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

3D chemical molecule visualizer for XYZ files.

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.

A small python script to create animation from multiply xyz files

How to plot a 3D surface with python by interpolation

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

Align atomic coordinates in xyz files. Align one or more atoms to x-, y- and z-axes. Set origin to a selected atom or a centroid of selected atoms. Rotate atomic coordinates about arbitrary angles. Translate atomic coordinates.

Color Voronoi diagram according to scalar property of points.

Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory

The comparison between two structures is based on the cartesian coords.

Fortran code that convert xyz file to bas file for Fireball

Fortran code that convert xyz-file to POSCAR file for VASP calculation

Fortran code that convert bas file to xyz file for Fireball.

Transfer XYZ file into POSCAR/CONTCAR file with re-center feature. Useful for single molecule calculation in VASP.

create allatom polymere system from .xyz file in VMD

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"

Converts .xyz coordinate files to povray scenes