Index

_

__init__() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig method) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) (ensembler.conditions.box_conditions.boxBoundaryCondition method) (ensembler.conditions.box_conditions.periodicBoundaryCondition method) (ensembler.conditions.restrain_conditions.positionRestraintCondition method) (ensembler.conditions.thermostats.andersonThermostat method) (ensembler.conditions.thermostats.berendsenThermostate method) (ensembler.ensemble.exchange_pattern.Exchange_pattern method) (ensembler.ensemble.replica_exchange.replicaExchangeEnvelopingDistributionSampling method) (ensembler.ensemble.replica_exchange.temperatureReplicaExchange method) (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.ND.harmonicOscillatorPotential method) (ensembler.potentials.ND.sumPotentials method) (ensembler.potentials.OneD._metadynamicsPotentialSympy method) (ensembler.potentials.OneD._timedependendBias method) (ensembler.potentials.OneD.addedPotentials method) (ensembler.potentials.OneD.coulombPotential method) (ensembler.potentials.OneD.doubleWellPotential method) (ensembler.potentials.OneD.dummyPotential method) (ensembler.potentials.OneD.envelopedPotential method) (ensembler.potentials.OneD.exponentialCoupledPotentials method) (ensembler.potentials.OneD.flatwellPotential method) (ensembler.potentials.OneD.fourWellPotential method) (ensembler.potentials.OneD.gaussPotential method) (ensembler.potentials.OneD.harmonicOscillatorPotential method) (ensembler.potentials.OneD.hybridCoupledPotentials method) (ensembler.potentials.OneD.lennardJonesForceFieldPotential method) (ensembler.potentials.OneD.lennardJonesPotential method) (ensembler.potentials.OneD.linearCoupledPotentials method) (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.OneD.sumPotentials method) (ensembler.potentials.OneD.torsionPotential method) (ensembler.potentials.OneD.wavePotential method) (ensembler.potentials.TwoD.addedPotentials method) (ensembler.potentials.TwoD.addedWavePotential method) (ensembler.potentials.TwoD.gaussPotential method) (ensembler.potentials.TwoD.harmonicOscillatorPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) (ensembler.potentials.TwoD.wavePotential method) (ensembler.samplers.newtonian.newtonianSampler method) (ensembler.samplers.optimizers.conjugate_gradient method) (ensembler.samplers.stochastic.langevinIntegrator method) (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator method) (ensembler.samplers.stochastic.monteCarloIntegrator method) (ensembler.system.basic_system.system method) (ensembler.system.eds_system.edsSystem method) (ensembler.system.perturbed_system.perturbedSystem method) _adapt_system_to_exchange_coordinate() (ensembler.ensemble.replica_exchange.replicaExchangeEnvelopingDistributionSampling method) (ensembler.ensemble.replica_exchange.temperatureReplicaExchange method) _baseClass (class in ensembler.util.basic_class)

_boundaryCondition (class in ensembler.conditions.box_conditions) _calc_bar() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) _calc_bar_mpmath() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) _calculate_current_temperature() (ensembler.conditions.thermostats.berendsenThermostate method) _calculate_dvdpos_singlePos_overwrite() (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.OneD.envelopedPotential method) _calculate_efficient() (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) _calculate_implementation_bruteForce() (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) _calculate_implementation_useZwanzig() (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig method) _calculate_meanEfficient() (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) _calculate_mpmath() (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) _calculate_optimize() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) _calculate_scaling_factor() (ensembler.conditions.thermostats.berendsenThermostate method) _collect_replica_energies() (ensembler.ensemble.exchange_pattern.localExchangeScheme method) _do_exchange() (ensembler.ensemble.exchange_pattern.Exchange_pattern method) _find_nearest() (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) _gen_rand_vel() (ensembler.system.basic_system.system method) _init_position() (ensembler.system.basic_system.system method) _init_velocities() (ensembler.system.basic_system.system method) _initialize_functions() (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.ND.harmonicOscillatorPotential method) (ensembler.potentials.ND.sumPotentials method) (ensembler.potentials.OneD.envelopedPotential method) (ensembler.potentials.OneD.sumPotentials method) (ensembler.potentials.TwoD.addedWavePotential method) (ensembler.potentials.TwoD.gaussPotential method) (ensembler.potentials.TwoD.harmonicOscillatorPotential method) (ensembler.potentials.TwoD.wavePotential method) _logsumexp_calc_gromos() (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.OneD.envelopedPotential method) _metadynamicsPotentialSympy (class in ensembler.potentials.OneD) _scale_velocities_fitting_to_temperature() (ensembler.ensemble.replica_exchange.temperatureReplicaExchange method) _swap_coordinates() (ensembler.ensemble.exchange_pattern.localExchangeScheme method) _timedependendBias (class in ensembler.potentials.OneD) _update_current_vars_from_current_state() (ensembler.system.basic_system.system method) _update_dHdLambda() (ensembler.system.perturbed_system.perturbedSystem method) _update_energies() (ensembler.system.basic_system.system method) _update_functions() (ensembler.potentials.ND.sumPotentials method) (ensembler.potentials.OneD.gaussPotential method) (ensembler.potentials.OneD.sumPotentials method) (ensembler.potentials.OneD.torsionPotential method) (ensembler.potentials.OneD.wavePotential method) (ensembler.potentials.TwoD.addedWavePotential method) (ensembler.potentials.TwoD.gaussPotential method) (ensembler.potentials.TwoD.wavePotential method) _update_potential() (ensembler.potentials.OneD._metadynamicsPotentialSympy method) (ensembler.potentials.OneD._timedependendBias method) (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) _update_state_from_traj() (ensembler.system.basic_system.system method) _update_temperature() (ensembler.system.basic_system.system method)

A

a (ensembler.conditions.thermostats.andersonThermostat attribute) (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.fourWellPotential attribute) A (ensembler.potentials.OneD.gaussPotential attribute) a (ensembler.tests.test_potentials.potentialCls_sumPotentials attribute) accept_move() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) add_replica() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) addedPotentials (class in ensembler.potentials.OneD) (class in ensembler.potentials.TwoD) addedWavePotential (class in ensembler.potentials.TwoD) ah (ensembler.potentials.OneD.fourWellPotential attribute) amplitude (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) andersonThermostat (class in ensembler.conditions.thermostats) animation_EDS_trajectory() (in module ensembler.visualisation.animationSimulation) animation_trajectory() (in module ensembler.visualisation.animationSimulation)

append_state() (ensembler.system.basic_system.system method) (ensembler.system.eds_system.edsSystem method) (ensembler.system.perturbed_system.perturbedSystem method) apply() (ensembler.conditions.box_conditions.boxBoundaryCondition method) (ensembler.conditions.box_conditions.periodicBoundaryCondition method) (ensembler.conditions.restrain_conditions.positionRestraintCondition method) (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) apply_conditions() (ensembler.system.basic_system.system method) apply_coupled() (ensembler.conditions.box_conditions.boxBoundaryCondition method) (ensembler.conditions.box_conditions.periodicBoundaryCondition method) (ensembler.conditions.restrain_conditions.positionRestraintCondition method) (ensembler.conditions.thermostats.andersonThermostat method) (ensembler.conditions.thermostats.berendsenThermostate method) (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) apply_mem() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method)

