diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
index 98127836..a29aee20 100644
--- a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
+++ b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -36,13 +36,18 @@
"source": [
"## 1. Set Input Parameters\n",
"\n",
- "### 1.1. Select Substrate and Layer from Input Materials"
+ "### 1.1. Set Substrate and Layer Parameters "
]
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
+ "execution_count": 1,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:36.375492Z",
+ "start_time": "2024-05-07T20:04:36.353678Z"
+ }
+ },
"outputs": [],
"source": [
"SUBSTRATE_PARAMETERS = {\n",
@@ -56,8 +61,9 @@
"}\n",
"\n",
"USE_CONVENTIONAL_CELL = True # if True, the surface plane is constructed using miller indices of the conventional cell\n",
+ "\n",
"IS_TERMINATION_SELECTION_INTERACTIVE = True # if True, the user can select the termination interactively\n",
- "DEFAULT_TERMINATION_INDEX = 0 # the default termination index to use if the interactive mode is disabled"
+ "TERMINATION_INDEX = 0 # the default termination index that is used if no termination selected"
]
},
{
@@ -71,13 +77,18 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
+ "execution_count": 2,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:36.397714Z",
+ "start_time": "2024-05-07T20:04:36.378928Z"
+ }
+ },
"outputs": [],
"source": [
"INTERFACE_PARAMETERS = {\n",
" \"DISTANCE_Z\": 3.0, # in Angstroms\n",
- " \"MAX_AREA\": 400, # in Angstroms^2\n",
+ " \"MAX_AREA\": 50, # in Angstroms^2\n",
"}"
]
},
@@ -90,8 +101,13 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
+ "execution_count": 3,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:36.399968Z",
+ "start_time": "2024-05-07T20:04:36.389404Z"
+ }
+ },
"outputs": [],
"source": [
"ZSL_PARAMETERS = {\n",
@@ -122,16 +138,24 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
+ "execution_count": 4,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:36.411153Z",
+ "start_time": "2024-05-07T20:04:36.402637Z"
+ }
+ },
"outputs": [],
"source": [
"import sys\n",
+ "\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
+ "\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" from utils.jupyterlite import install_packages\n",
- " await install_packages(\"create_interface_with_min_strain_zsl.ipynb\",\"../../config.yml\")"
+ "\n",
+ " await install_packages(\"create_interface_with_min_strain_zsl.ipynb\", \"../../config.yml\")"
]
},
{
@@ -143,7 +167,35 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Data from 0-Ni has been read successfully.\n",
+ "Data from 1-Graphene has been read successfully.\n",
+ "Data from 3-WS2 has been read successfully.\n",
+ "Data from 4-BN has been read successfully.\n",
+ "Data from 4-Te2Mo has been read successfully.\n",
+ "Data from B43 Te42 Mo21 W27 S54 N43 has been read successfully.\n",
+ "Data from Ni12 C8 has been read successfully.\n",
+ "Data from Ni3 C2 has been read successfully.\n",
+ "Data from Te14 Mo7 W9 S18 has been read successfully.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": "GridBox(children=(VBox(children=(Label(value='Ni - Material 0', layout=Layout(height='30px', overflow='hidden'…",
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 0,
+ "model_id": "868aae6d9d254aafb6e75472bb1fd341"
+ }
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"from mat3ra.made.material import Material\n",
"from utils.jupyterlite import get_data\n",
@@ -156,8 +208,13 @@
"visualize(materials, repetitions=[1, 1, 1], rotation=\"0x\")"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:40.253729Z",
+ "start_time": "2024-05-07T20:04:36.407859Z"
+ }
+ },
+ "execution_count": 5
},
{
"cell_type": "markdown",
@@ -179,18 +236,25 @@
"from mat3ra.made.tools.build import init_interface_builder\n",
"\n",
"interface_builder = init_interface_builder(\n",
- " materials[5],\n",
- " materials[3], settings=interface_settings\n",
- " )"
+ " materials[0],\n",
+ " materials[1],\n",
+ " settings=interface_settings\n",
+ ")"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:41.283030Z",
+ "start_time": "2024-05-07T20:04:40.296061Z"
+ }
+ },
+ "execution_count": 6
},
{
"cell_type": "markdown",
"source": [
- "### 4.2. Select the termination"
+ "### 4.2. Select the termination\n",
+ "Possible terminations for the interface are found by the interface builder. The user can select the termination interactively or use the default one."
