Index

_

__init__() (narupatools.app.client.Client method) (narupatools.app.client.OnFrameReceivedCallback method) (narupatools.app.session.OnTargetChanged method) (narupatools.app.session.Session method) (narupatools.app.shared_state.OnSharedStateAddedCallback method) (narupatools.app.shared_state.OnSharedStateChangedCallback method) (narupatools.app.shared_state.OnSharedStateRemovedCallback method) (narupatools.app.shared_state.SharedStateView method) (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.calculators.protocols.CalculatorSetAtoms method) (narupatools.ase.constraints.constraint.ASECellConstraint method) (narupatools.ase.constraints.constraint.ASEConstraint method) (narupatools.ase.constraints.constraint.ASEEnergyConstraint method) (narupatools.ase.constraints.constraint.ASEMomentaConstraint method) (narupatools.ase.constraints.constraint.ASEStressConstraint method) (narupatools.ase.constraints.imd_constraint.ASEAtomsWrapper method) (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.ase.constraints.observer.ASEObserver method) (narupatools.ase.converter.ASEConverter method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.imd.ASEDynamicsSupportsInteractions method) (narupatools.ase.imd.ASEIMDFeature method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.ase.system.ASESystem method) (narupatools.ase.trajectory.ASETrajectory method) (narupatools.core.broadcastable.Broadcastable method) (narupatools.core.broadcastable.Broadcaster method) (narupatools.core.dynamics.OnPostStepCallback method) (narupatools.core.dynamics.OnPreStepCallback method) (narupatools.core.dynamics.OnResetCallback method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) (narupatools.core.health_check.HealthCheck method) (narupatools.core.playable.Playable method) (narupatools.core.units.Prefix method) (narupatools.core.units.UnfinishedUnitOrQuantity method) (narupatools.core.units.Unit method) (narupatools.core.units.UnitConversion method) (narupatools.core.units.UnitSystem method) (narupatools.frame.converter.DictConverter method) (narupatools.frame.converter.FrameConverter method) (narupatools.frame.fields.FrameKey method) (narupatools.frame.frame.NarupaFrame method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.frame_producer.OnFrameProducedCallback method) (narupatools.frame.frame_producer.ProduceFrameCallback method) (narupatools.frame.frame_source.FrameSource method) (narupatools.frame.frame_source.FrameSourceWithNotify method) (narupatools.frame.frame_source.OnFieldsChangedCallback method) (narupatools.frame.frame_source.TrajectorySource method) (narupatools.frame.hdf5.trajectory.HDF5Topology method) (narupatools.frame.hdf5.trajectory.HDF5Trajectory method) (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.frame.hdf5.trajectory.InteractionView method) (narupatools.frame.hdf5.writer.HDF5Writer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.imd.feature.DynamicInteractions method) (narupatools.imd.feature.DynamicsSupportsInteractions method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature.OnEndInteractionCallback method) (narupatools.imd.feature.OnStartInteractionCallback method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.imd.forces.InteractiveForce method) (narupatools.imd.interaction.Interaction method) (narupatools.imd.interaction_source.InteractionsSource method) (narupatools.lammps.calculator.LAMMPSCalculator method) (narupatools.lammps.converter.LAMMPSConverter method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.lammps.dynamics.LAMMPSInteraction method) (narupatools.lammps.output_capture.OutputCapture method) (narupatools.lammps.region.Box method) (narupatools.lammps.region.Region method) (narupatools.lammps.region.RegionSpecification method) (narupatools.lammps.simulation.Compute method) (narupatools.lammps.simulation.LAMMPSSimulation method) (narupatools.mdanalysis.converter.MDAnalysisConverter method) (narupatools.mdanalysis.system.MDAnalysisSystem method) (narupatools.mdanalysis.trajectory.MDAnalysisTrajectory method) (narupatools.mdtraj.converter.MDTrajConverter method) (narupatools.mdtraj.trajectory.MDTrajTrajectory method) (narupatools.nglview.structure.ASEStructure method) (narupatools.nglview.structure.FrameDataStructure method) (narupatools.nglview.structure.NarupaToolsFrame method) (narupatools.nglview.structure.NarupaToolsTrajectory method) (narupatools.openmm.converter.OpenMMConverter method) (narupatools.openmm.dynamics.OpenMMDynamics method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) (narupatools.openmm.dynamics.OpenMMInteraction method) (narupatools.state.serializable_object.SerializableObject method) (narupatools.state.state_object.SharedStateObject method) (narupatools.state.typing.SerializableIterable method) (narupatools.state.typing.SerializableMapping method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.reference.SharedStateReference method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method)

A

active_interactions (narupatools.imd.interaction_source.InteractionsSource attribute) add() (narupatools.state.view.collection_view.SharedStateCollectionView method) add_callback() (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) add_dynamic_interactions_source() (narupatools.ase.imd.ASEIMDFeature method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) add_fields() (narupatools.frame.frame_producer.FrameProducer method) add_hdf5_writer() (in module narupatools.frame.hdf5.writer) add_imd_force() (narupatools.lammps.simulation.LAMMPSSimulation method) add_interaction() (narupatools.ase.imd.ASEIMDFeature method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) address (narupatools.app.session.Session attribute) adjust_cell() (narupatools.ase.constraints.constraint.ASECellConstraint method) (narupatools.ase.constraints.observer.ASEObserver method) adjust_forces() (narupatools.ase.constraints.constraint.ASECellConstraint method) (narupatools.ase.constraints.constraint.ASEConstraint method) (narupatools.ase.constraints.constraint.ASEEnergyConstraint method) (narupatools.ase.constraints.constraint.ASEMomentaConstraint method) (narupatools.ase.constraints.constraint.ASEStressConstraint method) (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.ase.constraints.observer.ASEObserver method) adjust_momenta() (narupatools.ase.constraints.constraint.ASEMomentaConstraint method) (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.ase.constraints.observer.ASEObserver method) adjust_positions() (narupatools.ase.constraints.constraint.ASECellConstraint method) (narupatools.ase.constraints.constraint.ASEConstraint method) (narupatools.ase.constraints.constraint.ASEEnergyConstraint method) (narupatools.ase.constraints.constraint.ASEMomentaConstraint method) (narupatools.ase.constraints.constraint.ASEStressConstraint method) (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.ase.constraints.observer.ASEObserver method) adjust_potential_energy() (narupatools.ase.constraints.constraint.ASEEnergyConstraint method) (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) adjust_stress() (narupatools.ase.constraints.constraint.ASEStressConstraint method)

