FEASST: Free Energy and Advanced Sampling Simulation Toolkit

Overview

The Free Energy and Advanced Sampling Simulation Toolkit (FEASST) is a free and open-source software to conduct molecular- and particle-based simulations with Monte Carlo methods. New users should start with the website (DOI) and the manuscript.

How to compile

FEASST requires C++14 and CMake, and is compiled with the following BASH commands:

#[apt/yum/dnf/brew] install g++ cmake
cd $HOME # replace this with your preference throughout
wget https://github.com/usnistgov/feasst/archive/refs/tags/v0.25.4.tar.gz
tar -xf v0.25.4.tar.gz --transform s/-/-v/
mkdir feasst-v0.25.4/build; cd $_
cmake ..
make install -j$(nproc)
# optional Python packages for feasst tutorials
pip install jupyter matplotlib pandas scipy ../pyfeasst # ../ ensures pyfeasst matches feasst

How to run a simulation

Input a text file to the compiled executable.

$HOME/feasst-v0.25.4/build/bin/fst < $HOME/feasst-v0.25.4/tutorial/example.txt

Example input text file

# Comments begin with the # symbol.
# Usage: ./fst < 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 decimal_places 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

This text input file is explained in detail in the first tutorial.

How to learn more

Review the first and second tutorial.
- Copy/paste or use the URL to find the code (e.g., https://pages.nist.gov/feasst/tutorial/launch.html is $HOME/feasst/tutorial/launch.py).
- See python launch.py --help (e.g., adjust --feasst_install or --hours_terminate).
Find Tutorials that are closest to what you would like to accomplish.
Reproduce the expected result of those Tutorials.
To modify Tutorials to accomplish your goals, refer to the Text Interface documentation.
Compare the energy of a reference configuration with a trusted source to ensure the model, Particle files and units return an expected result.
Contact us.

Features

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

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

Update to CMake 3 (https://cmake.org/download/)

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

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.

The data/software is provided by NIST as a public service and is expressly provided “AS IS.” NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT AND DATA ACCURACY. NIST does not warrant or make any representations regarding the use of the data/software or the results thereof, including but not limited to the correctness, accuracy, reliability or usefulness of the data/software. NIST SHALL NOT BE LIABLE AND YOU HEREBY RELEASE NIST FROM LIABILITY FOR ANY INDIRECT, CONSEQUENTIAL, SPECIAL, OR INCIDENTAL DAMAGES (INCLUDING DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, AND THE LIKE), WHETHER ARISING IN TORT, CONTRACT, OR OTHERWISE, ARISING FROM OR RELATING TO THE DATA (OR THE USE OF OR INABILITY TO USE THIS DATA), EVEN IF NIST HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

To the extent that NIST may hold copyright in countries other than the United States, you are hereby granted the non-exclusive irrevocable and unconditional right to print, publish, prepare derivative works and distribute the NIST data/software, in any medium, or authorize others to do so on your behalf, on a royalty-free basis throughout the World.

You may improve, modify, and create derivative works of the data/software or any portion of the data/software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the data/software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the data/software.

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Contents:

Index

Index