Builder: open and save CIF files (unit cell from symmetry operations)
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评估
调研方向
Start with the Builder’s existing periodic-cell import paths and the space-group tables it already uses; the payload names PDB (CRYST1), .gro, and .car as examples. The design brief is ready, but this work is scheduled after the GROMACS run settings and end-to-end clay system. Done means CIF import and P1 export round-trip, with the listed structures verified against Open Babel and Z × formula.
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描述
The Builder cannot open CIF files, which is how crystal structures come from the databases (COD, AMCSD, Materials Project, the IZA zeolite database). PDB (CRYST1), .gro and .car already bring their cell.
Scope:
- Import: cell,
_atom_site_loop, symmetry operations as listed (or, when only a space-group name is given, the space-group tables the Periodic Builder already uses), duplicates at special positions removed by periodic distance, result in the cell at 1×1×1. - Partial occupancy: the majority species on each site, with a warning listing the sites. A warning when hydrogens are absent (common in mineral CIFs).
- Export: P1 CIF of the current periodic structure; export → import round trip.
- Verification against Open Babel (
--fillUC strict) and against Z × formula, for pyrophyllite (Lee & Guggenheim 1981), quartz, graphite, NaCl, LiCoO₂, a zeolite, and a CIF with a space-group name only.
A design brief is ready; to be done after the GROMACS run settings and the end-to-end clay system.
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