FHI-aims IO Parsers (#3435)

* Move FHI-aims io from atomate2 into pymatgen 1) parsers and AimsOuput ojbects moved over 2) All ASE Atoms objects removed in favor of pymatgen structures 3) TO DO: Check name schemes 4) Create an AimsInputs object in the future * Initial aims input files 1) remove aims_outputs naming convention 2) Add AimsGeometryIn and AimsControlIn classes * Add test for the aims parsers Adjusted from ASE parser tests * Add tests for AimsOutputs 1) How to handle stress in properties? * Add aims output refrence files For aims outputs checks * Add tests for AimsGeometryIn inputs Test for both Si and H2O * Add tests for AimsCube Make sure that the AimsCubes are properly formatted * Add tests for aims_control_in Add test for aims control.in file generators * gzip all output files as requested all output files are gzipped * Gzip all refrence files 1) Species blocks can now read from gzipped file 2) geometry.in can now read a gzip file * Remove json dict comparision Error in the Actions from rounding errors, do more explicit test for as_dict * Add full type hinting for inputs.py and convert docstrings 1) Docstrings are googledoc format 2) All type hinting is done * Convert all AimsOutput docstrings to google doc Everything is also type hintted now * Add type hining and google doc strings to parsers * Fix tests Forgot pip install in the last commit * Requested changes to tests 1) Moved lines objects to seperate files 2) inline k_point_weights 3) Remove trailing comma 4) tmpdir -> tmp_path * Update pymatgen/io/aims/inputs.py use numpy eye instead of a full list Co-authored-by: Janosh Riebesell <[email protected]> Signed-off-by: Thomas Purcell <[email protected]> * pre-commit auto-fixes * Make more changes requested * Rename io.aims.output to io.aims.outputs Keep it consistent with inputs naming scheme * Add example for FHI-aims io * Make corrections suggested by @janosh 1) Remove copy of species file in examples 2) Typo corrections in docstrings 3) d -> dct for `from_dict` methods 4) error mesages for AimsCube 5) Shortened default checks in Inputs 6) Removal of chdir in tests * add nbstripout to pre-commit hooks apply to FHI-aims-example.ipynb * class AimsCube snake_case spin_state * fix doc str * refactor AimsCube.from_dict * fix typo * fix tests * mv tests/io/aims/(aims_->'')input_files tests/io/aims/(aims_->'')output_files tests/io/aims/(aims_->'')parser_checks * Correct refrence json files for aims_outputs aims.output -> aims.outputs module name --------- Signed-off-by: Thomas Purcell <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
materialsproject · Nov 8, 2023 · d4e253d · d4e253d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -56,3 +56,9 @@ repos:
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
         args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        args: [--drop-empty-cells, --keep-output]
diff --git a/examples/aims_io/FHI-aims-example.ipynb b/examples/aims_io/FHI-aims-example.ipynb
@@ -0,0 +1,161 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8e09cccf-4335-4c59-bfa7-d3e3caeef404",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pymatgen.io.aims.inputs import AimsGeometryIn, AimsCube, AimsControlIn\n",
+    "from pymatgen.io.aims.outputs import AimsOutput\n",
+    "\n",
+    "from pymatgen.core import Structure, Lattice\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
+    "from pathlib import Path\n",
+    "from subprocess import check_call\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "536af143-f892-4549-86d7-ff426ba265ed",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# AIMS_CMD should be modified to match your system\n",
+    "AIMS_CMD = \"aims.x\"\n",
+    "AIMS_OUTPUT = \"aims.out\"\n",
+    "AIMS_SD = \"species_dir\"\n",
+    "AIMS_TEST_DIR = \"../../tests/io/aims/species_directory/light/\"\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4d8d9fda-af37-45eb-971c-56fed59f3a27",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create test structure\n",
+    "structure = Structure(\n",
+    "    lattice=Lattice(\n",
+    "        np.array([[0, 2.715, 2.715],[2.715, 0, 2.715], [2.715, 2.715, 0]])\n",
+    "    ),\n",
+    "    species=[\"Si\", \"Si\"],\n",
+    "    coords=np.array([np.zeros(3), np.ones(3) *  0.25])\n",
+    ")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8e67e134-84f8-4c35-afe4-87cd66e2e781",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create the geometry file from the structure\n",
+    "geo_in = AimsGeometryIn.from_structure(structure)\n",
+    "\n",
+    "# Create the control.in file\n",
+    "cont_in = AimsControlIn(\n",
+    "    {\n",
+    "        \"xc\": \"pw-lda\",\n",
+    "        \"relax_geometry\": \"trm 0.01\",\n",
+    "        \"relax_unit_cell\": \"full\",\n",
+    "        \"species_dir\": AIMS_SD,\n",
+    "    }\n",
+    ")\n",
+    "\n",
+    "# Add new parameters as if AimsControl\n",
+    "cont_in[\"k_grid\"] = [1, 1, 1]\n",
+    "\n",
+    "# Output options to control in automatically append the list\n",
+    "cont_in[\"output\"] = \"hirshfeld\"\n",
+    "cont_in[\"output\"] = [\"eigenvectors\"]\n",
+    "\n",
+    "# Cube file output controlled by the AimsCube class\n",
+    "cont_in[\"cubes\"] = [\n",
+    "    AimsCube(\"total_density\", origin=[0,0,0], points=[11, 11, 11]),\n",
+    "    AimsCube(\"eigenstate_density 1\", origin=[0, 0, 0], points=[11, 11, 11]),\n",
+    "]\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "096337d6-871a-48dc-b4b3-a3c7c6fd812e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Write the input files\n",
+    "workdir = Path.cwd() / \"workdir/\"\n",
+    "workdir.mkdir(exist_ok=True)\n",
+    "\n",
+    "geo_in.write_file(workdir, overwrite=True)\n",
+    "cont_in.write_file(structure, workdir, overwrite=True)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c9994cd2-5e45-4071-ab87-b6b3e3af1174",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run the calculation\n",
+    "with open(f\"{workdir}/{AIMS_OUTPUT}\", \"w\") as outfile:\n",
+    "    aims_run = check_call([AIMS_CMD], cwd=workdir, stdout=outfile)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0c42a6c6-bb45-472f-a2cb-190cdd922047",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Read the aims output file and the final relaxed geometry\n",
+    "outputs = AimsOutput.from_outfile(f\"{workdir}/{AIMS_OUTPUT}\")\n",
+    "relaxed_structure = AimsGeometryIn.from_file(f\"{workdir}/geometry.in.next_step\")\n",
+    "\n",
+    "# Check the results\n",
+    "assert outputs.get_results_for_image(-1).lattice == relaxed_structure.structure.lattice\n",
+    "assert np.all(outputs.get_results_for_image(-1).frac_coords == relaxed_structure.structure.frac_coords)\n",
+    "\n",
+    "assert np.allclose(\n",
+    "    outputs.get_results_for_image(-1).properties[\"stress\"],\n",
+    "    outputs.stress\n",
+    ")\n",
+    "\n",
+    "assert np.allclose(\n",
+    "    outputs.get_results_for_image(-1).site_properties[\"force\"],\n",
+    "    outputs.forces\n",
+    ")\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/pymatgen/io/aims/__init__.py b/pymatgen/io/aims/__init__.py
@@ -0,0 +1 @@
+"""IO interface for FHI-aims."""