B

b (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.fourWellPotential attribute) (ensembler.tests.test_potentials.potentialCls_sumPotentials attribute) bar (class in ensembler.analysis.freeEnergyCalculation) bennetAcceptanceRatio (class in ensembler.analysis.freeEnergyCalculation) berendsenThermostate (class in ensembler.conditions.thermostats) beta (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute)

bh (ensembler.potentials.OneD.fourWellPotential attribute) bias_potential (ensembler.potentials.OneD.addedPotentials attribute) (ensembler.potentials.OneD.metadynamicsPotential attribute) (ensembler.potentials.TwoD.addedPotentials attribute) (ensembler.potentials.TwoD.metadynamicsPotential attribute) boundary1D (ensembler.tests.test_conditions.boxBoundaryCondition attribute) (ensembler.tests.test_conditions.periodicBoundaryCondition attribute) boundary2D (ensembler.tests.test_conditions.boxBoundaryCondition attribute) (ensembler.tests.test_conditions.periodicBoundaryCondition attribute) boxBoundaryCondition (class in ensembler.conditions.box_conditions) (class in ensembler.tests.test_conditions) build_mem() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method)

C

C (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) c (ensembler.potentials.OneD.fourWellPotential attribute) (ensembler.tests.test_potentials.potentialCls_sumPotentials attribute) c12 (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) c6 (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) calc_lam() (in module ensembler.visualisation.plotConveyorBelt) calculate() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig method) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) calculate_replica_lambda() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) calculate_total_ensemble_energy() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) calculate_total_kinetic_energy() (ensembler.system.basic_system.system method) calculate_total_potential_energy() (ensembler.system.basic_system.system method) cg (class in ensembler.samplers.optimizers) ch (ensembler.potentials.OneD.fourWellPotential attribute) charge1 (ensembler.potentials.OneD.coulombPotential attribute) charge2 (ensembler.potentials.OneD.coulombPotential attribute) check_for_metastep() (ensembler.potentials.OneD._metadynamicsPotentialSympy method) (ensembler.potentials.OneD._timedependendBias method) (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) clear_all_trajs() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) clear_trajectory() (ensembler.system.basic_system.system method) cm2inch() (in module ensembler.visualisation) condition_class (ensembler.tests.test_conditions.boxBoundaryCondition attribute) (ensembler.tests.test_conditions.periodicBoundaryCondition attribute) (ensembler.tests.test_conditions.positionRestraintCondition attribute) conditions() (ensembler.system.basic_system.system property) conjugate_gradient (class in ensembler.samplers.optimizers) constants (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) (ensembler.analysis.freeEnergyCalculation.zwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute)

convBelt (ensembler.tests.test_conveyorBelt.testEnsemble attribute) convergence_limit (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator attribute) convergence_radius (ensembler.analysis.freeEnergyCalculation.bar attribute) (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) conveyorBelt (class in ensembler.ensemble.replicas_dynamic_parameters) coordinate_dimensions (ensembler.ensemble.replica_exchange.replicaExchangeEnvelopingDistributionSampling attribute) (ensembler.ensemble.replica_exchange.temperatureReplicaExchange attribute) (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute) coulombPotential (class in ensembler.potentials.OneD) couple_system() (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) coupling (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) current_forces (ensembler.samplers.newtonian.leapFrogIntegrator attribute) (ensembler.samplers.newtonian.newtonianSampler attribute) (ensembler.samplers.newtonian.positionVerletIntegrator attribute) (ensembler.samplers.newtonian.velocityVerletIntegrator attribute) current_position (ensembler.samplers.newtonian.leapFrogIntegrator attribute) (ensembler.samplers.newtonian.newtonianSampler attribute) (ensembler.samplers.newtonian.positionVerletIntegrator attribute) (ensembler.samplers.newtonian.velocityVerletIntegrator attribute) current_state() (ensembler.system.basic_system.system property) current_velocity (ensembler.samplers.newtonian.leapFrogIntegrator attribute) (ensembler.samplers.newtonian.newtonianSampler attribute) (ensembler.samplers.newtonian.positionVerletIntegrator attribute) (ensembler.samplers.newtonian.velocityVerletIntegrator attribute) currentState (ensembler.system.perturbed_system.perturbedSystem attribute)

D

d (ensembler.potentials.OneD.fourWellPotential attribute) dfEDS (class in ensembler.analysis.freeEnergyCalculation) dh (ensembler.potentials.OneD.fourWellPotential attribute) doubleWellPotential (class in ensembler.potentials.OneD) drawCirc() (in module ensembler.visualisation.plotConveyorBelt)

drawFunicular() (in module ensembler.visualisation.plotConveyorBelt) dt (ensembler.samplers.newtonian.leapFrogIntegrator attribute) (ensembler.samplers.newtonian.newtonianSampler attribute) (ensembler.samplers.newtonian.positionVerletIntegrator attribute) (ensembler.samplers.newtonian.velocityVerletIntegrator attribute) dummyPotential (class in ensembler.potentials.OneD)

E

edsSystem (class in ensembler.system.eds_system) electric_permetivity (ensembler.potentials.OneD.coulombPotential attribute) ene() (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) ensembleCls (in module ensembler.util.ensemblerTypes) ensembler module ensembler.analysis module ensembler.analysis.freeEnergyCalculation module ensembler.conditions module ensembler.conditions.box_conditions module ensembler.conditions.restrain_conditions module ensembler.conditions.thermostats module ensembler.ensemble module ensembler.ensemble.exchange_pattern module ensembler.ensemble.replica_exchange module ensembler.ensemble.replicas_dynamic_parameters module ensembler.ensembler module ensembler.potentials module ensembler.potentials.ND module ensembler.potentials.OneD module ensembler.potentials.TwoD module ensembler.samplers module ensembler.samplers.newtonian module ensembler.samplers.optimizers module ensembler.samplers.stochastic module ensembler.system module ensembler.system.basic_system module ensembler.system.eds_system module ensembler.system.perturbed_system module ensembler.tests module ensembler.tests.test_analysis module ensembler.tests.test_conditions module ensembler.tests.test_conveyorBelt module ensembler.tests.test_ensemble module ensembler.tests.test_ensembler module

