pack-mm 0.0.15__tar.gz → 0.0.20__tar.gz
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- pack_mm-0.0.20/PKG-INFO +246 -0
- pack_mm-0.0.20/README.md +225 -0
- {pack_mm-0.0.15 → pack_mm-0.0.20}/pack_mm/cli/packmm.py +21 -14
- {pack_mm-0.0.15 → pack_mm-0.0.20}/pack_mm/core/core.py +78 -60
- {pack_mm-0.0.15 → pack_mm-0.0.20}/pyproject.toml +6 -1
- pack_mm-0.0.20/tests/test_core.py +178 -0
- {pack_mm-0.0.15 → pack_mm-0.0.20}/tests/test_packmm.py +8 -1
- pack_mm-0.0.15/PKG-INFO +0 -36
- pack_mm-0.0.15/README.md +0 -15
- {pack_mm-0.0.15 → pack_mm-0.0.20}/LICENSE +0 -0
- {pack_mm-0.0.15 → pack_mm-0.0.20}/pack_mm/__init__.py +0 -0
- {pack_mm-0.0.15 → pack_mm-0.0.20}/tests/__init__.py +0 -0
- {pack_mm-0.0.15 → pack_mm-0.0.20}/tests/utils.py +0 -0
pack_mm-0.0.20/PKG-INFO
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Metadata-Version: 2.1
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Name: pack-mm
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Version: 0.0.20
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Summary: packing materials and molecules in boxes using for machine learnt interatomic potentials
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Author: Alin M. Elena
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Natural Language :: English
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Classifier: Development Status :: 3 - Alpha
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Project-URL: Repository, https://github.com/ddmms/pack-mm/
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Project-URL: Documentation, https://ddmms.github.io/pack-mm/
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Requires-Python: >=3.10
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Requires-Dist: janus-core>=0.7.2
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Requires-Dist: typer<1.0.0,>=0.12.5
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Requires-Dist: typer-config<2.0.0,>=1.4.2
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Description-Content-Type: text/markdown
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[![Python versions][python-badge]][python-link]
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[![Build Status][ci-badge]][ci-link]
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[![Coverage Status][cov-badge]][cov-link]
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[![License][license-badge]][license-link]
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# what is packmm
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packmm is a simple python package that allows to build atomistic and molecular
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systems which are of interest for materials and molecular modelling.
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It tries to generate realistic starting configuration by employing machine learnt
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interatomic potential for describing interactions between atoms and Monte Carlo,
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Molecular Dynamics and hybrid Monte Carlo.
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It provides both a cli and a python api, with some examples below.
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## Quick install
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```bash
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uv pip install pack-mm
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```
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or install the lates
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```bash
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uv pip install git+https://github.com/ddmms/pack-mm.git
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```
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## CLI examples
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### MOF in spherical pocket
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```bash
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packmm --system examples/data/UiO-66.cif --molecule H2O --nmols 10 --where sphere --centre 10.0,10.0,10.0 --radius 5.0 --geometry
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```
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### Zeolite in cylindrical channel
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```bash
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packmm --system examples/data/MFI.cif --molecule H2O --nmols 30 --where cylinderY --centre 10.0,10.0,13.0 --radius 3.5 --height 19.00 --no-geometry
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```
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### NaCl on surface
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```bash
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packmm --system examples/data/NaCl.cif --molecule H2O --nmols 30 --where box --centre 8.5,8.5,16.0 --a 16.9 --b 16.9 --c 7.5 --no-geometry
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```
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### MOF ellipsoid
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first add a methanol
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```bash
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packmm --system examples/data/Cu2L.cif --molecule examples/data/Ethanol.xyz --nmols 1 --where sphere --centre 5.18,8.15,25.25 --radius 1 --model small-0b2 --geometry
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```
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!()[examples/pics/Cu2L-ethanol.png]
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``` bash
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packmm --system Cu2L-ethanol.cif --molecule H2O --nmols 10 --where ellipsoid --centre 5.18,8.15,25.25 --a 5.18 --b 8.15 --c 8.25 --no-geometry --model small-0b2
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```
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!()[examples/pics/Cu2l-ethanol-water.png]
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### Liquid water
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```bash
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packmm --molecule H2O --nmols 33 --where anywhere --cell-a 10.0 --cell-b 10.0 --cell-c 10.0 --model small-0b2
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```
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!()[examples/pics/water.png]
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### interstitials
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```bash
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packmm --system Pd-super.cif --molecule H2 --nmols 50 --where anywhere --model small-0b2
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```
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before optimisation
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!()[examples/pics/Pd-H2-noopt.png]
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after optimisation
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!()[examples/pics/Pd-H2.png]
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### full list of options
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```bash
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packmm --help
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Usage: packmm [OPTIONS]
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Pack molecules into a system based on the specified parameters.