],
"metadata": {
"collapsed": false
@@ -198,36 +262,29 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Selected termination: ('C_P6/mmm_2', 'Ni_R-3m_1')\n"
+ ]
+ }
+ ],
"source": [
"terminations = interface_builder.terminations\n",
+ "from utils.io import user_select_object_by_index\n",
"\n",
- "\n",
- "# TODO: move to utils (ot made?)\n",
- "def select_termination():\n",
- " prompt_text = \"Select termination by index:\\n\" + \"\\n\".join(\n",
- " f\"{i}: {t}\" for i, t in enumerate(terminations))\n",
- "\n",
- " selected_termination_index = input(prompt_text)\n",
- "\n",
- " try:\n",
- " selected_termination_index = int(selected_termination_index)\n",
- " except ValueError:\n",
- " print(\"Invalid input. Please enter a valid integer.\")\n",
- " return\n",
- "\n",
- " if selected_termination_index < 0 or selected_termination_index >= len(terminations):\n",
- " print(\"Invalid index. Please try again.\")\n",
- " else:\n",
- " selected_termination = terminations[selected_termination_index]\n",
- " print(\"Selected termination: \", selected_termination)\n",
- " return selected_termination\n",
- "\n",
- "selected_termination = select_termination() if IS_TERMINATION_SELECTION_INTERACTIVE else DEFAULT_TERMINATION_INDEX"
+ "selected_termination = user_select_object_by_index(terminations, object_name=\"termination\") if IS_TERMINATION_SELECTION_INTERACTIVE else terminations[TERMINATION_INDEX]"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:42.802069Z",
+ "start_time": "2024-05-07T20:04:41.284164Z"
+ }
+ },
+ "execution_count": 7
},
{
"cell_type": "markdown",
@@ -240,23 +297,35 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Creating interfaces...\n",
+ "Found 9 unique interfaces.\n"
+ ]
+ }
+ ],
"source": [
"from mat3ra.made.tools.build import create_interfaces\n",
"\n",
"interface_data_holder = create_interfaces(\n",
- " substrate=materials[5],\n",
- " layer=materials[3],\n",
" settings=interface_settings,\n",
" sort_by_strain_and_size=True,\n",
" remove_duplicates=True,\n",
" interface_builder=interface_builder,\n",
- " selected_termination=selected_termination,\n",
+ " termination=selected_termination,\n",
")"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.416835Z",
+ "start_time": "2024-05-07T20:04:42.759877Z"
+ }
+ },
+ "execution_count": 8
},
{
"cell_type": "markdown",
@@ -269,7 +338,17 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Interface with lowest strain for termination ('C_P6/mmm_2', 'Ni_R-3m_1') (index 0):\n",
+ " strain: 0.105%\n",
+ " number of atoms: 5\n"
+ ]
+ }
+ ],
"source": [
"print(f\"Interface with lowest strain for termination {selected_termination} (index 0):\")\n",
"interfaces = interface_data_holder.get_interfaces_for_termination(selected_termination)\n",
@@ -278,8 +357,13 @@
"print(\" number of atoms:\", first_interface.num_sites)"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.422060Z",
+ "start_time": "2024-05-07T20:04:44.416243Z"
+ }
+ },
+ "execution_count": 9
},
{
"cell_type": "markdown",
@@ -294,7 +378,1009 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": " \n "
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.plotly.v1+json": {
+ "data": [
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 0",
+ "text": [
+ "Index: 0
Strain: 0.11%
Atoms: 5"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 5
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 1",
+ "text": [
+ "Index: 1
Strain: 0.11%
Atoms: 10"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 10
