Index

A

a (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.Rhomboid attribute) add() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.constraints.Constraints method) (espressomd.electrokinetics.EKContainer method) (espressomd.electrokinetics.EKReactions method) (espressomd.interactions.BondedInteractions 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) (espressomd.particle_data.ParticleSlice method) add_boundary_from_shape() (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) add_dipole_particle() (in module espressomd.swimmer_helpers) add_drude_particle_to_core() (espressomd.drude_helpers.DrudeHelpers method) add_exclusion() (espressomd.particle_data.ParticleHandle method) (espressomd.particle_data.ParticleSlice method) add_ghost_particle() (espressomd.zn.EspressoConverter method) add_intramol_exclusion_bonds() (espressomd.drude_helpers.DrudeHelpers method) add_node_to_index() (espressomd.electrokinetics.EKIndexedReaction method) add_reaction() (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) (espressomd.reaction_methods.WidomInsertion method) add_thole_pair_damping() (espressomd.drude_helpers.DrudeHelpers method) add_verified_bond() (espressomd.particle_data.ParticleHandle method)

add_vtk_writer() (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) all() (espressomd.particle_data.ParticleList method) all_features() (in module espressomd.code_info) Analysis (class in espressomd.analyze) analysis (espressomd.system.System attribute) ANGLE_COSINE (espressomd.interactions.BONDED_IA attribute) ANGLE_COSSQUARE (espressomd.interactions.BONDED_IA attribute) ANGLE_HARMONIC (espressomd.interactions.BONDED_IA 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) array_variant (class in espressomd.script_interface) ase (espressomd.system.System property) ASEInterface (class in espressomd.plugins.ase) assert_features() (in module espressomd.code_features) auto_exclusions() (espressomd.particle_data.ParticleList method) (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() (espressomd.profiler.Caliper method) bin_centers() (espressomd.observables.ProfileObservable method) (espressomd.observables.RDF method) bin_edges() (espressomd.observables.ProfileObservable method) BindAtPointOfCollision (class in espressomd.collision_detection) BindCenters (class in espressomd.collision_detection) 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_COULOMB (espressomd.interactions.BONDED_IA attribute) BONDED_COULOMB_SR (espressomd.interactions.BONDED_IA attribute) BONDED_IA (class in espressomd.interactions) bonded_inter (espressomd.system.System attribute) BondedCoulomb (class in espressomd.interactions) BondedCoulombSRBond (class in espressomd.interactions) BondedInteraction (class in espressomd.interactions)

BondedInteractions (class in espressomd.interactions) bonds (espressomd.particle_data.ParticleHandle property) (espressomd.particle_data.ParticleSlice property) Boost boundary (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) boundary_force (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) box_l (espressomd.system.System attribute) BreakageSpec (class in espressomd.bond_breakage) BreakageSpecs (class in espressomd.bond_breakage) Brownian (class in espressomd.thermostat) BrownianDynamics (class in espressomd.integrate) BuckinghamInteraction (class in espressomd.interactions) build_type() (in module espressomd.code_info) 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_cylinder_tangential_vectors() (in module espressomd.lb) calc_quaternions_from_angles() (in module espressomd.math) 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.ParticleDipoleFields method) (espressomd.observables.ParticleDirectors 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_acceptance_probability() (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) calculate_excess_chemical_potential() (espressomd.reaction_methods.WidomInsertion method) calculate_particle_insertion_potential_energy() (espressomd.reaction_methods.WidomInsertion method) Caliper (class in espressomd.profiler) 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_reaction_method() (espressomd.reaction_methods.ReactionAlgorithm method) check_required_keys() (in module espressomd.utils)

