Index

_

__init__() (macrostate_distribution.MacrostateDistribution method)

A

accumulator module Accumulator (class in accumulator) add() (accumulator.Accumulator method)

all_sims_complete() (in module fstio) ASSERT (C macro), [1] average_macrostate() (macrostate_distribution.MacrostateDistribution method) AvogadroConstant (class in physical_constants)

B

BoltzmannConstant (class in physical_constants)

C

CATCH_PHRASE (C macro), [1] cd module

cd (class in cd) combine_tables_two_rigid_body() (in module fstio) concat_dataframe() (macrostate_distribution.MacrostateDistribution method)

D

dataframe() (macrostate_distribution.MacrostateDistribution method) DEBUG (C macro), [1]

dict_to_argparse() (in module fstio) display() (in module fstplot)

E

ElementaryCharge (class in physical_constants) ensemble_average() (macrostate_distribution.MacrostateDistribution method)

equilibrium() (macrostate_distribution.MacrostateDistribution method) ERROR (C macro), [1] ESqPerAngstromToKJPerMol (class in physical_constants)

F

FATAL (C macro), [1] feasst (C++ type), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27] feasst::Acceptance (C++ class), [1] feasst::Acceptance::add_to_energy_new (C++ function) feasst::Acceptance::add_to_energy_old (C++ function) feasst::Acceptance::add_to_energy_profile_new (C++ function) feasst::Acceptance::add_to_energy_profile_old (C++ function) feasst::Acceptance::add_to_ln_metropolis_prob (C++ function) feasst::Acceptance::add_to_macrostate_shift (C++ function) feasst::Acceptance::add_to_perturbed (C++ function) feasst::Acceptance::endpoint (C++ function) feasst::Acceptance::energy_new (C++ function) feasst::Acceptance::energy_old (C++ function) feasst::Acceptance::energy_profile_new (C++ function) feasst::Acceptance::energy_profile_old (C++ function) feasst::Acceptance::energy_ref (C++ function) feasst::Acceptance::ln_metropolis_prob (C++ function) feasst::Acceptance::macrostate_shift (C++ function) feasst::Acceptance::num_configurations (C++ function) feasst::Acceptance::perturbed (C++ function) feasst::Acceptance::reject (C++ function) feasst::Acceptance::reset (C++ function) feasst::Acceptance::set_endpoint (C++ function) feasst::Acceptance::set_energy_new (C++ function) feasst::Acceptance::set_energy_old (C++ function) feasst::Acceptance::set_energy_profile_new (C++ function) feasst::Acceptance::set_energy_profile_old (C++ function) feasst::Acceptance::set_energy_ref (C++ function) feasst::Acceptance::set_ln_metropolis_prob (C++ function) feasst::Acceptance::set_perturbed_state (C++ function) feasst::Acceptance::set_reject (C++ function) feasst::Acceptance::subtract_from_energy_profile_new (C++ function) feasst::Acceptance::updated (C++ function) feasst::Accumulator (C++ class), [1] feasst::Accumulator::accumulate (C++ function) feasst::Accumulator::average (C++ function) feasst::Accumulator::block_averages (C++ function) feasst::Accumulator::block_size (C++ function) feasst::Accumulator::block_std_of_std (C++ function) feasst::Accumulator::block_stdev (C++ function), [1] feasst::Accumulator::blocks (C++ function) feasst::Accumulator::is_equivalent (C++ function) feasst::Accumulator::largest_block_operation (C++ function) feasst::Accumulator::largest_blocks (C++ function) feasst::Accumulator::last_value (C++ function) feasst::Accumulator::max (C++ function) feasst::Accumulator::max_block_operations (C++ function) feasst::Accumulator::min (C++ function) feasst::Accumulator::moment (C++ function) feasst::Accumulator::moments (C++ function) feasst::Accumulator::num_moments (C++ function) feasst::Accumulator::num_values (C++ function) feasst::Accumulator::reset (C++ function) feasst::Accumulator::status (C++ function) feasst::Accumulator::status_header (C++ function) feasst::Accumulator::std (C++ function) feasst::Accumulator::stdev (C++ function) feasst::Accumulator::stdev_of_av (C++ function) feasst::Accumulator::str (C++ function) feasst::Accumulator::sum (C++ function) feasst::Accumulator::sum_dble (C++ function) feasst::Accumulator::sum_of_squared (C++ function) feasst::Accumulator::sum_of_squared_dble (C++ function) feasst::AccumulatorAverage (C++ class), [1] feasst::AccumulatorMoment (C++ class), [1] feasst::AccumulatorSum (C++ class), [1] feasst::AccumulatorSumOfSquared (C++ class), [1] feasst::Action (C++ class), [1] feasst::ActionExample (C++ class), [1] feasst::AEqualB (C++ class), [1] feasst::AHalfB (C++ class), [1] feasst::AlwaysReject (C++ class), [1] feasst::AlwaysReject::AlwaysReject (C++ function) feasst::AlwaysReject::is_accepted (C++ function) feasst::Analyze (C++ class), [1] feasst::Analyze::initialize (C++ function) feasst::Analyze::trial (C++ function) feasst::Analyze::update (C++ function) feasst::Analyze::write (C++ function) feasst::AnalyzeBonds (C++ class), [1] feasst::AnalyzeBonds::angle (C++ function) feasst::AnalyzeBonds::angle_hist (C++ function) feasst::AnalyzeBonds::bond (C++ function) feasst::AnalyzeBonds::bond_hist (C++ function) feasst::AnalyzeBonds::dihedral (C++ function) feasst::AnalyzeBonds::dihedral_hist (C++ function) feasst::AnalyzeBonds::initialize (C++ function) feasst::AnalyzeBonds::update (C++ function) feasst::AnalyzeBonds::write (C++ function) feasst::AnalyzeCluster (C++ class), [1] feasst::AnalyzeCluster::cluster_size (C++ function) feasst::AnalyzeCluster::header (C++ function) feasst::AnalyzeCluster::initialize (C++ function) feasst::AnalyzeCluster::update (C++ function) feasst::AnalyzeCluster::write (C++ function) feasst::AnalyzeData (C++ class), [1] feasst::AnalyzeExample (C++ class), [1] feasst::AnalyzeExample::geometric_center (C++ function), [1] feasst::AnalyzeExample::header (C++ function) feasst::AnalyzeExample::initialize (C++ function) feasst::AnalyzeExample::update (C++ function) feasst::AnalyzeExample::write (C++ function) feasst::AnalyzeFactory (C++ class), [1] feasst::AnalyzeFactory::add (C++ function) feasst::AnalyzeFactory::adjust_bounds (C++ function) feasst::AnalyzeFactory::analyze (C++ function) feasst::AnalyzeFactory::analyzers (C++ function) feasst::AnalyzeFactory::initialize (C++ function) feasst::AnalyzeFactory::num (C++ function) feasst::AnalyzeFactory::remove (C++ function) feasst::AnalyzeFactory::set_timer (C++ function) feasst::AnalyzeFactory::timer (C++ function) feasst::AnalyzeFactory::trial (C++ function) feasst::AnalyzeFactory::write_to_file (C++ function) feasst::AnalyzeUpdateOnly (C++ class), [1] feasst::AnalyzeWriteOnly (C++ class), [1] feasst::Angle (C++ class), [1] feasst::AngleHarmonic (C++ class), [1] feasst::AngleHarmonic::energy (C++ function) feasst::AngleHarmonic::random_branch (C++ function) feasst::AngleSquareWell (C++ class), [1] feasst::AngleSquareWell::energy (C++ function) feasst::Anisotropic (C++ class), [1] feasst::arglist (C++ type), [1] feasst::argtype (C++ type), [1] feasst::ArgumentParse (C++ class), [1] feasst::ArgumentParse::args (C++ function) feasst::ArgumentParse::ArgumentParse (C++ function), [1] feasst::ArgumentParse::get (C++ function) feasst::ArgumentParse::get_double (C++ function) feasst::ArgumentParse::get_int (C++ function) feasst::ArgumentParse::option_given (C++ function) feasst::ArgumentParse::parse (C++ function) feasst::ArgumentParse::str (C++ function) feasst::Background (C++ class), [1] feasst::Backmap (C++ class), [1] feasst::Backmap::initialize (C++ function) feasst::Backmap::write (C++ function) feasst::Bias (C++ class), [1] feasst::Bias::increment_phase (C++ function) feasst::Bias::infrequent_update (C++ function) feasst::Bias::ln_bias (C++ function) feasst::Bias::ln_prob (C++ function) feasst::Bias::num_iterations_to_complete (C++ function) feasst::Bias::phase (C++ function) feasst::Bias::set_ln_prob (C++ function) feasst::Bias::set_num_iterations_to_complete (C++ function) feasst::Bias::update (C++ function) feasst::Bond (C++ class), [1] feasst::Bond::add_site_index (C++ function) feasst::Bond::model (C++ function) feasst::Bond::num_sites (C++ function) feasst::Bond::set_model (C++ function) feasst::Bond::set_type (C++ function) feasst::Bond::site (C++ function) feasst::Bond::site_indices (C++ function) feasst::Bond::type (C++ function) feasst::BondFourBody (C++ class), [1] feasst::BondHarmonic (C++ class), [1] feasst::BondHarmonic::random_distance (C++ function) feasst::BondSquareWell (C++ class), [1] feasst::BondThreeBody (C++ class), [1] feasst::BondThreeBody::energy (C++ function), [1] feasst::BondThreeBody::random_angle_radians (C++ function) feasst::BondThreeBody::random_branch (C++ function) feasst::BondTwoBody (C++ class), [1] feasst::BondVisitor (C++ class), [1] feasst::BondVisitor::BondVisitor (C++ function) feasst::Cache (C++ class), [1] feasst::Cache::Cache (C++ function) feasst::Cache::is_loading (C++ function) feasst::Cache::is_unloading (C++ function), [1] feasst::Cache::load (C++ function) feasst::Cache::serialize (C++ function) feasst::Cache::set_load (C++ function) feasst::Cache::set_unload (C++ function), [1] feasst::CalculateCluster (C++ class), [1] feasst::CalculateCluster::cluster_size (C++ function) feasst::CalculateCluster::header (C++ function) feasst::CalculateCluster::initialize (C++ function) feasst::CalculateCluster::update (C++ function) feasst::CalculateCluster::write (C++ function) feasst::Cells (C++ class), [1] feasst::Cells::clear (C++ function) feasst::Cells::create (C++ function) feasst::Cells::group (C++ function) feasst::Cells::id (C++ function) feasst::Cells::neighbor (C++ function) feasst::Cells::num (C++ function), [1] feasst::Cells::num_sites (C++ function) feasst::Cells::num_total (C++ function) feasst::Cells::particles (C++ function) feasst::Cells::set_group (C++ function) feasst::Cells::set_type (C++ function) feasst::Cells::type (C++ function) feasst::Charge (C++ class), [1] feasst::ChargeScreened (C++ class), [1] feasst::ChargeScreened::erfc (C++ function) feasst::ChargeScreened::precompute (C++ function) feasst::ChargeScreened::serialize (C++ function) feasst::ChargeScreenedIntra (C++ class), [1] feasst::ChargeScreenedIntra::precompute (C++ function) feasst::ChargeScreenedIntra::serialize (C++ function) feasst::ChargeSelf (C++ class), [1] feasst::ChargeSelf::energy (C++ function) feasst::ChargeSelf::precompute (C++ function) feasst::ChargeSelf::serialize (C++ function) feasst::Check (C++ class), [1] feasst::Check::update (C++ function) feasst::CheckConstantVolume (C++ class), [1] feasst::CheckConstantVolume::update (C++ function) feasst::CheckEnergy (C++ class), [1] feasst::CheckEnergy::update (C++ function) feasst::CheckNetCharge (C++ class), [1] feasst::CheckNetCharge::update (C++ function) feasst::CheckPhysicality (C++ class), [1] feasst::CheckPhysicality::update (C++ function) feasst::Checkpoint (C++ class), [1] feasst::Checkpoint::check (C++ function) feasst::Checkpoint::Checkpoint (C++ function) feasst::Checkpoint::num_hours (C++ function) feasst::Checkpoint::read (C++ function) feasst::Checkpoint::serialize (C++ function) feasst::Checkpoint::write (C++ function) feasst::CheckProperties (C++ class), [1] feasst::CheckProperties::CheckProperties (C++ function) feasst::CheckProperties::update (C++ function) feasst::Chirality2D (C++ class), [1] feasst::Chirality2D::header (C++ function) feasst::Chirality2D::initialize (C++ function) feasst::Chirality2D::num_positive (C++ function) feasst::Chirality2D::update (C++ function) feasst::Chirality2D::write (C++ function) feasst::Clones (C++ class), [1] feasst::Clones::add (C++ function) feasst::Clones::clone (C++ function) feasst::Clones::Clones (C++ function) feasst::Clones::flat_histogram (C++ function) feasst::Clones::get_clone (C++ function) feasst::Clones::get_clones (C++ function) feasst::Clones::initialize (C++ function), [1] feasst::Clones::initialize_and_run_until_complete (C++ function) feasst::Clones::ln_prob (C++ function) feasst::Clones::num (C++ function) feasst::Clones::run_until_complete (C++ function) feasst::Clones::serialize (C++ function) feasst::Clones::set (C++ function) feasst::Clones::set_num_iterations_to_complete (C++ function) feasst::Clones::stitch (C++ function), [1] feasst::CODATA2010 (C++ class), [1] feasst::CODATA2010::avogadro_constant (C++ function) feasst::CODATA2010::boltzmann_constant (C++ function) feasst::CODATA2010::elementary_charge (C++ function) feasst::CODATA2010::permitivity_vacuum (C++ function) feasst::CODATA2014 (C++ class), [1] feasst::CODATA2014::avogadro_constant (C++ function) feasst::CODATA2014::boltzmann_constant (C++ function) feasst::CODATA2014::elementary_charge (C++ function) feasst::CODATA2014::permitivity_vacuum (C++ function) feasst::CODATA2018 (C++ class), [1] feasst::CODATA2018::avogadro_constant (C++ function) feasst::CODATA2018::boltzmann_constant (C++ function) feasst::CODATA2018::elementary_charge (C++ function) feasst::CODATA2018::permitivity_vacuum (C++ function) feasst::CollectionMatrix (C++ class), [1] feasst::CollectionMatrix::CollectionMatrix (C++ function), [1] feasst::CollectionMatrix::compute_ln_prob (C++ function) feasst::CollectionMatrix::increment (C++ function) feasst::CollectionMatrix::matrix (C++ function) feasst::CollectionMatrix::set (C++ function) feasst::CollectionMatrixSplice (C++ class), [1] feasst::CollectionMatrixSplice::add (C++ function) feasst::CollectionMatrixSplice::adjust_bounds (C++ function) feasst::CollectionMatrixSplice::are_all_complete (C++ function) feasst::CollectionMatrixSplice::clone (C++ function) feasst::CollectionMatrixSplice::collection_matrix (C++ function), [1] feasst::CollectionMatrixSplice::CollectionMatrixSplice (C++ function) feasst::CollectionMatrixSplice::flat_histogram (C++ function) feasst::CollectionMatrixSplice::get_clone (C++ function) feasst::CollectionMatrixSplice::get_clones (C++ function) feasst::CollectionMatrixSplice::ln_prob (C++ function) feasst::CollectionMatrixSplice::num (C++ function) feasst::CollectionMatrixSplice::run (C++ function) feasst::CollectionMatrixSplice::run_until_all_are_complete (C++ function) feasst::CollectionMatrixSplice::serialize (C++ function) feasst::CollectionMatrixSplice::set (C++ function), [1] feasst::CollectionMatrixSplice::set_size (C++ function) feasst::CollectionMatrixSplice::write (C++ function) feasst::CollectionMatrixSplice::write_bounds (C++ function) feasst::ComputeAddAVB (C++ class), [1] feasst::ComputeAddAVB::perturb_and_acceptance (C++ function) feasst::ComputeAddAVBDivalent (C++ class), [1] feasst::ComputeAddAVBDivalent::ComputeAddAVBDivalent (C++ function) feasst::ComputeAddAVBDivalent::perturb_and_acceptance (C++ function) feasst::ComputeAddMultiple (C++ class), [1] feasst::ComputeAddMultiple::ComputeAddMultiple (C++ function) feasst::ComputeAddMultiple::perturb_and_acceptance (C++ function) feasst::ComputeAVB2 (C++ class), [1] feasst::ComputeAVB2::ComputeAVB2 (C++ function) feasst::ComputeAVB2::perturb_and_acceptance (C++ function) feasst::ComputeAVB2::probability_out_to_in (C++ function) feasst::ComputeAVB4 (C++ class), [1] feasst::ComputeAVB4::perturb_and_acceptance (C++ function) feasst::ComputeBeta (C++ class), [1] feasst::ComputeBeta::perturb_and_acceptance (C++ function) feasst::ComputeGCA (C++ class), [1] feasst::ComputeGCA::perturb_and_acceptance (C++ function) feasst::ComputeGibbsParticleTransfer (C++ class), [1] feasst::ComputeGibbsParticleTransfer::perturb_and_acceptance (C++ function) feasst::ComputeGibbsVolumeTransfer (C++ class), [1] feasst::ComputeGibbsVolumeTransfer::perturb_and_acceptance (C++ function) feasst::ComputeModel (C++ class), [1] feasst::ComputeModel::perturb_and_acceptance (C++ function) feasst::ComputeMorph (C++ class), [1] feasst::ComputeMorph::perturb_and_acceptance (C++ function) feasst::ComputeMoveCluster (C++ class), [1] feasst::ComputeMoveCluster::perturb_and_acceptance (C++ function) feasst::ComputeRemoveAVB (C++ class), [1] feasst::ComputeRemoveAVB::perturb_and_acceptance (C++ function) feasst::ComputeRemoveAVBDivalent (C++ class), [1] feasst::ComputeRemoveAVBDivalent::ComputeRemoveAVBDivalent (C++ function) feasst::ComputeRemoveAVBDivalent::perturb_and_acceptance (C++ function) feasst::ComputeRemoveMultiple (C++ class), [1] feasst::ComputeRemoveMultiple::ComputeRemoveMultiple (C++ function) feasst::ComputeRemoveMultiple::perturb_and_acceptance (C++ function) feasst::Configuration (C++ class), [1] feasst::Configuration::add (C++ function), [1], [2] feasst::Configuration::add_model_param (C++ function) feasst::Configuration::add_non_ghost_particle_of_type (C++ function) feasst::Configuration::add_or_set_model_param (C++ function) feasst::Configuration::add_or_set_particle_type_site_property (C++ function) feasst::Configuration::add_or_set_site_property (C++ function) feasst::Configuration::add_particle_of_type (C++ function) feasst::Configuration::add_particle_type (C++ function) feasst::Configuration::add_site_property (C++ function) feasst::Configuration::are_all_sites_physical (C++ function) feasst::Configuration::check (C++ function) feasst::Configuration::check_dimensions (C++ function) feasst::Configuration::Configuration (C++ function) feasst::Configuration::copy_particles (C++ function) feasst::Configuration::dimension (C++ function) feasst::Configuration::displace (C++ function) feasst::Configuration::displace_particle (C++ function) feasst::Configuration::displace_particles (C++ function) feasst::Configuration::domain (C++ function) feasst::Configuration::ghosts (C++ function) feasst::Configuration::group_index (C++ function) feasst::Configuration::group_select (C++ function) feasst::Configuration::group_selects (C++ function) feasst::Configuration::increment_num_cell_lists (C++ function) feasst::Configuration::init_wrap (C++ function) feasst::Configuration::is_equal (C++ function) feasst::Configuration::max_sites_in_any_particle (C++ function) feasst::Configuration::model_params (C++ function) feasst::Configuration::neighbor_criteria (C++ function), [1] feasst::Configuration::newest_particle (C++ function) feasst::Configuration::newest_particle_index (C++ function) feasst::Configuration::num_angle_types (C++ function) feasst::Configuration::num_bond_types (C++ function) feasst::Configuration::num_cell_lists (C++ function) feasst::Configuration::num_dihedral_types (C++ function) feasst::Configuration::num_groups (C++ function) feasst::Configuration::num_particle_types (C++ function) feasst::Configuration::num_particles (C++ function) feasst::Configuration::num_particles_of_type (C++ function) feasst::Configuration::num_site_types (C++ function) feasst::Configuration::num_site_types_per_particle_type (C++ function) feasst::Configuration::num_sites (C++ function) feasst::Configuration::num_sites_of_type (C++ function), [1], [2], [3] feasst::Configuration::particle (C++ function), [1] feasst::Configuration::particle_type (C++ function) feasst::Configuration::particle_type_to_group (C++ function) feasst::Configuration::particle_type_to_group_create (C++ function) feasst::Configuration::particle_types (C++ function) feasst::Configuration::particles (C++ function) feasst::Configuration::physical_constants (C++ function) feasst::Configuration::remove_particle (C++ function) feasst::Configuration::remove_particles (C++ function) feasst::Configuration::replace_position (C++ function) feasst::Configuration::revive (C++ function) feasst::Configuration::select_particle (C++ function) feasst::Configuration::selection_of_all (C++ function) feasst::Configuration::serialize (C++ function) feasst::Configuration::set (C++ function) feasst::Configuration::set_model_param (C++ function), [1], [2] feasst::Configuration::set_particle_type (C++ function) feasst::Configuration::set_physical_constants (C++ function) feasst::Configuration::set_property (C++ function) feasst::Configuration::set_selection_physical (C++ function) feasst::Configuration::set_side_lengths (C++ function) feasst::Configuration::set_site_property (C++ function), [1] feasst::Configuration::set_site_type (C++ function) feasst::Configuration::site_type_to_particle_type (C++ function) feasst::Configuration::status (C++ function) feasst::Configuration::status_header (C++ function) feasst::Configuration::str (C++ function) feasst::Configuration::type_to_file_name (C++ function) feasst::Configuration::unique_type (C++ function), [1] feasst::Configuration::unique_types (C++ function) feasst::Configuration::update_positions (C++ function), [1], [2] feasst::Configuration::wrap_particle (C++ function) feasst::ConstrainModelIndex (C++ class), [1] feasst::ConstrainModelIndex::model_index (C++ function) feasst::ConstrainModelIndex::potential_index (C++ function) feasst::ConstrainNumParticles (C++ class), [1] feasst::ConstrainNumParticles::num_particles (C++ function) feasst::ConstrainNumParticles::type (C++ function) feasst::Constraint (C++ class), [1] feasst::ConstrainVolumeByCutoff (C++ class), [1] feasst::ContactObjective (C++ class), [1] feasst::CopyFollowingLines (C++ class), [1] feasst::CopyNextLine (C++ class), [1] feasst::CosPatchAngle (C++ class), [1] feasst::Coulomb (C++ class), [1] feasst::Coulomb::precompute (C++ function) feasst::Coulomb::serialize (C++ function) feasst::CPUTime (C++ class), [1] feasst::CPUTime::initialize (C++ function) feasst::CPUTime::write (C++ function) feasst::Criteria (C++ class), [1] feasst::Criteria::add (C++ function) feasst::Criteria::before_attempt (C++ function) feasst::Criteria::Criteria (C++ function) feasst::Criteria::current_energy (C++ function) feasst::Criteria::current_energy_profile (C++ function) feasst::Criteria::expanded_state (C++ function) feasst::Criteria::increment_phase (C++ function) feasst::Criteria::initialize (C++ function) feasst::Criteria::is_accepted (C++ function) feasst::Criteria::is_allowed (C++ function) feasst::Criteria::is_complete (C++ function) feasst::Criteria::is_equal (C++ function), [1] feasst::Criteria::num_expanded_states (C++ function) feasst::Criteria::num_iterations (C++ function) feasst::Criteria::num_iterations_to_complete (C++ function) feasst::Criteria::num_states (C++ function) feasst::Criteria::phase (C++ function) feasst::Criteria::set_complete (C++ function) feasst::Criteria::set_current_energy (C++ function) feasst::Criteria::set_current_energy_profile (C++ function) feasst::Criteria::set_expanded_state (C++ function) feasst::Criteria::set_num_iterations_to_complete (C++ function) feasst::Criteria::state (C++ function) feasst::Criteria::status (C++ function) feasst::Criteria::status_header (C++ function) feasst::Criteria::update (C++ function) feasst::Criteria::update_current_energy (C++ function) feasst::Criteria::was_accepted (C++ function) feasst::Criteria::write (C++ function) feasst::CriteriaUpdater (C++ class), [1] feasst::CriteriaUpdater::update (C++ function) feasst::CriteriaWriter (C++ class), [1] feasst::CriteriaWriter::write (C++ function) feasst::Cuboid (C++ class), [1] feasst::Cuboid::nearest_distance (C++ function) feasst::Cuboid::surface_area (C++ function) feasst::Cuboid::volume (C++ function) feasst::CustomException (C++ class), [1] feasst::CustomException::CustomException (C++ function) feasst::CustomException::what (C++ function) feasst::CutOff (C++ class), [1] feasst::CutoffOuter (C++ class), [1] feasst::Cylinder (C++ class), [1] feasst::Cylinder::nearest_distance (C++ function) feasst::DebyeHuckel (C++ class), [1] feasst::DebyeHuckel::precompute (C++ function) feasst::DebyeHuckel::serialize (C++ function) feasst::DeltaSigma (C++ class), [1] feasst::Density (C++ class), [1] feasst::Density::header (C++ function) feasst::Density::initialize (C++ function) feasst::Density::update (C++ function) feasst::Density::write (C++ function) feasst::DensityProfile (C++ class), [1] feasst::DensityProfile::header (C++ function) feasst::DensityProfile::initialize (C++ function) feasst::DensityProfile::profile (C++ function) feasst::DensityProfile::update (C++ function) feasst::DensityProfile::write (C++ function) feasst::Dihedral (C++ class), [1] feasst::DihedralHarmonic (C++ class), [1] feasst::DihedralRyckaertBellemans (C++ class), [1] feasst::DihedralTraPPE (C++ class), [1] feasst::Director (C++ class), [1] feasst::Domain (C++ class), [1] feasst::Domain::add_side_length (C++ function) feasst::Domain::dimension (C++ function) feasst::Domain::disable (C++ function) feasst::Domain::inscribed_sphere_diameter (C++ function) feasst::Domain::is_cubic (C++ function) feasst::Domain::max_side_length (C++ function) feasst::Domain::min_side_length (C++ function) feasst::Domain::periodic (C++ function) feasst::Domain::random_position (C++ function), [1] feasst::Domain::set_cubic (C++ function) feasst::Domain::set_side_length (C++ function) feasst::Domain::set_side_lengths (C++ function) feasst::Domain::shift (C++ function) feasst::Domain::shift_opt (C++ function) feasst::Domain::side_length (C++ function) feasst::Domain::side_lengths (C++ function) feasst::Domain::status (C++ function) feasst::Domain::status_header (C++ function) feasst::Domain::unwrap (C++ function) feasst::Domain::volume (C++ function) feasst::Domain::wrap (C++ function) feasst::Domain::xy (C++ function) feasst::Domain::xz (C++ function) feasst::Domain::yz (C++ function) feasst::DontVisitModel (C++ class), [1] feasst::ElectricField (C++ class), [1] feasst::ElectricField::energy (C++ function) feasst::ElectricField::precompute (C++ function) feasst::ElectricField::serialize (C++ function) feasst::EndCopy (C++ class), [1] feasst::EndToEndDistance (C++ class), [1] feasst::EndToEndDistance::end_to_end_distance (C++ function) feasst::EndToEndDistance::header (C++ function) feasst::EndToEndDistance::initialize (C++ function) feasst::EndToEndDistance::update (C++ function) feasst::EndToEndDistance::write (C++ function) feasst::Energy (C++ class), [1] feasst::Energy::energy (C++ function) feasst::Energy::header (C++ function) feasst::Energy::initialize (C++ function) feasst::Energy::update (C++ function) feasst::Energy::write (C++ function) feasst::EnergyAtCutOff (C++ class), [1] feasst::EnergyDerivAtCutOff (C++ class), [1] feasst::EnergyMap (C++ class), [1] feasst::EnergyMap::clear (C++ function) feasst::EnergyMap::default_value (C++ function) feasst::EnergyMap::energy (C++ function) feasst::EnergyMap::finalize (C++ function) feasst::EnergyMap::is_cluster_changed (C++ function) feasst::EnergyMap::is_queryable (C++ function) feasst::EnergyMap::neighbor_criteria (C++ function) feasst::EnergyMap::neighbors (C++ function) feasst::EnergyMap::precompute (C++ function) feasst::EnergyMap::revert (C++ function) feasst::EnergyMap::select_cluster (C++ function) feasst::EnergyMap::total_energy (C++ function) feasst::EnergyMap::update (C++ function) feasst::EnergyMapAll (C++ class), [1] feasst::EnergyMapAll::energy (C++ function) feasst::EnergyMapAll::finalize (C++ function) feasst::EnergyMapAll::is_cluster_changed (C++ function) feasst::EnergyMapAll::neighbors (C++ function) feasst::EnergyMapAll::revert (C++ function) feasst::EnergyMapAll::select_cluster (C++ function) feasst::EnergyMapAllCriteria (C++ class), [1] feasst::EnergyMapAllCriteria::is_queryable (C++ function) feasst::EnergyMapAllCriteria::update (C++ function) feasst::EnergyMapNeighbor (C++ class), [1] feasst::EnergyMapNeighbor::clear (C++ function) feasst::EnergyMapNeighbor::energy (C++ function) feasst::EnergyMapNeighbor::finalize (C++ function) feasst::EnergyMapNeighbor::is_cluster_changed (C++ function) feasst::EnergyMapNeighbor::neighbors (C++ function) feasst::EnergyMapNeighbor::revert (C++ function) feasst::EnergyMapNeighbor::select_cluster (C++ function) feasst::EnergyMapNeighbor::total_energy (C++ function) feasst::EnergyMapNeighbor::update (C++ function) feasst::EnergyMapNeighborCriteria (C++ class), [1] feasst::EnergyMapNeighborCriteria::is_queryable (C++ function) feasst::EnergyMapNeighborCriteria::update (C++ function) feasst::Ensemble (C++ class), [1] feasst::Ensemble::average (C++ function) feasst::Ensemble::average_macrostate (C++ function) feasst::Ensemble::conjugate (C++ function) feasst::Ensemble::Ensemble (C++ function), [1], [2] feasst::Ensemble::is_phase_boundary (C++ function) feasst::Ensemble::ln_prob (C++ function) feasst::Ensemble::ln_prob_original (C++ function) feasst::Ensemble::macrostates (C++ function) feasst::Ensemble::original_conjugate (C++ function) feasst::Ensemble::phase_boundary (C++ function) feasst::Ensemble::reweight (C++ function) feasst::Epsilon (C++ class), [1] feasst::Euler (C++ class), [1] feasst::Euler::compute_rotation_matrix (C++ function) feasst::Euler::Euler (C++ function) feasst::Euler::is_equal (C++ function) feasst::Euler::phi (C++ function) feasst::Euler::psi (C++ function) feasst::Euler::set (C++ function), [1] feasst::Euler::str (C++ function) feasst::Euler::theta (C++ function) feasst::Ewald (C++ class), [1] feasst::Ewald::change_volume (C++ function) feasst::Ewald::compute (C++ function), [1] feasst::Ewald::eik (C++ function) feasst::Ewald::kmax_squared (C++ function) feasst::Ewald::kxmax (C++ function) feasst::Ewald::kymax (C++ function) feasst::Ewald::kzmax (C++ function) feasst::Ewald::net_charge (C++ function) feasst::Ewald::num_kx (C++ function) feasst::Ewald::num_ky (C++ function) feasst::Ewald::num_kz (C++ function) feasst::Ewald::precompute (C++ function) feasst::Ewald::struct_fact_imag (C++ function), [1] feasst::Ewald::struct_fact_real (C++ function) feasst::Ewald::tolerance_to_alpha_ks (C++ function) feasst::Ewald::update_struct_fact_eik (C++ function) feasst::Ewald::update_wave_vectors (C++ function) feasst::Ewald::wave_num (C++ function) feasst::Ewald::wave_prefactor (C++ function) feasst::ExtensiveMoments (C++ class), [1] feasst::ExtensiveMoments::header (C++ function) feasst::ExtensiveMoments::initialize (C++ function) feasst::ExtensiveMoments::moments (C++ function) feasst::ExtensiveMoments::update (C++ function) feasst::ExtensiveMoments::write (C++ function) feasst::ExtrapolateBetaGCE (C++ class), [1] feasst::ExtrapolateBetaGCE::energy (C++ function) feasst::ExtrapolateBetaGCE::ExtrapolateBetaGCE (C++ function), [1] feasst::feasst::add (C++ function), [1], [2], [3], [4], [5], [6], [7] feasst::feasst::average (C++ function), [1] feasst::feasst::boolean (C++ function), [1], [2], [3] feasst::feasst::cumulative_probability (C++ function), [1] feasst::feasst::dble (C++ function), [1], [2], [3] feasst::feasst::deep_copy (C++ function), [1] feasst::feasst::deep_copy_derived (C++ function), [1], [2], [3] feasst::feasst::degrees_to_radians (C++ function), [1] feasst::feasst::factorial (C++ function), [1] feasst::feasst::feasst_check_all_used (C++ function), [1] feasst::feasst::feasst_deserialize (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31] feasst::feasst::feasst_deserialize_endcap (C++ function), [1] feasst::feasst::feasst_deserialize_fstobj (C++ function), [1], [2], [3], [4], [5] feasst::feasst::feasst_deserialize_version (C++ function), [1] feasst::feasst::feasst_difference (C++ function), [1] feasst::feasst::feasst_dir_trim_ (C++ function), [1] feasst::feasst::feasst_macro_output (C++ function), [1] feasst::feasst::feasst_omp_thread (C++ function), [1] feasst::feasst::feasst_serialize (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31] feasst::feasst::feasst_serialize_endcap (C++ function), [1] feasst::feasst::feasst_serialize_fstdr (C++ function), [1], [2], [3] feasst::feasst::feasst_serialize_fstobj (C++ function), [1], [2], [3], [4], [5] feasst::feasst::feasst_serialize_sp (C++ function), [1], [2], [3] feasst::feasst::feasst_serialize_version (C++ function), [1] feasst::feasst::feasst_sort (C++ function), [1] feasst::feasst::feasst_str (C++ function), [1], [2], [3], [4], [5] feasst::feasst::feasst_swap (C++ function), [1] feasst::feasst::feasst_union (C++ function), [1] feasst::feasst::file_backup (C++ function), [1] feasst::feasst::file_exists (C++ function), [1] feasst::feasst::fill (C++ function), [1], [2], [3] feasst::feasst::find (C++ function), [1], [2], [3] feasst::feasst::find_in_list (C++ function), [1], [2], [3], [4], [5] feasst::feasst::flt (C++ function), [1] feasst::feasst::has_bad_value (C++ function), [1], [2], [3] feasst::feasst::has_duplicate (C++ function), [1] feasst::feasst::install_dir (C++ function), [1] feasst::feasst::integer (C++ function), [1], [2], [3] feasst::feasst::is_equal (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9] feasst::feasst::is_found_in (C++ function), [1] feasst::feasst::is_in_interval (C++ function), [1] feasst::feasst::kelvin2kJpermol (C++ function), [1], [2], [3] feasst::feasst::line_to_argtype (C++ function), [1] feasst::feasst::local_minimum_indices (C++ function), [1] feasst::feasst::MakeTrialAnywhere (C++ function), [1] feasst::feasst::maximum (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] feasst::feasst::minimum (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] feasst::feasst::num_elements (C++ function), [1], [2], [3] feasst::feasst::num_spaces (C++ function), [1] feasst::feasst::parse_dimensional (C++ function), [1] feasst::feasst::parse_line (C++ function), [1] feasst::feasst::parse_mcs (C++ function), [1] feasst::feasst::product (C++ function), [1] feasst::feasst::quadratic_equation (C++ function), [1] feasst::feasst::radians_to_degrees (C++ function), [1] feasst::feasst::replace (C++ function), [1] feasst::feasst::replace_in_value (C++ function), [1] feasst::feasst::replace_value (C++ function), [1] feasst::feasst::resize (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9] feasst::feasst::round (C++ function), [1] feasst::feasst::sgn (C++ function), [1] feasst::feasst::sized_int_to_str (C++ function), [1] feasst::feasst::skip_characters (C++ function), [1] feasst::feasst::spherical_shell_volume (C++ function), [1] feasst::feasst::split (C++ function), [1] feasst::feasst::str (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] feasst::feasst::str_to_bool (C++ function), [1] feasst::feasst::str_to_double (C++ function), [1] feasst::feasst::str_to_int (C++ function), [1] feasst::feasst::sum (C++ function), [1], [2], [3], [4], [5] feasst::feasst::template_deserialize (C++ function), [1] feasst::feasst::template_factory (C++ function), [1] feasst::feasst::trim (C++ function), [1], [2], [3] feasst::feasst::used (C++ function), [1] feasst::feasst::version (C++ function), [1] feasst::FENE (C++ class), [1] feasst::FileParticle (C++ class), [1] feasst::FileParticle::read (C++ function) feasst::FileParticle::read_properties (C++ function) feasst::FileVMD (C++ class), [1] feasst::FileVMD::FileVMD (C++ function), [1] feasst::FileVMDPatch (C++ class), [1] feasst::FileVMDSpherocylinder (C++ class), [1] feasst::FileXYZ (C++ class), [1] feasst::FileXYZ::FileXYZ (C++ function), [1] feasst::FileXYZ::load (C++ function) feasst::FileXYZ::load_frame (C++ function) feasst::FileXYZ::write (C++ function) feasst::FileXYZPatch (C++ class), [1] feasst::FileXYZPatch::load (C++ function) feasst::FileXYZPatch::write (C++ function) feasst::FileXYZSpherocylinder (C++ class), [1] feasst::FileXYZSpherocylinder::load (C++ function) feasst::FileXYZSpherocylinder::write (C++ function) feasst::FiniteCylinder (C++ class), [1] feasst::FlatHistogram (C++ class), [1] feasst::FlatHistogram::before_attempt (C++ function) feasst::FlatHistogram::bias (C++ function) feasst::FlatHistogram::FlatHistogram (C++ function), [1] feasst::FlatHistogram::increment_phase (C++ function) feasst::FlatHistogram::is_accepted (C++ function) feasst::FlatHistogram::is_complete (C++ function) feasst::FlatHistogram::ln_prob (C++ function) feasst::FlatHistogram::macrostate (C++ function) feasst::FlatHistogram::num_iterations (C++ function) feasst::FlatHistogram::num_iterations_to_complete (C++ function) feasst::FlatHistogram::num_states (C++ function) feasst::FlatHistogram::phase (C++ function) feasst::FlatHistogram::set_complete (C++ function) feasst::FlatHistogram::set_ln_prob (C++ function) feasst::FlatHistogram::set_num_iterations_to_complete (C++ function) feasst::FlatHistogram::state (C++ function) feasst::FlatHistogram::update (C++ function) feasst::FlatHistogram::write (C++ function) feasst::Formula (C++ class), [1] feasst::Formula::Formula (C++ function) feasst::FormulaExponential (C++ class), [1] feasst::FormulaPolynomial (C++ class), [1] feasst::FormulaSineWave (C++ class), [1] feasst::FormulaSineWave::amplitude (C++ function) feasst::FormulaSineWave::default_shift (C++ function) feasst::FormulaSineWave::nearest_maximum (C++ function) feasst::FormulaSineWave::nearest_minimum (C++ function) feasst::FormulaSineWave::phase (C++ function) feasst::FormulaSineWave::shift (C++ function) feasst::FormulaSineWave::width (C++ function) feasst::Gamma (C++ class), [1] feasst::GhostTrialGrow (C++ class), [1] feasst::GhostTrialGrow::header (C++ function) feasst::GhostTrialGrow::initialize (C++ function) feasst::GhostTrialGrow::update (C++ function) feasst::GhostTrialGrow::write (C++ function) feasst::GhostTrialVolume (C++ class), [1] feasst::GhostTrialVolume::header (C++ function) feasst::GhostTrialVolume::initialize (C++ function) feasst::GhostTrialVolume::update (C++ function) feasst::GhostTrialVolume::write (C++ function) feasst::GibbsInitialize (C++ class), [1] feasst::GibbsInitialize::header (C++ function) feasst::GibbsInitialize::initialize (C++ function) feasst::GibbsInitialize::update (C++ function) feasst::GibbsInitialize::write (C++ function) feasst::GoldenSearch (C++ class), [1] feasst::GoldenSearch::bracket (C++ function) feasst::GrandCanonicalEnsemble (C++ class), [1] feasst::GrandCanonicalEnsemble::beta_mu (C++ function) feasst::GrandCanonicalEnsemble::betaPV (C++ function) feasst::GrandCanonicalEnsemble::GrandCanonicalEnsemble (C++ function) feasst::Group (C++ class), [1] feasst::Group::Group (C++ function) feasst::Group::is_dynamic (C++ function) feasst::Group::is_empty (C++ function) feasst::Group::is_in (C++ function), [1] feasst::Group::is_spatial (C++ function) feasst::Group::particle_types (C++ function) feasst::Group::remove_sites (C++ function) feasst::Group::site_indices (C++ function) feasst::Group::site_types (C++ function) feasst::HalfSpace (C++ class), [1] feasst::HalfSpace::dimension (C++ function) feasst::HalfSpace::direction (C++ function) feasst::HalfSpace::intersection (C++ function) feasst::HalfSpace::nearest_distance (C++ function) feasst::HalfSpaceSine (C++ class), [1] feasst::HalfSpaceSine::HalfSpaceSine (C++ function) feasst::HalfSpaceSine::is_inside (C++ function), [1] feasst::HalfSpaceSine::nearest_distance (C++ function) feasst::HalfSpaceSine::sine_wave (C++ function) feasst::HalfSpaceSine::wave_dimension (C++ function) feasst::HalfSpaceTilted (C++ class), [1] feasst::HalfSpaceTilted::distance_from_origin (C++ function) feasst::HalfSpaceTilted::HalfSpaceTilted (C++ function), [1] feasst::HalfSpaceTilted::nearest_distance (C++ function) feasst::HalfSpaceTilted::unit_normal (C++ function) feasst::HardSphere (C++ class), [1] feasst::HardSphere::serialize (C++ function) feasst::HeatCapacity (C++ class), [1] feasst::HeatCapacity::header (C++ function) feasst::HeatCapacity::initialize (C++ function) feasst::HeatCapacity::update (C++ function) feasst::HeatCapacity::write (C++ function) feasst::HenryCoefficient (C++ class), [1] feasst::HenryCoefficient::header (C++ function) feasst::HenryCoefficient::initialize (C++ function) feasst::HenryCoefficient::num_beta_taylor (C++ function) feasst::HenryCoefficient::update (C++ function) feasst::HenryCoefficient::write (C++ function) feasst::Histogram (C++ class), [1] feasst::Histogram::add (C++ function) feasst::Histogram::bin (C++ function) feasst::Histogram::center_of_bin (C++ function) feasst::Histogram::center_of_last_bin (C++ function) feasst::Histogram::edges (C++ function) feasst::Histogram::expandable (C++ function) feasst::Histogram::histogram (C++ function) feasst::Histogram::max (C++ function) feasst::Histogram::min (C++ function) feasst::Histogram::set_bin_size (C++ function) feasst::Histogram::set_edges (C++ function), [1] feasst::Histogram::set_not_expandable (C++ function) feasst::Histogram::set_width_center (C++ function) feasst::Histogram::set_width_min_max (C++ function) feasst::Histogram::size (C++ function) feasst::Histogram::str (C++ function) feasst::IdealGas (C++ class), [1] feasst::IdealGas::serialize (C++ function) feasst::Improper (C++ class), [1] feasst::IncrementPhase (C++ class), [1] feasst::IncrementPhase::update (C++ function) feasst::Jagla (C++ class), [1] feasst::Jagla::num_discretized_steps (C++ function) feasst::Jagla::precompute (C++ function) feasst::Jagla::serialize (C++ function) feasst::Lambda (C++ class), [1] feasst::LennardJones (C++ class), [1] feasst::LennardJones::hard_sphere_threshold (C++ function) feasst::LennardJones::serialize (C++ function) feasst::LennardJonesAlpha (C++ class), [1] feasst::LennardJonesAlpha::alpha (C++ function) feasst::LennardJonesAlpha::du_dr (C++ function) feasst::LennardJonesAlpha::precompute (C++ function) feasst::LennardJonesAlpha::serialize (C++ function) feasst::LennardJonesAlpha::set_wca (C++ function) feasst::LennardJonesCutShift (C++ class), [1] feasst::LennardJonesCutShift::precompute (C++ function) feasst::LennardJonesCutShift::serialize (C++ function) feasst::LennardJonesForceShift (C++ class), [1] feasst::LennardJonesForceShift::precompute (C++ function) feasst::LennardJonesForceShift::serialize (C++ function) feasst::Listen (C++ class), [1] feasst::LnProbability (C++ class), [1] feasst::LnProbability::add (C++ function) feasst::LnProbability::delta (C++ function) feasst::LnProbability::delta_values (C++ function) feasst::LnProbability::equilibrium_objective (C++ function) feasst::LnProbability::equilibrium_objective_boundary (C++ function) feasst::LnProbability::LnProbability (C++ function) feasst::LnProbability::minima (C++ function) feasst::LnProbability::normalize (C++ function) feasst::LnProbability::reduce (C++ function) feasst::LnProbability::resize (C++ function) feasst::LnProbability::set_value (C++ function) feasst::LnProbability::size (C++ function) feasst::LnProbability::sum_probability (C++ function), [1] feasst::LnProbability::value (C++ function) feasst::LnProbability::values (C++ function) feasst::Log (C++ class), [1] feasst::Log::header (C++ function) feasst::Log::initialize (C++ function) feasst::Log::write (C++ function) feasst::LongRangeCorrections (C++ class), [1] feasst::LongRangeCorrections::precompute (C++ function) feasst::LoopConfigOneBody (C++ class), [1] feasst::LoopOneBody (C++ class), [1] feasst::Macrostate (C++ class), [1] feasst::Macrostate::bin (C++ function) feasst::Macrostate::histogram (C++ function) feasst::Macrostate::is_allowed (C++ function) feasst::Macrostate::Macrostate (C++ function) feasst::Macrostate::num_macrostates_in_soft_range (C++ function) feasst::Macrostate::set (C++ function) feasst::Macrostate::soft_max (C++ function) feasst::Macrostate::soft_min (C++ function) feasst::Macrostate::value (C++ function), [1] feasst::MacrostateBeta (C++ class), [1] feasst::MacrostateBeta::value (C++ function) feasst::MacrostateEnergy (C++ class), [1] feasst::MacrostateEnergy::MacrostateEnergy (C++ function) feasst::MacrostateEnergy::value (C++ function) feasst::MacrostateModel (C++ class), [1] feasst::MacrostateModel::value (C++ function) feasst::MacrostateMorph (C++ class), [1] feasst::MacrostateMorph::value (C++ function) feasst::MacrostateNumParticles (C++ class), [1] feasst::MacrostateNumParticles::MacrostateNumParticles (C++ function) feasst::MacrostateNumParticles::value (C++ function) feasst::MacrostatePosition (C++ class), [1] feasst::MacrostatePosition::MacrostatePosition (C++ function) feasst::MacrostatePosition::value (C++ function) feasst::Matrix (C++ class), [1] feasst::Matrix::add (C++ function) feasst::Matrix::check (C++ function) feasst::Matrix::determinant (C++ function) feasst::Matrix::identity (C++ function) feasst::Matrix::invert (C++ function) feasst::Matrix::is_equal (C++ function) feasst::Matrix::is_identity (C++ function) feasst::Matrix::Matrix (C++ function) feasst::Matrix::matrix (C++ function) feasst::Matrix::multiply (C++ function), [1], [2], [3], [4] feasst::Matrix::num_columns (C++ function) feasst::Matrix::num_rows (C++ function) feasst::Matrix::set_size (C++ function) feasst::Matrix::set_value (C++ function) feasst::Matrix::skew_symmetric_cross_product (C++ function) feasst::Matrix::str (C++ function) feasst::Matrix::transpose (C++ function), [1] feasst::Matrix::value (C++ function) feasst::Matrix::zero (C++ function) feasst::MayerSampling (C++ class), [1] feasst::MayerSampling::beta_taylor (C++ function), [1] feasst::MayerSampling::is_accepted (C++ function) feasst::MayerSampling::mayer (C++ function) feasst::MayerSampling::mayer_ref (C++ function) feasst::MayerSampling::num_beta_taylor (C++ function) feasst::MayerSampling::precompute (C++ function) feasst::MayerSampling::second_virial_ratio (C++ function) feasst::MayerSampling::second_virial_ratio_block_stdev (C++ function) feasst::MayerSampling::write (C++ function) feasst::MeanSquaredDisplacement (C++ class), [1] feasst::MeanSquaredDisplacement::initialize (C++ function) feasst::MeanSquaredDisplacement::update (C++ function) feasst::MeanSquaredDisplacement::write (C++ function) feasst::Metropolis (C++ class), [1] feasst::Metropolis::is_accepted (C++ function) feasst::Metropolis::Metropolis (C++ function) feasst::Mie (C++ class), [1] feasst::Mie::precompute (C++ function) feasst::Mie::serialize (C++ function) feasst::MieLambdaA (C++ class), [1] feasst::MieLambdaR (C++ class), [1] feasst::MiePrefactor (C++ class), [1] feasst::Minimize (C++ class), [1] feasst::Minimize::bracket (C++ function) feasst::Minimize::lower (C++ function) feasst::Minimize::minimum (C++ function) feasst::Minimize::set_lower (C++ function) feasst::Minimize::set_upper (C++ function) feasst::Minimize::tolerance (C++ function) feasst::Minimize::upper (C++ function) feasst::Model (C++ class), [1] feasst::Model::charge_index (C++ function) feasst::Model::compute (C++ function), [1], [2], [3] feasst::Model::cutoff_index (C++ function) feasst::Model::deserialize (C++ function) feasst::Model::epsilon_index (C++ function) feasst::Model::factory (C++ function) feasst::Model::num_body (C++ function) feasst::Model::precompute (C++ function) feasst::Model::serialize (C++ function) feasst::Model::sigma_index (C++ function) feasst::ModelEmpty (C++ class), [1] feasst::ModelEmpty::energy (C++ function) feasst::ModelEmpty::serialize (C++ function) feasst::ModelExample (C++ class), [1] feasst::ModelExample::create (C++ function) feasst::ModelExample::energy (C++ function) feasst::ModelExample::num_discretized_steps (C++ function) feasst::ModelExample::precompute (C++ function) feasst::ModelExample::serialize (C++ function) feasst::ModelExpanded (C++ class), [1] feasst::ModelExpanded::energy (C++ function) feasst::ModelExpanded::model_index (C++ function) feasst::ModelExpanded::serialize (C++ function) feasst::ModelExpanded::set_model_index (C++ function) feasst::ModelHardShape (C++ class), [1] feasst::ModelHardShape::energy (C++ function) feasst::ModelHardShape::serialize (C++ function) feasst::ModelLJShape (C++ class), [1] feasst::ModelLJShape::energy (C++ function) feasst::ModelLJShape::epsilon (C++ function) feasst::ModelLJShape::precompute (C++ function) feasst::ModelLJShape::serialize (C++ function) feasst::ModelLJShape::sigma (C++ function) feasst::ModelLJShapeEnergyAtCutoff (C++ class), [1] feasst::ModelOneBody (C++ class), [1] feasst::ModelOneBody::compute (C++ function), [1], [2], [3] feasst::ModelOneBody::energy (C++ function) feasst::ModelOneBody::energy_no_wrap (C++ function) feasst::ModelOneBody::num_body (C++ function) feasst::ModelParam (C++ class), [1] feasst::ModelParam::add (C++ function), [1], [2] feasst::ModelParam::max (C++ function) feasst::ModelParam::mix (C++ function) feasst::ModelParam::mixed_max (C++ function) feasst::ModelParam::mixed_value (C++ function) feasst::ModelParam::mixed_values (C++ function) feasst::ModelParam::set (C++ function) feasst::ModelParam::set_max_and_mixed (C++ function) feasst::ModelParam::set_mixed (C++ function) feasst::ModelParam::set_param (C++ function) feasst::ModelParam::size (C++ function) feasst::ModelParam::str (C++ function) feasst::ModelParam::value (C++ function) feasst::ModelParam::values (C++ function) feasst::ModelParams (C++ class), [1] feasst::ModelParams::add (C++ function), [1] feasst::ModelParams::check (C++ function) feasst::ModelParams::constants (C++ function) feasst::ModelParams::deep_copy (C++ function) feasst::ModelParams::index (C++ function) feasst::ModelParams::mix (C++ function) feasst::ModelParams::physical_constants (C++ function) feasst::ModelParams::select (C++ function), [1] feasst::ModelParams::set (C++ function), [1], [2] feasst::ModelParams::set_cutoff_min_to_sigma (C++ function) feasst::ModelParams::set_physical_constants (C++ function), [1] feasst::ModelParams::size (C++ function) feasst::ModelParams::str (C++ function) feasst::ModelServer (C++ class), [1] feasst::ModelServer::hard_sphere_threshold (C++ function) feasst::ModelServer::serialize (C++ function) feasst::ModelSquareWellShape (C++ class), [1] feasst::ModelSquareWellShape::energy (C++ function) feasst::ModelSquareWellShape::serialize (C++ function) feasst::ModelTableCart1DHard (C++ class), [1] feasst::ModelTableCart1DHard::compute_table (C++ function) feasst::ModelTableCart1DHard::energy (C++ function) feasst::ModelTableCart1DHard::serialize (C++ function) feasst::ModelTableCart2DIntegr (C++ class), [1] feasst::ModelTableCart2DIntegr::compute_table (C++ function) feasst::ModelTableCart2DIntegr::compute_table_omp (C++ function) feasst::ModelTableCart2DIntegr::energy (C++ function) feasst::ModelTableCart2DIntegr::serialize (C++ function) feasst::ModelTableCart3DIntegr (C++ class), [1] feasst::ModelTableCart3DIntegr::compute_table (C++ function), [1], [2] feasst::ModelTableCart3DIntegr::compute_table_omp (C++ function), [1], [2] feasst::ModelTableCart3DIntegr::energy (C++ function) feasst::ModelTableCart3DIntegr::serialize (C++ function) feasst::ModelTableCart3DIntegr::table (C++ function) feasst::ModelThreeBody (C++ class), [1] feasst::ModelThreeBody::compute (C++ function), [1] feasst::ModelThreeBody::num_body (C++ function) feasst::ModelTwoBody (C++ class), [1] feasst::ModelTwoBody::compute (C++ function), [1], [2], [3] feasst::ModelTwoBody::num_body (C++ function) feasst::ModelTwoBodyFactory (C++ class), [1] feasst::ModelTwoBodyFactory::add (C++ function), [1] feasst::ModelTwoBodyFactory::model (C++ function) feasst::ModelTwoBodyFactory::num (C++ function) feasst::ModelTwoBodyFactory::precompute (C++ function) feasst::ModelTwoBodyFactory::serialize (C++ function) feasst::ModelTwoBodyTable (C++ class), [1] feasst::ModelTwoBodyTable::ModelTwoBodyTable (C++ function) feasst::ModelTwoBodyTable::precompute (C++ function) feasst::ModelTwoBodyTable::resize (C++ function) feasst::ModelTwoBodyTable::serialize (C++ function) feasst::ModelTwoBodyTable::set (C++ function), [1], [2] feasst::ModelTwoBodyTable::table (C++ function) feasst::Modify (C++ class), [1] feasst::Modify::initialize (C++ function) feasst::Modify::trial (C++ function) feasst::Modify::update (C++ function) feasst::Modify::write (C++ function) feasst::ModifyFactory (C++ class), [1] feasst::ModifyFactory::add (C++ function) feasst::ModifyFactory::adjust_bounds (C++ function) feasst::ModifyFactory::initialize (C++ function) feasst::ModifyFactory::modifiers (C++ function) feasst::ModifyFactory::modify (C++ function) feasst::ModifyFactory::num (C++ function) feasst::ModifyFactory::remove (C++ function) feasst::ModifyFactory::set_timer (C++ function) feasst::ModifyFactory::timer (C++ function) feasst::ModifyFactory::trial (C++ function) feasst::ModifyFactory::write_to_file (C++ function) feasst::ModifyUpdateOnly (C++ class), [1] feasst::MonteCarlo (C++ class), [1] feasst::MonteCarlo::add (C++ function), [1], [2], [3], [4], [5], [6], [7] feasst::MonteCarlo::add_args (C++ function) feasst::MonteCarlo::add_to_optimized (C++ function) feasst::MonteCarlo::add_to_reference (C++ function) feasst::MonteCarlo::analyze (C++ function) feasst::MonteCarlo::analyze_factory (C++ function) feasst::MonteCarlo::analyzers (C++ function) feasst::MonteCarlo::attempt (C++ function) feasst::MonteCarlo::attempt_trial (C++ function) feasst::MonteCarlo::begin (C++ function) feasst::MonteCarlo::clear_arguments (C++ function) feasst::MonteCarlo::configuration (C++ function) feasst::MonteCarlo::criteria (C++ function) feasst::MonteCarlo::initialize_analyzers (C++ function) feasst::MonteCarlo::initialize_criteria (C++ function) feasst::MonteCarlo::initialize_system (C++ function) feasst::MonteCarlo::initialize_trials (C++ function) feasst::MonteCarlo::modifiers (C++ function) feasst::MonteCarlo::modify (C++ function) feasst::MonteCarlo::modify_factory (C++ function) feasst::MonteCarlo::MonteCarlo (C++ function), [1] feasst::MonteCarlo::next_arg (C++ function) feasst::MonteCarlo::num_analyzers (C++ function) feasst::MonteCarlo::num_modifiers (C++ function) feasst::MonteCarlo::parse_args (C++ function) feasst::MonteCarlo::random (C++ function) feasst::MonteCarlo::remove_analyze (C++ function) feasst::MonteCarlo::remove_modify (C++ function) feasst::MonteCarlo::remove_trial (C++ function) feasst::MonteCarlo::reset_trial_stats (C++ function) feasst::MonteCarlo::resume (C++ function) feasst::MonteCarlo::run (C++ function) feasst::MonteCarlo::run_for_hours (C++ function) feasst::MonteCarlo::run_num_trials (C++ function) feasst::MonteCarlo::run_until_complete (C++ function) feasst::MonteCarlo::run_until_file_exists (C++ function) feasst::MonteCarlo::run_until_num_particles (C++ function) feasst::MonteCarlo::seed_random (C++ function) feasst::MonteCarlo::set (C++ function), [1], [2], [3], [4], [5] feasst::MonteCarlo::set_num_iterations_to_complete (C++ function) feasst::MonteCarlo::set_parse_for_num_configs (C++ function) feasst::MonteCarlo::set_parse_replace (C++ function) feasst::MonteCarlo::set_timer (C++ function) feasst::MonteCarlo::system (C++ function) feasst::MonteCarlo::thermo_params (C++ function) feasst::MonteCarlo::timer (C++ function) feasst::MonteCarlo::trial (C++ function) feasst::MonteCarlo::trial_factory (C++ function) feasst::MonteCarlo::trials (C++ function) feasst::MonteCarlo::write_checkpoint (C++ function) feasst::MonteCarlo::write_to_file (C++ function) feasst::Movie (C++ class), [1] feasst::Movie::initialize (C++ function) feasst::Movie::write (C++ function) feasst::MoviePatch (C++ class), [1] feasst::MoviePatch::initialize (C++ function) feasst::MoviePatch::write (C++ function) feasst::MovieSpherocylinder (C++ class), [1] feasst::MovieSpherocylinder::initialize (C++ function) feasst::MovieSpherocylinder::write (C++ function) feasst::NEAR_INFINITY (C++ member), [1] feasst::NEAR_ZERO (C++ member), [1] feasst::NeighborCriteria (C++ class), [1] feasst::NeighborCriteria::is_accepted (C++ function) feasst::NeighborCriteria::is_position_accepted (C++ function) feasst::NeighborCriteria::NeighborCriteria (C++ function) feasst::NeighborCriteria::serialize (C++ function) feasst::NeighborCriteria::volume (C++ function) feasst::NumParticles (C++ class), [1] feasst::NumParticles::header (C++ function) feasst::NumParticles::initialize (C++ function) feasst::NumParticles::update (C++ function) feasst::NumParticles::write (C++ function) feasst::PairDistribution (C++ class), [1] feasst::PairDistribution::header (C++ function) feasst::PairDistribution::initialize (C++ function) feasst::PairDistribution::update (C++ function) feasst::PairDistribution::write (C++ function) feasst::PairDistributionInner (C++ class), [1] feasst::PairDistributionInner::serialize (C++ function) feasst::Particle (C++ class), [1]