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╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
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│ --system TEXT The original box in which │
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│ you want to add particles. │
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│ If not provided, an empty │
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│ box will be created. │
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│ [default: None] │
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│ --molecule TEXT Name of the molecule to be │
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│ processed, ASE-recognizable │
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│ or ASE-readable file. │
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│ [default: H2O] │
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│ --nmols INTEGER Target number of molecules │
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│ to insert. │
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│ [default: -1] │
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│ --ntries INTEGER Maximum number of attempts │
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│ to insert each molecule. │
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│ [default: 50] │
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│ --seed INTEGER Random seed for │
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│ reproducibility. │
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│ [default: 2025] │
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│ --where [anywhere|sphere|box|cylin Where to insert the │
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│ derZ|cylinderY|cylinderX|e molecule. Choices: │
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│ llipsoid] 'anywhere', 'sphere', │
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│ 'box', 'cylinderZ', │
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│ 'cylinderY', 'cylinderX', │
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│ 'ellipsoid'. │
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│ [default: anywhere] │
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│ --centre TEXT Centre of the insertion │
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│ zone, coordinates in Å, │
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│ e.g., '5.0, 5.0, 5.0'. │
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│ [default: None] │
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│ --radius FLOAT Radius of the sphere or │
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│ cylinder in Å, depending on │
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│ the insertion volume. │
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│ [default: None] │
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│ --height FLOAT Height of the cylinder in │
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│ Å. │
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│ [default: None] │
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│ --a FLOAT Side of the box or │
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│ semi-axis of the ellipsoid, │
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│ in Å, depends on the │
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│ insertion method. │
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│ [default: None] │
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│ --b FLOAT Side of the box or │
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│ semi-axis of the ellipsoid, │
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│ in Å, depends on the │
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│ insertion method. │
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│ [default: None] │
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│ --c FLOAT Side of the box or │
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│ semi-axis of the ellipsoid, │
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│ in Å, depends on the │
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│ insertion method. │
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│ [default: None] │
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│ --device TEXT Device to run calculations │
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│ on (e.g., 'cpu' or 'cuda'). │
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│ [default: cpu] │
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│ --model TEXT ML model to use. │
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│ [default: medium-omat-0] │
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│ --arch TEXT MLIP architecture to use. │
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│ [default: mace_mp] │
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│ --temperature FLOAT Temperature for the Monte │
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│ Carlo acceptance rule. │
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│ [default: 300.0] │
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│ --cell-a FLOAT Side of the empty box along │
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│ the x-axis in Å. │
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│ [default: 20.0] │
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│ --cell-b FLOAT Side of the empty box along │
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│ the y-axis in Å. │
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│ [default: 20.0] │
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│ --cell-c FLOAT Side of the empty box along │
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│ the z-axis in Å. │
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│ [default: 20.0] │
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│ --fmax FLOAT force tollerance for │
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│ optimisation if needed. │
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│ [default: 0.1] │
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│ --geometry --no-geometry Perform geometry │
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│ optimization at the end. │
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│ [default: geometry] │
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│ --out-path TEXT path to save various │
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│ outputs. │
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│ [default: .] │
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│ --install-completion Install completion for the │
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│ current shell. │
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│ --show-completion Show completion for the │
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│ current shell, to copy it │
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│ or customize the │
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│ installation. │
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│ --help Show this message and exit. │
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╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
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```
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[python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
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[python-link]: https://pypi.org/project/pack-mm/
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[ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
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[ci-link]: https://github.com/ddmms/pack-mm/actions
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[cov-badge]: https://coveralls.io/repos/github/ddmms/pack-mm/badge.svg?branch=main
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[cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
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[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
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[license-link]: https://opensource.org/license/MIT
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pack_mm-0.0.20/README.md
ADDED
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@@ -0,0 +1,225 @@
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1
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+
[![Python versions][python-badge]][python-link]
|
|
2
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+
[![Build Status][ci-badge]][ci-link]
|
|
3
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+
[![Coverage Status][cov-badge]][cov-link]
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4
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[![License][license-badge]][license-link]
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5
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+
|
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6
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+
# what is packmm
|
|
7
|
+
|
|
8
|
+
packmm is a simple python package that allows to build atomistic and molecular
|
|
9
|
+
systems which are of interest for materials and molecular modelling.
|
|
10
|
+
|
|
11
|
+
It tries to generate realistic starting configuration by employing machine learnt
|
|
12
|
+
interatomic potential for describing interactions between atoms and Monte Carlo,
|
|
13
|
+
Molecular Dynamics and hybrid Monte Carlo.
|
|
14
|
+
|
|
15
|
+
It provides both a cli and a python api, with some examples below.
|
|
16
|
+
|
|
17
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+
## Quick install
|
|
18
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+
|
|
19
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+
```bash
|
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20
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+
|
|
21
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+
uv pip install pack-mm
|
|
22
|
+
|
|
23
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+
```
|
|
24
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+
or install the lates
|
|
25
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+
|
|
26
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+
```bash
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27
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+
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uv pip install git+https://github.com/ddmms/pack-mm.git
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```
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## CLI examples
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33
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+
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34
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35
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### MOF in spherical pocket
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36
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+
|
|
37
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```bash
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+
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39
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packmm --system examples/data/UiO-66.cif --molecule H2O --nmols 10 --where sphere --centre 10.0,10.0,10.0 --radius 5.0 --geometry
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```
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45
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### Zeolite in cylindrical channel
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```bash
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49
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packmm --system examples/data/MFI.cif --molecule H2O --nmols 30 --where cylinderY --centre 10.0,10.0,13.0 --radius 3.5 --height 19.00 --no-geometry
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```
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### NaCl on surface
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```bash
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packmm --system examples/data/NaCl.cif --molecule H2O --nmols 30 --where box --centre 8.5,8.5,16.0 --a 16.9 --b 16.9 --c 7.5 --no-geometry
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```
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64
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65
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### MOF ellipsoid
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66
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+
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67
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+
first add a methanol
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68
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+
|
|
69
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+
```bash
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70
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+
|
|
71
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+
packmm --system examples/data/Cu2L.cif --molecule examples/data/Ethanol.xyz --nmols 1 --where sphere --centre 5.18,8.15,25.25 --radius 1 --model small-0b2 --geometry
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72
|
+
|
|
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|
+
```
|
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|
+
|
|
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|
+
!()[examples/pics/Cu2L-ethanol.png]
|
|
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|
+
|
|
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|
+
``` bash
|
|
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|
+
|
|
79
|
+
packmm --system Cu2L-ethanol.cif --molecule H2O --nmols 10 --where ellipsoid --centre 5.18,8.15,25.25 --a 5.18 --b 8.15 --c 8.25 --no-geometry --model small-0b2
|
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+
|
|
81
|
+
|
|
82
|
+
```
|
|
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|
+
|
|
84
|
+
!()[examples/pics/Cu2l-ethanol-water.png]
|
|
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|
+
|
|
86
|
+
### Liquid water
|
|
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|
+
|
|
88
|
+
```bash
|
|
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|
+
|
|
90
|
+
packmm --molecule H2O --nmols 33 --where anywhere --cell-a 10.0 --cell-b 10.0 --cell-c 10.0 --model small-0b2
|
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|
+
|
|
92
|
+
|
|
93
|
+
```
|
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+
|
|
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|
+
!()[examples/pics/water.png]
|
|
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|
+
### interstitials
|
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|
+
|
|
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|
+
```bash
|
|
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|
+
|
|
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|
+
packmm --system Pd-super.cif --molecule H2 --nmols 50 --where anywhere --model small-0b2
|
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|
+
|
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|
+
```
|
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|
+
|
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|
+
before optimisation
|
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+
|
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|
+
!()[examples/pics/Pd-H2-noopt.png]
|
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+
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+
|
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+
after optimisation
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+
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|
+
!()[examples/pics/Pd-H2.png]
|
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+
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+
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+
|
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+
### full list of options
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+
|
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+
```bash
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+
|
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+
packmm --help
|
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+
|
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+
Usage: packmm [OPTIONS]
|
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+
|
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+
Pack molecules into a system based on the specified parameters.
