bjmorgan/python_in_chemistry

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Created about 7 years ago
Updated 3 months ago

bjmorgan/python_in_chemistry

bjmorgan

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vasppy

A Python suite for manipulating VASP input and output

lattice_mc

Lattice gas Monte Carlo simulation code

py-sc-fermi

py-sc-fermi is a materials modelling code for calculating self-consistent Fermi energies and defect concentrations under thermodynamic equilibrium (or quasi-equilibrium) given defect formation energies.

kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.

VASP-Utilities

A collection of command line utilities for manipulating VASP input / outpu

bsym

A Basic Symmetry Module (Python)

pyscses

PYthon Space-Charge Site-Explicit Solver

Jupyter Notebook

site-analysis

Tools for analysing molecular dynamics simulations using site occupations

garnet-lgmc-data

Dataset for garnet-lattice lattice-gas Monte Carlo simulations

Jupyter Notebook

Scripts

FastScript scripts

parsedoscar

Generates atom and site projected densities of states from a VASP DOSCAR

latex_typography_guide

Morgan group LaTeX typography guide

graph-opt

force-directed optimisation of a 3D-periodic graph

advent-of-code-2022

Jupyter Notebook

open-transmit-here-rb-appscript

rb-appscript designed to run as a OS X service to jump from a remote directory in Terminal to the same directory in a new Transmit window

MD-utilities

Analysis code for pimaim MD code

Snippets

point_charge_ewald

Module for simple MC optimisation of structures using a point charge Coulomb model (with Ewald sum)

pimaim

PIMAIM molecular dynamics code

msdcon

Mean-Squared-Displacements from Molecular Dynamics trajectories

neb-pimaim

Nudged Elastic Band implementation that uses the PIMAIM molecular dynamics code for evaluating image forces

rotate_poscar

Rotates the coordinates for a VASP POSCAR

data_F-TiO2_intercalation_anions

Data analysis for DFT calculations of intercalation into (F/OH)-TiO2

Jupyter Notebook

tlpy

Python scripts for generating defect transition level diagrams

Jupyter Notebook

interpolate_poscar

Interpolates the coordinates in two VASP POSCAR files

pdf_context

After performing a Spotlight search for pdfs, finds a string in those pdfs and prints the extract in context (set number of words before and after the search string). Currently outputs in a (bad) Markdown syntax, and includes links to the matched files. Inspired by http://bengoldacre.posterous.com/investigative-journalism-tools-id-like-and-ma

data_argyrodite_disorder

Jupyter Notebook