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 2",
+ "text": [
+ "Index: 2
Strain: 0.11%
Atoms: 15"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 15
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 3",
+ "text": [
+ "Index: 3
Strain: 0.11%
Atoms: 20"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 20
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 4",
+ "text": [
+ "Index: 4
Strain: 0.11%
Atoms: 25"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 25
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 5",
+ "text": [
+ "Index: 5
Strain: 0.11%
Atoms: 30"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 30
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 6",
+ "text": [
+ "Index: 6
Strain: 0.11%
Atoms: 35"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 35
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 7",
+ "text": [
+ "Index: 7
Strain: 0.11%
Atoms: 40"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 40
+ ],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "text",
+ "mode": "markers",
+ "name": "Index: 8",
+ "text": [
+ "Index: 8
Strain: 0.11%
Atoms: 45"
+ ],
+ "x": [
+ 0.10500000000000001
+ ],
+ "y": [
+ 45
+ ],
+ "type": "scatter"
+ }
+ ],
+ "layout": {
+ "height": 600,
+ "hovermode": "closest",
+ "legend": {
+ "title": {
+ "text": "Interfaces Indices"
+ }
+ },
+ "xaxis": {
+ "title": {
+ "text": "Strain (%)"
+ },
+ "type": "log"
+ },
+ "yaxis": {
+ "title": {
+ "text": "Number of atoms"
+ },
+ "type": "log"
+ },
+ "template": {
+ "data": {
+ "histogram2dcontour": [
+ {
+ "type": "histogram2dcontour",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "choropleth": [
+ {
+ "type": "choropleth",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ ],
+ "histogram2d": [
+ {
+ "type": "histogram2d",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "heatmap": [
+ {
+ "type": "heatmap",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "heatmapgl": [
+ {
+ "type": "heatmapgl",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "contourcarpet": [
+ {
+ "type": "contourcarpet",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ ],
+ "contour": [
+ {
+ "type": "contour",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "surface": [
+ {
+ "type": "surface",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ },
+ "colorscale": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ]
+ }
+ ],
+ "mesh3d": [
+ {
+ "type": "mesh3d",
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ ],
+ "scatter": [
+ {
+ "fillpattern": {
+ "fillmode": "overlay",
+ "size": 10,
+ "solidity": 0.2
+ },
+ "type": "scatter"
+ }
+ ],
+ "parcoords": [
+ {
+ "type": "parcoords",
+ "line": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scatterpolargl": [
+ {
+ "type": "scatterpolargl",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "bar": [
+ {
+ "error_x": {
+ "color": "#2a3f5f"
+ },
+ "error_y": {
+ "color": "#2a3f5f"
+ },
+ "marker": {
+ "line": {
+ "color": "#E5ECF6",
+ "width": 0.5
+ },
+ "pattern": {
+ "fillmode": "overlay",
+ "size": 10,
+ "solidity": 0.2
+ }
+ },
+ "type": "bar"
+ }
+ ],
+ "scattergeo": [
+ {
+ "type": "scattergeo",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scatterpolar": [
+ {
+ "type": "scatterpolar",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "histogram": [
+ {
+ "marker": {
+ "pattern": {
+ "fillmode": "overlay",
+ "size": 10,
+ "solidity": 0.2
+ }
+ },
+ "type": "histogram"
+ }
+ ],
+ "scattergl": [
+ {