all_frames (narupatools.app.client.Client attribute) always_dirty (narupatools.frame.frame_producer.FrameProducer attribute) angle (narupatools.core.units.UnitSystem attribute) angle() (in module narupatools.physics.vector) angular_velocity() (in module narupatools.physics.rigidbody) app (narupatools.app.session.Session attribute) are_frames_subscribed (narupatools.app.client.Client attribute) args() (narupatools.lammps.region.Box method) (narupatools.lammps.region.RegionSpecification method) ARRAY (narupatools.lammps.constants.VariableType attribute) array_keys (narupatools.frame.frame.NarupaFrame attribute) ase_atoms_to_frame() (in module narupatools.ase.converter) ASEAtomsWrapper (class in narupatools.ase.constraints.imd_constraint) ASECellConstraint (class in narupatools.ase.constraints.constraint) ASEConstraint (class in narupatools.ase.constraints.constraint) ASEConverter (class in narupatools.ase.converter) ASEDynamics (class in narupatools.ase.dynamics) ASEDynamicsSupportsInteractions (class in narupatools.ase.imd) ASEEnergyConstraint (class in narupatools.ase.constraints.constraint) ASEIMDFeature (class in narupatools.ase.imd) ASEMomentaConstraint (class in narupatools.ase.constraints.constraint) ASEObserver (class in narupatools.ase.constraints.observer) ASEOpenMMDynamics (class in narupatools.ase.openmm.dynamics) ASEStressConstraint (class in narupatools.ase.constraints.constraint) ASEStructure (class in narupatools.nglview.structure) ASESystem (class in narupatools.ase.system) ASETrajectory (class in narupatools.ase.trajectory) ATOM (narupatools.lammps.constants.VariableStyle attribute) atom_ids (narupatools.lammps.simulation.LAMMPSSimulation attribute) atomic_numbers_to_masses() (in module narupatools.frame.utils) atomic_numbers_to_symbols() (in module narupatools.frame.utils) atoms (narupatools.ase.constraints.imd_constraint.ASEAtomsWrapper attribute) (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEDynamicsSupportsInteractions attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.ase.system.ASESystem attribute) atoms_from_lammps_simulation() (in module narupatools.lammps.converter) attempt_update_multiplayer_locks() (narupatools.app.client.Client method) attempt_update_multiplayer_state() (narupatools.app.client.Client method) autoconnect() (narupatools.app.client.Client class method)

B

band_structure() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) bond_orders (narupatools.frame.frame.NarupaFrame attribute)

bond_pairs (narupatools.frame.frame.NarupaFrame attribute) bounds() (narupatools.lammps.region.Box class method) Box (class in narupatools.lammps.region) box_vectors (narupatools.frame.frame.NarupaFrame attribute) Broadcastable (class in narupatools.core.broadcastable) Broadcaster (class in narupatools.core.broadcastable)

C

calculate() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) calculate_cumulative_work() (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.frame.hdf5.trajectory.InteractionView method) calculate_energy() (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) calculate_force() (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) calculate_imd_force() (in module narupatools.imd.forces) calculate_numerical_forces() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) calculate_numerical_stress() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) calculate_per_particle_work() (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.frame.hdf5.trajectory.InteractionView method) calculate_power() (narupatools.frame.hdf5.trajectory.InteractionView method) calculate_properties() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) calculate_work() (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.frame.hdf5.trajectory.InteractionView method) calculation_required() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) CalculatorSetAtoms (class in narupatools.ase.calculators.protocols) catch_lammps_warnings_and_exceptions() (in module narupatools.lammps.simulation) center_of_mass() (in module narupatools.physics.rigidbody) center_of_mass_acceleration() (in module narupatools.physics.rigidbody) center_of_mass_velocity() (in module narupatools.physics.rigidbody) centripetal_force() (in module narupatools.physics.force) chain_count (narupatools.frame.frame.NarupaFrame attribute) chain_names (narupatools.frame.frame.NarupaFrame attribute) charge (narupatools.core.units.UnitSystem attribute) charges (narupatools.lammps.simulation.LAMMPSSimulation attribute) check_state() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) check_task() (narupatools.app.session.Session class method) (narupatools.ase.dynamics.ASEDynamics class method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics class method) (narupatools.core.dynamics.SimulationDynamics class method) (narupatools.core.health_check.HealthCheck class method) (narupatools.core.playable.Playable class method) (narupatools.frame.frame_producer.FrameProducer class method) (narupatools.frame.trajectory_playback.TrajectoryPlayback class method) (narupatools.imd.dynamics.InteractiveSimulationDynamics class method) (narupatools.lammps.dynamics.LAMMPSDynamics class method) (narupatools.openmm.dynamics.OpenMMDynamics class method) clear() (narupatools.app.shared_state.SharedStateView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) clear_imd_force() (narupatools.lammps.simulation.LAMMPSSimulation method)

