Index

A

a (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.Rhomboid attribute) active_actors (espressomd.actors.Actors attribute) active_list (espressomd.lb.FluidActor attribute) ActiveVirtualSitesHandle (class in espressomd.virtual_sites) Actors (class in espressomd.actors) actors (espressomd.system.System attribute) add() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.actors.Actors method) (espressomd.constraints.Constraints method) (espressomd.interactions.BondedInteractions method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.particle_data.ParticleList method) (espressomd.shapes.Union method) add_all_thole() (espressomd.drude_helpers.DrudeHelpers method) add_bond() (espressomd.particle_data.ParticleHandle method) add_boundary() (espressomd.electrokinetics.Electrokinetics method) add_drude_particle_to_core() (espressomd.drude_helpers.DrudeHelpers method) add_exclusion() (espressomd.particle_data.ParticleHandle method) add_intramol_exclusion_bonds() (espressomd.drude_helpers.DrudeHelpers method) add_reaction() (espressomd.electrokinetics.Electrokinetics method) (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) (espressomd.reaction_methods.WidomInsertion method)

add_species() (espressomd.electrokinetics.Electrokinetics method) add_thole_pair_damping() (espressomd.drude_helpers.DrudeHelpers method) add_verified_bond() (espressomd.particle_data.ParticleHandle method) agrid (espressomd.lb.HydrodynamicInteraction attribute) all() (espressomd.particle_data.ParticleList method) Analysis (class in espressomd.analyze) analysis (espressomd.system.System attribute) AngleCosine (class in espressomd.interactions) AngleCossquare (class in espressomd.interactions) AngleHarmonic (class in espressomd.interactions) angular_momentum() (espressomd.analyze.Analysis method) array_locked (class in espressomd.utils) assert_features() (in module espressomd) AssertThermostatType() (in module espressomd.thermostat) auto_exclusions() (espressomd.system.System method) auto_update_accumulators (espressomd.system.System attribute) autocorrelation() (in module espressomd.analyze) AutoUpdateAccumulators (class in espressomd.accumulators) axis (espressomd.shapes.Cylinder attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.SpheroCylinder attribute)

B

b (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.Rhomboid attribute) begin_section() (in module espressomd.profiler) bin_centers() (espressomd.observables.ProfileObservable method) (espressomd.observables.RDF method) bin_edges() (espressomd.observables.ProfileObservable method) bmhtf (espressomd.interactions.NonBondedInteractionHandle attribute) BMHTFInteraction (class in espressomd.interactions) bond_breakage (espressomd.system.System attribute) BondAngles (class in espressomd.observables) BondCriterion (class in espressomd.pair_criteria) BondDihedrals (class in espressomd.observables) bonded_inter (espressomd.system.System attribute) BondedCoulomb (class in espressomd.interactions) BondedCoulombSRBond (class in espressomd.interactions) BondedInteraction (class in espressomd.interactions) BondedInteractionNotDefined (class in espressomd.interactions)

BondedInteractions (class in espressomd.interactions) bonds (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) Boost boundary (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) box_l (espressomd.system.System attribute) BreakageSpec (class in espressomd.bond_breakage) BreakageSpecs (class in espressomd.bond_breakage) BrownianDynamics (class in espressomd.integrate) buckingham (espressomd.interactions.NonBondedInteractionHandle attribute) BuckinghamInteraction (class in espressomd.interactions) bulk_viscosity (espressomd.lb.HydrodynamicInteraction attribute) ButtonMotion (espressomd.visualization.MouseFireEvent attribute) ButtonPressed (espressomd.visualization.MouseFireEvent attribute) ButtonReleased (espressomd.visualization.MouseFireEvent attribute) by_id() (espressomd.particle_data.ParticleList method) by_ids() (espressomd.particle_data.ParticleList method)

C

c (espressomd.shapes.Rhomboid attribute) C++ compiler calc_re() (espressomd.analyze.Analysis method) calc_rg() (espressomd.analyze.Analysis method) calc_rh() (espressomd.analyze.Analysis method) calculate() (espressomd.observables.BondAngles method) (espressomd.observables.BondDihedrals method) (espressomd.observables.ComPosition method) (espressomd.observables.ComVelocity method) (espressomd.observables.CosPersistenceAngles method) (espressomd.observables.CylindricalDensityProfile method) (espressomd.observables.CylindricalFluxDensityProfile method) (espressomd.observables.CylindricalLBFluxDensityProfileAtParticlePositions method) (espressomd.observables.CylindricalLBVelocityProfile method) (espressomd.observables.CylindricalLBVelocityProfileAtParticlePositions method) (espressomd.observables.CylindricalVelocityProfile method) (espressomd.observables.DensityProfile method) (espressomd.observables.DipoleMoment method) (espressomd.observables.DPDStress method) (espressomd.observables.Energy method) (espressomd.observables.FluxDensityProfile method) (espressomd.observables.ForceDensityProfile method) (espressomd.observables.LBFluidPressureTensor method) (espressomd.observables.LBVelocityProfile method) (espressomd.observables.MagneticDipoleMoment method) (espressomd.observables.Observable method) (espressomd.observables.ParticleAngularVelocities method) (espressomd.observables.ParticleBodyAngularVelocities method) (espressomd.observables.ParticleBodyVelocities method) (espressomd.observables.ParticleDistances method) (espressomd.observables.ParticleForces method) (espressomd.observables.ParticlePositions method) (espressomd.observables.ParticleVelocities method) (espressomd.observables.Pressure method) (espressomd.observables.PressureTensor method) (espressomd.observables.RDF method) (espressomd.observables.TotalForce method) calculate_excess_chemical_potential() (espressomd.reaction_methods.WidomInsertion method) calculate_particle_insertion_potential_energy() (espressomd.reaction_methods.WidomInsertion method) call_method() (espressomd.script_interface.PScriptInterface method) callback_on_button() (espressomd.visualization.KeyboardManager method) Camera (class in espressomd.visualization) cell_system (espressomd.system.System attribute) CellSystem (class in espressomd.cell_system) center (espressomd.shapes.Cylinder attribute) (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Torus attribute) center_of_mass() (espressomd.analyze.Analysis method) (espressomd.cluster_analysis.Cluster method) central_angle (espressomd.shapes.HollowConicalFrustum attribute) change_reaction_constant() (espressomd.reaction_methods.ReactionAlgorithm method) change_volume_and_rescale_particles() (espressomd.system.System method) channel_width (espressomd.shapes.Slitpore attribute) charge_unit (espressomd.io.writer.h5md.H5md attribute)