ensembler.tests.test_potentials module ensembler.tests.test_sampler module ensembler.tests.test_system module ensembler.tests.test_visualization module ensembler.util module ensembler.util.basic_class module ensembler.util.dataStructure module ensembler.util.ensemblerTypes module ensembler.visualisation module ensembler.visualisation.animationSimulation module ensembler.visualisation.interactive_plots module ensembler.visualisation.plotConveyorBelt module ensembler.visualisation.plotPotentials module ensembler.visualisation.plotSimulations module ensembler.visualisation.style module envelopedPotential (class in ensembler.potentials.ND) (class in ensembler.potentials.OneD) envPot_differentS_overlay_min0_plot() (in module ensembler.visualisation.plotPotentials) envPot_differentS_overlay_plot() (in module ensembler.visualisation.plotPotentials) envPot_diffS_2stateMap_compare() (in module ensembler.visualisation.plotPotentials) envPot_diffS_compare() (in module ensembler.visualisation.plotPotentials) Eoff() (ensembler.potentials.ND.envelopedPotential property) (ensembler.potentials.OneD.envelopedPotential property) eoff() (ensembler.system.eds_system.edsSystem property) Eoff_i() (ensembler.potentials.ND.envelopedPotential property) (ensembler.potentials.OneD.envelopedPotential property) eoffA (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) eoffB (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) Eoffis (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) Eoffs (ensembler.visualisation.interactive_plots.interactive_eds attribute) epsilon (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.samplers.optimizers.cg attribute) (ensembler.samplers.optimizers.conjugate_gradient attribute) equation (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute) exchange() (ensembler.ensemble.exchange_pattern.Exchange_pattern method) (ensembler.ensemble.exchange_pattern.globalExchangeScheme method) (ensembler.ensemble.exchange_pattern.localExchangeScheme method) exchange_criterium() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) exchange_dimensions (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute) exchange_information (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute) exchange_offset (ensembler.ensemble.exchange_pattern.localExchangeScheme attribute) Exchange_pattern (class in ensembler.ensemble.exchange_pattern) exponentialCoupledPotentials (class in ensembler.potentials.OneD)

F

feCalculation (ensembler.tests.test_analysis.test_BAR attribute) (ensembler.tests.test_analysis.test_threeStateZwanzigReweighting attribute) (ensembler.tests.test_analysis.test_ZwanzigEquation attribute) fixedStepSize (ensembler.samplers.stochastic.langevinIntegrator attribute) (ensembler.samplers.stochastic.langevinVelocityIntegrator attribute) (ensembler.samplers.stochastic.monteCarloIntegrator attribute) (ensembler.samplers.stochastic.stochasticSampler attribute)

flatwellPotential (class in ensembler.potentials.OneD) force() (ensembler.potentials.OneD.metadynamicsPotential method) (ensembler.potentials.TwoD.metadynamicsPotential method) forceField (class in ensembler.potentials.OneD) fourWellPotential (class in ensembler.potentials.OneD) functional (ensembler.conditions.restrain_conditions.positionRestraintCondition attribute)

G

gaussPotential (class in ensembler.potentials.OneD) (class in ensembler.potentials.TwoD) get_conveyorbelt_trajectory() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method)

get_replica_trajectories() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) get_trajs() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) globalExchangeScheme (class in ensembler.ensemble.exchange_pattern)

H

HamiltonianReplicaExchange (class in ensembler.ensemble.replica_exchange) harmonicOscillatorPotential (class in ensembler.potentials.ND) (class in ensembler.potentials.OneD) (class in ensembler.potentials.TwoD)

higherbounds (ensembler.conditions.box_conditions._boundaryCondition attribute) hybridCoupledPotentials (class in ensembler.potentials.OneD)

I

i (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) (ensembler.potentials.OneD.sumPotentials attribute) (ensembler.potentials.OneD.torsionPotential attribute) (ensembler.potentials.TwoD.addedWavePotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) init_mem() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method)

initialise() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) (ensembler.system.basic_system.system method) integrator (ensembler.tests.test_ensemble.test_ReplicaExchangeCls attribute) integrator_class (ensembler.tests.test_sampler.standard_IntegratorTests attribute) (ensembler.tests.test_sampler.test_cg_Integrator attribute) (ensembler.tests.test_sampler.test_Langevin_Integrator attribute) (ensembler.tests.test_sampler.test_LangevinVelocity_Integrator attribute) (ensembler.tests.test_sampler.test_leapFrogIntegrator_Integrator attribute) (ensembler.tests.test_sampler.test_MetropolisMonteCarlo_Integrator attribute) (ensembler.tests.test_sampler.test_MonteCarlo_Integrator attribute) (ensembler.tests.test_sampler.test_positionVerletIntegrator_Integrator attribute) (ensembler.tests.test_sampler.test_verlocityVerletIntegrator_Integrator attribute) interactive_conveyor_belt() (in module ensembler.visualisation.interactive_plots) interactive_eds (class in ensembler.visualisation.interactive_plots)

K

k (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute) (ensembler.conditions.thermostats.andersonThermostat attribute) (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute)

kb (ensembler.conditions.thermostats.andersonThermostat attribute) (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute)

L

lam (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) lam() (ensembler.potentials.ND.lambdaEDSPotential property) (ensembler.potentials.OneD.lambdaEDSPotential property) (ensembler.system.perturbed_system.perturbedSystem property) lam_i() (ensembler.potentials.ND.lambdaEDSPotential property) (ensembler.potentials.OneD.lambdaEDSPotential property) lambdaEDSPotential (class in ensembler.potentials.ND) (class in ensembler.potentials.OneD) lamis (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute)

langevinIntegrator (class in ensembler.samplers.stochastic) langevinVelocityIntegrator (class in ensembler.samplers.stochastic) leapFrogIntegrator (class in ensembler.samplers.newtonian) lennardJonesForceFieldPotential (class in ensembler.potentials.OneD) lennardJonesPotential (class in ensembler.potentials.OneD) linearCoupledPotentials (class in ensembler.potentials.OneD) load() (ensembler.util.basic_class._baseClass class method) localExchangeScheme (class in ensembler.ensemble.exchange_pattern) lowerbounds (ensembler.conditions.box_conditions._boundaryCondition attribute)

