Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __call__() (hoomd.filter.All method) (hoomd.filter.CustomFilter method) (hoomd.filter.Intersection method) (hoomd.filter.Null method) (hoomd.filter.ParticleFilter method) (hoomd.filter.Rigid method) (hoomd.filter.SetDifference method) (hoomd.filter.Tags method) (hoomd.filter.Type method) (hoomd.filter.Union method) (hoomd.trigger.After method) (hoomd.trigger.And method) (hoomd.trigger.Before method) (hoomd.trigger.Not method) (hoomd.trigger.On method) (hoomd.trigger.Or method) (hoomd.trigger.Periodic method) (hoomd.trigger.Trigger method) (hoomd.variant.box.BoxVariant method) (hoomd.variant.box.Constant method) (hoomd.variant.box.Interpolate method) (hoomd.variant.box.InverseVolumeRamp method) (hoomd.variant.Constant method) (hoomd.variant.Cycle method) (hoomd.variant.Power method) (hoomd.variant.Ramp method) (hoomd.variant.Variant method) __contains__() (hoomd.md.alchemy.pair.AlchemicalDOFStore method) (hoomd.Operations method) __del__() (hoomd.Simulation method) __delitem__() (hoomd.data.TypeParameter method) __eq__() (hoomd.Box method) (hoomd.data.TypeParameter method) (hoomd.filter.All method) (hoomd.filter.CustomFilter method) (hoomd.filter.Intersection method) (hoomd.filter.Null method) (hoomd.filter.ParticleFilter method) (hoomd.filter.Rigid method) (hoomd.filter.SetDifference method) (hoomd.filter.Tags method) (hoomd.filter.Type method) (hoomd.filter.Union method) (hoomd.logging.Logger method) (hoomd.md.manifold.Manifold method) (hoomd.trigger.After method) (hoomd.trigger.And method) (hoomd.trigger.Before method) (hoomd.trigger.Not method) (hoomd.trigger.On method) (hoomd.trigger.Or method) (hoomd.trigger.Periodic method) (hoomd.tune.GradientDescent method) (hoomd.tune.GridOptimizer method) (hoomd.tune.ManualTuneDefinition method) (hoomd.tune.ScaleSolver method) (hoomd.tune.SecantSolver method) (hoomd.update.FilterUpdater method) __getattr__() (hoomd.custom.CustomOperation method) (hoomd.data.TypeParameter method) __getitem__() (hoomd.data.TypeParameter method) (hoomd.md.alchemy.pair.AlchemicalDOFStore method) __getstate__() (hoomd.data.TypeParameter method) (hoomd.Operations method) (hoomd.trigger.Trigger method) (hoomd.variant.Variant method) __hash__() (hoomd.filter.All method) (hoomd.filter.Intersection method) (hoomd.filter.Null method) (hoomd.filter.ParticleFilter method) (hoomd.filter.Rigid method) (hoomd.filter.SetDifference method) (hoomd.filter.Tags method) (hoomd.filter.Type method) (hoomd.filter.Union method) (hoomd.tune.ManualTuneDefinition method) __iadd__() (hoomd.logging.Logger method) (hoomd.Operations method) __isub__() (hoomd.logging.Logger method) (hoomd.Operations method) __iter__() (hoomd.data.TypeParameter method) (hoomd.md.alchemy.pair.AlchemicalDOFStore method) (hoomd.Operations method) __len__() (hoomd.data.TypeParameter method) (hoomd.md.alchemy.pair.AlchemicalDOFStore method) (hoomd.Operations method) (hoomd.write.Burst method) __neq__() (hoomd.Box method) __reduce__() (hoomd.Box method) (hoomd.trigger.And method) (hoomd.trigger.Not method) (hoomd.trigger.Or method) (hoomd.variant.box.Constant method) (hoomd.variant.box.Interpolate method) (hoomd.variant.box.InverseVolumeRamp method) __repr__() (hoomd.Box method) (hoomd.wall.Cylinder method) (hoomd.wall.Plane method) (hoomd.wall.Sphere method) __setattr__() (hoomd.md.Integrator method) __setitem__() (hoomd.data.TypeParameter method) (hoomd.logging.Logger method) __setstate__() (hoomd.custom.CustomOperation method) (hoomd.data.TypeParameter method) (hoomd.trigger.Trigger method) (hoomd.variant.Variant method) __str__() (hoomd.error.DataAccessError method) (hoomd.error.IsolationWarning method) (hoomd.error.MutabilityError method) (hoomd.filter.All method) (hoomd.filter.Intersection method) (hoomd.filter.Null method) (hoomd.filter.ParticleFilter method) (hoomd.filter.Rigid method) (hoomd.filter.SetDifference method) (hoomd.filter.Tags method) (hoomd.filter.Type method) (hoomd.filter.Union method) (hoomd.trigger.After method) (hoomd.trigger.And method) (hoomd.trigger.Before method) (hoomd.trigger.Not method) (hoomd.trigger.On method) (hoomd.trigger.Or method) (hoomd.trigger.Periodic method) (hoomd.wall.Cylinder method) (hoomd.wall.Plane method) (hoomd.wall.Sphere method) A a (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) A (hoomd.variant.Cycle attribute) (hoomd.variant.Power attribute) (hoomd.variant.Ramp attribute) acceleration (hoomd.data.ParticleLocalAccessBase attribute) accepted_categories (hoomd.write.HDF5Log attribute) act() (hoomd.custom.Action method) (hoomd.custom.CustomOperation method) (hoomd.tune.CustomTuner method) (hoomd.update.CustomUpdater method) (hoomd.write.CustomWriter method) Action (class in hoomd.custom) action (hoomd.custom.CustomOperation property) (hoomd.tune.CustomTuner property) (hoomd.update.CustomUpdater property) (hoomd.write.CustomWriter property) Action.Flags (class in hoomd.custom) Active (class in hoomd.md.force) active_force (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.update.ActiveRotationalDiffusion attribute) active_torque (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) ActiveOnManifold (class in hoomd.md.force) ActiveRotationalDiffusion (class in hoomd.md.update) add() (hoomd.logging.Logger method) (hoomd.Operations method) additional_energy (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) additional_virial (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) After (class in hoomd.trigger) alchemical_dof (hoomd.md.alchemy.methods.Alchemostat property) (hoomd.md.alchemy.methods.NVT attribute) alchemical_forces (hoomd.md.alchemy.pair.AlchemicalDOF property) alchemical_kT (hoomd.md.alchemy.methods.NVT attribute) alchemical_momentum (hoomd.md.alchemy.pair.AlchemicalDOF attribute) AlchemicalDOF (class in hoomd.md.alchemy.pair) AlchemicalDOFStore (class in hoomd.md.alchemy.pair) Alchemostat (class in hoomd.md.alchemy.methods) ALJ (class in hoomd.md.pair.aniso) All (class in hoomd.filter) ALL (hoomd.logging.LoggerCategories attribute) allocated_particles_per_cell (hoomd.md.nlist.Cell property) allow_unsafe_resize (hoomd.hpmc.update.QuickCompress attribute) alpha (hoomd.hpmc.external.Linear attribute) (hoomd.md.alchemy.pair.AlchemicalDOF attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.tune.GradientDescent property) alpha_start (hoomd.md.minimize.FIRE attribute) always_compute_pressure (hoomd.Simulation property) amplitude (hoomd.mpcd.force.SineForce attribute) (hoomd.mpcd.geometry.CosineChannel attribute) And (class in hoomd.trigger) AndersenThermostat (class in hoomd.mpcd.collide) Angle (class in hoomd.md.angle) angle (hoomd.logging.LoggerCategories attribute) (hoomd.mpcd.collide.StochasticRotationDynamics attribute) angle_types (hoomd.State property) angle_z (hoomd.write.DCD attribute) AngleLocalAccessBase (class in hoomd.data) angles (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.Snapshot property) angmom (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) angmom_tol (hoomd.md.minimize.FIRE attribute) angular_speed (hoomd.mpcd.geometry.ConcentricCylinders attribute) AngularStep (class in hoomd.hpmc.pair) AnisotropicPair (class in hoomd.md.pair.aniso) any() (hoomd.logging.LoggerCategories class method) Area (class in hoomd.md.mesh.conservation) area (hoomd.md.mesh.conservation.Area property) (hoomd.md.mesh.conservation.TriangleArea property) aspect (hoomd.hpmc.update.BoxMC attribute) aspect_moves (hoomd.hpmc.update.BoxMC property) attach() (hoomd.custom.Action method) auto_select() (in module hoomd.device) AutotunedObject (class in hoomd.operation) avg_cluster_size (hoomd.hpmc.update.GCA property) axis (hoomd.wall.Cylinder attribute) B B (hoomd.variant.Cycle attribute) (hoomd.variant.Power attribute) (hoomd.variant.Ramp attribute) barostat_dof (hoomd.md.methods.ConstantPressure attribute) barostat_energy (hoomd.md.methods.ConstantPressure property) barrier() (hoomd.communicator.Communicator method) barrier_all() (hoomd.communicator.Communicator method) Before (class in hoomd.trigger) BendingRigidity (class in hoomd.md.mesh.bending) Berendsen (class in hoomd.md.methods.thermostats) best_buffer_size (hoomd.md.tune.NeighborListBuffer property) betaP (hoomd.hpmc.compute.SDF property) BlockForce (class in hoomd.mpcd.force) body (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.hpmc.pair.Union attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.Snapshot.particles attribute) BodyForce (class in hoomd.mpcd.force) Bond (class in hoomd.md.bond) bond (hoomd.logging.LoggerCategories attribute) bond_types (hoomd.State property) BondLocalAccessBase (class in hoomd.data) bonds (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.mesh.Mesh property) (hoomd.Snapshot property) BounceBack (class in hoomd.mpcd.methods) (class in hoomd.mpcd.stream) Box (class in hoomd) box (hoomd.Snapshot attribute) (hoomd.State property) (hoomd.update.BoxResize attribute) (hoomd.variant.box.Constant property) box_dof (hoomd.md.methods.ConstantPressure attribute) box_like (in module hoomd.box) BoxInterface (class in hoomd.box) BoxMC (class in hoomd.hpmc.update) boxmc (hoomd.hpmc.tune.BoxMCMoveSize attribute) BoxMCMoveSize (class in hoomd.hpmc.tune) BoxResize (class in hoomd.update) BoxVariant (class in hoomd.variant.box) Brownian (class in hoomd.md.methods) (class in hoomd.md.methods.rattle) Buckingham (class in hoomd.md.pair) buffer (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) build_dir (in module hoomd.version) Bulk (class in hoomd.mpcd.stream) Burst (class in hoomd.write) Bussi (class in hoomd.md.methods.thermostats) C callback (hoomd.hpmc.shape_move.ShapeSpace attribute) categories (hoomd.logging.Logger property) Cell (class in hoomd.md.nlist) cell_list (hoomd.mpcd.Integrator property) cell_width (hoomd.md.nlist.Stencil attribute) CellList (class in hoomd.mpcd.collide) chain_probability (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) chain_time (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) chains_in_space (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere attribute) ChainTime (class in hoomd.hpmc.nec.tune) charge (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) check_dist (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) check_mpcd_particles() (hoomd.mpcd.stream.BounceBack method) check_particles() (hoomd.mpcd.methods.BounceBack method) clamp_into_domain() (hoomd.tune.ManualTuneDefinition method) clear_whole_buffer_after_dump (hoomd.write.Burst