check_type_or_throw_except() (in module espressomd.utils) check_valid_keys() (in module espressomd.utils) Checkpoint (class in espressomd.checkpointing) chunks() (espressomd.particle_data.ParticleSlice method) cid_for_particle() (espressomd.cluster_analysis.ClusterStructure method) clear() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.accumulators.TimeSeries method) (espressomd.cluster_analysis.ClusterStructure method) (espressomd.constraints.Constraints method) (espressomd.electrokinetics.EKContainer method) (espressomd.electrokinetics.EKReactions method) (espressomd.interactions.BondedInteractions method) (espressomd.particle_data.ParticleList method) (espressomd.script_interface.ScriptObjectMap method) (espressomd.shapes.Union method) clear_boundaries() (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) clear_density_boundaries() (espressomd.electrokinetics.EKSpecies method) clear_flux_boundaries() (espressomd.electrokinetics.EKSpecies method) clear_vtk_writers() (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla 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) Container (class in espressomd.electrostatics) (class in espressomd.magnetostatics) 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) cut_bond() (espressomd.zn.EspressoConverter method) cutoff (espressomd.interactions.LennardJonesCos2Interaction property) (espressomd.interactions.TabulatedNonBonded property) (espressomd.interactions.WCAInteraction property) 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

deactivate() (espressomd.interactions.NonBondedInteraction method) decode() (espressomd.zn.EspressoConverter method) decomposition_type (espressomd.cell_system.CellSystem attribute) default_params() (espressomd.detail.walberla.LatticeWalberla method) (espressomd.detail.walberla.VTKOutputBase method) (espressomd.electrokinetics.EKSpecies 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.P3M method) (espressomd.electrostatics.P3MGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.electrostatics.Scafacos 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.TholeInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.lb.LBFluidWalberla method) (espressomd.lb.LBFluidWalberlaGPU method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu 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) (espressomd.particle_data.ParticleSlice method) delete_bond() (espressomd.particle_data.ParticleHandle method) (espressomd.particle_data.ParticleSlice method) delete_exclusion() (espressomd.particle_data.ParticleHandle method) (espressomd.particle_data.ParticleSlice 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.EKSpeciesNode property) (espressomd.electrokinetics.EKSpeciesSlice property) (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property)

density_boundary (espressomd.electrokinetics.EKSpeciesNode property) (espressomd.electrokinetics.EKSpeciesSlice property) DensityBoundary (class in espressomd.electrokinetics) 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) DIHEDRAL (espressomd.interactions.BONDED_IA attribute) dip (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) dip_fld (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) dipm (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) DipolarDirectSumCpu (class in espressomd.magnetostatics) DipolarDirectSumGpu (class in espressomd.magnetostatics) DipolarP3M (class in espressomd.magnetostatics) dipole_fields() (espressomd.analyze.Analysis method) 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_stress() (espressomd.analyze.Analysis method) DPDInteraction (class in espressomd.interactions) DPDStress (class in espressomd.observables) DPDThermostat (class in espressomd.thermostat) 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_constraints() (espressomd.zn.Visualizer method) 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) edge_detection() (in module espressomd.lb) EKBulkReaction (class in espressomd.electrokinetics) EKContainer (class in espressomd.electrokinetics) ekcontainer (espressomd.system.System property) EKFFT (class in espressomd.electrokinetics) EKIndexedReaction (class in espressomd.electrokinetics) EKNone (class in espressomd.electrokinetics) EKReactant (class in espressomd.electrokinetics) EKReactions (class in espressomd.electrokinetics) EKSpecies (class in espressomd.electrokinetics) EKSpeciesNode (class in espressomd.electrokinetics) EKSpeciesSlice (class in espressomd.electrokinetics) ELC (class in espressomd.electrostatics) ElectricPlaneWave (class in espressomd.constraints) ElectricPotential (class in espressomd.constraints) ElectrostaticExtensions (class in espressomd.electrostatic_extensions) ElectrostaticInteraction (class in espressomd.electrostatics) Ellipsoid (class in espressomd.shapes) (class in espressomd.visualization) encode() (espressomd.zn.EspressoConverter method) end_section() (espressomd.profiler.Caliper method) Energy (class in espressomd.observables) energy() (espressomd.analyze.Analysis method) EnergyCriterion (class in espressomd.pair_criteria) ERR_MSG (espressomd.utils.array_locked attribute) error_tolerance (espressomd.io.vtk.VTKReader attribute) EspressoConverter (class in espressomd.zn) espressomd module espressomd.accumulators module espressomd.analyze module espressomd.bond_breakage module espressomd.cell_system module espressomd.checkpointing module espressomd.cluster_analysis module espressomd.code_features module espressomd.code_info module espressomd.collision_detection module espressomd.comfixed module espressomd.constraints module espressomd.cuda_init module espressomd.detail module espressomd.detail.walberla module espressomd.drude_helpers 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.vtk module espressomd.io.writer module espressomd.io.writer.h5md module espressomd.io.writer.vtf module espressomd.lb module espressomd.lees_edwards module espressomd.magnetostatics module espressomd.math module espressomd.observables module espressomd.pair_criteria module espressomd.particle_data module espressomd.plugins module espressomd.plugins.ase module espressomd.polymer module espressomd.profiler module espressomd.propagation module espressomd.reaction_methods module espressomd.rotation module espressomd.script_interface module espressomd.shapes module espressomd.swimmer_helpers module espressomd.system module espressomd.thermostat module espressomd.utils module espressomd.version module espressomd.visualization module espressomd.zn module exclusions (espressomd.particle_data.ParticleHandle property) (espressomd.particle_data.ParticleSlice property) exists() (espressomd.particle_data.ParticleList method) ext_force (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) ext_torque (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property)