clear_selections() (narupatools.app.client.Client method) Client (class in narupatools.app.client) close() (narupatools.app.client.Client method) (narupatools.app.session.Session method) (narupatools.ase.imd.ASEIMDFeature method) (narupatools.frame.hdf5.writer.HDF5Writer method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) collection() (narupatools.app.shared_state.SharedStateView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) command() (narupatools.lammps.simulation.LAMMPSSimulation method) command_history (narupatools.lammps.simulation.LAMMPSSimulation attribute) Compute (class in narupatools.lammps.simulation) computes (narupatools.lammps.simulation.LAMMPSSimulation attribute) connect() (narupatools.app.client.Client method) connect_imd() (narupatools.app.client.Client method) connect_multiplayer() (narupatools.app.client.Client method) connect_to_server() (narupatools.app.client.Client class method) connect_to_session() (narupatools.app.client.Client class method) connect_to_single_server() (narupatools.app.client.Client class method) connect_to_single_server_multiple_ports() (narupatools.app.client.Client class method) connect_trajectory() (narupatools.app.client.Client method) constant_interaction() (in module narupatools.imd.interactions) ConstantCalculator (class in narupatools.ase.calculators.constant_calculator) convert() (in module narupatools.frame.converter) convert_from_frame() (narupatools.ase.converter.ASEConverter class method) (narupatools.frame.converter.DictConverter class method) (narupatools.frame.converter.FrameConverter class method) (narupatools.lammps.converter.LAMMPSConverter class method) (narupatools.mdanalysis.converter.MDAnalysisConverter class method) (narupatools.mdtraj.converter.MDTrajConverter class method) (narupatools.openmm.converter.OpenMMConverter class method) convert_to_frame() (narupatools.ase.converter.ASEConverter class method) (narupatools.frame.converter.DictConverter class method) (narupatools.frame.converter.FrameConverter class method) (narupatools.lammps.converter.LAMMPSConverter class method) (narupatools.mdanalysis.converter.MDAnalysisConverter class method) (narupatools.mdtraj.converter.MDTrajConverter class method) (narupatools.openmm.converter.OpenMMConverter class method) coordinates (narupatools.frame.hdf5.writer.HDF5Writer attribute) copy() (narupatools.frame.frame.NarupaFrame method) create() (narupatools.ase.system.ASESystem static method) create_atom() (narupatools.lammps.simulation.LAMMPSSimulation method) create_box() (narupatools.lammps.simulation.LAMMPSSimulation method) create_from_object() (narupatools.ase.trajectory.ASETrajectory static method) (narupatools.frame.frame_source.TrajectorySource static method) (narupatools.frame.hdf5.trajectory.HDF5Trajectory static method) (narupatools.mdanalysis.trajectory.MDAnalysisTrajectory static method) (narupatools.mdtraj.trajectory.MDTrajTrajectory static method) create_interaction() (narupatools.frame.hdf5.writer.HDF5Writer method) create_langevin() (narupatools.ase.dynamics.ASEDynamics static method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) create_new() (narupatools.lammps.simulation.LAMMPSSimulation class method) create_region() (narupatools.lammps.simulation.LAMMPSSimulation method) create_selection() (narupatools.app.client.Client method) create_velocity_verlet() (narupatools.ase.dynamics.ASEDynamics static method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) critically_damped_spring_force() (in module narupatools.physics.force) cross_product() (in module narupatools.physics.vector) cross_product_matrix() (in module narupatools.physics.vector) current_frame (narupatools.app.client.Client attribute) current_interactions (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute)

D

damped_rotational_spring_forces() (in module narupatools.physics.force) damped_spring_force() (in module narupatools.physics.force) default_parameters (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) density (narupatools.core.units.UnitSystem attribute) density2d (narupatools.core.units.UnitSystem attribute) deserialize() (narupatools.state.serializable_object.SerializableObject class method) (narupatools.state.state_object.SharedStateObject class method) deserialize_simulation() (in module narupatools.openmm.serializer) DictConverter (class in narupatools.frame.converter) dictionary_to_protobuf() (in module narupatools.core.protobuf) dipole_moment (narupatools.core.units.UnitSystem attribute) directory (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) discard_results_on_any_change (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute)

distance() (in module narupatools.physics.vector) distribute_angular_velocity() (in module narupatools.physics.rigidbody) dot_product() (in module narupatools.physics.vector) duration (narupatools.frame.hdf5.trajectory.InteractionView attribute) dynamic_fields (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) dynamic_viscosity (narupatools.core.units.UnitSystem attribute) DynamicInteractions (class in narupatools.imd.feature) dynamics (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) DynamicsSupportsInteractions (class in narupatools.imd.feature)

E

elapsed_steps (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) elapsed_time (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEDynamicsSupportsInteractions attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.feature.DynamicsSupportsInteractions attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) electric_field (narupatools.core.units.UnitSystem attribute) end_broadcast() (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.broadcastable.Broadcastable method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method)

end_frame_index (narupatools.frame.hdf5.trajectory.InteractionView attribute) end_interaction() (narupatools.frame.hdf5.writer.HDF5Writer method) end_time (narupatools.frame.hdf5.trajectory.InteractionView attribute) energy (narupatools.core.units.UnitSystem attribute) eval() (narupatools.lammps.simulation.LAMMPSSimulation method) Event (class in narupatools.core.event) EventListener (class in narupatools.core.event) export_properties() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) extract_compute() (narupatools.lammps.simulation.LAMMPSSimulation method)

F

file() (narupatools.lammps.simulation.LAMMPSSimulation method) first_frame (narupatools.app.client.Client attribute) force (narupatools.core.units.UnitSystem attribute) forces (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) (narupatools.frame.hdf5.trajectory.InteractionsView attribute) (narupatools.frame.hdf5.trajectory.InteractionView attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) frame_data_to_dictionary() (in module narupatools.frame.converter) frame_indices (narupatools.frame.hdf5.trajectory.InteractionView attribute) frame_range (narupatools.frame.hdf5.trajectory.InteractionView attribute) frame_to_ase_atoms() (in module narupatools.ase.converter)

frame_to_mdanalysis_topology() (in module narupatools.mdanalysis.converter) frame_to_mdanalysis_universe() (in module narupatools.mdanalysis.converter) frame_to_openmm_system() (in module narupatools.openmm.converter) frame_to_openmm_topology() (in module narupatools.openmm.converter) frame_to_pdb_string() (in module narupatools.frame.converter) FrameConverter (class in narupatools.frame.converter) FrameDataStructure (class in narupatools.nglview.structure) FrameKey (class in narupatools.frame.fields) FrameProducer (class in narupatools.frame.frame_producer) frames (narupatools.app.client.Client attribute) FrameSource (class in narupatools.frame.frame_source) FrameSourceWithNotify (class in narupatools.frame.frame_source) from_ase_dynamics() (narupatools.ase.dynamics.ASEDynamics static method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) from_file() (narupatools.lammps.simulation.LAMMPSSimulation class method) from_simulation() (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) (narupatools.openmm.dynamics.OpenMMDynamics static method) from_string() (narupatools.frame.hdf5.trajectory.HDF5Topology class method) from_xml_file() (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) (narupatools.openmm.dynamics.OpenMMDynamics static method) from_xml_string() (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics static method) (narupatools.openmm.dynamics.OpenMMDynamics static method)

