├── .github └── workflows │ └── docs.yaml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin └── images │ ├── mof-5-6x6x6.gif │ ├── mof-5.gif │ ├── sod-decoration.png │ ├── sod-supercell.png │ └── zn-formate-8x8x8.gif ├── chic ├── __init__.py ├── atomic_cluster.py ├── bonds.py ├── cif.py ├── coarse_graining_methods │ ├── __init__.py │ └── defaults.py ├── decorate.py ├── gulp.py ├── lammps.py ├── linkers │ ├── Im-C4H4.xyz │ ├── Im-H.xyz │ ├── Im_raw.xyz │ ├── bIm_raw.xyz │ └── generate_molecule_template.py ├── net.py ├── rattle.py ├── scatty.py ├── sort_sites.py ├── structure.py ├── templates.py ├── tidy.py ├── utils.py ├── vasp.py ├── vector.py ├── xyz.py └── zif.py ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ ├── 1,3-BDC.html │ ├── custom.css │ ├── homepage-grab.png │ ├── mep-nodes.data │ ├── mep-nodes.png │ ├── mep.data │ ├── mep.html │ ├── mep.png │ ├── scripts │ │ ├── dihedral.py │ │ └── viz.py │ ├── visualisations │ │ ├── chem_commun_2023.gif │ │ ├── chem_commun_2023.jpeg │ │ ├── chem_mater_2021.jpeg │ │ ├── chem_sci_2020.png │ │ ├── crystengcomm_2024.gif │ │ ├── mIm-clean.html │ │ └── mIm-disordered.html │ ├── zif4-cg-d.html │ ├── zif4-cg.html │ ├── zif4.html │ ├── zif8-cg-d.html │ ├── zif8-cg.html │ └── zif8.html │ ├── api │ ├── atomic-clusters.rst │ ├── net.rst │ └── structure.rst │ ├── case-studies │ ├── cleaning.rst │ ├── coarse-graining.rst │ ├── decorating.rst │ ├── dihedrals.rst │ └── topology-data.rst │ ├── conf.py │ ├── favicon.svg │ ├── hide-title.html │ ├── index.rst │ ├── logo-short.svg │ ├── logo.svg │ └── publications │ └── pub-main.rst ├── examples ├── 1-coarse-graining-basics.ipynb ├── 2-removing-disorder.ipynb ├── 3-decorating-basics.ipynb ├── 4-supercells.ipynb ├── 5-building-units.ipynb ├── 6-protonating-zr-clusters.ipynb ├── UiO-66(Zr) │ ├── POSCAR │ ├── UKUDEL-with-H.cif │ ├── UKUDEL.cif │ ├── UiO-66_cdc-H2O-H.cif │ └── UiO-66_cdc-H2O.cif ├── cg_lammps_output │ ├── melt.plateau_400K.data │ └── plateau_400K.dump ├── cg_zif4 │ ├── POSCAR │ ├── ZIF-4-cag-cg.data │ ├── ZIF-4-cag-overlay.cif │ ├── ZIF-4-cag-tidy.cif │ ├── ZIF-4-cag-topocif.cif │ └── ZIF-4-cag.cif ├── cg_zif8 │ ├── POSCAR │ ├── ZIF-8-cg.xyz │ ├── ZIF-8-sod-cg-1x3x2.cif │ ├── ZIF-8-sod-cg-1x3x2.data │ ├── ZIF-8-sod-cg.cif │ ├── ZIF-8-sod-cg.data │ ├── ZIF-8-sod-overlay.cif │ └── ZIF-8-sod.cif ├── cg_zif_imidzb11 │ ├── IMIDZB11-symmetrised.data │ ├── imidzb11-cg.cif │ └── imidzb11-cg.data └── decorate_sod │ ├── ZIF-8-sod-cg-decorated-CH3-topology.data │ ├── ZIF-8-sod-cg-decorated-CH3.cif │ ├── ZIF-8-sod-cg-decorated-CH3.data │ ├── ZIF-8-sod-cg-decorated-H-1x3x2.data │ ├── ZIF-8-sod-cg-decorated-H-topology.data │ ├── ZIF-8-sod-cg-decorated-H.cif │ ├── ZIF-8-sod-cg-decorated-H.data │ ├── ZIF-8-sod-cg-decorated.data │ └── ZIF-8-sod-cg.cif ├── pyproject.toml ├── setup.py └── tests.py /.github/workflows/docs.yaml: -------------------------------------------------------------------------------- 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