feasst::Particle::add (C++ function) feasst::Particle::add_angle (C++ function) feasst::Particle::add_angle_model (C++ function) feasst::Particle::add_angle_property (C++ function) feasst::Particle::add_bond (C++ function) feasst::Particle::add_bond_model (C++ function) feasst::Particle::add_bond_property (C++ function) feasst::Particle::add_dihedral (C++ function) feasst::Particle::add_dihedral_model (C++ function) feasst::Particle::add_dihedral_property (C++ function) feasst::Particle::add_or_set_site_property (C++ function) feasst::Particle::add_site_property (C++ function) feasst::Particle::angle (C++ function), [1] feasst::Particle::angle_neighbors (C++ function) feasst::Particle::angles (C++ function) feasst::Particle::bond (C++ function), [1] feasst::Particle::bond_neighbors (C++ function) feasst::Particle::bonds (C++ function) feasst::Particle::check (C++ function) feasst::Particle::dihedral (C++ function), [1] feasst::Particle::dihedral_neighbors (C++ function) feasst::Particle::dihedrals (C++ function) feasst::Particle::displace (C++ function) feasst::Particle::erase_bonds (C++ function) feasst::Particle::increment_site_types (C++ function) feasst::Particle::is_isotropic (C++ function) feasst::Particle::max_distance (C++ function) feasst::Particle::num_angles (C++ function) feasst::Particle::num_bonds (C++ function) feasst::Particle::num_dihedrals (C++ function) feasst::Particle::num_sites (C++ function) feasst::Particle::num_sites_of_type (C++ function) feasst::Particle::remove_non_unique_types (C++ function) feasst::Particle::remove_site (C++ function) feasst::Particle::replace_position (C++ function), [1] feasst::Particle::replace_properties (C++ function) feasst::Particle::set_site (C++ function) feasst::Particle::set_site_physical (C++ function) feasst::Particle::set_site_property (C++ function) feasst::Particle::set_site_type (C++ function) feasst::Particle::set_type (C++ function) feasst::Particle::site (C++ function) feasst::Particle::sites (C++ function) feasst::Particle::type (C++ function) feasst::ParticleFactory (C++ class), [1] feasst::ParticleFactory::add (C++ function), [1], [2] feasst::ParticleFactory::add_model_param (C++ function) feasst::ParticleFactory::add_or_set_model_param (C++ function) feasst::ParticleFactory::add_or_set_site_property (C++ function) feasst::ParticleFactory::add_property (C++ function), [1] feasst::ParticleFactory::add_site_property (C++ function) feasst::ParticleFactory::check (C++ function) feasst::ParticleFactory::check_angle_types (C++ function) feasst::ParticleFactory::check_bond_types (C++ function) feasst::ParticleFactory::check_dihedral_types (C++ function) feasst::ParticleFactory::check_particle_types (C++ function) feasst::ParticleFactory::check_site_types (C++ function) feasst::ParticleFactory::check_types (C++ function), [1] feasst::ParticleFactory::displace (C++ function) feasst::ParticleFactory::model_params (C++ function) feasst::ParticleFactory::num (C++ function) feasst::ParticleFactory::num_angle_types (C++ function) feasst::ParticleFactory::num_angles (C++ function) feasst::ParticleFactory::num_bond_types (C++ function) feasst::ParticleFactory::num_bonds (C++ function) feasst::ParticleFactory::num_dihedral_types (C++ function) feasst::ParticleFactory::num_dihedrals (C++ function) feasst::ParticleFactory::num_particle_types (C++ function) feasst::ParticleFactory::num_site_types (C++ function) feasst::ParticleFactory::num_sites (C++ function) feasst::ParticleFactory::particle (C++ function) feasst::ParticleFactory::particles (C++ function) feasst::ParticleFactory::remove (C++ function), [1] feasst::ParticleFactory::replace_position (C++ function), [1] feasst::ParticleFactory::replace_properties (C++ function) feasst::ParticleFactory::scale_particle_positions (C++ function) feasst::ParticleFactory::set_cutoff_min_to_sigma (C++ function) feasst::ParticleFactory::set_model_param (C++ function), [1], [2] feasst::ParticleFactory::set_physical_constants (C++ function) feasst::ParticleFactory::set_property (C++ function) feasst::ParticleFactory::set_site_physical (C++ function) feasst::ParticleFactory::set_site_property (C++ function), [1] feasst::ParticleFactory::set_site_type (C++ function) feasst::ParticleFactory::unique_particles (C++ function) feasst::ParticleFactory::unique_types (C++ function) feasst::PatchAngle (C++ class), [1] feasst::Perturb (C++ class), [1] feasst::Perturb::before_select (C++ function) feasst::Perturb::finalize (C++ function) feasst::Perturb::finalize_possible (C++ function) feasst::Perturb::finalize_select (C++ function) feasst::Perturb::mid_stage (C++ function) feasst::Perturb::Perturb (C++ function) feasst::Perturb::perturb (C++ function) feasst::Perturb::revert (C++ function) feasst::Perturb::revert_possible (C++ function) feasst::Perturb::revert_select (C++ function) feasst::Perturb::set_finalize_possible (C++ function) feasst::Perturb::set_revert_possible (C++ function) feasst::Perturb::set_tunable (C++ function) feasst::Perturb::set_tunable_min_and_max (C++ function) feasst::Perturb::status (C++ function) feasst::Perturb::status_header (C++ function) feasst::Perturb::tunable (C++ function) feasst::Perturb::tune (C++ function) feasst::PerturbAdd (C++ class), [1] feasst::PerturbAdd::add (C++ function) feasst::PerturbAdd::before_select (C++ function) feasst::PerturbAdd::delay_add (C++ function) feasst::PerturbAdd::finalize (C++ function) feasst::PerturbAdd::perturb (C++ function) feasst::PerturbAdd::PerturbAdd (C++ function) feasst::PerturbAdd::revert (C++ function) feasst::PerturbAdd::status (C++ function) feasst::PerturbAdd::status_header (C++ function) feasst::PerturbAddAVB (C++ class), [1] feasst::PerturbAddAVB::delay_add (C++ function) feasst::PerturbAddAVB::finalize (C++ function) feasst::PerturbAddAVB::perturb (C++ function) feasst::PerturbAddAVB::PerturbAddAVB (C++ function) feasst::PerturbAddAVB::revert (C++ function) feasst::PerturbAddAVB::status (C++ function) feasst::PerturbAddAVB::status_header (C++ function) feasst::PerturbAnywhere (C++ class), [1] feasst::PerturbAnywhere::move (C++ function) feasst::PerturbAnywhere::set_position (C++ function) feasst::PerturbBeta (C++ class), [1] feasst::PerturbBeta::change_beta (C++ function) feasst::PerturbBeta::perturb (C++ function) feasst::PerturbBeta::PerturbBeta (C++ function), [1] feasst::PerturbBeta::revert (C++ function) feasst::PerturbBranch (C++ class), [1] feasst::PerturbBranch::move (C++ function) feasst::PerturbBranch::place_in_branch (C++ function) feasst::PerturbBranch::precompute (C++ function) feasst::PerturbConnector (C++ class), [1] feasst::PerturbConnector::move (C++ function) feasst::PerturbCrankshaft (C++ class), [1] feasst::PerturbCrankshaft::move (C++ function) feasst::PerturbCrankshaftSmall (C++ class), [1] feasst::PerturbCrankshaftSmall::move (C++ function) feasst::PerturbDihedral (C++ class), [1] feasst::PerturbDihedral::dihedral_type (C++ function) feasst::PerturbDihedral::old_dihedral_energy (C++ function) feasst::PerturbDihedral::place_dihedral (C++ function) feasst::PerturbDihedral::precompute (C++ function) feasst::PerturbDihedral::random_dihedral_radians (C++ function) feasst::PerturbDistance (C++ class), [1] feasst::PerturbDistance::bond_type (C++ function) feasst::PerturbDistance::move (C++ function) feasst::PerturbDistance::old_bond_energy (C++ function) feasst::PerturbDistance::PerturbDistance (C++ function), [1] feasst::PerturbDistance::precompute (C++ function) feasst::PerturbDistance::random_distance (C++ function) feasst::PerturbDistanceAngle (C++ class), [1] feasst::PerturbDistanceAngle::angle_type (C++ function) feasst::PerturbDistanceAngle::old_angle_energy (C++ function) feasst::PerturbDistanceAngle::place_in_circle (C++ function) feasst::PerturbDistanceAngle::precompute (C++ function) feasst::PerturbDistanceAngle::random_angle_radians (C++ function) feasst::PerturbDistanceAngleConnector (C++ class), [1] feasst::PerturbLibrary (C++ class), [1] feasst::PerturbLibrary::move (C++ function) feasst::PerturbLibrary::PerturbLibrary (C++ function) feasst::PerturbLibrary::precompute (C++ function) feasst::PerturbLibrary::xyz (C++ function) feasst::PerturbModel (C++ class), [1] feasst::PerturbModel::change_model_index (C++ function) feasst::PerturbModel::perturb (C++ function) feasst::PerturbModel::revert (C++ function) feasst::PerturbMove (C++ class), [1] feasst::PerturbMove::finalize (C++ function) feasst::PerturbMove::move (C++ function) feasst::PerturbMove::perturb (C++ function) feasst::PerturbMove::revert (C++ function) feasst::PerturbMoveAVB (C++ class), [1] feasst::PerturbMoveAVB::move (C++ function) feasst::PerturbMoveAVB::PerturbMoveAVB (C++ function) feasst::PerturbParticlePivot (C++ class), [1] feasst::PerturbParticlePivot::move (C++ function) feasst::PerturbParticleType (C++ class), [1] feasst::PerturbParticleType::finalize (C++ function) feasst::PerturbParticleType::perturb (C++ function) feasst::PerturbParticleType::PerturbParticleType (C++ function) feasst::PerturbParticleType::revert (C++ function) feasst::PerturbParticleType::status (C++ function) feasst::PerturbParticleType::status_header (C++ function) feasst::PerturbPivot (C++ class), [1] feasst::PerturbPivot::move (C++ function) feasst::PerturbPointReflect (C++ class), [1] feasst::PerturbPointReflect::move (C++ function), [1] feasst::PerturbPointReflect::precompute (C++ function) feasst::PerturbPointReflect::update_selection (C++ function) feasst::PerturbPositionSwap (C++ class), [1] feasst::PerturbPositionSwap::move (C++ function) feasst::PerturbRemove (C++ class), [1] feasst::PerturbRemove::before_select (C++ function) feasst::PerturbRemove::finalize (C++ function) feasst::PerturbRemove::perturb (C++ function) feasst::PerturbRemove::revert (C++ function) feasst::PerturbReptate (C++ class), [1] feasst::PerturbReptate::finalize (C++ function) feasst::PerturbReptate::move (C++ function) feasst::PerturbRotate (C++ class), [1] feasst::PerturbRotate::move (C++ function), [1], [2] feasst::PerturbRotate::update_eulers (C++ function) feasst::PerturbRotate::update_selection (C++ function) feasst::PerturbRotateCOM (C++ class), [1] feasst::PerturbRotateCOM::move (C++ function) feasst::PerturbSiteType (C++ class), [1] feasst::PerturbSiteType::finalize (C++ function) feasst::PerturbSiteType::perturb (C++ function) feasst::PerturbSiteType::PerturbSiteType (C++ function) feasst::PerturbSiteType::revert (C++ function) feasst::PerturbSiteType::set_site_type (C++ function) feasst::PerturbSiteType::status (C++ function) feasst::PerturbSiteType::status_header (C++ function) feasst::PerturbToAnchor (C++ class), [1] feasst::PerturbToAnchor::move (C++ function) feasst::PerturbTranslate (C++ class), [1] feasst::PerturbTranslate::mid_stage (C++ function) feasst::PerturbTranslate::move (C++ function), [1] feasst::PerturbTranslate::precompute (C++ function) feasst::PerturbTranslate::update_selection (C++ function) feasst::PerturbVolume (C++ class), [1] feasst::PerturbVolume::change_volume (C++ function) feasst::PerturbVolume::finalize (C++ function) feasst::PerturbVolume::perturb (C++ function) feasst::PerturbVolume::PerturbVolume (C++ function), [1] feasst::PerturbVolume::revert (C++ function) feasst::PerturbVolume::uniform_volume (C++ function) feasst::PhysicalConstants (C++ class), [1] feasst::PhysicalConstants::avogadro_constant (C++ function) feasst::PhysicalConstants::boltzmann_constant (C++ function) feasst::PhysicalConstants::charge_conversion (C++ function) feasst::PhysicalConstants::elementary_charge (C++ function) feasst::PhysicalConstants::grams_per_cm3_to_number_density (C++ function) feasst::PhysicalConstants::ideal_gas_constant (C++ function) feasst::PhysicalConstants::number_density_to_grams_per_cm3 (C++ function) feasst::PhysicalConstants::permitivity_vacuum (C++ function) feasst::PhysicalConstantsCustom (C++ class), [1] feasst::PhysicalConstantsCustom::avogadro_constant (C++ function) feasst::PhysicalConstantsCustom::boltzmann_constant (C++ function) feasst::PhysicalConstantsCustom::elementary_charge (C++ function) feasst::PhysicalConstantsCustom::permitivity_vacuum (C++ function) feasst::PI (C++ member), [1] feasst::Pool (C++ class), [1] feasst::Position (C++ class), [1] feasst::Position::add (C++ function) feasst::Position::add_to_coord (C++ function) feasst::Position::coord (C++ function), [1] feasst::Position::cosine (C++ function) feasst::Position::cross_product (C++ function) feasst::Position::dimension (C++ function) feasst::Position::distance (C++ function), [1] feasst::Position::divide (C++ function), [1] feasst::Position::dot_product (C++ function), [1] feasst::Position::is_equal (C++ function), [1] feasst::Position::multiply (C++ function) feasst::Position::nearest_distance_to_axis (C++ function) feasst::Position::normalize (C++ function) feasst::Position::orthogonal (C++ function) feasst::Position::Position (C++ function), [1] feasst::Position::push_back (C++ function) feasst::Position::reflect (C++ function) feasst::Position::set_coord (C++ function) feasst::Position::set_from_cartesian (C++ function) feasst::Position::set_from_spherical (C++ function), [1], [2] feasst::Position::set_to_origin (C++ function), [1] feasst::Position::set_to_origin_3D (C++ function) feasst::Position::set_vector (C++ function) feasst::Position::size (C++ function) feasst::Position::spherical (C++ function), [1] feasst::Position::squared_distance (C++ function), [1] feasst::Position::str (C++ function) feasst::Position::subtract (C++ function) feasst::Position::torsion_angle_radians (C++ function) feasst::Position::vertex_angle_radians (C++ function) feasst::Potential (C++ class), [1] feasst::Potential::cache (C++ function) feasst::Potential::cell_index (C++ function) feasst::Potential::change_volume (C++ function) feasst::Potential::does_cutoff_fit_domain (C++ function) feasst::Potential::energy (C++ function) feasst::Potential::finalize (C++ function) feasst::Potential::group_index (C++ function) feasst::Potential::load_cache (C++ function) feasst::Potential::model (C++ function) feasst::Potential::model_params (C++ function), [1] feasst::Potential::Potential (C++ function), [1], [2], [3] feasst::Potential::precompute (C++ function) feasst::Potential::revert (C++ function) feasst::Potential::select_energy (C++ function) feasst::Potential::serialize (C++ function) feasst::Potential::set (C++ function) feasst::Potential::set_model_param (C++ function), [1] feasst::Potential::set_model_params (C++ function) feasst::Potential::set_stored_energy (C++ function) feasst::Potential::stored_energy (C++ function) feasst::Potential::unload_cache (C++ function) feasst::Potential::visit_model (C++ function) feasst::PotentialFactory (C++ class), [1] feasst::PotentialFactory::add (C++ function) feasst::PotentialFactory::change_volume (C++ function) feasst::PotentialFactory::energy (C++ function) feasst::PotentialFactory::finalize (C++ function) feasst::PotentialFactory::load_cache (C++ function) feasst::PotentialFactory::num (C++ function) feasst::PotentialFactory::potential (C++ function) feasst::PotentialFactory::PotentialFactory (C++ function) feasst::PotentialFactory::potentials (C++ function) feasst::PotentialFactory::precompute (C++ function), [1] feasst::PotentialFactory::remove_opt_overlap (C++ function) feasst::PotentialFactory::revert (C++ function) feasst::PotentialFactory::select_energy (C++ function) feasst::PotentialFactory::serialize (C++ function) feasst::PotentialFactory::set (C++ function) feasst::PotentialFactory::stored_energy (C++ function) feasst::PotentialFactory::stored_energy_profile (C++ function) feasst::PotentialFactory::str (C++ function) feasst::PotentialFactory::unload_cache (C++ function) feasst::Prefetch (C++ class), [1] feasst::Prefetch::activate_prefetch (C++ function) feasst::Prefetch::Prefetch (C++ function) feasst::Prefetch::reset_trial_stats (C++ function) feasst::Prefetch::run (C++ function) feasst::Prefetch::run_num_trials (C++ function) feasst::Prefetch::run_until_file_exists (C++ function) feasst::Prefetch::run_until_num_particles (C++ function) feasst::Prefetch::trials_per_check (C++ function) feasst::PrinterXYZ (C++ class), [1] feasst::PrinterXYZPatch (C++ class), [1] feasst::PrinterXYZSpherocylinder (C++ class), [1] feasst::ProfileCPU (C++ class), [1] feasst::ProfileCPU::header (C++ function) feasst::ProfileCPU::initialize (C++ function) feasst::ProfileCPU::write (C++ function) feasst::ProfileTrials (C++ class), [1] feasst::ProfileTrials::header (C++ function) feasst::ProfileTrials::initialize (C++ function) feasst::ProfileTrials::update (C++ function) feasst::ProfileTrials::write (C++ function) feasst::ProgressReport (C++ class), [1] feasst::ProgressReport::check (C++ function) feasst::ProgressReport::percent (C++ function) feasst::ProgressReport::ProgressReport (C++ function), [1] feasst::ProgressReport::reset (C++ function) feasst::ProgressReport::serialize (C++ function) feasst::ProgressReport::set_num (C++ function) feasst::ProgressReport::write (C++ function) feasst::PropertiedEntity (C++ class), [1] feasst::PropertiedEntity::add_or_set_property (C++ function) feasst::PropertiedEntity::add_property (C++ function) feasst::PropertiedEntity::has_property (C++ function) feasst::PropertiedEntity::properties (C++ function) feasst::PropertiedEntity::property (C++ function) feasst::PropertiedEntity::set_properties (C++ function) feasst::PropertiedEntity::set_property (C++ function), [1] feasst::Properties (C++ class), [1] feasst::Properties::add (C++ function) feasst::Properties::add_or_set (C++ function) feasst::Properties::check (C++ function) feasst::Properties::has (C++ function) feasst::Properties::is_equal (C++ function), [1] feasst::Properties::names (C++ function) feasst::Properties::num (C++ function) feasst::Properties::set (C++ function) feasst::Properties::set_value (C++ function) feasst::Properties::str (C++ function) feasst::Properties::value (C++ function), [1], [2] feasst::Properties::values (C++ function) feasst::RadiusOfGyration (C++ class), [1] feasst::RadiusOfGyration::header (C++ function) feasst::RadiusOfGyration::histogram (C++ function) feasst::RadiusOfGyration::initialize (C++ function) feasst::RadiusOfGyration::radius_of_gyration (C++ function) feasst::RadiusOfGyration::rg_e (C++ function) feasst::RadiusOfGyration::update (C++ function) feasst::RadiusOfGyration::write (C++ function) feasst::Random (C++ class), [1] feasst::Random::alpha_numeric (C++ function) feasst::Random::cache (C++ function) feasst::Random::class_name (C++ function) feasst::Random::coin_flip (C++ function) feasst::Random::const_element (C++ function) feasst::Random::element (C++ function) feasst::Random::index (C++ function) feasst::Random::index_from_cumulative_probability (C++ function) feasst::Random::normal (C++ function) feasst::Random::position_in_cube (C++ function), [1] feasst::Random::position_in_cuboid (C++ function), [1] feasst::Random::position_in_spherical_shell (C++ function) feasst::Random::quaternion (C++ function) feasst::Random::rotation (C++ function), [1] feasst::Random::seed (C++ function) feasst::Random::seed_by_time (C++ function) feasst::Random::set_cache_to_load (C++ function) feasst::Random::set_cache_to_unload (C++ function) feasst::Random::standard_normal (C++ function) feasst::Random::uniform (C++ function), [1] feasst::Random::uniform_real (C++ function) feasst::Random::unit_sphere_surface (C++ function) feasst::RandomModulo (C++ class), [1] feasst::RandomMT19937 (C++ class), [1] feasst::RandomMT19937::standard_normal (C++ function) feasst::ReadConfigFromFile (C++ class), [1] feasst::ReadConfigFromFile::initialize (C++ function) feasst::ReadConfigFromFile::update (C++ function) feasst::RefPotential (C++ class), [1] feasst::RemoveAnalyze (C++ class), [1] feasst::RemoveModify (C++ class), [1] feasst::RemoveTrial (C++ class), [1] feasst::RigidAngle (C++ class), [1] feasst::RigidAngle::energy (C++ function) feasst::RigidAngle::random_angle_radians (C++ function) feasst::RigidAngle::random_branch (C++ function) feasst::RigidBond (C++ class), [1] feasst::RigidDihedral (C++ class), [1] feasst::Rosenbluth (C++ class), [1] feasst::Rosenbluth::chosen (C++ function) feasst::Rosenbluth::chosen_energy (C++ function) feasst::Rosenbluth::chosen_energy_profile (C++ function) feasst::Rosenbluth::chosen_step (C++ function) feasst::Rosenbluth::compute (C++ function) feasst::Rosenbluth::energy (C++ function) feasst::Rosenbluth::energy_profile (C++ function) feasst::Rosenbluth::ln_total_rosenbluth (C++ function) feasst::Rosenbluth::num (C++ function) feasst::Rosenbluth::resize (C++ function) feasst::Rosenbluth::Rosenbluth (C++ function) feasst::Rosenbluth::serialize (C++ function) feasst::Rosenbluth::set_energy (C++ function) feasst::Rosenbluth::store (C++ function) feasst::Rosenbluth::stored (C++ function) feasst::RotationMatrix (C++ class), [1] feasst::RotationMatrix::axis_angle (C++ function) feasst::RotationMatrix::axis_angle_opt (C++ function) feasst::RotationMatrix::check (C++ function) feasst::RotationMatrix::quaternion (C++ function) feasst::RotationMatrix::rotate (C++ function), [1] feasst::RotationMatrix::vector_onto_vector (C++ function), [1] feasst::Rotator (C++ class), [1] feasst::Run (C++ class), [1] feasst::Scattering (C++ class), [1] feasst::Scattering::initialize (C++ function) feasst::Scattering::update (C++ function) feasst::Scattering::write (C++ function) feasst::SeekAnalyze (C++ class), [1] feasst::SeekAnalyze::index (C++ function) feasst::SeekAnalyze::multistate_data (C++ function) feasst::SeekAnalyze::reference (C++ function) feasst::SeekModify (C++ class), [1] feasst::SeekModify::index (C++ function) feasst::Select (C++ class), [1] feasst::Select::add (C++ function) feasst::Select::add_particle (C++ function), [1] feasst::Select::add_site (C++ function) feasst::Select::add_sites (C++ function) feasst::Select::add_to_site_position (C++ function) feasst::Select::check (C++ function) feasst::Select::clear (C++ function) feasst::Select::exclude (C++ function) feasst::Select::excluded (C++ function) feasst::Select::geometric_center (C++ function) feasst::Select::group (C++ function) feasst::Select::has_positions (C++ function) feasst::Select::is_empty (C++ function) feasst::Select::is_equal (C++ function) feasst::Select::is_group_empty (C++ function) feasst::Select::is_overlap (C++ function) feasst::Select::load_position (C++ function) feasst::Select::load_positions (C++ function) feasst::Select::load_positions_of_last (C++ function) feasst::Select::new_bond (C++ function) feasst::Select::num_particles (C++ function) feasst::Select::num_sites (C++ function) feasst::Select::old_bond (C++ function) feasst::Select::particle_indices (C++ function) feasst::Select::random_particle (C++ function) feasst::Select::remove (C++ function) feasst::Select::remove_first_site (C++ function) feasst::Select::remove_first_sites (C++ function) feasst::Select::remove_last_particle (C++ function) feasst::Select::remove_last_site (C++ function) feasst::Select::remove_last_sites (C++ function) feasst::Select::remove_particle (C++ function) feasst::Select::remove_sites (C++ function) feasst::Select::replace_indices (C++ function) feasst::Select::reset_excluded_and_bond (C++ function) feasst::Select::Select (C++ function), [1] feasst::Select::set_group (C++ function) feasst::Select::set_new_bond (C++ function) feasst::Select::set_old_bond (C++ function) feasst::Select::set_particle (C++ function) feasst::Select::set_site (C++ function) feasst::Select::set_site_position (C++ function), [1] feasst::Select::set_site_properties (C++ function) feasst::Select::set_trial_state (C++ function) feasst::Select::site_indices (C++ function), [1] feasst::Select::site_positions (C++ function) feasst::Select::site_properties (C++ function) feasst::Select::str (C++ function) feasst::Select::trial_state (C++ function) feasst::SelectBranch (C++ class), [1] feasst::SelectBranch::precompute (C++ function) feasst::SelectCluster (C++ class), [1] feasst::SelectCluster::are_constraints_satisfied (C++ function) feasst::SelectCluster::precompute (C++ function) feasst::SelectCluster::select (C++ function) feasst::SelectCluster::select_cluster (C++ function) feasst::SelectCluster::select_clusters (C++ function) feasst::SelectCluster::SelectCluster (C++ function) feasst::SelectCrankshaftSmall (C++ class), [1] feasst::SelectCrankshaftSmall::precompute (C++ function) feasst::SelectCrankshaftSmall::select (C++ function) feasst::SelectEndSegment (C++ class), [1] feasst::SelectEndSegment::precompute (C++ function) feasst::SelectEndSegment::random_end_segment_in_particle (C++ function) feasst::SelectEndSegment::select (C++ function) feasst::SelectNothing (C++ class), [1] feasst::SelectNothing::select (C++ function) feasst::SelectParticleAVB (C++ class), [1] feasst::SelectParticleAVB::precompute (C++ function) feasst::SelectParticleAVB::select (C++ function) feasst::SelectParticleAVB::SelectParticleAVB (C++ function), [1] feasst::SelectParticleAVBDivalent (C++ class), [1] feasst::SelectParticleAVBDivalent::select (C++ function) feasst::SelectParticleAVBDivalent::SelectParticleAVBDivalent (C++ function), [1] feasst::SelectParticlePivot (C++ class), [1] feasst::SelectParticlePivot::precompute (C++ function) feasst::SelectParticlePivot::select (C++ function) feasst::SelectPerturbed (C++ class), [1] feasst::SelectPerturbed::select (C++ function) feasst::SelectReptate (C++ class), [1] feasst::SelectReptate::mid_stage (C++ function) feasst::SelectReptate::precompute (C++ function) feasst::SelectReptate::SelectReptate (C++ function) feasst::SelectSegment (C++ class), [1] feasst::SelectSegment::max_length (C++ function) feasst::SelectSegment::random_segment_in_particle (C++ function) feasst::SelectSegment::select (C++ function) feasst::SelectSiteOfType (C++ class), [1] feasst::SelectSiteOfType::random_site_in_particle (C++ function) feasst::SelectSiteOfType::select (C++ function) feasst::SelectSiteOfType::SelectSiteOfType (C++ function) feasst::SelectTwoSites (C++ class), [1] feasst::SelectTwoSites::mobile_site (C++ function) feasst::SelectTwoSites::mobile_site2 (C++ function) feasst::SelectTwoSites::precompute (C++ function) feasst::SelectTwoSites::select (C++ function) feasst::Server (C++ class), [1] feasst::Shape (C++ class), [1] feasst::Shape::grid (C++ function) feasst::Shape::integrate (C++ function) feasst::Shape::is_inside (C++ function), [1] feasst::Shape::nearest_distance (C++ function) feasst::Shape::surface_area (C++ function) feasst::Shape::volume (C++ function) feasst::ShapedEntity (C++ class), [1] feasst::ShapedEntity::shape (C++ function) feasst::ShapeFile (C++ class), [1] feasst::ShapeFile::is_inside (C++ function), [1] feasst::ShapeFile::nearest_distance (C++ function) feasst::ShapeIntersect (C++ class), [1] feasst::ShapeIntersect::is_inside (C++ function), [1] feasst::ShapeIntersect::nearest_distance (C++ function) feasst::ShapeIntersect::ShapeIntersect (C++ function) feasst::ShapeUnion (C++ class), [1] feasst::ShapeUnion::is_inside (C++ function), [1] feasst::ShapeUnion::nearest_distance (C++ function) feasst::Sigma (C++ class), [1] feasst::Site (C++ class), [1] feasst::Site::add_cell (C++ function) feasst::Site::add_position (C++ function) feasst::Site::add_property (C++ function) feasst::Site::cell (C++ function) feasst::Site::displace (C++ function) feasst::Site::euler (C++ function) feasst::Site::is_anisotropic (C++ function) feasst::Site::is_physical (C++ function) feasst::Site::num_cells (C++ function) feasst::Site::position (C++ function), [1] feasst::Site::set_anisotropic (C++ function) feasst::Site::set_cell (C++ function) feasst::Site::set_euler (C++ function) feasst::Site::set_physical (C++ function) feasst::Site::set_position (C++ function) feasst::Site::set_type (C++ function) feasst::Site::Site (C++ function) feasst::Site::type (C++ function) feasst::Slab (C++ class), [1] feasst::Slab::Slab (C++ function) feasst::SlabCorrection (C++ class), [1] feasst::SlabCorrection::compute (C++ function), [1] feasst::SlabCorrection::net_dipole (C++ function) feasst::SlabSine (C++ class), [1] feasst::SolidOfRevolutionTable (C++ class), [1] feasst::SolidOfRevolutionTable::is_energy_table (C++ function) feasst::Solver (C++ class), [1] feasst::Solver::guess (C++ function) feasst::Solver::is_lower (C++ function) feasst::Solver::is_upper (C++ function) feasst::Solver::lower (C++ function) feasst::Solver::root (C++ function) feasst::Solver::set_guess (C++ function) feasst::Solver::set_lower (C++ function) feasst::Solver::set_upper (C++ function) feasst::Solver::Solver (C++ function) feasst::Solver::tolerance (C++ function) feasst::Solver::upper (C++ function) feasst::SolverBisection (C++ class), [1] feasst::SolverBisection::root (C++ function) feasst::SolverBrentDekker (C++ class), [1] feasst::SolverBrentDekker::root (C++ function) feasst::SolverNewtonRaphson (C++ class), [1] feasst::SolverNewtonRaphson::root (C++ function) feasst::Sphere (C++ class), [1] feasst::Sphere::nearest_distance (C++ function) feasst::Sphere::surface_area (C++ function) feasst::Sphere::surface_mesh (C++ function) feasst::Sphere::volume (C++ function) feasst::Spherocylinder (C++ class), [1] feasst::SpherocylinderLength (C++ class), [1] feasst::SquareWell (C++ class), [1] feasst::SquareWell::serialize (C++ function) feasst::Stepper (C++ class), [1] feasst::Stepper::accumulator (C++ function) feasst::Stepper::append (C++ function) feasst::Stepper::configuration (C++ function) feasst::Stepper::configuration_index (C++ function) feasst::Stepper::empty_output_file (C++ function) feasst::Stepper::get_accumulator (C++ function) feasst::Stepper::header (C++ function) feasst::Stepper::is_multistate (C++ function) feasst::Stepper::is_multistate_aggregate (C++ function) feasst::Stepper::output_file (C++ function), [1] feasst::Stepper::output_file_append_phase (C++ function) feasst::Stepper::printer (C++ function) feasst::Stepper::rewrite_header (C++ function) feasst::Stepper::set_state (C++ function) feasst::Stepper::start_after_iteration (C++ function) feasst::Stepper::start_after_phase (C++ function) feasst::Stepper::state (C++ function) feasst::Stepper::Stepper (C++ function), [1] feasst::Stepper::stop_after_iteration (C++ function) feasst::Stepper::stop_after_phase (C++ function) feasst::Stepper::trials_per_update (C++ function) feasst::Stepper::trials_per_write (C++ function) feasst::Stepper::trials_since_update (C++ function) feasst::Stepper::trials_since_write (C++ function) feasst::Supertoroid (C++ class), [1] feasst::Supertoroid::is_inside (C++ function), [1] feasst::Supertoroid::nearest_distance (C++ function) feasst::Supertoroid::surface_area (C++ function) feasst::Supertoroid::volume (C++ function) feasst::SynchronizeData (C++ class), [1] feasst::SynchronizeData::dble_1D (C++ function) feasst::SynchronizeData::dble_2D (C++ function) feasst::SynchronizeData::dble_3D (C++ function) feasst::SynchronizeData::dble_5D (C++ function) feasst::SynchronizeData::dble_6D (C++ function) feasst::SynchronizeData::get_const_vpvpvpvpv (C++ function) feasst::SynchronizeData::get_const_vvvpvpv (C++ function) feasst::SynchronizeData::get_dble_1D (C++ function) feasst::SynchronizeData::get_dble_2D (C++ function) feasst::SynchronizeData::get_dble_3D (C++ function) feasst::SynchronizeData::get_dble_5D (C++ function) feasst::SynchronizeData::get_dble_6D (C++ function) feasst::SynchronizeData::get_int64_1D (C++ function) feasst::SynchronizeData::get_int_1D (C++ function) feasst::SynchronizeData::get_vpvpvpvpv (C++ function) feasst::SynchronizeData::get_vvvpvpv (C++ function) feasst::SynchronizeData::int64_1D (C++ function) feasst::SynchronizeData::int_1D (C++ function) feasst::System (C++ class), [1] feasst::System::add (C++ function), [1], [2] feasst::System::add_to_optimized (C++ function) feasst::System::add_to_reference (C++ function) feasst::System::add_to_unoptimized (C++ function) feasst::System::change_volume (C++ function) feasst::System::check (C++ function) feasst::System::configuration (C++ function) feasst::System::delta_volume_previous (C++ function) feasst::System::dimension (C++ function) feasst::System::energy (C++ function) feasst::System::finalize (C++ function) feasst::System::initialize (C++ function) feasst::System::load_cache (C++ function) feasst::System::neighbor_criteria (C++ function), [1] feasst::System::num_configurations (C++ function) feasst::System::num_references (C++ function) feasst::System::optimized (C++ function) feasst::System::perturbed_energy (C++ function) feasst::System::potential (C++ function) feasst::System::potentials (C++ function) feasst::System::precompute (C++ function) feasst::System::reference (C++ function) feasst::System::reference_energy (C++ function), [1] feasst::System::references (C++ function) feasst::System::remove_opt_overlap (C++ function) feasst::System::revert (C++ function) feasst::System::serialize (C++ function) feasst::System::set (C++ function) feasst::System::set_beta (C++ function) feasst::System::set_unoptimized (C++ function) feasst::System::status (C++ function) feasst::System::status_header (C++ function) feasst::System::stored_energy (C++ function) feasst::System::stored_energy_profile (C++ function) feasst::System::System (C++ function), [1] feasst::System::thermo_params (C++ function) feasst::System::total_volume (C++ function) feasst::System::unload_cache (C++ function) feasst::System::unoptimized (C++ function) feasst::System::unoptimized_energy (C++ function) feasst::Table (C++ class), [1] feasst::Table1D (C++ class), [1] feasst::Table1D::add (C++ function) feasst::Table1D::bin_to_value (C++ function) feasst::Table1D::data (C++ function) feasst::Table1D::forward_difference_interpolation (C++ function) feasst::Table1D::linear_interpolation (C++ function) feasst::Table1D::maximum (C++ function) feasst::Table1D::minimum (C++ function) feasst::Table1D::num (C++ function) feasst::Table1D::set_data (C++ function) feasst::Table1D::Table1D (C++ function) feasst::Table1D::value_to_nearest_bin (C++ function) feasst::Table2D (C++ class), [1] feasst::Table2D::add (C++ function) feasst::Table2D::bin_to_value (C++ function) feasst::Table2D::data (C++ function) feasst::Table2D::linear_interpolation (C++ function) feasst::Table2D::maximum (C++ function) feasst::Table2D::minimum (C++ function) feasst::Table2D::num (C++ function) feasst::Table2D::num0 (C++ function) feasst::Table2D::num1 (C++ function) feasst::Table2D::set_data (C++ function) feasst::Table2D::Table2D (C++ function) feasst::Table2D::value_to_nearest_bin (C++ function) feasst::Table3D (C++ class), [1] feasst::Table3D::add (C++ function) feasst::Table3D::bin_to_value (C++ function) feasst::Table3D::data (C++ function) feasst::Table3D::linear_interpolation (C++ function) feasst::Table3D::maximum (C++ function) feasst::Table3D::minimum (C++ function) feasst::Table3D::num (C++ function) feasst::Table3D::num0 (C++ function) feasst::Table3D::num1 (C++ function) feasst::Table3D::num2 (C++ function) feasst::Table3D::set_data (C++ function) feasst::Table3D::Table3D (C++ function), [1] feasst::Table3D::value_to_nearest_bin (C++ function) feasst::Table3D::write (C++ function) feasst::Table4D (C++ class), [1] feasst::Table4D::add (C++ function) feasst::Table4D::bin_to_value (C++ function) feasst::Table4D::data (C++ function) feasst::Table4D::linear_interpolation (C++ function) feasst::Table4D::maximum (C++ function) feasst::Table4D::minimum (C++ function) feasst::Table4D::num (C++ function) feasst::Table4D::num0 (C++ function) feasst::Table4D::num1 (C++ function) feasst::Table4D::num2 (C++ function) feasst::Table4D::num3 (C++ function) feasst::Table4D::set_data (C++ function) feasst::Table4D::Table4D (C++ function), [1] feasst::Table4D::value_to_nearest_bin (C++ function) feasst::Table4D::write (C++ function) feasst::Table5D (C++ class), [1] feasst::Table5D::add (C++ function) feasst::Table5D::bin_to_value (C++ function) feasst::Table5D::data (C++ function) feasst::Table5D::linear_interpolation (C++ function) feasst::Table5D::maximum (C++ function) feasst::Table5D::minimum (C++ function) feasst::Table5D::num (C++ function) feasst::Table5D::num0 (C++ function) feasst::Table5D::num1 (C++ function) feasst::Table5D::num2 (C++ function) feasst::Table5D::num3 (C++ function) feasst::Table5D::num4 (C++ function) feasst::Table5D::set_data (C++ function) feasst::Table5D::Table5D (C++ function), [1] feasst::Table5D::value_to_nearest_bin (C++ function) feasst::Table5D::write (C++ function) feasst::Table6D (C++ class), [1] feasst::Table6D::add (C++ function) feasst::Table6D::bin_to_value (C++ function) feasst::Table6D::data (C++ function) feasst::Table6D::linear_interpolation (C++ function) feasst::Table6D::maximum (C++ function) feasst::Table6D::minimum (C++ function) feasst::Table6D::num (C++ function) feasst::Table6D::num0 (C++ function) feasst::Table6D::num1 (C++ function) feasst::Table6D::num2 (C++ function) feasst::Table6D::num3 (C++ function) feasst::Table6D::num4 (C++ function) feasst::Table6D::num5 (C++ function) feasst::Table6D::set_data (C++ function) feasst::Table6D::Table6D (C++ function), [1] feasst::Table6D::value_to_nearest_bin (C++ function) feasst::Table6D::write (C++ function) feasst::Table::bin_spacing (C++ function) feasst::Table::maximum (C++ function) feasst::Table::minimum (C++ function) feasst::Table::write (C++ function) feasst::TablePotential (C++ class), [1] feasst::TablePotential::precompute (C++ function) feasst::TablePotential::serialize (C++ function) feasst::TabulateTwoRigidBody3D (C++ class), [1] feasst::TabulateTwoRigidBody3D::adjust_domain (C++ function) feasst::TabulateTwoRigidBody3D::combine_table (C++ function) feasst::TabulateTwoRigidBody3D::max_cubic_side_length (C++ function) feasst::TabulateTwoRigidBody3D::read_contact_table (C++ function) feasst::TabulateTwoRigidBody3D::write_table (C++ function) feasst::ThermoParams (C++ class), [1] feasst::ThermoParams::add_chemical_potential (C++ function) feasst::ThermoParams::beta (C++ function) feasst::ThermoParams::beta_mu (C++ function) feasst::ThermoParams::chemical_potential (C++ function) feasst::ThermoParams::is_equal (C++ function) feasst::ThermoParams::pH (C++ function) feasst::ThermoParams::pressure (C++ function) feasst::ThermoParams::set_beta (C++ function) feasst::ThermoParams::set_chemical_potential (C++ function) feasst::ThermoParams::set_pH (C++ function) feasst::ThermoParams::set_pressure (C++ function) feasst::ThermoParams::str (C++ function) feasst::Thread (C++ class), [1] feasst::Thread::in_chunk (C++ function) feasst::Thread::is_enabled (C++ function) feasst::Thread::num (C++ function) feasst::Thread::thread (C++ function) feasst::ThreadOMP (C++ class), [1] feasst::ThreadOMP::is_enabled (C++ function) feasst::ThreadOMP::num (C++ function) feasst::ThreadOMP::thread (C++ function) feasst::Timer (C++ class), [1] feasst::Timer::add (C++ function) feasst::Timer::clocks (C++ function) feasst::Timer::end (C++ function) feasst::Timer::hours (C++ function), [1], [2] feasst::Timer::missing_percent (C++ function) feasst::Timer::start (C++ function) feasst::Timer::sum_clocks (C++ function) feasst::TimerRDTSC (C++ class), [1] feasst::TimerRDTSC::add (C++ function) feasst::TimerRDTSC::erase (C++ function) feasst::TimerRDTSC::percents (C++ function) feasst::TimerRDTSC::start (C++ function) feasst::TimerRDTSC::TimerRDTSC (C++ function) feasst::TransitionMatrix (C++ class), [1] feasst::TransitionMatrix::infrequent_update (C++ function) feasst::TransitionMatrix::ln_prob (C++ function) feasst::TransitionMatrix::min_sweeps (C++ function) feasst::TransitionMatrix::num_iterations_to_complete (C++ function) feasst::TransitionMatrix::reset_sweeps (C++ function) feasst::TransitionMatrix::set_ln_prob (C++ function) feasst::TransitionMatrix::set_num_iterations_to_complete (C++ function) feasst::TransitionMatrix::update (C++ function) feasst::Trial (C++ class), [1] feasst::Trial::acceptance (C++ function) feasst::Trial::add_stage (C++ function), [1], [2] feasst::Trial::attempt (C++ function) feasst::Trial::compute (C++ function) feasst::Trial::description (C++ function) feasst::Trial::increment_num_attempts (C++ function) feasst::Trial::name_or_description (C++ function) feasst::Trial::num_attempts (C++ function) feasst::Trial::num_auto_reject (C++ function) feasst::Trial::num_stages (C++ function) feasst::Trial::num_success (C++ function) feasst::Trial::number_fraction_exclude_type (C++ function) feasst::Trial::precompute (C++ function) feasst::Trial::reset_stats (C++ function) feasst::Trial::revert (C++ function) feasst::Trial::set (C++ function), [1] feasst::Trial::set_description (C++ function) feasst::Trial::stage (C++ function) feasst::Trial::status (C++ function) feasst::Trial::status_header (C++ function) feasst::Trial::Trial (C++ function), [1] feasst::Trial::tune (C++ function) feasst::Trial::weight (C++ function) feasst::Trial::weight_per_number_fraction (C++ function) feasst::TrialAdd (C++ class), [1] feasst::TrialAddAVB (C++ class), [1] feasst::TrialAddAVBDivalent (C++ class), [1] feasst::TrialAddMultiple (C++ class), [1] feasst::TrialAVB2 (C++ class), [1] feasst::TrialAVB2Half (C++ class), [1] feasst::TrialAVB2Half::TrialAVB2Half (C++ function) feasst::TrialAVB4 (C++ class), [1] feasst::TrialBeta (C++ class), [1] feasst::TrialCompute (C++ class), [1] feasst::TrialCompute::compute_rosenbluth (C++ function) feasst::TrialCompute::perturb_and_acceptance (C++ function) feasst::TrialComputeAdd (C++ class), [1] feasst::TrialComputeAdd::perturb_and_acceptance (C++ function) feasst::TrialComputeMove (C++ class), [1] feasst::TrialComputeMove::perturb_and_acceptance (C++ function) feasst::TrialComputeRemove (C++ class), [1] feasst::TrialComputeRemove::perturb_and_acceptance (C++ function) feasst::TrialComputeTranslate (C++ class), [1] feasst::TrialComputeTranslate::perturb_and_acceptance (C++ function) feasst::TrialComputeVolume (C++ class), [1] feasst::TrialComputeVolume::perturb_and_acceptance (C++ function) feasst::TrialCrankshaft (C++ class), [1] feasst::TrialCrankshaftSmall (C++ class), [1] feasst::TrialFactory (C++ class), [1] feasst::TrialFactory::add (C++ function) feasst::TrialFactory::attempt (C++ function), [1] feasst::TrialFactory::cumulative_probability (C++ function) feasst::TrialFactory::last_index (C++ function) feasst::TrialFactory::num (C++ function) feasst::TrialFactory::precompute (C++ function) feasst::TrialFactory::random_index (C++ function) feasst::TrialFactory::remove (C++ function) feasst::TrialFactory::reset_stats (C++ function) feasst::TrialFactory::revert (C++ function) feasst::TrialFactory::set_timer (C++ function) feasst::TrialFactory::status (C++ function) feasst::TrialFactory::status_header (C++ function) feasst::TrialFactory::timer (C++ function) feasst::TrialFactory::trial (C++ function) feasst::TrialFactory::tune (C++ function) feasst::TrialFactoryNamed (C++ class), [1] feasst::TrialGibbsParticleTransfer (C++ class), [1] feasst::TrialGibbsParticleTransferOneWay (C++ class), [1] feasst::TrialGibbsParticleTransferOneWay::TrialGibbsParticleTransferOneWay (C++ function) feasst::TrialGibbsVolumeTransfer (C++ class), [1] feasst::TrialGrow (C++ class), [1] feasst::TrialGrow::TrialGrow (C++ function) feasst::TrialGrowFile (C++ class), [1] feasst::TrialGrowLinear (C++ class), [1] feasst::TrialGrowLinear::precompute (C++ function) feasst::TrialGrowLinear::TrialGrowLinear (C++ function) feasst::TrialModel (C++ class), [1] feasst::TrialMorph (C++ class), [1] feasst::TrialMorphExpanded (C++ class), [1] feasst::TrialMorphExpanded::attempt (C++ function) feasst::TrialMorphExpanded::precompute (C++ function) feasst::TrialMorphExpanded::TrialMorphExpanded (C++ function) feasst::TrialMove (C++ class), [1] feasst::TrialParticlePivot (C++ class), [1] feasst::TrialPivot (C++ class), [1] feasst::TrialRemove (C++ class), [1] feasst::TrialRemoveAVB (C++ class), [1] feasst::TrialRemoveAVBDivalent (C++ class), [1] feasst::TrialRemoveMultiple (C++ class), [1] feasst::TrialReptate (C++ class), [1] feasst::TrialReptate::TrialReptate (C++ function) feasst::TrialRigidCluster (C++ class), [1] feasst::TrialRotate (C++ class), [1] feasst::TrialRotate::TrialRotate (C++ function), [1] feasst::TrialRotateCluster (C++ class), [1] feasst::TrialSelect (C++ class), [1] feasst::TrialSelect::add_or_set_property (C++ function) feasst::TrialSelect::anchor (C++ function) feasst::TrialSelect::anchor_position (C++ function) feasst::TrialSelect::are_constraints_satisfied (C++ function) feasst::TrialSelect::before_select (C++ function) feasst::TrialSelect::configuration (C++ function) feasst::TrialSelect::configuration_index (C++ function) feasst::TrialSelect::get_configuration (C++ function) feasst::TrialSelect::group_index (C++ function) feasst::TrialSelect::has_property (C++ function) feasst::TrialSelect::is_ghost (C++ function) feasst::TrialSelect::is_isotropic (C++ function) feasst::TrialSelect::is_particle_type_set (C++ function) feasst::TrialSelect::mid_stage (C++ function) feasst::TrialSelect::mobile (C++ function) feasst::TrialSelect::mobile_original (C++ function) feasst::TrialSelect::particle_type (C++ function) feasst::TrialSelect::precompute (C++ function) feasst::TrialSelect::printable (C++ function) feasst::TrialSelect::probability (C++ function) feasst::TrialSelect::property (C++ function) feasst::TrialSelect::remove_unphysical_sites (C++ function) feasst::TrialSelect::replace_mobile (C++ function) feasst::TrialSelect::reset_mobile (C++ function) feasst::TrialSelect::sel (C++ function) feasst::TrialSelect::select (C++ function) feasst::TrialSelect::set_configuration_index (C++ function) feasst::TrialSelect::set_ghost (C++ function) feasst::TrialSelect::set_mobile (C++ function) feasst::TrialSelect::set_mobile_original (C++ function) feasst::TrialSelect::set_trial_state (C++ function) feasst::TrialSelectAll (C++ class), [1] feasst::TrialSelectAll::select (C++ function) feasst::TrialSelectAngle (C++ class), [1] feasst::TrialSelectAngle::anchor_site2 (C++ function) feasst::TrialSelectAngle::precompute (C++ function) feasst::TrialSelectBond (C++ class), [1] feasst::TrialSelectBond::anchor_site (C++ function) feasst::TrialSelectBond::mobile_site (C++ function) feasst::TrialSelectBond::precompute (C++ function) feasst::TrialSelectBond::select (C++ function) feasst::TrialSelectDihedral (C++ class), [1] feasst::TrialSelectDihedral::precompute (C++ function) feasst::TrialSelectParticle (C++ class), [1] feasst::TrialSelectParticle::ghost_particle (C++ function), [1] feasst::TrialSelectParticle::load_coordinates (C++ function) feasst::TrialSelectParticle::random_particle (C++ function), [1] feasst::TrialSelectParticle::select (C++ function) feasst::TrialSelectParticle::select_particle (C++ function) feasst::TrialSelectParticle::site (C++ function) feasst::TrialStage (C++ class), [1] feasst::TrialStage::are_constraints_satisfied (C++ function) feasst::TrialStage::attempt (C++ function) feasst::TrialStage::before_select (C++ function) feasst::TrialStage::finalize (C++ function) feasst::TrialStage::is_new_only (C++ function) feasst::TrialStage::mid_stage (C++ function) feasst::TrialStage::num_steps (C++ function) feasst::TrialStage::perturb (C++ function) feasst::TrialStage::precompute (C++ function) feasst::TrialStage::reference (C++ function) feasst::TrialStage::revert (C++ function) feasst::TrialStage::rosenbluth (C++ function) feasst::TrialStage::select (C++ function), [1] feasst::TrialStage::serialize (C++ function) feasst::TrialStage::set (C++ function), [1] feasst::TrialStage::set_mobile_physical (C++ function) feasst::TrialStage::status (C++ function) feasst::TrialStage::status_header (C++ function) feasst::TrialStage::TrialStage (C++ function), [1], [2] feasst::TrialStage::tune (C++ function) feasst::TrialSwapSites (C++ class), [1] feasst::TrialTransfer (C++ class), [1] feasst::TrialTransferAVB (C++ class), [1] feasst::TrialTransferAVBDivalent (C++ class), [1] feasst::TrialTransferMultiple (C++ class), [1] feasst::TrialTranslate (C++ class), [1] feasst::TrialTranslateCluster (C++ class), [1] feasst::TrialVolume (C++ class), [1] feasst::Tunable (C++ class), [1] feasst::Tunable::disable (C++ function) feasst::Tunable::enable (C++ function) feasst::Tunable::is_enabled (C++ function) feasst::Tunable::max (C++ function) feasst::Tunable::min (C++ function) feasst::Tunable::serialize (C++ function) feasst::Tunable::set_min_and_max (C++ function) feasst::Tunable::set_percent_change (C++ function) feasst::Tunable::set_target (C++ function) feasst::Tunable::set_value (C++ function) feasst::Tunable::Tunable (C++ function), [1], [2] feasst::Tunable::tune (C++ function) feasst::Tunable::value (C++ function) feasst::Tune (C++ class), [1] feasst::Tune::header (C++ function) feasst::Tune::initialize (C++ function) feasst::Tune::update (C++ function) feasst::Tune::write (C++ function) feasst::TwoBodyAlpha (C++ class), [1] feasst::TwoBodyAlpha::serialize (C++ function) feasst::TwoBodyAlpha::TwoBodyAlpha (C++ function) feasst::TwoBodyTable (C++ class), [1] feasst::TwoBodyTable::serialize (C++ function) feasst::TwoParticleContact (C++ class), [1] feasst::TwoParticleContactObjective (C++ class), [1] feasst::VERBOSE_LEVEL (C++ member), [1] feasst::VisitConfiguration (C++ class), [1] feasst::VisitModel (C++ class), [1] feasst::VisitModel::change_volume (C++ function) feasst::VisitModel::charge_index (C++ function) feasst::VisitModel::check_energy (C++ function) feasst::VisitModel::cutoff_index (C++ function) feasst::VisitModel::energy (C++ function) feasst::VisitModel::epsilon_index (C++ function) feasst::VisitModel::increment_energy (C++ function) feasst::VisitModel::set_energy (C++ function) feasst::VisitModel::sigma_index (C++ function) feasst::VisitModelBond (C++ class), [1] feasst::VisitModelCell (C++ class), [1] feasst::VisitModelCell::cell_id (C++ function) feasst::VisitModelCell::cell_id_opt_ (C++ function) feasst::VisitModelCell::cells (C++ function) feasst::VisitModelCell::change_volume (C++ function) feasst::VisitModelCell::precompute (C++ function) feasst::VisitModelCell::VisitModelCell (C++ function) feasst::VisitModelCutoffOuter (C++ class), [1] feasst::VisitModelCutoffOuter::VisitModelCutoffOuter (C++ function), [1] feasst::VisitModelInner (C++ class), [1] feasst::VisitModelInnerNN (C++ class), [1] feasst::VisitModelInnerPatch (C++ class), [1] feasst::VisitModelInnerServer (C++ class), [1] feasst::VisitModelInnerTable (C++ class), [1] feasst::VisitModelInnerTable::is_energy_table (C++ function) feasst::VisitModelInnerTable::second_virial_coefficient (C++ function) feasst::VisitModelIntra (C++ class), [1] feasst::VisitModelIntraMap (C++ class), [1] feasst::VisitModelIntraMap::include_map (C++ function) feasst::VisitModelIntraMap::precompute (C++ function) feasst::VisitModelOptLJ (C++ class), [1] feasst::VisitModelOptRPM (C++ class), [1] feasst::VisitParticles (C++ class), [1] feasst::Volume (C++ class), [1] feasst::Volume::header (C++ function) feasst::Volume::initialize (C++ function) feasst::Volume::update (C++ function) feasst::Volume::write (C++ function) feasst::WallClockLimit (C++ class), [1] feasst::WallClockLimit::update (C++ function) feasst::WangLandau (C++ class), [1] feasst::WangLandau::infrequent_update (C++ function) feasst::WangLandau::ln_prob (C++ function) feasst::WangLandau::num_iterations_to_complete (C++ function) feasst::WangLandau::set_ln_prob (C++ function) feasst::WangLandau::set_num_iterations_to_complete (C++ function) feasst::WangLandau::update (C++ function) feasst::Window (C++ class), [1] feasst::Window::boundaries (C++ function) feasst::Window::maximum (C++ function) feasst::Window::minimum (C++ function) feasst::Window::num (C++ function) feasst::Window::overlap (C++ function) feasst::Window::segment (C++ function) feasst::WindowCustom (C++ class), [1] feasst::WindowCustom::boundaries (C++ function) feasst::WindowCustom::maximum (C++ function) feasst::WindowCustom::minimum (C++ function) feasst::WindowCustom::num (C++ function) feasst::WindowCustom::segment (C++ function) feasst::WindowCustom::WindowCustom (C++ function) feasst::WindowExponential (C++ class), [1] feasst::WindowExponential::segment (C++ function) feasst::WLTM (C++ class), [1] feasst::WLTM::infrequent_update (C++ function) feasst::WLTM::ln_prob (C++ function) feasst::WLTM::num_iterations_to_complete (C++ function) feasst::WLTM::set_ln_prob (C++ function) feasst::WLTM::set_num_iterations_to_complete (C++ function) feasst::WLTM::update (C++ function) feasst::WrapParticles (C++ class), [1] feasst::WrapParticles::update (C++ function) feasst::WriteCheckpoint (C++ class), [1] feasst::WriteModelParams (C++ class), [1] feasst::WriteStepper (C++ class), [1] feasst::Yukawa (C++ class), [1] feasst::Yukawa::serialize (C++ function) feasst::Yukawa::set_kappa (C++ function) feasst::ZeroBackground (C++ class), [1] FEASST_MACRO_EXCEPTION (C macro), [1] FEASST_MACRO_OUTPUT (C macro), [1] FEASST_MAPPER (C macro), [1] FEASST_MAPPER_RENAME (C macro), [1] fstio module fstplot module