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+
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+
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
|
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+
│ --system TEXT The original box in which │
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│ you want to add particles. │
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│ If not provided, an empty │
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│ box will be created. │
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│ [default: None] │
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│ --molecule TEXT Name of the molecule to be │
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│ processed, ASE-recognizable │
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│ or ASE-readable file. │
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│ [default: H2O] │
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+
│ --nmols INTEGER Target number of molecules │
|
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│ to insert. │
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+
│ [default: -1] │
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+
│ --ntries INTEGER Maximum number of attempts │
|
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+
│ to insert each molecule. │
|
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+
│ [default: 50] │
|
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|
+
│ --seed INTEGER Random seed for │
|
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|
+
│ reproducibility. │
|
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|
+
│ [default: 2025] │
|
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+
│ --where [anywhere|sphere|box|cylin Where to insert the │
|
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|
+
│ derZ|cylinderY|cylinderX|e molecule. Choices: │
|
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+
│ llipsoid] 'anywhere', 'sphere', │
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+
│ 'box', 'cylinderZ', │
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+
│ 'cylinderY', 'cylinderX', │
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│ 'ellipsoid'. │
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+
│ [default: anywhere] │
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+
│ --centre TEXT Centre of the insertion │
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│ zone, coordinates in Å, │
|
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+
│ e.g., '5.0, 5.0, 5.0'. │
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│ [default: None] │
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│ --radius FLOAT Radius of the sphere or │
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+
│ cylinder in Å, depending on │
|
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|
+
│ the insertion volume. │
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+
│ [default: None] │
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+
│ --height FLOAT Height of the cylinder in │
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+
│ Å. │
|
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│ [default: None] │
|
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│ --a FLOAT Side of the box or │
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+
│ semi-axis of the ellipsoid, │
|
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+
│ in Å, depends on the │
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+
│ insertion method. │
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+
│ [default: None] │
|
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+
│ --b FLOAT Side of the box or │
|
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|
+
│ semi-axis of the ellipsoid, │
|
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|
+
│ in Å, depends on the │
|
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|
+
│ insertion method. │
|
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|
+
│ [default: None] │
|
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|
+
│ --c FLOAT Side of the box or │
|
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|
+
│ semi-axis of the ellipsoid, │
|
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|
+
│ in Å, depends on the │
|
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|
+
│ insertion method. │
|
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|
+
│ [default: None] │
|
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|
+
│ --device TEXT Device to run calculations │
|
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+
│ on (e.g., 'cpu' or 'cuda'). │
|
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|
+
│ [default: cpu] │
|
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|
+
│ --model TEXT ML model to use. │
|
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|
+
│ [default: medium-omat-0] │
|
|
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|
+
│ --arch TEXT MLIP architecture to use. │
|
|
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|
+
│ [default: mace_mp] │
|
|
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|
+
│ --temperature FLOAT Temperature for the Monte │
|
|
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|
+
│ Carlo acceptance rule. │
|
|
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|
+
│ [default: 300.0] │
|
|
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|
+
│ --cell-a FLOAT Side of the empty box along │
|
|
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|
+
│ the x-axis in Å. │
|
|
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|
+
│ [default: 20.0] │
|
|
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|
+
│ --cell-b FLOAT Side of the empty box along │
|
|
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|
+
│ the y-axis in Å. │
|
|
192
|
+
│ [default: 20.0] │
|
|
193
|
+
│ --cell-c FLOAT Side of the empty box along │
|
|
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|
+
│ the z-axis in Å. │
|
|
195
|
+
│ [default: 20.0] │
|
|
196
|
+
│ --fmax FLOAT force tollerance for │
|
|
197
|
+
│ optimisation if needed. │
|
|
198
|
+
│ [default: 0.1] │
|
|
199
|
+
│ --geometry --no-geometry Perform geometry │
|
|
200
|
+
│ optimization at the end. │
|
|
201
|
+
│ [default: geometry] │
|
|
202
|
+
│ --out-path TEXT path to save various │
|
|
203
|
+
│ outputs. │
|
|
204
|
+
│ [default: .] │
|
|
205
|
+
│ --install-completion Install completion for the │
|
|
206
|
+
│ current shell. │
|
|
207
|
+
│ --show-completion Show completion for the │
|
|
208
|
+
│ current shell, to copy it │
|
|
209
|
+
│ or customize the │
|
|
210
|
+
│ installation. │
|
|
211
|
+
│ --help Show this message and exit. │
|
|
212
|
+
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
|
|
213
|
+
|
|
214
|
+
|
|
215
|
+
```
|
|
216
|
+
|
|
217
|
+
|
|
218
|
+
[python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
|
|
219
|
+
[python-link]: https://pypi.org/project/pack-mm/
|
|
220
|
+
[ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
|
|
221
|
+
[ci-link]: https://github.com/ddmms/pack-mm/actions
|
|
222
|
+
[cov-badge]: https://coveralls.io/repos/github/ddmms/pack-mm/badge.svg?branch=main
|
|
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|
+
[cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
|
|
224
|
+
[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
|
|
225
|
+
[license-link]: https://opensource.org/license/MIT
|
|
@@ -52,30 +52,28 @@ def packmm(
|
|
|
52
52
|
),
|
|
53
53
|
centre: str | None = typer.Option(
|
|
54
54
|
None,
|
|
55
|
-
help="""Centre of the insertion zone in
|
|
56
|
-
e.g., '0.
