Pinned Repositories
Computational-Physics-Final
Simulating a three-body orbit of the Earth-Moon-Sun system using the Euler-Cromer method.
Femto-Research
Codes for femtosecond laser interaction research
gpaw
ising-monte-carlo
Statistical Mechanics 2D Ising Model Simulations
Lectures
marvel-college
Teaching materials for a high-school programming camp
mdevaluate
A Python package for the analysis of molecular dynamics simulations.
MODE-TASK
PCA and normal mode analysis of proteins
MonteCarloStepUpdater
2D Ising model with longer ranger interaction, using the Wolff-Luijten Method
newton-dynamics
Implentation of Velocity Verlet, Runge-Kutta (Rk4), for integrating Newton's equations of motions, for reference.
thonmaker's Repositories
thonmaker/Femto-Research
Codes for femtosecond laser interaction research
thonmaker/AutoMD.py
An asistant for automating your molecular dynamics
thonmaker/CNN-ASTLSTM
Code for paper "An end-to-end neural network framework for SOH estimation and RUL prediction of lithium battery"
thonmaker/coMD
This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization
thonmaker/CompFizz
Computational physics exercises following Jos Thijssen's 'Computational Physics' text book.
thonmaker/dft-learning
《能源环境材料计算模拟方法》学习笔记，包括linux基础命令、pbs作业管理系统、vasp、materials studio等。
thonmaker/DMFTwDFT3
A framework to treat strongly correlated materials using beyond-DFT methods
thonmaker/dynamics
Simple classical molecular dynamics code using custom potentials
thonmaker/DynaPhoPy
Phonon anharmonicity analysis from molecular dynamics
thonmaker/EssentialMath
thonmaker/IPMCsMD
Molecular dynamics simulations of ionic polymer metal composites (IPMCs)
thonmaker/Ising
thonmaker/lammpscn
thonmaker/Lattice_dynamics
thonmaker/learn-fireside
thonmaker/Linear_Algebra_With_Python
Lecture Notes for Linear Algebra Featuring Python
thonmaker/LVTHW
thonmaker/materials-for-max-qe2021-online-school
https://gitlab.com/QEF/materials-for-max-qe2021-online-school
thonmaker/MIT-Linear-Algebra-Notes
Notes for MIT-Linear-Algebra
thonmaker/Molecular-Dynamics
Molecular Dynamics implementation, part of the final assignment for the Computational Physics course at the university of Groningen.
thonmaker/mollab
emmm makes molecule manipulated. It is a framework to build and process data for molecule dynamics
thonmaker/pexmd
A parallel and extendable molecular dynamics code
thonmaker/polymer-in-simulation
thonmaker/Project_Fusion
thonmaker/Pyrazinamidase
A Molecular Dynamics simulation project of pyrazinamidase studying its influence in antibiotic resistance of pyrazinamide. The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In GROMACS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of harmonic and an angle style of harmonic or charmm should also be used.
thonmaker/python_for_data_analysis_2nd_chinese_version
《利用Python进行数据分析·第2版》
thonmaker/Simulation_and_modeling
Projects completed in the course "SI1336 Simulering och modellering" at KTH Royal Institute of Science.
thonmaker/Toy-MD
Python code for learning Molecular Dynamics simulations
thonmaker/Utilities
Bash, C and python useful scripts
thonmaker/yhkimlabwiki
Yoon Hoon Kim wiki page