check_array_type_or_throw_except() (in module espressomd.utils) check_required_keys() (in module espressomd.utils) check_topology() (espressomd.analyze.Analysis method) check_type_or_throw_except() (in module espressomd.utils) check_valid_keys() (in module espressomd.utils) Checkpoint (class in espressomd.checkpointing) cid_for_particle() (espressomd.cluster_analysis.ClusterStructure method) class_lookup() (espressomd.lb.FluidActor method) clear() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.accumulators.TimeSeries method) (espressomd.actors.Actors method) (espressomd.cluster_analysis.ClusterStructure method) (espressomd.constraints.Constraints method) (espressomd.interactions.BondedInteractions method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.particle_data.ParticleList method) (espressomd.script_interface.ScriptObjectMap method) (espressomd.shapes.Union method) close() (espressomd.io.writer.h5md.H5md method) Cluster (class in espressomd.cluster_analysis) cluster_ids() (espressomd.cluster_analysis.ClusterStructure method) Clusters (class in espressomd.cluster_analysis) clusters (espressomd.cluster_analysis.ClusterStructure property) ClusterStructure (class in espressomd.cluster_analysis) CMake collision_detection (espressomd.system.System attribute) CollisionDetection (class in espressomd.collision_detection) ComFixed (class in espressomd.comfixed) comfixed (espressomd.system.System attribute) ComPosition (class in espressomd.observables) ComVelocity (class in espressomd.observables) constant_pH (espressomd.reaction_methods.ConstantpHEnsemble attribute) ConstantpHEnsemble (class in espressomd.reaction_methods) Constraint (class in espressomd.constraints) Constraints (class in espressomd.constraints) constraints (espressomd.system.System attribute) convert_vector_body_to_space() (espressomd.particle_data.ParticleHandle method) convert_vector_space_to_body() (espressomd.particle_data.ParticleHandle method) corner (espressomd.shapes.Rhomboid attribute) Correlator (class in espressomd.accumulators) CosPersistenceAngles (class in espressomd.observables) CUDA cuda_init_handle (espressomd.system.System attribute) CudaInitHandle (class in espressomd.cuda_init) current_volume() (espressomd.interactions.IBM_VolCons method) cyl_transform_params (espressomd.shapes.HollowConicalFrustum attribute) Cylinder (class in espressomd.shapes) (class in espressomd.visualization) CylindricalDensityProfile (class in espressomd.observables) CylindricalFluxDensityProfile (class in espressomd.observables) CylindricalLBFluxDensityProfileAtParticlePositions (class in espressomd.observables) CylindricalLBVelocityProfile (class in espressomd.observables) CylindricalLBVelocityProfileAtParticlePositions (class in espressomd.observables) CylindricalProfileObservable (class in espressomd.observables) CylindricalTransformationParameters (class in espressomd.math) CylindricalVelocityProfile (class in espressomd.observables) Cython

D

decomposition_type (espressomd.cell_system.CellSystem attribute) default_params() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ElectrostaticExtensions method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.ELC method) (espressomd.electrostatics.ElectrostaticInteraction method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.electrostatics.Scafacos method) (espressomd.integrate.BrownianDynamics method) (espressomd.integrate.Integrator method) (espressomd.integrate.SteepestDescent method) (espressomd.integrate.StokesianDynamics method) (espressomd.integrate.VelocityVerlet method) (espressomd.integrate.VelocityVerletIsotropicNPT method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.FluidActor method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.DLC method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.magnetostatics.Scafacos method) define_bound_methods() (espressomd.script_interface.ScriptInterfaceHelper method) delete_all_bonds() (espressomd.particle_data.ParticleHandle method) delete_bond() (espressomd.particle_data.ParticleHandle method) delete_exclusion() (espressomd.particle_data.ParticleHandle method) delete_particle() (espressomd.reaction_methods.ReactionAlgorithm method) delete_reaction() (espressomd.reaction_methods.ReactionAlgorithm method) delete_verified_bond() (espressomd.particle_data.ParticleHandle method) density (espressomd.electrokinetics.SpecieRoutines attribute) (espressomd.lb.HydrodynamicInteraction attribute) (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property)

DensityProfile (class in espressomd.observables) device (espressomd.cuda_init.CudaInitHandle attribute) DH (class in espressomd.electrostatics) diagonalized_inertia_tensor() (in module espressomd.rotation) Dihedral (class in espressomd.interactions) dimensions (espressomd.MDA_ESP.Timestep property) dip (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) dipm (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) DipolarBarnesHutGpu (class in espressomd.magnetostatics) DipolarDirectSumCpu (class in espressomd.magnetostatics) DipolarDirectSumGpu (class in espressomd.magnetostatics) DipolarDirectSumWithReplicaCpu (class in espressomd.magnetostatics) DipolarP3M (class in espressomd.magnetostatics) DipoleMoment (class in espressomd.observables) direction (espressomd.shapes.Cylinder attribute) (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.HollowConicalFrustum attribute) (espressomd.shapes.Rhomboid attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Torus attribute) director (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) displacement_mc_move_for_particles_of_type() (espressomd.reaction_methods.ReactionAlgorithm method) dist (espressomd.shapes.Wall attribute) distance() (espressomd.system.System method) distance_vec() (espressomd.system.System method) DistanceCriterion (class in espressomd.pair_criteria) distribution() (espressomd.analyze.Analysis method) dividing_plane (espressomd.shapes.Slitpore attribute) DLC (class in espressomd.magnetostatics) DoubleClick (espressomd.visualization.MouseFireEvent attribute) dpd (espressomd.interactions.NonBondedInteractionHandle attribute) dpd_stress() (espressomd.analyze.Analysis method) DPDInteraction (class in espressomd.interactions) DPDStress (class in espressomd.observables) draw() (espressomd.visualization.Cylinder method) (espressomd.visualization.Ellipsoid method) (espressomd.visualization.HollowConicalFrustum method) (espressomd.visualization.Shape method) (espressomd.visualization.SimplePore method) (espressomd.visualization.Slitpore method) (espressomd.visualization.Sphere method) (espressomd.visualization.Spherocylinder method) (espressomd.visualization.Wall method) draw_arrow() (in module espressomd.visualization) draw_box() (in module espressomd.visualization) draw_cylinder() (in module espressomd.visualization) draw_plane() (in module espressomd.visualization) DrudeHelpers (class in espressomd.drude_helpers)

