atomipy
Copyright (c) 2024-2026 Michael Holmboe

The atomipy source code is licensed under the MIT License (see LICENSE).

This product bundles third-party reference data that retains its own license
and attribution. The MIT License covering the source code does not re-license
this data; the terms below apply to it.

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Molecular fragments — atomipy/structures/molecules/
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Derived from the Avogadro2 project.
Licensed under the BSD 3-Clause License.
Copyright (c) 2016 Geoffrey Hutchison, University of Pittsburgh.
Full license text: atomipy/structures/molecules/LICENSE

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Crystallographic structures — atomipy/structures/ (minerals, crystals, …)
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Derived from open crystallographic databases (e.g. the Crystallography Open
Database (COD) and the American Mineralogist Crystal Structure Database
(AMCSD)). Their original terms and attribution apply. When using a specific
structure, cite its original publication / database entry.

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Force-field parameters — atomipy/ffparams/min.ff/
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This covers the MINFF and CLAYFF files of that directory, that is forcefield.itp,
ffnonbonded.itp, ffbonded.itp, atomtypes.atp, atomname2type.n2t and the
ffnonbonded_tminff_*, ffnonbonded_gminff and Alternative_ffnonbonded_* variants.
The GROMACS files that live in the same directory are covered by the next
section.

The MINFF force field (https://github.com/mholmboe/minff) and the CLAYFF
parameters are compiled from the published literature. Cite the original papers
referenced in the force-field files when using these parameters, including:
  - MINFF: see https://github.com/mholmboe/minff
  - CLAYFF: Cygan, Liang & Kalinichev, J. Phys. Chem. B 2004, 108, 1255.

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GROMACS data and water models — atomipy/ffparams/min.ff/
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The same directory ships standard data and topology files taken unmodified from
the GROMACS distribution (https://www.gromacs.org), so that the generated force
field directory can be used directly with GROMACS. GROMACS is licensed under the
GNU Lesser General Public License version 2.1 or later, which governs these
files:

  atommass.dat, electroneg.dat, elements.dat, nsfactor.dat, residuetypes.dat,
  watermodels.dat

  flexwat-ferguson.itp, ions.itp, opc.itp, opc3.itp, spc.itp, spce.itp,
  tip3p.itp, tip3p-fb.itp, tip4p.itp, tip4p-fb.itp, tip4p2005.itp,
  tip4p2005f.itp, tip4p2005_nrexcl2.itp, tip4p2005_nrxcl1.itp, tip4pew.itp,
  tip4pice.itp, tip5p.itp, tips3p.itp

Note that atomipy itself does not link against GROMACS. The optional
atomipy/xdrfile.py is an independent ctypes wrapper that loads a libxdrfile
shared library supplied by the user at runtime; no GROMACS code is bundled with
atomipy.

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Reference data — atomipy/data/
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Tabulated values taken from the scientific literature, which should be cited
when the data is used:
  - bvparm2020.cif: the accumulated table of bond valence parameters
    distributed by the IUCr, https://www.iucr.org/resources/data/datasets/
    bond-valence-parameters
  - Revised_Shannon_radii.txt: the revised Shannon ionic and crystal radii
