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uw-cmg / MAST

MAterials Simulation Toolkit for use with pymatgen
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atom indexing #385

Closed cmgtam closed 7 years ago

cmgtam commented 10 years ago

Keep track of specific atoms by atom index. Useful for magmom, phonons, possibly NEBs, especially where atomic position changes drastically upon relaxation.

henry-wu commented 10 years ago

This requires MAST to initially index atoms which is matched up with their coordinates (applies for user inputted coordinates and scaled coordinates). Every time pymatgen does anything with atom coordinates, there needs to be a coordinate match done on the pymatgen output to determine the re-ordered index. Every time there is a VASP relaxation, the order of the POSCAR vs. CONTCAR needs to be matched up and the index-to-coordinate list needs to be updated.

cmgtam commented 7 years ago

Closing after major atom indexing fixes in version 1.3.4.