G

gather_atoms() (narupatools.lammps.simulation.LAMMPSSimulation method) gaussian_force_and_energy() (in module narupatools.physics.force) gaussian_interaction() (in module narupatools.imd.interactions) generate_topology() (in module narupatools.frame.hdf5.utils) get() (narupatools.app.shared_state.SharedStateView method) (narupatools.ase.constraints.observer.ASEObserver class method) (narupatools.frame.fields.FrameKey method) (narupatools.frame.frame.NarupaFrame method) (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) get_atoms() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_charges() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_coordinates() (narupatools.nglview.structure.NarupaToolsTrajectory method) get_default_parameters() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_dipole_moment() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_float_value() (narupatools.frame.frame.NarupaFrame method) get_force_function() (in module narupatools.imd.forces) get_forces() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_frame() (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.ase.system.ASESystem method) (narupatools.ase.trajectory.ASETrajectory method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.frame.frame_source.FrameSource method) (narupatools.frame.frame_source.FrameSourceWithNotify method) (narupatools.frame.frame_source.TrajectorySource method) (narupatools.frame.hdf5.trajectory.HDF5Topology method) (narupatools.frame.hdf5.trajectory.HDF5Trajectory method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.lammps.simulation.LAMMPSSimulation method) (narupatools.mdanalysis.system.MDAnalysisSystem method) (narupatools.mdanalysis.trajectory.MDAnalysisTrajectory method) (narupatools.mdtraj.trajectory.MDTrajTrajectory method) (narupatools.openmm.dynamics.OpenMMDynamics method)

get_frame_key() (in module narupatools.frame.fields) get_imd_forces() (narupatools.lammps.simulation.LAMMPSSimulation method) get_magnetic_moment() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_magnetic_moments() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_openmm_masses() (in module narupatools.openmm.converter) get_or_create() (narupatools.ase.constraints.observer.ASEObserver class method) get_positions() (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.imd.interaction.Interaction method) (narupatools.lammps.dynamics.LAMMPSInteraction method) (narupatools.openmm.dynamics.OpenMMInteraction method) get_potential_energies() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_potential_energy() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_property() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_selection() (narupatools.app.client.Client method) get_shared_value() (narupatools.app.client.Client method) get_stress() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_stresses() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) get_string_value() (narupatools.frame.frame.NarupaFrame method) get_structure_string() (narupatools.nglview.structure.ASEStructure method) (narupatools.nglview.structure.FrameDataStructure method) (narupatools.nglview.structure.NarupaToolsFrame method) (narupatools.nglview.structure.NarupaToolsTrajectory method) get_unit_system() (in module narupatools.lammps.units) get_with_default() (narupatools.frame.fields.FrameKey method) GLOBAL (narupatools.lammps.constants.VariableStyle attribute) guess_atomic_number() (in module narupatools.mdanalysis.utils) guess_elements() (in module narupatools.mdanalysis.utils)

H

has_value() (narupatools.state.view.reference.SharedStateReference method) HDF5Topology (class in narupatools.frame.hdf5.trajectory) HDF5Trajectory (class in narupatools.frame.hdf5.trajectory) HDF5Writer (class in narupatools.frame.hdf5.writer) health_check() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.health_check.HealthCheck method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method)

HealthCheck (class in narupatools.core.health_check)

I

id (narupatools.lammps.region.Region attribute) identity_matrix() (in module narupatools.physics.matrix) ignored_changes (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) imd (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) imd_forces (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) implemented_properties (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) index (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) indices (narupatools.frame.hdf5.trajectory.InteractionView attribute) Interaction (class in narupatools.imd.interaction) interaction (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) interaction_positions (narupatools.frame.hdf5.trajectory.InteractionView attribute) interaction_scales (narupatools.frame.hdf5.trajectory.InteractionView attribute) InteractionConstraint (class in narupatools.ase.constraints.imd_constraint) InteractionFeature (class in narupatools.imd.feature) interactions (narupatools.app.client.Client attribute) (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) InteractionsSource (class in narupatools.imd.interaction_source) InteractionsView (class in narupatools.frame.hdf5.trajectory)

InteractionView (class in narupatools.frame.hdf5.trajectory) InteractiveForce (class in narupatools.imd.forces) InteractiveSimulationDynamics (class in narupatools.imd.dynamics) invoke (narupatools.core.event.Event attribute) is_paused (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.playable.Playable attribute) (narupatools.frame.frame_producer.FrameProducer attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) is_playing (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.playable.Playable attribute) (narupatools.frame.frame_producer.FrameProducer attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) is_running (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.playable.Playable attribute) (narupatools.frame.frame_producer.FrameProducer attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) items() (narupatools.app.shared_state.SharedStateView method) (narupatools.frame.frame.NarupaFrame method) (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method)

K

keys() (narupatools.app.shared_state.SharedStateView method) (narupatools.frame.frame.NarupaFrame method) (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) kinetic_energies (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute)

kinetic_energy (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.frame.frame.NarupaFrame attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) kinetic_energy() (in module narupatools.physics.rigidbody) kronecker_delta() (in module narupatools.physics.matrix)

L

label (narupatools.ase.calculators.constant_calculator.ConstantCalculator attribute) (narupatools.ase.calculators.null_calculator.NullCalculator attribute) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator attribute) (narupatools.ase.openmm.calculator.OpenMMCalculator attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) lammps_packages (narupatools.lammps.simulation.LAMMPSSimulation attribute) LAMMPSCalculator (class in narupatools.lammps.calculator) LAMMPSConverter (class in narupatools.lammps.converter) LAMMPSDynamics (class in narupatools.lammps.dynamics) LAMMPSIMDFeature (class in narupatools.lammps.dynamics)

LAMMPSInteraction (class in narupatools.lammps.dynamics) LAMMPSSimulation (class in narupatools.lammps.simulation) latest_frame (narupatools.app.client.Client attribute) latest_multiplayer_values (narupatools.app.client.Client attribute) left_vector_triple_product_matrix() (in module narupatools.physics.vector) length (narupatools.core.units.UnitSystem attribute) linear_drag_force() (in module narupatools.physics.force) load_file() (narupatools.frame.hdf5.trajectory.HDF5Trajectory class method) LOCAL (narupatools.lammps.constants.VariableStyle attribute) looping (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute)

