ensembler.tests package

Submodules

ensembler.tests.test_analysis module

class ensembler.tests.test_analysis.test_BAR(methodName='runTest')

Bases: ensembler.tests.test_analysis.test_ZwanzigEquation

feCalculation

alias of ensembler.analysis.freeEnergyCalculation.bennetAcceptanceRatio

test_free_Energy1()

class ensembler.tests.test_analysis.test_ZwanzigEquation(methodName='runTest')

Bases: unittest.case.TestCase

feCalculation

alias of ensembler.analysis.freeEnergyCalculation.zwanzigEquation

test_constructor()

test_free_Energy1()

class ensembler.tests.test_analysis.test_threeStateZwanzigReweighting(methodName='runTest')

Bases: ensembler.tests.test_analysis.test_ZwanzigEquation

feCalculation

alias of ensembler.analysis.freeEnergyCalculation.threeStateZwanzig

test_free_Energy1()

ensembler.tests.test_conditions module

class ensembler.tests.test_conditions.boxBoundaryCondition(methodName='runTest')

Bases: unittest.case.TestCase

boundary1D = [0, 10]

boundary2D = [[0, 10], [0, 10]]

condition_class

alias of ensembler.conditions.box_conditions.boxBoundaryCondition

setUp() → None

Hook method for setting up the test fixture before exercising it.

test_apply1D()

test_apply2D()

test_constructor()

test_constructor2D()

test_load_str_path()

test_save_obj_str()

tmp_test_dir: str = None

class ensembler.tests.test_conditions.periodicBoundaryCondition(methodName='runTest')

Bases: unittest.case.TestCase

boundary1D = [0, 10]

boundary2D = [[0, 10], [0, 10]]

condition_class

alias of ensembler.conditions.box_conditions.periodicBoundaryCondition

setUp() → None

Hook method for setting up the test fixture before exercising it.

test_apply1D()

test_apply2D()

test_constructor()

test_constructor2D()

test_load_str_path()

test_save_obj_str()

tmp_test_dir = None

class ensembler.tests.test_conditions.positionRestraintCondition(methodName='runTest')

Bases: unittest.case.TestCase

condition_class

alias of ensembler.conditions.restrain_conditions.positionRestraintCondition

setUp() → None

Hook method for setting up the test fixture before exercising it.

test_apply1D()

test_apply2D()

test_constructor()

test_load_str_path()

test_save_obj_str()

tmp_test_dir = None

ensembler.tests.test_conveyorBelt module

class ensembler.tests.test_conveyorBelt.testEnsemble(methodName='runTest')

Bases: unittest.case.TestCase

convBelt

alias of ensembler.ensemble.replicas_dynamic_parameters.conveyorBelt

testTraj()

test_constructor()

test_run_step()

test_run_step_lambda1()

test_run_step_lambda2()

ensembler.tests.test_ensemble module

class ensembler.tests.test_ensemble.test_ReplicaExchangeCls(methodName='runTest')

Bases: unittest.case.TestCase

RE

alias of ensembler.ensemble._replica_graph._replicaExchange

integrator = <ensembler.samplers.stochastic.metropolisMonteCarloIntegrator object>

potential = <ensembler.potentials.OneD.harmonicOscillatorPotential object>

sys = <ensembler.system.basic_system.system object>

test_getTotPot_1DREnsemble()

test_getTraj_1DREnsemble()

test_init_1DREnsemble()

test_init_2DREnsemble()

test_run_1DREnsemble()

test_tearDown() → None

class ensembler.tests.test_ensemble.test_TemperatureReplicaExchangeCls(methodName='runTest')

Bases: unittest.case.TestCase

TRE

alias of ensembler.ensemble.replica_exchange.temperatureReplicaExchange

test_exchange_all()

test_init()

test_run()

test_simulate_good_exchange()

ensembler.tests.test_ensembler module

Unit and regression test for the ensembler package.

ensembler.tests.test_ensembler.test_ensembler_imported()

