Yury

Added handling of chimera-style indexing for PDB

6

There were already some workarounds for hex indexing by VMD. This fix generalizes the approach so new indexing styles can be added more easily. It also adds a style that...

problem with pickle

4

The problem: `.names` doubles after interacting with `pickle`, `cPickle` and `dill`. How to reproduce ([test.txt](https://github.com/Becksteinlab/GromacsWrapper/files/6217259/test.txt)): ```python import gromacs.formats as gmx import os import pickle def load_xvg(filepath, failsafe=2): xvg_file = gmx.XVG()...

Gaussian16.A.03 single-point E UCCSD(T,full) parsing

2

Hello, I found the package very helpful. I am using the conde-forge install. I have recently come across an issue. **Current behaviour:** A relatively simple Gussian [log file](https://github.com/PolyachenkoYA/lammps_questions/blob/main/cclib_singleE_parse/single_E.log) is parsed,...

**My setup** `python3.9`, install from `conda-forge::cp2k-input-tools` which seems to have 0.8.2 version. (Is this supported? I don't see a conda install option in this repo's install instructions, but conda-forge's [instructions](https://github.com/conda-forge/cp2k-input-tools-feedstock)...

Possible documentation improvement on RELAX_MULTIPLICITY

3

I wanted to do `UKS`, and the role of `RELAX_MULTIPLICITY` was not immediately clear. The [docs](https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT.html#CP2K_INPUT.FORCE_EVAL.DFT.RELAX_MULTIPLICITY) only say `Larger tolerance values increase the probability for a spin flip`. After searching...

**My setup** - cp2k: 2025.1 container - OS: (on a cluster) Red Hat Enterprise Linux 9.6 (Plow) **Current behaviour** Laucnhing this [input file](https://github.com/PolyachenkoYA/lammps_questions/blob/main/CP2K_segflt1/eq_MD.inp) using this [slurm script](https://github.com/PolyachenkoYA/lammps_questions/blob/main/CP2K_segflt1/eq_MD.slurm) results in the...