Text Interface

The syntax of a FEASST text input file is follows. Each line begins with the name of a class in FEASST, listed below. The class name is then proceeded by space-separated pairs of argument names and values. Minor version changes support the same text files, but major version changes do not. For example, all text files for version v0.23.0 should also work with v0.23.1, but may not work with v0.24.0. For updating to a newer version, see the change log below.

Random Number Generators

These are the number generators available for use.

Configuration

These classes describe the identity of the particles, their positions and the spatial domain in which they reside.

Nonbonded Isotropic Models

These classes include pair-wise (two-body) isotropic interactions models.

Nonbonded Potentials

These classes include various ways that interactions may be computed over a Selection or the entire Configuration.

Nonbonded Anisotropic Models

These classes include anisotropic interactions.

Long-Range Electrostatics

These classes include Ewald and long-range electrostatics.

Neighbor Lists

These classes store neighbors and their interaction energies.

One-Body Potentials

These classes include zero- and one-body interactions.

Bonded Interactions

The following bonded interactions are typically specified in fstprt files (see Particle files and units):

Thermodynamic Parameters

Acceptance Criteria

These classes determine if a MonteCarlo Trial is accepted or rejected.

Constraints

These classes impose Constraints on the acceptance Criteria.

Monte Carlo Trials

These classes add Trials.

Analyze

Analyze update/write every fixed number of trials, and do not change the simulation.

Modify

Modify update/write every fixed number of trials, but may change the simulation.

Actions

Action s happen once.

Flat Histogram

FlatHistogram simulations Bias along a 1-dimensional Macrostate.

Gibbs Ensemble

Simulate multiple Configuration s and transfer particles and/or volume between them.

Change Log

Below is a list text interface changes that may affect older scripts. Backwards incompatibility should remain for deprecated interface on minor version changes. Renamed arguments are shown as Class::old_argument->new_argument.

v0.25.13 to v0.25.14

  • Fixed issue when the order of first appearance of site types in the “Sites” section of a particle file did not match the order in “Site Properties”

v0.25.12 to v0.25.13

  • FEASST particle (fstprt) files now use strings instead of integers to represent sites, bonds, angles and dihedrals. Previous use of integers is still backwards compatible.

  • Deprecated configuration_index->config in RefPotential,Potential,Stepper,TrialSelect,Run,ZeroBackground,TrialGibbs[Particle,Volume]Transfer(csv)

  • Deprecated reference_index->ref in NeighborCriteria,RefPotential,TrialStage,WriteModelParams

  • Copy[Following,Next]Line::replace0/with0 deprecated. Use For.

  • Configuration::[parameter][i][j] replace with site type names

  • Configuration::particle_type,group csv

  • Configuration::add_particles_of_type[i]->add_num_[name]_particles

  • Cuboid::site_length[i]->side_lengths csv

  • Domain::side_length,periodic csv

  • Group::site_type,particle_type,particle_index csv

  • ModelTwoBodyFactory::model[i]->models csv

  • Position::x,y,z->csv

  • SelectParticleAVBDivalent::site_index->site_name

  • SelectParticleAVBDivalent::target_site_index->target_site_name

  • Remove::name,name_contains csv

  • ThermoParams::chemical_potential csv

  • Trial[Add,Remove,Transfer]Multiple::particle_type csv

  • TrialMorph::particle_type,particle_type_morph csv

  • VisitModelInnerServer::server_site[i]->server_sites csv

  • TrialSelect, Group and NeighborIndex, also use names instead of integers

v0.25.11 to v0.25.12

  • TablePotential bug fix for site types not in table.

v0.25.9 to v0.25.10

  • AngleSquareWell::minimum->min_degrees

  • AngleSquareWell::maximum->max_degrees

  • Random::seed, deprecated “time” and “default” options.

v0.25.6 to v0.25.7

  • LennardJonesAlpha::lambda fixed.

v0.25.4 to v0.25.5

  • Criteria::num_iterations_to_complete->cycles_to_complete

  • Metropolis/MayerSampling::num_trials_per_iteration->trials_per_cycle

  • Stepper::stop_after_iteration->stop_after_cycle

  • Stepper::start_after_iteration->start_after_cycle

  • Remove[Trial,Analyze,Modify]->Remove

  • Run::until_criteria_complete->until

v0.25.3 to v0.25.4

  • PressureFromTestVolume->GhostTrialVolume

v0.24.6 to v0.25.0

  • Mie::n,m arguments replaced with mie_lambda_r,mie_lambda_a “Site Properties”

  • TablePotential base class VisitModel->Model

  • Trial::weight_per_number->weight_per_number_fraction

v0.23.1 to v0.24.0

  • Stepper::file_name->output_file

  • WriteModelParams::file_name->output_file

  • Checkpoint::file_name->checkpoint_file

  • GhostTrialGrow::trial_grow_file->grow_file

  • TrialGrowFile::file_name->grow_file

  • ReadConfigFromFile::file_name->input_file

  • ShapeFile::file_name->shape_file

  • ModelTableCart3DIntegr::file_name->table_file

  • ModelTableCart3DIntegr::shape_file_name->shape_file

The information available above is pruned from the C++ Interface documentation, with only the class arguments and no member functions. Therefore the C++ Interface documentation represents all capabilities of FEASST, many of which are hidden from text users for various reasons (e.g., because the classes may be used only internally, in development, buggy, deprecated or debugging tools).