FEASST: Free Energy and Advanced Sampling Simulation Toolkit
Overview
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
Website: https://pages.nist.gov/feasst/
Website DOI: https://doi.org/10.18434/M3S095
Manuscript (v0.25.1): https://doi.org/10.1063/5.0224283
Code repository: https://github.com/usnistgov/feasst
Discussion list: https://groups.google.com/a/list.nist.gov/d/forum/feasst
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/v0.25.3.tar.gz
tar -xf v0.25.3.tar.gz --transform s/-/-v/
mkdir feasst-v0.25.3/build; cd $_
cmake ..
make install -j$(nproc)
# optional Python packages for feasst tutorials
pip install jupyter matplotlib pandas scipy ../pyfeasst # ../ ensures pyfeasst matches feasst
To run a text input file:
$HOME/feasst-v0.25.3/build/bin/fst < $HOME/feasst-v0.25.3/tutorial/example.txt
To restart a simulation from a Checkpoint
file, checkpoint.fst:
echo "Restart checkpoint.fst" | $HOME/feasst-v0.25.3/build/bin/fst
Text input file example
# 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 get started
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 the tutorial to accomplish your goals, refer to the Text Interface documentation.
Compare the energy of a reference configuration with a trusted source.
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
Email list
Issue tracker
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.
Permission to use this data/software is contingent upon your acceptance of the terms of this agreement and upon your providing appropriate acknowledgments of NIST’s creation of the data/software.
Contents:
- Overview
- Tutorials
- Lennard Jones in the canonical ensemble
- HPC/SLURM script with checkpointed restarts
- Lennard Jones potential test
- Modify a checkpoint file during restarting to run longer
- Reference configuration of SPC/E water in non-cuboid domain
- Average energy of a bulk SPC/E fluid in the canonical ensemble
- Lennard Jones Alpha potential test
- User defined tabular potentials
- Example TwoBodyAlpha potential: Feynman-Hibbs
- Make your own custom two body model
- Make your own custom analysis
- Make your own custom Action
- Ideal gas equation of state using grand canonical ensemble transition-matrix Monte Carlo
- Grand canonical ensemble transition-matrix Monte Carlo
- Analysis of a one-phase (supercritical) simulation
- Analysis of a two-phase (phase separated) simulation
- Grand Canonical Flat Histogram Simulation of Lennard-Jones
- Grand Canonical Flat Histogram Simulation of SPC/E
- Grand Canonical Flat Histogram Simulation of RPM
- Grand Canonical Flat Histogram Simulation of Hard Spheres.
- Grand Canonical Flat Histogram Simulation of Patchy Trimers
- Grand Canonical Flat Histogram Simulation of Kern-Frenkel Patches
- Grand Canonical Flat Histogram Simulation at low temperature
- Grand Canonical Flat Histogram Simulation of EMP2 CO2
- Grand Canonical Flat Histogram Simulation of TraPPE alkanes
- Efficiency of 1 or 2 bin Grand Canonical Flat Histogram Simulations
- Slab, cylindrical, spherical and mixed confinement
- Grand Canonical Flat Histogram Simulation of Lennard-Jones in a simple WCA porous network
- Grand Canonical Flat Histogram Simulation of TraPPE CO2 in ZIF8
- Simulation of a single freely-jointed chain
- Simulation of a single chain
- Simulation of a single 20-bead linear chain
- Scattering calculations for hard sphere coarse-grained mAb models
- Temperature extrapolation of the radius of gyration
- Testing angles and branches
- Monte Carlo with rigid cluster moves
- Compare scattering calculations for hard spheres
- Post process scattering calculations from file.
- Beta expanded ensemble
- Expanded Ensemble Grand Canonical Flat Histogram Simulation of RPM
- Second virial coefficient calculation of a Trimer using Mayer-Sampling
- Second virial coefficient calculation of TraPPE ethane using Mayer-Sampling
- Second virial coefficient calculation of a Kern-Frenkel patch using Mayer-Sampling
- Virial coefficients of all-atom mAb domains.
- Virial coefficients of 7-bead coarse-grained mAb model.
