Index

A

a (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.Rhomboid attribute) accuracy (espressomd.magnetostatics.DipolarP3M attribute) active_actors (espressomd.actors.Actors attribute) active_list (espressomd.actors.Actor attribute) ActiveVirtualSitesHandle (class in espressomd.virtual_sites) Actor (class in espressomd.actors) Actors (class in espressomd.actors) actors (espressomd.system.System attribute), [1] 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) add_all_thole() (in module espressomd.drude_helpers) add_bond() (espressomd.particle_data.ParticleHandle method) add_boundary() (espressomd.electrokinetics.Electrokinetics method) add_collective_variable_degree_of_association() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) add_collective_variable_potential_energy() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) add_drude_particle_to_core() (in module espressomd.drude_helpers) add_exclusion() (espressomd.particle_data.ParticleHandle method) add_intramol_exclusion_bonds() (in module espressomd.drude_helpers) add_reaction() (espressomd.electrokinetics.Electrokinetics method) (espressomd.reaction_ensemble.ConstantpHEnsemble method) (espressomd.reaction_ensemble.ReactionAlgorithm method)

add_species() (espressomd.electrokinetics.Electrokinetics method) add_thole_pair_damping() (in module espressomd.drude_helpers) add_verified_bond() (espressomd.particle_data.ParticleHandle method) AffinityInteraction (class in espressomd.interactions) agrid (espressomd.lb.HydrodynamicInteraction attribute) alpha (espressomd.magnetostatics.DipolarP3M attribute) (in module espressomd.drude_helpers) Analysis (class in espressomd.analyze) analysis (espressomd.system.System attribute), [1] AngleCosine (class in espressomd.interactions) AngleCossquare (class in espressomd.interactions) AngleHarmonic (class in espressomd.interactions) angular_momentum() (espressomd.analyze.Analysis method) append() (espressomd.analyze.Analysis method) array_locked (class in espressomd.utils) assert_agrid_tau_set() (in module espressomd.lb) assert_features() (in module espressomd) AssertThermostatType() (in module espressomd.thermostat) auto_exclusions() (espressomd.system.System method) auto_update_accumulators (espressomd.system.System attribute), [1] AutoUpdateAccumulators (class in espressomd.accumulators) available_methods() (in module espressomd.scafacos) axis (espressomd.shapes.Cylinder attribute) (espressomd.shapes.HollowCone attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Stomatocyte attribute)

B

b (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.Rhomboid attribute) begin_section() (in module espressomd.profiler) bmhtf (espressomd.interactions.NonBondedInteractionHandle attribute) BMHTFInteraction (class in espressomd.interactions) bond_site (espressomd.particle_data.ParticleHandle attribute) bond_site() (espressomd.particle_data.ParticleSlice property) BondAngles (class in espressomd.observables) BondCriterion (class in espressomd.pair_criteria) BondDihedrals (class in espressomd.observables) bonded_inter (espressomd.system.System attribute), [1] 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) bonds() (espressomd.particle_data.ParticleSlice property) boundary (espressomd.lb.LBFluidRoutines attribute) box_l (espressomd.globals.Globals attribute) (espressomd.system.System attribute) buckingham (espressomd.interactions.NonBondedInteractionHandle attribute) BuckinghamInteraction (class in espressomd.interactions) bulk_viscosity (espressomd.lb.HydrodynamicInteraction attribute) ButtonMotion (espressomd.visualization_opengl.MouseFireEvent attribute) ButtonPressed (espressomd.visualization_opengl.MouseFireEvent attribute) ButtonReleased (espressomd.visualization_opengl.MouseFireEvent attribute)

