pablopiaggi / environmentfinder Goto Github PK

Setup regression tests to make the code robust against different versions of python (e.g., 3.8 to 3.11), numpy, and ase.

Testing appmode, voila, ipywidgets, and nglview may be harder.

Useful information about the unique environments should be printed.

• The degeneracy of each environment
• The average number of atoms in the environments

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.