- Virial coefficients of spherocylinders.
- Virial coefficients of solids of revolusion.
- Virial coefficients of atomistic proteins in implicit solvent
- Canonical ensemble Lennard-Jones with Prefetching
- Test of an anisotropic, textured square well potential.
- CG simulation of a protein using anisotropic precomputed potentials
- Compare standard vs FFTW scattering calculations for hard spheres
- Semi-Grand Canonical Flat Histogram Simulation of a binary LJ mixture
- Semi-Grand Canonical Flat Histogram Simulation of CO2 and N2
- Compare XYZ (ascii) with netCDF
- Text file interface
- Python and C++ interface
- Text Interface
- Checkpoint
- Random Number Generators
- Configuration
- Nonbonded Isotropic Models
- Nonbonded Potentials
- Nonbonded Anisotropic Models
- Long-Range Electrostatics
- Neighbor Lists
- One-Body Potentials
- Bonded Interactions
- Thermodynamic Parameters
- Acceptance Criteria
- Constraints
- Monte Carlo Trials
- TrialTranslate
- TrialParticlePivot
- TrialTransfer
- TrialGrow
- TrialAdd
- TrialRemove
- TrialVolume
- TrialBeta
- TrialCrankshaft
- TrialCrankshaftSmall
- TrialPivot
- TrialSwapSites
- TrialAddMultiple
- TrialRemoveMultiple
- TrialTransferMultiple
- TrialAVB2
- TrialAVB4
- TrialRigidCluster
- TrialTranslateCluster
- TrialRotateCluster
- TrialTransferAVB
- TrialAddAVB
- TrialRemoveAVB
- TrialTransferAVBDivalent
- TrialAddAVBDivalent
- TrialRemoveAVBDivalent
- TrialMorph
- Analyze
- Modify
- Actions
- Flat Histogram
- Gibbs Ensemble
- Change Log
- Particle files and units
- C++ Interface
- Threads
- Utilities
- utils/include/arguments
- Cache
- CustomException
- utils/include/debug
- utils/include/file
- utils/include/max_precision
- utils/include/io
feasst
feasst::install_dir()
feasst::version()
feasst::feasst_str()
feasst::feasst_str()
feasst::feasst_str()
feasst::str()
feasst::split()
feasst::trim()
feasst::trim()
feasst::str()
feasst::num_spaces()
feasst::is_found_in()
feasst::replace()
feasst::str_to_int()
feasst::str_to_double()
feasst::str_to_bool()
feasst::sized_int_to_str()
- ProgressReport
- Timer
- Checkpoint
- utils/include/utils
feasst
feasst::find_in_list()
feasst::find_in_list()
feasst::find_in_list()
feasst::resize()
feasst::resize()
feasst::resize()
feasst::resize()
feasst::resize()
feasst::fill()
feasst::fill()
feasst::num_elements()
feasst::num_elements()
feasst::has_duplicate()
feasst::is_equal()
feasst::is_equal()
feasst::is_equal()
feasst::is_equal()
feasst::is_equal()
- ArgumentParse
- utils/include/arguments_extra
- utils/include/serialize
feasst
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize_version()
feasst::feasst_deserialize_version()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_deserialize()
feasst::feasst_deserialize()
feasst::feasst_serialize_fstobj()
feasst::feasst_deserialize_fstobj()
feasst::feasst_serialize_fstobj()
feasst::feasst_deserialize_fstobj()
feasst::feasst_serialize_fstobj()
feasst::feasst_deserialize_fstobj()
feasst::feasst_serialize_sp()
feasst::feasst_serialize_sp()
feasst::feasst_serialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize()
feasst::feasst_deserialize()
feasst::feasst_serialize_fstdr()
feasst::feasst_serialize()
feasst::feasst_serialize_fstdr()
feasst::feasst_serialize_endcap()
feasst::feasst_deserialize_endcap()
- utils/include/serialize_extra
- FEASST plugin dependencies
- Math
- math/include/constants
- Euler
- Formula
- FormulaPolynomial
- Matrix
- math/include/quadratic_equation
- Random
Random
seed_by_time()
seed()
uniform()
uniform()
coin_flip()
uniform_real()
