Zheyong Fan

nvalchemi-toolkit-ops. ALCHEMI Toolkit-Ops is a collection of optimized batch kernels to accelerate computational chemistry and material science workflows.

GPUMD-PySAGES. GPU-native interface between GPUMD and PySAGES for enhanced-sampling molecular dynamics

lammps-MatPL. The LAMMPS interface for the machine learning force field of MatPL.

anisotropic-ML. Python

Modern-CPP-Programming. Modern C++ Programming Course (C++03/11/14/17/20/23/26)

GPUMD_confinement. GPUMD code used for 2D confinement molecular simulations

nep_maker. Python

GPUMD-Wizard. Material structure processing software based on ASE (Atomic Simulation Environment)

modified_MLIP. The modified versions of the MLIP package and the LAMMPS-MLIP interface

NepTrain. An automated toolkit for training neuroevolution potential (NEP), integrating tools like GPUMD, VASP, and NEP for streamlined workflows including perturbation, active learning, single-point energy calculations, and potential training.

NepTrainKit. NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.

PWMLFF. Fortran

abacus-develop. An electronic structure package based on either plane wave basis or numerical atomic orbitals.

VaspTool. Python

atomistic-software. Tracking citations of atomistic simulation engines

udlbook. Understanding Deep Learning - Simon J.D. Prince

mdapy. A simple and fast python library to handle the data generated from molecular dynamics simulations

pykan. Kolmogorov Arnold Networks

tools. Some scripts for gpumd and nep

SPaMD. SPaMD (Scalable Parallel Materials/Molecular Design/Dynamics Studio) is an integrated software platform developed by the research group of Professor Ruifeng Zhang at Beihang University in the past five years. It is dedicated to the modeling, calculation/simulation, analysis and visualization of materials at atomic scale.

water_ice_nep. Supplement files of paper "Thermodynamics of Water and Ice from a Fast and Scalable First-Principles Neuroevolution Potential"

dota. Data-driven particle transport algorithm for fast dose calculations.

best-of-atomistic-machine-learning. 🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

CV-CUDA. CV-CUDA™ is an open-source, GPU accelerated library for cloud-scale image processing and computer vision.

NEP-ZBL-W. A repository for data related to the NEP-ZBL-W.

VASP_script. Useful scripts for VASP

VASPKIT_manual. VASPKIT_manual markdown source!

hityingph.github.io. Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

gpyumd. A Python interface for GPUMD

thermo. GPUMD and LAMMPS helper functions for thermal computations

DFTK.jl. Density-functional toolkit

somd_tutorials. Tutorials for the SOMD code.

somd. Molecular dynamics package designed for the SIESTA DFT code.

pimd-mooc. Interactive tutorials for the PIMD Massive Open Online Course

Ring-Polymer-Molecular-Dynamics-in-Python-and-cpp. In this project, we give python and C++ codes for the Ring Polymer Molecular Dynamics (RMPD) to calculate the time correlation function(TCF) of coordinate <q(0)q(t)>. Two kinds of thermostat have been tested.

i-pi. i-PI: a universal force engine

supporting-info. This GitHub repository contains additional information supporting published manuscripts

Spectral-decomposition-python-tools. Tools for computing spectral heat current distribution using LAMMPS NEMD simulations.

New-Version-Spectral-decomposition-python-tools. (NEW) Tools for computing spectral heat current distribution using LAMMPS NEMD simulations.

PPR-Phonon-Participation-Ratio. Calculation of phonon participation rates - used to characterize atomic vibrational information including the degree of localization and delocalization.

Phonon-Vibration-Viewer. Visualizing lattice vibration information from phonon dispersion to atoms (For GPUMD)

pySED. To implement the phonon SED (spectral energy desity) method in 2010, phonon lifetime can be calculated.

