db70268f99c46ec23dd\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9850>\n\n\n\ninput_dict_811eb58a852081af57d9d8db9199be2e->2_78df7e08d41d7db70268f99c46ec23dd\n\n\n\n\n\n2_54d3f470018f712d94b43362cb5614f2\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faaa1b0>\n\n\n\ninput_dict_811eb58a852081af57d9d8db9199be2e->2_54d3f470018f712d94b43362cb5614f2\n\n\n\n\n\n3_25174fe7df906bcbea5eab0c37f8c0ba\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8bf0>\n\n\n\ninput_dict_524ee86f5c443ec91b3b7be26ca077a8->3_25174fe7df906bcbea5eab0c37f8c0ba\n\n\n\n\n\n3_b70a098fcddf3aca598cafe9252716e4\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9fa0>\n\n\n\ninput_dict_524ee86f5c443ec91b3b7be26ca077a8->3_b70a098fcddf3aca598cafe9252716e4\n\n\n\n\n\n4_5fe4f431a207376dcfe8aa838521623e\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa8800>\n\n\n\ninput_dict_d68a1483bcccf569bef4e76ffedd1551->4_5fe4f431a207376dcfe8aa838521623e\n\n\n\n\n\n4_6f3d87fbd398bfb6ce97e69b03f91033\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x761e9faa9cd0>\n\n\n\ninput_dict_d68a1483bcccf569bef4e76ffedd1551->4_6f3d87fbd398bfb6ce97e69b03f91033\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_de0231a2cb57ae7c5f270591e461e498\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_f6f21f5be91964bd92bb0715985756ac\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_244ae7db7309f48a16fb16f358edb739\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_811eb58a852081af57d9d8db9199be2e\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_524ee86f5c443ec91b3b7be26ca077a8\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_d68a1483bcccf569bef4e76ffedd1551\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_f6f21f5be91964bd92bb0715985756ac\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_de0231a2cb57ae7c5f270591e461e498\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_f6f21f5be91964bd92bb0715985756ac\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_244ae7db7309f48a16fb16f358edb739\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_811eb58a852081af57d9d8db9199be2e\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_524ee86f5c443ec91b3b7be26ca077a8\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_d68a1483bcccf569bef4e76ffedd1551\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86\n\nstrain_lst=[0.9, 0.9500000000000001, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_ebabdb4e3893711b0b0b9bde48219a29\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_42401d269bf34371c3019bdc4bfb75a2\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_c78a04df8e59a6ea69048b21d98d8f35\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_035363b78ccad8fa3d1ed5663631f443\n\n\n\n\n\nstrain_lst_17d5bcbc7579ab5e0f98577d05347b86->structure_082651b60d0775f1e4fd226180d32ccd\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_de0231a2cb57ae7c5f270591e461e498\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_244ae7db7309f48a16fb16f358edb739\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_811eb58a852081af57d9d8db9199be2e\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_524ee86f5c443ec91b3b7be26ca077a8\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_d68a1483bcccf569bef4e76ffedd1551\n\n\n\n\n\n1_8f0b6b80405de7055941d933f333b118->volume_lst_3bbc92d0a53d92db965d7d7300f35662\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_8f0b6b80405de7055941d933f333b118\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_85e2b119e56f47d946031fd8b36e0cd8\n\n\n\n\n\n1_85e2b119e56f47d946031fd8b36e0cd8->energy_lst_0a36f26513e729da8bf6203d51de85ce\n\n\n\n\n\n2_78df7e08d41d7db70268f99c46ec23dd->volume_lst_3bbc92d0a53d92db965d7d7300f35662\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_78df7e08d41d7db70268f99c46ec23dd\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_54d3f470018f712d94b43362cb5614f2\n\n\n\n\n\n2_54d3f470018f712d94b43362cb5614f2->energy_lst_0a36f26513e729da8bf6203d51de85ce\n\n\n\n\n\n3_25174fe7df906bcbea5eab0c37f8c0ba->volume_lst_3bbc92d0a53d92db965d7d7300f35662\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_25174fe7df906bcbea5eab0c37f8c0ba\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_b70a098fcddf3aca598cafe9252716e4\n\n\n\n\n\n3_b70a098fcddf3aca598cafe9252716e4->energy_lst_0a36f26513e729da8bf6203d51de85ce\n\n\n\n\n\n4_5fe4f431a207376dcfe8aa838521623e->volume_lst_3bbc92d0a53d92db965d7d7300f35662\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_5fe4f431a207376dcfe8aa838521623e\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_6f3d87fbd398bfb6ce97e69b03f91033\n\n\n\n\n\n4_6f3d87fbd398bfb6ce97e69b03f91033->energy_lst_0a36f26513e729da8bf6203d51de85ce\n\n\n\n\n\nenergy_lst_0a36f26513e729da8bf6203d51de85ce->create_function_job_c1bd4fa8a953503eb91dd3a4c0e050c1\n\n\n\n\n" }, "metadata": {} } @@ -458,9 +353,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst[0].input['a'] = 4.05" - ], + "source": "delayed_object_lst[0].input['a'] = 4.05", "metadata": { "trusted": true }, @@ -469,9 +362,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst[-1].pull()" - ], + "source": "delayed_object_lst[-1].pull()", "metadata": { "trusted": true }, @@ -484,62 +375,62 @@ { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01906] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10178] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job generate_structures_a2be118b5bff59eaa11d83f99eaced4d was saved and received the ID: 4\nThe job get_dict_e6e21d04c5680e1114b80a92bc2e359c was saved and received the ID: 5\nThe job calculate_qe_51a232f4324d311c7fd4f7f769ddfdfe was saved and received the ID: 6\n" + "text": "The job generate_structures_758c1e24a8384d1f25f5126debddf480 was saved and received the ID: 4\nThe job get_dict_db80165b1c83d6fa1ef1eef8d8b3188b was saved and received the ID: 5\nThe job calculate_qe_c74608e7e5992312ade6c5737ad4d4f1 was saved and received the ID: 6\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01916] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10193] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_437c0ffaf598d0a286c53012d3d36f25 was saved and received the ID: 7\nThe job calculate_qe_8fb25b130b8e8e933d28d21f7c44b4ca was saved and received the ID: 8\n" + "text": "The job get_dict_97c2cc17b8b86f75ac4b6341cd45956c was saved and received the ID: 7\nThe job calculate_qe_3c59fd7824f74b10476745bf9830882f was saved and received the ID: 8\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01926] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10204] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_d1a00c031f330c896c8f5af25db5235b was saved and received the ID: 9\nThe job calculate_qe_042e4d560dcfc093eea3a34f7e523669 was saved and received the ID: 10\n" + "text": "The job get_dict_8c518d80d423ba91c334fe6a5d9543bd was saved and received the ID: 9\nThe job calculate_qe_38624f0e23e56cbc7b388ef79234a0cf was saved and received the ID: 10\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01938] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10215] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_ea36d0f502795b1fc4b32e62fce9820d was saved and received the ID: 11\nThe job calculate_qe_b4bd2031ca3d40580969fda1aecee94a was saved and received the ID: 12\n" + "text": "The job get_dict_85562edba169c3c58d84415c89cc95ec was saved and received the ID: 11\nThe job calculate_qe_78709c5d9efddf18fe3df6c5e14d06ed was saved and received the ID: 12\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01948] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10226] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_d190d6b6e585cababdcd49a344547984 was saved and received the ID: 13\nThe job calculate_qe_b3927880779bfca53ff78c00360e9527 was saved and received the ID: 14\n" + "text": "The job get_dict_c540734353f48fac14af5c29bd88abc9 was saved and received the ID: 13\nThe job calculate_qe_1e912623736f139236a98ac679574bb4 was saved and received the ID: 14\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-kk01elen:01958] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10242] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_list_90f0281f335962d10db1b3572abe82df was saved and received the ID: 15\nThe job get_list_09fa36007fd192f793a1f218b70fe87b was saved and received the ID: 16\nThe job plot_energy_volume_curve_8d8f280c69be12b1969d95cc53f9411b was saved and received the ID: 17\n" + "text": "The job get_list_eacb691fa58e50c0936b26623a5e36f9 was saved and received the ID: 15\nThe job get_list_069bfd570461c3607a17813d3ecb126c was saved and received the ID: 16\nThe job plot_energy_volume_curve_99f8fb836badb998aff830b255f6b0eb was saved and received the ID: 17\n" }, { "output_type": "display_data", @@ -554,7 +445,7 @@ }, { "cell_type": "code", - "source": [], + "source": "", "metadata": { "trusted": true }, diff --git a/example_workflows/quantum_espresso/pyiron_base.ipynb b/example_workflows/quantum_espresso/pyiron_base.ipynb index a1c94e0..ef34b5c 100644 --- a/example_workflows/quantum_espresso/pyiron_base.ipynb +++ b/example_workflows/quantum_espresso/pyiron_base.ipynb @@ -44,10 +44,8 @@ "execution_count": 1 }, { - "metadata": {}, + "id": "ea65c6275f956bdb", "cell_type": "code", - "outputs": [], - "execution_count": null, "source": [ "from workflow import (\n", " calculate_qe as _calculate_qe, \n", @@ -56,15 +54,21 @@ " plot_energy_volume_curve as _plot_energy_volume_curve,\n", ")" ], - "id": "ea65c6275f956bdb" + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 2 }, { - "metadata": {}, + "id": "686a6a5f54a0cef5", "cell_type": "code", - "outputs": [], - "execution_count": null, "source": "workflow_json_filename = \"pyiron_base_qe.json\"", - "id": "686a6a5f54a0cef5" + "metadata": { + "trusted": true + }, + "outputs": [], + "execution_count": 3 }, { "id": "208ddfb8-dfda-4227-aa1f-3dc29e34ea82", @@ -157,7 +161,7 @@ { "name": "stdout", "output_type": "stream", - "text": "{\"nodes\": [{\"id\": 0, \"function\": \"quantum_espresso_workflow.plot_energy_volume_curve\"}, {\"id\": 1, \"function\": \"python_workflow_definition.shared.get_list\"}, {\"id\": 2, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 3, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 4, \"function\": \"quantum_espresso_workflow.generate_structures\"}, {\"id\": 5, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 6, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 7, \"function\": \"quantum_espresso_workflow.get_bulk_structure\"}, {\"id\": 8, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 9, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 10, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 11, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 12, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 13, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 14, \"function\": \"quantum_espresso_workflow.calculate_qe\"}, {\"id\": 15, \"function\": \"python_workflow_definition.shared.get_dict\"}, {\"id\": 16, \"function\": \"python_workflow_definition.shared.get_list\"}, {\"id\": 17, \"value\": \"strain_0\"}, {\"id\": 18, \"value\": \"mini\"}, {\"id\": 19, \"value\": \"Al\"}, {\"id\": 20, \"value\": 4.04}, {\"id\": 21, \"value\": true}, {\"id\": 22, \"value\": {\"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"}}, {\"id\": 23, \"value\": [3, 3, 3]}, {\"id\": 24, \"value\": \"vc-relax\"}, {\"id\": 25, \"value\": 0.02}, {\"id\": 26, \"value\": [0.9, 0.9500000000000001, 1.0, 1.05, 1.1]}, {\"id\": 27, \"value\": \"scf\"}, {\"id\": 28, \"value\": \"strain_1\"}, {\"id\": 29, \"value\": \"strain_2\"}, {\"id\": 30, \"value\": \"strain_3\"}, {\"id\": 31, \"value\": \"strain_4\"}], \"edges\": [{\"target\": 0, \"targetPort\": \"volume_lst\", \"source\": 1, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"0\", \"source\": 2, \"sourcePort\": \"volume\"}, {\"target\": 2, \"targetPort\": \"working_directory\", \"source\": 17, \"sourcePort\": null}, {\"target\": 2, \"targetPort\": \"input_dict\", \"source\": 3, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"structure\", \"source\": 4, \"sourcePort\": \"s_0\"}, {\"target\": 4, \"targetPort\": \"structure\", \"source\": 5, \"sourcePort\": \"structure\"}, {\"target\": 5, \"targetPort\": \"working_directory\", \"source\": 18, \"sourcePort\": null}, {\"target\": 5, \"targetPort\": \"input_dict\", \"source\": 6, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"structure\", \"source\": 7, \"sourcePort\": null}, {\"target\": 7, \"targetPort\": \"element\", \"source\": 19, \"sourcePort\": null}, {\"target\": 7, \"targetPort\": \"a\", \"source\": 20, \"sourcePort\": null}, {\"target\": 7, \"targetPort\": \"cubic\", \"source\": 21, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"calculation\", \"source\": 24, \"sourcePort\": null}, {\"target\": 6, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 4, \"targetPort\": \"strain_lst\", \"source\": 26, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"calculation\", \"source\": 27, \"sourcePort\": null}, {\"target\": 3, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"1\", \"source\": 8, \"sourcePort\": \"volume\"}, {\"target\": 8, \"targetPort\": \"working_directory\", \"source\": 28, \"sourcePort\": null}, {\"target\": 8, \"targetPort\": \"input_dict\", \"source\": 9, \"sourcePort\": null}, {\"target\": 9, \"targetPort\": \"structure\", \"source\": 4, \"sourcePort\": \"s_1\"}, {\"target\": 9, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 9, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 9, \"targetPort\": \"calculation\", \"source\": 27, \"sourcePort\": null}, {\"target\": 9, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"2\", \"source\": 10, \"sourcePort\": \"volume\"}, {\"target\": 10, \"targetPort\": \"working_directory\", \"source\": 29, \"sourcePort\": null}, {\"target\": 10, \"targetPort\": \"input_dict\", \"source\": 11, \"sourcePort\": null}, {\"target\": 11, \"targetPort\": \"structure\", \"source\": 4, \"sourcePort\": \"s_2\"}, {\"target\": 11, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 11, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 11, \"targetPort\": \"calculation\", \"source\": 27, \"sourcePort\": null}, {\"target\": 11, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"3\", \"source\": 12, \"sourcePort\": \"volume\"}, {\"target\": 12, \"targetPort\": \"working_directory\", \"source\": 30, \"sourcePort\": null}, {\"target\": 12, \"targetPort\": \"input_dict\", \"source\": 13, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"structure\", \"source\": 4, \"sourcePort\": \"s_3\"}, {\"target\": 13, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"calculation\", \"source\": 27, \"sourcePort\": null}, {\"target\": 13, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 1, \"targetPort\": \"4\", \"source\": 14, \"sourcePort\": \"volume\"}, {\"target\": 14, \"targetPort\": \"working_directory\", \"source\": 31, \"sourcePort\": null}, {\"target\": 14, \"targetPort\": \"input_dict\", \"source\": 15, \"sourcePort\": null}, {\"target\": 15, \"targetPort\": \"structure\", \"source\": 4, \"sourcePort\": \"s_4\"}, {\"target\": 15, \"targetPort\": \"pseudopotentials\", \"source\": 22, \"sourcePort\": null}, {\"target\": 15, \"targetPort\": \"kpts\", \"source\": 23, \"sourcePort\": null}, {\"target\": 