pack-mm 0.0.19__py3-none-any.whl → 0.0.21__py3-none-any.whl

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Files changed (8) hide show
  1. pack_mm/core/core.py +3 -2
  2. pack_mm-0.0.21.dist-info/METADATA +246 -0
  3. pack_mm-0.0.21.dist-info/RECORD +8 -0
  4. pack_mm-0.0.19.dist-info/METADATA +0 -36
  5. pack_mm-0.0.19.dist-info/RECORD +0 -8
  6. {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/WHEEL +0 -0
  7. {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/entry_points.txt +0 -0
  8. {pack_mm-0.0.19.dist-info → pack_mm-0.0.21.dist-info}/licenses/LICENSE +0 -0
pack_mm/core/core.py CHANGED
@@ -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
@@ -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 * 8.6173303e-5 # Boltzmann constant in eV/K
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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)
@@ -358,5 +359,5 @@ def optimize_geometry(
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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()
pack_mm-0.0.21.dist-info/METADATA ADDED
@@ -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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+
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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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+ # what is packmm
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+
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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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+
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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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+
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+ 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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+
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+ ```
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+ 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.webp)
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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.webp)
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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.webp)
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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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+ 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.webp)
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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.webp)
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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.webp)
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+
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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.webp)
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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.webp)
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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. │
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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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+
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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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+ [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-0.0.21.dist-info/RECORD ADDED
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+ pack_mm/core/core.py,sha256=vNMQOVDIXyRCUWosww9sSHUxwqbjPRk5JLsb9muwpVA,11369
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pack_mm-0.0.19.dist-info/METADATA DELETED
@@ -1,36 +0,0 @@
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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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-
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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.dist-info/RECORD DELETED
@@ -1,8 +0,0 @@
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- pack_mm-0.0.19.dist-info/RECORD,,