M

magnitude() (in module narupatools.physics.vector) mark_dirty() (narupatools.frame.frame_producer.FrameProducer method) mass (narupatools.core.units.UnitSystem attribute) mass_weighted_forces() (in module narupatools.physics.force) masses (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) matrix_inverse() (in module narupatools.physics.matrix) mdanalysis_atomgroup_to_frame() (in module narupatools.mdanalysis.converter) mdanalysis_universe_to_frame() (in module narupatools.mdanalysis.converter) MDAnalysisConverter (class in narupatools.mdanalysis.converter) MDAnalysisSystem (class in narupatools.mdanalysis.system) MDAnalysisTrajectory (class in narupatools.mdanalysis.trajectory) mdtraj_topology_to_frame() (in module narupatools.mdtraj.converter) mdtraj_trajectory_to_frame() (in module narupatools.mdtraj.converter) MDTrajConverter (class in narupatools.mdtraj.converter) MDTrajTrajectory (class in narupatools.mdtraj.trajectory) modify() (narupatools.app.shared_state.SharedStateView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.reference.SharedStateReference method) (narupatools.state.view.view.SharedStateView method) module narupatools narupatools.app narupatools.app.client narupatools.app.session narupatools.app.shared_state narupatools.ase narupatools.ase.calculators narupatools.ase.calculators.constant_calculator narupatools.ase.calculators.null_calculator narupatools.ase.calculators.onebody_potential_calculator narupatools.ase.calculators.protocols narupatools.ase.constraints narupatools.ase.constraints.constraint narupatools.ase.constraints.imd_constraint narupatools.ase.constraints.observer narupatools.ase.converter narupatools.ase.dynamics narupatools.ase.imd narupatools.ase.openmm narupatools.ase.openmm.calculator narupatools.ase.openmm.converter narupatools.ase.openmm.dynamics narupatools.ase.system narupatools.ase.trajectory narupatools.ase.units narupatools.core narupatools.core.broadcastable narupatools.core.dynamics narupatools.core.event narupatools.core.health_check narupatools.core.patch narupatools.core.playable narupatools.core.protobuf narupatools.core.random narupatools.core.timing narupatools.core.units narupatools.frame narupatools.frame.converter narupatools.frame.fields narupatools.frame.frame narupatools.frame.frame_producer narupatools.frame.frame_source narupatools.frame.hdf5 narupatools.frame.hdf5.trajectory narupatools.frame.hdf5.utils narupatools.frame.hdf5.writer narupatools.frame.patch narupatools.frame.trajectory_playback narupatools.frame.utils narupatools.imd narupatools.imd.dynamics narupatools.imd.feature narupatools.imd.feature_setclear narupatools.imd.forces narupatools.imd.interaction narupatools.imd.interaction_source narupatools.imd.interactions narupatools.lammps narupatools.lammps.calculator narupatools.lammps.constants narupatools.lammps.converter narupatools.lammps.dynamics narupatools.lammps.exceptions narupatools.lammps.output_capture narupatools.lammps.region narupatools.lammps.simulation narupatools.lammps.units narupatools.lammps.warnings narupatools.mdanalysis narupatools.mdanalysis.converter narupatools.mdanalysis.system narupatools.mdanalysis.trajectory narupatools.mdanalysis.units narupatools.mdanalysis.utils narupatools.mdtraj narupatools.mdtraj.converter narupatools.mdtraj.trajectory narupatools.mdtraj.units narupatools.nglview narupatools.nglview.show narupatools.nglview.structure narupatools.openmm narupatools.openmm.converter narupatools.openmm.dynamics narupatools.openmm.integrators narupatools.openmm.serializer narupatools.openmm.units narupatools.physics narupatools.physics.force narupatools.physics.matrix narupatools.physics.random narupatools.physics.rigidbody narupatools.physics.rotations narupatools.physics.typing narupatools.physics.vector narupatools.state narupatools.state.serializable_object narupatools.state.state_object narupatools.state.typing narupatools.state.view narupatools.state.view.collection_view narupatools.state.view.dictionary_view narupatools.state.view.reference narupatools.state.view.view narupatools.state.view.wrappers

molecular_dynamics (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) moment_of_inertia_tensor() (in module narupatools.physics.rigidbody)

N

n_frames (narupatools.nglview.structure.NarupaToolsTrajectory attribute) name (narupatools.app.session.Session attribute) NarupaFrame (class in narupatools.frame.frame) narupatools module narupatools.app module narupatools.app.client module narupatools.app.session module narupatools.app.shared_state module narupatools.ase module narupatools.ase.calculators module narupatools.ase.calculators.constant_calculator module narupatools.ase.calculators.null_calculator module narupatools.ase.calculators.onebody_potential_calculator module narupatools.ase.calculators.protocols module narupatools.ase.constraints module narupatools.ase.constraints.constraint module narupatools.ase.constraints.imd_constraint module narupatools.ase.constraints.observer module narupatools.ase.converter module narupatools.ase.dynamics module narupatools.ase.imd module narupatools.ase.openmm module narupatools.ase.openmm.calculator module narupatools.ase.openmm.converter module narupatools.ase.openmm.dynamics module narupatools.ase.system module narupatools.ase.trajectory module narupatools.ase.units module narupatools.core module narupatools.core.broadcastable module narupatools.core.dynamics module narupatools.core.event module narupatools.core.health_check module narupatools.core.patch module narupatools.core.playable module narupatools.core.protobuf module narupatools.core.random module narupatools.core.timing module narupatools.core.units module narupatools.frame module narupatools.frame.converter module narupatools.frame.fields module narupatools.frame.frame module narupatools.frame.frame_producer module narupatools.frame.frame_source module narupatools.frame.hdf5 module narupatools.frame.hdf5.trajectory module narupatools.frame.hdf5.utils module narupatools.frame.hdf5.writer module narupatools.frame.patch module narupatools.frame.trajectory_playback module narupatools.frame.utils module narupatools.imd module narupatools.imd.dynamics module narupatools.imd.feature module narupatools.imd.feature_setclear module