15, \"targetPort\": \"calculation\", \"source\": 27, \"sourcePort\": null}, {\"target\": 15, \"targetPort\": \"smearing\", \"source\": 25, \"sourcePort\": null}, {\"target\": 0, \"targetPort\": \"energy_lst\", \"source\": 16, \"sourcePort\": null}, {\"target\": 16, \"targetPort\": \"0\", \"source\": 2, \"sourcePort\": \"energy\"}, {\"target\": 16, \"targetPort\": \"1\", \"source\": 8, \"sourcePort\": \"energy\"}, {\"target\": 16, \"targetPort\": \"2\", \"source\": 10, \"sourcePort\": \"energy\"}, {\"target\": 16, \"targetPort\": \"3\", \"source\": 12, \"sourcePort\": \"energy\"}, {\"target\": 16, \"targetPort\": \"4\", \"source\": 14, \"sourcePort\": \"energy\"}]}" + "text": "{\n \"version\": \"0.1.0\",\n \"nodes\": [\n {\n \"id\": 0,\n \"type\": \"function\",\n \"value\": \"workflow.plot_energy_volume_curve\"\n },\n {\n \"id\": 1,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 2,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 3,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 4,\n \"type\": \"function\",\n \"value\": \"workflow.generate_structures\"\n },\n {\n \"id\": 5,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 6,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 7,\n \"type\": \"function\",\n \"value\": \"workflow.get_bulk_structure\"\n },\n {\n \"id\": 8,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 9,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 10,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 11,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 12,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 13,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 14,\n \"type\": \"function\",\n \"value\": \"workflow.calculate_qe\"\n },\n {\n \"id\": 15,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_dict\"\n },\n {\n \"id\": 16,\n \"type\": \"function\",\n \"value\": \"python_workflow_definition.shared.get_list\"\n },\n {\n \"id\": 17,\n \"type\": \"input\",\n \"name\": \"working_directory_0\",\n \"value\": \"strain_0\"\n },\n {\n \"id\": 18,\n \"type\": \"input\",\n \"name\": \"working_directory_1\",\n \"value\": \"mini\"\n },\n {\n \"id\": 19,\n \"type\": \"input\",\n \"name\": \"element\",\n \"value\": \"Al\"\n },\n {\n \"id\": 20,\n \"type\": \"input\",\n \"name\": \"a\",\n \"value\": 4.04\n },\n {\n \"id\": 21,\n \"type\": \"input\",\n \"name\": \"cubic\",\n \"value\": true\n },\n {\n \"id\": 22,\n \"type\": \"input\",\n \"name\": \"pseudopotentials\",\n \"value\": {\n \"Al\": \"Al.pbe-n-kjpaw_psl.1.0.0.UPF\"\n }\n },\n {\n \"id\": 23,\n \"type\": \"input\",\n \"name\": \"kpts\",\n \"value\": [\n 3,\n 3,\n 3\n ]\n },\n {\n \"id\": 24,\n \"type\": \"input\",\n \"name\": \"calculation_0\",\n \"value\": \"vc-relax\"\n },\n {\n \"id\": 25,\n \"type\": \"input\",\n \"name\": \"smearing\",\n \"value\": 0.02\n },\n {\n \"id\": 26,\n \"type\": \"input\",\n \"name\": \"strain_lst\",\n \"value\": [\n 0.9,\n 0.9500000000000001,\n 1.0,\n 1.05,\n 1.1\n ]\n },\n {\n \"id\": 27,\n \"type\": \"input\",\n \"name\": \"calculation_1\",\n \"value\": \"scf\"\n },\n {\n \"id\": 28,\n \"type\": \"input\",\n \"name\": \"working_directory_2\",\n \"value\": \"strain_1\"\n },\n {\n \"id\": 29,\n \"type\": \"input\",\n \"name\": \"working_directory_3\",\n \"value\": \"strain_2\"\n },\n {\n \"id\": 30,\n \"type\": \"input\",\n \"name\": \"working_directory_4\",\n \"value\": \"strain_3\"\n },\n {\n \"id\": 31,\n \"type\": \"input\",\n \"name\": \"working_directory_5\",\n \"value\": \"strain_4\"\n },\n {\n \"id\": 32,\n \"type\": \"output\",\n \"name\": \"result\"\n }\n ],\n \"edges\": [\n {\n \"target\": 0,\n \"targetPort\": \"volume_lst\",\n \"source\": 1,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"0\",\n \"source\": 2,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 2,\n \"targetPort\": \"working_directory\",\n \"source\": 17,\n \"sourcePort\": null\n },\n {\n \"target\": 2,\n \"targetPort\": \"input_dict\",\n \"source\": 3,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"structure\",\n \"source\": 4,\n \"sourcePort\": \"s_0\"\n },\n {\n \"target\": 4,\n \"targetPort\": \"structure\",\n \"source\": 5,\n \"sourcePort\": \"structure\"\n },\n {\n \"target\": 5,\n \"targetPort\": \"working_directory\",\n \"source\": 18,\n \"sourcePort\": null\n },\n {\n \"target\": 5,\n \"targetPort\": \"input_dict\",\n \"source\": 6,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"structure\",\n \"source\": 7,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"element\",\n \"source\": 19,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"a\",\n \"source\": 20,\n \"sourcePort\": null\n },\n {\n \"target\": 7,\n \"targetPort\": \"cubic\",\n \"source\": 21,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"calculation\",\n \"source\": 24,\n \"sourcePort\": null\n },\n {\n \"target\": 6,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 4,\n \"targetPort\": \"strain_lst\",\n \"source\": 26,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"calculation\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 3,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"1\",\n \"source\": 8,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 8,\n \"targetPort\": \"working_directory\",\n \"source\": 28,\n \"sourcePort\": null\n },\n {\n \"target\": 8,\n \"targetPort\": \"input_dict\",\n \"source\": 9,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"structure\",\n \"source\": 4,\n \"sourcePort\": \"s_1\"\n },\n {\n \"target\": 9,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"calculation\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 9,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"2\",\n \"source\": 10,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 10,\n \"targetPort\": \"working_directory\",\n \"source\": 29,\n \"sourcePort\": null\n },\n {\n \"target\": 10,\n \"targetPort\": \"input_dict\",\n \"source\": 11,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"structure\",\n \"source\": 4,\n \"sourcePort\": \"s_2\"\n },\n {\n \"target\": 11,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"calculation\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 11,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"3\",\n \"source\": 12,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 12,\n \"targetPort\": \"working_directory\",\n \"source\": 30,\n \"sourcePort\": null\n },\n {\n \"target\": 12,\n \"targetPort\": \"input_dict\",\n \"source\": 13,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"structure\",\n \"source\": 4,\n \"sourcePort\": \"s_3\"\n },\n {\n \"target\": 13,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"calculation\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 13,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 1,\n \"targetPort\": \"4\",\n \"source\": 14,\n \"sourcePort\": \"volume\"\n },\n {\n \"target\": 14,\n \"targetPort\": \"working_directory\",\n \"source\": 31,\n \"sourcePort\": null\n },\n {\n \"target\": 14,\n \"targetPort\": \"input_dict\",\n \"source\": 15,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"structure\",\n \"source\": 4,\n \"sourcePort\": \"s_4\"\n },\n {\n \"target\": 15,\n \"targetPort\": \"pseudopotentials\",\n \"source\": 22,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"kpts\",\n \"source\": 23,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"calculation\",\n \"source\": 27,\n \"sourcePort\": null\n },\n {\n \"target\": 15,\n \"targetPort\": \"smearing\",\n \"source\": 25,\n \"sourcePort\": null\n },\n {\n \"target\": 0,\n \"targetPort\": \"energy_lst\",\n \"source\": 16,\n \"sourcePort\": null\n },\n {\n \"target\": 16,\n \"targetPort\": \"0\",\n \"source\": 2,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"1\",\n \"source\": 8,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"2\",\n \"source\": 10,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"3\",\n \"source\": 12,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 16,\n \"targetPort\": \"4\",\n \"source\": 14,\n \"sourcePort\": \"energy\"\n },\n {\n \"target\": 32,\n \"targetPort\": null,\n \"source\": 0,\n \"sourcePort\": null\n }\n ]\n}" } ], "execution_count": 12 @@ -180,7 +184,7 @@ "execution_count": 13, "output_type": "execute_result", "data": { - "text/plain": "Profile" + "text/plain": "Profile" }, "metadata": {} } @@ -228,7 +232,7 @@ { "name": "stderr", "output_type": "stream", - "text": "04/23/2025 09:47:03 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure8\n04/23/2025 09:47:04 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_bulk_structure8, type: PyFunction, finished.\n04/23/2025 09:47:04 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict7\n04/23/2025 09:47:05 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict7, type: PyFunction, finished.\n04/23/2025 09:47:05 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05529] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:47:58 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n04/23/2025 09:47:58 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n04/23/2025 09:47:58 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures5\n04/23/2025 09:47:59 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: generate_structures5, type: PyFunction, finished.\n04/23/2025 09:48:00 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict4,get_dict10,get_dict12,get_dict14,get_dict16\n04/23/2025 09:48:00 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict4, type: PyFunction, finished.\n04/23/2025 09:48:00 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe3,get_dict10,get_dict12,get_dict14,get_dict16\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05544] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:48:11 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:48:12 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe3, type: PyFunction, finished.\n04/23/2025 09:48:12 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10,get_dict12,get_dict14,get_dict16\n04/23/2025 09:48:12 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n04/23/2025 09:48:12 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe9,get_dict12,get_dict14,get_dict16\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05555] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:48:25 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:48:25 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe9, type: PyFunction, finished.\n04/23/2025 09:48:25 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict14,get_dict16\n04/23/2025 09:48:26 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n04/23/2025 09:48:26 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe11,get_dict14,get_dict16\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05567] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:48:40 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:48:41 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe11, type: PyFunction, finished.\n04/23/2025 09:48:41 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict16\n04/23/2025 09:48:41 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n04/23/2025 09:48:42 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe13,get_dict16\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05577] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:48:58 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:48:58 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe13, type: PyFunction, finished.\n04/23/2025 09:48:58 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict16\n04/23/2025 09:48:59 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_dict16, type: PyFunction, finished.\n04/23/2025 09:48:59 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe15\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05592] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:49:14 AM <5440> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:49:15 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: calculate_qe15, type: PyFunction, finished.\n04/23/2025 09:49:15 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list2,get_list17\n04/23/2025 09:49:16 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_list2, type: PyFunction, finished.\n04/23/2025 09:49:16 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n04/23/2025 09:49:16 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n04/23/2025 09:49:16 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve1\n04/23/2025 09:49:17 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve1, type: PyFunction, finished.\n04/23/2025 09:49:17 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/23/2025 09:49:17 AM <5440> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [193|WorkGraphEngine|finalize]: Finalize workgraph.\n" + "text": "05/24/2025 06:00:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure8\n05/24/2025 06:00:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_bulk_structure8, type: PyFunction, finished.\n05/24/2025 06:00:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict7\n05/24/2025 06:00:14 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict7, type: PyFunction, finished.\n05/24/2025 06:00:14 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6\n[jupyter-pythonworkflow-fl--x---d7231032:10471] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:01:04 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n05/24/2025 06:01:04 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n05/24/2025 06:01:04 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures5\n05/24/2025 06:01:05 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: generate_structures5, type: PyFunction, finished.\n05/24/2025 06:01:05 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict4,get_dict10,get_dict12,get_dict14,get_dict16\n05/24/2025 06:01:05 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict4, type: PyFunction, finished.\n05/24/2025 06:01:06 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe3,get_dict10,get_dict12,get_dict14,get_dict16\n[jupyter-pythonworkflow-fl--x---d7231032:10486] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:01:16 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:01:16 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe3, type: PyFunction, finished.\n05/24/2025 06:01:16 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10,get_dict12,get_dict14,get_dict16\n05/24/2025 06:01:18 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n05/24/2025 06:01:18 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe9,get_dict12,get_dict14,get_dict16\n[jupyter-pythonworkflow-fl--x---d7231032:10497] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:01:30 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:01:30 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe9, type: PyFunction, finished.\n05/24/2025 06:01:30 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict14,get_dict16\n05/24/2025 06:01:31 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n05/24/2025 06:01:31 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe11,get_dict14,get_dict16\n[jupyter-pythonworkflow-fl--x---d7231032:10508] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:01:43 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:01:43 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe11, type: PyFunction, finished.