|
|
55
|
+
help="""Centre of the insertion zone, coordinates in Å,
|
|
56
|
+
e.g., '5.0, 5.0, 5.0'.""",
|
|
57
57
|
),
|
|
58
58
|
radius: float | None = typer.Option(
|
|
59
59
|
None,
|
|
60
60
|
help="""Radius of the sphere or cylinder in Å,
|
|
61
61
|
depending on the insertion volume.""",
|
|
62
62
|
),
|
|
63
|
-
height: float | None = typer.Option(
|
|
64
|
-
None, help="Height of the cylinder in fractional coordinates."
|
|
65
|
-
),
|
|
63
|
+
height: float | None = typer.Option(None, help="Height of the cylinder in Å."),
|
|
66
64
|
a: float | None = typer.Option(
|
|
67
65
|
None,
|
|
68
|
-
help="""Side of the box or semi-axis of the ellipsoid,
|
|
66
|
+
help="""Side of the box or semi-axis of the ellipsoid, in Å,
|
|
69
67
|
depends on the insertion method.""",
|
|
70
68
|
),
|
|
71
69
|
b: float | None = typer.Option(
|
|
72
70
|
None,
|
|
73
|
-
help="""Side of the box or semi-axis of the ellipsoid,
|
|
71
|
+
help="""Side of the box or semi-axis of the ellipsoid, in Å,
|
|
74
72
|
depends on the insertion method.""",
|
|
75
73
|
),
|
|
76
74
|
c: float | None = typer.Option(
|
|
77
75
|
None,
|
|
78
|
-
help="""Side of the box or semi-axis of the ellipsoid,
|
|
76
|
+
help="""Side of the box or semi-axis of the ellipsoid, in Å,
|
|
79
77
|
depends on the insertion method.""",
|
|
80
78
|
),
|
|
81
79
|
device: str = typer.Option(
|
|
@@ -86,15 +84,22 @@ def packmm(
|
|
|
86
84
|
temperature: float = typer.Option(
|
|
87
85
|
300.0, help="Temperature for the Monte Carlo acceptance rule."
|
|
88
86
|
),
|
|
89
|
-
cell_a: float = typer.Option(
|
|
90
|
-
|
|
91
|
-
|
|
87
|
+
cell_a: float = typer.Option(
|
|
88
|
+
20.0, help="Side of the empty box along the x-axis in Å."
|
|
89
|
+
),
|
|
90
|
+
cell_b: float = typer.Option(
|
|
91
|
+
20.0, help="Side of the empty box along the y-axis in Å."
|
|
92
|
+
),
|
|
93
|
+
cell_c: float = typer.Option(
|
|
94
|
+
20.0, help="Side of the empty box along the z-axis in Å."
|
|
95
|
+
),
|
|
92
96
|
fmax: float = typer.Option(
|
|
93
97
|
0.1, help="force tollerance for optimisation if needed."
|
|
94
98
|
),
|
|
95
99
|
geometry: bool = typer.Option(
|
|
96
100
|
True, help="Perform geometry optimization at the end."
|
|
97
101
|
),
|
|
102
|
+
out_path: str = typer.Option(".", help="path to save various outputs."),
|
|
98
103
|
):
|
|
99
104
|
"""Pack molecules into a system based on the specified parameters."""
|
|
100
105
|
print("Script called with following input")
|
|
@@ -119,6 +124,7 @@ def packmm(
|
|
|
119
124
|
print(f"{temperature=}")
|
|
120
125
|
print(f"{fmax=}")
|
|
121
126
|
print(f"{geometry=}")
|
|
127
|
+
print(f"{out_path=}")
|
|
122
128
|
if nmols == -1:
|
|
123
129
|
print("nothing to do, no molecule to insert")
|
|
124
130
|
raise typer.Exit(0)
|
|
@@ -151,9 +157,10 @@ def packmm(
|
|
|
151
157
|
ntries=ntries,
|
|
152
158
|
fmax=fmax,
|
|
153
159
|
geometry=geometry,
|
|
154
|
-
|
|
155
|
-
|
|
156
|
-
|
|
160
|
+
cell_a=cell_a,
|
|
161
|
+
cell_b=cell_b,
|
|
162
|
+
cell_c=cell_c,
|
|
163
|
+
out_path=out_path,
|
|
157
164
|
)
|
|
158
165
|
|
|
159
166
|
|
|
@@ -11,6 +11,7 @@ from pathlib import Path
|
|
|
11
11
|
from ase import Atoms
|
|
12
12
|
from ase.build import molecule as build_molecule
|
|
13
13
|
from ase.io import read, write
|
|
14
|
+
from ase.units import kB
|
|
14
15
|
from janus_core.calculations.geom_opt import GeomOpt
|
|
15
16
|
from janus_core.helpers.mlip_calculators import choose_calculator
|
|
16
17
|
from numpy import cos, exp, pi, random, sin, sqrt
|
|
@@ -138,28 +139,29 @@ def validate_value(label, x):
|
|
|
138
139
|
|
|
139
140
|
|
|
140
141
|
def pack_molecules(
|
|
141
|
-
system: str
|
|
142
|
-
molecule: str,
|
|
143
|
-
nmols: int,
|
|
144
|
-
arch: str,
|
|
145
|
-
model: str,
|
|
146
|
-
device: str,
|
|
147
|
-
where: str,
|
|
148
|
-
center: tuple[float, float, float]
|
|
149
|
-
radius: float
|
|
150
|
-
height: float
|
|
151
|
-
a: float
|
|
152
|
-
b: float
|
|
153
|
-
c: float
|
|
154
|
-
seed: int,
|
|
155
|
-
temperature: float,
|
|
156
|
-
ntries: int,
|
|
157
|
-
geometry: bool,
|
|
158
|
-
fmax: float,
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
142
|
+
system: str = None,
|
|
143
|
+
molecule: str = "H2O",
|
|
144
|
+
nmols: int = -1,
|
|
145
|
+
arch: str = "cpu",
|
|
146
|
+
model: str = "mace_mp",
|
|
147
|
+
device: str = "medium-omat-0",
|
|
148
|
+
where: str = "anywhere",
|
|
149
|
+
center: tuple[float, float, float] = None,
|
|
150
|
+
radius: float = None,
|
|
151
|
+
height: float = None,
|
|
152
|
+
a: float = None,
|
|
153
|
+
b: float = None,
|
|
154
|
+
c: float = None,
|
|
155
|
+
seed: int = 2025,
|
|
156
|
+
temperature: float = 300.0,
|
|
157
|
+
ntries: int = 50,
|
|
158
|
+
geometry: bool = False,
|
|
159
|
+
fmax: float = 0.1,
|
|
160
|
+
cell_a: float = None,
|
|
161
|
+
cell_b: float = None,
|
|
162
|
+
cell_c: float = None,
|
|
163
|
+
out_path: str = ".",
|
|
164
|
+
) -> float:
|
|
163
165
|
"""
|
|
164
166
|
Pack molecules into a system based on the specified parameters.
