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PabloPiaggi / EnvironmentFinder

Tool for finding atomic environments in crystal structures
GNU General Public License v3.0
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PDB atom numbering starts from zero #3

Closed PabloPiaggi closed 3 years ago

PabloPiaggi commented 4 years ago

The numbering of atoms starts from zero in the output environments in PDB format. This is incompatible with PLUMED according to the manual.

The part of the code that prints the PDB files uses ASE and therefore is not easy to change from the EnvironmentFinder. I submitted a pull request to ASE to start the numbering from one and it was merged into the master branch. Therefore when the ASE version is updated this bug will be solved.

PabloPiaggi commented 4 years ago

Updating ASE will also solve a problem with reading lammps-data files. This was solved by this commit.

PabloPiaggi commented 3 years ago

Solved by e715b14