\n05/24/2025 06:01:43 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict16\n05/24/2025 06:01:44 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n05/24/2025 06:01:44 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe13,get_dict16\n[jupyter-pythonworkflow-fl--x---d7231032:10519] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:01:57 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:01:58 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe13, type: PyFunction, finished.\n05/24/2025 06:01:58 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict16\n05/24/2025 06:01:58 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_dict16, type: PyFunction, finished.\n05/24/2025 06:01:58 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe15\n[jupyter-pythonworkflow-fl--x---d7231032:10531] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:02:13 AM <10378> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:02:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: calculate_qe15, type: PyFunction, finished.\n05/24/2025 06:02:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list2,get_list17\n05/24/2025 06:02:13 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_list2, type: PyFunction, finished.\n05/24/2025 06:02:14 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n05/24/2025 06:02:14 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n05/24/2025 06:02:14 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve1\n05/24/2025 06:02:15 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve1, type: PyFunction, finished.\n05/24/2025 06:02:15 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 06:02:15 AM <10378> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [249|WorkGraphEngine|finalize]: Finalize workgraph.\n" }, { "output_type": "display_data", @@ -254,13 +258,7 @@ "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 18 }, { @@ -304,73 +302,73 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:49:19,623 INFO Started executing jobs locally\n2025-04-23 09:49:19,791 INFO Starting job - get_bulk_structure (3a79a0c7-c443-40e5-8c4c-030ccf176743)\n2025-04-23 09:49:19,795 INFO Finished job - get_bulk_structure (3a79a0c7-c443-40e5-8c4c-030ccf176743)\n2025-04-23 09:49:19,796 INFO Starting job - get_dict (d168da9a-66a0-4ab1-ab65-7b5b4b078fac)\n2025-04-23 09:49:19,799 INFO Finished job - get_dict (d168da9a-66a0-4ab1-ab65-7b5b4b078fac)\n2025-04-23 09:49:19,809 INFO Starting job - calculate_qe (0b40ca71-1ea2-4181-8d91-1de15ef3df17)\n" + "text": "2025-05-24 06:02:16,526 INFO Started executing jobs locally\n2025-05-24 06:02:16,619 INFO Starting job - get_bulk_structure (49008d34-c2c0-41a9-a7cb-17f68fd503d3)\n2025-05-24 06:02:16,622 INFO Finished job - get_bulk_structure (49008d34-c2c0-41a9-a7cb-17f68fd503d3)\n2025-05-24 06:02:16,623 INFO Starting job - get_dict (f81de048-62e5-448c-9783-fc9cb4d4bb7d)\n2025-05-24 06:02:16,625 INFO Finished job - get_dict (f81de048-62e5-448c-9783-fc9cb4d4bb7d)\n2025-05-24 06:02:16,625 INFO Starting job - calculate_qe (e7891e79-cd64-4e19-b474-4e5c4521807b)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05604] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10547] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:50:11,885 INFO Finished job - calculate_qe (0b40ca71-1ea2-4181-8d91-1de15ef3df17)\n2025-04-23 09:50:11,886 INFO Starting job - generate_structures (451e4839-7612-4530-bbdb-9cb3e77cc6b8)\n2025-04-23 09:50:11,891 INFO Finished job - generate_structures (451e4839-7612-4530-bbdb-9cb3e77cc6b8)\n2025-04-23 09:50:11,892 INFO Starting job - get_dict (b586638f-b882-4439-a28e-a2c76f50c0e2)\n2025-04-23 09:50:11,893 INFO Finished job - get_dict (b586638f-b882-4439-a28e-a2c76f50c0e2)\n2025-04-23 09:50:11,895 INFO Starting job - get_dict (974e6f28-2911-4b3b-bc55-786c2111e39e)\n2025-04-23 09:50:11,896 INFO Finished job - get_dict (974e6f28-2911-4b3b-bc55-786c2111e39e)\n2025-04-23 09:50:11,897 INFO Starting job - get_dict (1c0b7807-d38a-4e23-880f-bccd87c84b28)\n2025-04-23 09:50:11,899 INFO Finished job - get_dict (1c0b7807-d38a-4e23-880f-bccd87c84b28)\n2025-04-23 09:50:11,908 INFO Starting job - get_dict (8791b0c0-b424-4f62-80a9-3170660b35f9)\n2025-04-23 09:50:11,910 INFO Finished job - get_dict (8791b0c0-b424-4f62-80a9-3170660b35f9)\n2025-04-23 09:50:11,911 INFO Starting job - get_dict (b0e2cd7f-9e49-40b6-8c79-6a3c8588fed4)\n2025-04-23 09:50:11,913 INFO Finished job - get_dict (b0e2cd7f-9e49-40b6-8c79-6a3c8588fed4)\n2025-04-23 09:50:11,913 INFO Starting job - calculate_qe (146dc5e6-1415-4c92-9b81-c1dac13c4af7)\n" + "text": "2025-05-24 06:03:08,574 INFO Finished job - calculate_qe (e7891e79-cd64-4e19-b474-4e5c4521807b)\n2025-05-24 06:03:08,576 INFO Starting job - generate_structures (05513874-a1a3-428c-91ad-7ba4f44d13c4)\n2025-05-24 06:03:08,580 INFO Finished job - generate_structures (05513874-a1a3-428c-91ad-7ba4f44d13c4)\n2025-05-24 06:03:08,580 INFO Starting job - get_dict (4b033be6-d0c6-4bc4-8f10-eb0ff6ad94f8)\n2025-05-24 06:03:08,582 INFO Finished job - get_dict (4b033be6-d0c6-4bc4-8f10-eb0ff6ad94f8)\n2025-05-24 06:03:08,583 INFO Starting job - get_dict (8fb5c055-10cd-4cf0-adcc-57703638e0c8)\n2025-05-24 06:03:08,584 INFO Finished job - get_dict (8fb5c055-10cd-4cf0-adcc-57703638e0c8)\n2025-05-24 06:03:08,585 INFO Starting job - get_dict (0bc6f831-f685-4688-9f9a-194271b83d48)\n2025-05-24 06:03:08,586 INFO Finished job - get_dict (0bc6f831-f685-4688-9f9a-194271b83d48)\n2025-05-24 06:03:08,587 INFO Starting job - get_dict (90ac5a4e-6464-48c8-ae33-8efebb8ce336)\n2025-05-24 06:03:08,588 INFO Finished job - get_dict (90ac5a4e-6464-48c8-ae33-8efebb8ce336)\n2025-05-24 06:03:08,589 INFO Starting job - get_dict (d7a2d06e-aae2-40c6-914e-6145f1e22f35)\n2025-05-24 06:03:08,590 INFO Finished job - get_dict (d7a2d06e-aae2-40c6-914e-6145f1e22f35)\n2025-05-24 06:03:08,591 INFO Starting job - calculate_qe (7896c29a-eef8-425a-89b9-15c31c5b7555)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05619] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10573] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:50:23,619 INFO Finished job - calculate_qe (146dc5e6-1415-4c92-9b81-c1dac13c4af7)\n2025-04-23 09:50:23,620 INFO Starting job - calculate_qe (4760dd26-7403-4f3e-8d64-596893d84e95)\n" + "text": "2025-05-24 06:03:19,134 INFO Finished job - calculate_qe (7896c29a-eef8-425a-89b9-15c31c5b7555)\n2025-05-24 06:03:19,135 INFO Starting job - calculate_qe (b7eb8441-9b20-4560-8fee-06794bc3eb04)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05630] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:10584] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:50:35,807 INFO Finished job - calculate_qe (4760dd26-7403-4f3e-8d64-596893d84e95)\n2025-04-23 09:50:35,808 INFO Starting job - calculate_qe (e67d4ff9-8416-4eff-86da-8b82ca9e6a7b)\n" + "text": "2025-05-24 06:03:30,644 INFO Finished job - calculate_qe (b7eb8441-9b20-4560-8fee-06794bc3eb04)\n2025-05-24 06:03:30,645 INFO Starting job - calculate_qe (010f3f1a-792c-49ce-bbc8-d09be700575c)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05641] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:10595] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:50:49,609 INFO Finished job - calculate_qe (e67d4ff9-8416-4eff-86da-8b82ca9e6a7b)\n2025-04-23 09:50:49,610 INFO Starting job - calculate_qe (b351bbe7-8e96-4167-8eef-83fb97b952e9)\n" + "text": "2025-05-24 06:03:43,945 INFO Finished job - calculate_qe (010f3f1a-792c-49ce-bbc8-d09be700575c)\n2025-05-24 06:03:43,946 INFO Starting job - calculate_qe (b3b51b0e-49b7-4758-a561-94218cd03d6f)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05657] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:10605] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:51:03,448 INFO Finished job - calculate_qe (b351bbe7-8e96-4167-8eef-83fb97b952e9)\n2025-04-23 09:51:03,449 INFO Starting job - calculate_qe (2eee6b99-b12e-4e61-96f5-359461bf3c10)\n" + "text": "2025-05-24 06:03:57,230 INFO Finished job - calculate_qe (b3b51b0e-49b7-4758-a561-94218cd03d6f)\n2025-05-24 06:03:57,231 INFO Starting job - calculate_qe (29c5cbc6-5912-48df-9cf7-ced1c0aad822)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:05668] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:10615] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:51:14,516 INFO Finished job - calculate_qe (2eee6b99-b12e-4e61-96f5-359461bf3c10)\n2025-04-23 09:51:14,517 INFO Starting job - get_list (7bb19e3c-c167-4477-beee-c93a5148e5ca)\n2025-04-23 09:51:14,520 INFO Finished job - get_list (7bb19e3c-c167-4477-beee-c93a5148e5ca)\n2025-04-23 09:51:14,521 INFO Starting job - get_list (cb1ca4e3-b479-40af-8f27-0a2562b9e246)\n2025-04-23 09:51:14,524 INFO Finished job - get_list (cb1ca4e3-b479-40af-8f27-0a2562b9e246)\n2025-04-23 09:51:14,525 INFO Starting job - plot_energy_volume_curve (15aebe69-961a-4b8f-a3e3-2371ca361d64)\n2025-04-23 09:51:14,588 INFO Finished job - plot_energy_volume_curve (15aebe69-961a-4b8f-a3e3-2371ca361d64)\n2025-04-23 09:51:14,589 INFO Finished executing jobs locally\n" + "text": "2025-05-24 06:04:07,269 INFO Finished job - calculate_qe (29c5cbc6-5912-48df-9cf7-ced1c0aad822)\n2025-05-24 06:04:07,271 INFO Starting job - get_list (21df1d62-03ff-4f7c-ae36-34c9cb809b32)\n2025-05-24 06:04:07,277 INFO Finished job - get_list (21df1d62-03ff-4f7c-ae36-34c9cb809b32)\n2025-05-24 06:04:07,277 INFO Starting job - get_list (b1c1cd99-997b-4f4d-ad01-0e3af8c6a929)\n2025-05-24 06:04:07,288 INFO Finished job - get_list (b1c1cd99-997b-4f4d-ad01-0e3af8c6a929)\n2025-05-24 06:04:07,289 INFO Starting job - plot_energy_volume_curve (eb6fcf91-a5b3-4ddd-be2e-7406b51e5084)\n2025-05-24 06:04:07,353 INFO Finished job - plot_energy_volume_curve (eb6fcf91-a5b3-4ddd-be2e-7406b51e5084)\n2025-05-24 06:04:07,354 INFO Finished executing jobs locally\n" }, { "execution_count": 22, "output_type": "execute_result", "data": { - "text/plain": "{'3a79a0c7-c443-40e5-8c4c-030ccf176743': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'd168da9a-66a0-4ab1-ab65-7b5b4b078fac': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'vc-relax', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '0b40ca71-1ea2-4181-8d91-1de15ef3df17': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946928, 0.0, 0.0], [0.0, 4.045637215946928, 0.0], [0.0, 0.0, 4.045637215946928]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734636, 2.0228186079734636], [2.0228186079734636, 0.0, 2.0228186079734636], [2.0228186079734636, 2.0228186079734636, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365262253586, 'volume': 66.21567448236675}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '451e4839-7612-4530-bbdb-9cb3e77cc6b8': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859622328, 0.0, 0.0], [0.0, 3.9060197859622328, 0.0], [0.0, 0.0, 3.9060197859622328]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981116, 1.953009892981116], [1.953009892981116, 0.0, 1.953009892981116], [1.953009892981116, 1.953009892981116, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443181347, 0.0, 0.0], [0.0, 3.9770538443181347, 0.0], [0.0, 0.0, 3.9770538443181347]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.988526922159067, 1.988526922159067], [1.988526922159067, 0.0, 1.988526922159067], [1.988526922159067, 1.988526922159067, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946928, 0.0, 0.0], [0.0, 4.045637215946928, 0.0], [0.0, 0.0, 4.045637215946928]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734636, 2.0228186079734636], [2.0228186079734636, 0.0, 2.0228186079734636], [2.0228186079734636, 2.0228186079734636, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.1119709272830445, 0.0, 0.0], [0.0, 4.1119709272830445, 0.0], [0.0, 0.0, 4.1119709272830445]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.055985463641522, 2.055985463641522], [2.055985463641522, 0.0, 2.055985463641522], [2.055985463641522, 2.055985463641522, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372271, 0.0, 0.0], [0.0, 4.176230852372271, 0.0], [0.0, 0.0, 4.176230852372271]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.088115426186135, 2.088115426186135], [2.088115426186135, 0.0, 2.088115426186135], [2.088115426186135, 2.088115426186135, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'b586638f-b882-4439-a28e-a2c76f50c0e2': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443181347, 0.0, 0.0], [0.0, 3.9770538443181347, 0.0], [0.0, 0.0, 3.9770538443181347]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.988526922159067, 1.988526922159067], [1.988526922159067, 0.0, 1.988526922159067], [1.988526922159067, 1.988526922159067, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '974e6f28-2911-4b3b-bc55-786c2111e39e': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946928, 0.0, 0.0], [0.0, 4.045637215946928, 0.0], [0.0, 0.0, 4.045637215946928]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079734636, 2.0228186079734636], [2.0228186079734636, 0.0, 2.0228186079734636], [2.0228186079734636, 2.0228186079734636, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '1c0b7807-d38a-4e23-880f-bccd87c84b28': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.1119709272830445, 0.0, 0.0], [0.0, 4.1119709272830445, 0.0], [0.0, 0.0, 4.1119709272830445]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.055985463641522, 2.055985463641522], [2.055985463641522, 0.0, 2.055985463641522], [2.055985463641522, 2.055985463641522, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '8791b0c0-b424-4f62-80a9-3170660b35f9': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372271, 0.0, 0.0], [0.0, 4.176230852372271, 0.0], [0.0, 0.0, 4.176230852372271]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.088115426186135, 2.088115426186135], [2.088115426186135, 0.0, 2.088115426186135], [2.088115426186135, 2.088115426186135, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'b0e2cd7f-9e49-40b6-8c79-6a3c8588fed4': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859622328, 0.0, 0.0], [0.0, 3.9060197859622328, 0.0], [0.0, 0.0, 3.9060197859622328]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981116, 1.953009892981116], [1.953009892981116, 0.0, 1.953009892981116], [1.953009892981116, 1.953009892981116, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '146dc5e6-1415-4c92-9b81-c1dac13c4af7': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.97705382693468, 0.0, 0.0], [0.0, 3.97705382693468, 0.0], [0.0, 0.0, 3.97705382693468]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082746, 1.9885269135082746], [1.9885269135082746, 0.0, 1.9885269135082746], [1.9885269135082746, 1.9885269135082746, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9161488594584, 'volume': 62.90488993338832}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '4760dd26-7403-4f3e-8d64-596893d84e95': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263706, 0.0, 0.0], [0.0, 4.045637198263706, 0.0], [0.0, 0.0, 4.045637198263706]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583887, 2.0228185991583887], [2.0228185991583887, 0.0, 2.0228185991583887], [2.0228185991583887, 2.0228185991583887, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365241668336, 'volume': 