F

f (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) features() (in module espressomd.code_info) FeaturesError FENE (espressomd.interactions.BONDED_IA attribute) 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)

flush() (espressomd.io.writer.h5md.H5md method) flux_boundary (espressomd.electrokinetics.EKSpeciesNode property) (espressomd.electrokinetics.EKSpeciesSlice property) FluxBoundary (class in espressomd.electrokinetics) FluxDensityProfile (class in espressomd.observables) force_cap (espressomd.system.System property) force_unit (espressomd.io.writer.h5md.H5md attribute) ForceDensityProfile (class in espressomd.observables) ForceField (class in espressomd.constraints) 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) GaussianInteraction (class in espressomd.interactions) GayBerneInteraction (class in espressomd.interactions) generate_caller() (espressomd.script_interface.ScriptInterfaceHelper method) generic_oneway_reaction() (espressomd.reaction_methods.ReactionAlgorithm method) GenericLennardJonesInteraction (class in espressomd.interactions) get() (espressomd.plugins.ase.ASEInterface method) get_acceptance_rate_configurational_moves() (espressomd.reaction_methods.ReactionAlgorithm method) get_acceptance_rate_reaction() (espressomd.reaction_methods.ReactionAlgorithm method) get_array_names() (espressomd.io.vtk.VTKReader class method) get_available_methods() (espressomd.electrostatics.Scafacos method) (espressomd.magnetostatics.Scafacos method) get_bonds() (espressomd.zn.EspressoConverter method) get_camera_rotation_matrix() (espressomd.visualization.Camera method) get_default_colors() (espressomd.zn.EspressoConverter 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.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.ThermalizedBond method) (espressomd.interactions.Virtual method)