attribute) collision_method (hoomd.mpcd.Integrator attribute) CollisionMethod (class in hoomd.mpcd.collide) Communicator (class in hoomd.communicator) communicator (hoomd.device.CPU attribute) (hoomd.device.Device property) (hoomd.device.GPU attribute) (hoomd.Snapshot attribute) compile_date (in module hoomd.version) compile_flags (in module hoomd.version) complete (hoomd.hpmc.update.QuickCompress property) Compute (class in hoomd.operation) compute() (hoomd.trigger.After method) (hoomd.trigger.And method) (hoomd.trigger.Before method) (hoomd.trigger.Not method) (hoomd.trigger.On method) (hoomd.trigger.Or method) (hoomd.trigger.Periodic method) (hoomd.trigger.Trigger method) compute_capability (hoomd.device.GPU property) compute_energy() (hoomd.md.alchemy.pair.LJGauss method) (hoomd.md.pair.aniso.ALJ method) (hoomd.md.pair.aniso.AnisotropicPair method) (hoomd.md.pair.aniso.Dipole method) (hoomd.md.pair.aniso.GayBerne method) (hoomd.md.pair.aniso.Patchy method) (hoomd.md.pair.aniso.PatchyExpandedGaussian method) (hoomd.md.pair.aniso.PatchyExpandedLJ method) (hoomd.md.pair.aniso.PatchyExpandedMie method) (hoomd.md.pair.aniso.PatchyGaussian method) (hoomd.md.pair.aniso.PatchyLJ method) (hoomd.md.pair.aniso.PatchyMie method) (hoomd.md.pair.aniso.PatchyYukawa method) (hoomd.md.pair.Buckingham method) (hoomd.md.pair.DLVO method) (hoomd.md.pair.DPD method) (hoomd.md.pair.DPDConservative method) (hoomd.md.pair.DPDLJ method) (hoomd.md.pair.Ewald method) (hoomd.md.pair.ExpandedGaussian method) (hoomd.md.pair.ExpandedLJ method) (hoomd.md.pair.ExpandedMie method) (hoomd.md.pair.ForceShiftedLJ method) (hoomd.md.pair.Fourier method) (hoomd.md.pair.Gaussian method) (hoomd.md.pair.LJ method) (hoomd.md.pair.LJ0804 method) (hoomd.md.pair.LJ1208 method) (hoomd.md.pair.LJGauss method) (hoomd.md.pair.Mie method) (hoomd.md.pair.Moliere method) (hoomd.md.pair.Morse method) (hoomd.md.pair.OPP method) (hoomd.md.pair.Pair method) (hoomd.md.pair.ReactionField method) (hoomd.md.pair.Table method) (hoomd.md.pair.TWF method) (hoomd.md.pair.Yukawa method) (hoomd.md.pair.ZBL method) computes (hoomd.Operations property) ConcentricCylinders (class in hoomd.mpcd.geometry) configuration (hoomd.Snapshot property) Constant (class in hoomd.md.force) (class in hoomd.variant) (class in hoomd.variant.box) constant_force (hoomd.md.force.Constant attribute) constant_torque (hoomd.md.force.Constant attribute) ConstantForce (class in hoomd.mpcd.force) ConstantPressure (class in hoomd.md.methods) ConstantVolume (class in hoomd.md.methods) constituent_potential (hoomd.hpmc.pair.Union property) Constraint (class in hoomd.md.constrain) constraint (hoomd.logging.LoggerCategories attribute) ConstraintLocalAccessBase (class in hoomd.data) constraints (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.md.Integrator attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.mpcd.Integrator attribute) (hoomd.Snapshot property) contraction_separation (hoomd.mpcd.geometry.CosineExpansionContraction attribute) converged (hoomd.md.minimize.FIRE property) ConvexPolygon (class in hoomd.hpmc.integrate) ConvexPolyhedron (class in hoomd.hpmc.integrate) (class in hoomd.hpmc.nec.integrate) ConvexSpheropolygon (class in hoomd.hpmc.integrate) ConvexSpheropolyhedron (class in hoomd.hpmc.integrate) ConvexSpheropolyhedronUnion (class in hoomd.hpmc.integrate) CosineChannel (class in hoomd.mpcd.geometry) CosineExpansionContraction (class in hoomd.mpcd.geometry) CosineSquared (class in hoomd.md.angle) Coulomb (class in hoomd.md.long_range.pppm) (class in hoomd.md.special_pair) counter (hoomd.hpmc.update.BoxMC property) counters (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) couple (hoomd.md.methods.ConstantPressure attribute) CPU (class in hoomd.device) cpu_local_force_arrays (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) cpu_local_nlist_arrays (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) cpu_local_snapshot (hoomd.State property) create_bodies() (hoomd.md.constrain.Rigid method) create_diffusion_updater() (hoomd.md.force.Active method) create_state_from_gsd() (hoomd.Simulation method) create_state_from_snapshot() (hoomd.Simulation method) cube() (hoomd.Box class method) Custom (class in hoomd.md.force) CustomFilter (class in hoomd.filter) CustomOperation (class in hoomd.custom) CustomTuner (class in hoomd.tune) CustomUpdater (class in hoomd.update) CustomWriter (class in hoomd.write) cxx_compiler (in module hoomd.version) Cycle (class in hoomd.variant) Cylinder (class in hoomd.md.manifold) (class in hoomd.wall) D d (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) DataAccessError (class in hoomd.error) DCD (class in hoomd.write) default (hoomd.data.TypeParameter property) degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property) delimiter (hoomd.write.Table attribute) density (hoomd.mpcd.fill.GeometryFiller attribute) (hoomd.mpcd.fill.VirtualParticleFiller attribute) detach() (hoomd.custom.Action method) deterministic (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.Stencil attribute) Device (class in hoomd.device) device (hoomd.device.CPU property) (hoomd.device.Device property) (hoomd.device.GPU property) (hoomd.Simulation property) diameter (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) Diamond (class in hoomd.md.manifold) Dihedral (class in hoomd.md.dihedral) dihedral (hoomd.logging.LoggerCategories attribute) dihedral_types (hoomd.State property) DihedralLocalAccessBase (class in hoomd.data) dihedrals (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.Snapshot property) dimensions (hoomd.Box property) (hoomd.md.nlist.Cell property) (hoomd.Snapshot attribute) Dipole (class in hoomd.md.pair.aniso) directors (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) DisplacementCapped (class in hoomd.md.methods) (class in hoomd.md.methods.rattle) Distance (class in hoomd.md.constrain) DLVO (class in hoomd.md.pair) domain (hoomd.tune.ManualTuneDefinition property) domain_decomposition (hoomd.State property) domain_decomposition_split_fractions (hoomd.State property) DPD (class in hoomd.md.pair) DPDConservative (class in hoomd.md.pair) DPDLJ (class in hoomd.md.pair) dt (hoomd.md.Integrator attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.mpcd.Integrator attribute) dump() (hoomd.write.Burst method) dx (hoomd.hpmc.compute.SDF attribute) dynamic (hoomd.write.GSD attribute) E E (hoomd.md.external.field.Electric attribute) Elastic (class in hoomd.hpmc.shape_move) Electric (class in hoomd.md.external.field) Ellipsoid (class in hoomd.hpmc.integrate) (class in hoomd.md.manifold) embedded_particiles (hoomd.mpcd.collide.AndersenThermostat attribute) (hoomd.mpcd.collide.StochasticRotationDynamics attribute) embedded_particles (hoomd.mpcd.collide.CollisionMethod attribute) enable_profiling() (hoomd.device.GPU method) energies (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) energy (hoomd.hpmc.external.External property) (hoomd.hpmc.external.Harmonic property) (hoomd.hpmc.external.Linear property) (hoomd.hpmc.external.WallPotential property) (hoomd.hpmc.pair.AngularStep property) (hoomd.hpmc.pair.ExpandedGaussian property) (hoomd.hpmc.pair.LennardJones property) (hoomd.hpmc.pair.LJGauss property) (hoomd.hpmc.pair.OPP property) (hoomd.hpmc.pair.Pair property) (hoomd.hpmc.pair.Step property) (hoomd.hpmc.pair.Union property) (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.methods.thermostats.MTTK property) (hoomd.md.minimize.FIRE property) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) energy_tol (hoomd.md.minimize.FIRE attribute) epsilon (hoomd.md.alchemy.pair.LJGauss attribute) Ewald (class in hoomd.md.pair) exchange_moves (hoomd.hpmc.update.MuVT property) exclusions (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) ExpandedGaussian (class in hoomd.hpmc.pair) (class in hoomd.md.pair) ExpandedLJ (class in hoomd.md.pair) ExpandedMie (class in hoomd.md.pair) expansion_separation (hoomd.mpcd.geometry.CosineExpansionContraction attribute) External (class in hoomd.hpmc.external) external_energy (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) external_potentials (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) F FacetedEllipsoid (class in hoomd.hpmc.integrate) FacetedEllipsoidUnion (class in hoomd.hpmc.integrate) fdec_alpha (hoomd.md.minimize.FIRE attribute) fdec_dt (hoomd.md.minimize.FIRE attribute) FENEWCA (class in hoomd.md.bond) (class in hoomd.md.mesh.bond) Field (class in hoomd.md.external.field) filename (hoomd.write.DCD attribute) (hoomd.write.GSD attribute) (hoomd.write.HDF5Log attribute) filter (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.methods.Brownian attribute) (hoomd.md.methods.ConstantPressure attribute) (hoomd.md.methods.ConstantVolume attribute) (hoomd.md.methods.DisplacementCapped attribute) (hoomd.md.methods.Langevin attribute) (hoomd.md.methods.OverdampedViscous attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.DisplacementCapped attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.rattle.MethodRATTLE attribute) (hoomd.md.methods.rattle.NVE attribute) (hoomd.md.methods.rattle.OverdampedViscous attribute) (hoomd.md.update.ReversePerturbationFlow attribute) (hoomd.mpcd.methods.BounceBack attribute) (hoomd.update.BoxResize attribute) (hoomd.write.DCD attribute) (hoomd.write.GSD attribute) filter_like (in module hoomd.filter) filters (hoomd.update.FilterUpdater property) FilterUpdater (class in hoomd.update) final_bin (hoomd.md.tune.NeighborListBuffer property) final_box (hoomd.variant.box.Interpolate property) final_timestep (hoomd.Simulation property) final_volume (hoomd.variant.box.InverseVolumeRamp attribute) finc_dt (hoomd.md.minimize.FIRE attribute) FIRE (class in hoomd.md.minimize) flags (hoomd.custom.Action attribute) flip_probability (hoomd.hpmc.update.GCA attribute) floating_point_precision (in module hoomd.version) flow_direction (hoomd.md.update.ReversePerturbationFlow attribute) flow_target (hoomd.md.update.ReversePerturbationFlow attribute) flush() (hoomd.device.NoticeFile method) (hoomd.write.GSD method) (hoomd.write.HDF5Log method) Force (class in hoomd.md.force) force (hoomd.md.data.ForceLocalAccess attribute) (hoomd.md.data.ForceLocalAccessGPU attribute) (hoomd.mpcd.force.BlockForce attribute) (hoomd.mpcd.force.ConstantForce attribute) force_tol (hoomd.md.minimize.FIRE attribute) ForceLocalAccess (class in hoomd.md.data) ForceLocalAccessGPU (class in hoomd.md.data) forces (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.Integrator attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) (hoomd.mpcd.Integrator attribute) ForceShiftedLJ (class in hoomd.md.external.wall) (class in hoomd.md.pair) Fourier (class in hoomd.md.pair) free_volume (hoomd.hpmc.compute.FreeVolume property) FreeVolume (class in hoomd.hpmc.compute) from_basis_vectors() (hoomd.Box class method) from_box() (hoomd.Box class method) from_gsd_frame() (hoomd.Snapshot class method) from_matrix() (hoomd.Box class method) fugacity (hoomd.hpmc.update.MuVT attribute) G gamma (hoomd.md.methods.Brownian attribute) (hoomd.md.methods.ConstantPressure attribute) (hoomd.md.methods.Langevin attribute) (hoomd.md.methods.OverdampedViscous attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.rattle.OverdampedViscous attribute) gamma_r (hoomd.md.methods.Brownian attribute) (hoomd.md.methods.Langevin attribute) (hoomd.md.methods.OverdampedViscous attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.rattle.OverdampedViscous attribute) Gaussian (class in hoomd.md.external.wall) (class in hoomd.md.pair) GayBerne (class in hoomd.md.pair.aniso) GCA (class in hoomd.hpmc.update) Geometry (class in hoomd.mpcd.geometry) geometry (hoomd.mpcd.fill.GeometryFiller attribute) (hoomd.mpcd.methods.BounceBack attribute) (hoomd.mpcd.stream.BounceBack attribute) GeometryFiller (class in hoomd.mpcd.fill) get() (hoomd.data.TypeParameter method) get_available_devices() (hoomd.device.GPU static method) get_box() (hoomd.update.BoxResize method) get_snapshot() (hoomd.State method) get_unavailable_device_reasons() (hoomd.device.GPU static method) git_branch (in module hoomd.version) git_sha1 (in module hoomd.version) global_box (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) GPU (class in hoomd.device) gpu_api_version (in module hoomd.version) gpu_enabled (in module hoomd.version) gpu_error_checking (hoomd.device.GPU property) gpu_local_force_arrays (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) gpu_local_nlist_arrays (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) gpu_local_snapshot (hoomd.State property) gpu_platform (in module hoomd.version) GPUNotAvailableError (class in hoomd.error) GradientDescent (class in hoomd.tune) grid (hoomd.tune.ParticleSorter attribute) GridOptimizer (class in hoomd.tune) group (hoomd.Snapshot.angles attribute) (hoomd.Snapshot.bonds attribute) (hoomd.Snapshot.constraints attribute) (hoomd.Snapshot.dihedrals attribute) (hoomd.Snapshot.impropers attribute) (hoomd.Snapshot.pairs attribute) GSD (class in hoomd.write) Gyroid (class in hoomd.md.manifold) H half_nlist (hoomd.md.data.NeighborListLocalAccess attribute) (hoomd.md.data.NeighborListLocalAccessGPU attribute) half_step_hook (hoomd.md.Integrator attribute) (hoomd.mpcd.Integrator attribute) HalfStepHook (class in hoomd.md) Harmonic (class in hoomd.hpmc.external) (class in hoomd.md.angle) (class in hoomd.md.bond) (class in hoomd.md.improper) (class in hoomd.md.mesh.bond) harmonic_pressure (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute) HarmonicAveragedThermodynamicQuantities (class in hoomd.md.compute) HDF5Log (class in hoomd.write) head_list (hoomd.md.data.NeighborListLocalAccess attribute) (hoomd.md.data.NeighborListLocalAccessGPU attribute) header_sep (hoomd.write.Table attribute) Helfrich (class in hoomd.md.mesh.bending) hoomd module hoomd.box module hoomd.communicator module hoomd.custom module hoomd.data module hoomd.device module hoomd.error module hoomd.filter module hoomd.hpmc module hoomd.hpmc.compute module hoomd.hpmc.external module hoomd.hpmc.integrate module hoomd.hpmc.nec module hoomd.hpmc.nec.integrate module hoomd.hpmc.nec.tune module hoomd.hpmc.pair module hoomd.hpmc.shape_move module hoomd.hpmc.tune module hoomd.hpmc.update module hoomd.logging module hoomd.md module hoomd.md.alchemy module hoomd.md.alchemy.methods module hoomd.md.alchemy.pair module hoomd.md.angle module hoomd.md.bond module hoomd.md.compute module hoomd.md.constrain module hoomd.md.data module hoomd.md.dihedral module hoomd.md.external module hoomd.md.external.field module hoomd.md.external.wall module hoomd.md.force module hoomd.md.improper module hoomd.md.long_range module hoomd.md.long_range.pppm module hoomd.md.manifold module hoomd.md.many_body module hoomd.md.mesh module hoomd.md.mesh.bending module hoomd.md.mesh.bond module hoomd.md.mesh.conservation module hoomd.md.methods module hoomd.md.methods.rattle module hoomd.md.methods.thermostats module hoomd.md.minimize module hoomd.md.nlist module hoomd.md.pair module hoomd.md.pair.aniso module hoomd.md.special_pair module hoomd.md.tune module hoomd.md.update module hoomd.mesh module hoomd.mpcd module hoomd.mpcd.collide module hoomd.mpcd.fill module hoomd.mpcd.force module hoomd.mpcd.geometry module hoomd.mpcd.methods module hoomd.mpcd.stream module hoomd.mpcd.tune module hoomd.operation module hoomd.trigger module hoomd.tune module hoomd.update module hoomd.util module hoomd.variant module hoomd.variant.box module hoomd.version module hoomd.wall module hoomd.write module HOOMDArray (class in hoomd.data) HOOMDGPUArray (class in hoomd.data) hpmc_built (in module hoomd.version) HPMCIntegrator (class in hoomd.hpmc.integrate) HPMCNECIntegrator (class in hoomd.hpmc.nec.integrate) I image (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) Improper (class in hoomd.md.improper) improper (hoomd.logging.LoggerCategories attribute) improper_types (hoomd.State property) ImproperLocalAccessBase (class in hoomd.data) impropers (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.Snapshot property) in_domain() (hoomd.tune.ManualTuneDefinition method) IncompleteSpecificationError (class in hoomd.error) initial_box (hoomd.variant.box.Interpolate property) (hoomd.variant.box.InverseVolumeRamp property) initial_timestep (hoomd.Simulation property) inner_radius (hoomd.mpcd.geometry.ConcentricCylinders attribute) insert_moves (hoomd.hpmc.update.MuVT property) inside (hoomd.wall.Cylinder attribute) (hoomd.wall.Sphere attribute) install_dir (in module hoomd.version) instance (hoomd.hpmc.update.BoxMC attribute) (hoomd.hpmc.update.QuickCompress attribute) integrate_rotational_dof (hoomd.md.Integrator attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.mpcd.Integrator attribute) Integrator (class in hoomd.md) (class in hoomd.mpcd) (class in hoomd.operation) integrator (hoomd.Operations property) interaction_matrix (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) Interpolate (class in hoomd.variant.box) Intersection (class in hoomd.filter) InverseVolumeRamp (class in hoomd.variant.box) is2D (hoomd.Box property) is_available() (hoomd.device.GPU static method) is_tuning_complete (hoomd.custom.CustomOperation property) (hoomd.hpmc.compute.FreeVolume property) (hoomd.hpmc.compute.SDF property) (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) (hoomd.hpmc.nec.tune.ChainTime property) (hoomd.hpmc.tune.BoxMCMoveSize property) (hoomd.hpmc.tune.MoveSize property) (hoomd.hpmc.update.BoxMC property) (hoomd.hpmc.update.GCA property) (hoomd.hpmc.update.MuVT property) (hoomd.hpmc.update.QuickCompress property) (hoomd.hpmc.update.Shape property) (hoomd.md.alchemy.methods.Alchemostat property) (hoomd.md.alchemy.methods.NVT property) (hoomd.md.alchemy.pair.LJGauss property) (hoomd.md.angle.Angle property) (hoomd.md.angle.CosineSquared property) (hoomd.md.angle.Harmonic property) (hoomd.md.angle.Table property) (hoomd.md.bond.Bond property) (hoomd.md.bond.FENEWCA property) (hoomd.md.bond.Harmonic property) (hoomd.md.bond.Table property) (hoomd.md.bond.Tether property) (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities property) (hoomd.md.compute.ThermodynamicQuantities property) (hoomd.md.constrain.Constraint property) (hoomd.md.constrain.Distance property) (hoomd.md.constrain.Rigid property) (hoomd.md.dihedral.Dihedral property) (hoomd.md.dihedral.OPLS property) (hoomd.md.dihedral.Periodic property) (hoomd.md.dihedral.Table property) (hoomd.md.external.field.Electric property) (hoomd.md.external.field.Field property) (hoomd.md.external.field.Magnetic property) (hoomd.md.external.field.Periodic property) (hoomd.md.external.wall.ForceShiftedLJ property) (hoomd.md.external.wall.Gaussian property) (hoomd.md.external.wall.LJ property) (hoomd.md.external.wall.Mie property) (hoomd.md.external.wall.Morse property) (hoomd.md.external.wall.WallPotential property) (hoomd.md.external.wall.Yukawa property) (hoomd.md.force.Active property) (hoomd.md.force.ActiveOnManifold property) (hoomd.md.force.Constant property) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic property) (hoomd.md.improper.Improper property) (hoomd.md.improper.Periodic property) (hoomd.md.Integrator property) (hoomd.md.long_range.pppm.Coulomb property) (hoomd.md.many_body.RevCross property) (hoomd.md.many_body.SquareDensity property) (hoomd.md.many_body.Tersoff property) (hoomd.md.many_body.Triplet property) (hoomd.md.mesh.bending.BendingRigidity property) (hoomd.md.mesh.bending.Helfrich property) (hoomd.md.mesh.bond.FENEWCA property) (hoomd.md.mesh.bond.Harmonic property) (hoomd.md.mesh.bond.Tether property) (hoomd.md.mesh.conservation.Area property) (hoomd.md.mesh.conservation.MeshConservationPotential property) (hoomd.md.mesh.conservation.TriangleArea property) (hoomd.md.mesh.conservation.Volume property) (hoomd.md.mesh.MeshPotential property) (hoomd.md.methods.Brownian property) (hoomd.md.methods.ConstantPressure property) (hoomd.md.methods.ConstantVolume property) (hoomd.md.methods.DisplacementCapped property) (hoomd.md.methods.Langevin property) (hoomd.md.methods.Method property) (hoomd.md.methods.OverdampedViscous property) (hoomd.md.methods.rattle.Brownian property) (hoomd.md.methods.rattle.DisplacementCapped property) (hoomd.md.methods.rattle.Langevin property) (hoomd.md.methods.rattle.MethodRATTLE property) (hoomd.md.methods.rattle.NVE property) (hoomd.md.methods.rattle.OverdampedViscous property) (hoomd.md.methods.Thermostatted property) (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) (hoomd.md.pair.aniso.ALJ property) (hoomd.md.pair.aniso.AnisotropicPair property) (hoomd.md.pair.aniso.Dipole property) (hoomd.md.pair.aniso.GayBerne property) (hoomd.md.pair.aniso.Patchy property) (hoomd.md.pair.aniso.PatchyExpandedGaussian property) (hoomd.md.pair.aniso.PatchyExpandedLJ property) (hoomd.md.pair.aniso.PatchyExpandedMie property) (hoomd.md.pair.aniso.PatchyGaussian property) (hoomd.md.pair.aniso.PatchyLJ property) (hoomd.md.pair.aniso.PatchyMie property) (hoomd.md.pair.aniso.PatchyYukawa