M

make_eoff_sliders() (ensembler.visualisation.interactive_plots.interactive_eds method) mass() (ensembler.system.basic_system.system property) max_iterations (ensembler.analysis.freeEnergyCalculation.bar attribute) (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) maxIterationTillAccept (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator attribute) maxStepSize (ensembler.samplers.optimizers.optimizer attribute) mean (ensembler.potentials.TwoD.gaussPotential attribute) metadynamicsPotential (class in ensembler.potentials.OneD) (class in ensembler.potentials.TwoD) metropolis_criterion() (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator method) metropolisMonteCarloIntegrator (class in ensembler.samplers.stochastic) min_iterations (ensembler.analysis.freeEnergyCalculation.bar attribute) (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) minStepSize (ensembler.samplers.stochastic.stochasticSampler attribute) module ensembler ensembler.analysis ensembler.analysis.freeEnergyCalculation ensembler.conditions ensembler.conditions.box_conditions ensembler.conditions.restrain_conditions ensembler.conditions.thermostats ensembler.ensemble ensembler.ensemble.exchange_pattern ensembler.ensemble.replica_exchange ensembler.ensemble.replicas_dynamic_parameters ensembler.ensembler ensembler.potentials ensembler.potentials.ND ensembler.potentials.OneD ensembler.potentials.TwoD ensembler.samplers ensembler.samplers.newtonian ensembler.samplers.optimizers ensembler.samplers.stochastic ensembler.system ensembler.system.basic_system ensembler.system.eds_system ensembler.system.perturbed_system ensembler.tests ensembler.tests.test_analysis ensembler.tests.test_conditions ensembler.tests.test_conveyorBelt ensembler.tests.test_ensemble ensembler.tests.test_ensembler ensembler.tests.test_potentials ensembler.tests.test_sampler ensembler.tests.test_system ensembler.tests.test_visualization ensembler.util ensembler.util.basic_class ensembler.util.dataStructure ensembler.util.ensemblerTypes ensembler.visualisation ensembler.visualisation.animationSimulation ensembler.visualisation.interactive_plots ensembler.visualisation.plotConveyorBelt ensembler.visualisation.plotPotentials ensembler.visualisation.plotSimulations ensembler.visualisation.style

monteCarloIntegrator (class in ensembler.samplers.stochastic) mu (ensembler.potentials.OneD.gaussPotential attribute) multiplicity (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) multiState_overlays() (in module ensembler.visualisation.plotPotentials)

N

N (ensembler.conditions.thermostats.andersonThermostat attribute) (ensembler.potentials.OneD.torsionPotential attribute) N_dens (ensembler.conditions.thermostats.andersonThermostat attribute) name (ensembler.conditions.box_conditions.boxBoundaryCondition attribute) (ensembler.conditions.box_conditions.periodicBoundaryCondition attribute) (ensembler.conditions.restrain_conditions.positionRestraintCondition attribute) (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD._metadynamicsPotentialSympy attribute) (ensembler.potentials.OneD._timedependendBias attribute) (ensembler.potentials.OneD.addedPotentials attribute) (ensembler.potentials.OneD.coulombPotential attribute) (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.dummyPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.flatwellPotential attribute) (ensembler.potentials.OneD.fourWellPotential attribute) (ensembler.potentials.OneD.gaussPotential attribute) (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) (ensembler.potentials.OneD.metadynamicsPotential attribute) (ensembler.potentials.OneD.sumPotentials attribute) (ensembler.potentials.OneD.torsionPotential attribute) (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.addedPotentials attribute) (ensembler.potentials.TwoD.addedWavePotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.metadynamicsPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) (ensembler.samplers.newtonian.leapFrogIntegrator attribute) (ensembler.samplers.newtonian.positionVerletIntegrator attribute) (ensembler.samplers.newtonian.velocityVerletIntegrator attribute) (ensembler.samplers.stochastic.langevinIntegrator attribute) (ensembler.samplers.stochastic.langevinVelocityIntegrator attribute) (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator attribute) (ensembler.samplers.stochastic.monteCarloIntegrator attribute) (ensembler.system.basic_system.system attribute) (ensembler.system.eds_system.edsSystem attribute) (ensembler.system.perturbed_system.perturbedSystem attribute) (ensembler.util.basic_class._baseClass attribute)

nDimensions (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) (ensembler.system.basic_system.system attribute) newtonianSampler (class in ensembler.samplers.newtonian) notImplementedERR() (in module ensembler.util.basic_class) nParticles (ensembler.system.basic_system.system attribute) nPotentials (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD.sumPotentials attribute) nStates (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) (ensembler.system.basic_system.system attribute) nstates (ensembler.visualisation.interactive_plots.interactive_eds attribute) nSteps_between_trials (ensembler.ensemble.replica_exchange.HamiltonianReplicaExchange attribute) (ensembler.ensemble.replica_exchange.replicaExchangeEnvelopingDistributionSampling attribute) (ensembler.ensemble.replica_exchange.temperatureReplicaExchange attribute) (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute) nWavePotentials (ensembler.potentials.TwoD.addedWavePotential attribute)

O

oneD_biased_simulation_analysis_plot() (in module ensembler.visualisation.plotSimulations) oneD_simulation_analysis_plot() (in module ensembler.visualisation.plotSimulations)

optimize() (ensembler.samplers.optimizers.conjugate_gradient method) optimizer (class in ensembler.samplers.optimizers)

P

periodicBoundaryCondition (class in ensembler.conditions.box_conditions) (class in ensembler.tests.test_conditions) perturbedSystem (class in ensembler.system.perturbed_system) phase (ensembler.potentials.OneD.torsionPotential attribute) phase_shift (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) plot_1DPotential() (in module ensembler.visualisation.plotPotentials) plot_1DPotential_dhdpos() (in module ensembler.visualisation.plotPotentials) plot_1DPotential_Termoverlay() (in module ensembler.visualisation.plotPotentials) plot_1DPotential_V() (in module ensembler.visualisation.plotPotentials) plot_2D_2State_EDS_potential() (in module ensembler.visualisation.plotPotentials) plot_2D_2State_EDS_potential_sDependency() (in module ensembler.visualisation.plotPotentials) plot_2D_2states() (in module ensembler.visualisation.plotPotentials) plot_2D_potential_V() (in module ensembler.visualisation.plotPotentials) plot_2DPotential() (in module ensembler.visualisation.plotPotentials) plot_2perturbedEnergy_landscape() (in module ensembler.visualisation.plotPotentials) plot_envelopedPotential_2State_System() (in module ensembler.visualisation.plotPotentials) plot_envelopedPotential_system() (in module ensembler.visualisation.plotPotentials) plot_potential() (in module ensembler.visualisation.plotPotentials) plotEnsembler() (in module ensembler.visualisation.plotConveyorBelt) position (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD._metadynamicsPotentialSympy attribute) (ensembler.potentials.OneD._timedependendBias attribute) (ensembler.potentials.OneD.addedPotentials attribute) (ensembler.potentials.OneD.coulombPotential attribute) (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.dummyPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.fourWellPotential attribute) (ensembler.potentials.OneD.gaussPotential attribute) (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) (ensembler.potentials.OneD.metadynamicsPotential attribute) (ensembler.potentials.OneD.sumPotentials attribute) (ensembler.potentials.OneD.torsionPotential attribute) (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.addedPotentials attribute) (ensembler.potentials.TwoD.addedWavePotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.metadynamicsPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) position() (ensembler.system.basic_system.system property) position_0 (ensembler.conditions.restrain_conditions.positionRestraintCondition attribute) positionRestraintCondition (class in ensembler.conditions.restrain_conditions) (class in ensembler.tests.test_conditions) positionVerletIntegrator (class in ensembler.samplers.newtonian) posShift (ensembler.samplers.stochastic.stochasticSampler attribute) potential (ensembler.tests.test_ensemble.test_ReplicaExchangeCls attribute)