+ "type": "scattergl",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scatter3d": [
+ {
+ "type": "scatter3d",
+ "line": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ },
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scattermapbox": [
+ {
+ "type": "scattermapbox",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scatterternary": [
+ {
+ "type": "scatterternary",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "scattercarpet": [
+ {
+ "type": "scattercarpet",
+ "marker": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ }
+ }
+ ],
+ "carpet": [
+ {
+ "aaxis": {
+ "endlinecolor": "#2a3f5f",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "minorgridcolor": "white",
+ "startlinecolor": "#2a3f5f"
+ },
+ "baxis": {
+ "endlinecolor": "#2a3f5f",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "minorgridcolor": "white",
+ "startlinecolor": "#2a3f5f"
+ },
+ "type": "carpet"
+ }
+ ],
+ "table": [
+ {
+ "cells": {
+ "fill": {
+ "color": "#EBF0F8"
+ },
+ "line": {
+ "color": "white"
+ }
+ },
+ "header": {
+ "fill": {
+ "color": "#C8D4E3"
+ },
+ "line": {
+ "color": "white"
+ }
+ },
+ "type": "table"
+ }
+ ],
+ "barpolar": [
+ {
+ "marker": {
+ "line": {
+ "color": "#E5ECF6",
+ "width": 0.5
+ },
+ "pattern": {
+ "fillmode": "overlay",
+ "size": 10,
+ "solidity": 0.2
+ }
+ },
+ "type": "barpolar"
+ }
+ ],
+ "pie": [
+ {
+ "automargin": true,
+ "type": "pie"
+ }
+ ]
+ },
+ "layout": {
+ "autotypenumbers": "strict",
+ "colorway": [
+ "#636efa",
+ "#EF553B",
+ "#00cc96",
+ "#ab63fa",
+ "#FFA15A",
+ "#19d3f3",
+ "#FF6692",
+ "#B6E880",
+ "#FF97FF",
+ "#FECB52"
+ ],
+ "font": {
+ "color": "#2a3f5f"
+ },
+ "hovermode": "closest",
+ "hoverlabel": {
+ "align": "left"
+ },
+ "paper_bgcolor": "white",
+ "plot_bgcolor": "#E5ECF6",
+ "polar": {
+ "bgcolor": "#E5ECF6",
+ "angularaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "radialaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ }
+ },
+ "ternary": {
+ "bgcolor": "#E5ECF6",
+ "aaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "baxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "caxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ }
+ },
+ "coloraxis": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ },
+ "colorscale": {
+ "sequential": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ],
+ "sequentialminus": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
+ 0.1111111111111111,
+ "#46039f"
+ ],
+ [
+ 0.2222222222222222,
+ "#7201a8"
+ ],
+ [
+ 0.3333333333333333,
+ "#9c179e"
+ ],
+ [
+ 0.4444444444444444,
+ "#bd3786"
+ ],
+ [
+ 0.5555555555555556,
+ "#d8576b"
+ ],
+ [
+ 0.6666666666666666,
+ "#ed7953"
+ ],
+ [
+ 0.7777777777777778,
+ "#fb9f3a"
+ ],
+ [
+ 0.8888888888888888,
+ "#fdca26"
+ ],
+ [
+ 1.0,
+ "#f0f921"
+ ]
+ ],
+ "diverging": [
+ [
+ 0,
+ "#8e0152"
+ ],
+ [
+ 0.1,
+ "#c51b7d"
+ ],
+ [
+ 0.2,
+ "#de77ae"
+ ],
+ [
+ 0.3,
+ "#f1b6da"
+ ],
+ [
+ 0.4,
+ "#fde0ef"
+ ],
+ [
+ 0.5,
+ "#f7f7f7"
+ ],
+ [
+ 0.6,
+ "#e6f5d0"
+ ],
+ [
+ 0.7,
+ "#b8e186"
+ ],
+ [
+ 0.8,
+ "#7fbc41"
+ ],
+ [
+ 0.9,
+ "#4d9221"
+ ],
+ [
+ 1,
+ "#276419"
+ ]
+ ]
+ },
+ "xaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": "",
+ "title": {
+ "standoff": 15
+ },
+ "zerolinecolor": "white",
+ "automargin": true,
+ "zerolinewidth": 2
+ },
+ "yaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": "",
+ "title": {
+ "standoff": 15
+ },
+ "zerolinecolor": "white",
+ "automargin": true,
+ "zerolinewidth": 2
+ },
+ "scene": {