66.21567361409329}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'e67d4ff9-8416-4eff-86da-8b82ca9e6a7b': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309876, 0.0, 0.0], [0.0, 4.111970909309876, 0.0], [0.0, 0.0, 4.111970909309876]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025814, 'volume': 69.52645729479767}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'b351bbe7-8e96-4167-8eef-83fb97b952e9': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411823, 0.0, 0.0], [0.0, 4.17623083411823, 0.0], [0.0, 0.0, 4.17623083411823]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.08811541707298, 2.08811541707298], [2.08811541707298, 0.0, 2.08811541707298], [2.08811541707298, 2.08811541707298, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8737904693405, 'volume': 72.83724097550255}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '2eee6b99-b12e-4e61-96f5-359461bf3c10': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197688892653, 0.0, 0.0], [0.0, 3.9060197688892653, 0.0], [0.0, 0.0, 3.9060197688892653]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8457446150649, 'volume': 59.59410625268378}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '7bb19e3c-c167-4477-beee-c93a5148e5ca': {1: Response(output=[-1074.8457446150649, -1074.9161488594584, -1074.9365241668336, -1074.9192860025814, -1074.8737904693405], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'cb1ca4e3-b479-40af-8f27-0a2562b9e246': {1: Response(output=[59.59410625268378, 62.90488993338832, 66.21567361409329, 69.52645729479767, 72.83724097550255], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '15aebe69-961a-4b8f-a3e3-2371ca361d64': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" + "text/plain": "{'49008d34-c2c0-41a9-a7cb-17f68fd503d3': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'f81de048-62e5-448c-9783-fc9cb4d4bb7d': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'vc-relax', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'e7891e79-cd64-4e19-b474-4e5c4521807b': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946847, 0.0, 0.0], [0.0, 4.045637215946847, 0.0], [0.0, 0.0, 4.045637215946846]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973423, 2.022818607973423], [2.022818607973423, 0.0, 2.022818607973423], [2.022818607973423, 2.022818607973423, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365262253593, 'volume': 66.21567448236276}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '05513874-a1a3-428c-91ad-7ba4f44d13c4': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859621546, 0.0, 0.0], [0.0, 3.9060197859621546, 0.0], [0.0, 0.0, 3.9060197859621537]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810769, 1.9530098929810769], [1.9530098929810769, 0.0, 1.9530098929810769], [1.9530098929810769, 1.9530098929810769, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844318055, 0.0, 0.0], [0.0, 3.977053844318055, 0.0], [0.0, 0.0, 3.9770538443180543]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590272, 1.9885269221590272], [1.9885269221590272, 0.0, 1.9885269221590272], [1.9885269221590272, 1.9885269221590272, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946847, 0.0, 0.0], [0.0, 4.045637215946847, 0.0], [0.0, 0.0, 4.045637215946846]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973423, 2.022818607973423], [2.022818607973423, 0.0, 2.022818607973423], [2.022818607973423, 2.022818607973423, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282963, 0.0, 0.0], [0.0, 4.111970927282963, 0.0], [0.0, 0.0, 4.111970927282961]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414805, 2.05598546364148], [2.0559854636414805, 0.0, 2.05598546364148], [2.0559854636414805, 2.0559854636414805, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372187, 0.0, 0.0], [0.0, 4.176230852372187, 0.0], [0.0, 0.0, 4.1762308523721865]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860932, 2.0881154261860932], [2.0881154261860932, 0.0, 2.0881154261860932], [2.0881154261860932, 2.0881154261860932, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '4b033be6-d0c6-4bc4-8f10-eb0ff6ad94f8': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844318055, 0.0, 0.0], [0.0, 3.977053844318055, 0.0], [0.0, 0.0, 3.9770538443180543]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221590272, 1.9885269221590272], [1.9885269221590272, 0.0, 1.9885269221590272], [1.9885269221590272, 1.9885269221590272, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '8fb5c055-10cd-4cf0-adcc-57703638e0c8': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946847, 0.0, 0.0], [0.0, 4.045637215946847, 0.0], [0.0, 0.0, 4.045637215946846]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.022818607973423, 2.022818607973423], [2.022818607973423, 0.0, 2.022818607973423], [2.022818607973423, 2.022818607973423, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '0bc6f831-f685-4688-9f9a-194271b83d48': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282963, 0.0, 0.0], [0.0, 4.111970927282963, 0.0], [0.0, 0.0, 4.111970927282961]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414805, 2.05598546364148], [2.0559854636414805, 0.0, 2.05598546364148], [2.0559854636414805, 2.0559854636414805, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '90ac5a4e-6464-48c8-ae33-8efebb8ce336': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372187, 0.0, 0.0], [0.0, 4.176230852372187, 0.0], [0.0, 0.0, 4.1762308523721865]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860932, 2.0881154261860932], [2.0881154261860932, 0.0, 2.0881154261860932], [2.0881154261860932, 2.0881154261860932, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'd7a2d06e-aae2-40c6-914e-6145f1e22f35': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859621546, 0.0, 0.0], [0.0, 3.9060197859621546, 0.0], [0.0, 0.0, 3.9060197859621537]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810769, 1.9530098929810769], [1.9530098929810769, 0.0, 1.9530098929810769], [1.9530098929810769, 1.9530098929810769, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '7896c29a-eef8-425a-89b9-15c31c5b7555': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.97705382693461, 0.0, 0.0], [0.0, 3.97705382693461, 0.0], [0.0, 0.0, 3.9770538269346]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082753, 1.9885269135082753], [1.9885269135082753, 0.0, 1.9885269135082753], [1.9885269135082753, 1.9885269135082753, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9161488594596, 'volume': 62.90488993338486}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'b7eb8441-9b20-4560-8fee-06794bc3eb04': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263626, 0.0, 0.0], [0.0, 4.045637198263626, 0.0], [0.0, 0.0, 4.045637198263626]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583882, 2.0228185991583882], [2.0228185991583882, 0.0, 2.0228185991583882], [2.0228185991583882, 2.0228185991583882, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.936524166835, 'volume': 66.21567361408935}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '010f3f1a-792c-49ce-bbc8-d09be700575c': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309796, 0.0, 0.0], [0.0, 4.111970909309796, 0.0], [0.0, 0.0, 4.111970909309796]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025805, 'volume': 69.52645729479359}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'b3b51b0e-49b7-4758-a561-94218cd03d6f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411815, 0.0, 0.0], [0.0, 4.17623083411815, 0.0], [0.0, 0.0, 4.17623083411815]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154170729803, 2.0881154170729803], [2.0881154170729803, 0.0, 2.0881154170729803], [2.0881154170729803, 2.0881154170729803, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8737904693437, 'volume': 72.83724097549829}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '29c5cbc6-5912-48df-9cf7-ced1c0aad822': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197688891853, 0.0, 0.0], [0.0, 3.9060197688891853, 0.0], [0.0, 0.0, 3.9060197688891853]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.845744615063, 'volume': 59.59410625268013}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '21df1d62-03ff-4f7c-ae36-34c9cb809b32': {1: Response(output=[-1074.845744615063, -1074.9161488594596, -1074.936524166835, -1074.9192860025805, -1074.8737904693437], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'b1c1cd99-997b-4f4d-ad01-0e3af8c6a929': {1: Response(output=[59.59410625268013, 62.90488993338486, 66.21567361408935, 69.52645729479359, 72.83724097549829], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'eb6fcf91-a5b3-4ddd-be2e-7406b51e5084': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))}}" }, "metadata": {} }, diff --git a/example_workflows/quantum_espresso/universal_workflow.ipynb b/example_workflows/quantum_espresso/universal_workflow.ipynb index 958ffe1..42453c4 100644 --- a/example_workflows/quantum_espresso/universal_workflow.ipynb +++ b/example_workflows/quantum_espresso/universal_workflow.ipynb @@ -51,7 +51,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\n0\n\nquantum_espresso_workflow.get_bulk_structure\n\n\n\n13\n\npython_workflow_definition.shared.get_dict\n\n\n\n0->13\n\n\nstructure\n\n\n\n1\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n13->1\n\n\ninput_dict\n\n\n\n2\n\nquantum_espresso_workflow.generate_structures\n\n\n\n1->2\n\n\nstructure=result[structure]\n\n\n\n20\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->20\n\n\nstructure=result[s_0]\n\n\n\n23\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->23\n\n\nstructure=result[s_1]\n\n\n\n25\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->25\n\n\nstructure=result[s_2]\n\n\n\n27\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->27\n\n\nstructure=result[s_3]\n\n\n\n29\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->29\n\n\nstructure=result[s_4]\n\n\n\n3\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n20->3\n\n\ninput_dict\n\n\n\n4\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n23->4\n\n\ninput_dict\n\n\n\n5\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n25->5\n\n\ninput_dict\n\n\n\n6\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n27->6\n\n\ninput_dict\n\n\n\n7\n\nquantum_espresso_workflow.calculate_qe\n\n\n\n29->7\n\n\ninput_dict\n\n\n\n30\n\npython_workflow_definition.shared.get_list\n\n\n\n3->30\n\n\n0=result[volume]\n\n\n\n31\n\npython_workflow_definition.shared.get_list\n\n\n\n3->31\n\n\n0=result[energy]\n\n\n\n8\n\nquantum_espresso_workflow.plot_energy_volume_curve\n\n\n\n30->8\n\n\nvolume_lst\n\n\n\n31->8\n\n\nenergy_lst\n\n\n\n4->30\n\n\n1=result[volume]\n\n\n\n4->31\n\n\n1=result[energy]\n\n\n\n5->30\n\n\n2=result[volume]\n\n\n\n5->31\n\n\n2=result[energy]\n\n\n\n6->30\n\n\n3=result[volume]\n\n\n\n6->31\n\n\n3=result[energy]\n\n\n\n7->30\n\n\n4=result[volume]\n\n\n\n7->31\n\n\n4=result[energy]\n\n\n\n9\n\nAl\n\n\n\n9->0\n\n\nelement\n\n\n\n10\n\n4.05\n\n\n\n10->0\n\n\na\n\n\n\n11\n\nTrue\n\n\n\n11->0\n\n\ncubic\n\n\n\n12\n\nmini\n\n\n\n12->1\n\n\nworking_directory\n\n\n\n14\n\n{'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\n14->13\n\n\npseudopotentials\n\n\n\n14->20\n\n\npseudopotentials\n\n\n\n14->23\n\n\npseudopotentials\n\n\n\n14->25\n\n\npseudopotentials\n\n\n\n14->27\n\n\npseudopotentials\n\n\n\n14->29\n\n\npseudopotentials\n\n\n\n15\n\n[3, 3, 3]\n\n\n\n15->13\n\n\nkpts\n\n\n\n15->20\n\n\nkpts\n\n\n\n15->23\n\n\nkpts\n\n\n\n15->25\n\n\nkpts\n\n\n\n15->27\n\n\nkpts\n\n\n\n15->29\n\n\nkpts\n\n\n\n16\n\nvc-relax\n\n\n\n16->13\n\n\ncalculation\n\n\n\n17\n\n0.02\n\n\n\n17->13\n\n\nsmearing\n\n\n\n17->20\n\n\nsmearing\n\n\n\n17->23\n\n\nsmearing\n\n\n\n17->25\n\n\nsmearing\n\n\n\n17->27\n\n\nsmearing\n\n\n\n17->29\n\n\nsmearing\n\n\n\n18\n\n[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\n18->2\n\n\nstrain_lst\n\n\n\n19\n\nstrain_0\n\n\n\n19->3\n\n\nworking_directory\n\n\n\n21\n\nscf\n\n\n\n21->20\n\n\ncalculation\n\n\n\n21->23\n\n\ncalculation\n\n\n\n21->25\n\n\ncalculation\n\n\n\n21->27\n\n\ncalculation\n\n\n\n21->29\n\n\ncalculation\n\n\n\n22\n\nstrain_1\n\n\n\n22->4\n\n\nworking_directory\n\n\n\n24\n\nstrain_2\n\n\n\n24->5\n\n\nworking_directory\n\n\n\n26\n\nstrain_3\n\n\n\n26->6\n\n\nworking_directory\n\n\n\n28\n\nstrain_4\n\n\n\n28->7\n\n\nworking_directory\n\n\n" + "image/svg+xml": "\n\n\n\n\n0\n\nworkflow.get_bulk_structure\n\n\n\n13\n\npython_workflow_definition.shared.get_dict\n\n\n\n0->13\n\n\nstructure\n\n\n\n1\n\nworkflow.calculate_qe\n\n\n\n13->1\n\n\ninput_dict\n\n\n\n2\n\nworkflow.generate_structures\n\n\n\n1->2\n\n\nstructure=result[structure]\n\n\n\n20\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->20\n\n\nstructure=result[s_0]\n\n\n\n23\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->23\n\n\nstructure=result[s_1]\n\n\n\n25\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->25\n\n\nstructure=result[s_2]\n\n\n\n27\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->27\n\n\nstructure=result[s_3]\n\n\n\n29\n\npython_workflow_definition.shared.get_dict\n\n\n\n2->29\n\n\nstructure=result[s_4]\n\n\n\n3\n\nworkflow.calculate_qe\n\n\n\n20->3\n\n\ninput_dict\n\n\n\n4\n\nworkflow.calculate_qe\n\n\n\n23->4\n\n\ninput_dict\n\n\n\n5\n\nworkflow.calculate_qe\n\n\n\n25->5\n\n\ninput_dict\n\n\n\n6\n\nworkflow.calculate_qe\n\n\n\n27->6\n\n\ninput_dict\n\n\n\n7\n\nworkflow.calculate_qe\n\n\n\n29->7\n\n\ninput_dict\n\n\n\n30\n\npython_workflow_definition.shared.get_list\n\n\n\n3->30\n\n\n0=result[volume]\n\n\n\n31\n\npython_workflow_definition.shared.get_list\n\n\n\n3->31\n\n\n0=result[energy]\n\n\n\n8\n\nworkflow.plot_energy_volume_curve\n\n\n\n30->8\n\n\nvolume_lst\n\n\n\n31->8\n\n\nenergy_lst\n\n\n\n4->30\n\n\n1=result[volume]\n\n\n\n4->31\n\n\n1=result[energy]\n\n\n\n5->30\n\n\n2=result[volume]\n\n\n\n5->31\n\n\n2=result[energy]\n\n\n\n6->30\n\n\n3=result[volume]\n\n\n\n6->31\n\n\n3=result[energy]\n\n\n\n7->30\n\n\n4=result[volume]\n\n\n\n7->31\n\n\n4=result[energy]\n\n\n\n32\n\nresult\n\n\n\n8->32\n\n\n\n\n\n9\n\nAl\n\n\n\n9->0\n\n\nelement\n\n\n\n10\n\n4.05\n\n\n\n10->0\n\n\na\n\n\n\n11\n\nTrue\n\n\n\n11->0\n\n\ncubic\n\n\n\n12\n\nmini\n\n\n\n12->1\n\n\nworking_directory\n\n\n\n14\n\n{'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\n14->13\n\n\npseudopotentials\n\n\n\n14->20\n\n\npseudopotentials\n\n\n\n14->23\n\n\npseudopotentials\n\n\n\n14->25\n\n\npseudopotentials\n\n\n\n14->27\n\n\npseudopotentials\n\n\n\n14->29\n\n\npseudopotentials\n\n\n\n15\n\n[3, 3, 3]\n\n\n\n15->13\n\n\nkpts\n\n\n\n15->20\n\n\nkpts\n\n\n\n15->23\n\n\nkpts\n\n\n\n15->25\n\n\nkpts\n\n\n\n15->27\n\n\nkpts\n\n\n\n15->29\n\n\nkpts\n\n\n\n16\n\nvc-relax\n\n\n\n16->13\n\n\ncalculation\n\n\n\n17\n\n0.02\n\n\n\n17->13\n\n\nsmearing\n\n\n\n17->20\n\n\nsmearing\n\n\n\n17->23\n\n\nsmearing\n\n\n\n17->25\n\n\nsmearing\n\n\n\n17->27\n\n\nsmearing\n\n\n\n17->29\n\n\nsmearing\n\n\n\n18\n\n[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\n18->2\n\n\nstrain_lst\n\n\n\n19\n\nstrain_0\n\n\n\n19->3\n\n\nworking_directory\n\n\n\n21\n\nscf\n\n\n\n21->20\n\n\ncalculation\n\n\n\n21->23\n\n\ncalculation\n\n\n\n21->25\n\n\ncalculation\n\n\n\n21->27\n\n\ncalculation\n\n\n\n21->29\n\n\ncalculation\n\n\n\n22\n\nstrain_1\n\n\n\n22->4\n\n\nworking_directory\n\n\n\n24\n\nstrain_2\n\n\n\n24->5\n\n\nworking_directory\n\n\n\n26\n\nstrain_3\n\n\n\n26->6\n\n\nworking_directory\n\n\n\n28\n\nstrain_4\n\n\n\n28->7\n\n\nworking_directory\n\n\n" }, "metadata": {} } @@ -74,7 +74,7 @@ "execution_count": 3, "output_type": "execute_result", "data": { - "text/plain": "Profile" + "text/plain": "Profile" }, "metadata": {} } @@ -105,7 +105,7 @@ "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 1, - "model_id": "5af0ea14112b49749055805432385d2e" + "model_id": "ee61bd4c7d90449593a86d50e9eb6acc" } }, "metadata": {} @@ -123,7 +123,7 @@ { "name": "stderr", "output_type": "stream", - "text": "04/23/2025 09:54:08 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure1\n04/23/2025 09:54:09 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_bulk_structure1, type: PyFunction, finished.