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) 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) alpha (espressomd.magnetostatics.DipolarP3M attribute) (in module espressomd.drude_helpers) Analysis (class in espressomd.analyze) analysis (espressomd.system.System attribute) analyze_linear_momentum() (espressomd.analyze.Analysis method) 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_features() (in module espressomd) AssertThermostatType() (in module espressomd.thermostat) auto_exclusions() (espressomd.system.System method) auto_update_accumulators (espressomd.system.System attribute) AutoUpdateAccumulators (class in espressomd.accumulators) 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) bmhtf (espressomd.interactions.NonBondedInteractionHandle attribute) BMHTFInteraction (class in espressomd.interactions) bond_site (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) BondCriterion (class in espressomd.pair_criteria) bonded_inter (espressomd.system.System attribute) BondedCoulomb (class in espressomd.interactions) BondedCoulombP3MSRBond (class in espressomd.interactions) BondedInteraction (class in espressomd.interactions)

BondedInteractionNotDefined (class in espressomd.interactions) BondedInteractions (class in espressomd.interactions) bonds (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) 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) 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) 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) 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) checkpoint() (espressomd.electrokinetics.Electrokinetics method) cid_for_particle() (espressomd.cluster_analysis.ClusterStructure method) class_lookup() (espressomd.actors.Actor method) clear() (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), [1] ClusterStructure (class in espressomd.cluster_analysis) collision_detection (espressomd.system.System attribute) CollisionDetection (class in espressomd.collision_detection) ComFixed (class in espressomd.comfixed) comfixed (espressomd.system.System attribute) 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) 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) coulomb_prefactor (in module espressomd.drude_helpers) create_polymer() (in module espressomd.polymer) cuda_init_handle (espressomd.system.System attribute) 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) cylrad (espressomd.shapes.Maze attribute)

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.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.lb.LBFluid 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.swimmer_reaction.Reaction method) default_scale (espressomd.constraints.ForceField attribute) (espressomd.constraints.PotentialField attribute) 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.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) dim (espressomd.shapes.Maze attribute) dimensions (espressomd.MDA_ESP.Timestep attribute) dip (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) dipm (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice 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) director (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) 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) DLC (class in espressomd.magnetostatic_extensions) DoubleClick (espressomd.visualization_opengl.MouseFireEvent attribute) dpd (espressomd.interactions.NonBondedInteractionHandle attribute) DPDInteraction (class in espressomd.interactions) 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_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 attribute), [1] ek_init() (espressomd.electrokinetics.Electrokinetics method) EKBoundaries (class in espressomd.ekboundaries) ekboundaries (espressomd.system.System attribute) EKBoundary (class in espressomd.ekboundaries) ELC (class in espressomd.electrostatic_extensions) 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) 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.reaction_ensemble (module) espressomd.scafacos (module) espressomd.script_interface (module) espressomd.shapes (module) espressomd.swimmer_reaction (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) (espressomd.particle_data.ParticleSlice attribute) exists() (espressomd.particle_data.ParticleList method) ext_force (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) ext_torque (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute)

F

f (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) far_cut (espressomd.magnetostatic_extensions.DLC attribute) FeneBond (class in espressomd.interactions) find_particle() (espressomd.system.System method) fix (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) 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 attribute), [1] 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 attribute) gamma_rot (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) 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_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.LBFluid 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.magnetostatics.MagnetostaticInteraction method) (espressomd.script_interface.PScriptInterface method) (espressomd.swimmer_reaction.Reaction 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_unravelled_index() (in module espressomd.utils) 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) 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) (espressomd.particle_data.ParticleSlice attribute) id() (espressomd.script_interface.PScriptInterface method) id_drude (in module espressomd.drude_helpers) image_box (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) implementation (espressomd.virtual_sites.ActiveVirtualSitesHandle 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) 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)

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

K

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)