get_default_radii() (espressomd.zn.EspressoConverter method) get_extra_clip_plane() (in module espressomd.visualization) get_interpolated_velocity() (espressomd.lb.LBFluidWalberla method) get_intersections() (espressomd.zn.WallIntersection 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_node_indices_inside_shape() (espressomd.detail.walberla.LatticeWalberla method) get_nodes_inside_shape() (espressomd.detail.walberla.LatticeModel method) get_non_interacting_type() (espressomd.reaction_methods.ReactionAlgorithm method) get_pairs() (espressomd.cell_system.CellSystem method) get_parameter() (espressomd.script_interface.PScriptInterface method) get_params() (espressomd.io.writer.h5md.H5md method) (espressomd.script_interface.PScriptInterface method) get_piece_topology() (espressomd.io.vtk.VTKReader class method) get_registered_objects() (espressomd.checkpointing.Checkpoint method) get_shape_bitmask() (espressomd.detail.walberla.LatticeModel method) (espressomd.detail.walberla.LatticeWalberla method) get_sip() (espressomd.script_interface.PScriptInterface method) get_slice_bounding_box() (in module espressomd.detail.walberla) get_state() (espressomd.cell_system.CellSystem method) get_status() (espressomd.reaction_methods.ReactionAlgorithm 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) GlueToSurface (class in espressomd.collision_detection) 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) handle_sigint() (espressomd.integrate.Integrator method) HARMONIC (espressomd.interactions.BONDED_IA attribute) HarmonicBond (class in espressomd.interactions) has_checkpoints() (espressomd.checkpointing.Checkpoint method) has_features() (in module espressomd.code_features)

HatInteraction (class in espressomd.interactions) HertzianInteraction (class in espressomd.interactions) highest_particle_id (espressomd.particle_data.ParticleList property) 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_TRIBEND (espressomd.interactions.BONDED_IA attribute) IBM_Triel (class in espressomd.interactions) IBM_TRIEL (espressomd.interactions.BONDED_IA attribute) IBM_VolCons (class in espressomd.interactions) IBM_VOLUME_CONSERVATION (espressomd.interactions.BONDED_IA attribute) ICC (class in espressomd.electrostatic_extensions) id (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) image_box (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) index (espressomd.electrokinetics.EKSpeciesNode property) (espressomd.lb.LBFluidNodeWalberla property)

inertia_tensor() (in module espressomd.rotation) instance (espressomd.zn.EspressoConverter attribute) Integrator (class in espressomd.integrate) integrator (espressomd.system.System attribute) IntegratorHandle (class in espressomd.integrate) interaction_range (espressomd.cell_system.CellSystem attribute) is_boundary (espressomd.electrokinetics.EKSpeciesNode property) (espressomd.electrokinetics.EKSpeciesSlice property) (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) is_valid_type() (in module espressomd.utils) is_virtual() (espressomd.particle_data.ParticleHandle method) IsotropicNpt (class in espressomd.thermostat) 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)

L

lag_times() (espressomd.accumulators.Correlator method) Langevin (class in espressomd.thermostat) last_applied_force (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) last_iterations() (espressomd.electrostatic_extensions.ICC method) LatticeModel (class in espressomd.detail.walberla) LatticeWalberla (class in espressomd.detail.walberla) lb (espressomd.system.System property) LBField (class in espressomd.zn) LBFluidNodeWalberla (class in espressomd.lb) LBFluidPressureTensor (class in espressomd.observables) LBFluidSliceWalberla (class in espressomd.lb) LBFluidWalberla (class in espressomd.lb) LBFluidWalberlaGPU (class in espressomd.lb) LBThermostat (class in espressomd.thermostat) 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) LennardJonesCos2Interaction (class in espressomd.interactions) LennardJonesCosInteraction (class in espressomd.interactions) LennardJonesInteraction (class in espressomd.interactions) level (espressomd.zn.EspressoConverter attribute) 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.detail.walberla.LatticeModel method) (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) longest_distance() (espressomd.cluster_analysis.Cluster method) lower_smoothing_radius (espressomd.shapes.Slitpore attribute)