property) (hoomd.md.pair.Buckingham property) (hoomd.md.pair.DLVO property) (hoomd.md.pair.DPD property) (hoomd.md.pair.DPDConservative property) (hoomd.md.pair.DPDLJ property) (hoomd.md.pair.Ewald property) (hoomd.md.pair.ExpandedGaussian property) (hoomd.md.pair.ExpandedLJ property) (hoomd.md.pair.ExpandedMie property) (hoomd.md.pair.ForceShiftedLJ property) (hoomd.md.pair.Fourier property) (hoomd.md.pair.Gaussian property) (hoomd.md.pair.LJ property) (hoomd.md.pair.LJ0804 property) (hoomd.md.pair.LJ1208 property) (hoomd.md.pair.LJGauss property) (hoomd.md.pair.Mie property) (hoomd.md.pair.Moliere property) (hoomd.md.pair.Morse property) (hoomd.md.pair.OPP property) (hoomd.md.pair.Pair property) (hoomd.md.pair.ReactionField property) (hoomd.md.pair.Table property) (hoomd.md.pair.TWF property) (hoomd.md.pair.Yukawa property) (hoomd.md.pair.ZBL property) (hoomd.md.special_pair.Coulomb property) (hoomd.md.special_pair.LJ property) (hoomd.md.special_pair.SpecialPair property) (hoomd.md.update.ActiveRotationalDiffusion property) (hoomd.md.update.ReversePerturbationFlow property) (hoomd.md.update.ZeroMomentum property) (hoomd.mpcd.collide.AndersenThermostat property) (hoomd.mpcd.collide.CellList property) (hoomd.mpcd.collide.CollisionMethod property) (hoomd.mpcd.collide.StochasticRotationDynamics property) (hoomd.mpcd.fill.GeometryFiller property) (hoomd.mpcd.fill.VirtualParticleFiller property) (hoomd.mpcd.Integrator property) (hoomd.mpcd.methods.BounceBack property) (hoomd.mpcd.stream.BounceBack property) (hoomd.mpcd.stream.Bulk property) (hoomd.mpcd.stream.StreamingMethod property) (hoomd.mpcd.tune.ParticleSorter property) (hoomd.operation.AutotunedObject property) (hoomd.operation.Compute property) (hoomd.operation.Integrator property) (hoomd.operation.Operation property) (hoomd.operation.TriggeredOperation property) (hoomd.operation.Tuner property) (hoomd.operation.Updater property) (hoomd.operation.Writer property) (hoomd.Operations property) (hoomd.tune.CustomTuner property) (hoomd.tune.LoadBalancer property) (hoomd.tune.ParticleSorter property) (hoomd.update.BoxResize property) (hoomd.update.CustomUpdater property) (hoomd.update.FilterUpdater property) (hoomd.update.RemoveDrift property) (hoomd.write.Burst property) (hoomd.write.CustomWriter property) (hoomd.write.DCD property) (hoomd.write.GSD property) (hoomd.write.HDF5Log property) (hoomd.write.Table property) IsolationWarning (class in hoomd.error) isotropic_potential (hoomd.hpmc.pair.AngularStep property) K k_rotational (hoomd.hpmc.external.Harmonic attribute) k_translational (hoomd.hpmc.external.Harmonic attribute) kappa (hoomd.tune.GradientDescent attribute) kernel_parameters (hoomd.custom.CustomOperation property) (hoomd.hpmc.compute.FreeVolume property) (hoomd.hpmc.compute.SDF property) (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) (hoomd.hpmc.nec.tune.ChainTime property) (hoomd.hpmc.tune.BoxMCMoveSize property) (hoomd.hpmc.tune.MoveSize property) (hoomd.hpmc.update.BoxMC property) (hoomd.hpmc.update.GCA property) (hoomd.hpmc.update.MuVT property) (hoomd.hpmc.update.QuickCompress property) (hoomd.hpmc.update.Shape property) (hoomd.md.alchemy.methods.Alchemostat property) (hoomd.md.alchemy.methods.NVT property) (hoomd.md.alchemy.pair.LJGauss property) (hoomd.md.angle.Angle property) (hoomd.md.angle.CosineSquared property) (hoomd.md.angle.Harmonic property) (hoomd.md.angle.Table property) (hoomd.md.bond.Bond property) (hoomd.md.bond.FENEWCA property) (hoomd.md.bond.Harmonic property) (hoomd.md.bond.Table property) (hoomd.md.bond.Tether property) (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities property) (hoomd.md.compute.ThermodynamicQuantities property) (hoomd.md.constrain.Constraint property) (hoomd.md.constrain.Distance property) (hoomd.md.constrain.Rigid property) (hoomd.md.dihedral.Dihedral property) (hoomd.md.dihedral.OPLS property) (hoomd.md.dihedral.Periodic property) (hoomd.md.dihedral.Table property) (hoomd.md.external.field.Electric property) (hoomd.md.external.field.Field property) (hoomd.md.external.field.Magnetic property) (hoomd.md.external.field.Periodic property) (hoomd.md.external.wall.ForceShiftedLJ property) (hoomd.md.external.wall.Gaussian property) (hoomd.md.external.wall.LJ property) (hoomd.md.external.wall.Mie property) (hoomd.md.external.wall.Morse property) (hoomd.md.external.wall.WallPotential property) (hoomd.md.external.wall.Yukawa property) (hoomd.md.force.Active property) (hoomd.md.force.ActiveOnManifold property) (hoomd.md.force.Constant property) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic property) (hoomd.md.improper.Improper property) (hoomd.md.improper.Periodic property) (hoomd.md.Integrator property) (hoomd.md.long_range.pppm.Coulomb property) (hoomd.md.many_body.RevCross property) (hoomd.md.many_body.SquareDensity property) (hoomd.md.many_body.Tersoff property) (hoomd.md.many_body.Triplet property) (hoomd.md.mesh.bending.BendingRigidity property) (hoomd.md.mesh.bending.Helfrich property) (hoomd.md.mesh.bond.FENEWCA property) (hoomd.md.mesh.bond.Harmonic property) (hoomd.md.mesh.bond.Tether property) (hoomd.md.mesh.conservation.Area property) (hoomd.md.mesh.conservation.MeshConservationPotential property) (hoomd.md.mesh.conservation.TriangleArea property) (hoomd.md.mesh.conservation.Volume property) (hoomd.md.mesh.MeshPotential property) (hoomd.md.methods.Brownian property) (hoomd.md.methods.ConstantPressure property) (hoomd.md.methods.ConstantVolume property) (hoomd.md.methods.DisplacementCapped property) (hoomd.md.methods.Langevin property) (hoomd.md.methods.Method property) (hoomd.md.methods.OverdampedViscous property) (hoomd.md.methods.rattle.Brownian property) (hoomd.md.methods.rattle.DisplacementCapped property) (hoomd.md.methods.rattle.Langevin property) (hoomd.md.methods.rattle.MethodRATTLE property) (hoomd.md.methods.rattle.NVE property) (hoomd.md.methods.rattle.OverdampedViscous property) (hoomd.md.methods.Thermostatted property) (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) (hoomd.md.pair.aniso.ALJ property) (hoomd.md.pair.aniso.AnisotropicPair property) (hoomd.md.pair.aniso.Dipole property) (hoomd.md.pair.aniso.GayBerne property) (hoomd.md.pair.aniso.Patchy property) (hoomd.md.pair.aniso.PatchyExpandedGaussian property) (hoomd.md.pair.aniso.PatchyExpandedLJ property) (hoomd.md.pair.aniso.PatchyExpandedMie property) (hoomd.md.pair.aniso.PatchyGaussian property) (hoomd.md.pair.aniso.PatchyLJ property) (hoomd.md.pair.aniso.PatchyMie property) (hoomd.md.pair.aniso.PatchyYukawa property) (hoomd.md.pair.Buckingham property) (hoomd.md.pair.DLVO property) (hoomd.md.pair.DPD property) (hoomd.md.pair.DPDConservative property) (hoomd.md.pair.DPDLJ property) (hoomd.md.pair.Ewald property) (hoomd.md.pair.ExpandedGaussian property) (hoomd.md.pair.ExpandedLJ property) (hoomd.md.pair.ExpandedMie property) (hoomd.md.pair.ForceShiftedLJ property) (hoomd.md.pair.Fourier property) (hoomd.md.pair.Gaussian property) (hoomd.md.pair.LJ property) (hoomd.md.pair.LJ0804 property) (hoomd.md.pair.LJ1208 property) (hoomd.md.pair.LJGauss property) (hoomd.md.pair.Mie property) (hoomd.md.pair.Moliere property) (hoomd.md.pair.Morse property) (hoomd.md.pair.OPP property) (hoomd.md.pair.Pair property) (hoomd.md.pair.ReactionField property) (hoomd.md.pair.Table property) (hoomd.md.pair.TWF property) (hoomd.md.pair.Yukawa property) (hoomd.md.pair.ZBL property) (hoomd.md.special_pair.Coulomb property) (hoomd.md.special_pair.LJ property) (hoomd.md.special_pair.SpecialPair property) (hoomd.md.update.ActiveRotationalDiffusion property) (hoomd.md.update.ReversePerturbationFlow property) (hoomd.md.update.ZeroMomentum property) (hoomd.mpcd.collide.AndersenThermostat property) (hoomd.mpcd.collide.CellList property) (hoomd.mpcd.collide.CollisionMethod property) (hoomd.mpcd.collide.StochasticRotationDynamics property) (hoomd.mpcd.fill.GeometryFiller property) (hoomd.mpcd.fill.VirtualParticleFiller property) (hoomd.mpcd.Integrator property) (hoomd.mpcd.methods.BounceBack property) (hoomd.mpcd.stream.BounceBack property) (hoomd.mpcd.stream.Bulk property) (hoomd.mpcd.stream.StreamingMethod property) (hoomd.mpcd.tune.ParticleSorter property) (hoomd.operation.AutotunedObject property) (hoomd.operation.Compute property) (hoomd.operation.Integrator property) (hoomd.operation.Operation property) (hoomd.operation.TriggeredOperation property) (hoomd.operation.Tuner property) (hoomd.operation.Updater property) (hoomd.operation.Writer property) (hoomd.tune.CustomTuner property) (hoomd.tune.LoadBalancer property) (hoomd.tune.ParticleSorter property) (hoomd.update.BoxResize property) (hoomd.update.CustomUpdater property) (hoomd.update.FilterUpdater property) (hoomd.update.RemoveDrift property) (hoomd.write.Burst property) (hoomd.write.CustomWriter property) (hoomd.write.DCD property) (hoomd.write.GSD property) (hoomd.write.HDF5Log property) (hoomd.write.Table property) kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property) kinetic_temperature (hoomd.md.compute.ThermodynamicQuantities property) kT (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute) (hoomd.md.methods.Brownian attribute) (hoomd.md.methods.Langevin attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.thermostats.Berendsen attribute) (hoomd.md.methods.thermostats.Bussi attribute) (hoomd.md.methods.thermostats.MTTK attribute) (hoomd.mpcd.collide.AndersenThermostat attribute) (hoomd.mpcd.collide.StochasticRotationDynamics attribute) (hoomd.mpcd.fill.GeometryFiller attribute) (hoomd.mpcd.fill.VirtualParticleFiller attribute) L L (hoomd.Box property) Langevin (class in hoomd.md.methods) (class in hoomd.md.methods.rattle) last_tps (hoomd.md.tune.NeighborListBuffer property) leaf_capacity (hoomd.hpmc.pair.Union attribute) length (hoomd.hpmc.update.BoxMC attribute) (hoomd.mpcd.geometry.PlanarPore attribute) LennardJones (class in hoomd.hpmc.pair) Linear (class in hoomd.hpmc.external) linear_momentum (hoomd.md.Integrator property) (hoomd.mpcd.Integrator property) LJ (class in hoomd.md.external.wall) (class in hoomd.md.pair) (class in hoomd.md.special_pair) LJ0804 (class in hoomd.md.pair) LJ1208 (class in hoomd.md.pair) LJGauss (class in hoomd.hpmc.pair) (class in hoomd.md.alchemy.pair) (class in hoomd.md.pair) LoadBalancer (class in hoomd.tune) local_box (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) local_pair_list (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) localize_abort() (hoomd.communicator.Communicator