E

E (espressomd.constraints.LinearElectricPotential property) E0 (espressomd.constraints.ElectricPlaneWave property) ek_init() (espressomd.electrokinetics.Electrokinetics method) EKBoundaries (class in espressomd.ekboundaries) ekboundaries (espressomd.system.System attribute) EKBoundary (class in espressomd.ekboundaries) ELC (class in espressomd.electrostatics) ElectricPlaneWave (class in espressomd.constraints) ElectricPotential (class in espressomd.constraints) Electrokinetics (class in espressomd.electrokinetics) ElectrokineticsRoutines (class in espressomd.electrokinetics) ElectrostaticExtensions (class in espressomd.electrostatic_extensions) ElectrostaticInteraction (class in espressomd.electrostatics) Ellipsoid (class in espressomd.shapes) (class in espressomd.visualization) empty() (espressomd.lbboundaries.LBBoundaries method) end_section() (in module espressomd.profiler) Energy (class in espressomd.observables) energy() (espressomd.analyze.Analysis method) EnergyCriterion (class in espressomd.pair_criteria) ERR_MSG (espressomd.utils.array_locked attribute) ESPParser (class in espressomd.MDA_ESP) ESPReader (class in espressomd.MDA_ESP) espressomd module espressomd.accumulators module espressomd.actors module espressomd.analyze module espressomd.bond_breakage module espressomd.cell_system module espressomd.checkpointing module espressomd.cluster_analysis module espressomd.collision_detection module espressomd.comfixed module espressomd.constraints module espressomd.cuda_init module espressomd.drude_helpers module espressomd.ekboundaries module espressomd.electrokinetics module espressomd.electrostatic_extensions module espressomd.electrostatics module espressomd.galilei module espressomd.highlander module espressomd.integrate module

espressomd.interactions module espressomd.io module espressomd.io.mpiio module espressomd.io.writer module espressomd.io.writer.h5md module espressomd.io.writer.vtf module espressomd.lb module espressomd.lbboundaries module espressomd.lees_edwards module espressomd.magnetostatics module espressomd.math module espressomd.MDA_ESP module espressomd.observables module espressomd.pair_criteria module espressomd.particle_data module espressomd.polymer module espressomd.profiler module espressomd.reaction_methods module espressomd.rotation module espressomd.script_interface module espressomd.shapes module espressomd.system module espressomd.thermostat module espressomd.utils module espressomd.version module espressomd.virtual_sites module espressomd.visualization module exclusions (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) exists() (espressomd.particle_data.ParticleList method) ext_force (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) ext_force_density (espressomd.lb.HydrodynamicInteraction attribute) ext_torque (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

F

f (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) FeaturesError FeneBond (class in espressomd.interactions) FFTW fields (espressomd.io.writer.h5md.H5md attribute) file_path (espressomd.io.writer.h5md.H5md attribute) fix (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) FlowField (class in espressomd.constraints) FluidActor (class in espressomd.lb) flush() (espressomd.io.writer.h5md.H5md method)

flux (espressomd.electrokinetics.SpecieRoutines attribute) FluxDensityProfile (class in espressomd.observables) force_cap (espressomd.integrate.IntegratorHandle attribute) (espressomd.system.System attribute) force_unit (espressomd.io.writer.h5md.H5md attribute) ForceDensityProfile (class in espressomd.observables) ForceField (class in espressomd.constraints) format (espressomd.MDA_ESP.ESPParser attribute) (espressomd.MDA_ESP.ESPReader attribute) fractal_dimension() (espressomd.cluster_analysis.Cluster method) FreeMotion (espressomd.visualization.MouseFireEvent attribute) friendly() (in module espressomd.version)

G

g (espressomd.constraints.Gravity property) galilei (espressomd.system.System attribute) galilei_transform() (espressomd.galilei.GalileiTransform method) GalileiTransform (class in espressomd.galilei) gamma (espressomd.constraints.HomogeneousFlowField attribute) (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) gamma_rot (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) gaussian (espressomd.interactions.NonBondedInteractionHandle attribute) GaussianInteraction (class in espressomd.interactions) gay_berne (espressomd.interactions.NonBondedInteractionHandle attribute) GayBerneInteraction (class in espressomd.interactions) generate_caller() (espressomd.script_interface.ScriptInterfaceHelper method) generic_lennard_jones (espressomd.interactions.NonBondedInteractionHandle attribute) GenericLennardJonesInteraction (class in espressomd.interactions) get_acceptance_rate_reaction() (espressomd.reaction_methods.ReactionAlgorithm method) get_available_methods() (espressomd.electrostatics.Scafacos method) (espressomd.magnetostatics.Scafacos method) get_bonded_interaction_type_from_es_core() (in module espressomd.interactions) get_camera_rotation_matrix() (espressomd.visualization.Camera method) get_default_params() (espressomd.interactions.AngleCosine method) (espressomd.interactions.AngleCossquare method) (espressomd.interactions.AngleHarmonic method) (espressomd.interactions.BondedCoulomb method) (espressomd.interactions.BondedCoulombSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.Dihedral method) (espressomd.interactions.FeneBond method) (espressomd.interactions.HarmonicBond method) (espressomd.interactions.IBM_Tribend method) (espressomd.interactions.IBM_Triel method) (espressomd.interactions.IBM_VolCons method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method)