potential() (ensembler.system.basic_system.system property) potential_class (ensembler.tests.test_potentials.potentialCls_2D_harmonicOscillatorPotential attribute) (ensembler.tests.test_potentials.potentialCls_2D_sumPotentials attribute) (ensembler.tests.test_potentials.potentialCls_2D_torsionPotential attribute) (ensembler.tests.test_potentials.potentialCls_2D_wavePotential attribute) (ensembler.tests.test_potentials.potentialCls_addedPotentials attribute) (ensembler.tests.test_potentials.potentialCls_addedPotentials2D attribute) (ensembler.tests.test_potentials.potentialCls_coulombPotential attribute) (ensembler.tests.test_potentials.potentialCls_doubleWellPot1D attribute) (ensembler.tests.test_potentials.potentialCls_flatwell attribute) (ensembler.tests.test_potentials.potentialCls_fourWellPot1D attribute) (ensembler.tests.test_potentials.potentialCls_gaussPotential1D attribute) (ensembler.tests.test_potentials.potentialCls_harmonicOsc1D attribute) (ensembler.tests.test_potentials.potentialCls_lennardJonesForceFieldPotential attribute) (ensembler.tests.test_potentials.potentialCls_lennardJonesPotential attribute) (ensembler.tests.test_potentials.potentialCls_metadynamics attribute) (ensembler.tests.test_potentials.potentialCls_metadynamics2D attribute) (ensembler.tests.test_potentials.potentialCls_ND_harmonicOscillatorPotential attribute) (ensembler.tests.test_potentials.potentialCls_ND_sumPotentials attribute) (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials attribute) (ensembler.tests.test_potentials.potentialCls_perturbed_exponentialCoupledPotentials attribute) (ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials attribute) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials attribute) (ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials attribute) (ensembler.tests.test_potentials.potentialCls_sumPotentials attribute) (ensembler.tests.test_potentials.potentialCls_torsionPotential attribute) (ensembler.tests.test_potentials.potentialCls_wavePotential attribute) (ensembler.tests.test_potentials.test_potentialCls attribute) potentialCls_2D_harmonicOscillatorPotential (class in ensembler.tests.test_potentials) potentialCls_2D_sumPotentials (class in ensembler.tests.test_potentials) potentialCls_2D_torsionPotential (class in ensembler.tests.test_potentials) potentialCls_2D_wavePotential (class in ensembler.tests.test_potentials) potentialCls_addedPotentials (class in ensembler.tests.test_potentials) potentialCls_addedPotentials2D (class in ensembler.tests.test_potentials) potentialCls_coulombPotential (class in ensembler.tests.test_potentials) potentialCls_doubleWellPot1D (class in ensembler.tests.test_potentials) potentialCls_flatwell (class in ensembler.tests.test_potentials) potentialCls_fourWellPot1D (class in ensembler.tests.test_potentials) potentialCls_gaussPotential1D (class in ensembler.tests.test_potentials) potentialCls_harmonicOsc1D (class in ensembler.tests.test_potentials) potentialCls_lennardJonesForceFieldPotential (class in ensembler.tests.test_potentials) potentialCls_lennardJonesPotential (class in ensembler.tests.test_potentials) potentialCls_metadynamics (class in ensembler.tests.test_potentials) potentialCls_metadynamics2D (class in ensembler.tests.test_potentials) potentialCls_ND_harmonicOscillatorPotential (class in ensembler.tests.test_potentials) potentialCls_ND_sumPotentials (class in ensembler.tests.test_potentials) potentialCls_perturbed_envelopedPotentials (class in ensembler.tests.test_potentials) potentialCls_perturbed_exponentialCoupledPotentials (class in ensembler.tests.test_potentials) potentialCls_perturbed_hybridCoupledPotentials (class in ensembler.tests.test_potentials) potentialCls_perturbed_lambdaEnvelopedPotentials (class in ensembler.tests.test_potentials) potentialCls_perturbedLinearCoupledPotentials (class in ensembler.tests.test_potentials) potentialCls_sumPotentials (class in ensembler.tests.test_potentials) potentialCls_torsionPotential (class in ensembler.tests.test_potentials) potentialCls_wavePotential (class in ensembler.tests.test_potentials) potentialNDCls (class in ensembler.tests.test_potentials) potentials (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD.sumPotentials attribute) propagate() (ensembler.system.basic_system.system method)

R

r_shift (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) random_position() (ensembler.system.basic_system.system method) random_shift() (ensembler.samplers.stochastic.stochasticSampler method) RE (ensembler.tests.test_ensemble.test_ReplicaExchangeCls attribute) redraw() (ensembler.visualisation.interactive_plots.interactive_eds method) redraw_eoff() (ensembler.visualisation.interactive_plots.interactive_eds method) redraw_s() (ensembler.visualisation.interactive_plots.interactive_eds method) redraw_states() (ensembler.visualisation.interactive_plots.interactive_eds method)

replica_graph (ensembler.ensemble.exchange_pattern.Exchange_pattern attribute) replica_graph_dimensions (ensembler.ensemble.replica_exchange.replicaExchangeEnvelopingDistributionSampling attribute) (ensembler.ensemble.replica_exchange.temperatureReplicaExchange attribute) (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute) replicaExchangeEnvelopingDistributionSampling (class in ensembler.ensemble.replica_exchange) resolution (ensembler.samplers.stochastic.stochasticSampler attribute) Restraint (class in ensembler.conditions.restrain_conditions) revert() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) revert_step() (ensembler.system.basic_system.system method) run() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method)