narupatools.imd.forces module narupatools.imd.interaction module narupatools.imd.interaction_source module narupatools.imd.interactions module narupatools.lammps module narupatools.lammps.calculator module narupatools.lammps.constants module narupatools.lammps.converter module narupatools.lammps.dynamics module narupatools.lammps.exceptions module narupatools.lammps.output_capture module narupatools.lammps.region module narupatools.lammps.simulation module narupatools.lammps.units module narupatools.lammps.warnings module narupatools.mdanalysis module narupatools.mdanalysis.converter module narupatools.mdanalysis.system module narupatools.mdanalysis.trajectory module narupatools.mdanalysis.units module narupatools.mdanalysis.utils module narupatools.mdtraj module narupatools.mdtraj.converter module narupatools.mdtraj.trajectory module narupatools.mdtraj.units module narupatools.nglview module narupatools.nglview.show module narupatools.nglview.structure module narupatools.openmm module narupatools.openmm.converter module narupatools.openmm.dynamics module narupatools.openmm.integrators module narupatools.openmm.serializer module narupatools.openmm.units module narupatools.physics module narupatools.physics.force module narupatools.physics.matrix module narupatools.physics.random module narupatools.physics.rigidbody module narupatools.physics.rotations module narupatools.physics.typing module narupatools.physics.vector module narupatools.state module narupatools.state.serializable_object module narupatools.state.state_object module narupatools.state.typing module narupatools.state.view module narupatools.state.view.collection_view module narupatools.state.view.dictionary_view module narupatools.state.view.reference module narupatools.state.view.view module narupatools.state.view.wrappers module NarupaToolsFrame (class in narupatools.nglview.structure) NarupaToolsTrajectory (class in narupatools.nglview.structure) normalized() (in module narupatools.physics.vector) NullCalculator (class in narupatools.ase.calculators.null_calculator)

O

on_dictionary_update() (narupatools.app.shared_state.SharedStateView method) on_end_interaction (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) on_field_changed (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.frame.frame_source.FrameSourceWithNotify attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) on_frame_produced (narupatools.frame.frame_producer.FrameProducer attribute) on_frame_received (narupatools.app.client.Client attribute) on_post_step (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEDynamicsSupportsInteractions attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.feature.DynamicsSupportsInteractions attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) on_post_step() (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.imd.interaction.Interaction method) (narupatools.lammps.dynamics.LAMMPSInteraction method) (narupatools.openmm.dynamics.OpenMMInteraction method) on_pre_step (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEDynamicsSupportsInteractions attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.feature.DynamicsSupportsInteractions attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) on_pre_step() (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.imd.interaction.Interaction method) (narupatools.lammps.dynamics.LAMMPSInteraction method) (narupatools.openmm.dynamics.OpenMMInteraction method) on_reset (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEDynamicsSupportsInteractions attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.feature.DynamicsSupportsInteractions attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute)

on_set_cell (narupatools.ase.constraints.observer.ASEObserver attribute) on_set_momenta (narupatools.ase.constraints.observer.ASEObserver attribute) on_set_positions (narupatools.ase.constraints.observer.ASEObserver attribute) on_shared_state_added() (narupatools.app.shared_state.SharedStateView method) on_shared_state_changed() (narupatools.app.shared_state.SharedStateView method) on_shared_state_removed() (narupatools.app.shared_state.SharedStateView method) on_start_interaction (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) OneBodyPotentialCalculator (class in narupatools.ase.calculators.onebody_potential_calculator) OnEndInteractionCallback (class in narupatools.imd.feature) OnFieldsChangedCallback (class in narupatools.frame.frame_source) OnFrameProducedCallback (class in narupatools.frame.frame_producer) OnFrameReceivedCallback (class in narupatools.app.client) OnPostStepCallback (class in narupatools.core.dynamics) OnPreStepCallback (class in narupatools.core.dynamics) OnResetCallback (class in narupatools.core.dynamics) OnSharedStateAddedCallback (class in narupatools.app.shared_state) OnSharedStateChangedCallback (class in narupatools.app.shared_state) OnSharedStateRemovedCallback (class in narupatools.app.shared_state) OnStartInteractionCallback (class in narupatools.imd.feature) OnTargetChanged (class in narupatools.app.session) openmm_context_to_frame() (in module narupatools.openmm.converter) openmm_simulation_to_ase_atoms() (in module narupatools.ase.openmm.converter) openmm_simulation_to_ase_molecular_dynamics() (in module narupatools.ase.openmm.converter) openmm_simulation_to_frame() (in module narupatools.openmm.converter) openmm_state_to_frame() (in module narupatools.openmm.converter) openmm_topology_to_frame() (in module narupatools.openmm.converter) OpenMMCalculator (class in narupatools.ase.openmm.calculator) OpenMMConverter (class in narupatools.openmm.converter) OpenMMDynamics (class in narupatools.openmm.dynamics) OpenMMIMDFeature (class in narupatools.openmm.dynamics) OpenMMInteraction (class in narupatools.openmm.dynamics) orbital_angular_momentum() (in module narupatools.physics.rigidbody) outer_product() (in module narupatools.physics.vector) output (narupatools.lammps.output_capture.OutputCapture attribute) OutputCapture (class in narupatools.lammps.output_capture)

P

particle_count (narupatools.frame.frame.NarupaFrame attribute) particle_elements (narupatools.frame.frame.NarupaFrame attribute) particle_indices (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) particle_names (narupatools.frame.frame.NarupaFrame attribute) particle_positions (narupatools.frame.frame.NarupaFrame attribute) particle_residues (narupatools.frame.frame.NarupaFrame attribute) particle_types (narupatools.frame.frame.NarupaFrame attribute) pause() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) play() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) Playable (class in narupatools.core.playable) playback_interval (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.playable.Playable attribute) (narupatools.frame.frame_producer.FrameProducer attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) playback_rate (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.playable.Playable attribute) (narupatools.frame.frame_producer.FrameProducer attribute) (narupatools.frame.trajectory_playback.TrajectoryPlayback attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute)

pop() (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) popitem() (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) port (narupatools.app.session.Session attribute) positions (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) potential_energies (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) (narupatools.frame.hdf5.trajectory.InteractionsView attribute) (narupatools.frame.hdf5.trajectory.InteractionView attribute) potential_energy (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.frame.frame.NarupaFrame attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) Prefix (class in narupatools.core.units) pressure (narupatools.core.units.UnitSystem attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) ProduceFrameCallback (class in narupatools.frame.frame_producer) PropertyType (class in narupatools.lammps.constants)

