• Constraint
  • Constraint
• ConstrainNumParticles
  • ConstrainNumParticles
    • type()
    • num_particles()
• Perturb
  • Perturb
    • Perturb()
    • tunable()
    • set_tunable_min_and_max()
    • set_tunable()
    • tune()
    • before_select()
    • mid_stage()
    • perturb()
    • revert_possible()
    • set_revert_possible()
    • revert_select()
    • revert()
    • finalize_possible()
    • set_finalize_possible()
    • finalize_select()
    • finalize()
    • status_header()
    • status()
• Action
  • Action
• RemoveModify
  • RemoveModify
• WriteCheckpoint
  • WriteCheckpoint
• ConstrainVolumeByCutoff
  • ConstrainVolumeByCutoff
• Acceptance
  • Acceptance
    • ln_metropolis_prob()
    • set_ln_metropolis_prob()
    • add_to_ln_metropolis_prob()
    • reject()
    • set_reject()
    • endpoint()
    • set_endpoint()
    • reset()
    • updated()
    • energy_new()
    • set_energy_new()
    • add_to_energy_new()
    • num_configurations()
    • energy_profile_new()
    • set_energy_profile_new()
    • add_to_energy_profile_new()
    • subtract_from_energy_profile_new()
    • energy_old()
    • set_energy_old()
    • add_to_energy_old()
    • energy_profile_old()
    • set_energy_profile_old()
    • add_to_energy_profile_old()
    • energy_ref()
    • set_energy_ref()
    • macrostate_shift()
    • add_to_macrostate_shift()
    • add_to_perturbed()
    • set_perturbed_state()
    • perturbed()
• Run
  • Run
• TrialCompute
  • TrialCompute
    • compute_rosenbluth()
    • perturb_and_acceptance()
• TrialComputeMove
  • TrialComputeMove
    • perturb_and_acceptance()
• Remove
  • Remove
• WriteModelParams
  • WriteModelParams
• PerturbMove
  • PerturbMove
    • move()
    • perturb()
    • revert()
    • finalize()
• Criteria
  • Criteria
    • Criteria()
    • add()
    • is_allowed()
    • before_attempt()
    • is_accepted()
    • was_accepted()
    • set_current_energy()
    • current_energy()
    • set_current_energy_profile()
    • current_energy_profile()
    • update_current_energy()
    • status_header()
    • status()
    • write()
    • phase()
    • increment_phase()
    • cycles_to_complete()
    • set_cycles_to_complete()
    • num_cycles()
    • is_complete()
    • set_complete()
    • state()
    • num_states()
    • set_expanded_state()
    • expanded_state()
    • num_expanded_states()
    • update()
    • is_equal()
    • is_equal()
    • initialize()
• TrialComputeAddRemove
  • TrialComputeAddRemove
    • perturb_and_acceptance()
• TrialSelect
  • TrialSelect
    • group_index()
    • particle_type()
    • particle_type_name()
    • configuration_index()
    • configuration()
    • get_configuration()
    • set_configuration_index()
    • set_config()
    • config()
    • before_select()
    • select()
    • sel()
    • precompute()
    • mobile()
    • set_mobile()
    • mobile_original()
    • set_mobile_original()
    • anchor()
    • anchor_position()
    • set_trial_state()
    • reset_mobile()
    • probability()
    • mid_stage()
    • set_ghost()
    • is_ghost()
    • printable()
    • are_constraints_satisfied()
    • is_particle_type_set()
    • remove_unphysical_sites()
    • replace_mobile()
    • property()
    • has_property()
    • add_or_set_property()
    • is_isotropic()
• TrialSelectAll
  • TrialSelectAll
    • select()
• TrialSelectParticle
  • TrialSelectParticle
    • precompute()
    • load_coordinates()
    • site()
    • random_particle()
    • random_particle()
    • ghost_particle()
    • ghost_particle()