index()
element()
const_element()
alpha_numeric()
position_in_cube()
position_in_cube()
position_in_cuboid()
position_in_cuboid()
unit_sphere_surface()
position_in_spherical_shell()
index_from_cumulative_probability()
quaternion()
rotation()
rotation()
standard_normal()
normal()
cache()
set_cache_to_load()
set_cache_to_unload()
class_name()
- RandomModulo
- RandomMT19937
- Solver
- SolverBisection
- SolverBrentDekker
- SolverNewtonRaphson
- Table
- FormulaExponential
- Histogram
- Minimize
- GoldenSearch
- Position
Position
Position()
Position()
coord()
set_vector()
set_from_cartesian()
push_back()
set_from_spherical()
set_from_spherical()
set_from_spherical()
spherical()
spherical()
coord()
set_coord()
add_to_coord()
size()
dimension()
set_to_origin_3D()
set_to_origin()
set_to_origin()
add()
subtract()
divide()
divide()
multiply()
dot_product()
dot_product()
cross_product()
squared_distance()
distance()
squared_distance()
distance()
str()
cosine()
vertex_angle_radians()
torsion_angle_radians()
normalize()
is_equal()
is_equal()
nearest_distance_to_axis()
orthogonal()
reflect()
- Accumulator
Accumulator
max_block_operations()
num_moments()
accumulate()
average()
stdev()
std()
stdev_of_av()
block_stdev()
block_std_of_std()
block_averages()
block_size()
blocks()
num_values()
sum()
sum_dble()
sum_of_squared()
sum_of_squared_dble()
reset()
max()
min()
moment()
moments()
status_header()
status()
str()
last_value()
is_equivalent()
- math/include/utils_math
feasst
feasst::round()
feasst::average()
feasst::product()
feasst::minimum()
feasst::minimum()
feasst::minimum()
feasst::minimum()
feasst::minimum()
feasst::minimum()
feasst::maximum()
feasst::maximum()
feasst::maximum()
feasst::maximum()
feasst::maximum()
feasst::maximum()
feasst::sum()
feasst::sum()
feasst::sum()
feasst::local_minimum_indices()
feasst::feasst_union()
feasst::feasst_difference()
feasst::sgn()
feasst::radians_to_degrees()
feasst::degrees_to_radians()
feasst::feasst_swap()
feasst::feasst_sort()
feasst::is_in_interval()
feasst::cumulative_probability()
feasst::spherical_shell_volume()
feasst::add()
feasst::add()
feasst::add()
feasst::add()
feasst::factorial()
feasst::has_bad_value()
feasst::has_bad_value()
- FEASST plugin dependencies
- Configuration
- NeighborCriteria
- PhysicalConstants
- Properties
- ModelParam
- Group
- Bond
- VisitParticles
- VisitConfiguration
- Configuration
Configuration
serialize()
Configuration()
add_particle_type()
num_particle_types()
num_site_types()
num_bond_types()
num_angle_types()
num_dihedral_types()
particle_type()
type_to_file_name()
particle_types()
add()
model_params()
set_model_param()
set_model_param()
set_model_param()
add_model_param()
add_or_set_model_param()
set_physical_constants()
physical_constants()
unique_types()
unique_type()
unique_type()
max_sites_in_any_particle()
set_site_type()
site_type_to_particle_type()
num_site_types_per_particle_type()
add()
num_groups()
particle_type_to_group()
particle_type_to_group_create()
group_index()
group_selects()
group_select()
add_particle_of_type()
particle()
particle()
selection_of_all()
num_particles()
num_sites()
num_particles_of_type()
newest_particle()
num_sites_of_type()
num_sites_of_type()
num_sites_of_type()
num_sites_of_type()
update_positions()
update_positions()
update_positions()
copy_particles()
displace_particles()
displace_particle()
displace()
replace_position()
remove_particles()
remove_particle()
set()
domain()
set_side_lengths()
dimension()
init_wrap()
num_cell_lists()
increment_num_cell_lists()
revive()
particles()