+ "xaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ },
+ "yaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ },
+ "zaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ }
+ },
+ "shapedefaults": {
+ "line": {
+ "color": "#2a3f5f"
+ }
+ },
+ "annotationdefaults": {
+ "arrowcolor": "#2a3f5f",
+ "arrowhead": 0,
+ "arrowwidth": 1
+ },
+ "geo": {
+ "bgcolor": "white",
+ "landcolor": "#E5ECF6",
+ "subunitcolor": "white",
+ "showland": true,
+ "showlakes": true,
+ "lakecolor": "white"
+ },
+ "title": {
+ "x": 0.05
+ },
+ "mapbox": {
+ "style": "light"
+ }
+ }
+ }
+ },
+ "config": {
+ "plotlyServerURL": "https://plot.ly"
+ }
+ },
+ "text/html": ""
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Terminations: \n",
+ " [('C_P6/mmm_2', 'Ni_R-3m_1')]\n"
+ ]
+ }
+ ],
"source": [
"from utils.plot import plot_strain_vs_atoms\n",
"\n",
@@ -309,8 +1395,13 @@
"print(\"Terminations: \\n\", interface_data_holder.terminations)"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.633104Z",
+ "start_time": "2024-05-07T20:04:44.420896Z"
+ }
+ },
+ "execution_count": 10
},
{
"cell_type": "markdown",
@@ -337,8 +1428,13 @@
" interfaces_slice_range_or_index)"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.633708Z",
+ "start_time": "2024-05-07T20:04:44.630001Z"
+ }
+ },
+ "execution_count": 11
},
{
"cell_type": "markdown",
@@ -351,13 +1447,31 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "GridBox(children=(VBox(children=(Label(value='Ni3C2 - Material 0', layout=Layout(height='30px', overflow='hidd…",
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 0,
+ "model_id": "015146a9876848f1a0b0fbebd9340312"
+ }
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
- "visualize(selected_interfaces, repetitions=[1,1,1], rotation=\"0x\")"
+ "visualize(selected_interfaces, repetitions=[1, 1, 1], rotation=\"0x\")"
],
"metadata": {
- "collapsed": false
- }
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.633998Z",
+ "start_time": "2024-05-07T20:04:44.630076Z"
+ }
+ },
+ "execution_count": 12
},
{
"cell_type": "markdown",
@@ -368,11 +1482,25 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
+ "execution_count": 13,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-05-07T20:04:44.634051Z",
+ "start_time": "2024-05-07T20:04:44.630525Z"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Data for materials written to uploads/Ni3 C2.json\n"
+ ]
+ }
+ ],
"source": [
"from utils.jupyterlite import set_data\n",
+ "\n",
"set_data(\"materials\", selected_interfaces)"
]
}
diff --git a/utils/io.py b/utils/io.py
new file mode 100644
index 00000000..ce6f9750
--- /dev/null
+++ b/utils/io.py
@@ -0,0 +1,24 @@
+from typing import Any, List, Optional
+
+
+def user_select_object_by_index(
+ objects: List[Any], object_name: str = "object", prompt_head: Optional[str] = None
+) -> Any:
+ prompt_head = prompt_head or f"Select {object_name} by index:\n"
+ prompt_body = "\n".join(f"{i}: {t}" for i, t in enumerate(objects))
+
+ selected_index_str = input(prompt_head + prompt_body)
+ try:
+ selected_index = int(selected_index_str)
+ except ValueError:
+ print("Invalid input. Please enter a valid integer.")
+ return user_select_object_by_index(objects, object_name, prompt_head)
+
+ assert isinstance(selected_index, int)
+
+ if selected_index < 0 or selected_index >= len(objects):
+ print("Invalid index.")
+ return user_select_object_by_index(objects, object_name, prompt_head)
+
+ print(f"Selected {object_name}: ", objects[selected_index])
+ return objects[selected_index]