HOOMD-blue
v3.2.0
Getting started
Features
Installing binaries
Building from source
Migrating to HOOMD v3
Change Log
Citing HOOMD-blue
Tutorials
Introducing HOOMD-blue
Introducing Molecular Dynamics
Logging
Parallel Simulation With MPI
Custom Actions in Python
Organizing and Executing Simulations
How to guides
How to model molecular systems
Python API
hoomd
hoomd.hpmc
hoomd.md
Developer guide
Contributing
Code style
Testing
Components
Reference
Notation
Units
Deprecated
License
Credits
Index
HOOMD-blue
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Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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W
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Z
_
__call__() (hoomd.filter.CustomFilter method)
(hoomd.filter.ParticleFilter method)
(hoomd.trigger.Trigger method)
(hoomd.variant.Variant method)
__contains__() (hoomd.md.alchemy.pair.AlchemicalDOFStore method)
(hoomd.Operations method)
__dir__() (hoomd.hpmc.integrate.HPMCIntegrator method)
(hoomd.operation.Operation method)
__eq__() (hoomd.Box method)
(hoomd.filter.ParticleFilter method)
(hoomd.logging.Logger method)
(hoomd.md.manifold.Manifold method)
(hoomd.tune.ManualTuneDefinition method)
(hoomd.tune.ScaleSolver method)
(hoomd.tune.SecantSolver method)
(hoomd.update.FilterUpdater method)
(hoomd.variant.Constant method)
(hoomd.variant.Cycle method)
(hoomd.variant.Power method)
(hoomd.variant.Ramp method)
__getattr__() (hoomd.custom.CustomOperation method)
__getitem__() (hoomd.md.alchemy.pair.AlchemicalDOFStore method)
__getstate__() (hoomd.Operations method)
(hoomd.variant.Variant method)
__hash__() (hoomd.filter.ParticleFilter method)
(hoomd.tune.ManualTuneDefinition method)
__iadd__() (hoomd.logging.Logger method)
(hoomd.Operations method)
__isub__() (hoomd.logging.Logger method)
(hoomd.Operations method)
__iter__() (hoomd.md.alchemy.pair.AlchemicalDOFStore method)
(hoomd.Operations method)
__len__() (hoomd.md.alchemy.pair.AlchemicalDOFStore method)
(hoomd.Operations method)
__neq__() (hoomd.Box method)
__reduce__() (hoomd.Box method)
__repr__() (hoomd.Box method)
(hoomd.wall.Cylinder method)
(hoomd.wall.Plane method)
(hoomd.wall.Sphere method)
__setattr__() (hoomd.md.Integrator method)
__setitem__() (hoomd.logging.Logger method)
__setstate__() (hoomd.custom.CustomOperation method)
(hoomd.variant.Variant method)
__str__() (hoomd.error.DataAccessError method)
(hoomd.error.MutabilityError method)
(hoomd.filter.ParticleFilter method)
(hoomd.wall.Cylinder method)
(hoomd.wall.Plane method)
(hoomd.wall.Sphere method)
A
a (hoomd.hpmc.integrate.HPMCIntegrator attribute)
A (hoomd.variant.Cycle attribute)
(hoomd.variant.Power attribute)
(hoomd.variant.Ramp attribute)
acceleration (hoomd.data.ParticleLocalAccessBase attribute)
act() (hoomd.custom.Action method)
(hoomd.custom.CustomOperation method)
Action (class in hoomd.custom)
action (hoomd.custom.CustomOperation 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.force.Force property)
additional_virial (hoomd.md.force.Force property)
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)
alpha (hoomd.md.alchemy.pair.AlchemicalDOF attribute)
(hoomd.md.long_range.pppm.Coulomb attribute)
(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)
alpha_start (hoomd.md.minimize.FIRE attribute)
always_compute_pressure (hoomd.Simulation property)
And (class in hoomd.trigger)
Angle (class in hoomd.md.angle)
angle (hoomd.logging.LoggerCategories 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)
AnisotropicPair (class in hoomd.md.pair.aniso)
any() (hoomd.logging.LoggerCategories class method)