select_particle()
newest_particle_index()
ghosts()
wrap_particle()
add_non_ghost_particle_of_type()
set_selection_physical()
set_property()
add_site_property()
add_or_set_site_property()
add_or_set_particle_type_site_property()
set_site_property()
set_site_property()
set_particle_type()
add()
neighbor_criteria()
neighbor_criteria()
check()
are_all_sites_physical()
is_equal()
check_dimensions()
status_header()
status()
str()
- PrinterXYZ
- FileVMD
- Domain
Domain
side_lengths()
side_length()
set_side_lengths()
set_side_length()
add_side_length()
set_cubic()
is_cubic()
xy()
xz()
yz()
disable()
periodic()
dimension()
volume()
shift()
shift_opt()
wrap()
random_position()
random_position()
min_side_length()
max_side_length()
inscribed_sphere_diameter()
unwrap()
status_header()
status()
- Select
Select
check()
is_equal()
random_particle()
str()
is_empty()
clear()
add_site()
set_site()
set_particle()
add_sites()
remove_sites()
add_particle()
add_particle()
num_particles()
num_sites()
add()
remove()
remove_last_particle()
remove_last_site()
remove_last_sites()
remove_first_site()
remove_first_sites()
remove_particle()
particle_indices()
site_indices()
site_indices()
replace_indices()
is_overlap()
is_group_empty()
set_group()
group()
Select()
Select()
has_positions()
site_positions()
site_properties()
set_site_position()
set_site_position()
add_to_site_position()
set_site_properties()
load_position()
load_positions()
load_positions_of_last()
geometric_center()
trial_state()
set_trial_state()
exclude()
excluded()
set_new_bond()
new_bond()
set_old_bond()
old_bond()
reset_excluded_and_bond()
- Site
- Particle
Particle
max_distance()
add()
site()
set_site()
sites()
num_sites()
remove_site()
is_isotropic()
set_site_physical()
check()
increment_site_types()
remove_non_unique_types()
set_site_type()
num_sites_of_type()
displace()
replace_position()
replace_position()
replace_properties()
add_site_property()
add_or_set_site_property()
set_site_property()
num_bonds()
bond()
bonds()
add_bond()
add_bond_property()
add_bond_model()
erase_bonds()
bond()
bond_neighbors()
num_angles()
angle()
angles()
add_angle()
add_angle_property()
add_angle_model()
angle()
angle_neighbors()
num_dihedrals()
dihedral()
dihedrals()
add_dihedral()
add_dihedral_property()
add_dihedral_model()
dihedral()
dihedral_neighbors()
type()
set_type()
- FileParticle
- ParticleFactory
ParticleFactory
unique_particles()
unique_types()
check_types()
check_types()
check_site_types()
check_particle_types()
check_bond_types()
check_angle_types()
check_dihedral_types()
add()
add()
remove()
particle()
particles()
num()
replace_position()
replace_position()
replace_properties()
scale_particle_positions()
check()
num_site_types()
num_sites()
num_particle_types()
num_bond_types()
num_bonds()
num_angle_types()
num_angles()
num_dihedral_types()
num_dihedrals()
set_site_type()
remove()
displace()
model_params()
add()
set_model_param()
set_model_param()
set_model_param()
add_model_param()
add_or_set_model_param()
set_cutoff_min_to_sigma()
set_physical_constants()
set_site_physical()
add_property()
add_property()
set_property()
add_site_property()
add_or_set_site_property()
set_site_property()
set_site_property()
- FEASST plugin dependencies
- System
- FEASST plugin dependencies
- API
- BondFourBody
- BondThreeBody
- AngleSquareWell
- BondTwoBody
- BondSquareWell
- CutoffOuter
- Model
- ModelOneBody
- ModelEmpty
- ModelThreeBody
- ModelTwoBody
- LennardJones
- IdealGas
- HardSphere
- ModelTwoBodyFactory
- ModelTwoBodyTable
- PotentialFactory
- RigidAngle