get_extra_clip_plane() (in module espressomd.visualization) get_indices() (espressomd.lb.LBSlice method) get_interpolated_fluid_velocity_at_positions() (espressomd.lb.LBFluidGPU method) get_interpolated_velocity() (espressomd.lb.HydrodynamicInteraction method) get_last_checkpoint_index() (espressomd.checkpointing.Checkpoint method) get_magnetostatics_prefactor() (espressomd.magnetostatics.MagnetostaticInteraction method) get_near_field_delegation() (espressomd.electrostatics.Scafacos method) get_neighbors() (espressomd.cell_system.CellSystem method) get_non_interacting_type() (espressomd.reaction_methods.ReactionAlgorithm method) get_pairs() (espressomd.cell_system.CellSystem method) get_parameter() (espressomd.collision_detection.CollisionDetection method) (espressomd.script_interface.PScriptInterface method) get_params() (espressomd.collision_detection.CollisionDetection method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.integrate.Integrator method) (espressomd.interactions.NonBondedInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.FluidActor method) (espressomd.script_interface.PScriptInterface method) get_registered_objects() (espressomd.checkpointing.Checkpoint method) get_sip() (espressomd.script_interface.PScriptInterface method) get_state() (espressomd.cell_system.CellSystem method) (espressomd.integrate.IntegratorHandle method) (espressomd.thermostat.Thermostat method) get_status() (espressomd.reaction_methods.ReactionAlgorithm method) get_ts() (espressomd.thermostat.Thermostat method) get_values() (espressomd.lb.LBSlice method) get_volume() (espressomd.reaction_methods.ReactionAlgorithm method) get_wall_constraints_in_z_direction() (espressomd.reaction_methods.ReactionAlgorithm method) git_branch() (in module espressomd.version) git_commit() (in module espressomd.version) git_state() (in module espressomd.version) gpu_available() (in module espressomd.cuda_init) Gravity (class in espressomd.constraints) gyration_tensor() (espressomd.analyze.Analysis method)

H

H (espressomd.constraints.HomogeneousMagneticField attribute) H5md (class in espressomd.io.writer.h5md) handle_errors() (in module espressomd.utils) handle_input() (espressomd.visualization.KeyboardManager method) HarmonicBond (class in espressomd.interactions) has_checkpoints() (espressomd.checkpointing.Checkpoint method) has_features() (in module espressomd) hat (espressomd.interactions.NonBondedInteractionHandle attribute) HatInteraction (class in espressomd.interactions) have_quaternion (espressomd.virtual_sites.ActiveVirtualSitesHandle attribute)

hertzian (espressomd.interactions.NonBondedInteractionHandle attribute) HertzianInteraction (class in espressomd.interactions) highest_particle_id (espressomd.particle_data.ParticleList attribute) highlander() (in module espressomd.highlander) Hold (espressomd.visualization.KeyboardFireEvent attribute) HollowConicalFrustum (class in espressomd.shapes) (class in espressomd.visualization) HomogeneousFlowField (class in espressomd.constraints) HomogeneousMagneticField (class in espressomd.constraints) HydrodynamicInteraction (class in espressomd.lb)

I

IBM_Tribend (class in espressomd.interactions) IBM_Triel (class in espressomd.interactions) IBM_VolCons (class in espressomd.interactions) ICC (class in espressomd.electrostatic_extensions) id (espressomd.electrokinetics.Species attribute) (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) image_box (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) index (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) inertia_tensor() (in module espressomd.rotation) Integrator (class in espressomd.integrate) integrator (espressomd.system.System attribute) IntegratorHandle (class in espressomd.integrate) interaction_range (espressomd.cell_system.CellSystem attribute) is_active() (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.FluidActor method)

is_valid() (espressomd.interactions.NonBondedInteraction method) (espressomd.lb.FluidActor method) is_valid_type() (in module espressomd.utils) items() (espressomd.script_interface.ScriptObjectMap method)

K

k (espressomd.constraints.ElectricPlaneWave property) keyboard_down() (espressomd.visualization.KeyboardManager method) keyboard_up() (espressomd.visualization.KeyboardManager method) KeyboardButtonEvent (class in espressomd.visualization) KeyboardFireEvent (class in espressomd.visualization)

KeyboardManager (class in espressomd.visualization) keys() (espressomd.script_interface.ScriptObjectMap method) kill_particle_forces() (espressomd.galilei.GalileiTransform method) kill_particle_motion() (espressomd.galilei.GalileiTransform method) kT (espressomd.lb.HydrodynamicInteraction attribute)

L

lag_times() (espressomd.accumulators.Correlator method) last_iterations() (espressomd.electrostatic_extensions.ICC method) LBBoundaries (class in espressomd.lbboundaries) lbboundaries (espressomd.system.System attribute) LBBoundary (class in espressomd.lbboundaries) LBFluid (class in espressomd.lb) LBFluidGPU (class in espressomd.lb) LBFluidPressureTensor (class in espressomd.observables) LBFluidRoutines (class in espressomd.lb) LBSlice (class in espressomd.lb) LBVelocityProfile (class in espressomd.observables) lees_edwards (espressomd.system.System attribute) lees_edwards_flag (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) lees_edwards_offset (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) LeesEdwards (class in espressomd.lees_edwards) length (espressomd.shapes.Cylinder attribute) (espressomd.shapes.HollowConicalFrustum attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.SpheroCylinder attribute)

length_unit (espressomd.io.writer.h5md.H5md attribute) lennard_jones (espressomd.interactions.NonBondedInteractionHandle attribute) lennard_jones_cos (espressomd.interactions.NonBondedInteractionHandle attribute) lennard_jones_cos2 (espressomd.interactions.NonBondedInteractionHandle attribute) LennardJonesCos2Interaction (class in espressomd.interactions) LennardJonesCosInteraction (class in espressomd.interactions) LennardJonesInteraction (class in espressomd.interactions) linear_momentum() (espressomd.analyze.Analysis method) linear_polymer_positions() (in module espressomd.polymer) LinearElectricPotential (class in espressomd.constraints) LinearShear (class in espressomd.lees_edwards) list_devices() (espressomd.cuda_init.CudaInitHandle method) list_devices_properties() (espressomd.cuda_init.CudaInitHandle method) load() (espressomd.checkpointing.Checkpoint method) load_checkpoint() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) longest_distance() (espressomd.cluster_analysis.Cluster method) lower_smoothing_radius (espressomd.shapes.Slitpore attribute)