C

c (espressomd.shapes.Rhomboid attribute) calc_re() (espressomd.analyze.Analysis method) calc_rg() (espressomd.analyze.Analysis method) calc_rh() (espressomd.analyze.Analysis method) call_method() (espressomd.script_interface.PScriptInterface method) callback_on_button() (espressomd.visualization_opengl.KeyboardManager method) Camera (class in espressomd.visualization_opengl) cao (espressomd.magnetostatics.DipolarP3M attribute) cell_system (espressomd.system.System attribute), [1] CellSystem (class in espressomd.cellsystem) center (espressomd.shapes.Cylinder attribute) (espressomd.shapes.Ellipsoid attribute) (espressomd.shapes.HollowCone attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Stomatocyte attribute) (espressomd.shapes.Torus attribute) center_of_mass() (espressomd.analyze.Analysis method) change_volume_and_rescale_particles() (espressomd.system.System method) channel_width (espressomd.shapes.Slitpore attribute) check_bond_or_throw_exception() (espressomd.particle_data.ParticleHandle method) check_neutrality() (in module espressomd.electrostatics) check_topology() (espressomd.analyze.Analysis method) check_type_or_throw_except() (in module espressomd.utils) check_valid_type() (espressomd.system.System method) Checkpoint (class in espressomd.checkpointing) cid_for_particle() (espressomd.cluster_analysis.ClusterStructure method) class_lookup() (espressomd.actors.Actor method) clear() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.accumulators.TimeSeries method) (espressomd.actors.Actors method) (espressomd.cluster_analysis.ClusterStructure method) (espressomd.constraints.Constraints method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.particle_data.ParticleList 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 attribute) clusters() (espressomd.cluster_analysis.ClusterStructure property) ClusterStructure (class in espressomd.cluster_analysis) collision_detection (espressomd.system.System attribute), [1] CollisionDetection (class in espressomd.collision_detection) ComFixed (class in espressomd.comfixed) comfixed (espressomd.system.System attribute), [1] ComForce (class in espressomd.observables) ComPosition (class in espressomd.observables) ComVelocity (class in espressomd.observables) conjugated() (espressomd.visualization_opengl.Quaternion method) constant_pH (espressomd.reaction_ensemble.ConstantpHEnsemble attribute) ConstantpHEnsemble (class in espressomd.reaction_ensemble) Constraint (class in espressomd.constraints) Constraints (class in espressomd.constraints) constraints (espressomd.system.System attribute), [1] convert_vector_body_to_space() (espressomd.particle_data.ParticleHandle method) convert_vector_space_to_body() (espressomd.particle_data.ParticleHandle method) core_ids (in module espressomd.drude_helpers) corner (espressomd.shapes.Rhomboid attribute) Correlator (class in espressomd.accumulators) CosPersistenceAngles (class in espressomd.observables) coulomb_prefactor (in module espressomd.drude_helpers) cuda_init_handle (espressomd.system.System attribute), [1] CudaInitHandle (class in espressomd.cuda_init) Current (class in espressomd.observables) Cylinder (class in espressomd.shapes) cylindrical_average() (espressomd.analyze.Analysis method) 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) CylindricalVelocityProfile (class in espressomd.observables)

D

default_params() (espressomd.actors.Actor method) (espressomd.diamond.Diamond method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ELC method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.MMM2D method) (espressomd.electrostatics.P3M method) (espressomd.electrostatics.P3MGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.electrostatics.Scafacos method) (espressomd.interactions.AffinityInteraction 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.MembraneCollisionInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.TholeInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatic_extensions.DLC method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.Scafacos method) (espressomd.minimize_energy.MinimizeEnergy method) (espressomd.scafacos.ScafacosConnector 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_ensemble.ReactionAlgorithm method) delete_verified_bond() (espressomd.particle_data.ParticleHandle method) density (espressomd.electrokinetics.SpecieRoutines attribute) (espressomd.lb.HydrodynamicInteraction attribute) (espressomd.lb.LBFluidRoutines attribute) DensityProfile (class in espressomd.observables)

device (espressomd.cuda_init.CudaInitHandle attribute) device_list (espressomd.cuda_init.CudaInitHandle attribute) DH (class in espressomd.electrostatics) Diamond (class in espressomd.diamond) Dihedral (class in espressomd.interactions) dimensions() (espressomd.MDA_ESP.Timestep property) dip (espressomd.particle_data.ParticleHandle attribute) dip() (espressomd.particle_data.ParticleSlice property) dipm (espressomd.particle_data.ParticleHandle attribute) dipm() (espressomd.particle_data.ParticleSlice property) dipolar (espressomd.electrostatics.Scafacos attribute) (espressomd.magnetostatics.Scafacos attribute) 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.HollowCone attribute) (espressomd.shapes.Rhomboid attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Stomatocyte attribute) (espressomd.shapes.Torus attribute) director (espressomd.particle_data.ParticleHandle attribute) director() (espressomd.particle_data.ParticleSlice property) displacement_mc_move_for_particles_of_type() (espressomd.reaction_ensemble.ReactionAlgorithm method) (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) dist (espressomd.shapes.Wall attribute) dist_to() (espressomd.analyze.Analysis method) 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.magnetostatic_extensions) DoubleClick (espressomd.visualization_opengl.MouseFireEvent attribute) dpd (espressomd.interactions.NonBondedInteractionHandle attribute) dpd_stress() (espressomd.analyze.Analysis method) DPDInteraction (class in espressomd.interactions) DPDStress (class in espressomd.observables) draw_arrow() (in module espressomd.visualization_opengl) draw_box() (in module espressomd.visualization_opengl) draw_cylinder() (in module espressomd.visualization_opengl) draw_ellipsoid() (in module espressomd.visualization_opengl) draw_plane() (in module espressomd.visualization_opengl) draw_points() (in module espressomd.visualization_opengl) draw_simple_pore() (in module espressomd.visualization_opengl) draw_slitpore() (in module espressomd.visualization_opengl) draw_sphere() (in module espressomd.visualization_opengl) draw_sphero_cylinder() (in module espressomd.visualization_opengl) drude_ids (in module 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), [1] EKBoundary (class in espressomd.ekboundaries) ELC (class in espressomd.electrostatic_extensions) 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) empty() (espressomd.lbboundaries.LBBoundaries method) end_section() (in module espressomd.profiler) 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.__cinit__ (module) espressomd._init (module) espressomd.accumulators (module) espressomd.actors (module) espressomd.analyze (module) espressomd.cellsystem (module) espressomd.checkpointing (module) espressomd.cluster_analysis (module) espressomd.collision_detection (module) espressomd.comfixed (module) espressomd.constraints (module) espressomd.cuda_init (module) espressomd.diamond (module) espressomd.drude_helpers (module) espressomd.ekboundaries (module) espressomd.electrokinetics (module) espressomd.electrostatic_extensions (module) espressomd.electrostatics (module)