- RigidBond
- RigidDihedral
- System
System
set()
thermo_params()
set_beta()
change_volume()
delta_volume_previous()
total_volume()
revert()
finalize()
load_cache()
unload_cache()
status_header()
status()
check()
serialize()
System()
add()
num_configurations()
configuration()
dimension()
add()
set_unoptimized()
add_to_unoptimized()
unoptimized()
potential()
add_to_optimized()
optimized()
add_to_reference()
num_references()
reference()
references()
potentials()
remove_opt_overlap()
add()
neighbor_criteria()
neighbor_criteria()
precompute()
unoptimized_energy()
energy()
perturbed_energy()
stored_energy()
stored_energy_profile()
reference_energy()
reference_energy()
System()
- ThermoParams
- BondVisitor
- Cells
- Potential
Potential
group_index()
cell_index()
Potential()
model()
Potential()
visit_model()
Potential()
set()
set_model_params()
set_model_param()
set_model_param()
model_params()
model_params()
does_cutoff_fit_domain()
precompute()
energy()
select_energy()
stored_energy()
set_stored_energy()
change_volume()
revert()
finalize()
cache()
load_cache()
unload_cache()
serialize()
Potential()
- SynchronizeData
- EnergyMap
- VisitModel
- LongRangeCorrections
- DontVisitModel
- VisitModelIntraMap
- VisitModelIntra
- VisitModelCutoffOuter
- VisitModelCell
- VisitModelBond
- VisitModelInner
- Monte Carlo
- Tutorial
- FEASST plugin dependencies
- API
- Action
- Constraint
- ConstrainNumParticles
- Perturb
- PerturbMove
- PerturbRemove
- PerturbVolume
- RefPotential
- RemoveAnalyze
- RemoveModify
- RemoveTrial
- Stepper
Stepper
trials_per_update()
trials_per_write()
output_file()
output_file()
output_file_append_phase()
empty_output_file()
append()
rewrite_header()
stop_after_phase()
start_after_phase()
stop_after_iteration()
start_after_iteration()
configuration_index()
configuration()
set_state()
is_multistate()
state()
accumulator()
get_accumulator()
trials_since_update()
trials_since_write()
is_multistate_aggregate()
header()
printer()
Stepper()
- Modify
- ModifyFactory
- Analyze
- AnalyzeFactory
- TrialCompute
- TrialComputeAdd
- TrialComputeMove
- TrialComputeRemove
- TrialComputeTranslate
- TrialComputeVolume
- TrialSelect
TrialSelect
group_index()
particle_type()
configuration_index()
configuration()
get_configuration()
set_configuration_index()
before_select()
select()
sel()
precompute()
mobile()
set_mobile()
mobile_original()
set_mobile_original()
anchor()
anchor_position()
set_trial_state()
reset_mobile()
probability()
mid_stage()
set_ghost()
is_ghost()
printable()
are_constraints_satisfied()
is_particle_type_set()
remove_unphysical_sites()
replace_mobile()
property()
has_property()
add_or_set_property()
is_isotropic()
- TrialSelectAll
- TrialSelectBond
- TrialSelectAngle
- TrialSelectDihedral
- TrialSelectParticle
- TrialStage
- Tunable
- WriteCheckpoint
- WriteModelParams
- Run
- Acceptance
Acceptance
ln_metropolis_prob()
set_ln_metropolis_prob()
add_to_ln_metropolis_prob()
reject()
set_reject()
endpoint()
set_endpoint()
reset()
updated()
energy_new()
set_energy_new()
add_to_energy_new()
num_configurations()
energy_profile_new()
set_energy_profile_new()
add_to_energy_profile_new()
subtract_from_energy_profile_new()
energy_old()
set_energy_old()
add_to_energy_old()
energy_profile_old()
set_energy_profile_old()
add_to_energy_profile_old()
energy_ref()
set_energy_ref()
macrostate_shift()
add_to_macrostate_shift()
add_to_perturbed()
set_perturbed_state()
perturbed()
- ConstrainVolumeByCutoff
- MonteCarlo
MonteCarlo
MonteCarlo()
MonteCarlo()
begin()
parse_args()
add_args()
resume()