method) LocalSnapshot (class in hoomd.data) LocalSnapshotGPU (class in hoomd.data) log() (hoomd.logging.Logger method) (in module hoomd.logging) loggables (hoomd.custom.Action property) (hoomd.Simulation property) Logger (class in hoomd.logging) logger (hoomd.write.GSD property) (hoomd.write.HDF5Log attribute) (hoomd.write.Table attribute) LoggerCategories (class in hoomd.logging) Lx (hoomd.Box property) (hoomd.box.BoxInterface property) Ly (hoomd.Box property) (hoomd.box.BoxInterface property) Lz (hoomd.Box property) (hoomd.box.BoxInterface property) M Magnetic (class in hoomd.md.external.field) make_example_simulation() (in module hoomd.util) make_pppm_coulomb_forces() (in module hoomd.md.long_range.pppm) Manifold (class in hoomd.md.manifold) manifold_constraint (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.DisplacementCapped attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.rattle.MethodRATTLE attribute) (hoomd.md.methods.rattle.NVE attribute) (hoomd.md.methods.rattle.OverdampedViscous attribute) ManualTuneDefinition (class in hoomd.tune) map_overlaps (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) mask (hoomd.hpmc.pair.AngularStep attribute) mass (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.md.alchemy.pair.AlchemicalDOF attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.particles attribute) max (hoomd.variant.Constant property) (hoomd.variant.Cycle property) (hoomd.variant.Power property) (hoomd.variant.Ramp property) (hoomd.variant.Variant property) max_burst_size (hoomd.write.Burst attribute) max_chain_time (hoomd.hpmc.nec.tune.ChainTime attribute) max_delta (hoomd.tune.GradientDescent attribute) max_header_len (hoomd.write.Table attribute) max_iterations (hoomd.tune.LoadBalancer attribute) max_move_size (hoomd.hpmc.tune.BoxMCMoveSize attribute) max_overlaps_per_particle (hoomd.hpmc.update.QuickCompress attribute) max_precision (hoomd.write.Table attribute) max_rotation_move (hoomd.hpmc.tune.MoveSize attribute) max_slab (hoomd.md.update.ReversePerturbationFlow attribute) max_tps (hoomd.md.tune.NeighborListBuffer property) max_translation_move (hoomd.hpmc.tune.MoveSize attribute) max_volume_rescale (hoomd.hpmc.update.MuVT attribute) max_x (hoomd.tune.ManualTuneDefinition property) maximize (hoomd.tune.GradientDescent attribute) maximum_buffer (hoomd.md.tune.NeighborListBuffer attribute) maximum_displacement (hoomd.md.methods.DisplacementCapped attribute) (hoomd.md.methods.rattle.DisplacementCapped attribute) maximum_write_buffer_size (hoomd.write.GSD attribute) md_built (in module hoomd.version) members (hoomd.data.AngleLocalAccessBase attribute) (hoomd.data.BondLocalAccessBase attribute) (hoomd.data.ConstraintLocalAccessBase attribute) (hoomd.data.DihedralLocalAccessBase attribute) (hoomd.data.ImproperLocalAccessBase attribute) (hoomd.data.PairLocalAccessBase attribute) Mesh (class in hoomd.mesh) mesh (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential property) (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) MeshConservationPotential (class in hoomd.md.mesh.conservation) MeshPotential (class in hoomd.md.mesh) message_filename (hoomd.device.CPU property) (hoomd.device.Device property) (hoomd.device.GPU property) Method (class in hoomd.md.methods) MethodRATTLE (class in hoomd.md.methods.rattle) methods (hoomd.md.Integrator attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.mpcd.Integrator attribute) Mie (class in hoomd.md.external.wall) (class in hoomd.md.pair) min (hoomd.variant.Constant property) (hoomd.variant.Cycle property) (hoomd.variant.Power property) (hoomd.variant.Ramp property) (hoomd.variant.Variant property) min_column_width (hoomd.write.Table attribute) min_scale (hoomd.hpmc.update.QuickCompress attribute) min_slab (hoomd.md.update.ReversePerturbationFlow attribute) min_steps_adapt (hoomd.md.minimize.FIRE attribute) min_steps_conv (hoomd.md.minimize.FIRE attribute) min_x (hoomd.tune.ManualTuneDefinition property) minimum_buffer (hoomd.md.tune.NeighborListBuffer attribute) mode (hoomd.hpmc.pair.ExpandedGaussian attribute) (hoomd.hpmc.pair.LennardJones attribute) (hoomd.hpmc.pair.LJGauss attribute) (hoomd.hpmc.pair.OPP attribute) (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.write.GSD attribute) (hoomd.write.HDF5Log attribute) modify_namespace() (in module hoomd.logging) module hoomd hoomd.box hoomd.communicator hoomd.custom hoomd.data hoomd.device hoomd.error hoomd.filter hoomd.hpmc hoomd.hpmc.compute hoomd.hpmc.external hoomd.hpmc.integrate hoomd.hpmc.nec hoomd.hpmc.nec.integrate hoomd.hpmc.nec.tune hoomd.hpmc.pair hoomd.hpmc.shape_move hoomd.hpmc.tune hoomd.hpmc.update hoomd.logging hoomd.md hoomd.md.alchemy hoomd.md.alchemy.methods hoomd.md.alchemy.pair hoomd.md.angle hoomd.md.bond hoomd.md.compute hoomd.md.constrain hoomd.md.data hoomd.md.dihedral hoomd.md.external hoomd.md.external.field hoomd.md.external.wall hoomd.md.force hoomd.md.improper hoomd.md.long_range hoomd.md.long_range.pppm hoomd.md.manifold hoomd.md.many_body hoomd.md.mesh hoomd.md.mesh.bending hoomd.md.mesh.bond hoomd.md.mesh.conservation hoomd.md.methods hoomd.md.methods.rattle hoomd.md.methods.thermostats hoomd.md.minimize hoomd.md.nlist hoomd.md.pair hoomd.md.pair.aniso hoomd.md.special_pair hoomd.md.tune hoomd.md.update hoomd.mesh hoomd.mpcd hoomd.mpcd.collide hoomd.mpcd.fill hoomd.mpcd.force hoomd.mpcd.geometry hoomd.mpcd.methods hoomd.mpcd.stream hoomd.mpcd.tune hoomd.operation hoomd.trigger hoomd.tune hoomd.update hoomd.util hoomd.variant hoomd.variant.box hoomd.version hoomd.wall hoomd.write Moliere (class in hoomd.md.pair) moment_inertia (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) Morse (class in hoomd.md.external.wall) (class in hoomd.md.pair) move_ratio (hoomd.hpmc.update.MuVT attribute) moves (hoomd.hpmc.tune.BoxMCMoveSize attribute) (hoomd.hpmc.tune.MoveSize attribute) MoveSize (class in hoomd.hpmc.tune) mpcd (hoomd.Snapshot property) mpcd_built (in module hoomd.version) mpcd_particle_force (hoomd.mpcd.stream.BounceBack attribute) (hoomd.mpcd.stream.Bulk attribute) (hoomd.mpcd.stream.StreamingMethod attribute) mpcd_particle_sorter (hoomd.mpcd.Integrator attribute) mpi_enabled (in module hoomd.version) MPINotAvailableError (class in hoomd.error) mps (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) MTTK (class in hoomd.md.methods.thermostats) mu (hoomd.md.alchemy.pair.AlchemicalDOF attribute) (hoomd.md.pair.aniso.Dipole attribute) MutabilityError (class in hoomd.error) MuVT (class in hoomd.hpmc.update) N N (hoomd.hpmc.update.MuVT property) (hoomd.Snapshot.angles attribute) (hoomd.Snapshot.bonds attribute) (hoomd.Snapshot.constraints attribute) (hoomd.Snapshot.dihedrals attribute) (hoomd.Snapshot.impropers attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.pairs attribute) (hoomd.Snapshot.particles attribute) N_angles (hoomd.State property) N_bonds (hoomd.State property) N_constraints (hoomd.State property) N_dihedrals (hoomd.State property) N_impropers (hoomd.State property) n_neigh (hoomd.md.data.NeighborListLocalAccess attribute) (hoomd.md.data.NeighborListLocalAccessGPU attribute) N_particles (hoomd.State property) n_slabs (hoomd.md.update.ReversePerturbationFlow attribute) N_special_pairs (hoomd.State property) nec_counters (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere attribute) NeighborList (class in hoomd.md.nlist) NeighborListBuffer (class in hoomd.md.tune) NeighborListLocalAccess (class in hoomd.md.data) NeighborListLocalAccessGPU (class in hoomd.md.data) net_alchemical_force (hoomd.md.alchemy.pair.AlchemicalDOF property) net_energy (hoomd.data.ParticleLocalAccessBase attribute) net_force (hoomd.data.ParticleLocalAccessBase attribute) net_torque (hoomd.data.ParticleLocalAccessBase attribute) net_virial (hoomd.data.ParticleLocalAccessBase attribute) nlist (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.data.NeighborListLocalAccess attribute) (hoomd.md.data.NeighborListLocalAccessGPU attribute) (hoomd.md.long_range.pppm.Coulomb property) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) no_slip (hoomd.mpcd.geometry.ConcentricCylinders attribute) (hoomd.mpcd.geometry.CosineChannel attribute) (hoomd.mpcd.geometry.CosineExpansionContraction attribute) (hoomd.mpcd.geometry.Geometry attribute) (hoomd.mpcd.geometry.ParallelPlates attribute) (hoomd.mpcd.geometry.PlanarPore attribute) (hoomd.mpcd.geometry.Sphere attribute) NONE (hoomd.logging.LoggerCategories attribute) normal (hoomd.wall.Plane attribute) normal_shear_ratio (hoomd.hpmc.shape_move.Elastic attribute) Not (class in hoomd.trigger) notice() (hoomd.device.CPU method) (hoomd.device.Device method) (hoomd.device.GPU method) notice_level (hoomd.device.CPU property) (hoomd.device.Device property) (hoomd.device.GPU property) NoticeFile (class in hoomd.device) nselect (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) nsweeps (hoomd.hpmc.update.Shape attribute) Null (class in hoomd.filter) num_builds (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) num_cells (hoomd.mpcd.collide.CellList property) num_particles (hoomd.md.compute.ThermodynamicQuantities property) num_partitions (hoomd.communicator.Communicator property) num_ranks (hoomd.communicator.Communicator property) num_samples (hoomd.hpmc.compute.FreeVolume attribute) NVE (class in hoomd.md.methods.rattle) NVT (class in hoomd.md.alchemy.methods) O object (hoomd.logging.LoggerCategories attribute) On (class in hoomd.trigger) only_default (hoomd.logging.Logger property) open (hoomd.wall.Cylinder attribute) (hoomd.wall.Plane attribute) (hoomd.wall.Sphere attribute) Operation (class in hoomd.operation) Operations (class in hoomd) operations (hoomd.Simulation property) OPLS (class in hoomd.md.dihedral) OPP (class in hoomd.hpmc.pair) (class in hoomd.md.pair) Optimizer (class in hoomd.tune) Or (class in hoomd.trigger) order (hoomd.md.long_range.pppm.Coulomb attribute) orientation (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.particles attribute) origin (hoomd.wall.Cylinder attribute) (hoomd.wall.Plane attribute) (hoomd.wall.Sphere attribute) outer_radius (hoomd.mpcd.geometry.ConcentricCylinders attribute) output (hoomd.write.Table attribute) OverdampedViscous (class in hoomd.md.methods) (class in hoomd.md.methods.rattle) overlaps (hoomd.hpmc.external.WallPotential property) (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) overwrite (hoomd.write.DCD attribute) P P (hoomd.hpmc.compute.SDF property) (hoomd.hpmc.update.BoxMC attribute) Pair (class in hoomd.hpmc.pair) (class