Feature/SOF-7339 update: rewrite ZSL notebook to use made-tools #118
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@@ -46,13 +46,11 @@ | |
| "outputs": [], | ||
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There was a problem hiding this comment. There was a problem hiding this comment. There was a problem hiding this comment. We can just pass
substrate = materials[0] layer = materials[1] There was a problem hiding this comment. There was a problem hiding this comment. Line #5. interfaces_range = slice(0, 1) # select the first interface with the lowest strain Let's move the comment above and add with the lowest strain and number of atoms
The actual selection by termination and slice functionality can go to the holder class itself too Reply via ReviewNB There was a problem hiding this comment. Line #4. materials = list(map(lambda interface_config: from_pymatgen(interface_config), selected_interface)) This lambda function can go to interface_data_holder Reply via ReviewNB There was a problem hiding this comment. Line #4. await micropip.install('mat3ra-api-examples[dev]', deps=False)
Remove Reply via ReviewNB There was a problem hiding this comment. Line #1. print(interface_data_holder.terminations)
Maybe we should print the number of interfaces for the first termination, not all of them Should be:
print(f"Terminations found: {interface_data_holder.terminations)}")
print(f"Interfaces for the first termination: {interface_data_holder.get_interfaces_for_termination(0))}")
Reply via ReviewNB There was a problem hiding this comment. Line #3. materials = list(selected_interface) We should not need Reply via ReviewNB There was a problem hiding this comment. We probably don't need print statement here either. We should instead add a visualization function to plot the selected interface(s) in a subsequent task |
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| "source": [ | ||
| "SUBSTRATE_PARAMETERS = {\n", | ||
| " \"MILLER_INDICES\": (1, 1, 1), # the miller indices of the interfacial plane\n", | ||
| " \"THICKNESS\": 3, # in layers\n", | ||
| "}\n", | ||
| "\n", | ||
| "LAYER_PARAMETERS = {\n", | ||
| " \"MILLER_INDICES\": (0, 0, 1), # the miller indices of the interfacial plane\n", | ||
| " \"THICKNESS\": 1, # in layers\n", | ||
| "}\n", | ||
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@@ -107,7 +105,8 @@ | |
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 2. 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." | ||
| ] | ||
| }, | ||
| { | ||
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@@ -120,35 +119,30 @@ | |
| "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\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 3. Load input Materials\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import get_data\n", | ||
| "from mat3ra.made.material import Material\n", | ||
| "\n", | ||
| "# Get the list of input materials and load them into `materials_in` variable\n", | ||
| "get_data(\"materials_in\", globals())\n", | ||
| "materials = [] \n", | ||
| "for material_config in globals()[\"materials_in\"]:\n", | ||
| " print(material_config, \"\\n\")\n", | ||
| " materials.append(Material(material_config))" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
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@@ -177,66 +171,28 @@ | |
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build import create_interfaces\n", | ||
| "\n", | ||
| "interface_data_holder = create_interfaces(\n", | ||
| " substrate=materials[0],\n", | ||
| " layer=materials[1],\n", | ||
| " settings={\n", | ||
| " \"SUBSTRATE_PARAMETERS\": SUBSTRATE_PARAMETERS,\n", | ||
| " \"LAYER_PARAMETERS\": LAYER_PARAMETERS,\n", | ||
| " \"USE_CONVENTIONAL_CELL\": USE_CONVENTIONAL_CELL,\n", | ||
| " \"ZSL_PARAMETERS\": ZSL_PARAMETERS,\n", | ||
| " \"INTERFACE_PARAMETERS\": INTERFACE_PARAMETERS,\n", | ||
| " },\n", | ||
| " sort_by_strain_and_size=True,\n", | ||
| " remove_duplicates=True,\n", | ||
| ")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 4.2. Print out the interfaces and terminations" | ||
| ] | ||
| }, | ||
| { | ||
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@@ -245,18 +201,15 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "print(\"Found terminations:\", interface_data_holder.terminations)\n", | ||
| "print(f\"Number of interfaces for a termination: {len(interface_data_holder.get_interfaces_for_termination(0))}\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 4.2. Print out interfaces with the lowest strain for each termination" | ||
| ] | ||
| }, | ||
| { | ||
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@@ -265,48 +218,19 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "for termination in interface_data_holder.terminations:\n", | ||
| " print(f\"Interface with lowest strain for termination {termination} (index 0):\")\n", | ||
| " interfaces = interface_data_holder.get_interfaces_for_termination(termination)\n", | ||
| " first_interface = interfaces[0]\n", | ||
| " print(f\" strain: {first_interface.get_mean_abs_strain() * 100:.3f}%\")\n", | ||
| " print(\" number of atoms:\", first_interface.num_sites)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 5. Plot the results\n", | ||
| "\n", | ||
| "Plot the number of atoms vs strain. Adjust the parameters as needed.\n" | ||
| ] | ||
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@@ -317,91 +241,26 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.plot import plot_strain_vs_atoms\n", | ||
| "\n", | ||
| "PLOT_SETTINGS = {\n", | ||
| " \"HEIGHT\": 600,\n", | ||
| " \"X_SCALE\": \"log\", # or linear\n", | ||
| " \"Y_SCALE\": \"log\", # or linear\n", | ||
| "}\n", | ||
| "\n", | ||
| "plot_strain_vs_atoms(interface_data_holder, PLOT_SETTINGS)\n", | ||
| "\n", | ||
| "print(\"Terminations: \\n\", interface_data_holder.terminations)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 6. Select the interface to pass outside this kernel\n", | ||
| "\n", | ||
| "### 6.1. Select the interface with the desired termination and strain\n", | ||
| "\n", | ||
| "Select the index for termination first, and for it - the index in the list of corresponding interfaces sorted by strain (index 0 has minimum strain)." | ||
| ] | ||
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@@ -412,19 +271,18 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Could be either the termination as tuple, e.g. `('Ni_P6/mmm_1', 'C_C2/m_2')` or its index: `0`\n", | ||
| "termination_or_its_index = 0\n", | ||
| "# select the first interface with the lowest strain and the smallest number of atoms\n", | ||
| "interfaces_slice_range_or_index = 0\n", | ||
| "selected_interfaces = interface_data_holder.get_interfaces_as_materials(termination_or_its_index, interfaces_slice_range_or_index)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 6.2. Pass data to the outside runtime\n" | ||
| ] | ||
| }, | ||
| { | ||
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@@ -433,12 +291,10 @@ | |
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import set_data\n", | ||
| "\n", | ||
| "set_data(\"materials\", selected_interfaces)\n", | ||
| "print(selected_interfaces)" | ||
| ] | ||
| } | ||
| ], | ||
|
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Line #6. await install_packages("create_interface_with_min_strain_zsl.ipynb","../../config.yml")Are we keeping this change? If yes, then how will the packages be installed in Python (not Pyodide)?
Reply via ReviewNB