pack-mm 0.0.19__tar.gz → 0.0.20__tar.gz

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Files changed (13) hide show
  1. pack_mm-0.0.20/PKG-INFO +246 -0
  2. pack_mm-0.0.20/README.md +225 -0
  3. {pack_mm-0.0.19 → pack_mm-0.0.20}/pack_mm/core/core.py +3 -2
  4. {pack_mm-0.0.19 → pack_mm-0.0.20}/pyproject.toml +1 -1
  5. pack_mm-0.0.19/PKG-INFO +0 -36
  6. pack_mm-0.0.19/README.md +0 -15
  7. {pack_mm-0.0.19 → pack_mm-0.0.20}/LICENSE +0 -0
  8. {pack_mm-0.0.19 → pack_mm-0.0.20}/pack_mm/__init__.py +0 -0
  9. {pack_mm-0.0.19 → pack_mm-0.0.20}/pack_mm/cli/packmm.py +0 -0
  10. {pack_mm-0.0.19 → pack_mm-0.0.20}/tests/__init__.py +0 -0
  11. {pack_mm-0.0.19 → pack_mm-0.0.20}/tests/test_core.py +0 -0
  12. {pack_mm-0.0.19 → pack_mm-0.0.20}/tests/test_packmm.py +0 -0
  13. {pack_mm-0.0.19 → pack_mm-0.0.20}/tests/utils.py +0 -0
pack_mm-0.0.20/PKG-INFO ADDED
@@ -0,0 +1,246 @@
1
+ Metadata-Version: 2.1
2
+ Name: pack-mm
3
+ 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
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
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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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+
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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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+
27
+ # what is packmm
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+
29
+ packmm is a simple python package that allows to build atomistic and molecular
30
+ systems which are of interest for materials and molecular modelling.
31
+
32
+ It tries to generate realistic starting configuration by employing machine learnt
33
+ interatomic potential for describing interactions between atoms and Monte Carlo,
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+ Molecular Dynamics and hybrid Monte Carlo.
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+
36
+ It provides both a cli and a python api, with some examples below.
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+
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+ ## Quick install
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+
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+ ```bash
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+
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+ uv pip install pack-mm
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+
44
+ ```
45
+ or install the lates
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+
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+ ```bash
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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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+ ```
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+
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+ ## CLI examples
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+
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+
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+ ### MOF in spherical pocket
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+
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+ ```bash
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+
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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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+ ```
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+
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+ ![](examples/pics/UiO66water.png)
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+
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+ ### Zeolite in cylindrical channel
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+
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+
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+ ```bash
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+
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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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+ ```
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+
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+ ![](examples/pics/MFIwater.png)
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+
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+ ### NaCl on surface
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+
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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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+ ```
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+
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+ ![](examples/pics/NaClwater.png)
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+
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+ ### MOF ellipsoid
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+
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+ first add a methanol
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+
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+ ```bash
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+
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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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+ ```