in hoomd.md.pair) pair (hoomd.logging.LoggerCategories attribute) pair_energy (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) pair_list (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) pair_potentials (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) PairLocalAccessBase (class in hoomd.data) pairs (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.Snapshot property) ParallelPlates (class in hoomd.mpcd.geometry) param_move_probability (hoomd.hpmc.shape_move.ShapeSpace attribute) parameter (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) params (hoomd.hpmc.pair.ExpandedGaussian attribute) (hoomd.hpmc.pair.LennardJones attribute) (hoomd.hpmc.pair.LJGauss attribute) (hoomd.hpmc.pair.OPP attribute) (hoomd.hpmc.pair.Step attribute) (hoomd.hpmc.shape_move.ShapeSpace attribute) (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) particle (hoomd.logging.LoggerCategories attribute) particle_types (hoomd.State property) particle_volumes (hoomd.hpmc.update.Shape property) ParticleFilter (class in hoomd.filter) ParticleLocalAccessBase (class in hoomd.data) particles (hoomd.data.LocalSnapshot property) (hoomd.data.LocalSnapshotGPU property) (hoomd.Snapshot property) particles_per_chain (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere attribute) ParticleSorter (class in hoomd.mpcd.tune) (class in hoomd.tune) partition (hoomd.communicator.Communicator property) Patchy (class in hoomd.md.pair.aniso) PatchyExpandedGaussian (class in hoomd.md.pair.aniso) PatchyExpandedLJ (class in hoomd.md.pair.aniso) PatchyExpandedMie (class in hoomd.md.pair.aniso) PatchyGaussian (class in hoomd.md.pair.aniso) PatchyLJ (class in hoomd.md.pair.aniso) PatchyMie (class in hoomd.md.pair.aniso) PatchyYukawa (class in hoomd.md.pair.aniso) period (hoomd.md.alchemy.methods.NVT attribute) (hoomd.mpcd.collide.AndersenThermostat attribute) (hoomd.mpcd.collide.CollisionMethod attribute) (hoomd.mpcd.collide.StochasticRotationDynamics attribute) (hoomd.mpcd.stream.BounceBack attribute) (hoomd.mpcd.stream.Bulk attribute) (hoomd.mpcd.stream.StreamingMethod attribute) (hoomd.trigger.Periodic attribute) Periodic (class in hoomd.md.dihedral) (class in hoomd.md.external.field) (class in hoomd.md.improper) (class in hoomd.trigger) periodic (hoomd.Box property) phase (hoomd.trigger.Periodic attribute) pivot_move_probability (hoomd.hpmc.update.GCA attribute) PlanarPore (class in hoomd.mpcd.geometry) Plane (class in hoomd.md.manifold) (class in hoomd.wall) plane_normal (hoomd.hpmc.external.Linear attribute) plane_origin (hoomd.hpmc.external.Linear attribute) Polyhedron (class in hoomd.hpmc.integrate) position (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.particles attribute) potential_energy (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities property) (hoomd.md.compute.ThermodynamicQuantities property) (hoomd.md.data.ForceLocalAccess attribute) (hoomd.md.data.ForceLocalAccessGPU attribute) Power (class in hoomd.variant) power (hoomd.variant.Power attribute) pressure (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities property) (hoomd.md.compute.ThermodynamicQuantities property) pressure_tensor (hoomd.md.compute.ThermodynamicQuantities property) pretend (hoomd.hpmc.update.Shape attribute) pretty (hoomd.write.Table attribute) Primitive (class in hoomd.md.manifold) Q QuickCompress (class in hoomd.hpmc.update) R r0 (hoomd.md.alchemy.pair.LJGauss attribute) r_cut (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) r_on (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) radius (hoomd.mpcd.geometry.Sphere attribute) (hoomd.wall.Cylinder attribute) (hoomd.wall.Sphere attribute) Ramp (class in hoomd.variant) rank (hoomd.communicator.Communicator property) ReactionField (class in hoomd.md.pair) rebuild_check_delay (hoomd.md.nlist.Cell attribute) (hoomd.md.nlist.NeighborList attribute) (hoomd.md.nlist.Stencil attribute) (hoomd.md.nlist.Tree attribute) reference_orientations (hoomd.hpmc.external.Harmonic attribute) reference_positions (hoomd.hpmc.external.Harmonic attribute) (hoomd.update.RemoveDrift attribute) reference_shape (hoomd.hpmc.shape_move.Elastic attribute) remove() (hoomd.logging.Logger method) (hoomd.Operations method) remove_moves (hoomd.hpmc.update.MuVT property) RemoveDrift (class in hoomd.update) repeat_length (hoomd.mpcd.geometry.CosineChannel attribute) (hoomd.mpcd.geometry.CosineExpansionContraction attribute) replicate() (hoomd.Snapshot method) (hoomd.State method) rescale_all (hoomd.md.methods.ConstantPressure attribute) reservoir_energy (hoomd.md.methods.Langevin property) reset() (hoomd.md.minimize.FIRE method) (hoomd.tune.GradientDescent method) (hoomd.tune.GridOptimizer method) (hoomd.tune.ScaleSolver method) (hoomd.tune.SecantSolver method) (hoomd.tune.SolverStep method) resolution (hoomd.md.long_range.pppm.Coulomb attribute) RevCross (class in hoomd.md.many_body) ReversePerturbationFlow (class in hoomd.md.update) Rigid (class in hoomd.filter) (class in hoomd.md.constrain) rigid (hoomd.md.Integrator attribute) (hoomd.md.minimize.FIRE attribute) (hoomd.mpcd.Integrator attribute) RootSolver (class in hoomd.tune) rotate_moves (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) rotational_degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property) rotational_diffusion (hoomd.md.update.ActiveRotationalDiffusion attribute) rotational_dof (hoomd.md.methods.thermostats.MTTK attribute) rotational_kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property) rtag (hoomd.data.AngleLocalAccessBase attribute) (hoomd.data.BondLocalAccessBase attribute) (hoomd.data.ConstraintLocalAccessBase attribute) (hoomd.data.DihedralLocalAccessBase attribute) (hoomd.data.ImproperLocalAccessBase attribute) (hoomd.data.PairLocalAccessBase attribute) (hoomd.data.ParticleLocalAccessBase attribute) run() (hoomd.Simulation method) S S (hoomd.md.methods.ConstantPressure attribute) scalar (hoomd.logging.LoggerCategories attribute) scale() (hoomd.Box method) scale_solver() (hoomd.hpmc.nec.tune.ChainTime class method) (hoomd.hpmc.tune.BoxMCMoveSize class method) (hoomd.hpmc.tune.MoveSize class method) ScaleSolver (class in hoomd.tune) SDF (class in hoomd.hpmc.compute) sdf_compression (hoomd.hpmc.compute.SDF property) sdf_expansion (hoomd.hpmc.compute.SDF property) secant_solver() (hoomd.hpmc.nec.tune.ChainTime class method) (hoomd.hpmc.tune.BoxMCMoveSize class method) (hoomd.hpmc.tune.MoveSize class method) SecantSolver (class in hoomd.tune) seed (hoomd.Simulation property) separation (hoomd.mpcd.force.BlockForce attribute) (hoomd.mpcd.geometry.CosineChannel attribute) (hoomd.mpcd.geometry.ParallelPlates attribute) (hoomd.mpcd.geometry.PlanarPore attribute) sequence (hoomd.logging.LoggerCategories attribute) set_box() (hoomd.State method) set_forces() (hoomd.md.force.Custom method) set_snapshot() (hoomd.State method) setdefault() (hoomd.data.TypeParameter method) SetDifference (class in hoomd.filter) Shape (class in hoomd.hpmc.update) shape (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) (hoomd.md.pair.aniso.ALJ attribute) shape_move (hoomd.hpmc.update.Shape attribute) shape_move_energy (hoomd.hpmc.update.Shape property) shape_moves (hoomd.hpmc.update.Shape property) ShapeMove (class in hoomd.hpmc.shape_move) ShapeSpace (class in hoomd.hpmc.shape_move) shear (hoomd.hpmc.update.BoxMC attribute) shear_moves (hoomd.hpmc.update.BoxMC property) shift (hoomd.mpcd.collide.CellList attribute) shortest_rebuild (hoomd.md.nlist.Cell property) (hoomd.md.nlist.NeighborList property) (hoomd.md.nlist.Stencil property) (hoomd.md.nlist.Tree property) sigma (hoomd.md.alchemy.pair.LJGauss attribute) SimplePolygon (class in hoomd.hpmc.integrate) Simulation (class in hoomd) SimulationDefinitionError (class in hoomd.error) SineForce (class in hoomd.mpcd.force) size (hoomd.mesh.Mesh property) slab_direction (hoomd.md.update.ReversePerturbationFlow attribute) Snapshot (class in hoomd) solve() (hoomd.tune.GradientDescent method) (hoomd.tune.SolverStep method) solve_one() (hoomd.tune.GradientDescent method) (hoomd.tune.GridOptimizer method) (hoomd.tune.ScaleSolver method) (hoomd.tune.SecantSolver method) (hoomd.tune.SolverStep method) solver (hoomd.hpmc.nec.tune.ChainTime attribute) (hoomd.hpmc.tune.BoxMCMoveSize attribute) (hoomd.hpmc.tune.MoveSize attribute) (hoomd.md.tune.NeighborListBuffer attribute) SolverStep (class in hoomd.tune) source_dir (in module hoomd.version) special_pair_types (hoomd.State property) SpecialPair (class in hoomd.md.special_pair) speed (hoomd.mpcd.geometry.ParallelPlates attribute) Sphere (class in hoomd.hpmc.integrate) (class in hoomd.hpmc.nec.integrate) (class in hoomd.md.manifold) (class in hoomd.mpcd.geometry) (class in hoomd.wall) SphereUnion (class in hoomd.hpmc.integrate) Sphinx (class in hoomd.hpmc.integrate) square() (hoomd.Box class method) SquareDensity (class in hoomd.md.many_body) State (class in hoomd) state (hoomd.Simulation property) Stencil (class in hoomd.md.nlist) Step (class in hoomd.hpmc.pair) step_size (hoomd.hpmc.shape_move.Elastic attribute) (hoomd.hpmc.shape_move.ShapeMove attribute) (hoomd.hpmc.shape_move.ShapeSpace attribute) (hoomd.hpmc.shape_move.Vertex attribute) stiffness (hoomd.hpmc.shape_move.Elastic attribute) StochasticRotationDynamics (class in hoomd.mpcd.collide) streaming_method (hoomd.mpcd.Integrator attribute) StreamingMethod (class in hoomd.mpcd.stream) string (hoomd.logging.LoggerCategories attribute) string_categories (hoomd.logging.Logger property) strings (hoomd.logging.LoggerCategories attribute) summed_exchanged_momentum (hoomd.md.update.ReversePerturbationFlow property) symmetries (hoomd.hpmc.external.Harmonic attribute) T t_A (hoomd.variant.Cycle attribute) t_AB (hoomd.variant.Cycle attribute) t_B (hoomd.variant.Cycle attribute) t_BA (hoomd.variant.Cycle attribute) t_ramp (hoomd.variant.box.InverseVolumeRamp attribute) (hoomd.variant.Power attribute) (hoomd.variant.Ramp attribute) t_start (hoomd.variant.box.InverseVolumeRamp attribute) (hoomd.variant.Cycle attribute) (hoomd.variant.Power attribute) (hoomd.variant.Ramp attribute) Table (class in hoomd.md.angle) (class in hoomd.md.bond) (class in hoomd.md.dihedral) (class in hoomd.md.pair) (class in hoomd.write) tag (hoomd.data.AngleLocalAccessBase attribute) (hoomd.data.BondLocalAccessBase attribute) (hoomd.data.ConstraintLocalAccessBase attribute) (hoomd.data.DihedralLocalAccessBase attribute) (hoomd.data.ImproperLocalAccessBase attribute) (hoomd.data.PairLocalAccessBase