|
|
165
167
|
|
|
@@ -181,9 +183,10 @@ def pack_molecules(
|
|
|
181
183
|
temperature (float): Temperature in Kelvin for acceptance probability.
|
|
182
184
|
ntries (int): Maximum number of attempts to insert each molecule.
|
|
183
185
|
geometry (bool): Whether to perform geometry optimization after insertion.
|
|
184
|
-
|
|
186
|
+
cell_a, cell_b, cell_c (float): Cell dimensions if system is empty.
|
|
187
|
+
out_path (str): path to save various outputs
|
|
185
188
|
"""
|
|
186
|
-
kbt = temperature *
|
|
189
|
+
kbt = temperature * kB
|
|
187
190
|
validate_value("temperature", temperature)
|
|
188
191
|
validate_value("radius", radius)
|
|
189
192
|
validate_value("height", height)
|
|
@@ -193,10 +196,10 @@ def pack_molecules(
|
|
|
193
196
|
validate_value("box b", b)
|
|
194
197
|
validate_value("box c", c)
|
|
195
198
|
validate_value("ntries", ntries)
|
|
196
|
-
validate_value("cell box a",
|
|
197
|
-
validate_value("cell box b",
|
|
199
|
+
validate_value("cell box cell a", cell_a)
|
|
200
|
+
validate_value("cell box cell b", cell_b)
|
|
198
201
|
validate_value("nmols", nmols)
|
|
199
|
-
validate_value("cell box c",
|
|
202
|
+
validate_value("cell box cell c", cell_c)
|
|
200
203
|
|
|
201
204
|
random.seed(seed)
|
|
202
205
|
|
|
@@ -204,25 +207,21 @@ def pack_molecules(
|
|
|
204
207
|
sys = read(system)
|
|
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sysname = Path(system).stem
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except Exception:
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sys = Atoms(cell=[
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sys = Atoms(cell=[cell_a, cell_b, cell_c], pbc=[True, True, True])
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cell = sys.cell.lengths()
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# Print
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# Print summary
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print(f"Using {arch} model {model} on {device}.")
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print(f"Insert in {where}.")
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# Set center of insertion region
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center = (cell[0] * 0.5, cell[1] * 0.5, cell[2] * 0.5)
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else:
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center = tuple(ci * cell[i] for i, ci in enumerate(center))
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# Set parameters based on insertion region
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a, b, c =
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a, b, c = cell[0], cell[1], cell[2]
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radius = min(cell) * 0.5
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@@ -230,20 +229,22 @@ def pack_molecules(
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if height is None:
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height = 0.5 * cell[2]
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if height is None:
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height = 0.5 * cell[1]
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radius = min(cell[2], cell[1]) * 0.5
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if height is None:
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height = 0.5 * cell[0]
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elif where == "box":
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a, b, c = a or
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a, b, c = a or cell[0], b or cell[1], c or cell[2]
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a, b, c = a or 0
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a, b, c = a or cell[0], b or cell[1], c or cell[2]
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calc = choose_calculator(
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arch=arch, model_path=model, device=device, default_dtype="float64"
|
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)
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calc = choose_calculator(arch=arch, model_path=model, device=device)
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sys.calc = calc
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e = sys.get_potential_energy() if len(sys) > 0 else 0.0
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accept = False
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for _itry in range(ntries):
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mol = load_molecule(molecule)
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tv = get_insertion_position(where, center,
|
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tv = get_insertion_position(where, center, a, b, c, radius, height)
|
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mol = rotate_molecule(mol)
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mol.translate(tv)
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@@ -274,18 +275,31 @@ def pack_molecules(
|
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csys = tsys.copy()
|
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e = en
|
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277
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print(f"Inserted particle {i + 1}")
|
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|
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write(f"{sysname}+{i + 1}{Path(molecule).stem}.cif", csys)
|
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+
write(Path(out_path) / f"{sysname}+{i + 1}{Path(molecule).stem}.cif", csys)
|
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else:
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# Things are bad, maybe geomatry optimisation saves us
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print(f"Failed to insert particle {i + 1} after {ntries} tries")
|
|
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|
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optimize_geometry(
|
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|
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f"{sysname}+{i + 1}{Path(molecule).stem}.cif",
|
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|
+
_ = optimize_geometry(
|
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f"{sysname}+{i + 1}{Path(molecule).stem}.cif",
|
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device,
|
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arch,
|
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model,
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fmax,
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out_path,
|
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289
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)
|
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energy_final = e
|
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|
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|
# Perform final geometry optimization if requested
|
|
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293
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if geometry:
|
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|
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optimize_geometry(
|
|
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|
-
f"{sysname}+{nmols}{Path(molecule).stem}.cif",
|
|
294
|
+
energy_final = optimize_geometry(
|
|
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|
+
f"{sysname}+{nmols}{Path(molecule).stem}.cif",
|
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+
device,
|
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arch,
|
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+
model,
|
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|
+
fmax,
|
|
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+
out_path,
|
|
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301
|
)
|
|
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+
return energy_final
|
|
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303
|
|
|
290
304
|
|
|
291
305
|
def load_molecule(molecule: str):
|
|
@@ -299,25 +313,24 @@ def load_molecule(molecule: str):
|
|
|
299
313
|
def get_insertion_position(
|
|
300
314
|
where: str,
|
|
301
315
|
center: tuple[float, float, float],
|
|
302
|
-
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
|
|
306
|
-
|
|
307
|
-
height: float | None,
|
|
316
|
+
a: float = None,
|
|
317
|
+
b: float = None,
|
|
318
|
+
c: float = None,
|
|
319
|
+
radius: float = None,
|
|
320
|
+
height: float = None,
|
|
308
321
|
) -> tuple[float, float, float]:
|
|
309
322
|
"""Get a random insertion position based on the region."""