M

mach_limit() (espressomd.lb.HydrodynamicInteraction method) 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 property) max_cut_nonbonded (espressomd.cell_system.CellSystem attribute) (espressomd.system.System property) 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.code_features) MMM1D (class in espressomd.electrostatics) module espressomd espressomd.accumulators espressomd.analyze espressomd.bond_breakage espressomd.cell_system espressomd.checkpointing espressomd.cluster_analysis espressomd.code_features espressomd.code_info espressomd.collision_detection espressomd.comfixed espressomd.constraints espressomd.cuda_init espressomd.detail espressomd.detail.walberla espressomd.drude_helpers espressomd.electrokinetics espressomd.electrostatic_extensions espressomd.electrostatics espressomd.galilei espressomd.highlander espressomd.integrate espressomd.interactions espressomd.io espressomd.io.mpiio espressomd.io.vtk espressomd.io.writer espressomd.io.writer.h5md espressomd.io.writer.vtf espressomd.lb espressomd.lees_edwards espressomd.magnetostatics espressomd.math espressomd.observables espressomd.pair_criteria espressomd.particle_data espressomd.plugins espressomd.plugins.ase espressomd.polymer espressomd.profiler espressomd.propagation espressomd.reaction_methods espressomd.rotation espressomd.script_interface espressomd.shapes espressomd.swimmer_helpers espressomd.system espressomd.thermostat espressomd.utils espressomd.version espressomd.visualization espressomd.zn

mol_id (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) moment_of_inertia_matrix() (espressomd.analyze.Analysis method) 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

name() (espressomd.script_interface.PScriptInterface method) nbhood() (espressomd.analyze.Analysis method) nesting_level() (in module espressomd.utils) node (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) node_grid (espressomd.cell_system.CellSystem attribute) 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) NONE (espressomd.interactions.BONDED_IA attribute) (espressomd.propagation.Propagation attribute) 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.collision_detection) (class in espressomd.lees_edwards) OIF_GLOBAL_FORCES (espressomd.interactions.BONDED_IA attribute) OIF_LOCAL_FORCES (espressomd.interactions.BONDED_IA attribute) 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)

P

P3M (class in espressomd.electrostatics) P3MGPU (class in espressomd.electrostatics) pairs() (espressomd.particle_data.ParticleList method) params (espressomd.interactions.BondedInteraction property) parse() (espressomd.io.vtk.VTKReader method) part (espressomd.system.System attribute) particle_energy() (espressomd.analyze.Analysis method) particle_ids() (espressomd.cluster_analysis.Cluster method) particle_neighbor_pids() (espressomd.analyze.Analysis 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) ParticleDipoleFields (class in espressomd.observables) ParticleDirectors (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) plane_intersection_with_line() (espressomd.zn.WallIntersection method)

PObjectRef (class in espressomd.script_interface) population (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla 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) (espressomd.particle_data.ParticleSlice property) pos_offset (espressomd.lees_edwards.LeesEdwards 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 property) (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) pressure_tensor() (espressomd.analyze.Analysis method) pressure_tensor_neq (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) PressureTensor (class in espressomd.observables) print_sip() (espressomd.script_interface.PObjectRef method) process_bonds() (espressomd.zn.EspressoConverter method) ProfileObservable (class in espressomd.observables) Propagation (class in espressomd.propagation) propagation (espressomd.particle_data.ParticleHandle property) (espressomd.particle_data.ParticleSlice property) protocol (espressomd.collision_detection.CollisionDetection attribute) (espressomd.lees_edwards.LeesEdwards attribute) PScriptInterface (class in espressomd.script_interface) Python

Q

q (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) QUARTIC (espressomd.interactions.BONDED_IA attribute)

