Python4ChemistryTools

My personal Python toolbox for theoretical chemistry. Some Bash scripts also sneaked in.

Trajectories and File Conversion

• ase2adf.py: Convert any type of ASE readable input file (or files, including asterisk expressions) given as arguments to ADF style XYZ files.
• ase2xst.py: Convert any type of ASE readable input file given as argument to XST file (e.g. to read cell info in VMD).
• aseSupercell.py: Read ASE compatible input and save a supercell xyz-Trajectory file.
• cp2krestart2xyz: Extract single xyz file from CP2K restart/input files and save them as an ASE ext-xyz file.
• crystal2traj.py: Convert Crystal geometry optimization output to a ASE compatible ext-xyz trajectory file.
• dftb+2traj.py: Extract trajectory including periodicity from DFTB+ MD simulation.
• gaussian2traj.py: Convert Gaussian geometry output to ASE compatible ext-xyz trajectory file.
• print-traj-cell.py: Prints volume and cell vectors from an ASE compatible trajectory.
• supercell.py: Generate Supercell from xyz-Trajectory file, can be used as module or standalone.

Structure Manipulation and Analysis

• move_atom.py: Move a single atom from an ASE-compatible input around in space and save all resulting coordinates as xyz. Can be used as a script or module.
• geometryAnalyzer: Some functions for geometric analysis of ASE-format molecules and trajectories. Copy functions into your code or import the file.

Other

• cp2k-bsse.py: Analyze output of a CP2K BSSE calculation with two components using PLAMS.
• dothemath.py: Script to process all math expressions in a text file. Useful for many things, e.g. processing manually written force field definitions.
• moffunctions.py: Some functions for analyzing MOFs, pretty specific to DUT-8.
• mpl-settings.py: My favorite Matplotlib settings.
• plams_defaults: Options for PLAMS to work on clusters.
• sumCube.py: Make the sum of an arbitrary number of cube files. Also supports subtraction.
• print-cell-params.py: Prints the cell parameters of any ASE compatible file.