Add NVT post-processing for TDEP input generation #698
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,231 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "acfd5c8f", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Anharmonic Phonons From NVT Molecular Dynamics\n", | ||
| "\n", | ||
| "[](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/python/anharmonic_phonons.ipynb)\n", | ||
| "\n", | ||
| "This tutorial shows how to generate standard [TDEP](https://tdep-developers.github.io/tdep/) input files through `post_process_kwargs` while running an NVT molecular dynamics simulation with `janus-core`, and then use them to compute anharmonic phonon properties with TDEP.\n", | ||
| "\n", | ||
| "The workflow is:\n", | ||
| "\n", | ||
| "1. Build a unit cell and supercell.\n", | ||
| "2. Run a small NVT molecular dynamics simulation with `janus-core`.\n", | ||
| "3. Automatically generate standard TDEP input files.\n", | ||
| "4. Run TDEP separately to extract force constants and compute anharmonic phonon properties.\n", | ||
| "\n", | ||
| "> [!NOTE]\n", | ||
| "> The `janus-core` part of this tutorial can be run directly in Python, but the TDEP commands require a local environment where TDEP is installed.\n", | ||
| "\n", | ||
| "\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "9751041e", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from pathlib import Path\n", | ||
| "\n", | ||
| "from ase.build import bulk\n", | ||
| "from ase.io import write\n", | ||
| "from IPython.display import Image\n", | ||
| "\n", | ||
| "from janus_core.calculations.md import NVT\n", | ||
| "from janus_core.calculations.single_point import SinglePoint\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "5b840b9c", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Build The Unit Cell And Supercell\n", | ||
| "\n", | ||
| "We first construct a rocksalt NaCl unit cell and expand it to a `2 x 2 x 2` supercell.\n", | ||
| "\n", | ||
| "The unit-cell structure is used to generate `infile.ucposcar`, while the supercell structure is used both for the molecular dynamics simulation and to generate `infile.ssposcar`.\n", | ||
| "\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "9cfcc50b", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "unit_cell = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n", | ||
| "supercell = unit_cell * (2, 2, 2)\n", | ||
| "\n", | ||
| "write(\"unit_cell.cif\", unit_cell)\n", | ||
| "write(\"supercell.cif\", supercell)\n", | ||
| "\n", | ||
| "Path(\"unit_cell.cif\"), Path(\"supercell.cif\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "036f06e1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Run NVT Molecular Dynamics And Generate TDEP Inputs\n", | ||
| "\n", | ||
| "We now run a small NVT molecular dynamics simulation using the supercell structure.\n", | ||
| "\n", | ||
| "TDEP input generation is enabled through `post_process_kwargs`. This automatically writes the following files into `tdep-inputs/` after the MD run finishes:\n", | ||
| "\n", | ||
| "- `infile.ucposcar`\n", | ||
| "- `infile.ssposcar`\n", | ||
| "- `infile.positions`\n", | ||
| "- `infile.forces`\n", | ||
| "- `infile.stat`\n", | ||
| "- `infile.meta`\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "b3c201e8", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "single_point = SinglePoint(\n", | ||
| " struct=\"supercell.cif\",\n", | ||
| " arch=\"mace_mp\",\n", | ||
| " model=\"small\",\n", | ||
| ")\n", | ||
| "\n", | ||
| "nvt = NVT(\n", | ||
| " struct=single_point.struct,\n", | ||
| " temp=300.0,\n", | ||
| " steps=200,\n", | ||
| " timestep=1.0,\n", | ||
| " traj_every=20,\n", | ||
| " stats_every=20,\n", | ||
| " file_prefix=\"janus_results/NaCl-nvt-T300\",\n", | ||
| " post_process_kwargs={\n", | ||
| " \"tdep_compute\": True,\n", | ||
| " \"tdep_unit_cell_file\": \"unit_cell.cif\",\n", | ||
| " \"tdep_supercell_file\": \"supercell.cif\",\n", | ||
| " \"tdep_output_dir\": \"janus_results/tdep-inputs\",\n", | ||
| " },\n", | ||
| ")\n", | ||
| "\n", | ||
| "nvt.run()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "28caa974", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Check The Generated TDEP Input Files\n", | ||
| "\n", | ||
| "After the molecular dynamics simulation completes, the TDEP input files should be available in the `tdep-inputs/` directory.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "4c69c025", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "required_files = [\n", | ||
| " \"infile.ucposcar\",\n", | ||
| " \"infile.ssposcar\",\n", | ||
| " \"infile.positions\",\n", | ||
| " \"infile.forces\",\n", | ||
| " \"infile.stat\",\n", | ||
| " \"infile.meta\",\n", | ||
| "]\n", | ||
| "\n", | ||
| "for name in required_files:\n", | ||
| " path = Path(\"janus_results/tdep-inputs\") / name\n", | ||
| " print(name, path.exists(), path)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "54941085", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Run TDEP And Plot The Phonon Dispersion\n", | ||
| "\n", | ||
| "With the input files in place, we run the [TDEP](https://tdep-developers.github.io/tdep/) executables directly from the notebook. The `-p` flag asks TDEP to emit a gnuplot script that targets a PDF; we then convert that PDF to a PNG with `pdftoppm` so the figure can be embedded inline.\n", | ||
| "\n", | ||
| "\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "3d2fbdb8", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "%%bash\n", | ||
| "set -e\n", | ||
| "cd janus_results/tdep-inputs\n", | ||
| "\n", | ||
| "extract_forceconstants -rc2 100\n", | ||
| "cp outfile.forceconstant infile.forceconstant\n", | ||
| "phonon_dispersion_relations --dos -p\n", | ||
| "gnuplot outfile.dispersion_relations.gnuplot_pdf\n", | ||
| "pdftoppm -png -r 150 outfile.dispersion_relations.pdf outfile.dispersion_relations\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "4246dbef", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Inspect The Phonon Dispersion\n", | ||
| "\n", | ||
| "The figure below is the TDEP-generated phonon dispersion rendered by gnuplot.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "cba90ea0", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "Image(filename=\"janus_results/tdep-inputs/outfile.dispersion_relations-1.png\")\n" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "janus-core", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.12.13" | ||
| }, | ||
| "nbsphinx": { | ||
| "execute": "always", | ||
| "timeout": 600 | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -12,3 +12,4 @@ Python Tutorials | |
| phonons | ||
| neb | ||
| elasticity | ||
| anharmonic_phonons | ||
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I'm concerned this is being done on the docs workflow.
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In case it's not clear, @junwen94, the docs that are built during
ci.yml(which runs on every push, and for every PR) do not run the notebook tutorials (make all), they just check the docs build from the .rst files (make html).The tutorials will be run as part of the
publish-on-pypi.ymlworkflow, which is triggered on new tagged releases, so you should still test locally that bothmakecommands work.You will need installations in
ci.yml, but only for thetestssection of the workflow, as we have for PLUMED (assuming, as I suggest elsewhere, we actually run tdep, and not just test the input generation).