set()
random()
seed_random()
add()
configuration()
add()
add()
set()
add_to_optimized()
add_to_reference()
add()
set()
thermo_params()
set()
system()
initialize_system()
set()
criteria()
initialize_criteria()
add()
add()
remove_trial()
trials()
trial()
initialize_trials()
add()
remove_analyze()
analyzers()
analyze()
num_analyzers()
initialize_analyzers()
add()
remove_modify()
modify()
num_modifiers()
set()
write_checkpoint()
run()
attempt()
reset_trial_stats()
run_num_trials()
run_until_num_particles()
run_for_hours()
run_until_complete()
run_until_file_exists()
set_num_iterations_to_complete()
attempt_trial()
write_to_file()
next_arg()
- Rosenbluth
- PerturbRotate
- PerturbTranslate
- PerturbAnywhere
- PerturbAdd
- PerturbDistance
- PerturbDistanceAngle
- PerturbDihedral
- Criteria
Criteria
Criteria()
add()
is_allowed()
before_attempt()
is_accepted()
was_accepted()
set_current_energy()
current_energy()
set_current_energy_profile()
current_energy_profile()
update_current_energy()
status_header()
status()
write()
phase()
increment_phase()
num_iterations_to_complete()
set_num_iterations_to_complete()
num_iterations()
is_complete()
set_complete()
state()
num_states()
set_expanded_state()
expanded_state()
num_expanded_states()
update()
is_equal()
is_equal()
- AlwaysReject
- Metropolis
- Trial
Trial
weight()
weight_per_number_fraction()
number_fraction_exclude_type()
add_stage()
add_stage()
add_stage()
set()
num_stages()
stage()
num_success()
num_attempts()
num_auto_reject()
increment_num_attempts()
acceptance()
reset_stats()
status_header()
status()
tune()
precompute()
set()
compute()
revert()
attempt()
description()
set_description()
Trial()
- TrialMove
- TrialFactory
- TrialTransfer
- TrialAdd
- TrialRotate
- TrialRemove
- TrialTranslate
- TrialVolume
- SeekNumParticles
- Models
- Steppers
- Check
- CheckPhysicality
- CheckProperties
- Chirality2D
- CriteriaUpdater
- CriteriaWriter
- Density
- DensityProfile
- Energy
- ExtensiveMoments
- HeatCapacity
- IncrementPhase
- Movie
- NumParticles
- ReadConfigFromFile
- Scattering
- AnalyzeData
- SeekModify
- Tune
- Volume
- WallClockLimit
- WrapParticles
- WriteStepper
- MeanSquaredDisplacement
- ProfileTrials
- CheckEnergy
- Log
- PairDistributionInner
- CPUTime
- Tutorial
- FEASST plugin dependencies
- Flat histogram
- Tutorial
- Ideal gas equation of state using grand canonical ensemble transition-matrix Monte Carlo
- Grand canonical ensemble transition-matrix Monte Carlo
- Analysis of a one-phase (supercritical) simulation
- Analysis of a two-phase (phase separated) simulation
- Grand Canonical Flat Histogram Simulation of Lennard-Jones
- Grand Canonical Flat Histogram Simulation of SPC/E
- Grand Canonical Flat Histogram Simulation of RPM
- Grand Canonical Flat Histogram Simulation of Hard Spheres.
- Grand Canonical Flat Histogram Simulation of Patchy Trimers
- Grand Canonical Flat Histogram Simulation of Kern-Frenkel Patches
- Grand Canonical Flat Histogram Simulation at low temperature
- Grand Canonical Flat Histogram Simulation of EMP2 CO2
- Grand Canonical Flat Histogram Simulation of TraPPE alkanes
- Efficiency of 1 or 2 bin Grand Canonical Flat Histogram Simulations
- FEASST plugin dependencies
- API
- Tutorial
- Patch
- Mayer
- MayerSampling
- Tutorial
- Second virial coefficient calculation of a Trimer using Mayer-Sampling
- Second virial coefficient calculation of TraPPE ethane using Mayer-Sampling
- Second virial coefficient calculation of a Kern-Frenkel patch using Mayer-Sampling
- Virial coefficients of all-atom mAb domains.