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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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+
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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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+
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+ ```
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+
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+ !()[examples/pics/Cu2l-ethanol-water.png]
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+
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+ ### Liquid water
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+
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+ ```bash
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+
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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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+
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+ ```
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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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+
146
+ ╭─ 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 │
163
+ │ 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. │
179
+ │ [default: None] │
180
+ │ --height FLOAT Height of the cylinder in │
181
+ │ 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] │
193
+ │ --c FLOAT Side of the box or │
194
+ │ 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] │
198
+ │ --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] │
203
+ │ --arch TEXT MLIP architecture to use. │
204
+ │ [default: mace_mp] │
205
+ │ --temperature FLOAT Temperature for the Monte │
206
+ │ Carlo acceptance rule. │
207
+ │ [default: 300.0] │
208
+ │ --cell-a FLOAT Side of the empty box along │
209
+ │ the x-axis in Å. │
210
+ │ [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. │
213
+ │ [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 │
218
+ │ optimisation if needed. │
219
+ │ [default: 0.1] │
220
+ │ --geometry --no-geometry Perform geometry │
221
+ │ optimization at the end. │
222
+ │ [default: geometry] │
223
+ │ --out-path TEXT path to save various │
224
+ │ outputs. │
225
+ │ [default: .] │
226
+ │ --install-completion Install completion for the │
227
+ │ current shell. │
228
+ │ --show-completion Show completion for the │
229
+ │ current shell, to copy it │
230
+ │ or customize the │
231
+ │ installation. │
232
+ │ --help Show this message and exit. │
233
+ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
234
+
235
+
236
+ ```
237
+
238
+
239
+ [python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
240
+ [python-link]: https://pypi.org/project/pack-mm/
241
+ [ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
242
+ [ci-link]: https://github.com/ddmms/pack-mm/actions
243
+ [cov-badge]: https://coveralls.io/repos/github/ddmms/pack-mm/badge.svg?branch=main
244
+ [cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
245
+ [license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
246
+ [license-link]: https://opensource.org/license/MIT
pack_mm-0.0.20/README.md ADDED
@@ -0,0 +1,225 @@
1
+ [![Python versions][python-badge]][python-link]
2
+ [![Build Status][ci-badge]][ci-link]
3
+ [![Coverage Status][cov-badge]][cov-link]
4
+ [![License][license-badge]][license-link]
5
+
6
+ # 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
+ ## Quick install
18
+
19
+ ```bash
20
+
21
+ uv pip install pack-mm
22
+
23
+ ```
24
+ or install the lates
25
+
26
+ ```bash
27
+
28
+ uv pip install git+https://github.com/ddmms/pack-mm.git
29
+
30
+ ```
31
+
32
+ ## CLI examples
33
+
34
+
35
+ ### MOF in spherical pocket
36
+
37
+ ```bash
38
+
39
+ packmm --system examples/data/UiO-66.cif --molecule H2O --nmols 10 --where sphere --centre 10.0,10.0,10.0 --radius 5.0 --geometry
40
+
41
+ ```
42
+
43
+ ![](examples/pics/UiO66water.png)
44
+
45
+ ### Zeolite in cylindrical channel
46
+
47
+
48
+ ```bash
49
+
50
+ 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
51
+
52
+ ```
53
+
54
+ ![](examples/pics/MFIwater.png)
55
+
56
+ ### NaCl on surface
57
+
58
+ ```bash
59
+ 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
60
+
61
+ ```
62
+
63
+ ![](examples/pics/NaClwater.png)
64
+
65
+ ### MOF ellipsoid
66
+
67
+ first add a methanol
68
+
69
+ ```bash
70
+
71
+ 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
72
+
73
+ ```
74
+
75
+ !()[examples/pics/Cu2L-ethanol.png]
76
+
77
+ ``` bash
78
+
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
80
+
81
+
82
+ ```
83
+
84
+ !()[examples/pics/Cu2l-ethanol-water.png]
85
+
86
+ ### Liquid water
87
+
88
+ ```bash
89
+
90
+ packmm --molecule H2O --nmols 33 --where anywhere --cell-a 10.0 --cell-b 10.0 --cell-c 10.0 --model small-0b2
91
+
92
+
93
+ ```
94
+
95
+ !()[examples/pics/water.png]
96
+ ### interstitials
97
+
98
+ ```bash
99
+
100
+ packmm --system Pd-super.cif --molecule H2 --nmols 50 --where anywhere --model small-0b2
101
+
102
+ ```
103
+
104
+ before optimisation
105
+
106
+ !()[examples/pics/Pd-H2-noopt.png]
107
+
108
+
109
+ after optimisation
110
+
111
+ !()[examples/pics/Pd-H2.png]
112
+
113
+
114
+
115
+ ### full list of options
116
+
117
+ ```bash
118
+
119
+ packmm --help
120
+
121
+ Usage: packmm [OPTIONS]
122
+
123
+ Pack molecules into a system based on the specified parameters.