|
|
310
323
|
if where == "sphere":
|
|
311
324
|
return random_point_in_sphere(center, radius)
|
|
312
325
|
if where == "box":
|
|
313
|
-
return random_point_in_box(center,
|
|
326
|
+
return random_point_in_box(center, a, b, c)
|
|
314
327
|
if where == "ellipsoid":
|
|
315
|
-
return random_point_in_ellipsoid(center,
|
|
328
|
+
return random_point_in_ellipsoid(center, a, b, c)
|
|
316
329
|
if where in ["cylinderZ", "cylinderY", "cylinderX"]:
|
|
317
330
|
axis = where[-1].lower()
|
|
318
|
-
return random_point_in_cylinder(center, radius,
|
|
331
|
+
return random_point_in_cylinder(center, radius, height, axis)
|
|
319
332
|
# now is anywhere
|
|
320
|
-
return random.random(3) * [a, b, c]
|
|
333
|
+
return random.random(3) * [a, b, c]
|
|
321
334
|
|
|
322
335
|
|
|
323
336
|
def rotate_molecule(mol):
|
|
@@ -330,16 +343,21 @@ def rotate_molecule(mol):
|
|
|
330
343
|
|
|
331
344
|
|
|
332
345
|
def optimize_geometry(
|
|
333
|
-
struct_path: str,
|
|
346
|
+
struct_path: str,
|
|
347
|
+
device: str,
|
|
348
|
+
arch: str,
|
|
349
|
+
model: str,
|
|
350
|
+
fmax: float,
|
|
351
|
+
out_path: str = ".",
|
|
334
352
|
) -> float:
|
|
335
353
|
"""Optimize the geometry of a structure."""
|
|
336
354
|
geo = GeomOpt(
|
|
337
355
|
struct_path=struct_path,
|
|
338
356
|
device=device,
|
|
339
357
|
fmax=fmax,
|
|
340
|
-
calc_kwargs={"model_paths": model
|
|
358
|
+
calc_kwargs={"model_paths": model},
|
|
341
359
|
filter_kwargs={"hydrostatic_strain": True},
|
|
342
360
|
)
|
|
343
361
|
geo.run()
|
|
344
|
-
write(f"{struct_path}-opt.cif", geo.struct)
|
|
362
|
+
write(Path(out_path) / f"{Path(struct_path).stem}-opt.cif", geo.struct)
|
|
345
363
|
return geo.struct.get_potential_energy()
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
[project]
|
|
2
2
|
name = "pack-mm"
|
|
3
|
-
version = "0.0.
|
|
3
|
+
version = "0.0.20"
|
|
4
4
|
description = "packing materials and molecules in boxes using for machine learnt interatomic potentials"
|
|
5
5
|
authors = [
|
|
6
6
|
{ name = "Alin M. Elena" },
|
|
@@ -44,6 +44,7 @@ docs = [
|
|
|
44
44
|
"furo<2025.0.0,>=2024.1.29",
|
|
45
45
|
"jupyter>=1.1.1",
|
|
46
46
|
"markupsafe<2.1",
|
|
47
|
+
"sphinx-immaterial",
|
|
47
48
|
"nbsphinx>=0.9.6",
|
|
48
49
|
"numpydoc<2.0.0,>=1.6.0",
|
|
49
50
|
"sphinx<9.0.0,>=8.0.2",
|
|
@@ -136,3 +137,7 @@ default-groups = [
|
|
|
136
137
|
"docs",
|
|
137
138
|
"pre-commit",
|
|
138
139
|
]
|
|
140
|
+
|
|
141
|
+
[tool.uv.sources.sphinx-immaterial]
|
|
142
|
+
git = "https://github.com/jbms/sphinx-immaterial.git"
|
|
143
|
+
rev = "main"
|
|
@@ -0,0 +1,178 @@
|
|
|
1
|
+
"""Test cli for core."""
|
|
2
|
+
|
|
3
|
+
# -*- coding: utf-8 -*-
|
|
4
|
+
# Author; alin m elena, alin@elena.re
|
|
5
|
+
# Contribs;
|
|
6
|
+
# Date: 22-02-2025
|
|
7
|
+
# ©alin m elena,
|
|
8
|
+
from __future__ import annotations
|
|
9
|
+
|
|
10
|
+
from ase import Atoms
|
|
11
|
+
from ase.build import molecule as build_molecule
|
|
12
|
+
from ase.io import write
|
|
13
|
+
import numpy as np
|
|
14
|
+
from numpy import random
|
|
15
|
+
import pytest
|
|
16
|
+
|
|
17
|
+
from pack_mm.core.core import (
|
|
18
|
+
get_insertion_position,
|
|
19
|
+
load_molecule,
|
|
20
|
+
optimize_geometry,
|
|
21
|
+
pack_molecules,
|
|
22
|
+
random_point_in_box,
|
|
23
|
+
random_point_in_cylinder,
|
|
24
|
+
random_point_in_ellipsoid,
|
|
25
|
+
random_point_in_sphere,
|
|
26
|
+
rotate_molecule,
|
|
27
|
+
validate_value,
|
|
28
|
+
)
|
|
29
|
+
|
|
30
|
+
|
|
31
|
+
# Set a fixed seed for reproducibility in tests
|
|
32
|
+
@pytest.fixture(autouse=True)
|
|
33
|
+
def set_random_seed():
|
|
34
|
+
"""Set random seed."""
|
|
35
|
+
random.seed(2042)
|
|
36
|
+
|
|
37
|
+
|
|
38
|
+
def test_random_point_in_sphere():
|
|
39
|
+
"""Test point in sphere."""