espressomd.galilei (module) espressomd.globals (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.magnetostatic_extensions (module) espressomd.magnetostatics (module) espressomd.MDA_ESP (module) espressomd.minimize_energy (module) espressomd.observables (module) espressomd.pair_criteria (module) espressomd.particle_data (module) espressomd.polymer (module) espressomd.profiler (module) espressomd.reaction_ensemble (module) espressomd.scafacos (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) espressomd.visualization_mayavi (module) espressomd.visualization_opengl (module) exclusions (espressomd.particle_data.ParticleHandle attribute) exclusions() (espressomd.particle_data.ParticleSlice property) exists() (espressomd.particle_data.ParticleList method) ext_force (espressomd.particle_data.ParticleHandle attribute) ext_force() (espressomd.particle_data.ParticleSlice property) ext_force_density (espressomd.lb.HydrodynamicInteraction attribute) ext_torque (espressomd.particle_data.ParticleHandle attribute) ext_torque() (espressomd.particle_data.ParticleSlice property)

F

f (espressomd.particle_data.ParticleHandle attribute) f() (espressomd.particle_data.ParticleSlice property) far_cut (espressomd.magnetostatic_extensions.DLC attribute) FeaturesError FeneBond (class in espressomd.interactions) fix (espressomd.particle_data.ParticleHandle attribute) fix() (espressomd.particle_data.ParticleSlice property) FlowField (class in espressomd.constraints) flush() (espressomd.io.writer.h5md.H5md method)

flux (espressomd.electrokinetics.SpecieRoutines attribute) FluxDensityProfile (class in espressomd.observables) force_cap (espressomd.globals.Globals attribute) (espressomd.system.System attribute) ForceDensityProfile (class in espressomd.observables) ForceField (class in espressomd.constraints) format (espressomd.MDA_ESP.ESPParser attribute) (espressomd.MDA_ESP.ESPReader attribute) FreeMotion (espressomd.visualization_opengl.MouseFireEvent attribute) friendly() (in module espressomd.version)

G

g() (espressomd.constraints.Gravity property) galilei (espressomd.system.System attribute), [1] galilei_transform() (espressomd.galilei.GalileiTransform method) GalileiTransform (class in espressomd.galilei) gamma (espressomd.constraints.HomogeneousFlowField attribute) (espressomd.particle_data.ParticleHandle attribute) gamma() (espressomd.particle_data.ParticleSlice property) gamma_rot (espressomd.particle_data.ParticleHandle attribute) gamma_rot() (espressomd.particle_data.ParticleSlice property) gap_size (espressomd.magnetostatic_extensions.DLC attribute) 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_configurational_moves() (espressomd.reaction_ensemble.ReactionAlgorithm method) get_acceptance_rate_reaction() (espressomd.reaction_ensemble.ReactionAlgorithm method) get_camera_rotation_matrix() (espressomd.visualization_opengl.Camera method) get_extra_clip_plane() (in module espressomd.visualization_opengl) 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_mean() (espressomd.accumulators.MeanVarianceCalculator method) get_non_interacting_type() (espressomd.reaction_ensemble.ReactionAlgorithm method)

