pymatgen-analysis-molcrys
Pymatgen namespace addon that exposes MolCrysKit
molecular-crystal workflows under pymatgen.analysis.molcrys.
After installation:
from pymatgen.core import Structure
from pymatgen.analysis.molcrys import TopologicalSlabGenerator, generate_topological_slab
structure = Structure.from_file("molecular_crystal.cif")
slab = generate_topological_slab(structure, (0, 0, 1), layers=3, vacuum=15.0)
# slab is a pymatgen Structure; molecules are not cut through
Install
From this monorepo (development):
pip install -e . # molcrys-kit at repo root
pip install -e addons/pymatgen-analysis-molcrys
From PyPI (when published):
pip install pymatgen-analysis-molcrys
Design
- This package is a thin Structure-facing facade.
- Algorithms live in
molcrys-kit. - Conversion uses MolCrysKit's occupancy-preserving pymatgen bridge
(
MolecularCrystal.to_pymatgen/from_pymatgen), notAseAtomsAdaptor(which rejects partially occupied structures).
Versioning
This addon has its own semver (0.1.0 initially) and depends on
molcrys-kit>=0.8.0b2. Bump the lower bound when the facade needs a newer
engine API.
1 maintainer
Metadata
1 maintainer
Release files for pymatgen-analysis-molcrys 0.1.0
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Release files / pymatgen_analysis_molcrys-0.1.0.tar.gz
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