- Virial coefficients of 7-bead coarse-grained mAb model.
- Virial coefficients of spherocylinders.
- Virial coefficients of solids of revolusion.
- Virial coefficients of atomistic proteins in implicit solvent
- FEASST plugin dependencies
- XTC
- Chain
- PerturbSiteType
- PerturbToAnchor
- PerturbPositionSwap
- SelectTwoSites
- SelectPerturbed
- SelectParticlePivot
- SelectSiteOfType
- SelectBranch
- SelectSegment
- SelectEndSegment
- SelectCrankshaftSmall
- PerturbConnector
- SelectReptate
- PerturbCrankshaft
- PerturbCrankshaftSmall
- PerturbLibrary
- PerturbParticlePivot
- PerturbPivot
- RadiusOfGyration
- EndToEndDistance
- PerturbDistanceAngleConnector
- PerturbBranch
- PerturbReptate
- AnalyzeBonds
- TrialCrankshaft
- TrialCrankshaftSmall
- TrialParticlePivot
- TrialPivot
- TrialReptate
- TrialSwapSites
- GhostTrialGrow
- TrialGrow
- TrialGrowLinear
- Tutorial
- FEASST plugin dependencies
- Shape
- Confinement
- Slab, cylindrical, spherical and mixed confinement
- Grand Canonical Flat Histogram Simulation of Lennard-Jones in a simple WCA porous network
- Grand Canonical Flat Histogram Simulation of TraPPE CO2 in ZIF8
- FEASST plugin dependencies
- API
- Charge
- Optimized Lennard-Jones
- Cluster
- Monte Carlo with rigid cluster moves
- FEASST plugin dependencies
- API
- ComputeMoveCluster
- SelectCluster
- PerturbPointReflect
- SelectParticleAVBDivalent
- SelectParticleAVB
- PerturbRotateCOM
- PerturbMoveAVB
- PerturbAddAVB
- CalculateCluster
- AnalyzeCluster
- ComputeRemoveAVBDivalent
- ComputeRemoveAVB
- ComputeGCA
- ComputeAVB4
- ComputeAVB2
- ComputeAddAVBDivalent
- ComputeAddAVB
- TrialAVB4
- TrialTranslateCluster
- TrialTransferAVBDivalent
- TrialTransferAVB
- TrialRotateCluster
- TrialRigidCluster
- TrialRemoveAVBDivalent
- TrialRemoveAVB
- TrialAVB2
- TrialAddAVBDivalent
- TrialAddAVB
- EnergyMapNeighbor
- EnergyMapNeighborCriteria
- EnergyMapAll
- EnergyMapAllCriteria
- Expanded Grand Canonical Ensemble
- Morph
- Beta expanded
- Prefetch
- Aniso
- Modify FEASST
- Gibbs
- Server
- Model Expanded
- FFTW
- NetCDF
- MPI
- Modify FEASST
- pyfeasst
- accumulator
- cd
- fstio
- fstplot
- macrostate_distribution
MacrostateDistribution
MacrostateDistribution.__init__()
MacrostateDistribution.set_dataframe()
MacrostateDistribution.concat_dataframe()
MacrostateDistribution.dataframe()
MacrostateDistribution.set_macrostates()
MacrostateDistribution.macrostates()
MacrostateDistribution.set_ln_prob()
MacrostateDistribution.ln_prob()
MacrostateDistribution.set_minimum_smoothing()
MacrostateDistribution.minimum_smoothing()
MacrostateDistribution.normalize()
MacrostateDistribution.average_macrostate()
MacrostateDistribution.ensemble_average()
MacrostateDistribution.plot()
MacrostateDistribution.minimums()
MacrostateDistribution.split()
MacrostateDistribution.reweight()
MacrostateDistribution.reweight_to_macrostate()
MacrostateDistribution.equilibrium()
splice()
splice_files()
read_appended()
splice_collection_matrix()
- multistate_accumulator
- physical_constants
- Python Interface
- Contact
- Contributing
- For contributing code
- Guidelines for collaboration with FEASST developers
- Acknowledgement
- Citation