I

INFO (C macro), [1]

L

ln_prob() (macrostate_distribution.MacrostateDistribution method)

M

macrostate_distribution module MacrostateDistribution (class in macrostate_distribution) macrostates() (macrostate_distribution.MacrostateDistribution method) MAX_PRECISION (C macro), [1] mean() (accumulator.Accumulator method) minimum_smoothing() (macrostate_distribution.MacrostateDistribution method) minimums() (macrostate_distribution.MacrostateDistribution method) module accumulator cd fstio fstplot macrostate_distribution multistate_accumulator physical_constants

MolarGasConstant (class in physical_constants) multistate_accumulator module

N

normalize() (macrostate_distribution.MacrostateDistribution method)

num_moments() (accumulator.Accumulator method) num_values() (accumulator.Accumulator method)

P

physical_constants module

plot() (macrostate_distribution.MacrostateDistribution method)

R

read_appended() (in module macrostate_distribution) read_checkpoint() (in module fstio) reweight() (macrostate_distribution.MacrostateDistribution method)

reweight_to_macrostate() (macrostate_distribution.MacrostateDistribution method) run_simulations() (in module fstio) run_single() (in module fstio)

S

set_dataframe() (macrostate_distribution.MacrostateDistribution method) set_ln_prob() (macrostate_distribution.MacrostateDistribution method) set_macrostates() (macrostate_distribution.MacrostateDistribution method) set_minimum_smoothing() (macrostate_distribution.MacrostateDistribution method) slurm_single_node() (in module fstio) splice() (in module macrostate_distribution) splice_by_max_column() (in module multistate_accumulator)

splice_by_node() (in module multistate_accumulator) splice_collection_matrix() (in module macrostate_distribution) splice_files() (in module macrostate_distribution) split() (in module fstio) (macrostate_distribution.MacrostateDistribution method) stdev() (accumulator.Accumulator method) STRINGIFY (C macro), [1] sum_moment() (accumulator.Accumulator method)

T

TRACE (C macro), [1]

TRY (C macro), [1]

U

units() (physical_constants.AvogadroConstant method) (physical_constants.BoltzmannConstant method) (physical_constants.ElementaryCharge method) (physical_constants.ESqPerAngstromToKJPerMol method) (physical_constants.MolarGasConstant method) (physical_constants.VacuumElectricPermittivity method)

V

VacuumElectricPermittivity (class in physical_constants) val2map() (in module fstplot) value() (physical_constants.AvogadroConstant method) (physical_constants.BoltzmannConstant method) (physical_constants.ElementaryCharge method) (physical_constants.ESqPerAngstromToKJPerMol method) (physical_constants.MolarGasConstant method) (physical_constants.VacuumElectricPermittivity method)

vector3d_to_list() (in module fstio)

W

WARN (C macro), [1]