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Use dict keys as strings #13

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Merged
merged 3 commits into from
Mar 14, 2025
Merged

Use dict keys as strings #13

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dde3ae0
Use dict keys as strings
jan-janssen Mar 14, 2025
7c92f0a
bug fix
jan-janssen Mar 14, 2025
e187f5e
another fix
jan-janssen Mar 14, 2025
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23 changes: 21 additions & 2 deletions jobflow_to_pyiron_base_qe.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,12 @@
{
"id": "07598344-0f75-433b-8902-bea21a42088c",
"cell_type": "code",
"source": "calculate_qe = job(_calculate_qe, data=[\"energy\", \"volume\", \"structure\"])\ngenerate_structures = job(_generate_structures, data=[\"i\" for i in range(100)])\nplot_energy_volume_curve = job(_plot_energy_volume_curve)\nget_bulk_structure = job(_get_bulk_structure)",
"source": [
"calculate_qe = job(_calculate_qe, data=[\"energy\", \"volume\", \"structure\"])\n",
"generate_structures = job(_generate_structures, data=[f\"s_{i}\" for i in range(100)])\n",
"plot_energy_volume_curve = job(_plot_energy_volume_curve)\n",
"get_bulk_structure = job(_get_bulk_structure)"
],
"metadata": {
"trusted": true
},
Expand Down Expand Up @@ -140,7 +145,21 @@
{
"id": "53e979ac-21db-4aa5-ae58-7cfc08dfa87b",
"cell_type": "code",
"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, str(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 = []\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)"
],
"metadata": {
"trusted": true
},
Expand Down
4 changes: 2 additions & 2 deletions quantum_espresso_workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def generate_structures(structure, strain_lst):
structure_strain.cell * strain ** (1 / 3), scale_atoms=True
)
structure_lst.append(structure_strain)
return {str(i): atoms_to_json_dict(atoms=s) for i, s in enumerate(structure_lst)}
return {f"s_{i}": atoms_to_json_dict(atoms=s) for i, s in enumerate(structure_lst)}


def plot_energy_volume_curve(volume_lst, energy_lst):
Expand Down Expand Up @@ -110,4 +110,4 @@ def atoms_to_json_dict(atoms):
else:
json_dict[key] = value

return json_dict
return json_dict
10 changes: 5 additions & 5 deletions workflow_qe.json
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Original file line number Diff line number Diff line change
Expand Up @@ -47,35 +47,35 @@
{"target": 2, "targetHandle": "structure", "source": 1, "sourceHandle": "structure"},
{"target": 2, "targetHandle": "strain_lst", "source": 18, "sourceHandle": null},
{"target": 3, "targetHandle": "working_directory", "source": 19, "sourceHandle": null},
{"target": 20, "targetHandle": "structure", "source": 2, "sourceHandle": "0"},
{"target": 20, "targetHandle": "structure", "source": 2, "sourceHandle": "s_0"},
{"target": 20, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
{"target": 20, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
{"target": 20, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
{"target": 20, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
{"target": 3, "targetHandle": "input_dict", "source": 20, "sourceHandle": null},
{"target": 4, "targetHandle": "working_directory", "source": 22, "sourceHandle": null},
{"target": 23, "targetHandle": "structure", "source": 2, "sourceHandle": "1"},
{"target": 23, "targetHandle": "structure", "source": 2, "sourceHandle": "s_1"},
{"target": 23, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
{"target": 23, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
{"target": 23, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
{"target": 23, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
{"target": 4, "targetHandle": "input_dict", "source": 23, "sourceHandle": null},
{"target": 5, "targetHandle": "working_directory", "source": 24, "sourceHandle": null},
{"target": 25, "targetHandle": "structure", "source": 2, "sourceHandle": "2"},
{"target": 25, "targetHandle": "structure", "source": 2, "sourceHandle": "s_2"},
{"target": 25, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
{"target": 25, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
{"target": 25, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
{"target": 25, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
{"target": 5, "targetHandle": "input_dict", "source": 25, "sourceHandle": null},
{"target": 6, "targetHandle": "working_directory", "source": 26, "sourceHandle": null},
{"target": 27, "targetHandle": "structure", "source": 2, "sourceHandle": "3"},
{"target": 27, "targetHandle": "structure", "source": 2, "sourceHandle": "s_3"},
{"target": 27, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
{"target": 27, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
{"target": 27, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
{"target": 27, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
{"target": 6, "targetHandle": "input_dict", "source": 27, "sourceHandle": null},
{"target": 7, "targetHandle": "working_directory", "source": 28, "sourceHandle": null},
{"target": 29, "targetHandle": "structure", "source": 2, "sourceHandle": "4"},
{"target": 29, "targetHandle": "structure", "source": 2, "sourceHandle": "s_4"},
{"target": 29, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
{"target": 29, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
{"target": 29, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
Expand Down
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