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polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories

License: MIT License

Python 89.99% TeX 10.01%

monte-carlo-simulation molecular-dynamics-simulation materials-science solid-state-chemistry solid-state-physics simulation chemistry

polypy's Introduction

Hi there 👋

My name is Adam Symington, a scientist and programmer. I am the data science lead at Fraym. I am own and build the PythonMaps project, a small data visualisation project aimed at showing off the power of Python programming in geospatial data visulationsation. During my academic career I used ab initio and classical simulation techniques to predict and analyse the properties batteries, fuel cells, catalysts and nuclear fuel. In addition to research, I have taught several undergraduate and postgraduate courses in the Department of Chemistry at the University of Bath, introducing students to Python programming and it's application in the chemical sciences.

Where: Bristol / Belfast / Washington
Work: Fraym
Contact: [email protected]
Website: https://www.pythonmaps.com
Twitter: https://twitter.com/PythonMaps
linkedin: https://www.linkedin.com/in/adam-symington/

polypy's People

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sylvesterlali ab5424

polypy's Issues

Atom Reading

Bug - The program currently will only consider the first letter of the atom name when reading. So for a system with Fe and F it will return the coordinates of both.

Write Setup.py

Write a setup script

Documentation

Create documentation with sphinx

Problem in using the tool

Currently, I am working on a similar topic where I am interested in the diffusion along and across the grain boundary. As I am using Lammps for my MD simulations. I found it a bit difficult to convert lammps trajectory to DL_Poly history format. However, I found the following code which converts XYZ to dl_poly format (https://www.projectaten.com/dlputils/docs/utilities/xyz2his). When I read this file through polypy it reads everything but the problem that I am facing is that the given tool is unable to calculate MSD and diffusion coefficient. In addition, if the trajectory is too large then it also fails to load.

Having problem with using it

Hello Adam,

I have tried to use PolyPy but, did not work. Please, can you add more description on how to use it?
In addition, it would be great if you have a script to convert HISTORY file to PDB format that can be read in different packages. I tried with VMD but the results were as attached snapshot.
Thanks
Ali

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