S

s (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.visualisation.interactive_plots.interactive_eds attribute) s() (ensembler.potentials.ND.envelopedPotential property) (ensembler.potentials.OneD.envelopedPotential property) (ensembler.system.eds_system.edsSystem property) s_i() (ensembler.potentials.ND.envelopedPotential property) (ensembler.potentials.OneD.envelopedPotential property) sampler() (ensembler.system.basic_system.system property) save() (ensembler.util.basic_class._baseClass method) set_current_state() (ensembler.system.basic_system.system method) (ensembler.system.eds_system.edsSystem method) (ensembler.system.perturbed_system.perturbedSystem method) set_degrees() (ensembler.potentials.OneD.torsionPotential method) (ensembler.potentials.OneD.wavePotential method) (ensembler.potentials.TwoD.addedWavePotential method) (ensembler.potentials.TwoD.wavePotential method) set_Eoff() (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.OneD.envelopedPotential method) (ensembler.potentials.OneD.exponentialCoupledPotentials method) (ensembler.potentials.OneD.hybridCoupledPotentials method) set_eoff() (ensembler.system.eds_system.edsSystem method) set_lam() (ensembler.potentials.ND.lambdaEDSPotential method) (ensembler.potentials.OneD.lambdaEDSPotential method) set_lambda() (ensembler.system.perturbed_system.perturbedSystem method) set_parameters() (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio method) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation method) set_phaseshift() (ensembler.potentials.TwoD.wavePotential method) set_position() (ensembler.system.basic_system.system method) set_radians() (ensembler.potentials.OneD.torsionPotential method) (ensembler.potentials.OneD.wavePotential method) (ensembler.potentials.TwoD.addedWavePotential method) (ensembler.potentials.TwoD.wavePotential method) set_s() (ensembler.potentials.ND.envelopedPotential method) (ensembler.potentials.OneD.envelopedPotential method) (ensembler.potentials.OneD.exponentialCoupledPotentials method) (ensembler.potentials.OneD.hybridCoupledPotentials method) (ensembler.system.eds_system.edsSystem method) set_simulation_n_steps_between_trials() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) set_temperature() (ensembler.system.basic_system.system method) set_velocities() (ensembler.system.basic_system.system method) setUp() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) (ensembler.tests.test_potentials.test_potentialCls method) (ensembler.tests.test_sampler.standard_IntegratorTests method) (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method)

sigma (ensembler.potentials.OneD.gaussPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) significant_decimals() (in module ensembler.visualisation.plotPotentials) simulate() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) (ensembler.system.basic_system.system method) simulation_analysis_plot() (in module ensembler.visualisation.plotSimulations) sis (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) spaceRange (ensembler.samplers.stochastic.stochasticSampler attribute) spline() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt static method) standard_IntegratorTests (class in ensembler.tests.test_sampler) state (ensembler.system.basic_system.system attribute) (ensembler.system.eds_system.edsSystem attribute) (ensembler.system.perturbed_system.perturbedSystem attribute) step() (ensembler.samplers.newtonian.leapFrogIntegrator method) (ensembler.samplers.newtonian.positionVerletIntegrator method) (ensembler.samplers.newtonian.velocityVerletIntegrator method) (ensembler.samplers.optimizers.conjugate_gradient method) (ensembler.samplers.stochastic.langevinIntegrator method) (ensembler.samplers.stochastic.metropolisMonteCarloIntegrator method) (ensembler.samplers.stochastic.monteCarloIntegrator method) step_size_coefficient (ensembler.samplers.stochastic.stochasticSampler attribute) stochasticSampler (class in ensembler.samplers.stochastic) sumPotentials (class in ensembler.potentials.ND) (class in ensembler.potentials.OneD) sys (ensembler.tests.test_ensemble.test_ReplicaExchangeCls attribute) system (class in ensembler.system.basic_system) (ensembler.potentials.TwoD.metadynamicsPotential attribute) system_class (ensembler.tests.test_system.test_edsSystem1D attribute) (ensembler.tests.test_system.test_perturbedSystem1D attribute) (ensembler.tests.test_system.test_System attribute) system_trajs (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt attribute)

