pack-mm 0.0.19__py3-none-any.whl → 0.0.21__py3-none-any.whl
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- pack_mm/core/core.py +3 -2
- pack_mm-0.0.21.dist-info/METADATA +246 -0
- pack_mm-0.0.21.dist-info/RECORD +8 -0
- pack_mm-0.0.19.dist-info/METADATA +0 -36
- pack_mm-0.0.19.dist-info/RECORD +0 -8
- {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/WHEEL +0 -0
- {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/entry_points.txt +0 -0
- {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/licenses/LICENSE +0 -0
pack_mm/core/core.py
CHANGED
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@@ -11,6 +11,7 @@ from pathlib import Path
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from ase import Atoms
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from ase.build import molecule as build_molecule
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from ase.io import read, write
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from ase.units import kB
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from janus_core.calculations.geom_opt import GeomOpt
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from janus_core.helpers.mlip_calculators import choose_calculator
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from numpy import cos, exp, pi, random, sin, sqrt
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@@ -185,7 +186,7 @@ def pack_molecules(
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cell_a, cell_b, cell_c (float): Cell dimensions if system is empty.
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out_path (str): path to save various outputs
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"""
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kbt = temperature *
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kbt = temperature * kB
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validate_value("temperature", temperature)
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validate_value("radius", radius)
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validate_value("height", height)
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filter_kwargs={"hydrostatic_strain": True},
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)
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geo.run()
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write(Path(out_path) / f"{struct_path}-opt.cif", geo.struct)
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write(Path(out_path) / f"{Path(struct_path).stem}-opt.cif", geo.struct)
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return geo.struct.get_potential_energy()
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@@ -0,0 +1,246 @@
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Metadata-Version: 2.1
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Name: pack-mm
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Version: 0.0.21
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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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``` 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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### 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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### 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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after optimisation
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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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@@ -0,0 +1,8 @@
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pack_mm-0.0.21.dist-info/METADATA,sha256=jW4IZ3HFn-e7AxJ8dAteajsDSs1dsybX3G9l080Gr5Y,13506
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pack_mm-0.0.21.dist-info/WHEEL,sha256=thaaA2w1JzcGC48WYufAs8nrYZjJm8LqNfnXFOFyCC4,90
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pack_mm-0.0.21.dist-info/entry_points.txt,sha256=ajKA2oehIa_LCVCP2XTRxV0VNgjGl9c2wYkwk0BasrQ,66
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pack_mm-0.0.21.dist-info/licenses/LICENSE,sha256=ZOYkPdn_vQ8wYJqZnjesow79F_grMbVlHcJ9V91G1pE,1100
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pack_mm/__init__.py,sha256=ct7qfCmTDwhLYip6JKYWRLasmmaGYt0ColbK0CpvYZk,150
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pack_mm/cli/packmm.py,sha256=VqumDT_f1Nf1LCZ1WsF5D6MoLmKEQPEimYenibQHIU4,4944
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pack_mm/core/core.py,sha256=vNMQOVDIXyRCUWosww9sSHUxwqbjPRk5JLsb9muwpVA,11369
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pack_mm-0.0.21.dist-info/RECORD,,
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Metadata-Version: 2.1
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Name: pack-mm
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Version: 0.0.19
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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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# pack materials and molecules
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