aspect (hoomd.hpmc.update.BoxMC attribute)
aspect_moves (hoomd.hpmc.update.BoxMC property)
attach() (hoomd.custom.Action method)
auto_select() (in module hoomd.device)
avg_cluster_size (hoomd.hpmc.update.Clusters 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.NPH attribute)
(hoomd.md.methods.NPT attribute)
barostat_energy (hoomd.md.methods.NPH property)
(hoomd.md.methods.NPT property)
barrier() (hoomd.communicator.Communicator method)
barrier_all() (hoomd.communicator.Communicator method)
Before (class in hoomd.trigger)
betaP (hoomd.hpmc.compute.SDF property)
body (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.md.constrain.Rigid attribute)
(hoomd.Snapshot.particles attribute)
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)
Box (class in hoomd)
box (hoomd.Snapshot attribute)
(hoomd.State property)
box1 (hoomd.update.BoxResize attribute)
box2 (hoomd.update.BoxResize attribute)
box_dof (hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT attribute)
BoxMC (class in hoomd.hpmc.update)
boxmc (hoomd.hpmc.tune.BoxMCMoveSize attribute)
BoxMCMoveSize (class in hoomd.hpmc.tune)
BoxResize (class in hoomd.update)
Brownian (class in hoomd.md.methods)
(class in hoomd.md.methods.rattle)
Buckingham (class in hoomd.md.pair)
buffer (hoomd.md.nlist.NeighborList attribute)
build_dir (in module hoomd.version)
C
callback (hoomd.hpmc.shape_move.ShapeSpace attribute)
categories (hoomd.logging.Logger property)
Cell (class in hoomd.md.nlist)
cell_width (hoomd.md.nlist.Stencil attribute)
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.HPMCNECIntegrator property)
ChainTime (class in hoomd.hpmc.nec.tune)
charge (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.Snapshot.particles attribute)
charges (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
check_dist (hoomd.md.nlist.NeighborList attribute)
clamp_into_domain() (hoomd.tune.ManualTuneDefinition method)
Clusters (class in hoomd.hpmc.update)
code (hoomd.hpmc.external.user.CPPExternalPotential attribute)
(hoomd.hpmc.pair.user.CPPPotential attribute)
code_constituent (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
code_isotropic (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
Communicator (class in hoomd.communicator)
communicator (hoomd.device.Device property)
(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.Trigger method)
compute_capability (hoomd.device.GPU property)
compute_energy() (hoomd.md.pair.Pair method)
computes (hoomd.Operations property)
configuration (hoomd.Snapshot property)
Constant (class in hoomd.variant)
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.Snapshot property)
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)
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.HPMCIntegrator property)
couple (hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT attribute)
CPPExternalPotential (class in hoomd.hpmc.external.user)
CPPPotential (class in hoomd.hpmc.pair.user)
CPPPotentialBase (class in hoomd.hpmc.pair.user)
CPPPotentialUnion (class in hoomd.hpmc.pair.user)
CPU (class in hoomd.device)
cpu_local_force_arrays (hoomd.md.force.Force property)
cpu_local_snapshot (hoomd.State property)
create_bodies() (hoomd.md.constrain.Rigid method)
create_diffusion_updater() (hoomd.md.force.Active method)
(hoomd.md.force.ActiveOnManifold method)
create_state_from_gsd() (hoomd.Simulation method)
create_state_from_snapshot() (hoomd.Simulation method)
cube() (hoomd.Box class method)
cuda_devrt_library (in module hoomd.version)
cuda_include_path (in module hoomd.version)
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.HPMCIntegrator attribute)