get_pairs_() (espressomd.cellsystem.CellSystem method) get_parameter() (espressomd.collision_detection.CollisionDetection method) (espressomd.script_interface.PScriptInterface method) get_params() (espressomd.actors.Actor method) (espressomd.collision_detection.CollisionDetection method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.interactions.NonBondedInteraction method) (espressomd.io.writer.h5md.H5md method) (espressomd.scafacos.ScafacosConnector method) (espressomd.script_interface.PScriptInterface method) get_registered_objects() (espressomd.checkpointing.Checkpoint method) get_state() (espressomd.cellsystem.CellSystem method) (espressomd.thermostat.Thermostat method) get_status() (espressomd.reaction_ensemble.ReactionAlgorithm method) get_ts() (espressomd.thermostat.Thermostat method) get_variance() (espressomd.accumulators.MeanVarianceCalculator method) get_volume() (espressomd.reaction_ensemble.ReactionAlgorithm method) get_wall_constraints_in_z_direction() (espressomd.reaction_ensemble.ReactionAlgorithm method) git_branch() (in module espressomd.version) git_commit() (in module espressomd.version) git_state() (in module espressomd.version) Globals (class in espressomd.globals) globals (espressomd.system.System attribute), [1] 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_opengl.KeyboardManager method) harmonic_bond (in module espressomd.drude_helpers) HarmonicBond (class in espressomd.interactions) HarmonicDumbbellBond (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_velocity (espressomd.virtual_sites.VirtualSitesRelative 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_opengl.KeyboardFireEvent attribute) HollowCone (class in espressomd.shapes) 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) id() (espressomd.particle_data.ParticleSlice property) (espressomd.script_interface.PScriptInterface method) id_drude (in module espressomd.drude_helpers) image_box (espressomd.particle_data.ParticleHandle attribute) image_box() (espressomd.particle_data.ParticleSlice property) implementation (espressomd.virtual_sites.ActiveVirtualSitesHandle attribute) index (espressomd.lb.LBFluidRoutines attribute) init() (espressomd.minimize_energy.MinimizeEnergy method) (in module espressomd.script_interface) inner_radius (espressomd.shapes.HollowCone attribute) (espressomd.shapes.Stomatocyte attribute) integ_switch (espressomd.system.System attribute) Integrator (class in espressomd.integrate) integrator (espressomd.system.System attribute), [1] is_active() (espressomd.actors.Actor method) (espressomd.interactions.AffinityInteraction 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.MembraneCollisionInteraction 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)

is_valid() (espressomd.actors.Actor method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.NonBondedInteraction method) is_valid_type() (in module espressomd.utils)

K

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

KeyboardFireEvent (class in espressomd.visualization_opengl) KeyboardManager (class in espressomd.visualization_opengl) kill_particle_forces() (espressomd.galilei.GalileiTransform method) kill_particle_motion() (espressomd.galilei.GalileiTransform method) kT (espressomd.lb.HydrodynamicInteraction attribute)

L

last_iterations() (espressomd.electrostatic_extensions.ICC method) layer_width (espressomd.shapes.Stomatocyte attribute) LBBoundaries (class in espressomd.lbboundaries) lbboundaries (espressomd.system.System attribute), [1] LBBoundary (class in espressomd.lbboundaries) LBFluid (class in espressomd.lb) LBFluidGPU (class in espressomd.lb) LBFluidRoutines (class in espressomd.lb) LBFluidStress (class in espressomd.observables) LBVelocityProfile (class in espressomd.observables) length (espressomd.shapes.Cylinder attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.SpheroCylinder 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) LinearElectricPotential (class in espressomd.constraints) load() (espressomd.checkpointing.Checkpoint method) load_checkpoint() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) load_wang_landau_checkpoint() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) lower_smoothing_radius (espressomd.shapes.Slitpore attribute)

M

MagneticDipoleMoment (class in espressomd.observables) MagnetostaticExtension (class in espressomd.magnetostatic_extensions) MagnetostaticInteraction (class in espressomd.magnetostatics) major() (in module espressomd.version) mass (espressomd.particle_data.ParticleHandle attribute) mass() (espressomd.particle_data.ParticleSlice property) mass_drude (in module espressomd.drude_helpers) materials (espressomd.visualization.openGLLive attribute) (espressomd.visualization_opengl.openGLLive attribute) max_cut_bonded (espressomd.system.System attribute) max_cut_nonbonded (espressomd.system.System attribute) max_num_cells (espressomd.cellsystem.CellSystem attribute) max_oif_objects (espressomd.system.System attribute) maxPWerror (espressomd.magnetostatic_extensions.DLC attribute) mayaviLive (class in espressomd.visualization) (class in espressomd.visualization_mayavi) MeanVarianceCalculator (class in espressomd.accumulators) measure_excess_chemical_potential() (espressomd.reaction_ensemble.WidomInsertion method) membrane_collision (espressomd.interactions.NonBondedInteractionHandle attribute) MembraneCollisionInteraction (class in espressomd.interactions) mesh (espressomd.magnetostatics.DipolarP3M attribute) mesh_off (espressomd.magnetostatics.DipolarP3M attribute) method_name (espressomd.magnetostatics.Scafacos attribute) method_params (espressomd.magnetostatics.Scafacos attribute) min_dist() (espressomd.analyze.Analysis method) (espressomd.constraints.ShapeBasedConstraint method) min_dist2() (espressomd.analyze.Analysis method) min_global_cut (espressomd.globals.Globals attribute) (espressomd.system.System attribute) min_num_cells (espressomd.cellsystem.CellSystem attribute) minimize() (espressomd.minimize_energy.MinimizeEnergy method)

