feature/SOF-7347 update: use interface settings as class + add metadata to interface #124
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@@ -11,7 +11,7 @@ | |
| "<h2 style=\"color:green\">Usage</h2>\n", | ||
|
There was a problem hiding this comment. Line #5. distance_z=3.0, # distance between two planes, in Angstroms distance between substrate and layer Reply via ReviewNB |
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| "\n", | ||
| "1. Make sure to select Input Materials\n", | ||
| "2. Set Interface Parameters (e.g. `distance_z`, `max_area`, `miller_indices`) below or use the default values\n", | ||
| "3. Click \"Run\" > \"Run All Cells\" to run all cells\n", | ||
| "4. Wait for the run to complete (depending on the area, it can take 1-2 min or more). Scroll down to view cell results.\n", | ||
| "5. Review the strain plot and modify its parameters as needed\n", | ||
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@@ -32,62 +32,40 @@ | |
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "## 1. Install Packages\n", | ||
| "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` as directed in README." | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| } | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "import sys\n", | ||
| "\n", | ||
| "if sys.platform == \"emscripten\":\n", | ||
| " import micropip\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\")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 2. Set Interface Parameters\n", | ||
| "\n", | ||
| "### 2.1. Set Substrate and Layer Parameters \n", | ||
| "Imported `InterfaceSettings` is a class that specifies the parameters for the construction of the interface. The default values are assumed if properties are not set during the initialization.\n", | ||
| "Additionally, specify if the termination selection is done using interactive prompt, or the via selecting the termination index in the code." | ||
| ] | ||
| }, | ||
| { | ||
|
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@@ -96,46 +74,50 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.interface import InterfaceSettings\n", | ||
| "\n", | ||
| "# Parameters can be set during the class initialization:\n", | ||
| "interface_builder_settings = InterfaceSettings(\n", | ||
| " distance_z=3.0, # distance between two planes, in Angstroms\n", | ||
| " use_conventional_cell=True, # if True, the surface plane is constructed using miller indices of the conventional cell\n", | ||
| ")\n", | ||
| "\n", | ||
| "# Parameters can be set after the initialization:\n", | ||
| "interface_builder_settings.SubstrateParameters.miller_indices = (1, 1, 1) # the Miller indices of the interfacial plane of the substrate\n", | ||
| "interface_builder_settings.SubstrateParameters.thickness = 3 # substrate thickness in layers\n", | ||
| "interface_builder_settings.LayerParameters.miller_indices = (0, 0, 1) # the Miller indices of the interfacial plane of the layer\n", | ||
| "interface_builder_settings.LayerParameters.thickness = 1 # layer thickness in layers\n", | ||
| "\n", | ||
| "IS_TERMINATION_SELECTION_INTERACTIVE = False # if True, the user can select the termination interactively\n", | ||
| "TERMINATION_INDEX = 0 # the default termination index that is used if no termination selected, ignored in interactive mode" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 2.2. Set Strain Matching Algorithm Parameters (Optional)\n", | ||
| "The search algorithm for supercells matching can be tuned by setting its parameters directly, otherwise the default values are used." | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| } | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.interface import ZSLParameters\n", | ||
| "interface_builder_settings.ZSLParameters = ZSLParameters(\n", | ||
| " max_area=50, # maximum area of the generated interfaces, in Angstroms^2\n", | ||
| " max_area_tol=0.09, # maximum tolerance on ratio of super-lattices to consider equal\n", | ||
| " max_length_tol=0.03, # maximum length tolerance for two vectors to be considered equal\n", | ||
| " max_angle_tol=0.01, # maximum angle tolerance for two sets of vectors to have equal angles\n", | ||
| ")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
|
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@@ -185,7 +167,7 @@ | |
| "interface_builder = init_interface_builder(\n", | ||
| " substrate=materials[0],\n", | ||
| " layer=materials[1],\n", | ||
| " settings=interface_builder_settings\n", | ||
| ")" | ||
| ], | ||
| "metadata": { | ||
|
|
@@ -239,7 +221,6 @@ | |
| "from mat3ra.made.tools.build import create_interfaces\n", | ||
| "\n", | ||
| "interface_data_holder = create_interfaces(\n", | ||
| " sort_by_strain_and_size=True,\n", | ||
| " remove_duplicates=True,\n", | ||
| " interface_builder=interface_builder,\n", | ||
|
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@@ -254,7 +235,7 @@ | |
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 4.4. Print out interface with the lowest strain for selected termination" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
|
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@@ -359,7 +340,8 @@ | |
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 6.3. Pass data to the outside runtime\n", | ||
| "Enrich the selected interfaces names with the strain values and pass them to the application runtime." | ||
| ] | ||
| }, | ||
| { | ||
|
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@@ -370,6 +352,10 @@ | |
| "source": [ | ||
| "from utils.jupyterlite import set_data\n", | ||
| "\n", | ||
| "for interface in selected_interfaces:\n", | ||
| " if \"Interface, Strain:\" not in interface[\"name\"]:\n", | ||
| " interface[\"name\"] = f'{interface[\"name\"]}, Interface, Strain:{interface[\"metadata\"][\"interface_properties\"][\"mean_abs_strain\"]*100:.3f}%'\n", | ||
| "\n", | ||
| "set_data(\"materials\", selected_interfaces)" | ||
| ] | ||
| } | ||
|
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specify whether termination selection is done
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Smth like: Choose the termination selection mode: interactive with prompt or by index in the code ?