AGF-phonon-transport. A 200-line Matlab implementation of the Atomistic Green's function (AGF) method for phonon transport

sportran. A code to estimate transport coefficients from the cepstral analysis of a (multi)variate current stationary time series -- [FKA "thermocepstrum"]

gpyumd. A Python interface for GPUMD

PyNEP. A python interface of NEP

gpuqt. A CUDA-implementation of linear-scaling quantum transport methods

cusolver_stream. test stream of cusolver

NVIDIA_SGEMM_PRACTICE. Step-by-step optimization of CUDA SGEMM

nnpot. Python

Tutorial-on-atomic-simulations. Tutorials on atomic simulations related to my research

abacus-develop. An electronic structure package based on either plane wave basis or numerical atomic orbitals.

turbogap. The TurboGAP code

Machine-Learning_ZhouZhihua. Exercises answers to the book "machine-learning" written by Prof. Zhou Zhihua of Nanjing University

parallelGBC. Parallel Groebner Basis Computation

deepmd-kit. A deep learning package for many-body potential energy representation and molecular dynamics

ParallelComputing. well done is quickly done

kaldo. Anharmonic Lattice Dynamics

scilab. Read only copy of https://gitlab.com/scilab/scilab

SENPAI. Molecular dynamics simulation software

OpenRDM. An open-source library for reduced-density matrix-based analysis and computation

cpp-code-snippets. Some useful C++ code snippets

CUDA-Programming-with-Python. 关于书籍CUDA Programming使用了pycuda模块的Python版本的示例代码

Lammps_Toolbox. Toolbox used to construct model analysis output data for lammps based on Matlab

cmake-demo. 《CMake入门实战》源码

Virgilio. Your new Mentor for Data Science E-Learning.

pfc. Tools for phase field crystal modeling of two-dimensional materials.

code-samples. Source code examples from the Parallel Forall Blog

scaled-particle-theory. The formulation of scaled particle theory (SPT) is presented for a quite general model of fluids confined in a random porous media, i.e., a multicomponent hard sphere (HS) fluid in a multicomponent hard sphere or a multicomponent overlapping hard sphere (OHS) matrix. The analytical expressions for pressure, Helmholtz free energy, and chemical potential are derived. The thermodynamic consistency of the proposed theory is established. I provided the code here based on SPT2 for computing the chemical potential of hard sphere fluid confined by porous media. Reference: W. Chen, S.L. Zhao, M. Holovko, X. S. Chen,and W. Dong, J. Phys. Chem. B accepted

GPUGA. Graphics Processing Units Genetic Algorithm

LSQT-Jupyter. A tutorial on the linear scaling quantum transport methods using Jupyter (with Python3)

CUDA-Programming. Sample codes for my CUDA programming book

dft-book. A book on modeling materials using VASP, ase and vasp

proyectormp.github.io. pagina del grupo

kinematicAlgebra. This project is to generate the kinematic algebra in Yang-Mills amplitude

For_gpumd. Some examples of GPUMD

tbmd. Tight binding molecular dynamics code to model carbon structures (linear carbon chains, fullerenes, graphene, etc.)

JuliaByExample. Examples of Julia

atomistica. Atomistica is a library of interatomic potentials that is compatible with ASE and LAMMPS

thermo. GPUMD and LAMMPS helper functions for thermal computations

DynaPhoPy. Phonon anharmonicity analysis from molecular dynamics

REBO. Molecular dynamics code for the Reactive Empirical Bond Order (REBO) potential with carbon, hydrogen and oxygen interactions or carbon, hydrogen and sulfur interactions

cppbestpractices. Collaborative Collection of C++ Best Practices. This online resource is part of Jason Turner's collection of C++ Best Practices resources. See README.md for more information.

PWDFT.jl. Plane wave density functional theory using Julia programming language

potfit. potfit force-matching code

lammps. Public development project of the LAMMPS MD software package

examples. Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Code" button, or follow the "Releases" link below.

mcmd. Monte Carlo and Molecular Dynamics Simulation Package

old_pfc. High-performance phase field crystal (PFC) code for generating realistic model systems of polycrystalline graphene.

free-programming-books. :books: Freely available programming books