minimize_energy (espressomd.system.System attribute), [1] MinimizeEnergy (class in espressomd.minimize_energy) minor() (in module espressomd.version) missing_features() (in module espressomd) MMM1D (class in espressomd.electrostatics) MMM1DGPU (class in espressomd.electrostatics) MMM2D (class in espressomd.electrostatics) mol_core_partial_charges (in module espressomd.drude_helpers) mol_core_types (in module espressomd.drude_helpers) mol_drude_types (in module espressomd.drude_helpers) mol_id (espressomd.particle_data.ParticleHandle attribute) mol_id() (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_opengl.MouseManager method) mouse_move() (espressomd.visualization_opengl.MouseManager method) MouseButtonEvent (class in espressomd.visualization_opengl) MouseFireEvent (class in espressomd.visualization_opengl) MouseManager (class in espressomd.visualization_opengl) move_backward() (espressomd.visualization_opengl.Camera method) move_down() (espressomd.visualization_opengl.Camera method) move_forward() (espressomd.visualization_opengl.Camera method) move_left() (espressomd.visualization_opengl.Camera method) move_right() (espressomd.visualization_opengl.Camera method) move_up() (espressomd.visualization_opengl.Camera method) Mpiio (class in espressomd.io.mpiio) mu_E (espressomd.particle_data.ParticleHandle attribute) mu_E() (espressomd.particle_data.ParticleSlice property) mult_q() (espressomd.visualization_opengl.Quaternion method) mult_v() (espressomd.visualization_opengl.Quaternion method)

N

n_part_types (espressomd.particle_data.ParticleList attribute) n_replica (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu 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) node() (espressomd.particle_data.ParticleSlice property) node_grid (espressomd.cellsystem.CellSystem attribute)

nodes() (espressomd.lb.HydrodynamicInteraction method) non_bonded_inter (espressomd.system.System attribute), [1] 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() (espressomd.visualization_opengl.Camera method) normalized() (espressomd.visualization_opengl.Camera method) number_of_particles() (espressomd.system.System method)

O

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

only_positive (espressomd.constraints.ShapeBasedConstraint attribute) open (espressomd.shapes.Cylinder attribute) openGLLive (class in espressomd.visualization) (class in espressomd.visualization_opengl) opening_angle (espressomd.shapes.HollowCone attribute) out_direction (espressomd.particle_data.ParticleHandle attribute) out_direction() (espressomd.particle_data.ParticleSlice property) outer_radius (espressomd.shapes.HollowCone attribute) (espressomd.shapes.Stomatocyte attribute)

P

P3M (class in espressomd.electrostatics) P3MGPU (class in espressomd.electrostatics) p_core (in module espressomd.drude_helpers) pair_criterion (espressomd.cluster_analysis.ClusterStructure attribute) pairs() (espressomd.particle_data.ParticleList method) params (espressomd.interactions.BondedInteraction attribute) parse() (espressomd.MDA_ESP.ESPParser method) part (espressomd.system.System attribute), [1] 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.globals.Globals attribute) (espressomd.system.System attribute) phi() (espressomd.constraints.ElectricPlaneWave property) phi0() (espressomd.constraints.LinearElectricPotential property) pi (espressomd.interactions.TabulatedAngle attribute) (espressomd.interactions.TabulatedDihedral attribute) PObjectId (class in espressomd.script_interface) policy_ (espressomd.script_interface.PScriptInterface attribute) population (espressomd.lb.LBFluidRoutines attribute) pore_length (espressomd.shapes.Slitpore attribute) pore_mouth (espressomd.shapes.Slitpore attribute) pore_width (espressomd.shapes.Slitpore attribute) pos (espressomd.particle_data.ParticleHandle attribute)

pos() (espressomd.particle_data.ParticleSlice property) pos_folded (espressomd.particle_data.ParticleHandle attribute) positions() (in module espressomd.polymer) potential (espressomd.electrokinetics.ElectrokineticsRoutines attribute) PotentialField (class in espressomd.constraints) prefactor (espressomd.magnetostatics.DipolarDirectSumCpu attribute) (espressomd.magnetostatics.DipolarDirectSumGpu attribute) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu attribute) (espressomd.magnetostatics.DipolarP3M attribute) (espressomd.magnetostatics.MagnetostaticInteraction attribute) (espressomd.magnetostatics.Scafacos attribute) Pressed (espressomd.visualization_opengl.KeyboardFireEvent attribute) pressure (espressomd.electrokinetics.ElectrokineticsRoutines attribute) pressure() (espressomd.analyze.Analysis method) print_boundary() (espressomd.lb.HydrodynamicInteraction method) print_velocity() (espressomd.lb.HydrodynamicInteraction method) print_vtk_boundary() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) print_vtk_density() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) print_vtk_flux() (espressomd.electrokinetics.Species method) print_vtk_flux_fluc() (espressomd.electrokinetics.Species method) print_vtk_flux_link() (espressomd.electrokinetics.Species method) print_vtk_lbforce() (espressomd.electrokinetics.Electrokinetics method) print_vtk_particle_potential() (espressomd.electrokinetics.Electrokinetics method) print_vtk_potential() (espressomd.electrokinetics.Electrokinetics method) print_vtk_velocity() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) processGuiEvents() (espressomd.visualization.mayaviLive method) (espressomd.visualization_mayavi.mayaviLive method) PScriptInterface (class in espressomd.script_interface) py_number_of_species (espressomd.electrokinetics.Species attribute) python_dp3m_adaptive_tune() (espressomd.magnetostatics.DipolarP3M method) python_dp3m_set_mesh_offset() (espressomd.magnetostatics.DipolarP3M method) python_dp3m_set_params() (espressomd.magnetostatics.DipolarP3M method) python_dp3m_set_tune_params() (espressomd.magnetostatics.DipolarP3M method)

