Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

• UpdatedMar 10, 2025
• Python

Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables

• UpdatedFeb 22, 2024
• Python

3D chemical molecule visualizer for XYZ files.

• UpdatedAug 8, 2017
• C++

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.

• UpdatedMay 3, 2024
• Python

A small python script to create animation from multiply xyz files

• UpdatedAug 28, 2019
• Python

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.

• UpdatedOct 20, 2024
• Python

How to plot a 3D surface with python by interpolation

• UpdatedFeb 12, 2022
• Python

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

• UpdatedMar 9, 2023
• Python

Color Voronoi diagram according to scalar property of points.

• UpdatedNov 5, 2019
• Jupyter Notebook

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

• UpdatedApr 8, 2018
• Perl

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

• UpdatedDec 2, 2017
• Python

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

• UpdatedSep 16, 2021
• Python

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

• UpdatedDec 24, 2022
• Fortran

Fortran code that convert xyz file to bas file for Fireball

• UpdatedDec 21, 2022
• Fortran

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

• UpdatedDec 21, 2022
• Fortran

• UpdatedJul 13, 2018
• Jupyter Notebook

create allatom polymere system from .xyz file in VMD

• UpdatedDec 28, 2022

Converts .xyz coordinate files to povray scenes

• UpdatedJan 30, 2025
• Python

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"

• UpdatedJan 19, 2020
• Python

• UpdatedAug 27, 2017