    • select()
    • select_particle()
• TrialSelectBond
  • TrialSelectBond
    • anchor_site_name()
    • mobile_site_name()
    • precompute()
    • select()
• TrialSelectAngle
  • TrialSelectAngle
    • anchor_site2_name()
    • precompute()
• TrialSelectDihedral
  • TrialSelectDihedral
    • precompute()
• RefPotential
  • RefPotential
• TrialComputeVolume
  • TrialComputeVolume
    • perturb_and_acceptance()
• PerturbAddRemove
  • PerturbAddRemove
    • before_select()
    • perturb()
    • revert()
    • finalize()
    • status_header()
    • status()
• AlwaysReject
  • AlwaysReject
    • AlwaysReject()
    • is_accepted()
• TrialComputeTranslate
  • TrialComputeTranslate
    • perturb_and_acceptance()
• RemoveTrial
  • RemoveTrial
• TrialComputeRemove
  • TrialComputeRemove
    • perturb_and_acceptance()
• MonteCarlo
  • MonteCarlo
    • MonteCarlo()
    • MonteCarlo()
    • begin()
    • parse_args()
    • add_args()
    • resume()
    • clear_arguments()
    • set()
    • random()
    • seed_random()
    • add()
    • configuration()
    • add()
    • add()
    • set()
    • add_to_optimized()
    • add_to_reference()
    • add()
    • set()
    • thermo_params()
    • set()
    • system()
    • initialize_system()
    • trial_factory()
    • analyze_factory()
    • modify_factory()
    • set()
    • criteria()
    • initialize_criteria()
    • add()
    • add()
    • remove_trial()
    • trials()
    • trial()
    • initialize_trials()
    • add()
    • remove_analyze()
    • analyzers()
    • analyze()
    • num_analyzers()
    • initialize_analyzers()
    • add()
    • remove_modify()
    • modifiers()
    • modify()
    • num_modifiers()
    • set()
    • write_checkpoint()
    • run()
    • attempt()
    • reset_trial_stats()
    • run_num_trials()
    • run_until_num_particles()
    • run_for_hours()
    • run_until_complete()
    • run_until_file_exists()
    • set_cycles_to_complete()
    • attempt_trial()
    • write_to_file()
    • next_arg()
    • set_parse_for_num_configs()
    • set_parse_replace()
    • set_parse_for()
    • set_replace_with_index()
    • set_timer()
    • timer()
• Tunable
  • Tunable
    • set_min_and_max()
    • max()
    • min()
    • set_value()
    • value()
    • disable()
    • enable()
    • is_enabled()
    • set_percent_change()
    • set_target()
    • tune()
    • serialize()
    • Tunable()
    • Tunable()
• RemoveAnalyze
  • RemoveAnalyze
• PerturbVolume
  • PerturbVolume
    • uniform_volume()
    • perturb()
    • change_volume()
    • revert()
    • finalize()
    • PerturbVolume()
• Metropolis
  • Metropolis
    • Metropolis()
    • is_accepted()
• Stepper
  • Stepper
    • trials_per_update()
    • trials_per_write()
    • output_file()
    • output_file()
    • output_file_append_phase()
    • empty_output_file()
    • append()
    • rewrite_header()
    • stop_after_phase()
    • start_after_phase()
    • stop_after_cycle()
    • start_after_cycle()
    • configuration_index()
    • configuration()
    • set_state()
    • is_multistate()
    • state()
    • accumulator()
    • get_accumulator()
    • trials_since_update()
    • trials_since_write()
    • is_multistate_aggregate()
    • header()
    • printer()
    • initialize()
    • Stepper()
• Analyze
  • Analyze
    • initialize()
    • trial()
    • update()
    • write()
  • AnalyzeWriteOnly
  • AnalyzeUpdateOnly
• Modify
  • Modify
    • initialize()
    • trial()
    • update()
    • write()
  • ModifyUpdateOnly
• ModifyFactory
  • ModifyFactory