M

MagneticDipoleMoment (class in espressomd.observables) MagnetostaticInteraction (class in espressomd.magnetostatics) major() (in module espressomd.version) make_backward_reaction() (espressomd.reaction_methods.SingleReaction method) mass (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) mass_unit (espressomd.io.writer.h5md.H5md attribute) materials (espressomd.visualization.openGLLive attribute) matrix_to_quat() (in module espressomd.rotation) max_cut_bonded (espressomd.cell_system.CellSystem attribute) (espressomd.system.System attribute) max_cut_nonbonded (espressomd.cell_system.CellSystem attribute) (espressomd.system.System attribute) max_oif_objects (espressomd.system.System attribute) mean() (espressomd.accumulators.MeanVarianceCalculator method) MeanVarianceCalculator (class in espressomd.accumulators) min_dist() (espressomd.analyze.Analysis method) (espressomd.constraints.ShapeBasedConstraint method) min_global_cut (espressomd.system.System attribute) minor() (in module espressomd.version) missing_features() (in module espressomd) MMM1D (class in espressomd.electrostatics) MMM1DGPU (class in espressomd.electrostatics) module espressomd espressomd.accumulators espressomd.actors espressomd.analyze espressomd.bond_breakage espressomd.cell_system espressomd.checkpointing espressomd.cluster_analysis espressomd.collision_detection espressomd.comfixed espressomd.constraints espressomd.cuda_init espressomd.drude_helpers espressomd.ekboundaries espressomd.electrokinetics espressomd.electrostatic_extensions espressomd.electrostatics espressomd.galilei espressomd.highlander espressomd.integrate espressomd.interactions espressomd.io espressomd.io.mpiio espressomd.io.writer espressomd.io.writer.h5md espressomd.io.writer.vtf espressomd.lb espressomd.lbboundaries espressomd.lees_edwards espressomd.magnetostatics espressomd.math espressomd.MDA_ESP espressomd.observables espressomd.pair_criteria espressomd.particle_data espressomd.polymer espressomd.profiler espressomd.reaction_methods espressomd.rotation espressomd.script_interface espressomd.shapes espressomd.system espressomd.thermostat espressomd.utils espressomd.version espressomd.virtual_sites espressomd.visualization

mol_id (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) moment_of_inertia_matrix() (espressomd.analyze.Analysis method) morse (espressomd.interactions.NonBondedInteractionHandle attribute) MorseInteraction (class in espressomd.interactions) mouse_click() (espressomd.visualization.MouseManager method) mouse_move() (espressomd.visualization.MouseManager method) MouseButtonEvent (class in espressomd.visualization) MouseFireEvent (class in espressomd.visualization) MouseManager (class in espressomd.visualization) move_backward() (espressomd.visualization.Camera method) move_down() (espressomd.visualization.Camera method) move_forward() (espressomd.visualization.Camera method) move_left() (espressomd.visualization.Camera method) move_right() (espressomd.visualization.Camera method) move_up() (espressomd.visualization.Camera method) MPI Mpiio (class in espressomd.io.mpiio) mu_E (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

N

n_part_types (espressomd.particle_data.ParticleList attribute) n_rigidbonds (espressomd.particle_data.ParticleList attribute) name() (espressomd.script_interface.PScriptInterface method) nbhood() (espressomd.analyze.Analysis method) nesting_level() (in module espressomd.utils) neutralize_system() (espressomd.electrokinetics.Electrokinetics method) node (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) node_grid (espressomd.cell_system.CellSystem attribute)

nodes() (espressomd.lb.HydrodynamicInteraction method) non_bonded_inter (espressomd.system.System attribute) non_bonded_loop_trace() (espressomd.cell_system.CellSystem method) NonBondedInteraction (class in espressomd.interactions) NonBondedInteractionHandle (class in espressomd.interactions) NonBondedInteractions (class in espressomd.interactions) normal (espressomd.shapes.Torus attribute) (espressomd.shapes.Wall attribute) normalize_and_check_bond_or_throw_exception() (espressomd.particle_data.ParticleHandle method) number_of_particles() (espressomd.system.System method)

O

Observable (class in espressomd.observables) Off (class in espressomd.lees_edwards) OifGlobalForces (class in espressomd.interactions) OifLocalForces (class in espressomd.interactions) omega (espressomd.constraints.ElectricPlaneWave property) omega_body (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

omega_lab (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) only_positive (espressomd.constraints.ShapeBasedConstraint attribute) open (espressomd.shapes.Cylinder attribute) openGLLive (class in espressomd.visualization) OscillatoryShear (class in espressomd.lees_edwards) override_cutoff_check (espressomd.virtual_sites.ActiveVirtualSitesHandle attribute)

P

P3M (class in espressomd.electrostatics) P3MGPU (class in espressomd.electrostatics) pairs() (espressomd.particle_data.ParticleList method) params (espressomd.interactions.BondedInteraction property) parse() (espressomd.MDA_ESP.ESPParser method) part (espressomd.system.System attribute) particle_energy() (espressomd.analyze.Analysis method) particle_ids() (espressomd.cluster_analysis.Cluster method) particle_type (espressomd.constraints.ShapeBasedConstraint attribute) particle_velocity (espressomd.constraints.ShapeBasedConstraint attribute) ParticleAngularVelocities (class in espressomd.observables) ParticleBodyAngularVelocities (class in espressomd.observables) ParticleBodyVelocities (class in espressomd.observables) ParticleDistances (class in espressomd.observables) ParticleForces (class in espressomd.observables) ParticleHandle (class in espressomd.particle_data) ParticleList (class in espressomd.particle_data) ParticlePositions (class in espressomd.observables) particles() (espressomd.cluster_analysis.Cluster method) ParticleSlice (class in espressomd.particle_data) ParticleVelocities (class in espressomd.observables) penetrable (espressomd.constraints.ShapeBasedConstraint attribute) periodicity (espressomd.system.System attribute) phi (espressomd.constraints.ElectricPlaneWave property) phi0 (espressomd.constraints.LinearElectricPotential property) pi (espressomd.interactions.TabulatedAngle attribute) (espressomd.interactions.TabulatedDihedral attribute)