\n04/23/2025 09:54:09 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10\n04/23/2025 09:54:10 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n04/23/2025 09:54:10 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe2\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09908] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:55:03 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n04/23/2025 09:55:03 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe2, type: PyFunction, finished.\n04/23/2025 09:55:03 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures3\n04/23/2025 09:55:04 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: generate_structures3, type: PyFunction, finished.\n04/23/2025 09:55:04 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict11,get_dict12,get_dict13,get_dict14,get_dict15\n04/23/2025 09:55:05 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict11, type: PyFunction, finished.\n04/23/2025 09:55:05 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe4,get_dict12,get_dict13,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09923] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:55:16 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:55:17 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe4, type: PyFunction, finished.\n04/23/2025 09:55:17 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict13,get_dict14,get_dict15\n04/23/2025 09:55:17 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n04/23/2025 09:55:17 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe5,get_dict13,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09934] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:55:29 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:55:29 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe5, type: PyFunction, finished.\n04/23/2025 09:55:29 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict13,get_dict14,get_dict15\n04/23/2025 09:55:30 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict13, type: PyFunction, finished.\n04/23/2025 09:55:30 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6,get_dict14,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09945] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:55:42 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:55:43 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n04/23/2025 09:55:43 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict15\n04/23/2025 09:55:44 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n04/23/2025 09:55:44 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe7,get_dict15\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09957] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:55:59 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:55:59 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe7, type: PyFunction, finished.\n04/23/2025 09:55:59 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict15\n04/23/2025 09:56:00 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_dict15, type: PyFunction, finished.\n04/23/2025 09:56:00 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe8\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:09972] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n04/23/2025 09:56:17 AM <9828> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n04/23/2025 09:56:18 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: calculate_qe8, type: PyFunction, finished.\n04/23/2025 09:56:18 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list16,get_list17\n04/23/2025 09:56:19 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_list16, type: PyFunction, finished.\n04/23/2025 09:56:19 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n04/23/2025 09:56:19 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n04/23/2025 09:56:19 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve9\n04/23/2025 09:56:20 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve9, type: PyFunction, finished.\n04/23/2025 09:56:20 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/23/2025 09:56:20 AM <9828> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [327|WorkGraphEngine|finalize]: Finalize workgraph.\n" + "text": "05/24/2025 06:05:21 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_bulk_structure1\n05/24/2025 06:05:21 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_bulk_structure1, type: PyFunction, finished.\n05/24/2025 06:05:21 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict10\n05/24/2025 06:05:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict10, type: PyFunction, finished.\n05/24/2025 06:05:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe2\n[jupyter-pythonworkflow-fl--x---d7231032:10748] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:06:12 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['energy', 'volume'])\n05/24/2025 06:06:12 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe2, type: PyFunction, finished.\n05/24/2025 06:06:12 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: generate_structures3\n05/24/2025 06:06:13 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: generate_structures3, type: PyFunction, finished.\n05/24/2025 06:06:13 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict11,get_dict12,get_dict13,get_dict14,get_dict15\n05/24/2025 06:06:14 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict11, type: PyFunction, finished.\n05/24/2025 06:06:14 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe4,get_dict12,get_dict13,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10760] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:06:24 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:06:24 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe4, type: PyFunction, finished.\n05/24/2025 06:06:24 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict12,get_dict13,get_dict14,get_dict15\n05/24/2025 06:06:25 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict12, type: PyFunction, finished.\n05/24/2025 06:06:25 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe5,get_dict13,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10770] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:06:36 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:06:36 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe5, type: PyFunction, finished.\n05/24/2025 06:06:36 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict13,get_dict14,get_dict15\n05/24/2025 06:06:37 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict13, type: PyFunction, finished.\n05/24/2025 06:06:37 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe6,get_dict14,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10781] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:06:49 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:06:49 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe6, type: PyFunction, finished.\n05/24/2025 06:06:49 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict14,get_dict15\n05/24/2025 06:06:50 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict14, type: PyFunction, finished.\n05/24/2025 06:06:50 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe7,get_dict15\n[jupyter-pythonworkflow-fl--x---d7231032:10792] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:07:05 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:07:06 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe7, type: PyFunction, finished.\n05/24/2025 06:07:06 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_dict15\n05/24/2025 06:07:06 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_dict15, type: PyFunction, finished.\n05/24/2025 06:07:06 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: calculate_qe8\n[jupyter-pythonworkflow-fl--x---d7231032:10804] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n05/24/2025 06:07:21 AM <10674> aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode: [WARNING] Found extra results that are not included in the output: dict_keys(['structure'])\n05/24/2025 06:07:21 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: calculate_qe8, type: PyFunction, finished.\n05/24/2025 06:07:21 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list16,get_list17\n05/24/2025 06:07:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_list16, type: PyFunction, finished.\n05/24/2025 06:07:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: get_list17\n05/24/2025 06:07:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: get_list17, type: PyFunction, finished.\n05/24/2025 06:07:22 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: plot_energy_volume_curve9\n05/24/2025 06:07:23 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|update_task_state]: Task: plot_energy_volume_curve9, type: PyFunction, finished.\n05/24/2025 06:07:23 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n05/24/2025 06:07:23 AM <10674> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [342|WorkGraphEngine|finalize]: Finalize workgraph.\n" }, { "output_type": "display_data", @@ -161,10 +161,7 @@ }, { "cell_type": "code", - "source": [ - "with SingleNodeExecutor(max_workers=1) as exe:\n", - " result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()" - ], + "source": "with SingleNodeExecutor(max_workers=1) as exe:\n result = load_workflow_json(file_name=\"workflow.json\", exe=exe).result()", "metadata": { "trusted": true }, @@ -172,7 +169,7 @@ { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:10149] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:10867] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:10938] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11002] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11066] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11130] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:10932] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:11164] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:11230] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:11301] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:11367] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:11433] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" } ], "execution_count": 9 @@ -197,13 +194,7 @@ "metadata": { "trusted": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n" - } - ], + "outputs": [], "execution_count": 11 }, { @@ -234,67 +225,67 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 09:59:48,753 INFO Started executing jobs locally\n2025-04-23 09:59:48,761 INFO Starting job - get_bulk_structure (35ed74db-cf3f-4c0f-99bd-a7ff1db0d988)\n2025-04-23 09:59:48,764 INFO Finished job - get_bulk_structure (35ed74db-cf3f-4c0f-99bd-a7ff1db0d988)\n2025-04-23 09:59:48,764 INFO Starting job - get_dict (7774021f-6e06-4c7f-92a9-46955c99ecd4)\n2025-04-23 09:59:48,767 INFO Finished job - get_dict (7774021f-6e06-4c7f-92a9-46955c99ecd4)\n2025-04-23 09:59:48,767 INFO Starting job - calculate_qe (61858f11-6889-471c-8c11-dcb40ddb9fc5)\n" + "text": "2025-05-24 06:11:19,085 INFO Started executing jobs locally\n2025-05-24 06:11:19,088 INFO Starting job - get_bulk_structure (13fb19e6-ff0a-4b2e-9cdd-391f43580ede)\n2025-05-24 06:11:19,091 INFO Finished job - get_bulk_structure (13fb19e6-ff0a-4b2e-9cdd-391f43580ede)\n2025-05-24 06:11:19,091 INFO Starting job - get_dict (9d93f23c-2f31-4943-95eb-c30d527e0a7c)\n2025-05-24 06:11:19,093 INFO Finished job - get_dict (9d93f23c-2f31-4943-95eb-c30d527e0a7c)\n2025-05-24 06:11:19,093 INFO Starting job - calculate_qe (031ec4f2-37b7-4837-941d-943eb1a3a36f)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11842] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12088] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:00:38,712 INFO Finished job - calculate_qe (61858f11-6889-471c-8c11-dcb40ddb9fc5)\n2025-04-23 10:00:38,713 INFO Starting job - generate_structures (6677baf4-a206-48d3-ac40-1553c1978514)\n2025-04-23 10:00:38,717 INFO Finished job - generate_structures (6677baf4-a206-48d3-ac40-1553c1978514)\n2025-04-23 10:00:38,718 INFO Starting job - get_dict (e08257f2-54ce-417e-9d4a-3be382e98632)\n2025-04-23 10:00:38,719 INFO Finished job - get_dict (e08257f2-54ce-417e-9d4a-3be382e98632)\n2025-04-23 10:00:38,720 INFO Starting job - get_dict (09257370-ee8d-4fb4-b1df-c68470f77d6e)\n2025-04-23 10:00:38,721 INFO Finished job - get_dict (09257370-ee8d-4fb4-b1df-c68470f77d6e)\n2025-04-23 10:00:38,721 INFO Starting job - get_dict (f54bd010-a381-4fb9-a6a2-327603f25c6c)\n2025-04-23 10:00:38,723 INFO Finished job - get_dict (f54bd010-a381-4fb9-a6a2-327603f25c6c)\n2025-04-23 10:00:38,723 INFO Starting job - get_dict (a7796fe7-6fa9-46ff-938c-747a1216db5a)\n2025-04-23 10:00:38,724 INFO Finished job - get_dict (a7796fe7-6fa9-46ff-938c-747a1216db5a)\n2025-04-23 10:00:38,725 INFO Starting job - get_dict (51a90fa6-a6fc-458e-9039-ccc9dcfb55db)\n2025-04-23 10:00:38,726 INFO Finished job - get_dict (51a90fa6-a6fc-458e-9039-ccc9dcfb55db)\n2025-04-23 10:00:38,726 INFO Starting job - calculate_qe (0060409e-3f07-4950-a306-f4b2b5e19fde)\n" + "text": "2025-05-24 06:12:09,004 INFO Finished job - calculate_qe (031ec4f2-37b7-4837-941d-943eb1a3a36f)\n2025-05-24 06:12:09,005 INFO Starting job - generate_structures (c26bc0f8-4833-4913-ae54-676004a2cee5)\n2025-05-24 06:12:09,009 INFO Finished job - generate_structures (c26bc0f8-4833-4913-ae54-676004a2cee5)\n2025-05-24 06:12:09,009 INFO Starting job - get_dict (d68d9722-53d8-489e-b3dd-831637c677ce)\n2025-05-24 06:12:09,011 INFO Finished job - get_dict (d68d9722-53d8-489e-b3dd-831637c677ce)\n2025-05-24 06:12:09,011 INFO Starting job - get_dict (a2a5e5ca-2862-48d4-a3d2-3090bc48ee44)\n2025-05-24 06:12:09,013 INFO Finished job - get_dict (a2a5e5ca-2862-48d4-a3d2-3090bc48ee44)\n2025-05-24 06:12:09,014 INFO Starting job - get_dict (752bccfa-8200-4fee-bcae-799506e75b3f)\n2025-05-24 06:12:09,015 INFO Finished job - get_dict (752bccfa-8200-4fee-bcae-799506e75b3f)\n2025-05-24 06:12:09,016 INFO Starting job - get_dict (8f26bac2-370b-431a-8e67-16205b118a8e)\n2025-05-24 06:12:09,017 INFO Finished job - get_dict (8f26bac2-370b-431a-8e67-16205b118a8e)\n2025-05-24 06:12:09,018 INFO Starting job - get_dict (86078da3-b1d1-47e5-98b6-666c8d1c925f)\n2025-05-24 06:12:09,019 INFO Finished job - get_dict (86078da3-b1d1-47e5-98b6-666c8d1c925f)\n2025-05-24 06:12:09,020 INFO Starting job - calculate_qe (8bf26748-191f-48c0-b55a-3c00dc23cbd4)\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11856] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12101] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:00:49,710 