Q

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

quat (espressomd.particle_data.ParticleHandle attribute) quat() (espressomd.particle_data.ParticleSlice property) Quaternion (class in espressomd.visualization_opengl)

R

r_cut (espressomd.magnetostatics.DipolarP3M attribute) radius (espressomd.shapes.Cylinder attribute) (espressomd.shapes.SimplePore attribute) (espressomd.shapes.Sphere attribute) (espressomd.shapes.SpheroCylinder attribute) (espressomd.shapes.Torus attribute) random_number_generator_state (espressomd.system.System attribute) rdf() (espressomd.analyze.Analysis method) reaction() (espressomd.reaction_ensemble.ReactionAlgorithm method) (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) ReactionAlgorithm (class in espressomd.reaction_ensemble) ReactionEnsemble (class in espressomd.reaction_ensemble) 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_opengl.KeyboardManager method) (espressomd.visualization_opengl.MouseManager method) register_callback() (espressomd.visualization.mayaviLive method) (espressomd.visualization.openGLLive method) (espressomd.visualization_mayavi.mayaviLive method) (espressomd.visualization_opengl.openGLLive method) register_signal() (espressomd.checkpointing.Checkpoint method) Released (espressomd.visualization_opengl.KeyboardFireEvent attribute) remove() (espressomd.accumulators.AutoUpdateAccumulators method) (espressomd.actors.Actors method) (espressomd.constraints.Constraints method) (espressomd.lbboundaries.LBBoundaries method) (espressomd.particle_data.ParticleHandle method) required_keys() (espressomd.actors.Actor method) (espressomd.diamond.Diamond method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ELC method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.MMM2D method) (espressomd.electrostatics.P3M method) (espressomd.electrostatics.P3MGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.interactions.AffinityInteraction method) (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.HarmonicDumbbellBond 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.MembraneCollisionInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.OifOutDirection method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.TholeInteraction method) (espressomd.interactions.Virtual method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatic_extensions.DLC method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.minimize_energy.MinimizeEnergy method) (espressomd.scafacos.ScafacosConnector method)

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

S

save() (espressomd.checkpointing.Checkpoint method) save_checkpoint() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.HydrodynamicInteraction method) Scafacos (class in espressomd.electrostatics) (class in espressomd.magnetostatics) ScafacosConnector (class in espressomd.scafacos) screenshot() (espressomd.visualization.openGLLive method) (espressomd.visualization_opengl.openGLLive method) script_interface_register() (in module espressomd.script_interface) ScriptInterfaceHelper (class in espressomd.script_interface) ScriptObjectRegistry (class in espressomd.script_interface) seed (espressomd.lb.HydrodynamicInteraction attribute) (espressomd.system.System attribute) select() (espressomd.particle_data.ParticleList method) set_camera() (espressomd.visualization_opengl.Camera method) set_cylindrical_constraint_in_z_direction() (espressomd.reaction_ensemble.ReactionAlgorithm method) set_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.HarmonicDumbbellBond 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.OifOutDirection method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method) set_density() (espressomd.electrokinetics.Electrokinetics method) set_domain_decomposition() (espressomd.cellsystem.CellSystem method) set_dpd() (espressomd.thermostat.Thermostat method) set_interpolation_order() (espressomd.lb.HydrodynamicInteraction method) set_isotropic_npt() (espressomd.integrate.Integrator method) set_langevin() (espressomd.thermostat.Thermostat method) set_layered() (espressomd.cellsystem.CellSystem method) set_lb() (espressomd.thermostat.Thermostat method) set_magnetostatics_prefactor() (espressomd.magnetostatics.MagnetostaticInteraction method) set_n_square() (espressomd.cellsystem.CellSystem method) set_non_interacting_type() (espressomd.reaction_ensemble.ReactionAlgorithm method) set_npt() (espressomd.thermostat.Thermostat method) set_nvt() (espressomd.integrate.Integrator method) set_params() (espressomd.actors.Actor method) (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.TholeInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.scafacos.ScafacosConnector method) (espressomd.script_interface.PScriptInterface method)

