SOF-7599 update: use new made for slab generation #227
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -42,12 +42,12 @@ | |
| "cell_type": "code", | ||
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There was a problem hiding this comment. Line #2. print("Available terminations:", [str(t) for t in terminations])
The numbering needs to be fixed, the logic should be:
2. Find possible terminations and select one
3. Create a slab for the selected termination Reply via ReviewNB |
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| "source": [ | ||
| "# Enable interactive selection of terminations via UI prompt\n", | ||
| "IS_TERMINATIONS_SELECTION_INTERACTIVE = False\n", | ||
| "\n", | ||
| "MILLER_INDICES = (0, 1, 1)\n", | ||
| "THICKNESS = 3 # in atomic layers\n", | ||
| "VACUUM = 10.0 # in angstroms\n", | ||
| "XY_SUPERCELL_MATRIX = [[2, 0], [0, 2]]\n", | ||
| "USE_ORTHOGONAL_Z = True\n", | ||
| "USE_CONVENTIONAL_CELL = True\n", | ||
| "\n", | ||
|
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@@ -79,10 +79,11 @@ | |
| "\n", | ||
| "if sys.platform == \"emscripten\":\n", | ||
| " import micropip\n", | ||
| "\n", | ||
| " await micropip.install('mat3ra-api-examples', deps=False)\n", | ||
| " await micropip.install('mat3ra-utils')\n", | ||
| " from mat3ra.utils.jupyterlite.packages import install_packages\n", | ||
| "\n", | ||
| " await install_packages(\"\")" | ||
| ], | ||
| "metadata": { | ||
|
|
@@ -108,6 +109,7 @@ | |
| "from utils.jupyterlite import get_materials\n", | ||
| "\n", | ||
| "materials = get_materials(globals())\n", | ||
| "print(globals()[\"materials_in\"][0])\n", | ||
| "material = materials[0]" | ||
| ], | ||
| "metadata": { | ||
|
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@@ -131,6 +133,7 @@ | |
| "cell_type": "code", | ||
| "source": [ | ||
| "from utils.visualize import visualize_materials as visualize\n", | ||
| "\n", | ||
| "visualize(material, repetitions=[3, 3, 1], rotation=\"0x\")\n", | ||
| "visualize(material, repetitions=[3, 3, 1], rotation=\"-90x\")" | ||
| ], | ||
|
|
@@ -155,47 +158,35 @@ | |
| "id": "6634dae92a6c07b9" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.slab.configuration import CrystalLatticePlanes\n", | ||
| "\n", | ||
| "crystal_lattice_planes = CrystalLatticePlanes(\n", | ||
| " crystal=material,\n", | ||
| " miller_indices=MILLER_INDICES,\n", | ||
| " use_conventional_cell=USE_CONVENTIONAL_CELL\n", | ||
| ")" | ||
| ], | ||
| "id": "ec30720293c64ecc", | ||
| "outputs": [], | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 2.1. Get terminations", | ||
| "id": "eb3aeb119d8726ba" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "terminations = crystal_lattice_planes.get_terminations()\n", | ||
| "print(\"Available terminations:\", [str(t) for t in terminations])" | ||
| ], | ||
| "id": "68bb05623903b05c", | ||
| "outputs": [], | ||
| "execution_count": null | ||
| }, | ||
|
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@@ -212,11 +203,12 @@ | |
| { | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "# from mat3ra.made.tools.build.slab import create_slab\n", | ||
| "#\n", | ||
| "# slabs = [create_slab(slab_configuration, termination) for termination in slab_terminations]\n", | ||
| "#\n", | ||
| "# visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in slabs], repetitions=[3, 3, 1],\n", | ||
| "# rotation=\"-90x\")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -239,7 +231,7 @@ | |
| "cell_type": "code", | ||
| "source": [ | ||
| "print(\"Terminations\")\n", | ||
| "for idx, termination in enumerate(terminations):\n", | ||
| " print(f\" {idx}: {termination}\")" | ||
| ], | ||
| "metadata": { | ||
|
|
@@ -266,12 +258,13 @@ | |
| "\n", | ||
| "termination_index = TERMINATION_INDEX\n", | ||
| "\n", | ||
| "termination = terminations[termination_index]\n", | ||
| "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n", | ||
| " if sys.platform == \"emscripten\":\n", | ||
| " termination = await ui_prompt_select_array_element_by_index_pyodide(terminations,\n", | ||
| " element_name=\"termination\")\n", | ||
| " else:\n", | ||
| " termination = ui_prompt_select_array_element_by_index(terminations, element_name=\"termination\")\n" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -282,20 +275,84 @@ | |
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": "## 3. Create Atomic Layers", | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "143bc82b430b37d5" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.slab.configuration import AtomicLayersUniqueRepeated\n", | ||
| "\n", | ||
| "top_termination = termination\n", | ||
| "# TODO: should use `from_parameters`\n", | ||
| "atomic_layers = AtomicLayersUniqueRepeated(\n", | ||
| " crystal=material,\n", | ||
| " miller_indices=MILLER_INDICES,\n", | ||
| " use_conventional_cell=True,\n", | ||
| " number_of_repetitions=THICKNESS,\n", | ||
| " termination_top=top_termination,\n", | ||
| ")" | ||
| ], | ||
| "id": "f08dc6f4372930e4", | ||
| "outputs": [], | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "### 3.1. Specify vacuum", | ||
| "id": "c483e6aae37766b1" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.slab.configuration import VacuumConfiguration, AxisEnum\n", | ||
| "\n", | ||
| "vacuum = VacuumConfiguration(direction=AxisEnum.z, size=VACUUM, is_orthogonal=True)" | ||
| ], | ||
| "id": "ca440d1dad2061da", | ||
| "outputs": [], | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "### 3.2. Create slab configuration", | ||
| "id": "41066bf389dfd216" | ||
| }, | ||
| { | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.slab import SlabConfiguration\n", | ||
| "\n", | ||
| "slab_configuration = SlabConfiguration(\n", | ||
| " supercell_xy=XY_SUPERCELL_MATRIX, stack_components=[atomic_layers, vacuum], direction=AxisEnum.z\n", | ||
| ")" | ||
| ], | ||
| "id": "ee1be3faa5341c70", | ||
| "outputs": [], | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "### 3.3. Create slab", | ||
| "id": "7869f1b09ecd62c6" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.slab import create_slab\n", | ||
| "\n", | ||
| "slab = create_slab(slab_configuration)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -316,9 +373,7 @@ | |
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "source": "visualize(slab, repetitions=[1, 1, 1], rotation=\"0x\", viewer=\"wave\")", | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
|
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@@ -340,6 +395,7 @@ | |
| "cell_type": "code", | ||
| "source": [ | ||
| "from utils.jupyterlite import set_materials\n", | ||
| "\n", | ||
| "set_materials(slab)" | ||
| ], | ||
| "metadata": { | ||
|
|
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We should use
get_slabsfromcrystal_lattice_planesReply via ReviewNB