INFO Finished job - calculate_qe (0060409e-3f07-4950-a306-f4b2b5e19fde)\n2025-04-23 10:00:49,711 INFO Starting job - calculate_qe (d40b5716-3dee-4eb6-9c82-5335f13e2ed5)\n" + "text": "2025-05-24 06:12:19,833 INFO Finished job - calculate_qe (8bf26748-191f-48c0-b55a-3c00dc23cbd4)\n2025-05-24 06:12:19,834 INFO Starting job - calculate_qe (e248cdb3-3984-4c9e-8ed9-2d8ea4d0053b)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11866] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12111] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:01:00,507 INFO Finished job - calculate_qe (d40b5716-3dee-4eb6-9c82-5335f13e2ed5)\n2025-04-23 10:01:00,508 INFO Starting job - calculate_qe (ca9b7260-0409-45d0-b0a5-cd07b9e34fff)\n" + "text": "2025-05-24 06:12:30,295 INFO Finished job - calculate_qe (e248cdb3-3984-4c9e-8ed9-2d8ea4d0053b)\n2025-05-24 06:12:30,296 INFO Starting job - calculate_qe (b99732df-2c29-471a-a9dd-b43cf0765295)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11876] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12121] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:01:14,075 INFO Finished job - calculate_qe (ca9b7260-0409-45d0-b0a5-cd07b9e34fff)\n2025-04-23 10:01:14,076 INFO Starting job - calculate_qe (7ef9bf5f-2ca4-4005-8389-9cc19488c6ba)\n" + "text": "2025-05-24 06:12:42,189 INFO Finished job - calculate_qe (b99732df-2c29-471a-a9dd-b43cf0765295)\n2025-05-24 06:12:42,189 INFO Starting job - calculate_qe (5316d29c-cdf2-4a43-934d-02518422acf5)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11886] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12131] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:01:28,946 INFO Finished job - calculate_qe (7ef9bf5f-2ca4-4005-8389-9cc19488c6ba)\n2025-04-23 10:01:28,951 INFO Starting job - calculate_qe (223364ac-72f3-4a33-848e-bd19d97d5d03)\n" + "text": "2025-05-24 06:12:55,607 INFO Finished job - calculate_qe (5316d29c-cdf2-4a43-934d-02518422acf5)\n2025-05-24 06:12:55,608 INFO Starting job - calculate_qe (dc161c3a-22d0-456d-9a79-bc0126f7296b)\n" }, { "name": "stderr", "output_type": "stream", - "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11896] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" + "text": "Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12141] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n" }, { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:01:44,264 INFO Finished job - calculate_qe (223364ac-72f3-4a33-848e-bd19d97d5d03)\n2025-04-23 10:01:44,265 INFO Starting job - get_list (2154d54f-07fe-487a-aca2-fa00d90f90a4)\n2025-04-23 10:01:44,269 INFO Finished job - get_list (2154d54f-07fe-487a-aca2-fa00d90f90a4)\n2025-04-23 10:01:44,269 INFO Starting job - get_list (1d4c09d5-7f97-4496-8cfd-1ec336c467d8)\n2025-04-23 10:01:44,274 INFO Finished job - get_list (1d4c09d5-7f97-4496-8cfd-1ec336c467d8)\n2025-04-23 10:01:44,275 INFO Starting job - plot_energy_volume_curve (43ed7824-5c9c-46f4-96fd-e6bc56809e5b)\n" + "text": "2025-05-24 06:13:09,051 INFO Finished job - calculate_qe (dc161c3a-22d0-456d-9a79-bc0126f7296b)\n2025-05-24 06:13:09,052 INFO Starting job - get_list (a23aaea4-d7dc-4223-bedc-213cbf38f436)\n2025-05-24 06:13:09,054 INFO Finished job - get_list (a23aaea4-d7dc-4223-bedc-213cbf38f436)\n2025-05-24 06:13:09,055 INFO Starting job - get_list (09e90050-8621-403e-8f78-c50a7180f23c)\n2025-05-24 06:13:09,057 INFO Finished job - get_list (09e90050-8621-403e-8f78-c50a7180f23c)\n2025-05-24 06:13:09,058 INFO Starting job - plot_energy_volume_curve (1e007ae5-e596-4e71-baa0-7ac7a604a5fd)\n" }, { "name": "stderr", @@ -304,13 +295,13 @@ { "name": "stdout", "output_type": "stream", - "text": "2025-04-23 10:01:44,359 INFO Finished job - plot_energy_volume_curve (43ed7824-5c9c-46f4-96fd-e6bc56809e5b)\n2025-04-23 10:01:44,360 INFO Finished executing jobs locally\n" + "text": "2025-05-24 06:13:09,114 INFO Finished job - plot_energy_volume_curve (1e007ae5-e596-4e71-baa0-7ac7a604a5fd)\n2025-05-24 06:13:09,115 INFO Finished executing jobs locally\n" }, { "execution_count": 14, "output_type": "execute_result", "data": { - "text/plain": "{'35ed74db-cf3f-4c0f-99bd-a7ff1db0d988': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '7774021f-6e06-4c7f-92a9-46955c99ecd4': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'vc-relax', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '61858f11-6889-471c-8c11-dcb40ddb9fc5': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946779, 0.0, 0.0], [0.0, 4.045637215946779, 0.0], [0.0, 0.0, 4.045637215946779]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079733894, 2.0228186079733894], [2.0228186079733894, 0.0, 2.0228186079733894], [2.0228186079733894, 2.0228186079733894, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365262253605, 'volume': 66.21567448235946}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '6677baf4-a206-48d3-ac40-1553c1978514': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859620884, 0.0, 0.0], [0.0, 3.9060197859620884, 0.0], [0.0, 0.0, 3.9060197859620884]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810442, 1.9530098929810442], [1.9530098929810442, 0.0, 1.9530098929810442], [1.9530098929810442, 1.9530098929810442, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844317988, 0.0, 0.0], [0.0, 3.977053844317988, 0.0], [0.0, 0.0, 3.977053844317988]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221589943, 1.9885269221589943], [1.9885269221589943, 0.0, 1.9885269221589943], [1.9885269221589943, 1.9885269221589943, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946779, 0.0, 0.0], [0.0, 4.045637215946779, 0.0], [0.0, 0.0, 4.045637215946779]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079733894, 2.0228186079733894], [2.0228186079733894, 0.0, 2.0228186079733894], [2.0228186079733894, 2.0228186079733894, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282893, 0.0, 0.0], [0.0, 4.111970927282893, 0.0], [0.0, 0.0, 4.111970927282893]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414463, 2.0559854636414463], [2.0559854636414463, 0.0, 2.0559854636414463], [2.0559854636414463, 2.0559854636414463, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372117, 0.0, 0.0], [0.0, 4.176230852372117, 0.0], [0.0, 0.0, 4.176230852372117]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860586, 2.0881154261860586], [2.0881154261860586, 0.0, 2.0881154261860586], [2.0881154261860586, 2.0881154261860586, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'e08257f2-54ce-417e-9d4a-3be382e98632': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9060197859620884, 0.0, 0.0], [0.0, 3.9060197859620884, 0.0], [0.0, 0.0, 3.9060197859620884]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098929810442, 1.9530098929810442], [1.9530098929810442, 0.0, 1.9530098929810442], [1.9530098929810442, 1.9530098929810442, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '09257370-ee8d-4fb4-b1df-c68470f77d6e': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.977053844317988, 0.0, 0.0], [0.0, 3.977053844317988, 0.0], [0.0, 0.0, 3.977053844317988]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221589943, 1.9885269221589943], [1.9885269221589943, 0.0, 1.9885269221589943], [1.9885269221589943, 1.9885269221589943, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'f54bd010-a381-4fb9-a6a2-327603f25c6c': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215946779, 0.0, 0.0], [0.0, 4.045637215946779, 0.0], [0.0, 0.0, 4.045637215946779]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079733894, 2.0228186079733894], [2.0228186079733894, 0.0, 2.0228186079733894], [2.0228186079733894, 2.0228186079733894, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'a7796fe7-6fa9-46ff-938c-747a1216db5a': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927282893, 0.0, 0.0], [0.0, 4.111970927282893, 0.0], [0.0, 0.0, 4.111970927282893]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636414463, 2.0559854636414463], [2.0559854636414463, 0.0, 2.0559854636414463], [2.0559854636414463, 2.0559854636414463, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '51a90fa6-a6fc-458e-9039-ccc9dcfb55db': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372117, 0.0, 0.0], [0.0, 4.176230852372117, 0.0], [0.0, 0.0, 4.176230852372117]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261860586, 2.0881154261860586], [2.0881154261860586, 0.0, 2.0881154261860586], [2.0881154261860586, 2.0881154261860586, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '0060409e-3f07-4950-a306-f4b2b5e19fde': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019768889126, 0.0, 0.0], [0.0, 3.906019768889126, 0.0], [0.0, 0.0, 3.906019768889126]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8457446150614, 'volume': 59.59410625267737}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'd40b5716-3dee-4eb6-9c82-5335f13e2ed5': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538269345397, 0.0, 0.0], [0.0, 3.9770538269345397, 0.0], [0.0, 0.0, 3.9770538269345397]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082746, 1.9885269135082746], [1.9885269135082746, 0.0, 1.9885269135082746], [1.9885269135082746, 1.9885269135082746, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9161488594598, 'volume': 62.90488993338167}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'ca9b7260-0409-45d0-b0a5-cd07b9e34fff': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263556, 0.0, 0.0], [0.0, 4.045637198263556, 0.0], [0.0, 0.0, 4.045637198263556]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583882, 2.0228185991583882], [2.0228185991583882, 0.0, 2.0228185991583882], [2.0228185991583882, 2.0228185991583882, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365241668365, 'volume': 66.21567361408594}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '7ef9bf5f-2ca4-4005-8389-9cc19488c6ba': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309726, 0.0, 0.0], [0.0, 4.111970909309726, 0.0], [0.0, 0.0, 4.111970909309726]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025814, 'volume': 69.52645729479006}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '223364ac-72f3-4a33-848e-bd19d97d5d03': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411808, 0.0, 0.0], [0.0, 4.17623083411808, 0.0], [0.0, 0.0, 4.17623083411808]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.08811541707298, 2.08811541707298], [2.08811541707298, 0.0, 2.08811541707298], [2.08811541707298, 2.08811541707298, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8737904693435, 'volume': 72.83724097549467}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '2154d54f-07fe-487a-aca2-fa00d90f90a4': {1: Response(output=[59.59410625267737, 62.90488993338167, 66.21567361408594, 69.52645729479006, 72.83724097549467], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '1d4c09d5-7f97-4496-8cfd-1ec336c467d8': {1: Response(output=[-1074.8457446150614, -1074.9161488594598, -1074.9365241668365, -1074.9192860025814, -1074.8737904693435], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '43ed7824-5c9c-46f4-96fd-e6bc56809e5b': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}" + "text/plain": "{'13fb19e6-ff0a-4b2e-9cdd-391f43580ede': {1: Response(output='{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '9d93f23c-2f31-4943-95eb-c30d527e0a7c': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'vc-relax', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '031ec4f2-37b7-4837-941d-943eb1a3a36f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215947026, 0.0, 0.0], [0.0, 4.045637215947026, 0.0], [0.0, 0.0, 4.045637215947025]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079735124, 2.0228186079735124], [2.0228186079735124, 0.0, 2.0228186079735124], [2.0228186079735124, 2.0228186079735124, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365262253532, 'volume': 66.21567448237158}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'c26bc0f8-4833-4913-ae54-676004a2cee5': {1: Response(output={'s_0': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019785962327, 0.0, 0.0], [0.0, 3.906019785962327, 0.0], [0.0, 0.0, 3.906019785962326]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981163, 1.9530098929811628], [1.953009892981163, 0.0, 1.9530098929811628], [1.953009892981163, 1.953009892981163, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_1': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443182306, 0.0, 0.0], [0.0, 3.9770538443182306, 0.0], [0.0, 0.0, 3.9770538443182297]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221591149, 1.9885269221591149], [1.9885269221591149, 0.0, 1.9885269221591149], [1.9885269221591149, 1.9885269221591149, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_2': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215947026, 0.0, 0.0], [0.0, 4.045637215947026, 0.0], [0.0, 0.0, 4.045637215947025]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079735124, 2.0228186079735124], [2.0228186079735124, 0.0, 2.0228186079735124], [2.0228186079735124, 2.0228186079735124, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_3': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927283144, 0.0, 0.0], [0.0, 4.111970927283144, 0.0], [0.0, 0.0, 4.111970927283143]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636415715, 2.0559854636415715], [2.0559854636415715, 0.0, 2.0559854636415715], [2.0559854636415715, 2.0559854636415715, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 's_4': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372372, 0.0, 0.0], [0.0, 4.176230852372372, 0.0], [0.0, 0.0, 4.176230852372371]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261861856, 2.0881154261861856], [2.0881154261861856, 0.0, 2.0881154261861856], [2.0881154261861856, 2.0881154261861856, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}'}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'd68d9722-53d8-489e-b3dd-831637c677ce': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019785962327, 0.0, 0.0], [0.0, 3.906019785962327, 0.0], [0.0, 0.0, 3.906019785962326]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.953009892981163, 1.9530098929811628], [1.953009892981163, 0.0, 1.9530098929811628], [1.953009892981163, 1.953009892981163, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'a2a5e5ca-2862-48d4-a3d2-3090bc48ee44': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.9770538443182306, 0.0, 0.0], [0.0, 3.9770538443182306, 0.0], [0.0, 0.0, 3.9770538443182297]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269221591149, 1.9885269221591149], [1.9885269221591149, 0.0, 1.9885269221591149], [1.9885269221591149, 1.9885269221591149, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '752bccfa-8200-4fee-bcae-799506e75b3f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637215947026, 0.0, 0.0], [0.0, 4.045637215947026, 0.0], [0.0, 0.0, 4.045637215947025]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228186079735124, 2.0228186079735124], [2.0228186079735124, 0.0, 2.0228186079735124], [2.0228186079735124, 2.0228186079735124, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '8f26bac2-370b-431a-8e67-16205b118a8e': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970927283144, 0.0, 0.0], [0.0, 4.111970927283144, 0.0], [0.0, 0.0, 