T

T (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute) (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) temp (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) temperature (ensembler.conditions.thermostats.andersonThermostat attribute) temperature() (ensembler.system.basic_system.system property) temperature_noise_range (ensembler.conditions.thermostats.andersonThermostat attribute) temperatureReplicaExchange (class in ensembler.ensemble.replica_exchange) test_1D_animation() (ensembler.tests.test_visualization.test_plot_Animations method) test_1D_cvb() (ensembler.tests.test_visualization.test_interactive_widgets method) test_1D_eds() (ensembler.tests.test_visualization.test_interactive_widgets method) test_1D_plotEnsembler() (ensembler.tests.test_visualization.test_plot_ConveyorBelt method) test_1DPotential_V() (ensembler.tests.test_visualization.test_plot_Potentials method) test_append_state() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_apply1D() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) test_apply2D() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) test_applyConditions() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_BAR (class in ensembler.tests.test_analysis) test_cg_Integrator (class in ensembler.tests.test_sampler) test_constructor() (ensembler.tests.test_analysis.test_ZwanzigEquation method) (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) (ensembler.tests.test_conveyorBelt.testEnsemble method) (ensembler.tests.test_potentials.potentialCls_perturbed_exponentialCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials method) (ensembler.tests.test_potentials.test_potentialCls method) (ensembler.tests.test_sampler.standard_IntegratorTests method) test_constructor2D() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) test_constructor_ListPotentials() (ensembler.tests.test_potentials.potentialCls_2D_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_2D_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_ND_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_torsionPotential method) test_constructor_SinglePotential() (ensembler.tests.test_potentials.potentialCls_torsionPotential method) test_dHdlam() (ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials method) test_dHdpos() (ensembler.tests.test_potentials.potentialCls_2D_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_2D_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_ND_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_sumPotentials method) test_dHdpos2D1Pos() (ensembler.tests.test_potentials.potentialCls_2D_wavePotential method) test_dHdpos2DNPos() (ensembler.tests.test_potentials.potentialCls_2D_harmonicOscillatorPotential method) (ensembler.tests.test_potentials.potentialCls_2D_wavePotential method) test_dHdpos3DNPos() (ensembler.tests.test_potentials.potentialCls_ND_harmonicOscillatorPotential method) test_dVdpos() (ensembler.tests.test_potentials.potentialCls_addedPotentials method) (ensembler.tests.test_potentials.potentialCls_addedPotentials2D method) (ensembler.tests.test_potentials.potentialCls_coulombPotential method) (ensembler.tests.test_potentials.potentialCls_doubleWellPot1D method) (ensembler.tests.test_potentials.potentialCls_flatwell method) (ensembler.tests.test_potentials.potentialCls_fourWellPot1D method) (ensembler.tests.test_potentials.potentialCls_gaussPotential1D method) (ensembler.tests.test_potentials.potentialCls_harmonicOsc1D method) (ensembler.tests.test_potentials.potentialCls_lennardJonesForceFieldPotential method) (ensembler.tests.test_potentials.potentialCls_lennardJonesPotential method) (ensembler.tests.test_potentials.potentialCls_metadynamics2D method) (ensembler.tests.test_potentials.potentialCls_perturbed_exponentialCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_wavePotential method) test_dVdpos_1Pos() (ensembler.tests.test_potentials.potentialCls_metadynamics method) (ensembler.tests.test_potentials.potentialCls_metadynamics2D method) test_dVdpos_NPos() (ensembler.tests.test_potentials.potentialCls_metadynamics method) test_edsSystem1D (class in ensembler.tests.test_system) test_ene_1Pos() (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials method) test_ene_NPos() (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials method) test_energies() (ensembler.tests.test_potentials.potentialCls_2D_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_2D_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_addedPotentials method) (ensembler.tests.test_potentials.potentialCls_addedPotentials2D method) (ensembler.tests.test_potentials.potentialCls_coulombPotential method) (ensembler.tests.test_potentials.potentialCls_doubleWellPot1D method) (ensembler.tests.test_potentials.potentialCls_flatwell method) (ensembler.tests.test_potentials.potentialCls_fourWellPot1D method) (ensembler.tests.test_potentials.potentialCls_gaussPotential1D method) (ensembler.tests.test_potentials.potentialCls_harmonicOsc1D method) (ensembler.tests.test_potentials.potentialCls_lennardJonesForceFieldPotential method) (ensembler.tests.test_potentials.potentialCls_lennardJonesPotential method) (ensembler.tests.test_potentials.potentialCls_metadynamics method) (ensembler.tests.test_potentials.potentialCls_metadynamics2D method) (ensembler.tests.test_potentials.potentialCls_ND_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_exponentialCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials method) (ensembler.tests.test_potentials.potentialCls_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_wavePotential method) test_energies2D1Pos() (ensembler.tests.test_potentials.potentialCls_2D_wavePotential method) test_energies2DNPos() (ensembler.tests.test_potentials.potentialCls_2D_harmonicOscillatorPotential method) (ensembler.tests.test_potentials.potentialCls_2D_wavePotential method) test_energies3DNPos() (ensembler.tests.test_potentials.potentialCls_ND_harmonicOscillatorPotential method) test_energies_phase_shifted() (ensembler.tests.test_potentials.potentialCls_2D_sumPotentials method) (ensembler.tests.test_potentials.potentialCls_2D_torsionPotential method) (ensembler.tests.test_potentials.potentialCls_torsionPotential method) test_energies_singlepo_list() (ensembler.tests.test_potentials.potentialCls_torsionPotential method) test_energies_singlepot() (ensembler.tests.test_potentials.potentialCls_torsionPotential method) test_ensembler_imported() (in module ensembler.tests.test_ensembler) test_exchange_all() (ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls method) test_force_1Pos() (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials method) test_force_NPos() (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials method) test_free_Energy1() (ensembler.tests.test_analysis.test_BAR method) (ensembler.tests.test_analysis.test_threeStateZwanzigReweighting method) (ensembler.tests.test_analysis.test_ZwanzigEquation method)

test_get_Pot() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_get_Trajectory() (ensembler.tests.test_system.test_System method) test_getTotPot_1DREnsemble() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_getTraj_1DREnsemble() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_init() (ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls method) test_init_1DREnsemble() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_init_2DREnsemble() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_initVel() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_instantiationError() (ensembler.tests.test_potentials.potentialNDCls method) test_integrate() (ensembler.tests.test_sampler.test_cg_Integrator method) (ensembler.tests.test_sampler.test_Langevin_Integrator method) (ensembler.tests.test_sampler.test_LangevinVelocity_Integrator method) (ensembler.tests.test_sampler.test_leapFrogIntegrator_Integrator method) (ensembler.tests.test_sampler.test_MetropolisMonteCarlo_Integrator method) (ensembler.tests.test_sampler.test_MonteCarlo_Integrator method) (ensembler.tests.test_sampler.test_positionVerletIntegrator_Integrator method) (ensembler.tests.test_sampler.test_verlocityVerletIntegrator_Integrator method) test_interactive_widgets (class in ensembler.tests.test_visualization) test_Langevin_Integrator (class in ensembler.tests.test_sampler) test_LangevinVelocity_Integrator (class in ensembler.tests.test_sampler) test_leapFrogIntegrator_Integrator (class in ensembler.tests.test_sampler) test_load_integrator() (ensembler.tests.test_sampler.standard_IntegratorTests method) test_load_str_path() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) (ensembler.tests.test_potentials.test_potentialCls method) (ensembler.tests.test_system.test_System method) test_MetropolisMonteCarlo_Integrator (class in ensembler.tests.test_sampler) test_MonteCarlo_Integrator (class in ensembler.tests.test_sampler) test_perturbedSystem1D (class in ensembler.tests.test_system) test_plot_1DPotential() (ensembler.tests.test_visualization.test_plot_Potentials method) test_plot_1DPotential_dhdpos() (ensembler.tests.test_visualization.test_plot_Potentials method) test_plot_Animations (class in ensembler.tests.test_visualization) test_plot_ConveyorBelt (class in ensembler.tests.test_visualization) test_plot_Potentials (class in ensembler.tests.test_visualization) test_plot_Simulations (class in ensembler.tests.test_visualization) test_positionVerletIntegrator_Integrator (class in ensembler.tests.test_sampler) test_potentialCls (class in ensembler.tests.test_potentials) test_propergate() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_ReplicaExchangeCls (class in ensembler.tests.test_ensemble) test_revertStep() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_run() (ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls method) test_run_1DREnsemble() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_run_step() (ensembler.tests.test_conveyorBelt.testEnsemble method) test_run_step_lambda1() (ensembler.tests.test_conveyorBelt.testEnsemble method) test_run_step_lambda2() (ensembler.tests.test_conveyorBelt.testEnsemble method) test_s_change() (ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials method) (ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials method) test_save_integrator() (ensembler.tests.test_sampler.standard_IntegratorTests method) test_save_obj_str() (ensembler.tests.test_conditions.boxBoundaryCondition method) (ensembler.tests.test_conditions.periodicBoundaryCondition method) (ensembler.tests.test_conditions.positionRestraintCondition method) (ensembler.tests.test_potentials.test_potentialCls method) (ensembler.tests.test_system.test_System method) test_setTemperature() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_simulate() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_simulate_good_exchange() (ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls method) test_static_sim_plots() (ensembler.tests.test_visualization.test_plot_Simulations method) test_step() (ensembler.tests.test_sampler.test_cg_Integrator method) (ensembler.tests.test_sampler.test_Langevin_Integrator method) (ensembler.tests.test_sampler.test_LangevinVelocity_Integrator method) (ensembler.tests.test_sampler.test_leapFrogIntegrator_Integrator method) (ensembler.tests.test_sampler.test_MetropolisMonteCarlo_Integrator method) (ensembler.tests.test_sampler.test_MonteCarlo_Integrator method) (ensembler.tests.test_sampler.test_positionVerletIntegrator_Integrator method) (ensembler.tests.test_sampler.test_verlocityVerletIntegrator_Integrator method) test_System (class in ensembler.tests.test_system) test_system_constructor() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_system_constructor_detail() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_tearDown() (ensembler.tests.test_ensemble.test_ReplicaExchangeCls method) test_TemperatureReplicaExchangeCls (class in ensembler.tests.test_ensemble) test_threeStateZwanzigReweighting (class in ensembler.tests.test_analysis) test_totKin() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_totPot() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_twoD_simulation_ana_plot() (ensembler.tests.test_visualization.test_plot_Simulations method) test_updateEne() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_updateTemp() (ensembler.tests.test_system.test_edsSystem1D method) (ensembler.tests.test_system.test_perturbedSystem1D method) (ensembler.tests.test_system.test_System method) test_verlocityVerletIntegrator_Integrator (class in ensembler.tests.test_sampler) test_Visualization (class in ensembler.tests.test_visualization) test_ZwanzigEquation (class in ensembler.tests.test_analysis) testEnsemble (class in ensembler.tests.test_conveyorBelt) testTraj() (ensembler.tests.test_conveyorBelt.testEnsemble method) thermostat (class in ensembler.conditions.thermostats) threeStateZwanzig (class in ensembler.analysis.freeEnergyCalculation) tmp_test_dir (ensembler.tests.test_conditions.boxBoundaryCondition attribute) (ensembler.tests.test_conditions.periodicBoundaryCondition attribute) (ensembler.tests.test_conditions.positionRestraintCondition attribute) (ensembler.tests.test_potentials.test_potentialCls attribute) (ensembler.tests.test_sampler.standard_IntegratorTests attribute) (ensembler.tests.test_system.test_edsSystem1D attribute) (ensembler.tests.test_system.test_perturbedSystem1D attribute) (ensembler.tests.test_system.test_System attribute) torsionPotential (class in ensembler.potentials.OneD) total_kinetic_energy() (ensembler.system.basic_system.system property) total_potential_energy() (ensembler.system.basic_system.system property) total_system_energy() (ensembler.system.basic_system.system property) trajectory() (ensembler.system.basic_system.system property) TRE (ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls attribute) twoD_simulation_analysis_plot() (in module ensembler.visualisation.plotSimulations)