PObjectRef (class in espressomd.script_interface) population (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) pore_length (espressomd.shapes.Slitpore attribute) pore_mouth (espressomd.shapes.Slitpore attribute) pore_width (espressomd.shapes.Slitpore attribute) pos (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) pos_folded (espressomd.particle_data.ParticleHandle attribute) pos_offset (espressomd.lees_edwards.LeesEdwards attribute) potential (espressomd.electrokinetics.ElectrokineticsRoutines attribute) PotentialField (class in espressomd.constraints) Pressed (espressomd.visualization.KeyboardFireEvent attribute) Pressure (class in espressomd.observables) pressure() (espressomd.analyze.Analysis method) pressure_tensor (espressomd.lb.HydrodynamicInteraction attribute) (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) pressure_tensor() (espressomd.analyze.Analysis method) pressure_tensor_neq (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) PressureTensor (class in espressomd.observables) print_sip() (espressomd.script_interface.PObjectRef method) ProfileObservable (class in espressomd.observables) protocol (espressomd.lees_edwards.LeesEdwards attribute) PScriptInterface (class in espressomd.script_interface) py_number_of_species (espressomd.electrokinetics.Species attribute) Python

Q

q (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

QuarticBond (class in espressomd.interactions) quat (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

R

r1 (espressomd.shapes.HollowConicalFrustum attribute) r2 (espressomd.shapes.HollowConicalFrustum attribute) radius (espressomd.shapes.Cylinder attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Torus attribute) RDF (class in espressomd.observables) reaction() (espressomd.reaction_methods.ReactionAlgorithm method) ReactionAlgorithm (class in espressomd.reaction_methods) ReactionEnsemble (class in espressomd.reaction_methods) ReactionField (class in espressomd.electrostatics) read() (espressomd.io.mpiio.Mpiio method) read_signals() (espressomd.checkpointing.Checkpoint method) recover() (espressomd.thermostat.Thermostat method) register() (espressomd.checkpointing.Checkpoint method) register_button() (espressomd.visualization.KeyboardManager method) (espressomd.visualization.MouseManager method) register_callback() (espressomd.visualization.openGLLive method) register_signal() (espressomd.checkpointing.Checkpoint method) Released (espressomd.visualization.KeyboardFireEvent attribute) remove() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.actors.Actors method) (espressomd.constraints.Constraints method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.particle_data.ParticleHandle method) (espressomd.script_interface.ScriptObjectMap method) (espressomd.shapes.Union method) remove_constraint() (espressomd.reaction_methods.ReactionAlgorithm method) required_keys() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ElectrostaticExtensions method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.ELC method) (espressomd.electrostatics.ElectrostaticInteraction method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.electrostatics.Scafacos method) (espressomd.integrate.BrownianDynamics method) (espressomd.integrate.Integrator method) (espressomd.integrate.SteepestDescent method) (espressomd.integrate.StokesianDynamics method) (espressomd.integrate.VelocityVerlet method) (espressomd.integrate.VelocityVerletIsotropicNPT method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.WCAInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.FluidActor method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.DLC method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.magnetostatics.Scafacos method) (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) (espressomd.reaction_methods.SingleReaction method) (espressomd.reaction_methods.WidomInsertion method)

reset() (espressomd.interactions.NonBondedInteractions method) resort() (espressomd.cell_system.CellSystem method) result() (espressomd.accumulators.Correlator method) Rhomboid (class in espressomd.shapes) RigidBond (class in espressomd.interactions) rinertia (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) rotate() (espressomd.particle_data.ParticleHandle method) rotate_camera() (espressomd.visualization.Camera method) rotate_system() (espressomd.system.System method) rotate_system_x() (espressomd.visualization.Camera method) rotate_system_XL() (espressomd.visualization.Camera method) rotate_system_XR() (espressomd.visualization.Camera method) rotate_system_y() (espressomd.visualization.Camera method) rotate_system_YL() (espressomd.visualization.Camera method) rotate_system_YR() (espressomd.visualization.Camera method) rotate_system_z() (espressomd.visualization.Camera method) rotate_system_ZL() (espressomd.visualization.Camera method) rotate_system_ZR() (espressomd.visualization.Camera method) rotate_vector() (espressomd.visualization.Camera method) rotation (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) rotation_helper() (in module espressomd.visualization) run() (espressomd.integrate.Integrator method) (espressomd.integrate.IntegratorHandle method) (espressomd.integrate.SteepestDescent method) (espressomd.visualization.openGLLive method) run_for_all_pairs() (espressomd.cluster_analysis.ClusterStructure method) run_for_bonded_particles() (espressomd.cluster_analysis.ClusterStructure method)