124
+
125
+ ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
126
+ │ --system TEXT The original box in which │
127
+ │ you want to add particles. │
128
+ │ If not provided, an empty │
129
+ │ box will be created. │
130
+ │ [default: None] │
131
+ │ --molecule TEXT Name of the molecule to be │
132
+ │ processed, ASE-recognizable │
133
+ │ or ASE-readable file. │
134
+ │ [default: H2O] │
135
+ │ --nmols INTEGER Target number of molecules │
136
+ │ to insert. │
137
+ │ [default: -1] │
138
+ │ --ntries INTEGER Maximum number of attempts │
139
+ │ to insert each molecule. │
140
+ │ [default: 50] │
141
+ │ --seed INTEGER Random seed for │
142
+ │ reproducibility. │
143
+ │ [default: 2025] │
144
+ │ --where [anywhere|sphere|box|cylin Where to insert the │
145
+ │ derZ|cylinderY|cylinderX|e molecule. Choices: │
146
+ │ llipsoid] 'anywhere', 'sphere', │
147
+ │ 'box', 'cylinderZ', │
148
+ │ 'cylinderY', 'cylinderX', │
149
+ │ 'ellipsoid'. │
150
+ │ [default: anywhere] │
151
+ │ --centre TEXT Centre of the insertion │
152
+ │ zone, coordinates in Å, │
153
+ │ e.g., '5.0, 5.0, 5.0'. │
154
+ │ [default: None] │
155
+ │ --radius FLOAT Radius of the sphere or │
156
+ │ cylinder in Å, depending on │
157
+ │ the insertion volume. │
158
+ │ [default: None] │
159
+ │ --height FLOAT Height of the cylinder in │
160
+ │ Å. │
161
+ │ [default: None] │
162
+ │ --a FLOAT Side of the box or │
163
+ │ semi-axis of the ellipsoid, │
164
+ │ in Å, depends on the │
165
+ │ insertion method. │
166
+ │ [default: None] │
167
+ │ --b FLOAT Side of the box or │
168
+ │ semi-axis of the ellipsoid, │
169
+ │ in Å, depends on the │
170
+ │ insertion method. │
171
+ │ [default: None] │
172
+ │ --c FLOAT Side of the box or │
173
+ │ semi-axis of the ellipsoid, │
174
+ │ in Å, depends on the │
175
+ │ insertion method. │
176
+ │ [default: None] │
177
+ │ --device TEXT Device to run calculations │
178
+ │ on (e.g., 'cpu' or 'cuda'). │
179
+ │ [default: cpu] │
180
+ │ --model TEXT ML model to use. │
181
+ │ [default: medium-omat-0] │
182
+ │ --arch TEXT MLIP architecture to use. │
183
+ │ [default: mace_mp] │
184
+ │ --temperature FLOAT Temperature for the Monte │
185
+ │ Carlo acceptance rule. │
186
+ │ [default: 300.0] │
187
+ │ --cell-a FLOAT Side of the empty box along │
188
+ │ the x-axis in Å. │
189
+ │ [default: 20.0] │
190
+ │ --cell-b FLOAT Side of the empty box along │
191
+ │ the y-axis in Å. │
192
+ │ [default: 20.0] │
193
+ │ --cell-c FLOAT Side of the empty box along │
194
+ │ 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
223
+ [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
{pack_mm-0.0.19 → pack_mm-0.0.20}/pack_mm/core/core.py RENAMED
@@ -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
@@ -185,7 +186,7 @@ def pack_molecules(
185
186
  cell_a, cell_b, cell_c (float): Cell dimensions if system is empty.
186
187
  out_path (str): path to save various outputs
187
188
  """
188
- kbt = temperature * 8.6173303e-5 # Boltzmann constant in eV/K
189
+ kbt = temperature * kB
189
190
  validate_value("temperature", temperature)
190
191
  validate_value("radius", radius)
191
192
  validate_value("height", height)
@@ -358,5 +359,5 @@ def optimize_geometry(
358
359
  filter_kwargs={"hydrostatic_strain": True},
359
360
  )
360
361
  geo.run()
361
- write(Path(out_path) / f"{struct_path}-opt.cif", geo.struct)
362
+ write(Path(out_path) / f"{Path(struct_path).stem}-opt.cif", geo.struct)
362
363
  return geo.struct.get_potential_energy()
{pack_mm-0.0.19 → pack_mm-0.0.20}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "pack-mm"
3
- version = "0.0.19"
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" },
pack_mm-0.0.19/PKG-INFO DELETED
@@ -1,36 +0,0 @@
1
- Metadata-Version: 2.1
2
- Name: pack-mm
3
- Version: 0.0.19
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/
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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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-
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- # pack materials and molecules
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-
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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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-
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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
pack_mm-0.0.19/README.md DELETED
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- # pack materials and molecules
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-
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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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-
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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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