4.111970927283143]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854636415715, 2.0559854636415715], [2.0559854636415715, 0.0, 2.0559854636415715], [2.0559854636415715, 2.0559854636415715, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '86078da3-b1d1-47e5-98b6-666c8d1c925f': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.176230852372372, 0.0, 0.0], [0.0, 4.176230852372372, 0.0], [0.0, 0.0, 4.176230852372371]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0881154261861856, 2.0881154261861856], [2.0881154261861856, 0.0, 2.0881154261861856], [2.0881154261861856, 2.0881154261861856, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'pseudopotentials': {'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}, 'kpts': [3, 3, 3], 'calculation': 'scf', 'smearing': 0.02}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '8bf26748-191f-48c0-b55a-3c00dc23cbd4': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.906019768889365, 0.0, 0.0], [0.0, 3.906019768889365, 0.0], [0.0, 0.0, 3.906019768889365]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9530098844635175, 1.9530098844635175], [1.9530098844635175, 0.0, 1.9530098844635175], [1.9530098844635175, 1.9530098844635175, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8457446150635, 'volume': 59.594106252688384}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'e248cdb3-3984-4c9e-8ed9-2d8ea4d0053b': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[3.97705382693478, 0.0, 0.0], [0.0, 3.97705382693478, 0.0], [0.0, 0.0, 3.97705382693478]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 1.9885269135082746, 1.9885269135082746], [1.9885269135082746, 0.0, 1.9885269135082746], [1.9885269135082746, 1.9885269135082746, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.916148859456, 'volume': 62.90488993339307}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'b99732df-2c29-471a-a9dd-b43cf0765295': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.045637198263806, 0.0, 0.0], [0.0, 4.045637198263806, 0.0], [0.0, 0.0, 4.045637198263797]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0228185991583887, 2.0228185991583887], [2.0228185991583887, 0.0, 2.0228185991583887], [2.0228185991583887, 2.0228185991583887, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9365241668336, 'volume': 66.21567361409807}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '5316d29c-cdf2-4a43-934d-02518422acf5': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.111970909309976, 0.0, 0.0], [0.0, 4.111970909309976, 0.0], [0.0, 0.0, 4.111970909309976]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.0559854546134178, 2.0559854546134178], [2.0559854546134178, 0.0, 2.0559854546134178], [2.0559854546134178, 2.0559854546134178, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.9192860025798, 'volume': 69.52645729480278}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'dc161c3a-22d0-456d-9a79-bc0126f7296b': {1: Response(output={'structure': '{\"immutable_id\": null, \"last_modified\": null, \"elements\": [\"Al\"], \"nelements\": 1, \"elements_ratios\": [1.0], \"chemical_formula_descriptive\": \"Al4\", \"chemical_formula_reduced\": \"Al\", \"chemical_formula_hill\": null, \"chemical_formula_anonymous\": \"A\", \"dimension_types\": [1, 1, 1], \"nperiodic_dimensions\": 3, \"lattice_vectors\": [[4.17623083411833, 0.0, 0.0], [0.0, 4.17623083411833, 0.0], [0.0, 0.0, 4.17623083411833]], \"space_group_symmetry_operations_xyz\": null, \"space_group_symbol_hall\": null, \"space_group_symbol_hermann_mauguin\": null, \"space_group_symbol_hermann_mauguin_extended\": null, \"space_group_it_number\": null, \"cartesian_site_positions\": [[0.0, 0.0, 0.0], [0.0, 2.08811541707298, 2.08811541707298], [2.08811541707298, 0.0, 2.08811541707298], [2.08811541707298, 2.08811541707298, 0.0]], \"nsites\": 4, \"species\": [{\"name\": \"Al\", \"chemical_symbols\": [\"Al\"], \"concentration\": [1.0], \"mass\": null, \"original_name\": null, \"attached\": null, \"nattached\": null}], \"species_at_sites\": [\"Al\", \"Al\", \"Al\", \"Al\"], \"assemblies\": null, \"structure_features\": []}', 'energy': -1074.8737904693403, 'volume': 72.8372409755078}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n 'a23aaea4-d7dc-4223-bedc-213cbf38f436': {1: Response(output=[59.594106252688384, 62.90488993339307, 66.21567361409807, 69.52645729480278, 72.8372409755078], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '09e90050-8621-403e-8f78-c50a7180f23c': {1: Response(output=[-1074.8457446150635, -1074.916148859456, -1074.9365241668336, -1074.9192860025798, -1074.8737904693403], detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))},\n '1e007ae5-e596-4e71-baa0-7ac7a604a5fd': {1: Response(output=None, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan/example_workflows/quantum_espresso'))}}" }, "metadata": {} }, @@ -341,10 +332,7 @@ }, { "cell_type": "code", - "source": [ - "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\n", - "delayed_object_lst[-1].draw()" - ], + "source": "delayed_object_lst = load_workflow_json(file_name=\"workflow.json\")\ndelayed_object_lst[-1].draw()", "metadata": { "trusted": true }, @@ -353,7 +341,7 @@ "output_type": "display_data", "data": { "text/plain": "", - "image/svg+xml": "\n\n\n\n\ncreate_function_job_985eb2c5b23ed5677690754a7d6b54b0\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaaf30>\n\n\n\nvolume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa94f0>\n\n\n\nvolume_lst_b5f2fd1e32e4e01ea2626029ed68b478->create_function_job_985eb2c5b23ed5677690754a7d6b54b0\n\n\n\n\n\n0_cfd4cf6c1025f44cf76a26492950ed54\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9970>\n\n\n\n0_cfd4cf6c1025f44cf76a26492950ed54->volume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_cfd4cf6c1025f44cf76a26492950ed54\n\n\n\n\n\n0_cc627152090a464ac0fcf4a27e06bbb5\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baab710>\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_cc627152090a464ac0fcf4a27e06bbb5\n\n\n\n\n\nenergy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa89b0>\n\n\n\n0_cc627152090a464ac0fcf4a27e06bbb5->energy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\n\n\n\n\ninput_dict_0c62beeaf41ac41d9f675982e41165f1\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa8ce0>\n\n\n\ninput_dict_0c62beeaf41ac41d9f675982e41165f1->0_cfd4cf6c1025f44cf76a26492950ed54\n\n\n\n\n\ninput_dict_0c62beeaf41ac41d9f675982e41165f1->0_cc627152090a464ac0fcf4a27e06bbb5\n\n\n\n\n\nstructure_df04e4d893c5690957f89611b7345b28\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9be0>\n\n\n\nstructure_df04e4d893c5690957f89611b7345b28->input_dict_0c62beeaf41ac41d9f675982e41165f1\n\n\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa8fe0>\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8->structure_df04e4d893c5690957f89611b7345b28\n\n\n\n\n\nstructure_2b7ddbcc5cb639c73affda9ede67dec5\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9f70>\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8->structure_2b7ddbcc5cb639c73affda9ede67dec5\n\n\n\n\n\nstructure_aa5ccf55b0a0454daa8ad56aaa4c1b75\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaa570>\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8->structure_aa5ccf55b0a0454daa8ad56aaa4c1b75\n\n\n\n\n\nstructure_8cca8f18cbbe5fb77bb757dffc3ae643\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaa5d0>\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8->structure_8cca8f18cbbe5fb77bb757dffc3ae643\n\n\n\n\n\nstructure_b84beabc3985a89fc046a65b9a67e983\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaa8d0>\n\n\n\nstructure_140732db3f49342de208b33a5c1eaaa8->structure_b84beabc3985a89fc046a65b9a67e983\n\n\n\n\n\ninput_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9af0>\n\n\n\nstructure_2b7ddbcc5cb639c73affda9ede67dec5->input_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\n\n\n\n\ninput_dict_14cfa30c74c4da7397c159da09a99d0f\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9eb0>\n\n\n\nstructure_aa5ccf55b0a0454daa8ad56aaa4c1b75->input_dict_14cfa30c74c4da7397c159da09a99d0f\n\n\n\n\n\ninput_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaa5a0>\n\n\n\nstructure_8cca8f18cbbe5fb77bb757dffc3ae643->input_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\n\n\n\n\ninput_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaac00>\n\n\n\nstructure_b84beabc3985a89fc046a65b9a67e983->input_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_140732db3f49342de208b33a5c1eaaa8\n\n\n\n\n\ninput_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baab170>\n\n\n\ninput_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17->structure_140732db3f49342de208b33a5c1eaaa8\n\n\n\n\n\nstructure_282f0db80018c1bdf8d2119a70f01182\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9880>\n\n\n\nstructure_282f0db80018c1bdf8d2119a70f01182->input_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_282f0db80018c1bdf8d2119a70f01182\n\n\n\n\n\na_aea0574e321c6f75f923c059730e9537\n\na=4.05\n\n\n\na_aea0574e321c6f75f923c059730e9537->structure_282f0db80018c1bdf8d2119a70f01182\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_282f0db80018c1bdf8d2119a70f01182\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_0c62beeaf41ac41d9f675982e41165f1\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_14cfa30c74c4da7397c159da09a99d0f\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\n\n\n\n\n1_081d0cbb5f75d5202dfdffa9d67c3b22\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa8980>\n\n\n\ninput_dict_2380e4d6d0edfa808bc57fcfeec4447f->1_081d0cbb5f75d5202dfdffa9d67c3b22\n\n\n\n\n\n1_5bd086346009762990f93ec30f88dcd7\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baab6e0>\n\n\n\ninput_dict_2380e4d6d0edfa808bc57fcfeec4447f->1_5bd086346009762990f93ec30f88dcd7\n\n\n\n\n\n2_146e8d22689b52e89f9c92b365734f80\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa82c0>\n\n\n\ninput_dict_14cfa30c74c4da7397c159da09a99d0f->2_146e8d22689b52e89f9c92b365734f80\n\n\n\n\n\n2_323db0344dea52dc7aae9026884bb4bf\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaba40>\n\n\n\ninput_dict_14cfa30c74c4da7397c159da09a99d0f->2_323db0344dea52dc7aae9026884bb4bf\n\n\n\n\n\n3_c95ed4f75c0e100499869a1c2682a919\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa9df0>\n\n\n\ninput_dict_c307ef11e5f328f32eeaa1bbe51c4de9->3_c95ed4f75c0e100499869a1c2682a919\n\n\n\n\n\n3_ae3c4c3451f55bb975d471c4a248a4bc\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baa80b0>\n\n\n\ninput_dict_c307ef11e5f328f32eeaa1bbe51c4de9->3_ae3c4c3451f55bb975d471c4a248a4bc\n\n\n\n\n\n4_b7507f656125f365dc5dfea1575f24e8\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baaa390>\n\n\n\ninput_dict_36a7fa9f3c0b6814f4ae6120416e2c1d->4_b7507f656125f365dc5dfea1575f24e8\n\n\n\n\n\n4_c6fc275eedc1dad3222d092b24c3382c\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x72c31baabc50>\n\n\n\ninput_dict_36a7fa9f3c0b6814f4ae6120416e2c1d->4_c6fc275eedc1dad3222d092b24c3382c\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_0c62beeaf41ac41d9f675982e41165f1\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_14cfa30c74c4da7397c159da09a99d0f\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_0c62beeaf41ac41d9f675982e41165f1\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_2929e5a6d1a8b6c0a02d6fb9fd7cec17\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_14cfa30c74c4da7397c159da09a99d0f\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781\n\nstrain_lst=[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_df04e4d893c5690957f89611b7345b28\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_2b7ddbcc5cb639c73affda9ede67dec5\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_aa5ccf55b0a0454daa8ad56aaa4c1b75\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_8cca8f18cbbe5fb77bb757dffc3ae643\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_b84beabc3985a89fc046a65b9a67e983\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_0c62beeaf41ac41d9f675982e41165f1\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_2380e4d6d0edfa808bc57fcfeec4447f\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_14cfa30c74c4da7397c159da09a99d0f\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_c307ef11e5f328f32eeaa1bbe51c4de9\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_36a7fa9f3c0b6814f4ae6120416e2c1d\n\n\n\n\n\n1_081d0cbb5f75d5202dfdffa9d67c3b22->volume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_081d0cbb5f75d5202dfdffa9d67c3b22\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_5bd086346009762990f93ec30f88dcd7\n\n\n\n\n\n1_5bd086346009762990f93ec30f88dcd7->energy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\n\n\n\n\n2_146e8d22689b52e89f9c92b365734f80->volume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_146e8d22689b52e89f9c92b365734f80\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_323db0344dea52dc7aae9026884bb4bf\n\n\n\n\n\n2_323db0344dea52dc7aae9026884bb4bf->energy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\n\n\n\n\n3_c95ed4f75c0e100499869a1c2682a919->volume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_c95ed4f75c0e100499869a1c2682a919\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_ae3c4c3451f55bb975d471c4a248a4bc\n\n\n\n\n\n3_ae3c4c3451f55bb975d471c4a248a4bc->energy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\n\n\n\n\n4_b7507f656125f365dc5dfea1575f24e8->volume_lst_b5f2fd1e32e4e01ea2626029ed68b478\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_b7507f656125f365dc5dfea1575f24e8\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_c6fc275eedc1dad3222d092b24c3382c\n\n\n\n\n\n4_c6fc275eedc1dad3222d092b24c3382c->energy_lst_15dd456e7182ea1aeeb3eb8a96e8d855\n\n\n\n\n\nenergy_lst_15dd456e7182ea1aeeb3eb8a96e8d855->create_function_job_985eb2c5b23ed5677690754a7d6b54b0\n\n\n\n\n" + "image/svg+xml": "\n\n\n\n\ncreate_function_job_9adf79b116ef7d1bd6234b8bd3fb8790\n\ncreate_function_job=<pyiron_base.project.delayed.DelayedObject object at 0x768578177f50>\n\n\n\nvolume_lst_9ecc37695722ff26a909e7df66fad761\n\nvolume_lst=<pyiron_base.project.delayed.DelayedObject object at 0x768578177ec0>\n\n\n\nvolume_lst_9ecc37695722ff26a909e7df66fad761->create_function_job_9adf79b116ef7d1bd6234b8bd3fb8790\n\n\n\n\n\n0_9ec2b766eb40591013f27b281c10fdf6\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x7685781761e0>\n\n\n\n0_9ec2b766eb40591013f27b281c10fdf6->volume_lst_9ecc37695722ff26a909e7df66fad761\n\n\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add\n\nworking_directory=strain_0\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_9ec2b766eb40591013f27b281c10fdf6\n\n\n\n\n\n0_2ee29abc84e19e2a89c493d954bca047\n\n0=<pyiron_base.project.delayed.DelayedObject object at 0x768578177470>\n\n\n\nworking_directory_2e9abb255f1a31f7d29b4451ad422add->0_2ee29abc84e19e2a89c493d954bca047\n\n\n\n\n\nenergy_lst_d41078de6fda3484043c8f3407845d97\n\nenergy_lst=<pyiron_base.project.delayed.DelayedObject object at 