    • add()
    • remove()
    • num()
    • modifiers()
    • modify()
    • initialize()
    • write_to_file()
    • adjust_bounds()
    • trial()
    • set_timer()
    • timer()
• PerturbRemove
  • PerturbRemove
    • perturb()
    • before_select()
    • finalize()
    • revert()
• TrialStage
  • TrialStage
    • reference()
    • ref()
    • is_new_only()
    • rosenbluth()
    • num_steps()
    • set()
    • select()
    • precompute()
    • before_select()
    • select()
    • set()
    • perturb()
    • set_mobile_physical()
    • attempt()
    • mid_stage()
    • are_constraints_satisfied()
    • revert()
    • finalize()
    • tune()
    • status_header()
    • status()
    • serialize()
    • TrialStage()
    • TrialStage()
• Trial
  • Trial
    • weight()
    • weight_per_number_fraction()
    • number_fraction_exclude_type()
    • add_stage()
    • add_stage()
    • add_stage()
    • set()
    • num_stages()
    • stage()
    • num_success()
    • num_attempts()
    • num_auto_reject()
    • increment_num_attempts()
    • acceptance()
    • reset_stats()
    • status_header()
    • name_or_description()
    • status()
    • tune()
    • precompute()
    • set()
    • compute()
    • revert()
    • attempt()
    • description()
    • set_description()
    • Trial()
• TrialMove
  • TrialMove
• TrialVolume
  • TrialVolume
• TrialFactory
  • TrialFactory
    • add()
    • remove()
    • num()
    • trial()
    • random_index()
    • attempt()
    • attempt()
    • last_index()
    • cumulative_probability()
    • revert()
    • status_header()
    • status()
    • reset_stats()
    • tune()
    • precompute()
    • set_timer()
    • timer()
  • TrialFactoryNamed
• TrialTransfer
  • TrialTransfer
• TrialAdd
  • TrialAdd
• TrialTranslate
  • TrialTranslate
• TrialAddRemove
  • TrialAddRemove
• TrialRotate
  • TrialRotate
    • TrialRotate()
• TrialRemove
  • TrialRemove
• AnalyzeFactory
  • AnalyzeFactory
    • initialize()
    • add()
    • remove()
    • num()
    • analyzers()
    • analyze()
    • write_to_file()
    • adjust_bounds()
    • trial()
    • set_timer()
    • timer()
• TrialComputeAdd
  • TrialComputeAdd
    • perturb_and_acceptance()
• OptPotential
  • OptPotential
• PerturbTranslate
  • PerturbTranslate
    • precompute()
    • mid_stage()
    • update_selection()
    • move()
    • move()
• PerturbDistance
  • PerturbDistance
    • precompute()
    • bond_type()
    • old_bond_energy()
    • random_distance()
    • move()
    • PerturbDistance()
• PerturbDistanceAngle
  • PerturbDistanceAngle
    • precompute()
    • angle_type()
    • old_angle_energy()
    • random_angle_radians()
    • place_in_circle()
• PerturbDihedral
  • PerturbDihedral
    • precompute()
    • dihedral_type()
    • old_dihedral_energy()
    • random_dihedral_radians()
    • place_dihedral()
• PerturbRotate
  • PerturbRotate
    • update_selection()
    • update_eulers()
    • move()
    • move()
    • move()
• PerturbAnywhere
  • PerturbAnywhere
    • set_position()
    • move()
• PerturbAdd
  • PerturbAdd
    • PerturbAdd()
    • delay_add()
    • before_select()
    • perturb()
    • add()
    • revert()
    • finalize()
    • status_header()
    • status()
• Rosenbluth
  • Rosenbluth
    • resize()
    • num()
    • store()
    • set_energy()
    • compute()
    • stored()
    • chosen()
    • chosen_energy()
    • chosen_energy_profile()
    • ln_total_rosenbluth()
    • energy()
    • energy_profile()
    • chosen_step()
    • serialize()
    • Rosenbluth()