Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
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Updated
Jun 25, 2023 - Python
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables
Transfer XYZ file into POSCAR/CONTCAR file with re-center feature. Useful for single molecule calculation in VASP.
These are important tools written for working with ORCA (a computational chemistry open source package) in a super-computing environment. They include multiple job submission scripts (BASH), multiple job cancellation (BASH), job setup with different geometries (in python), data extraction (BASH), final optimized geometry extraction (BASH) and
A small python script to create animation from multiply xyz files
The comparison between two structures is based on the cartesian coords.
This repository contains the working files used in the work "Hot Electron Cooling in Silicon Nanoclusters via Landau-Zener Non-Adiabatic Molecular Dynamics: Size Dependence and Role of Surface Termination"
How to plot a 3D surface with python by interpolation
A small tool for converting npz files to xyz files.
Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory
Converts .xyz coordinate files to povray scenes
Python 3 script for overlaying or superimposing two or more molecules. The overlayed / superimposed molecules can be displayed and the modified coordinates can be saved as xyz files. Coloring by atom or molecule is possible.
Some codes that I prepared for fundamental research interests.
Fortran code that convert xyz-file to POSCAR file for VASP calculation
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