Sample test, will always pass so long as import statement worked

ensembler.tests.test_potentials module

class ensembler.tests.test_potentials.potentialCls_2D_harmonicOscillatorPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.TwoD.harmonicOscillatorPotential

test_dHdpos2DNPos()

test_energies2DNPos()

class ensembler.tests.test_potentials.potentialCls_2D_sumPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.ND.sumPotentials

test_constructor_ListPotentials()

test_dHdpos()

test_energies()

test_energies_phase_shifted()

class ensembler.tests.test_potentials.potentialCls_2D_torsionPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.TwoD.addedWavePotential

test_constructor_ListPotentials()

test_dHdpos()

test_energies()

test_energies_phase_shifted()

class ensembler.tests.test_potentials.potentialCls_2D_wavePotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.TwoD.wavePotential

test_dHdpos2D1Pos()

test_dHdpos2DNPos()

test_energies2D1Pos()

test_energies2DNPos()

class ensembler.tests.test_potentials.potentialCls_ND_harmonicOscillatorPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.ND.harmonicOscillatorPotential

test_dHdpos3DNPos()

test_energies3DNPos()

class ensembler.tests.test_potentials.potentialCls_ND_sumPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.ND.sumPotentials

test_constructor_ListPotentials()

test_dHdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_addedPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.addedPotentials

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_addedPotentials2D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.TwoD.addedPotentials

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_coulombPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.coulombPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_doubleWellPot1D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.doubleWellPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_flatwell(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.flatwellPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_fourWellPot1D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.fourWellPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_gaussPotential1D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.gaussPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_harmonicOsc1D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.harmonicOscillatorPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_lennardJonesForceFieldPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.lennardJonesForceFieldPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_lennardJonesPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.lennardJonesPotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_metadynamics(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.metadynamicsPotential

test_dVdpos_1Pos()

test_dVdpos_NPos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_metadynamics2D(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.TwoD.metadynamicsPotential

test_dVdpos()

test_dVdpos_1Pos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_perturbedLinearCoupledPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.linearCoupledPotentials

test_constructor()

test_dHdlam()

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_perturbed_envelopedPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.envelopedPotential

test_ene_1Pos()

test_ene_NPos()

test_force_1Pos()

test_force_NPos()

test_s_change()

class ensembler.tests.test_potentials.potentialCls_perturbed_exponentialCoupledPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.exponentialCoupledPotentials

test_constructor()

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_perturbed_hybridCoupledPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.hybridCoupledPotentials

test_constructor()

test_dHdlam()

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_perturbed_lambdaEnvelopedPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.lambdaEDSPotential

test_ene_1Pos()

test_ene_NPos()

test_force_1Pos()

test_force_NPos()

test_s_change()

class ensembler.tests.test_potentials.potentialCls_sumPotentials(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

a = <ensembler.potentials.OneD.harmonicOscillatorPotential object>

b = <ensembler.potentials.OneD.harmonicOscillatorPotential object>

c = <ensembler.potentials.OneD.harmonicOscillatorPotential object>

potential_class

alias of ensembler.potentials.OneD.sumPotentials

test_constructor_ListPotentials()

test_dHdpos()

test_energies()

class ensembler.tests.test_potentials.potentialCls_torsionPotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.torsionPotential

test_constructor_ListPotentials()

test_constructor_SinglePotential()

test_dVdpos()

test_energies()

test_energies_phase_shifted()

test_energies_singlepo_list()

test_energies_singlepot()

class ensembler.tests.test_potentials.potentialCls_wavePotential(methodName='runTest')

Bases: ensembler.tests.test_potentials.test_potentialCls

potential_class

alias of ensembler.potentials.OneD.wavePotential

test_dVdpos()

test_energies()

class ensembler.tests.test_potentials.potentialNDCls(methodName='runTest')

Bases: unittest.case.TestCase

test_instantiationError()

class ensembler.tests.test_potentials.test_potentialCls(methodName='runTest')

Bases: unittest.case.TestCase

potential_class

alias of ensembler.potentials._basicPotentials._potentialCls

setUp() → None

Hook method for setting up the test fixture before exercising it.

test_constructor()

test_load_str_path()

test_save_obj_str()

tmp_test_dir: str = None

ensembler.tests.test_sampler module

class ensembler.tests.test_sampler.standard_IntegratorTests(methodName='runTest')

Bases: unittest.case.TestCase

integrator_class

alias of ensembler.samplers._basicSamplers._samplerCls

setUp() → None

Hook method for setting up the test fixture before exercising it.

test_constructor()

test_load_integrator()

test_save_integrator()

tmp_test_dir: str = None

class ensembler.tests.test_sampler.test_LangevinVelocity_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.stochastic.langevinVelocityIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_Langevin_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.stochastic.langevinIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_MetropolisMonteCarlo_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.stochastic.metropolisMonteCarloIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_MonteCarlo_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.stochastic.metropolisMonteCarloIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_cg_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.optimizers.conjugate_gradient