|
|
40
|
+
center = (0, 0, 0)
|
|
41
|
+
radius = 10.0
|
|
42
|
+
point = random_point_in_sphere(center, radius)
|
|
43
|
+
assert len(point) == 3
|
|
44
|
+
distance = np.linalg.norm(np.array(point) - np.array(center))
|
|
45
|
+
assert distance <= radius
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
def test_random_point_in_ellipsoid():
|
|
49
|
+
"""Test point in ellipsoid."""
|
|
50
|
+
center = (0, 0, 0)
|
|
51
|
+
a, b, c = 1.0, 2.0, 3.0
|
|
52
|
+
point = random_point_in_ellipsoid(center, a, b, c)
|
|
53
|
+
assert len(point) == 3
|
|
54
|
+
x, y, z = point
|
|
55
|
+
assert (x**2 / a**2) + (y**2 / b**2) + (z**2 / c**2) <= 1.0
|
|
56
|
+
|
|
57
|
+
|
|
58
|
+
def test_random_point_in_box():
|
|
59
|
+
"""Test point in box."""
|
|
60
|
+
center = (0, 0, 0)
|
|
61
|
+
a, b, c = 1.0, 2.0, 3.0
|
|
62
|
+
point = random_point_in_box(center, a, b, c)
|
|
63
|
+
assert len(point) == 3
|
|
64
|
+
x, y, z = point
|
|
65
|
+
assert center[0] - a * 0.5 <= x <= center[0] + a * 0.5
|
|
66
|
+
assert center[1] - b * 0.5 <= y <= center[1] + b * 0.5
|
|
67
|
+
assert center[2] - c * 0.5 <= z <= center[2] + c * 0.5
|
|
68
|
+
|
|
69
|
+
|
|
70
|
+
def test_random_point_in_cylinder():
|
|
71
|
+
"""Test point in cylinder."""
|
|
72
|
+
center = (0, 0, 0)
|
|
73
|
+
radius = 1.0
|
|
74
|
+
height = 2.0
|
|
75
|
+
direction = "z"
|
|
76
|
+
point = random_point_in_cylinder(center, radius, height, direction)
|
|
77
|
+
assert len(point) == 3
|
|
78
|
+
x, y, z = point
|
|
79
|
+
assert x**2 + y**2 <= radius**2
|
|
80
|
+
assert center[2] - height * 0.5 <= z <= center[2] + height * 0.5
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
def test_validate_value_positive():
|
|
84
|
+
"""Test point in test value."""
|
|
85
|
+
validate_value("test_value", 1.0) # Should not raise an exception
|
|
86
|
+
|
|
87
|
+
|
|
88
|
+
def test_validate_value_negative():
|
|
89
|
+
"""Test point in test value."""
|
|
90
|
+
with pytest.raises(Exception, match="Invalid test_value, needs to be positive"):
|
|
91
|
+
validate_value("test_value", -1.0)
|
|
92
|
+
|
|
93
|
+
|
|
94
|
+
def test_load_molecule_from_file(tmp_path):
|
|
95
|
+
"""Test point in load molecule."""
|
|
96
|
+
molecule = build_molecule("H2O")
|
|
97
|
+
molecule_file = tmp_path / "water.xyz"
|
|
98
|
+
molecule.write(molecule_file)
|
|
99
|
+
loaded_molecule = load_molecule(str(molecule_file))
|
|
100
|
+
assert isinstance(loaded_molecule, Atoms)
|
|
101
|
+
assert len(loaded_molecule) == 3 # H2O has 3 atoms
|
|
102
|
+
|
|
103
|
+
|
|
104
|
+
def test_load_molecule_from_name():
|
|
105
|
+
"""Test point in load molecule."""
|
|
106
|
+
molecule = load_molecule("H2O")
|
|
107
|
+
assert isinstance(molecule, Atoms)
|
|
108
|
+
assert len(molecule) == 3 # H2O has 3 atoms
|
|
109
|
+
|
|
110
|
+
|
|
111
|
+
def test_get_insertion_position_sphere():
|
|
112
|
+
"""Test point in sphere."""
|
|
113
|
+
center = (0, 0, 0)
|
|
114
|
+
radius = 10.0
|
|
115
|
+
point = get_insertion_position("sphere", center, radius=radius)
|
|
116
|
+
assert len(point) == 3
|
|
117
|
+
distance = np.linalg.norm(np.array(point) - np.array(center))
|
|
118
|
+
assert distance <= radius
|
|
119
|
+
|
|
120
|
+
|
|
121
|
+
def test_rotate_molecule():
|
|
122
|
+
"""Test rotate molecule."""
|
|
123
|
+
molecule = build_molecule("H2O")
|
|
124
|
+
rotated_molecule = rotate_molecule(molecule)
|
|
125
|
+
assert isinstance(rotated_molecule, Atoms)
|
|
126
|
+
assert len(rotated_molecule) == 3 # H2O has 3 atoms
|
|
127
|
+
|
|
128
|
+
|
|
129
|
+
def test_optimize_geometry(tmp_path):
|
|
130
|
+
"""Test go."""
|
|
131
|
+
# Create a temporary structure file
|
|
132
|
+
molecule = build_molecule("H2O")
|
|
133
|
+
molecule.set_cell([10, 10, 10])
|
|
134
|
+
molecule.set_pbc([True, True, True])
|
|
135
|
+
structure_file = tmp_path / "water.cif"
|
|
136
|
+
write(structure_file, molecule)
|
|
137
|
+
optimized_energy = optimize_geometry(
|
|
138
|
+
str(structure_file),
|
|
139
|
+
device="cpu",
|
|
140
|
+
arch="mace_mp",
|
|
141
|
+
model="medium-omat-0",
|
|
142
|
+
fmax=0.01,
|
|
143
|
+
)
|
|
144
|
+
assert optimized_energy == pytest.approx(-13.759273983276572, abs=1.0e-8)
|
|
145
|
+
|
|
146
|
+
|
|
147
|
+
# Test pack_molecules with a simple case
|
|
148
|
+
def test_pack_molecules(tmp_path):
|
|
149
|
+
"""Test pack molecule."""
