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.

Note

Manuscript: https://doi.org/10.6028/jres.123.004

Website: https://pages.nist.gov/feasst/

Website DOI: https://doi.org/10.18434/M3S095

Code repository: https://github.com/usnistgov/feasst

Discussion list: https://groups.google.com/a/list.nist.gov/d/forum/feasst

Features

_images/feasst.png

The features available in the Text Interface are summarized as follows:

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

  • Gibbs ensemble

Interaction potentials

  • Lennard-Jones and Mie with cut/force shift and corrections

  • Hard spheres and square wells

  • Patchy and anisotropic 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

Monte Carlo trials

  • Translation, rotation, crankshaft and pivot

  • Rigid cluster rotation and translation

  • Configurational bias transfers and partial regrowth

  • Dual-cut configurational bias

  • Aggregation volume bias

  • Reptation

  • Branches

Modern software

  • Interface as text input, C++ or Python module

  • Server interface to C++ or Python clients

  • OpenMP parallelization and prefetching

  • Checkpoint files to save, restart and analyze simulations

How to compile

#[apt/yum/dnf/brew] install g++ cmake git python3
cd $HOME # replace this with your preference throughout
git clone https://github.com/usnistgov/feasst.git
mkdir feasst/build
cd feasst/build
cmake ..
make install -j$(nproc)
# optional python packages for feasst tutorials
pip install jupyter matplotlib pandas scipy ../pyfeasst

FEASST requires a C++14 compiler, CMake and Python3, while git is optional. The executables fst and rst should appear in $HOME/feasst/build/bin/. Text input files are run using fst < input.txt and simulations are restarted using rst checkpoint.txt. For pyfeasst, provide pip a path to the specific pyfeasst directory in feasst to ensure the versions match (e.g., do not leave out the “../”).

Basic simulation example

The following text input file is explained in detail in the first tutorial.

# This is a text input file located at $HOME/feasst/tutorial/example.txt.
# Comments begin with the # symbol.
# Usage: $HOME/feasst/build/bin/fst < $HOME/feasst/tutorial/example.txt
MonteCarlo
RandomMT19937 seed 1572362164
Configuration cubic_side_length 55.0321208149104 particle_type0 /feasst/particle/lj.fstprt
Potential Model LennardJones VisitModel VisitModelCell min_length max_cutoff
Potential VisitModel LongRangeCorrections
ThermoParams beta 1.111111111111111 chemical_potential0 -1
Metropolis
TrialTranslate weight 1 tunable_param 2
Tune
CheckEnergy trials_per_update 1e4 tolerance 1e-8
TrialAdd weight 2 particle_type 0
Run until_num_particles 500
RemoveTrial name TrialAdd
Run num_trials 1e5
RemoveModify name Tune
Log trials_per_write 1e4 output_file lj.csv
Energy trials_per_write 1e4 output_file lj_en.csv
Movie trials_per_write 1e4 output_file lj.xyz
Metropolis num_trials_per_iteration 1e4 num_iterations_to_complete 1e2
Run until_criteria_complete true

How to get started

Troubleshooting install

Please Contact us if you run into an issue not listed below.

Ubuntu 18, 20, 22, 24 and Rocky 8 and 9

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

Ubuntu 16

CentOS 7

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

Cray (NERSC CORI)

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

macOS Mojave

  • for omp, try brew install libomp

Windows 10

  • Install Windows subsystem for Linux (Ubuntu 16)

  • See Ubuntu 16

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

Contact

Project lead

Harold Wickes Hatch

https://www.nist.gov/people/harold-wickes-hatch

harold.hatch@nist.gov

Email list

https://list.nist.gov/feasst

Issue tracker

https://github.com/usnistgov/feasst/issues

Bug reporting

Any and all bug reports are greatly appreciated in order to improve FEASST.

The following checklist is recommended to improve reproducibility so that I can get back to you more quickly.

  • Reproduce the issue with a minimal example to reduce the complexity, run time and file size.

  • Provide all output.

  • Provide the version (for a git install, bash command “git describe –abbrev=10 –dirty –always –tags” and commit from git log).

  • Provide the user code (e.g., input text file, C++ with int main() or .py file).

  • For installation errors, include the output of the “cmake ..” command on an empty build directory.

Disclaimer

Certain commercial firms and trade names are identified in this document in order to specify the installation and usage procedures adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, nor is it intended to imply that related products are necessarily the best available for the purpose.

License

This license was obtained from https://www.nist.gov/director/licensing (revised as of July 2017).

This data/software was developed by employees of the National Institute of Standards and Technology (NIST), an agency of the Federal Government. Pursuant to title 15 United States Code Section 105, works of NIST employees are not subject to copyright protection in the United States and are considered to be in the public domain.

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