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_leapFrogIntegrator_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.newtonian.leapFrogIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_positionVerletIntegrator_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.newtonian.positionVerletIntegrator

test_integrate()

test_step()

class ensembler.tests.test_sampler.test_verlocityVerletIntegrator_Integrator(methodName='runTest')

Bases: ensembler.tests.test_sampler.standard_IntegratorTests

integrator_class

alias of ensembler.samplers.newtonian.velocityVerletIntegrator

test_integrate()

test_step()

ensembler.tests.test_system module

class ensembler.tests.test_system.test_System(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

Hook method for setting up the test fixture before exercising it.

system_class

alias of ensembler.system.basic_system.system

test_append_state()

uses init_state, updateEne, randomPos, self.state :return:

test_applyConditions()

NOT IMPLEMENTED!

test_get_Pot()

test_get_Trajectory()

test_initVel()

uses init_state, updateEne, randomPos, self.state :return:

test_load_str_path()

test_propergate()

test_revertStep()

test_save_obj_str()

test_setTemperature()

test_simulate()

test_system_constructor()

test_system_constructor_detail()

uses init_state, updateEne, randomPos, self.state :return:

test_totKin()

uses init_state, updateEne, randomPos, self.state :return:

test_totPot()

uses init_state, updateEne, randomPos, self.state :return:

test_updateEne()

test_updateTemp()

NOT IMPLEMENTED

tmp_test_dir: str = None

class ensembler.tests.test_system.test_edsSystem1D(methodName='runTest')

Bases: ensembler.tests.test_system.test_System

setUp() → None

Hook method for setting up the test fixture before exercising it.

system_class

alias of ensembler.system.eds_system.edsSystem

test_append_state()

uses init_state, updateEne, randomPos, self.state :return:

test_applyConditions()

NOT IMPLEMENTED!

test_get_Pot()

test_initVel()

uses init_state, updateEne, randomPos, self.state :return:

test_propergate()

test_revertStep()

test_setTemperature()

test_simulate()

test_system_constructor()

uses init_state, updateEne, randomPos, self.state :return:

test_system_constructor_detail()

uses init_state, updateEne, randomPos, self.state :return:

test_totKin()

uses init_state, updateEne, randomPos, self.state :return:

test_totPot()

uses init_state, updateEne, randomPos, self.state :return:

test_updateEne()

test_updateTemp()

NOT IMPLEMENTED

tmp_test_dir: str = None

class ensembler.tests.test_system.test_perturbedSystem1D(methodName='runTest')

Bases: ensembler.tests.test_system.test_System

setUp() → None

Hook method for setting up the test fixture before exercising it.

system_class

alias of ensembler.system.perturbed_system.perturbedSystem

test_append_state()

uses init_state, updateEne, randomPos, self.state :return:

test_applyConditions()

NOT IMPLEMENTED!

test_get_Pot()

test_initVel()

uses init_state, updateEne, randomPos, self.state :return:

test_propergate()

test_revertStep()

test_setTemperature()

test_simulate()

test_system_constructor()

uses init_state, updateEne, randomPos, self.state :return:

test_system_constructor_detail()

uses init_state, updateEne, randomPos, self.state :return:

test_totKin()

uses init_state, updateEne, randomPos, self.state :return:

test_totPot()

uses init_state, updateEne, randomPos, self.state :return:

test_updateEne()

test_updateTemp()

NOT IMPLEMENTED

tmp_test_dir: str = None

ensembler.tests.test_visualization module

class ensembler.tests.test_visualization.test_Visualization(methodName='runTest')

Bases: unittest.case.TestCase

class ensembler.tests.test_visualization.test_interactive_widgets(methodName='runTest')

Bases: ensembler.tests.test_visualization.test_Visualization

test_1D_cvb()

test_1D_eds()

class ensembler.tests.test_visualization.test_plot_Animations(methodName='runTest')

Bases: ensembler.tests.test_visualization.test_Visualization

test_1D_animation()

class ensembler.tests.test_visualization.test_plot_ConveyorBelt(methodName='runTest')

Bases: ensembler.tests.test_visualization.test_Visualization

test_1D_plotEnsembler()

class ensembler.tests.test_visualization.test_plot_Potentials(methodName='runTest')

Bases: ensembler.tests.test_visualization.test_Visualization

test_1DPotential_V()

test_plot_1DPotential()

test_plot_1DPotential_dhdpos()

class ensembler.tests.test_visualization.test_plot_Simulations(methodName='runTest')

Bases: ensembler.tests.test_visualization.test_Visualization

test_static_sim_plots()

test_twoD_simulation_ana_plot()

Module contents

Test suite, containing automatic tests.