|
|
150
|
+
# Create a temporary system file
|
|
151
|
+
system = Atoms(
|
|
152
|
+
"Ca", positions=[(5.0, 5.0, 5.0)], cell=[10, 10, 10], pbc=[True, True, True]
|
|
153
|
+
)
|
|
154
|
+
system_file = tmp_path / "system.cif"
|
|
155
|
+
write(system_file, system)
|
|
156
|
+
|
|
157
|
+
# Test packing molecules
|
|
158
|
+
e = pack_molecules(
|
|
159
|
+
system=str(system_file),
|
|
160
|
+
molecule="H2O",
|
|
161
|
+
nmols=2,
|
|
162
|
+
arch="mace_mp",
|
|
163
|
+
model="medium-omat-0",
|
|
164
|
+
device="cpu",
|
|
165
|
+
where="sphere",
|
|
166
|
+
center=(5.0, 5.0, 5.0),
|
|
167
|
+
radius=5.0,
|
|
168
|
+
seed=2042,
|
|
169
|
+
temperature=300,
|
|
170
|
+
ntries=10,
|
|
171
|
+
geometry=False,
|
|
172
|
+
fmax=0.1,
|
|
173
|
+
out_path=tmp_path,
|
|
174
|
+
)
|
|
175
|
+
|
|
176
|
+
assert (tmp_path / "system+1H2O.cif").exists()
|
|
177
|
+
assert (tmp_path / "system+2H2O.cif").exists()
|
|
178
|
+
assert e == pytest.approx(-28.251229837533085, abs=1.0e-6)
|
|
@@ -3,7 +3,7 @@
|
|
|
3
3
|
# Author; alin m elena, alin@elena.re
|
|
4
4
|
# Contribs;
|
|
5
5
|
# Date: 22-02-2025
|
|
6
|
-
# ©alin m elena,
|
|
6
|
+
# ©alin m elena,
|
|
7
7
|
from __future__ import annotations
|
|
8
8
|
|
|
9
9
|
from typer.testing import CliRunner
|
|
@@ -88,6 +88,13 @@ def test_packmm_mlip():
|
|
|
88
88
|
assert "device='cuda'" in strip_ansi_codes(result.output)
|
|
89
89
|
|
|
90
90
|
|
|
91
|
+
def test_packmm_out_path():
|
|
92
|
+
"""Check out_path."""
|
|
93
|
+
result = runner.invoke(app, ["--out-path", "out"])
|
|
94
|
+
assert result.exit_code == 0
|
|
95
|
+
assert "out_path='out'" in strip_ansi_codes(result.output)
|
|
96
|
+
|
|
97
|
+
|
|
91
98
|
def test_packmm_custom_box_dimensions():
|
|
92
99
|
"""Check box."""
|
|
93
100
|
result = runner.invoke(app, ["--a", "30.0", "--b", "30.0", "--c", "30.0"])
|
pack_mm-0.0.15/PKG-INFO
DELETED
|
@@ -1,36 +0,0 @@
|
|
|
1
|
-
Metadata-Version: 2.1
|
|
2
|
-
Name: pack-mm
|
|
3
|
-
Version: 0.0.15
|
|
4
|
-
Summary: packing materials and molecules in boxes using for machine learnt interatomic potentials
|
|
5
|
-
Author: Alin M. Elena
|
|
6
|
-
Classifier: Programming Language :: Python
|
|
7
|
-
Classifier: Programming Language :: Python :: 3.10
|
|
8
|
-
Classifier: Programming Language :: Python :: 3.11
|
|
9
|
-
Classifier: Programming Language :: Python :: 3.12
|
|
10
|
-
Classifier: Intended Audience :: Science/Research
|
|
11
|
-
Classifier: License :: OSI Approved :: MIT License
|
|
12
|
-
Classifier: Natural Language :: English
|
|
13
|
-
Classifier: Development Status :: 3 - Alpha
|
|
14
|
-
Project-URL: Repository, https://github.com/ddmms/pack-mm/
|
|
15
|
-
Project-URL: Documentation, https://ddmms.github.io/pack-mm/
|
|
16
|
-
Requires-Python: >=3.10
|
|
17
|
-
Requires-Dist: janus-core>=0.7.2
|
|
18
|
-
Requires-Dist: typer<1.0.0,>=0.12.5
|
|
19
|
-
Requires-Dist: typer-config<2.0.0,>=1.4.2
|
|
20
|
-
Description-Content-Type: text/markdown
|
|
21
|
-
|
|
22
|
-
# pack materials and molecules
|
|
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|
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|
|
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|
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[![Python versions][python-badge]][python-link]
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|
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|
|
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|
|
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|
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[python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
|
|
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|
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[python-link]: https://pypi.org/project/pack-mm/
|
|
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|
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[ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
|
|
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|
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[ci-link]: https://github.com/ddmms/pack-mm/actions
|
|
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[cov-badge]: https://coveralls.io/repos/github/ddmms/pack-mm/badge.svg?branch=main
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|
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|
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[cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
|
|
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|
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[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
|
|
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|
-
[license-link]: https://opensource.org/license/MIT
|
pack_mm-0.0.15/README.md
DELETED
|
@@ -1,15 +0,0 @@
|
|
|
1
|
-
# pack materials and molecules
|
|
2
|
-
|
|
3
|
-
[![Python versions][python-badge]][python-link]
|
|
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|
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[![Build Status][ci-badge]][ci-link]
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[![Coverage Status][cov-badge]][cov-link]
|
|
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|
-
[![License][license-badge]][license-link]
|
|
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|
-
|
|
8
|
-
[python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
|
|
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|
-
[python-link]: https://pypi.org/project/pack-mm/
|
|
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|
-
[ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
|
|
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|
-
[ci-link]: https://github.com/ddmms/pack-mm/actions
|
|
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[cov-badge]: https://coveralls.io/repos/github/ddmms/pack-mm/badge.svg?branch=main
|
|
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|
-
[cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
|
|
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|
-
[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
|
|
15
|
-
[license-link]: https://opensource.org/license/MIT
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|