S

sample_sizes() (espressomd.accumulators.Correlator method) save() (espressomd.checkpointing.Checkpoint method) save_checkpoint() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) Scafacos (class in espressomd.electrostatics) (class in espressomd.magnetostatics) screenshot() (espressomd.visualization.openGLLive method) script_interface_register() (in module espressomd.script_interface) script_path (espressomd.io.writer.h5md.H5md attribute) ScriptInterfaceHelper (class in espressomd.script_interface) ScriptObjectList (class in espressomd.script_interface) ScriptObjectMap (class in espressomd.script_interface) seed (espressomd.lb.HydrodynamicInteraction attribute) select() (espressomd.particle_data.ParticleList method) set_boundary_conditions() (espressomd.lees_edwards.LeesEdwards method) set_brownian() (espressomd.thermostat.Thermostat method) set_brownian_dynamics() (espressomd.integrate.IntegratorHandle method) set_cylindrical_constraint_in_z_direction() (espressomd.reaction_methods.ReactionAlgorithm method) set_default_params() (espressomd.interactions.TabulatedNonBonded method) set_density() (espressomd.electrokinetics.Electrokinetics method) set_dpd() (espressomd.thermostat.Thermostat method) set_hybrid_decomposition() (espressomd.cell_system.CellSystem method) set_interpolation_order() (espressomd.lb.HydrodynamicInteraction method) set_isotropic_npt() (espressomd.integrate.IntegratorHandle method) set_langevin() (espressomd.thermostat.Thermostat method) set_lb() (espressomd.thermostat.Thermostat method) set_n_square() (espressomd.cell_system.CellSystem method) set_near_field_delegation() (espressomd.electrostatics.Scafacos method) set_non_interacting_type() (espressomd.reaction_methods.ReactionAlgorithm method) set_npt() (espressomd.thermostat.Thermostat method) set_nvt() (espressomd.integrate.IntegratorHandle method) set_params() (espressomd.collision_detection.CollisionDetection method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.FluidActor method) (espressomd.script_interface.PScriptInterface method) set_regular_decomposition() (espressomd.cell_system.CellSystem method) set_slice_one_for_all() (in module espressomd.particle_data) set_slice_one_for_each() (in module espressomd.particle_data)

set_solid_material() (in module espressomd.visualization) set_steepest_descent() (espressomd.integrate.IntegratorHandle method) set_stokesian() (espressomd.thermostat.Thermostat method) set_stokesian_dynamics() (espressomd.integrate.IntegratorHandle method) set_values() (espressomd.lb.LBSlice method) set_volume() (espressomd.reaction_methods.ReactionAlgorithm method) set_vv() (espressomd.integrate.IntegratorHandle method) set_wall_constraints_in_z_direction() (espressomd.reaction_methods.ReactionAlgorithm method) setup_and_add_drude_exclusion_bonds() (espressomd.drude_helpers.DrudeHelpers method) setup_diamond_polymer() (in module espressomd.polymer) setup_intramol_exclusion_bonds() (espressomd.drude_helpers.DrudeHelpers method) setup_type_map() (espressomd.system.System method) Shape (class in espressomd.shapes) (class in espressomd.visualization) shape (espressomd.constraints.ShapeBasedConstraint attribute) (espressomd.lb.HydrodynamicInteraction attribute) shape() (espressomd.observables.Observable method) ShapeBasedConstraint (class in espressomd.constraints) shear_direction (espressomd.lees_edwards.LeesEdwards attribute) shear_plane_normal (espressomd.lees_edwards.LeesEdwards attribute) shear_velocity (espressomd.lees_edwards.LeesEdwards attribute) SimplePore (class in espressomd.shapes) (class in espressomd.visualization) SingleReaction (class in espressomd.reaction_methods) sip (espressomd.script_interface.PScriptInterface attribute) size() (espressomd.cluster_analysis.Cluster method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.shapes.Union method) skin (espressomd.cell_system.CellSystem attribute) Slitpore (class in espressomd.shapes) (class in espressomd.visualization) smooth_step (espressomd.interactions.NonBondedInteractionHandle attribute) smoothing_radius (espressomd.shapes.SimplePore attribute) SmoothStepInteraction (class in espressomd.interactions) soft_sphere (espressomd.interactions.NonBondedInteractionHandle attribute) SoftSphereInteraction (class in espressomd.interactions) SpecieRoutines (class in espressomd.electrokinetics) Species (class in espressomd.electrokinetics) Sphere (class in espressomd.shapes) (class in espressomd.visualization) SpheroCylinder (class in espressomd.shapes) Spherocylinder (class in espressomd.visualization) start() (espressomd.visualization.openGLLive method) std_error() (espressomd.accumulators.MeanVarianceCalculator method) SteepestDescent (class in espressomd.integrate) StokesianDynamics (class in espressomd.integrate) Stream (class in espressomd.MDA_ESP) structure_factor() (espressomd.analyze.Analysis method) suspend() (espressomd.thermostat.Thermostat method) swimming (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) System (class in espressomd.system) system (espressomd.lb.FluidActor attribute) system_CMS() (espressomd.galilei.GalileiTransform method) system_CMS_velocity() (espressomd.galilei.GalileiTransform method)

T

tabulated (espressomd.interactions.NonBondedInteractionHandle attribute) TabulatedAngle (class in espressomd.interactions) TabulatedDihedral (class in espressomd.interactions) TabulatedDistance (class in espressomd.interactions) TabulatedNonBonded (class in espressomd.interactions) tau (espressomd.lb.HydrodynamicInteraction attribute) ThereCanOnlyBeOne ThermalizedBond (class in espressomd.interactions) Thermostat (class in espressomd.thermostat) thermostat (espressomd.system.System attribute) thickness (espressomd.shapes.HollowConicalFrustum attribute) thole (espressomd.interactions.NonBondedInteractionHandle attribute) time (espressomd.integrate.IntegratorHandle attribute) (espressomd.system.System attribute) time_series() (espressomd.accumulators.TimeSeries method) time_step (espressomd.integrate.IntegratorHandle attribute) (espressomd.system.System attribute) time_unit (espressomd.io.writer.h5md.H5md attribute) TimeSeries (class in espressomd.accumulators) Timestep (class in espressomd.MDA_ESP) to_char_pointer() (in module espressomd.utils) to_dict() (espressomd.particle_data.ParticleHandle method) (espressomd.particle_data.ParticleSlice method) to_str() (in module espressomd.utils) torque_lab (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) Torus (class in espressomd.shapes) total_force() (espressomd.constraints.ShapeBasedConstraint method) total_normal_force() (espressomd.constraints.ShapeBasedConstraint method) TotalForce (class in espressomd.observables) trajectory (espressomd.MDA_ESP.Stream property) tube_radius (espressomd.shapes.Torus attribute) tune_skin() (espressomd.cell_system.CellSystem method) turn_off() (espressomd.thermostat.Thermostat method) type (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) type1 (espressomd.interactions.NonBondedInteractionHandle attribute) type2 (espressomd.interactions.NonBondedInteractionHandle attribute) type_name() (espressomd.interactions.AngleCosine method) (espressomd.interactions.AngleCossquare method) (espressomd.interactions.AngleHarmonic method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BondedCoulomb method) (espressomd.interactions.BondedCoulombSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.Dihedral method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.FeneBond method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HarmonicBond method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.IBM_Tribend method) (espressomd.interactions.IBM_Triel method) (espressomd.interactions.IBM_VolCons method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedAngle method) (espressomd.interactions.TabulatedDihedral method) (espressomd.interactions.TabulatedDistance method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method) (espressomd.interactions.WCAInteraction method)