DataAccessError
DCD (class in hoomd.write)
default (hoomd.data.typeparam.TypeParameter property)
degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property)
delimiter (hoomd.write.Table attribute)
depletant_fugacity (hoomd.hpmc.integrate.HPMCIntegrator attribute)
depletant_ntrial (hoomd.hpmc.integrate.HPMCIntegrator attribute)
detach() (hoomd.custom.Action method)
deterministic (hoomd.md.nlist.Cell attribute)
(hoomd.md.nlist.Stencil attribute)
Device (class in hoomd.device)
device (hoomd.Simulation property)
devices (hoomd.device.Device property)
diameter (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.Snapshot.particles attribute)
diameters (hoomd.hpmc.pair.user.CPPPotentialUnion 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)
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)
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)
enable_profiling() (hoomd.device.GPU method)
energies (hoomd.md.force.Force property)
energy (hoomd.hpmc.external.field.Harmonic property)
(hoomd.hpmc.external.user.CPPExternalPotential property)
(hoomd.hpmc.pair.user.CPPPotential attribute)
(hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
(hoomd.md.force.Force property)
(hoomd.md.minimize.FIRE property)
energy_rotational (hoomd.hpmc.external.field.Harmonic property)
energy_tol (hoomd.md.minimize.FIRE attribute)
energy_translational (hoomd.hpmc.external.field.Harmonic property)
epsilon (hoomd.md.alchemy.pair.LJGauss attribute)
Ewald (class in hoomd.md.pair)
exchange_moves (hoomd.hpmc.update.MuVT property)
exclusions (hoomd.md.nlist.NeighborList attribute)
ExpandedLJ (class in hoomd.md.pair)
ExpandedMie (class in hoomd.md.pair)
external_potential (hoomd.hpmc.integrate.HPMCIntegrator property)
ExternalField (class in hoomd.hpmc.external.field)
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)
filter (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute)
(hoomd.md.force.Active attribute)
(hoomd.md.force.ActiveOnManifold attribute)
(hoomd.md.methods.Brownian attribute)
(hoomd.md.methods.Langevin attribute)
(hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT attribute)
(hoomd.md.methods.NVE attribute)
(hoomd.md.methods.NVT attribute)
(hoomd.md.methods.OverdampedViscous attribute)
(hoomd.md.methods.rattle.Brownian attribute)
(hoomd.md.methods.rattle.Langevin attribute)
(hoomd.md.methods.rattle.NVE attribute)
(hoomd.md.methods.rattle.OverdampedViscous attribute)
(hoomd.md.update.ReversePerturbationFlow attribute)
(hoomd.update.BoxResize attribute)
(hoomd.write.DCD attribute)
(hoomd.write.GSD attribute)
filters (hoomd.update.FilterUpdater property)
FilterUpdater (class in hoomd.update)
final_timestep (hoomd.Simulation property)
finc_dt (hoomd.md.minimize.FIRE attribute)
FIRE (class in hoomd.md.minimize)
flags (hoomd.custom.Action attribute)
flip_probability (hoomd.hpmc.update.Clusters attribute)
floating_point_precision (in module hoomd.version)
flow_direction (hoomd.md.update.ReversePerturbationFlow attribute)
flow_target (hoomd.md.update.ReversePerturbationFlow attribute)
Force (class in hoomd.md.force)
force (hoomd.md.data.ForceLocalAccess attribute)
(hoomd.md.data.ForceLocalAccessGPU attribute)
force_tol (hoomd.md.minimize.FIRE attribute)
ForceLocalAccess (class in hoomd.md.data)
ForceLocalAccessGPU (class in hoomd.md.data)
forces (hoomd.md.force.Force property)
(hoomd.md.Integrator attribute)
(hoomd.md.minimize.FIRE 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_box() (hoomd.Box class method)
from_gsd_snapshot() (hoomd.Snapshot class method)
from_matrix() (hoomd.Box class method)
