feasst 0.25.19

https://pages.nist.gov/feasst

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 can start with the website (DOI), manuscript, GitHub discussion and a five minute video. Support FEASST with a GitHub star or manuscript citation!

Quickstart

sudo apt install g++ cmake python3-venv               # C++, CMake and Python3
python3 -m venv feasst; source ~/feasst/bin/activate  # or use existing env/conda
CMAKE_BUILD_PARALLEL_LEVEL=8 pip3 install feasst      # install
feasst-menu                                           # interactive tutorial

For Mac/Linux use apt, yum, dnf, brew(homebrew), etc. For Windows, use WSL. For HPC, use “module avail/load.”

C++ Executable

Run with BASH/etc:

#!/bin/bash
num_particles=500
density=0.003
beta=`python3 -c "print(1./0.9)"`
length=`python3 -c "print(($num_particles/$density)**(1./3.))"`
tpc=1e4
feasst << EOF
# Comments begin with the # symbol.
# Compute average energy of LJ at T*=0.9, rho*=0.003
# See https://mmlapps.nist.gov/srs/LJ_PURE/mc.htm
MonteCarlo
RandomMT19937
#seed=1572362164
Configuration cubic_side_length=$length particle_type=lj:/feasst/particle/lj.txt
Potential Model=LennardJones VisitModel=VisitModelCell
Potential VisitModel=LongRangeCorrections
Checkpoint checkpoint_file=checkpoint.fst
ThermoParams beta=$beta chemical_potential=-1
Metropolis
TrialTranslate weight=1 tunable_param=2
Tune
CheckEnergy trials_per_update=$tpc decimal_places=8
Log trials_per_write=$tpc output_file=lj_eq.csv
Run until_num_particles=$num_particles particle_type=lj Trial=TrialAdd weight=2
Run num_trials=1e5
Remove name=Tune,Log
WriteCheckpoint
EOF

Restart with checkpoint.fst and BASH/etc:

#!/bin/bash
write="trials_per_write=1e4 output_file=lj"
feasst << EOF
Restart checkpoint_file=checkpoint.fst
Log $write.csv
Movie $write.xyz
Energy ${write}_en.csv
Metropolis trials_per_cycle=1e4 cycles_to_complete=1e2
Run until=complete
EOF

Run with script.txt and BASH/etc:

feasst < script.txt

Python Module

Install with BASH/etc:

sudo apt install g++ cmake python3-dev python3-venv
python3 -m venv feasst; source ~/feasst/bin/activate
CMAKE_BUILD_PARALLEL_LEVEL=8 CMAKE_ARGS="-DUSE_PYBIND11=ON" pip install feasst

Run in Python:

import numpy as np
import pandas as pd
import feasst

# Compare with T*=0.9,rho*=0.003 in https://mmlapps.nist.gov/srs/LJ_PURE/mc.htm.
num_particles=500
density=0.003
beta=1./0.9
length=np.power(num_particles/density, 1./3.)
prefix='lj'
write=f'trials_per_write=1e4 output_file={prefix}'

mc = feasst.MonteCarlo()
feasst.parse(mc, f"""RandomMT19937 seed=416974832
Configuration cubic_side_length={length} particle_type=lj:/feasst/particle/lj_new.txt
Potential Model=LennardJones VisitModel=VisitModelCell
ThermoParams beta={beta} chemical_potential=1
Metropolis
TrialTranslate tunable_param=2
Checkpoint checkpoint_file={prefix}_checkpoint.fst num_hours=1 num_hours_terminate=117.5667
CheckEnergy trials_per_update=1e4 decimal_places=8
Log {write}_eq.csv
Movie {write}_eq.xyz
Run until_num_particles={num_particles} Trial=TrialAdd particle_type=lj
Metropolis trials_per_cycle=1e4 cycles_to_complete=10
Run until=complete Stepper=Tune
Remove name=Log,Movie""")

print('# x-position of first particle/site.', mc.configuration(0).particle(0).site(0).position(0))
assert mc.configuration(0).particle(0).site(0).position(0) != 0.

feasst.parse(mc, f"""Metropolis trials_per_cycle=1e4 cycles_to_complete=1e2
Log {write}.csv
Movie {write}.xyz
Energy {write}_en.csv
CPUTime {write}_cpu.csv
ProfileCPU {write}_profile.csv
GhostTrialVolume {write}_pressure.csv trials_per_update=1e4
Run until=complete""")

print('# compare average energy with SRSW https://mmlapps.nist.gov/srs/LJ_PURE/mc.htm.')
en = pd.read_csv('lj_en.csv')
print('<U> =', en['average'][0]/num_particles, '+/-', en['block_stdev'][0]/num_particles)

Documentation

See https://pages.nist.gov/feasst. View documentation for your specific version by downloading FEASST and opening the html/index.html file as shown by the following Bash commands.

curl -OL https://github.com/usnistgov/feasst/archive/refs/tags/v0.25.19.tar.gz
tar -xf v0.25.19.tar.gz
open feasst-0.25.19/html/index.html