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) reactions (espressomd.electrokinetics.EKContainer property) read() (espressomd.io.mpiio.Mpiio method) read_signals() (espressomd.checkpointing.Checkpoint method) reconstruct_array() (espressomd.io.vtk.VTKReader class 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) register_system() (espressomd.plugins.ase.ASEInterface method) Released (espressomd.visualization.KeyboardFireEvent attribute) remove() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.constraints.Constraints method) (espressomd.electrokinetics.EKContainer method) (espressomd.electrokinetics.EKReactions method) (espressomd.interactions.BondedInteractions method) (espressomd.particle_data.ParticleHandle method) (espressomd.particle_data.ParticleSlice method) (espressomd.script_interface.ScriptObjectMap method) (espressomd.shapes.Union method) remove_constraint() (espressomd.reaction_methods.ReactionAlgorithm method) remove_node_from_index() (espressomd.electrokinetics.EKIndexedReaction method) remove_vtk_writer() (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) representation (espressomd.zn.EspressoConverter attribute) required_keys() (espressomd.detail.walberla.LatticeWalberla method) (espressomd.electrokinetics.EKSpeciesNode method) (espressomd.electrokinetics.EKSpeciesSlice method) (espressomd.electrokinetics.VTKOutput 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.ReactionField method) (espressomd.electrostatics.Scafacos method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.lb.LBFluidNodeWalberla method) (espressomd.lb.LBFluidSliceWalberla method) (espressomd.lb.VTKOutput method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu 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.NonBondedInteractionHandle method) (espressomd.interactions.NonBondedInteractions method) resort() (espressomd.cell_system.CellSystem method) result() (espressomd.accumulators.Correlator method) Rhomboid (class in espressomd.shapes) RIGID_BOND (espressomd.interactions.BONDED_IA attribute) RigidBond (class in espressomd.interactions) rinertia (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) ROT_BROWNIAN (espressomd.propagation.Propagation attribute) ROT_EULER (espressomd.propagation.Propagation attribute) ROT_LANGEVIN (espressomd.propagation.Propagation attribute) ROT_STOKESIAN (espressomd.propagation.Propagation attribute) ROT_VS_RELATIVE (espressomd.propagation.Propagation attribute) 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.detail.walberla.LatticeModel method) (espressomd.electrokinetics.EKSpecies method) (espressomd.lb.LBFluidWalberla method) Scafacos (class in espressomd.electrostatics) (class in espressomd.magnetostatics) scafacos_methods() (in module espressomd.code_info) 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) select() (espressomd.particle_data.ParticleList method) SERVER_PORT (espressomd.zn.Visualizer attribute) set_boundary_conditions() (espressomd.lees_edwards.LeesEdwards method) set_brownian() (espressomd.thermostat.Thermostat method) set_brownian_dynamics() (espressomd.integrate.IntegratorHandle method) set_colors() (espressomd.zn.EspressoConverter method) set_cylindrical_constraint_in_z_direction() (espressomd.reaction_methods.ReactionAlgorithm method) set_dpd() (espressomd.thermostat.Thermostat method) set_hybrid_decomposition() (espressomd.cell_system.CellSystem 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_parameter() (espressomd.particle_data.ParticleHandle method) set_params() (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.TholeInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.particle_data.ParticleHandle method) (espressomd.script_interface.PScriptInterface method)

set_radii() (espressomd.zn.EspressoConverter 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_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) 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.shapes.Union method) skin (espressomd.cell_system.CellSystem attribute) Slitpore (class in espressomd.shapes) (class in espressomd.visualization) smoothing_radius (espressomd.shapes.SimplePore attribute) SmoothStepInteraction (class in espressomd.interactions) SOCKET_PORT (espressomd.zn.Visualizer attribute) SoftSphereInteraction (class in espressomd.interactions) 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) Stokesian (class in espressomd.thermostat) StokesianDynamics (class in espressomd.integrate) structure_factor() (espressomd.analyze.Analysis method) swimming (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) System (class in espressomd.system) system_CMS() (espressomd.galilei.GalileiTransform method) system_CMS_velocity() (espressomd.galilei.GalileiTransform method) SYSTEM_DEFAULT (espressomd.propagation.Propagation attribute)