set_random_state_PRNG() (espressomd.system.System method) set_sip_via_oid() (espressomd.script_interface.PScriptInterface 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_opengl) set_steepest_descent() (espressomd.integrate.Integrator method) set_volume() (espressomd.reaction_ensemble.ReactionAlgorithm method) set_vv() (espressomd.integrate.Integrator method) set_wall_constraints_in_z_direction() (espressomd.reaction_ensemble.ReactionAlgorithm method) set_wang_landau_parameters() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) setup_and_add_drude_exclusion_bonds() (in module espressomd.drude_helpers) setup_intramol_exclusion_bonds() (in module espressomd.drude_helpers) setup_type_map() (espressomd.system.System method) Shape (class in espressomd.shapes) shape (espressomd.constraints.ShapeBasedConstraint attribute) (espressomd.lb.HydrodynamicInteraction attribute) ShapeBasedConstraint (class in espressomd.constraints) SimplePore (class in espressomd.shapes) sip (espressomd.script_interface.PScriptInterface attribute) size() (espressomd.lbboundaries.LBBoundaries method) skin (espressomd.cellsystem.CellSystem attribute) Slitpore (class in espressomd.shapes) 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) SpheroCylinder (class in espressomd.shapes) start() (espressomd.visualization.mayaviLive method) (espressomd.visualization.openGLLive method) (espressomd.visualization_mayavi.mayaviLive method) (espressomd.visualization_opengl.openGLLive method) Stomatocyte (class in espressomd.shapes) Stream (class in espressomd.MDA_ESP) stress (espressomd.lb.HydrodynamicInteraction attribute) (espressomd.lb.LBFluidRoutines attribute) stress_neq (espressomd.lb.LBFluidRoutines attribute) stress_tensor() (espressomd.analyze.Analysis method) StressTensor (class in espressomd.observables) structure_factor() (espressomd.analyze.Analysis method) SubtLJ (class in espressomd.interactions) suspend() (espressomd.thermostat.Thermostat method) swimming (espressomd.particle_data.ParticleHandle attribute) swimming() (espressomd.particle_data.ParticleSlice property) System (class in espressomd.system) system (espressomd.actors.Actor attribute) (in module espressomd.drude_helpers), [1], [2], [3], [4], [5] system_CMS() (espressomd.galilei.GalileiTransform method) system_CMS_velocity() (espressomd.galilei.GalileiTransform method)

T

t1 (in module espressomd.drude_helpers) t2 (in module espressomd.drude_helpers) 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) temp (espressomd.particle_data.ParticleHandle attribute) temp() (espressomd.particle_data.ParticleSlice property) ThereCanOnlyBeOne thermalized_bond (in module espressomd.drude_helpers) ThermalizedBond (class in espressomd.interactions) Thermostat (class in espressomd.thermostat) thermostat (espressomd.system.System attribute), [1] thole (espressomd.interactions.NonBondedInteractionHandle attribute) thole_damping (in module espressomd.drude_helpers) TholeInteraction (class in espressomd.interactions) time (espressomd.globals.Globals attribute) (espressomd.system.System attribute) time_series() (espressomd.accumulators.TimeSeries method) time_step (espressomd.globals.Globals attribute) (espressomd.system.System attribute) TimeSeries (class in espressomd.accumulators) Timestep (class in espressomd.MDA_ESP) timings (espressomd.globals.Globals attribute) (espressomd.system.System attribute) to_char_pointer() (in module espressomd.utils) to_str() (in module espressomd.utils) torque_lab (espressomd.particle_data.ParticleHandle attribute) torque_lab() (espressomd.particle_data.ParticleSlice property) Torus (class in espressomd.shapes) total_force() (espressomd.constraints.ShapeBasedConstraint method) total_normal_force() (espressomd.constraints.ShapeBasedConstraint method) trajectory() (espressomd.MDA_ESP.Stream property) tube_radius (espressomd.shapes.Torus attribute) tune (espressomd.magnetostatics.DipolarP3M attribute) tune() (espressomd.electrostatics.ElectrostaticInteraction method) tune_skin() (espressomd.cellsystem.CellSystem method) turn_off() (espressomd.thermostat.Thermostat method) type (espressomd.particle_data.ParticleHandle attribute) type() (espressomd.particle_data.ParticleSlice property) type1 (espressomd.interactions.NonBondedInteractionHandle attribute) type2 (espressomd.interactions.NonBondedInteractionHandle attribute) type_drude (in module espressomd.drude_helpers) type_name() (espressomd.interactions.AffinityInteraction method) (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.HarmonicDumbbellBond 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.MembraneCollisionInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.OifOutDirection method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.TabulatedAngle method) (espressomd.interactions.TabulatedDihedral method) (espressomd.interactions.TabulatedDistance method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.TholeInteraction 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.HarmonicDumbbellBond 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.OifOutDirection method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SubtLJ 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 attribute) u() (espressomd.constraints.HomogeneousFlowField property) units (espressomd.MDA_ESP.ESPReader attribute) unregister() (espressomd.checkpointing.Checkpoint method) update() (espressomd.accumulators.MeanVarianceCalculator method) (espressomd.accumulators.TimeSeries method) (espressomd.particle_data.ParticleHandle method) (espressomd.visualization.mayaviLive method) (espressomd.visualization.openGLLive method) (espressomd.visualization_mayavi.mayaviLive method) (espressomd.visualization_opengl.openGLLive method)