Q

quaternion_as_rotation_matrix() (in module narupatools.physics.rotations)

quaternion_conjugate() (in module narupatools.physics.rotations) quaternion_inverse() (in module narupatools.physics.rotations)

R

random_float() (in module narupatools.core.random) random_integer() (in module narupatools.core.random) random_letter() (in module narupatools.core.random) random_quaternion() (in module narupatools.physics.random) random_sphere() (in module narupatools.physics.random) random_vector() (in module narupatools.physics.random) random_word() (in module narupatools.core.random) raw (narupatools.frame.frame.NarupaFrame attribute) read() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) read_atoms() (narupatools.ase.calculators.constant_calculator.ConstantCalculator class method) (narupatools.ase.calculators.null_calculator.NullCalculator class method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator class method) (narupatools.ase.openmm.calculator.OpenMMCalculator class method) (narupatools.lammps.calculator.LAMMPSCalculator class method) realtime (narupatools.frame.hdf5.writer.HDF5Writer attribute) Region (class in narupatools.lammps.region) region_ids (narupatools.lammps.simulation.LAMMPSSimulation attribute) RegionSpecification (class in narupatools.lammps.region) register_imd_force_type() (in module narupatools.imd.forces) remove() (narupatools.state.view.reference.SharedStateReference method) remove_callback() (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) remove_dynamic_interactions_source() (narupatools.ase.imd.ASEIMDFeature method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) remove_fields() (narupatools.frame.frame_producer.FrameProducer method) remove_interaction() (narupatools.ase.imd.ASEIMDFeature method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) remove_selection() (narupatools.app.client.Client method) remove_shared_value() (narupatools.app.client.Client method) reopen() (narupatools.frame.hdf5.writer.HDF5Writer method) reset() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.calculator.LAMMPSCalculator method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method)

residue_chains (narupatools.frame.frame.NarupaFrame attribute) residue_count (narupatools.frame.frame.NarupaFrame attribute) residue_ids (narupatools.frame.frame.NarupaFrame attribute) residue_names (narupatools.frame.frame.NarupaFrame attribute) restart() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) right_cross_product_matrix() (in module narupatools.physics.vector) root_selection (narupatools.app.client.Client attribute) rotate_around_center_of_mass() (in module narupatools.physics.rotations) rotate_around_origin() (in module narupatools.physics.rotations) rotate_around_point() (in module narupatools.physics.rotations) run() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.lammps.simulation.LAMMPSSimulation method) (narupatools.openmm.dynamics.OpenMMDynamics method) run_command() (narupatools.app.client.Client method) run_imd_command() (narupatools.app.client.Client method) run_multiplayer_command() (narupatools.app.client.Client method) run_pause() (narupatools.app.client.Client method) run_play() (narupatools.app.client.Client method) run_reset() (narupatools.app.client.Client method) run_step() (narupatools.app.client.Client method) run_trajectory_command() (narupatools.app.client.Client method)

S

save_frame() (narupatools.frame.hdf5.writer.HDF5Writer method) save_interaction() (narupatools.frame.hdf5.writer.HDF5Writer method) save_topology() (narupatools.frame.hdf5.writer.HDF5Writer method) SCALAR (narupatools.lammps.constants.VariableType attribute) selections (narupatools.app.client.Client attribute) SerializableIterable (class in narupatools.state.typing) SerializableMapping (class in narupatools.state.typing) SerializableObject (class in narupatools.state.serializable_object) serialize() (narupatools.state.serializable_object.SerializableObject method) (narupatools.state.state_object.SharedStateObject method) serialize_simulation() (in module narupatools.openmm.serializer) server_timestamp (narupatools.frame.frame.NarupaFrame attribute) Session (class in narupatools.app.session) set() (narupatools.app.shared_state.SharedStateView method) (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.frame.fields.FrameKey method) (narupatools.lammps.calculator.LAMMPSCalculator method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.reference.SharedStateReference method) (narupatools.state.view.view.SharedStateView method) set_atoms() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.protocols.CalculatorSetAtoms method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) set_float_array() (narupatools.frame.frame.NarupaFrame method) set_float_value() (narupatools.frame.frame.NarupaFrame method) set_imd_force() (narupatools.lammps.simulation.LAMMPSSimulation method) set_index_array() (narupatools.frame.frame.NarupaFrame method) set_label() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) set_mass() (narupatools.lammps.simulation.LAMMPSSimulation method) set_shared_value() (narupatools.app.client.Client method) set_string_array() (narupatools.frame.frame.NarupaFrame method) set_string_value() (narupatools.frame.frame.NarupaFrame method) SetAndClearInteractionFeature (class in narupatools.imd.feature_setclear) setdefault() (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) setup_langevin() (narupatools.lammps.simulation.LAMMPSSimulation method) shared_state (narupatools.app.client.Client attribute) (narupatools.app.session.Session attribute) SharedStateClientWrapper (class in narupatools.state.view.wrappers) SharedStateCollectionView (class in narupatools.state.view.collection_view) SharedStateDictionaryView (class in narupatools.state.view.dictionary_view) SharedStateObject (class in narupatools.state.state_object) SharedStateReference (class in narupatools.state.view.reference) SharedStateServerWrapper (class in narupatools.state.view.wrappers) SharedStateView (class in narupatools.app.shared_state) (class in narupatools.state.view.view) shortcuts (narupatools.frame.frame.NarupaFrame attribute) show() (narupatools.app.session.Session method) show_ase() (in module narupatools.nglview.show) show_narupa() (in module narupatools.nglview.show) show_narupatools_traj() (in module narupatools.nglview.show) simulation (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.lammps.calculator.LAMMPSCalculator attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute)