attribute) (hoomd.data.ParticleLocalAccessBase attribute) Tags (class in hoomd.filter) tags (hoomd.filter.Tags property) tail_correction (hoomd.md.pair.LJ attribute) tally_reservoir_energy (hoomd.md.methods.Langevin attribute) target (hoomd.hpmc.nec.tune.ChainTime attribute) (hoomd.hpmc.tune.BoxMCMoveSize attribute) (hoomd.hpmc.tune.MoveSize attribute) (hoomd.tune.ManualTuneDefinition property) target_box (hoomd.hpmc.update.QuickCompress attribute) tau (hoomd.md.methods.thermostats.Berendsen attribute) (hoomd.md.methods.thermostats.Bussi attribute) (hoomd.md.methods.thermostats.MTTK attribute) tauS (hoomd.md.methods.ConstantPressure attribute) Tersoff (class in hoomd.md.many_body) test_particle_type (hoomd.hpmc.compute.FreeVolume attribute) Tether (class in hoomd.md.bond) (class in hoomd.md.mesh.bond) thermalize_barostat_dof() (hoomd.md.methods.ConstantPressure method) thermalize_dof() (hoomd.md.methods.thermostats.MTTK method) thermalize_particle_momenta() (hoomd.State method) ThermodynamicQuantities (class in hoomd.md.compute) Thermostat (class in hoomd.md.methods.thermostats) thermostat (hoomd.md.methods.ConstantPressure attribute) (hoomd.md.methods.ConstantVolume attribute) (hoomd.md.methods.DisplacementCapped attribute) (hoomd.md.methods.Thermostatted attribute) Thermostatted (class in hoomd.md.methods) tilts (hoomd.Box property) timestep (hoomd.Simulation property) (hoomd.trigger.After attribute) (hoomd.trigger.Before attribute) (hoomd.trigger.On attribute) to_base() (hoomd.data.TypeParameter method) to_dict() (hoomd.wall.Cylinder method) (hoomd.wall.Plane method) (hoomd.wall.Sphere method) (hoomd.wall.WallGeometry method) to_matrix() (hoomd.Box method) tol (hoomd.tune.GradientDescent attribute) tolerance (hoomd.md.constrain.Distance attribute) (hoomd.md.methods.rattle.Brownian attribute) (hoomd.md.methods.rattle.DisplacementCapped attribute) (hoomd.md.methods.rattle.Langevin attribute) (hoomd.md.methods.rattle.MethodRATTLE attribute) (hoomd.md.methods.rattle.NVE attribute) (hoomd.md.methods.rattle.OverdampedViscous attribute) (hoomd.tune.LoadBalancer attribute) torque (hoomd.md.data.ForceLocalAccess attribute) (hoomd.md.data.ForceLocalAccessGPU attribute) torques (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) tps (hoomd.Simulation property) transfer_types (hoomd.hpmc.update.MuVT attribute) translate_moves (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoid property) (hoomd.hpmc.integrate.FacetedEllipsoidUnion property) (hoomd.hpmc.integrate.HPMCIntegrator property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.integrate.Sphinx property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere property) translation_move_probability (hoomd.hpmc.integrate.ConvexPolygon attribute) (hoomd.hpmc.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolygon attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedron attribute) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion attribute) (hoomd.hpmc.integrate.Ellipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoid attribute) (hoomd.hpmc.integrate.FacetedEllipsoidUnion attribute) (hoomd.hpmc.integrate.HPMCIntegrator attribute) (hoomd.hpmc.integrate.Polyhedron attribute) (hoomd.hpmc.integrate.SimplePolygon attribute) (hoomd.hpmc.integrate.Sphere attribute) (hoomd.hpmc.integrate.SphereUnion attribute) (hoomd.hpmc.integrate.Sphinx attribute) (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) translational_degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property) translational_dof (hoomd.md.methods.thermostats.MTTK attribute) translational_kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property) Tree (class in hoomd.md.nlist) TriangleArea (class in hoomd.md.mesh.conservation) triangles (hoomd.mesh.Mesh property) triangulation (hoomd.mesh.Mesh attribute) Trigger (class in hoomd.trigger) trigger (hoomd.custom.CustomOperation attribute) (hoomd.hpmc.nec.tune.ChainTime attribute) (hoomd.hpmc.tune.BoxMCMoveSize attribute) (hoomd.hpmc.tune.MoveSize attribute) (hoomd.hpmc.update.BoxMC attribute) (hoomd.hpmc.update.GCA attribute) (hoomd.hpmc.update.MuVT attribute) (hoomd.hpmc.update.QuickCompress attribute) (hoomd.hpmc.update.Shape attribute) (hoomd.md.tune.NeighborListBuffer attribute) (hoomd.md.update.ActiveRotationalDiffusion attribute) (hoomd.md.update.ReversePerturbationFlow attribute) (hoomd.md.update.ZeroMomentum attribute) (hoomd.mpcd.tune.ParticleSorter attribute) (hoomd.operation.TriggeredOperation attribute) (hoomd.operation.Tuner attribute) (hoomd.operation.Updater attribute) (hoomd.operation.Writer attribute) (hoomd.trigger.Not attribute) (hoomd.tune.CustomTuner attribute) (hoomd.tune.LoadBalancer attribute) (hoomd.tune.ParticleSorter attribute) (hoomd.update.BoxResize attribute) (hoomd.update.CustomUpdater attribute) (hoomd.update.FilterUpdater attribute) (hoomd.update.RemoveDrift attribute) (hoomd.write.Burst attribute) (hoomd.write.CustomWriter attribute) (hoomd.write.DCD attribute) (hoomd.write.GSD attribute) (hoomd.write.HDF5Log attribute) (hoomd.write.Table attribute) trigger_like (in module hoomd.trigger) TriggeredOperation (class in hoomd.operation) triggers (hoomd.trigger.And attribute) (hoomd.trigger.Or attribute) Triplet (class in hoomd.md.many_body) truncate (hoomd.write.GSD attribute) tune_kernel_parameters() (hoomd.custom.CustomOperation method) (hoomd.hpmc.compute.FreeVolume method) (hoomd.hpmc.compute.SDF method) (hoomd.hpmc.integrate.ConvexPolygon method) (hoomd.hpmc.integrate.ConvexPolyhedron method) (hoomd.hpmc.integrate.ConvexSpheropolygon method) (hoomd.hpmc.integrate.ConvexSpheropolyhedron method) (hoomd.hpmc.integrate.ConvexSpheropolyhedronUnion method) (hoomd.hpmc.integrate.Ellipsoid method) (hoomd.hpmc.integrate.FacetedEllipsoid method) (hoomd.hpmc.integrate.FacetedEllipsoidUnion method) (hoomd.hpmc.integrate.HPMCIntegrator method) (hoomd.hpmc.integrate.Polyhedron method) (hoomd.hpmc.integrate.SimplePolygon method) (hoomd.hpmc.integrate.Sphere method) (hoomd.hpmc.integrate.SphereUnion method) (hoomd.hpmc.integrate.Sphinx method) (hoomd.hpmc.nec.integrate.ConvexPolyhedron method) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator method) (hoomd.hpmc.nec.integrate.Sphere method) (hoomd.hpmc.nec.tune.ChainTime method) (hoomd.hpmc.tune.BoxMCMoveSize method) (hoomd.hpmc.tune.MoveSize method) (hoomd.hpmc.update.BoxMC method) (hoomd.hpmc.update.GCA method) (hoomd.hpmc.update.MuVT method) (hoomd.hpmc.update.QuickCompress method) (hoomd.hpmc.update.Shape method) (hoomd.md.alchemy.methods.Alchemostat method) (hoomd.md.alchemy.methods.NVT method) (hoomd.md.alchemy.pair.LJGauss method) (hoomd.md.angle.Angle method) (hoomd.md.angle.CosineSquared method) (hoomd.md.angle.Harmonic method) (hoomd.md.angle.Table method) (hoomd.md.bond.Bond method) (hoomd.md.bond.FENEWCA method) (hoomd.md.bond.Harmonic method) (hoomd.md.bond.Table method) (hoomd.md.bond.Tether method) (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities method) (hoomd.md.compute.ThermodynamicQuantities method) (hoomd.md.constrain.Constraint method) (hoomd.md.constrain.Distance method) (hoomd.md.constrain.Rigid method) (hoomd.md.dihedral.Dihedral method) (hoomd.md.dihedral.OPLS method) (hoomd.md.dihedral.Periodic method) (hoomd.md.dihedral.Table method) (hoomd.md.external.field.Electric method) (hoomd.md.external.field.Field method) (hoomd.md.external.field.Magnetic method) (hoomd.md.external.field.Periodic method) (hoomd.md.external.wall.ForceShiftedLJ method) (hoomd.md.external.wall.Gaussian method) (hoomd.md.external.wall.LJ method) (hoomd.md.external.wall.Mie method) (hoomd.md.external.wall.Morse method) (hoomd.md.external.wall.WallPotential method) (hoomd.md.external.wall.Yukawa method) (hoomd.md.force.Active method) (hoomd.md.force.ActiveOnManifold method) (hoomd.md.force.Constant method) (hoomd.md.force.Force method) (hoomd.md.improper.Harmonic method) (hoomd.md.improper.Improper method) (hoomd.md.improper.Periodic method) (hoomd.md.Integrator method) (hoomd.md.long_range.pppm.Coulomb method) (hoomd.md.many_body.RevCross method) (hoomd.md.many_body.SquareDensity method) (hoomd.md.many_body.Tersoff method) (hoomd.md.many_body.Triplet method) (hoomd.md.mesh.bending.BendingRigidity method) (hoomd.md.mesh.bending.Helfrich method) (hoomd.md.mesh.bond.FENEWCA method) (hoomd.md.mesh.bond.Harmonic method) (hoomd.md.mesh.bond.Tether method) (hoomd.md.mesh.conservation.Area method) (hoomd.md.mesh.conservation.MeshConservationPotential method) (hoomd.md.mesh.conservation.TriangleArea method) (hoomd.md.mesh.conservation.Volume method) (hoomd.md.mesh.MeshPotential method) (hoomd.md.methods.Brownian method) (hoomd.md.methods.ConstantPressure method) (hoomd.md.methods.ConstantVolume method) (hoomd.md.methods.DisplacementCapped method) (hoomd.md.methods.Langevin method) (hoomd.md.methods.Method method) (hoomd.md.methods.OverdampedViscous method) (hoomd.md.methods.rattle.Brownian method) (hoomd.md.methods.rattle.DisplacementCapped method) (hoomd.md.methods.rattle.Langevin method) (hoomd.md.methods.rattle.MethodRATTLE method) (hoomd.md.methods.rattle.NVE method) (hoomd.md.methods.rattle.OverdampedViscous method) (hoomd.md.methods.Thermostatted method) (hoomd.md.nlist.Cell method) (hoomd.md.nlist.NeighborList method) (hoomd.md.nlist.Stencil method) (hoomd.md.nlist.Tree method) (hoomd.md.pair.aniso.ALJ method) (hoomd.md.pair.aniso.AnisotropicPair method) (hoomd.md.pair.aniso.Dipole method) (hoomd.md.pair.aniso.GayBerne method) (hoomd.md.pair.aniso.Patchy method) (hoomd.md.pair.aniso.PatchyExpandedGaussian method) (hoomd.md.pair.aniso.PatchyExpandedLJ method) (hoomd.md.pair.aniso.PatchyExpandedMie method) (hoomd.md.pair.aniso.PatchyGaussian method) (hoomd.md.pair.aniso.PatchyLJ method) (hoomd.md.pair.aniso.PatchyMie method) (hoomd.md.pair.aniso.PatchyYukawa method) (hoomd.md.pair.Buckingham method) (hoomd.md.pair.DLVO method) (hoomd.md.pair.DPD method) (hoomd.md.pair.DPDConservative method) (hoomd.md.pair.DPDLJ method) (hoomd.md.pair.Ewald method) (hoomd.md.pair.ExpandedGaussian method) (hoomd.md.pair.ExpandedLJ method) (hoomd.md.pair.ExpandedMie method) (hoomd.md.pair.ForceShiftedLJ method) (hoomd.md.pair.Fourier method) (hoomd.md.pair.Gaussian method) (hoomd.md.pair.LJ method) (hoomd.md.pair.LJ0804 method) (hoomd.md.pair.LJ1208 method) (hoomd.md.pair.LJGauss method) (hoomd.md.pair.Mie method) (hoomd.md.pair.Moliere method) (hoomd.md.pair.Morse method) (hoomd.md.pair.OPP method) (hoomd.md.pair.Pair method) (hoomd.md.pair.ReactionField