L

lattice_switch (espressomd.system.System attribute) layer_width (espressomd.shapes.Stomatocyte attribute) LBBoundaries (class in espressomd.lbboundaries) lbboundaries (espressomd.system.System attribute) LBBoundary (class in espressomd.lbboundaries) LBFluid (class in espressomd.lb) LBFluidGPU (class in espressomd.lb) LBFluidRoutines (class in espressomd.lb) 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) LinearElectricPotential (class in espressomd.constraints) load() (espressomd.checkpointing.Checkpoint method) load_checkpoint() (espressomd.lb.LBFluid method) load_wang_landau_checkpoint() (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) local_stress_tensor() (espressomd.analyze.Analysis 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) (espressomd.particle_data.ParticleSlice attribute) mass_drude (in module espressomd.drude_helpers) 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) Maze (class in espressomd.shapes) 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) 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)

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) (espressomd.particle_data.ParticleSlice attribute) 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) (espressomd.particle_data.ParticleSlice attribute) 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) (espressomd.particle_data.ParticleSlice attribute)

node_grid (espressomd.cellsystem.CellSystem attribute) non_bonded_inter (espressomd.system.System attribute) NonBondedInteraction (class in espressomd.interactions) NonBondedInteractionHandle (class in espressomd.interactions) NonBondedInteractions (class in espressomd.interactions) normal (espressomd.shapes.Wall attribute) normalize() (espressomd.visualization_opengl.Camera method) normalized() (espressomd.visualization_opengl.Camera method) nsphere (espressomd.shapes.Maze attribute) 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_body (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) omega_lab (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute)

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) (espressomd.particle_data.ParticleSlice attribute) 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) particle_scales (espressomd.constraints.ForceField attribute) (espressomd.constraints.PotentialField attribute) 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) 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) phi0 (espressomd.constraints.LinearElectricPotential attribute), [1] pi (espressomd.lb.LBFluidRoutines attribute) pi_neq (espressomd.lb.LBFluidRoutines attribute) PObjectId (class in espressomd.script_interface) 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) (espressomd.particle_data.ParticleSlice attribute) pos_folded (espressomd.particle_data.ParticleHandle attribute) 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) Pressed (espressomd.visualization_opengl.KeyboardFireEvent attribute) pressure (espressomd.electrokinetics.ElectrokineticsRoutines attribute) pressure() (espressomd.analyze.Analysis method) print_boundary() (espressomd.lb.LBFluid method) print_velocity() (espressomd.lb.LBFluid method) print_vtk_boundary() (espressomd.electrokinetics.Electrokinetics method) (espressomd.lb.LBFluid method) print_vtk_density() (espressomd.electrokinetics.Electrokinetics method) (espressomd.electrokinetics.Species method) print_vtk_flux() (espressomd.electrokinetics.Species method) print_vtk_lbforce_density() (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.LBFluid 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) (espressomd.particle_data.ParticleSlice attribute)

quat (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) 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) random_number_generator_state (espressomd.system.System attribute) rdf() (espressomd.analyze.Analysis method) Reaction (class in espressomd.swimmer_reaction) reaction() (espressomd.reaction_ensemble.ReactionAlgorithm method) (espressomd.reaction_ensemble.WangLandauReactionEnsemble method) ReactionAlgorithm (class in espressomd.reaction_ensemble) ReactionEnsemble (class in espressomd.reaction_ensemble) 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) remove_total_momentum() (espressomd.lb.LBFluidGPU 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.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.BondedCoulombP3MSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.Dihedral 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.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.Tabulated method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method) (espressomd.lb.LBFluid 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.swimmer_reaction.Reaction method)