SimulationDynamics (class in narupatools.core.dynamics) snapshot() (narupatools.app.shared_state.SharedStateView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.reference.SharedStateReference method) (narupatools.state.view.view.SharedStateView method) specification (narupatools.lammps.region.Region attribute) spin_angular_momentum() (in module narupatools.physics.rigidbody) spring_force() (in module narupatools.physics.force) spring_force_and_energy() (in module narupatools.physics.force) spring_interaction() (in module narupatools.imd.interactions) sqr_distance() (in module narupatools.physics.vector) sqr_magnitude() (in module narupatools.physics.vector) start() (narupatools.app.session.Session class method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) start_broadcast() (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.broadcastable.Broadcastable method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) start_frame_index (narupatools.frame.hdf5.trajectory.InteractionView attribute) start_interaction() (narupatools.app.client.Client method) start_loop() (narupatools.app.session.Session method) start_time (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.frame.hdf5.trajectory.InteractionView attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) step() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) stop() (narupatools.app.session.Session method) (narupatools.ase.dynamics.ASEDynamics method) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.playable.Playable method) (narupatools.frame.frame_producer.FrameProducer method) (narupatools.frame.trajectory_playback.TrajectoryPlayback method) (narupatools.imd.dynamics.InteractiveSimulationDynamics method) (narupatools.lammps.dynamics.LAMMPSDynamics method) (narupatools.openmm.dynamics.OpenMMDynamics method) stop_interaction() (narupatools.app.client.Client method) style (narupatools.lammps.region.Box attribute) (narupatools.lammps.region.RegionSpecification attribute) subscribe_multiplayer() (narupatools.app.client.Client method) subscribe_to_all_frames() (narupatools.app.client.Client method) subscribe_to_frames() (narupatools.app.client.Client method)

T

target (narupatools.app.session.Session attribute) temperature (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.core.units.UnitSystem attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) time (narupatools.core.units.UnitSystem attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) times (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) timestep (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) todict() (narupatools.ase.calculators.constant_calculator.ConstantCalculator method) (narupatools.ase.calculators.null_calculator.NullCalculator method) (narupatools.ase.calculators.onebody_potential_calculator.OneBodyPotentialCalculator method) (narupatools.ase.openmm.calculator.OpenMMCalculator method) (narupatools.lammps.calculator.LAMMPSCalculator method) topology (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) torque (narupatools.core.units.UnitSystem attribute)

total_steps (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) total_time (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.core.dynamics.SimulationDynamics attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) total_work (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute) TrajectoryPlayback (class in narupatools.frame.trajectory_playback) TrajectorySource (class in narupatools.frame.frame_source) type (narupatools.frame.hdf5.trajectory.InteractionView attribute) typed_collection() (narupatools.state.view.collection_view.SharedStateCollectionView class method) typed_reference() (narupatools.state.view.reference.SharedStateReference class method)

U

UnfinishedUnitOrQuantity (class in narupatools.core.units) Unit (class in narupatools.core.units) UnitConversion (class in narupatools.core.units) UnitSystem (class in narupatools.core.units) universe (narupatools.lammps.simulation.LAMMPSSimulation attribute) untyped_collection() (narupatools.state.view.collection_view.SharedStateCollectionView class method) untyped_reference() (narupatools.state.view.reference.SharedStateReference class method) update() (narupatools.app.shared_state.SharedStateView method) (narupatools.imd.feature.DynamicInteractions method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.reference.SharedStateReference method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method)

update_available_commands() (narupatools.app.client.Client method) update_energy_and_forces() (narupatools.ase.constraints.imd_constraint.InteractionConstraint method) (narupatools.imd.interaction.Interaction method) (narupatools.lammps.dynamics.LAMMPSInteraction method) (narupatools.openmm.dynamics.OpenMMInteraction method) update_interaction() (narupatools.app.client.Client method) (narupatools.ase.imd.ASEIMDFeature method) (narupatools.imd.feature.InteractionFeature method) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature method) (narupatools.lammps.dynamics.LAMMPSIMDFeature method) (narupatools.openmm.dynamics.OpenMMIMDFeature method) update_selection() (narupatools.app.client.Client method) update_struct() (in module narupatools.core.protobuf) used_shortcuts (narupatools.frame.frame.NarupaFrame attribute)

V

value_keys (narupatools.frame.frame.NarupaFrame attribute) values() (narupatools.app.shared_state.SharedStateView method) (narupatools.frame.frame.NarupaFrame method) (narupatools.frame.hdf5.trajectory.InteractionsView method) (narupatools.state.view.collection_view.SharedStateCollectionView method) (narupatools.state.view.dictionary_view.SharedStateDictionaryView method) (narupatools.state.view.view.SharedStateView method) (narupatools.state.view.wrappers.SharedStateClientWrapper method) (narupatools.state.view.wrappers.SharedStateServerWrapper method) VariableStyle (class in narupatools.lammps.constants) VariableType (class in narupatools.lammps.constants) VECTOR (narupatools.lammps.constants.VariableType attribute)

vector() (in module narupatools.physics.vector) vector_projection() (in module narupatools.physics.vector) vector_rejection() (in module narupatools.physics.vector) velocities (narupatools.ase.dynamics.ASEDynamics attribute) (narupatools.ase.openmm.dynamics.ASEOpenMMDynamics attribute) (narupatools.frame.hdf5.trajectory.HDF5Trajectory attribute) (narupatools.frame.hdf5.writer.HDF5Writer attribute) (narupatools.imd.dynamics.InteractiveSimulationDynamics attribute) (narupatools.lammps.dynamics.LAMMPSDynamics attribute) (narupatools.lammps.simulation.LAMMPSSimulation attribute) (narupatools.openmm.dynamics.OpenMMDynamics attribute) velocity (narupatools.core.units.UnitSystem attribute) velocity_verlet_integrator() (in module narupatools.openmm.integrators)

W

wait_for() (in module narupatools.core.timing) wait_until_first_frame() (narupatools.app.client.Client method) work_last_step (narupatools.ase.constraints.imd_constraint.InteractionConstraint attribute) (narupatools.ase.imd.ASEIMDFeature attribute) (narupatools.imd.feature.InteractionFeature attribute) (narupatools.imd.feature_setclear.SetAndClearInteractionFeature attribute) (narupatools.imd.interaction.Interaction attribute) (narupatools.lammps.dynamics.LAMMPSIMDFeature attribute) (narupatools.lammps.dynamics.LAMMPSInteraction attribute) (narupatools.openmm.dynamics.OpenMMIMDFeature attribute) (narupatools.openmm.dynamics.OpenMMInteraction attribute)

wrap_interaction_source() (in module narupatools.imd.interaction_source)

Z

zero_matrix() (in module narupatools.physics.matrix)

zero_vector() (in module narupatools.physics.vector)