U

update_all_lambda() (ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt method) update_current_state() (ensembler.system.basic_system.system method) (ensembler.system.eds_system.edsSystem method) (ensembler.system.perturbed_system.perturbedSystem method) update_exchange_information() (ensembler.ensemble.exchange_pattern.Exchange_pattern method)

update_positon() (ensembler.samplers.stochastic.langevinIntegrator method) (ensembler.samplers.stochastic.langevinVelocityIntegrator method) update_system_properties() (ensembler.system.basic_system.system method) (ensembler.system.perturbed_system.perturbedSystem method) updateEnsembler() (in module ensembler.visualisation.plotConveyorBelt)

V

V_dim (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) V_functional (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.ND.sumPotentials attribute) (ensembler.potentials.OneD.coulombPotential attribute) (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.fourWellPotential attribute) (ensembler.potentials.OneD.gaussPotential attribute) (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.potentials.OneD.sumPotentials attribute) (ensembler.potentials.OneD.torsionPotential attribute) (ensembler.potentials.OneD.wavePotential attribute) (ensembler.potentials.TwoD.addedWavePotential attribute) (ensembler.potentials.TwoD.gaussPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.wavePotential attribute) V_is (ensembler.visualisation.interactive_plots.interactive_eds attribute) V_is() (ensembler.potentials.ND.envelopedPotential property) (ensembler.potentials.OneD.envelopedPotential property)

Va (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) Vb (ensembler.potentials.OneD.exponentialCoupledPotentials attribute) (ensembler.potentials.OneD.hybridCoupledPotentials attribute) (ensembler.potentials.OneD.linearCoupledPotentials attribute) velocity() (ensembler.system.basic_system.system property) velocityVerletIntegrator (class in ensembler.samplers.newtonian) verbose (ensembler.conditions.box_conditions.periodicBoundaryCondition attribute) verbose() (ensembler.util.basic_class._baseClass property) Vi (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute) Vi_i (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) Vi_j (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) Vis (ensembler.potentials.ND.envelopedPotential attribute) (ensembler.potentials.ND.lambdaEDSPotential attribute) (ensembler.potentials.OneD.envelopedPotential attribute) (ensembler.potentials.OneD.lambdaEDSPotential attribute) Vj (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute) (ensembler.analysis.freeEnergyCalculation.zwanzigEquation attribute) Vj_i (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) Vj_j (ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio attribute) Vmax (ensembler.potentials.OneD.doubleWellPotential attribute) (ensembler.potentials.OneD.fourWellPotential attribute) Voff (ensembler.potentials.ND.harmonicOscillatorPotential attribute) (ensembler.potentials.TwoD.harmonicOscillatorPotential attribute) Vr (ensembler.analysis.freeEnergyCalculation.threeStateZwanzig attribute)

W

wave_potentials (ensembler.potentials.TwoD.addedWavePotential attribute) wavePotential (class in ensembler.potentials.OneD) (class in ensembler.potentials.TwoD)

wavePotentials (ensembler.potentials.OneD.torsionPotential attribute) write_trajectory() (ensembler.system.basic_system.system method)

X

x_max (ensembler.potentials.OneD.flatwellPotential attribute) x_min (ensembler.potentials.OneD.flatwellPotential attribute)

x_shift (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute)

Y

y_max (ensembler.potentials.OneD.flatwellPotential attribute) y_min (ensembler.potentials.OneD.flatwellPotential attribute) y_shift (ensembler.potentials.OneD.dummyPotential attribute) (ensembler.potentials.OneD.harmonicOscillatorPotential attribute) (ensembler.potentials.OneD.lennardJonesForceFieldPotential attribute) (ensembler.potentials.OneD.lennardJonesPotential attribute) (ensembler.potentials.OneD.wavePotential attribute)

yOffset (ensembler.potentials.TwoD.wavePotential attribute)

Z

zwanzig (class in ensembler.analysis.freeEnergyCalculation)

zwanzigEquation (class in ensembler.analysis.freeEnergyCalculation)