T

TABULATED_ANGLE (espressomd.interactions.BONDED_IA attribute) TABULATED_DIHEDRAL (espressomd.interactions.BONDED_IA attribute) TABULATED_DISTANCE (espressomd.interactions.BONDED_IA attribute) TabulatedAngle (class in espressomd.interactions) TabulatedDihedral (class in espressomd.interactions) TabulatedDistance (class in espressomd.interactions) TabulatedNonBonded (class in espressomd.interactions) ThereCanOnlyBeOne THERMALIZED_DIST (espressomd.interactions.BONDED_IA attribute) ThermalizedBond (class in espressomd.interactions) (class in espressomd.thermostat) Thermostat (class in espressomd.thermostat) thermostat (espressomd.system.System attribute) thickness (espressomd.shapes.HollowConicalFrustum attribute) TholeInteraction (class in espressomd.interactions) time (espressomd.system.System property) time_series() (espressomd.accumulators.TimeSeries method) time_step (espressomd.system.System property) time_unit (espressomd.io.writer.h5md.H5md attribute) TimeSeries (class in espressomd.accumulators) 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) TRANS_BROWNIAN (espressomd.propagation.Propagation attribute) TRANS_LANGEVIN (espressomd.propagation.Propagation attribute) TRANS_LANGEVIN_NPT (espressomd.propagation.Propagation attribute) TRANS_LB_MOMENTUM_EXCHANGE (espressomd.propagation.Propagation attribute) TRANS_LB_TRACER (espressomd.propagation.Propagation attribute) TRANS_NEWTON (espressomd.propagation.Propagation attribute) TRANS_STOKESIAN (espressomd.propagation.Propagation attribute) TRANS_VS_RELATIVE (espressomd.propagation.Propagation attribute) 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) type_mapping (espressomd.plugins.ase.ASEInterface attribute)

U

u (espressomd.constraints.HomogeneousFlowField property) Union (class in espressomd.shapes) 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.particle_data.ParticleSlice method) (espressomd.visualization.openGLLive method) (espressomd.zn.Visualizer 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)

V

v (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice property) valid_fields() (espressomd.io.writer.h5md.H5md method) valid_keys() (espressomd.detail.walberla.LatticeWalberla method) (espressomd.detail.walberla.VTKOutputBase method) (espressomd.electrostatic_extensions.ElectrostaticExtensions method) (espressomd.electrostatic_extensions.ICC method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.lb.LBFluidWalberla method) (espressomd.reaction_methods.ConstantpHEnsemble method) (espressomd.reaction_methods.ReactionAlgorithm method) (espressomd.reaction_methods.SingleReaction method) (espressomd.reaction_methods.WidomInsertion method) valid_observables() (espressomd.detail.walberla.VTKOutputBase method) validate_params() (espressomd.electrokinetics.EKSpeciesNode method) (espressomd.electrokinetics.EKSpeciesSlice method) (espressomd.electrostatics.ELC method) (espressomd.electrostatics.ElectrostaticInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.lb.LBFluidSliceWalberla method) (espressomd.lb.LBFluidWalberla method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.DLC method) (espressomd.magnetostatics.MagnetostaticInteraction method)

variance() (espressomd.accumulators.MeanVarianceCalculator method) VectorField (class in espressomd.zn) velocity (espressomd.lb.LBFluidNodeWalberla property) (espressomd.lb.LBFluidSliceWalberla property) velocity_difference() (espressomd.system.System method) velocity_unit (espressomd.io.writer.h5md.H5md attribute) VelocityBounceBack (class in espressomd.lb) VelocityVerlet (class in espressomd.integrate) VelocityVerletIsotropicNPT (class in espressomd.integrate) version() (in module espressomd.version) Virtual (class in espressomd.interactions) virtual (espressomd.particle_data.ParticleHandle attribute) VIRTUAL_BOND (espressomd.interactions.BONDED_IA attribute) Visualizer (class in espressomd.zn) 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) VTKOutput (class in espressomd.electrokinetics) (class in espressomd.lb) VTKOutputBase (class in espressomd.detail.walberla) VTKReader (class in espressomd.io.vtk)

W

Wall (class in espressomd.shapes) (class in espressomd.visualization) WallIntersection (class in espressomd.zn) WCAInteraction (class in espressomd.interactions) WidomInsertion (class in espressomd.reaction_methods)

write() (espressomd.io.mpiio.Mpiio method) (espressomd.io.writer.h5md.H5md method) writevcf() (in module espressomd.io.writer.vtf) writevsf() (in module espressomd.io.writer.vtf) writevtk() (espressomd.particle_data.ParticleList method)