0x768578176240>\n\n\n\n0_2ee29abc84e19e2a89c493d954bca047->energy_lst_d41078de6fda3484043c8f3407845d97\n\n\n\n\n\ninput_dict_87f4e1381ab79d513e7ddd2deecdd386\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7685781773b0>\n\n\n\ninput_dict_87f4e1381ab79d513e7ddd2deecdd386->0_9ec2b766eb40591013f27b281c10fdf6\n\n\n\n\n\ninput_dict_87f4e1381ab79d513e7ddd2deecdd386->0_2ee29abc84e19e2a89c493d954bca047\n\n\n\n\n\nstructure_24283480cde4a82cb11a95ad8315004b\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7685781770b0>\n\n\n\nstructure_24283480cde4a82cb11a95ad8315004b->input_dict_87f4e1381ab79d513e7ddd2deecdd386\n\n\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x7685780d7170>\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6->structure_24283480cde4a82cb11a95ad8315004b\n\n\n\n\n\nstructure_02eea1a3dae4b8a2111c575ca7b757e4\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x768578176db0>\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6->structure_02eea1a3dae4b8a2111c575ca7b757e4\n\n\n\n\n\nstructure_f70fbf61dbacde3f86dbc99a31f544d6\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x768578176a80>\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6->structure_f70fbf61dbacde3f86dbc99a31f544d6\n\n\n\n\n\nstructure_5bb5ba75f27ad166411ec7f96a67d795\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x768578176750>\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6->structure_5bb5ba75f27ad166411ec7f96a67d795\n\n\n\n\n\nstructure_2a68a68e8c70db7870ac8e42f8b1865d\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x768578176420>\n\n\n\nstructure_199228a058c6c2abd4059cca704f33e6->structure_2a68a68e8c70db7870ac8e42f8b1865d\n\n\n\n\n\ninput_dict_adda488913baad1684ada5811fc1bf07\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x768578177020>\n\n\n\nstructure_02eea1a3dae4b8a2111c575ca7b757e4->input_dict_adda488913baad1684ada5811fc1bf07\n\n\n\n\n\ninput_dict_d5e1009e9a3698a7a581d7920d3308ba\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x768578176d20>\n\n\n\nstructure_f70fbf61dbacde3f86dbc99a31f544d6->input_dict_d5e1009e9a3698a7a581d7920d3308ba\n\n\n\n\n\ninput_dict_e4951879c0adfc1ee95c3f213d3670aa\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7685781769f0>\n\n\n\nstructure_5bb5ba75f27ad166411ec7f96a67d795->input_dict_e4951879c0adfc1ee95c3f213d3670aa\n\n\n\n\n\ninput_dict_a404d97e273a3ac600efe8c07b153592\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x7685781766c0>\n\n\n\nstructure_2a68a68e8c70db7870ac8e42f8b1865d->input_dict_a404d97e273a3ac600efe8c07b153592\n\n\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7\n\nworking_directory=mini\n\n\n\nworking_directory_a17ade9a563d8dcadb655fb2e1c743a7->structure_199228a058c6c2abd4059cca704f33e6\n\n\n\n\n\ninput_dict_537467c3235749e6bbce7787ac63fcf2\n\ninput_dict=<pyiron_base.project.delayed.DelayedObject object at 0x768578175910>\n\n\n\ninput_dict_537467c3235749e6bbce7787ac63fcf2->structure_199228a058c6c2abd4059cca704f33e6\n\n\n\n\n\nstructure_1143d046335e4294dac52196bc2767db\n\nstructure=<pyiron_base.project.delayed.DelayedObject object at 0x768578175b50>\n\n\n\nstructure_1143d046335e4294dac52196bc2767db->input_dict_537467c3235749e6bbce7787ac63fcf2\n\n\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0\n\nelement=Al\n\n\n\nelement_467734216d9bd2497ffd28d5cd6daba0->structure_1143d046335e4294dac52196bc2767db\n\n\n\n\n\na_aea0574e321c6f75f923c059730e9537\n\na=4.05\n\n\n\na_aea0574e321c6f75f923c059730e9537->structure_1143d046335e4294dac52196bc2767db\n\n\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a\n\ncubic=True\n\n\n\ncubic_bad787c53fa02a5559fe570238fdb23a->structure_1143d046335e4294dac52196bc2767db\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10\n\npseudopotentials={'Al': 'Al.pbe-n-kjpaw_psl.1.0.0.UPF'}\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_87f4e1381ab79d513e7ddd2deecdd386\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_537467c3235749e6bbce7787ac63fcf2\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_adda488913baad1684ada5811fc1bf07\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_d5e1009e9a3698a7a581d7920d3308ba\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_e4951879c0adfc1ee95c3f213d3670aa\n\n\n\n\n\npseudopotentials_453cdcc0d627a851e196cd899d956d10->input_dict_a404d97e273a3ac600efe8c07b153592\n\n\n\n\n\n1_191bdde6d29a8110f9185c2dc2f36d40\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x768578176210>\n\n\n\ninput_dict_adda488913baad1684ada5811fc1bf07->1_191bdde6d29a8110f9185c2dc2f36d40\n\n\n\n\n\n1_4fc4ea22f90e9c5395aebcd832723a0b\n\n1=<pyiron_base.project.delayed.DelayedObject object at 0x768578177740>\n\n\n\ninput_dict_adda488913baad1684ada5811fc1bf07->1_4fc4ea22f90e9c5395aebcd832723a0b\n\n\n\n\n\n2_19f8c443d3f233fce65b180b8671f9d3\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x768578176810>\n\n\n\ninput_dict_d5e1009e9a3698a7a581d7920d3308ba->2_19f8c443d3f233fce65b180b8671f9d3\n\n\n\n\n\n2_a91f85ab07dda5e77e64539693175399\n\n2=<pyiron_base.project.delayed.DelayedObject object at 0x7685781771a0>\n\n\n\ninput_dict_d5e1009e9a3698a7a581d7920d3308ba->2_a91f85ab07dda5e77e64539693175399\n\n\n\n\n\n3_3ede2f537cf839143078e1512ff2ef2f\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x7685781759d0>\n\n\n\ninput_dict_e4951879c0adfc1ee95c3f213d3670aa->3_3ede2f537cf839143078e1512ff2ef2f\n\n\n\n\n\n3_5d8eeb1260eb131e15c0788d790e6449\n\n3=<pyiron_base.project.delayed.DelayedObject object at 0x768578176ed0>\n\n\n\ninput_dict_e4951879c0adfc1ee95c3f213d3670aa->3_5d8eeb1260eb131e15c0788d790e6449\n\n\n\n\n\n4_25a83d640c1b83e1d1be6ab4ab2fe22d\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x768578177c50>\n\n\n\ninput_dict_a404d97e273a3ac600efe8c07b153592->4_25a83d640c1b83e1d1be6ab4ab2fe22d\n\n\n\n\n\n4_24178a0d53ab74cdcd2d82759a89311b\n\n4=<pyiron_base.project.delayed.DelayedObject object at 0x768578177140>\n\n\n\ninput_dict_a404d97e273a3ac600efe8c07b153592->4_24178a0d53ab74cdcd2d82759a89311b\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa\n\nkpts=[3, 3, 3]\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_87f4e1381ab79d513e7ddd2deecdd386\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_537467c3235749e6bbce7787ac63fcf2\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_adda488913baad1684ada5811fc1bf07\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_d5e1009e9a3698a7a581d7920d3308ba\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_e4951879c0adfc1ee95c3f213d3670aa\n\n\n\n\n\nkpts_e961a9390797b0f6f8887a402ea3e9aa->input_dict_a404d97e273a3ac600efe8c07b153592\n\n\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34\n\ncalculation=vc-relax\n\n\n\ncalculation_77b75a01e65d83962d14fa8a882d6c34->input_dict_537467c3235749e6bbce7787ac63fcf2\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9\n\nsmearing=0.02\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_87f4e1381ab79d513e7ddd2deecdd386\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_537467c3235749e6bbce7787ac63fcf2\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_adda488913baad1684ada5811fc1bf07\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_d5e1009e9a3698a7a581d7920d3308ba\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_e4951879c0adfc1ee95c3f213d3670aa\n\n\n\n\n\nsmearing_64a632a7e5bfbb7d0c6face9b82082a9->input_dict_a404d97e273a3ac600efe8c07b153592\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781\n\nstrain_lst=[0.9, 0.95, 1.0, 1.05, 1.1]\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_24283480cde4a82cb11a95ad8315004b\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_02eea1a3dae4b8a2111c575ca7b757e4\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_f70fbf61dbacde3f86dbc99a31f544d6\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_5bb5ba75f27ad166411ec7f96a67d795\n\n\n\n\n\nstrain_lst_2d8c38dac8f1aeeeecfa3c0b1cc8a781->structure_2a68a68e8c70db7870ac8e42f8b1865d\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83\n\ncalculation=scf\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_87f4e1381ab79d513e7ddd2deecdd386\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_adda488913baad1684ada5811fc1bf07\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_d5e1009e9a3698a7a581d7920d3308ba\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_e4951879c0adfc1ee95c3f213d3670aa\n\n\n\n\n\ncalculation_bc91e0ce7227762f507f47b85f2f0a83->input_dict_a404d97e273a3ac600efe8c07b153592\n\n\n\n\n\n1_191bdde6d29a8110f9185c2dc2f36d40->volume_lst_9ecc37695722ff26a909e7df66fad761\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd\n\nworking_directory=strain_1\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_191bdde6d29a8110f9185c2dc2f36d40\n\n\n\n\n\nworking_directory_5423d2cc67129a6d0383af6f347df5bd->1_4fc4ea22f90e9c5395aebcd832723a0b\n\n\n\n\n\n1_4fc4ea22f90e9c5395aebcd832723a0b->energy_lst_d41078de6fda3484043c8f3407845d97\n\n\n\n\n\n2_19f8c443d3f233fce65b180b8671f9d3->volume_lst_9ecc37695722ff26a909e7df66fad761\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992\n\nworking_directory=strain_2\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_19f8c443d3f233fce65b180b8671f9d3\n\n\n\n\n\nworking_directory_cc646e064ddfc4b2811aba3d86d27992->2_a91f85ab07dda5e77e64539693175399\n\n\n\n\n\n2_a91f85ab07dda5e77e64539693175399->energy_lst_d41078de6fda3484043c8f3407845d97\n\n\n\n\n\n3_3ede2f537cf839143078e1512ff2ef2f->volume_lst_9ecc37695722ff26a909e7df66fad761\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f\n\nworking_directory=strain_3\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_3ede2f537cf839143078e1512ff2ef2f\n\n\n\n\n\nworking_directory_e27768d53df6cd8dc245c52054ecf31f->3_5d8eeb1260eb131e15c0788d790e6449\n\n\n\n\n\n3_5d8eeb1260eb131e15c0788d790e6449->energy_lst_d41078de6fda3484043c8f3407845d97\n\n\n\n\n\n4_25a83d640c1b83e1d1be6ab4ab2fe22d->volume_lst_9ecc37695722ff26a909e7df66fad761\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7\n\nworking_directory=strain_4\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_25a83d640c1b83e1d1be6ab4ab2fe22d\n\n\n\n\n\nworking_directory_72bba39b22d2b7ce154d37c7e8c658b7->4_24178a0d53ab74cdcd2d82759a89311b\n\n\n\n\n\n4_24178a0d53ab74cdcd2d82759a89311b->energy_lst_d41078de6fda3484043c8f3407845d97\n\n\n\n\n\nenergy_lst_d41078de6fda3484043c8f3407845d97->create_function_job_9adf79b116ef7d1bd6234b8bd3fb8790\n\n\n\n\n" }, "metadata": {} } @@ -370,67 +358,67 @@ { "name": "stdout", "output_type": "stream", - "text": "The job get_bulk_structure_f1e730ed97e30e5439e855d2ac41396f was saved and received the ID: 1\nThe job get_dict_1e47509b88d63a21fd421686554c8f4a was saved and received the ID: 2\nThe job calculate_qe_e3c0bf43f7edf24d215901bf93271e87 was saved and received the ID: 3\n" + "text": "The job get_bulk_structure_2ca4aeae204ceaa28593c93054b07908 was saved and received the ID: 1\nThe job get_dict_1e47509b88d63a21fd421686554c8f4a was saved and received the ID: 2\nThe job calculate_qe_411e578f2700d09ba2df9a4c682b4582 was saved and received the ID: 3\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11926] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12175] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job generate_structures_5ee3c796287c1d44e6fcdeec1fcc55e5 was saved and received the ID: 4\nThe job get_dict_a6c6a93d0a4d3f93b67cd4f2f527f113 was saved and received the ID: 5\nThe job calculate_qe_30b838d672325385dbf68abbd0dc920f was saved and received the ID: 6\n" + "text": "The job generate_structures_29f44e1952b8f5678d84a2b016899fce was saved and received the ID: 4\nThe job get_dict_ef87933d61756398c7394b1132327107 was saved and received the ID: 5\nThe job calculate_qe_7a90048d1de9ecbd9a0d65912ce16a05 was saved and received the ID: 6\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11942] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12194] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_56c7baf33180a622d02de781bb5d83b8 was saved and received the ID: 7\nThe job calculate_qe_9be8c05a4037c09a47b17e782e3af791 was saved and received the ID: 8\n" + "text": "The job get_dict_8df97e882e2a6b51191dddf174e87731 was saved and received the ID: 7\nThe job calculate_qe_78019c29f3a9ab2782b972a871cf7b97 was saved and received the ID: 8\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11953] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12205] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_13814149cf915b88a341f5932909d0c5 was saved and received the ID: 9\nThe job calculate_qe_ca75104e062b66d78cb4990513466ad9 was saved and received the ID: 10\n" + "text": "The job get_dict_be1c027670e9498836f67834851d04cc was saved and received the ID: 9\nThe job calculate_qe_aaa66ba36e55a9cc577037576b1e6ccb was saved and received the ID: 10\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11963] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12216] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_2aa82e83accc35e7ebb2ab9e1f450b85 was saved and received the ID: 11\nThe job calculate_qe_bf556bcb1e352359c372a2ccc2bc060e was saved and received the ID: 12\n" + "text": "The job get_dict_52b5c75d597a1c4b528615e1125a0896 was saved and received the ID: 11\nThe job calculate_qe_62d76f231acf9ea944e9c695277ff831 was saved and received the ID: 12\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11973] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12227] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_dict_fe77eeeb61b97b67635aae94093a7e1d was saved and received the ID: 13\nThe job calculate_qe_ef80e3efb1f1b5c06bfbcec3bf1b4905 was saved and received the ID: 14\n" + "text": "The job get_dict_1c3ed4191b35cf54ac773bb8172f6947 was saved and received the ID: 13\nThe job calculate_qe_2589d637ad774f38e26fdd2b4529fcca was saved and received the ID: 14\n" }, { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11985] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12237] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "name": "stdout", "output_type": "stream", - "text": "The job get_list_2691e781d16d4171a2d5e93468359d9f was saved and received the ID: 15\nThe job get_list_31e21423c6b0488ff776e3739a542d92 was saved and received the ID: 16\nThe job plot_energy_volume_curve_204ada257bb5f43b38f0b8818e86bdaa was saved and received the ID: 17\n" + "text": "The job get_list_274bff6e81bec86553cdd07a055e2b5e was saved and received the ID: 15\nThe job get_list_4457d79d3504f678b6f74963dd8f0e4c was saved and received the ID: 16\nThe job plot_energy_volume_curve_33e1f4fbca145ac4d2a72d20544cad9d was saved and received the ID: 17\n" }, { "output_type": "display_data", @@ -467,7 +455,7 @@ { "name": "stderr", "output_type": "stream", - "text": "[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:11996] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:12014] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:12025] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:12036] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:12047] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pyiron-dev-pyth-flow-definition-5x990k36:12057] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" + "text": "[jupyter-pythonworkflow-fl--x---d7231032:12248] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12262] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12277] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12289] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12299] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n[jupyter-pythonworkflow-fl--x---d7231032:12309] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\nNote: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG\n" }, { "output_type": "display_data",