update/SOF 7461 #145
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -50,8 +50,27 @@ | |
| "source": [ | ||
|
Member
There was a problem hiding this comment. Line #8. print("Please select a film material. Film is set to substrate.")
Film material not found. Re-using substrate material as film. Reply via ReviewNB |
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| "# Enable interactive selection of terminations via UI prompt\n", | ||
| "IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n", | ||
| "\n", | ||
| "FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]\n", | ||
| "FILM_MILLER_INDICES = (0, 0, 1)\n", | ||
| "FILM_THICKNESS = 1 # in atomic layers\n", | ||
| "FILM_VACUUM = 0.0 # in angstroms\n", | ||
| "FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n", | ||
| "FILM_USE_ORTHOGONAL_Z = True\n", | ||
| "\n", | ||
| "SUBSTRATE_INDEX = 0\n", | ||
| "SUBSTRATE_MILLER_INDICES = (1, 1, 1)\n", | ||
| "SUBSTRATE_THICKNESS = 3 # in atomic layers\n", | ||
| "SUBSTRATE_VACUUM = 3.0 # in angstroms\n", | ||
| "SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n", | ||
| "SUBSTRATE_USE_ORTHOGONAL_Z = True\n", | ||
| "\n", | ||
| "# Maximum area for the superlattice search algorithm\n", | ||
| "MAX_AREA = 50 # in Angstrom^2\n", | ||
| "# Set the termination pair indices\n", | ||
| "TERMINATION_PAIR_INDEX = 0 # Will be overridden in interactive selection is used\n", | ||
| "INTERFACE_DISTANCE = 3.0 # in Angstrom\n", | ||
| "INTERFACE_VACUUM = 20.0 # in Angstrom" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
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@@ -76,6 +95,7 @@ | |
| "\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\")" | ||
|
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@@ -97,14 +117,15 @@ | |
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import get_materials\n", | ||
| "\n", | ||
| "materials = get_materials(globals())\n", | ||
| "substrate = materials[SUBSTRATE_INDEX]\n", | ||
| "try: \n", | ||
| " film = materials[FILM_INDEX]\n", | ||
| "except IndexError:\n", | ||
| " print(\"Film material not found. Re-using substrate material as film.\")\n", | ||
| " film = substrate" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -151,20 +172,20 @@ | |
| "\n", | ||
| "film_slab_configuration = SlabConfiguration(\n", | ||
| " bulk=film,\n", | ||
| " miller_indices=FILM_MILLER_INDICES,\n", | ||
| " thickness=FILM_THICKNESS, # in atomic layers\n", | ||
| " vacuum=FILM_VACUUM, # in angstroms\n", | ||
| " xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n", | ||
| " use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n", | ||
| ")\n", | ||
| "\n", | ||
| "substrate_slab_configuration = SlabConfiguration(\n", | ||
| " bulk=substrate,\n", | ||
| " miller_indices=SUBSTRATE_MILLER_INDICES,\n", | ||
| " thickness=SUBSTRATE_THICKNESS, # in atomic layers\n", | ||
| " vacuum=SUBSTRATE_VACUUM, # in angstroms\n", | ||
| " xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n", | ||
| " use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n", | ||
| ")" | ||
| ], | ||
| "metadata": {}, | ||
|
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@@ -255,10 +276,9 @@ | |
| "source": [ | ||
| "from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n", | ||
| "\n", | ||
| "termination_pair_index = TERMINATION_PAIR_INDEX\n", | ||
| "\n", | ||
| "termination_pair = termination_pairs[termination_pair_index]\n", | ||
| "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n", | ||
| " if sys.platform == \"emscripten\":\n", | ||
| " termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"film/substrate termination pair\")\n", | ||
|
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@@ -293,8 +313,8 @@ | |
| " substrate_configuration=substrate_slab_configuration,\n", | ||
| " film_termination=film_termination,\n", | ||
| " substrate_termination=substrate_termination,\n", | ||
| " distance=INTERFACE_DISTANCE,\n", | ||
| " vacuum= INTERFACE_VACUUM\n", | ||
| ")" | ||
| ], | ||
| "metadata": { | ||
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@@ -437,10 +457,8 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import set_materials\n", | ||
| "set_materials(selected_interfaces)" | ||
| ] | ||
| } | ||
| ], | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -43,7 +43,26 @@ | |
| "# Enable interactive selection of terminations via UI prompt\n", | ||
|
Member