update_maximum_and_minimum_energies_at_current_state() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) update_modelview() (espressomd.visualization_opengl.Camera method) update_system_info() (espressomd.visualization.openGLLive method) (espressomd.visualization_opengl.openGLLive method) upper_smoothing_radius (espressomd.shapes.Slitpore attribute) user_interactions (espressomd.interactions.NonBondedInteraction attribute)

V

v (espressomd.particle_data.ParticleHandle attribute) v() (espressomd.particle_data.ParticleSlice property) v_kappa() (espressomd.analyze.Analysis method) valid_keys() (espressomd.actors.Actor method) (espressomd.diamond.Diamond method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) (espressomd.electrostatic_extensions.ELC method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.MMM2D method) (espressomd.electrostatics.P3M method) (espressomd.electrostatics.P3MGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.interactions.AffinityInteraction method) (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.HarmonicDumbbellBond 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.MembraneCollisionInteraction method) (espressomd.interactions.MorseInteraction method) (espressomd.interactions.NonBondedInteraction method) (espressomd.interactions.OifGlobalForces method) (espressomd.interactions.OifLocalForces method) (espressomd.interactions.OifOutDirection method) (espressomd.interactions.QuarticBond method) (espressomd.interactions.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.TholeInteraction method) (espressomd.interactions.Virtual method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatic_extensions.DLC method) (espressomd.magnetostatics.DipolarBarnesHutGpu method) (espressomd.magnetostatics.DipolarDirectSumCpu method) (espressomd.magnetostatics.DipolarDirectSumGpu method) (espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.scafacos.ScafacosConnector method)

validate() (espressomd.collision_detection.CollisionDetection method) validate_params() (espressomd.actors.Actor method) (espressomd.diamond.Diamond method) (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrostatic_extensions.ELC method) (espressomd.electrostatic_extensions.ICC method) (espressomd.electrostatics.DH method) (espressomd.electrostatics.MMM1D method) (espressomd.electrostatics.MMM1DGPU method) (espressomd.electrostatics.MMM2D method) (espressomd.electrostatics.P3M method) (espressomd.electrostatics.P3MGPU method) (espressomd.electrostatics.ReactionField method) (espressomd.interactions.AffinityInteraction method) (espressomd.interactions.BMHTFInteraction method) (espressomd.interactions.BondedInteraction 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.MembraneCollisionInteraction 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.TabulatedDistance method) (espressomd.interactions.TholeInteraction method) (espressomd.interactions.WCAInteraction method) (espressomd.lb.HydrodynamicInteraction method) (espressomd.magnetostatic_extensions.DLC method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.minimize_energy.MinimizeEnergy method) (espressomd.scafacos.ScafacosConnector method) (in module espressomd.polymer) velocity (espressomd.electrokinetics.ElectrokineticsRoutines attribute) (espressomd.lb.LBFluidRoutines attribute) verbose (in module espressomd.drude_helpers), [1], [2], [3], [4], [5] Virtual (class in espressomd.interactions) virtual (espressomd.particle_data.ParticleHandle attribute) virtual() (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) vs_quat() (espressomd.particle_data.ParticleSlice property) vs_relative (espressomd.particle_data.ParticleHandle attribute) vs_relative() (espressomd.particle_data.ParticleSlice property) vtf_pid_map() (in module espressomd.io.writer.vtf)

W

Wall (class in espressomd.shapes) WangLandauHasConverged WangLandauReactionEnsemble (class in espressomd.reaction_ensemble) WCAInteraction (class in espressomd.interactions) WidomInsertion (class in espressomd.reaction_ensemble) width (espressomd.shapes.HollowCone attribute) write() (espressomd.io.mpiio.Mpiio method) (espressomd.io.writer.h5md.H5md method)

write_out_preliminary_energy_run_results() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) write_wang_landau_checkpoint() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) write_wang_landau_results_to_file() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) writevcf() (in module espressomd.io.writer.vtf) writevsf() (in module espressomd.io.writer.vtf) writevtk() (espressomd.particle_data.ParticleList method)