G
gamma (hoomd.md.methods.Brownian attribute)
(hoomd.md.methods.Langevin attribute)
(hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT 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)
Gauss (class in hoomd.md.external.wall)
(class in hoomd.md.pair)
GayBerne (class in hoomd.md.pair.aniso)
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.force.Force property)
gpu_local_snapshot (hoomd.State property)
gpu_platform (in module hoomd.version)
grid (hoomd.tune.ParticleSorter attribute)
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
Harmonic (class in hoomd.hpmc.external.field)
(class in hoomd.md.angle)
(class in hoomd.md.bond)
(class in hoomd.md.dihedral)
(class in hoomd.md.improper)
(class in hoomd.md.mesh.bond)
harmonic_pressure (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute)
HarmonicAveragedThermodynamicQuantities (class in hoomd.md.compute)
header_sep (hoomd.write.Table attribute)
hoomd
module
hoomd.communicator
module
hoomd.custom
module
hoomd.data
module
hoomd.data.array
module
hoomd.device
module
hoomd.error
module
hoomd.filter
module
hoomd.hpmc
module
hoomd.hpmc.compute
module
hoomd.hpmc.external
module
hoomd.hpmc.external.field
module
hoomd.hpmc.external.user
module
hoomd.hpmc.external.wall
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.pair.user
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.bond
module
hoomd.md.methods
module
hoomd.md.methods.rattle
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.update
module
hoomd.mesh
module
hoomd.operation
module
hoomd.trigger
module
hoomd.tune
module
hoomd.update
module
hoomd.variant
module
hoomd.version
module
hoomd.wall
module
hoomd.write
module
HOOMDArray (class in hoomd.data.array)
HOOMDGPUArray (class in hoomd.data.array)
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)
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)
Integrator (class in hoomd.md)
(class in hoomd.operation)
integrator (hoomd.Operations property)
interaction_matrix (hoomd.hpmc.integrate.HPMCIntegrator attribute)
Intersection (class in hoomd.filter)
is2D (hoomd.Box property)
is_available() (hoomd.device.GPU static method)
K
k_rotational (hoomd.hpmc.external.field.Harmonic attribute)
k_translational (hoomd.hpmc.external.field.Harmonic attribute)
kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property)
kinetic_temperature (hoomd.md.compute.ThermodynamicQuantities property)
kT (hoomd.md.compute.HarmonicAveragedThermodynamicQuantities attribute)
(hoomd.md.methods.Brownian attribute)
(hoomd.md.methods.Langevin attribute)
(hoomd.md.methods.NPT attribute)
(hoomd.md.methods.NVT attribute)
(hoomd.md.methods.rattle.Brownian attribute)
(hoomd.md.methods.rattle.Langevin attribute)
L
L (hoomd.Box property)
Langevin (class in hoomd.md.methods)
(class in hoomd.md.methods.rattle)
leaf_capacity (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
length (hoomd.hpmc.update.BoxMC attribute)
linear_momentum (hoomd.md.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.md.alchemy.pair)
(class in hoomd.md.pair)
llvm_enabled (in module hoomd.version)
LoadBalancer (class in hoomd.tune)
local_box (hoomd.data.LocalSnapshot property)
(hoomd.data.LocalSnapshotGPU property)
localize_abort() (hoomd.communicator.Communicator method)
LocalSnapshot (class in hoomd.data)
LocalSnapshotGPU (class in hoomd.data)
log (hoomd.write.GSD property)
log() (hoomd.logging.Logger method)
(in module hoomd.logging)
loggables (hoomd.custom.Action property)
(hoomd.hpmc.integrate.HPMCIntegrator property)
(hoomd.operation.Operation property)
(hoomd.Simulation property)
Logger (class in hoomd.logging)