method) (hoomd.md.pair.Table method) (hoomd.md.pair.TWF method) (hoomd.md.pair.Yukawa method) (hoomd.md.pair.ZBL method) (hoomd.md.special_pair.Coulomb method) (hoomd.md.special_pair.LJ method) (hoomd.md.special_pair.SpecialPair method) (hoomd.md.update.ActiveRotationalDiffusion method) (hoomd.md.update.ReversePerturbationFlow method) (hoomd.md.update.ZeroMomentum method) (hoomd.mpcd.collide.AndersenThermostat method) (hoomd.mpcd.collide.CellList method) (hoomd.mpcd.collide.CollisionMethod method) (hoomd.mpcd.collide.StochasticRotationDynamics method) (hoomd.mpcd.fill.GeometryFiller method) (hoomd.mpcd.fill.VirtualParticleFiller method) (hoomd.mpcd.Integrator method) (hoomd.mpcd.methods.BounceBack method) (hoomd.mpcd.stream.BounceBack method) (hoomd.mpcd.stream.Bulk method) (hoomd.mpcd.stream.StreamingMethod method) (hoomd.mpcd.tune.ParticleSorter method) (hoomd.operation.AutotunedObject method) (hoomd.operation.Compute method) (hoomd.operation.Integrator method) (hoomd.operation.Operation method) (hoomd.operation.TriggeredOperation method) (hoomd.operation.Tuner method) (hoomd.operation.Updater method) (hoomd.operation.Writer method) (hoomd.Operations method) (hoomd.tune.CustomTuner method) (hoomd.tune.LoadBalancer method) (hoomd.tune.ParticleSorter method) (hoomd.update.BoxResize method) (hoomd.update.CustomUpdater method) (hoomd.update.FilterUpdater method) (hoomd.update.RemoveDrift method) (hoomd.write.Burst method) (hoomd.write.CustomWriter method) (hoomd.write.DCD method) (hoomd.write.GSD method) (hoomd.write.HDF5Log method) (hoomd.write.Table method) tuned (hoomd.hpmc.tune.BoxMCMoveSize property) (hoomd.hpmc.tune.MoveSize property) (hoomd.md.tune.NeighborListBuffer property) Tuner (class in hoomd.operation) tuners (hoomd.Operations property) TWF (class in hoomd.md.pair) Type (class in hoomd.filter) type (hoomd.mpcd.fill.GeometryFiller attribute) (hoomd.mpcd.fill.VirtualParticleFiller attribute) type_ids (hoomd.mesh.Mesh property) type_select (hoomd.hpmc.update.Shape attribute) type_shapes (hoomd.hpmc.integrate.ConvexPolygon property) (hoomd.hpmc.integrate.ConvexPolyhedron property) (hoomd.hpmc.integrate.ConvexSpheropolygon property) (hoomd.hpmc.integrate.ConvexSpheropolyhedron property) (hoomd.hpmc.integrate.Ellipsoid property) (hoomd.hpmc.integrate.Polyhedron property) (hoomd.hpmc.integrate.SimplePolygon property) (hoomd.hpmc.integrate.Sphere property) (hoomd.hpmc.integrate.SphereUnion property) (hoomd.hpmc.nec.integrate.ConvexPolyhedron property) (hoomd.hpmc.nec.integrate.Sphere property) (hoomd.md.pair.aniso.ALJ property) (hoomd.md.pair.aniso.GayBerne property) TypeConversionError (class in hoomd.error) typeid (hoomd.data.AngleLocalAccessBase attribute) (hoomd.data.BondLocalAccessBase attribute) (hoomd.data.DihedralLocalAccessBase attribute) (hoomd.data.ImproperLocalAccessBase attribute) (hoomd.data.PairLocalAccessBase attribute) (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.angles attribute) (hoomd.Snapshot.bonds attribute) (hoomd.Snapshot.dihedrals attribute) (hoomd.Snapshot.impropers attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.pairs attribute) (hoomd.Snapshot.particles attribute) TypeParameter (class in hoomd.data) types (hoomd.filter.Type property) (hoomd.hpmc.tune.MoveSize attribute) (hoomd.mesh.Mesh attribute) (hoomd.Snapshot.angles attribute) (hoomd.Snapshot.bonds attribute) (hoomd.Snapshot.dihedrals attribute) (hoomd.Snapshot.impropers attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.pairs attribute) (hoomd.Snapshot.particles attribute) (hoomd.State property) U Union (class in hoomd.filter) (class in hoomd.hpmc.pair) unwrap_full (hoomd.write.DCD attribute) unwrap_rigid (hoomd.write.DCD attribute) update() (hoomd.md.HalfStepHook method) (hoomd.update.BoxResize static method) update_fraction (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.Sphere attribute) update_group_dof() (hoomd.State method) Updater (class in hoomd.operation) updaters (hoomd.Operations property) V value (hoomd.data.ConstraintLocalAccessBase attribute) (hoomd.md.alchemy.pair.AlchemicalDOF property) (hoomd.Snapshot.constraints attribute) (hoomd.variant.Constant attribute) Variant (class in hoomd.variant) variant (hoomd.variant.box.Interpolate attribute) variant_like (in module hoomd.variant) velocity (hoomd.data.ParticleLocalAccessBase attribute) (hoomd.Snapshot.mpcd attribute) (hoomd.Snapshot.particles attribute) version (in module hoomd.version) Vertex (class in hoomd.hpmc.shape_move) vertex_move_probability (hoomd.hpmc.shape_move.Vertex attribute) virial (hoomd.md.data.ForceLocalAccess attribute) (hoomd.md.data.ForceLocalAccessGPU attribute) virial_pressure (hoomd.hpmc.nec.integrate.ConvexPolyhedron attribute) (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property) (hoomd.hpmc.nec.integrate.Sphere attribute) virials (hoomd.md.alchemy.pair.LJGauss attribute) (hoomd.md.angle.Angle attribute) (hoomd.md.angle.CosineSquared attribute) (hoomd.md.angle.Harmonic attribute) (hoomd.md.angle.Table attribute) (hoomd.md.bond.Bond attribute) (hoomd.md.bond.FENEWCA attribute) (hoomd.md.bond.Harmonic attribute) (hoomd.md.bond.Table attribute) (hoomd.md.bond.Tether attribute) (hoomd.md.constrain.Constraint attribute) (hoomd.md.constrain.Distance attribute) (hoomd.md.constrain.Rigid attribute) (hoomd.md.dihedral.Dihedral attribute) (hoomd.md.dihedral.OPLS attribute) (hoomd.md.dihedral.Periodic attribute) (hoomd.md.dihedral.Table attribute) (hoomd.md.external.field.Electric attribute) (hoomd.md.external.field.Field attribute) (hoomd.md.external.field.Magnetic attribute) (hoomd.md.external.field.Periodic attribute) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential attribute) (hoomd.md.external.wall.Yukawa attribute) (hoomd.md.force.Active attribute) (hoomd.md.force.ActiveOnManifold attribute) (hoomd.md.force.Constant attribute) (hoomd.md.force.Force property) (hoomd.md.improper.Harmonic attribute) (hoomd.md.improper.Improper attribute) (hoomd.md.improper.Periodic attribute) (hoomd.md.long_range.pppm.Coulomb attribute) (hoomd.md.many_body.RevCross attribute) (hoomd.md.many_body.SquareDensity attribute) (hoomd.md.many_body.Tersoff attribute) (hoomd.md.many_body.Triplet attribute) (hoomd.md.mesh.bending.BendingRigidity attribute) (hoomd.md.mesh.bending.Helfrich attribute) (hoomd.md.mesh.bond.FENEWCA attribute) (hoomd.md.mesh.bond.Harmonic attribute) (hoomd.md.mesh.bond.Tether attribute) (hoomd.md.mesh.conservation.Area attribute) (hoomd.md.mesh.conservation.MeshConservationPotential attribute) (hoomd.md.mesh.conservation.TriangleArea attribute) (hoomd.md.mesh.conservation.Volume attribute) (hoomd.md.mesh.MeshPotential attribute) (hoomd.md.pair.aniso.ALJ attribute) (hoomd.md.pair.aniso.AnisotropicPair attribute) (hoomd.md.pair.aniso.Dipole attribute) (hoomd.md.pair.aniso.GayBerne attribute) (hoomd.md.pair.aniso.Patchy attribute) (hoomd.md.pair.aniso.PatchyExpandedGaussian attribute) (hoomd.md.pair.aniso.PatchyExpandedLJ attribute) (hoomd.md.pair.aniso.PatchyExpandedMie attribute) (hoomd.md.pair.aniso.PatchyGaussian attribute) (hoomd.md.pair.aniso.PatchyLJ attribute) (hoomd.md.pair.aniso.PatchyMie attribute) (hoomd.md.pair.aniso.PatchyYukawa attribute) (hoomd.md.pair.Buckingham attribute) (hoomd.md.pair.DLVO attribute) (hoomd.md.pair.DPD attribute) (hoomd.md.pair.DPDConservative attribute) (hoomd.md.pair.DPDLJ attribute) (hoomd.md.pair.Ewald attribute) (hoomd.md.pair.ExpandedGaussian attribute) (hoomd.md.pair.ExpandedLJ attribute) (hoomd.md.pair.ExpandedMie attribute) (hoomd.md.pair.ForceShiftedLJ attribute) (hoomd.md.pair.Fourier attribute) (hoomd.md.pair.Gaussian attribute) (hoomd.md.pair.LJ attribute) (hoomd.md.pair.LJ0804 attribute) (hoomd.md.pair.LJ1208 attribute) (hoomd.md.pair.LJGauss attribute) (hoomd.md.pair.Mie attribute) (hoomd.md.pair.Moliere attribute) (hoomd.md.pair.Morse attribute) (hoomd.md.pair.OPP attribute) (hoomd.md.pair.Pair attribute) (hoomd.md.pair.ReactionField attribute) (hoomd.md.pair.Table attribute) (hoomd.md.pair.TWF attribute) (hoomd.md.pair.Yukawa attribute) (hoomd.md.pair.ZBL attribute) (hoomd.md.special_pair.Coulomb attribute) (hoomd.md.special_pair.LJ attribute) (hoomd.md.special_pair.SpecialPair attribute) virtual_particle_fillers (hoomd.mpcd.Integrator property) VirtualParticleFiller (class in hoomd.mpcd.fill) Volume (class in hoomd.md.mesh.conservation) volume (hoomd.Box property) (hoomd.hpmc.shape_move.Vertex attribute) (hoomd.hpmc.update.BoxMC attribute) (hoomd.md.compute.ThermodynamicQuantities property) (hoomd.md.mesh.conservation.Volume property) volume_moves (hoomd.hpmc.update.BoxMC property) (hoomd.hpmc.update.MuVT property) W WallGeometry (class in hoomd.wall) WallPotential (class in hoomd.hpmc.external) (class in hoomd.md.external.wall) walls (hoomd.hpmc.external.WallPotential property) (hoomd.md.external.wall.ForceShiftedLJ attribute) (hoomd.md.external.wall.Gaussian attribute) (hoomd.md.external.wall.LJ attribute) (hoomd.md.external.wall.Mie attribute) (hoomd.md.external.wall.Morse attribute) (hoomd.md.external.wall.WallPotential property) (hoomd.md.external.wall.Yukawa attribute) walltime (hoomd.communicator.Communicator property) (hoomd.Simulation property) wavenumber (hoomd.mpcd.force.SineForce attribute) width (hoomd.md.angle.Table attribute) (hoomd.md.bond.Table attribute) (hoomd.md.dihedral.Table attribute) (hoomd.mpcd.force.BlockForce attribute) with_gradient_descent() (hoomd.md.tune.NeighborListBuffer class method) with_grid() (hoomd.md.tune.NeighborListBuffer class method) wrap() (hoomd.Snapshot method) writable() (hoomd.device.NoticeFile method) write() (hoomd.device.NoticeFile method) (hoomd.write.GSD static method) (hoomd.write.Table method) write_at_start (hoomd.write.Burst attribute) write_diameter (hoomd.write.GSD attribute) Writer (class in hoomd.operation) writers (hoomd.Operations property) X x (hoomd.tune.LoadBalancer attribute) (hoomd.tune.ManualTuneDefinition property) x_compression (hoomd.hpmc.compute.SDF property) x_expansion (hoomd.hpmc.compute.SDF property) xmax (hoomd.hpmc.compute.SDF attribute) xy (hoomd.Box property) (hoomd.box.BoxInterface property) xz (hoomd.Box property) (hoomd.box.BoxInterface property) Y y (hoomd.tune.LoadBalancer attribute) (hoomd.tune.ManualTuneDefinition property) Yukawa (class in hoomd.md.external.wall) (class in hoomd.md.pair) yz (hoomd.Box property) (hoomd.box.BoxInterface property) Z z (hoomd.tune.LoadBalancer attribute) ZBL (class in hoomd.md.pair) ZeroMomentum (class in hoomd.md.update)