type_number() (espressomd.interactions.AngleCosine method) (espressomd.interactions.AngleCossquare method) (espressomd.interactions.AngleHarmonic method) (espressomd.interactions.BondedCoulomb method) (espressomd.interactions.BondedCoulombSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.Dihedral method) (espressomd.interactions.FeneBond method) (espressomd.interactions.HarmonicBond method) (espressomd.interactions.IBM_Tribend method) (espressomd.interactions.IBM_Triel method) (espressomd.interactions.IBM_VolCons method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.TabulatedAngle method) (espressomd.interactions.TabulatedDihedral method) (espressomd.interactions.TabulatedDistance method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method)

U

u (espressomd.constraints.HomogeneousFlowField property) Union (class in espressomd.shapes) units (espressomd.MDA_ESP.ESPReader attribute) UnitSystem (class in espressomd.io.writer.h5md) unregister() (espressomd.checkpointing.Checkpoint method) update() (espressomd.accumulators.MeanVarianceCalculator method) (espressomd.accumulators.TimeSeries method) (espressomd.particle_data.ParticleHandle method) (espressomd.visualization.openGLLive method)

update_modelview() (espressomd.visualization.Camera method) update_system_info() (espressomd.visualization.openGLLive method) upper_smoothing_radius (espressomd.shapes.Slitpore attribute) use_verlet_lists (espressomd.cell_system.CellSystem attribute) user_interactions (espressomd.interactions.NonBondedInteraction attribute)

V

v (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) valid_fields() (espressomd.io.writer.h5md.H5md method) valid_keys() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ElectrostaticExtensions method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.ELC method) (espressomd.electrostatics.ElectrostaticInteraction method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.electrostatics.Scafacos method) (espressomd.integrate.BrownianDynamics method) (espressomd.integrate.Integrator method) (espressomd.integrate.SteepestDescent method) (espressomd.integrate.StokesianDynamics method) (espressomd.integrate.VelocityVerlet method) (espressomd.integrate.VelocityVerletIsotropicNPT method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.IBM_Tribend method) (espressomd.interactions.IBM_Triel method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.WCAInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.FluidActor method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.DLC method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.magnetostatics.Scafacos method) (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) (espressomd.reaction_methods.SingleReaction method) (espressomd.reaction_methods.WidomInsertion method) validate_params() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrostatic_extensions.ElectrostaticExtensions method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.ELC method) (espressomd.electrostatics.ElectrostaticInteraction method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.Scafacos method) (espressomd.integrate.BrownianDynamics method) (espressomd.integrate.Integrator method) (espressomd.integrate.SteepestDescent method) (espressomd.integrate.StokesianDynamics method) (espressomd.integrate.VelocityVerlet method) (espressomd.integrate.VelocityVerletIsotropicNPT method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.Dihedral method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.GaussianInteraction method) (espressomd.interactions.GayBerneInteraction method) (espressomd.interactions.GenericLennardJonesInteraction method) (espressomd.interactions.HatInteraction method) (espressomd.interactions.HertzianInteraction method) (espressomd.interactions.IBM_Tribend method) (espressomd.interactions.IBM_Triel method) (espressomd.interactions.LennardJonesCos2Interaction method) (espressomd.interactions.LennardJonesCosInteraction method) (espressomd.interactions.LennardJonesInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TabulatedAngle method) (espressomd.interactions.TabulatedDihedral method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.WCAInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.FluidActor method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.DLC method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.magnetostatics.Scafacos method) (in module espressomd.polymer)

variance() (espressomd.accumulators.MeanVarianceCalculator method) velocity (espressomd.lb.LBFluidRoutines attribute) (espressomd.lb.LBSlice property) velocity_difference() (espressomd.system.System method) velocity_unit (espressomd.io.writer.h5md.H5md attribute) VelocityVerlet (class in espressomd.integrate) VelocityVerletIsotropicNPT (class in espressomd.integrate) Virtual (class in espressomd.interactions) virtual (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) virtual_sites (espressomd.system.System attribute) VirtualSitesInertialessTracers (class in espressomd.virtual_sites) VirtualSitesOff (class in espressomd.virtual_sites) VirtualSitesRelative (class in espressomd.virtual_sites) viscosity (espressomd.lb.HydrodynamicInteraction attribute) volume() (espressomd.system.System method) vs_auto_relate_to() (espressomd.particle_data.ParticleHandle method) vs_quat (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) vs_relative (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) vtf_pid_map() (in module espressomd.io.writer.vtf)

W

Wall (class in espressomd.shapes) (class in espressomd.visualization) WCAInteraction (class in espressomd.interactions) WidomInsertion (class in espressomd.reaction_methods) write() (espressomd.io.mpiio.Mpiio method) (espressomd.io.writer.h5md.H5md method) write_boundary() (espressomd.lb.HydrodynamicInteraction method) write_velocity() (espressomd.lb.HydrodynamicInteraction method) write_vtk_boundary() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) write_vtk_density() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method)

write_vtk_flux() (espressomd.electrokinetics.Species method) write_vtk_flux_fluc() (espressomd.electrokinetics.Species method) write_vtk_flux_link() (espressomd.electrokinetics.Species method) write_vtk_lbforce() (espressomd.electrokinetics.Electrokinetics method) write_vtk_particle_potential() (espressomd.electrokinetics.Electrokinetics method) write_vtk_potential() (espressomd.electrokinetics.Electrokinetics method) write_vtk_velocity() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) writevcf() (in module espressomd.io.writer.vtf) writevsf() (in module espressomd.io.writer.vtf) writevtk() (espressomd.particle_data.ParticleList method)