There was a problem hiding this comment. Line #21. TERMINATION_PAIR_INDEX = 0 TERMINATION_PAIR_INDEX # Will be overriden in interactive selection is used Reply via ReviewNB |
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| "IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n", | ||
| "# Enable scaling of the film slab atomic coordinates to match the substrate lattice (preserve coordinates in crystal units).\n", | ||
| "ENABLE_FILM_SCALING = True\n", | ||
| "\n", | ||
| "FILM_INDEX = 1\n", | ||
| "FILM_MILLER_INDICES = (0, 0, 1)\n", | ||
| "FILM_THICKNESS = 1 # in atomic layers\n", | ||
| "FILM_VACUUM = 0.0 # in angstroms\n", | ||
| "FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n", | ||
| "FILM_USE_ORTHOGONAL_Z = True\n", | ||
| "\n", | ||
| "SUBSTRATE_INDEX = 0\n", | ||
| "SUBSTRATE_MILLER_INDICES = (1, 1, 1)\n", | ||
| "SUBSTRATE_THICKNESS = 3 # in atomic layers\n", | ||
| "SUBSTRATE_VACUUM = 3.0 # in angstroms\n", | ||
| "SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n", | ||
| "SUBSTRATE_USE_ORTHOGONAL_Z = True\n", | ||
| "\n", | ||
| "# Set the termination pair indices\n", | ||
| "TERMINATION_PAIR_INDEX = 0 # Will be overridden in interactive selection is used\n", | ||
| "INTERFACE_DISTANCE = 3.0 # in Angstrom\n", | ||
| "INTERFACE_VACUUM = 20.0 # in Angstrom" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -92,14 +111,15 @@ | |
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import get_materials\n", | ||
| "\n", | ||
| "materials = get_materials(globals())\n", | ||
| "substrate = materials[SUBSTRATE_INDEX]\n", | ||
| "try: \n", | ||
| " film = materials[FILM_INDEX]\n", | ||
| "except IndexError:\n", | ||
| " print(\"Please select a film material. Film is set to substrate.\")\n", | ||
| " film = substrate" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -148,20 +168,20 @@ | |
| "\n", | ||
| "film_slab_configuration = SlabConfiguration(\n", | ||
| " bulk=film,\n", | ||
| " miller_indices=FILM_MILLER_INDICES,\n", | ||
| " thickness=FILM_THICKNESS, # in atomic layers\n", | ||
| " vacuum=FILM_VACUUM, # in angstroms\n", | ||
| " xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n", | ||
| " use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n", | ||
| ")\n", | ||
| "\n", | ||
| "substrate_slab_configuration = SlabConfiguration(\n", | ||
| " bulk=substrate,\n", | ||
| " miller_indices=SUBSTRATE_MILLER_INDICES,\n", | ||
| " thickness=SUBSTRATE_THICKNESS, # in atomic layers\n", | ||
| " vacuum=SUBSTRATE_VACUUM, # in angstroms\n", | ||
| " xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n", | ||
| " use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n", | ||
| ")" | ||
| ], | ||
| "metadata": { | ||
|
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@@ -206,8 +226,8 @@ | |
| "film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n", | ||
| "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n", | ||
| "\n", | ||
| "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n", | ||
| "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\") " | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -255,10 +275,9 @@ | |
| "source": [ | ||
| "from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n", | ||
| "\n", | ||
| "termination_pair_index = TERMINATION_PAIR_INDEX\n", | ||
| "\n", | ||
| "termination_pair = termination_pairs[termination_pair_index]\n", | ||
| "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n", | ||
| " if sys.platform == \"emscripten\":\n", | ||
| " termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"film/substrate termination pair\")\n", | ||
|
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@@ -293,6 +312,8 @@ | |
| " substrate_configuration=substrate_slab_configuration,\n", | ||
| " film_termination=film_termination,\n", | ||
| " substrate_termination=substrate_termination,\n", | ||
| " interface_distance=INTERFACE_DISTANCE, # in Angstrom\n", | ||
| " interface_vacuum=INTERFACE_VACUUM # in Angstrom\n", | ||
| ")\n", | ||
| "\n", | ||
| "interface = create_interface(interface_configuration)" | ||
|
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@@ -355,9 +376,8 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import set_materials\n", | ||
| "set_materials(interface)" | ||
| ] | ||
| } | ||
| ], | ||
|
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FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]Reply via ReviewNB
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ok