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) (espressomd.particle_data.ParticleSlice attribute) 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) (espressomd.particle_data.ParticleSlice attribute) 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.lb.LBFluid method) screenshot() (espressomd.visualization.openGLLive method) (espressomd.visualization_opengl.openGLLive method) script_interface_register() (in module espressomd.script_interface) ScriptInterfaceHelper (class in espressomd.script_interface) seed (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.BondedCoulombP3MSRBond 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.RigidBond method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.Tabulated 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_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.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() (espressomd.swimmer_reaction.Reaction 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 (espressomd.constraints.ShapeBasedConstraint attribute) ShapeBasedConstraint (class in espressomd.constraints) SimplePore (class in espressomd.shapes) 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) species_list (espressomd.electrokinetics.Electrokinetics attribute) Sphere (class in espressomd.shapes) SpheroCylinder (class in espressomd.shapes) sphrad (espressomd.shapes.Maze attribute) start() (espressomd.swimmer_reaction.Reaction method) (espressomd.visualization.mayaviLive method) (espressomd.visualization.openGLLive method) (espressomd.visualization_mayavi.mayaviLive method) (espressomd.visualization_opengl.openGLLive method) Stomatocyte (class in espressomd.shapes) stop() (espressomd.swimmer_reaction.Reaction method) Stream (class in espressomd.MDA_ESP) 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) (espressomd.particle_data.ParticleSlice attribute) 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 (class in espressomd.interactions) tabulated (espressomd.interactions.NonBondedInteractionHandle attribute) TabulatedNonBonded (class in espressomd.interactions) temp (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) ThereCanOnlyBeOne thermalized_bond (in module espressomd.drude_helpers) ThermalizedBond (class in espressomd.interactions) Thermostat (class in espressomd.thermostat) thermostat (espressomd.system.System attribute) thole (espressomd.interactions.NonBondedInteractionHandle attribute) thole_damping (in module espressomd.drude_helpers) time (espressomd.globals.Globals attribute) (espressomd.system.System attribute) time_step (espressomd.globals.Globals attribute) (espressomd.system.System attribute) 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) (espressomd.particle_data.ParticleSlice attribute) total_force() (espressomd.constraints.ShapeBasedConstraint method) total_normal_force() (espressomd.constraints.ShapeBasedConstraint method) trajectory (espressomd.MDA_ESP.Stream 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) (espressomd.particle_data.ParticleSlice attribute) 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.BondedCoulombP3MSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.Dihedral 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.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.Tabulated method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method)

type_number() (espressomd.interactions.AngleCosine method) (espressomd.interactions.AngleCossquare method) (espressomd.interactions.AngleHarmonic method) (espressomd.interactions.BondedCoulomb method) (espressomd.interactions.BondedCoulombP3MSRBond 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.RigidBond method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.Tabulated method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method)

U

u (espressomd.constraints.HomogeneousFlowField attribute), [1] units (espressomd.MDA_ESP.ESPReader attribute) unregister() (espressomd.checkpointing.Checkpoint method) update() (espressomd.accumulators.MeanVarianceCalculator 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) (espressomd.particle_data.ParticleSlice attribute) 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.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.BondedCoulombP3MSRBond method) (espressomd.interactions.BondedInteraction method) (espressomd.interactions.BondedInteractionNotDefined method) (espressomd.interactions.BuckinghamInteraction method) (espressomd.interactions.DPDInteraction method) (espressomd.interactions.Dihedral 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.RigidBond method) (espressomd.interactions.SmoothStepInteraction method) (espressomd.interactions.SoftSphereInteraction method) (espressomd.interactions.SubtLJ method) (espressomd.interactions.Tabulated method) (espressomd.interactions.TabulatedNonBonded method) (espressomd.interactions.ThermalizedBond method) (espressomd.interactions.Virtual method) (espressomd.lb.LBFluid 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.swimmer_reaction.Reaction 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.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.lb.LBFluid method) (espressomd.magnetostatic_extensions.DLC method) (espressomd.magnetostatics.DipolarP3M method) (espressomd.magnetostatics.MagnetostaticInteraction method) (espressomd.minimize_energy.MinimizeEnergy method) (espressomd.swimmer_reaction.Reaction 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) (espressomd.particle_data.ParticleSlice attribute) virtual_sites (espressomd.system.System attribute) VirtualSitesInertialessTracers (class in espressomd.virtual_sites) VirtualSitesOff (class in espressomd.virtual_sites) VirtualSitesRelative (class in espressomd.virtual_sites) 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 attribute) vs_relative (espressomd.particle_data.ParticleHandle attribute) (espressomd.particle_data.ParticleSlice attribute) vtf_pid_map() (in module espressomd.io.writer.vtf)

W

Wall (class in espressomd.shapes) WangLandauHasConverged WangLandauReactionEnsemble (class in espressomd.reaction_ensemble) 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)