Code Monkey home page Code Monkey logo

jinruiamophy / feasst Goto Github PK

View Code? Open in Web Editor NEW

This project forked from usnistgov/feasst

0.0 0.0 0.0 25.58 MB

The Free Energy and Advanced Sampling Simulation Toolkit (FEASST) is a free, open-source, modular program to conduct molecular and particle-based simulations with flat-histogram Monte Carlo methods.

Home Page: http://pages.nist.gov/feasst

License: Other

Shell 0.41% JavaScript 0.02% C++ 79.09% Python 8.82% HTML 0.28% CMake 0.92% Jupyter Notebook 10.33% GDB 0.01% Dockerfile 0.03% Roff 0.09%

feasst's Introduction

README

The Free Energy and Advanced Sampling Simulation Toolkit (FEASST) is a free, open-source, public domain software to conduct molecular and particle-based simulations with Monte Carlo methods.

Features

dev/sphinx/feasst.png

:doc:`/plugin/README` contains the list of features available. Some features include but are not limited to the following:

Monte Carlo simulation techniques

  • Metropolis
  • Wang-Landau
  • Transition-matrix
  • Mayer-sampling

Thermodynamic ensembles

  • Microcanonical ensemble
  • Canonical ensemble
  • Grand canonical ensemble
  • Temperature and growth expanded ensembles

Monte Carlo trials

  • Translation, rotation, crankshaft, pivot
  • Rigid cluster rotation and translation
  • Configurational bias transfers and partial regrowth
  • Dual-cut configurational bias
  • Aggregation volume bias
  • Reptation
  • Branches

Interaction potentials

  • Hard spheres
  • Lennard-Jones with LRC, cut and force shift
  • Patchy particles
  • Yukawa and charged interactions
  • Ewald summation and 2D slab correction
  • Bonds, angles and dihedrals
  • TraPPE small molecules and n-alkanes
  • Slab, cylindrical and spherical confinement
  • Cell list and neighbor list

Modern software

  • Interface with C++ or as a Python module
  • OpenMP parallelization and prefetching
  • Checkpoint files to save, restart and analyze simulations

How to install (e.g., compile the executables).

[apt/yum/brew] install g++ cmake git python3
git clone https://github.com/usnistgov/feasst.git
mkdir feasst/build
cd feasst/build
cmake ..
make install -j4
# optional python packages for feasst tutorials
pip install ../pyfeasst jupyter matplotlib pandas scipy

The executables fst, which is used to start a simulation, and rst, which is used to restart a simulation, should now be located in /path/to/feasst/build/bin/.

Troubleshooting install

Please :doc:`/CONTACT` us if you run into an issue not listed below.

CentOS 7

CMake version is usually too old. Try the command cmake3 instead of cmake.

Windows 10

  • Install Windows subsystem for Linux (Ubuntu 16)
  • See Ubuntu 16

Ubuntu 16

macOS Mojave

  • for omp, try brew install libomp

Cray (NERSC CORI)

  • OpenMP functions apparently do not work unless the cray programming environment is disabled.

Ubuntu 18, 20, 22

  • We are not aware of any issues with these OS.

Documentation for a specific version of FEASST

You can access the documentation of a specific version of FEASST as follows.

git clone https://github.com/usnistgov/feasst.git
cd feasst
git checkout nist-pages
git log
# find the commit of your version from git log
# (e.g., 0.19.0 is a50b4fe943832f012373f23658a9497990d70d21)
git checkout a50b4fe943832f012373f23658a9497990d70d21
google-chrome index.html

feasst's People

Contributors

dwsideriusnist avatar haroldhatchnist avatar hhatch avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.