logger (hoomd.write.Table attribute)
LoggerCategories (class in hoomd.logging)
Lx (hoomd.Box property)
Ly (hoomd.Box property)
Lz (hoomd.Box property)
M
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.Langevin attribute)
(hoomd.md.methods.rattle.NVE attribute)
(hoomd.md.methods.rattle.OverdampedViscous attribute)
ManualTuneDefinition (class in hoomd.tune)
map_overlaps (hoomd.hpmc.integrate.HPMCIntegrator property)
mass (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.md.alchemy.pair.AlchemicalDOF attribute)
(hoomd.Snapshot.particles attribute)
max (hoomd.variant.Variant property)
max_chain_time (hoomd.hpmc.nec.tune.ChainTime 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_translation_move (hoomd.hpmc.tune.MoveSize attribute)
max_volume_rescale (hoomd.hpmc.update.MuVT attribute)
max_x (hoomd.tune.ManualTuneDefinition property)
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)
memory_traceback (hoomd.device.GPU property)
Mesh (class in hoomd.mesh)
mesh (hoomd.md.mesh.MeshPotential property)
(hoomd.md.nlist.NeighborList attribute)
MeshPotential (class in hoomd.md.mesh)
metal_built (in module hoomd.version)
Method (class in hoomd.md.methods)
MethodRATTLE (class in hoomd.md.methods.rattle)
methods (hoomd.md.Integrator attribute)
(hoomd.md.minimize.FIRE attribute)
Mie (class in hoomd.md.external.wall)
(class in hoomd.md.pair)
min (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)
mode (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.ExpandedLJ attribute)
(hoomd.md.pair.ExpandedMie attribute)
(hoomd.md.pair.ForceShiftedLJ attribute)
(hoomd.md.pair.Fourier attribute)
(hoomd.md.pair.Gauss attribute)
(hoomd.md.pair.LJ attribute)
(hoomd.md.pair.LJ0804 attribute)
(hoomd.md.pair.LJ1208 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)
module
hoomd
hoomd.communicator
hoomd.custom
hoomd.data
hoomd.data.array
hoomd.device
hoomd.error
hoomd.filter
hoomd.hpmc
hoomd.hpmc.compute
hoomd.hpmc.external
hoomd.hpmc.external.field
hoomd.hpmc.external.user
hoomd.hpmc.external.wall
hoomd.hpmc.integrate
hoomd.hpmc.nec
hoomd.hpmc.nec.integrate
hoomd.hpmc.nec.tune
hoomd.hpmc.pair
hoomd.hpmc.pair.user
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.bond
hoomd.md.methods
hoomd.md.methods.rattle
hoomd.md.minimize
hoomd.md.nlist
hoomd.md.pair
hoomd.md.pair.aniso
hoomd.md.special_pair
hoomd.md.update
hoomd.mesh
hoomd.operation
hoomd.trigger
hoomd.tune
hoomd.update
hoomd.variant
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_built (in module hoomd.version)
mpi_enabled (in module hoomd.version)
mps (hoomd.hpmc.integrate.HPMCIntegrator property)
msg_file (hoomd.device.Device property)
mu (hoomd.md.alchemy.pair.AlchemicalDOF attribute)
(hoomd.md.pair.aniso.Dipole attribute)
MutabilityError
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.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_particles (hoomd.State property)
n_slabs (hoomd.md.update.ReversePerturbationFlow attribute)
N_special_pairs (hoomd.State property)
nec_counters (hoomd.hpmc.nec.integrate.HPMCNECIntegrator property)
NeighborList (class in hoomd.md.nlist)
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.long_range.pppm.Coulomb property)
(hoomd.md.many_body.Triplet attribute)
(hoomd.md.pair.Pair 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_level (hoomd.device.Device property)
NPH (class in hoomd.md.methods)
NPT (class in hoomd.md.methods)
nselect (hoomd.hpmc.integrate.HPMCIntegrator attribute)
nsweeps (hoomd.hpmc.update.Shape attribute)
ntrial (hoomd.hpmc.update.MuVT attribute)
Null (class in hoomd.filter)
num_cpu_threads (hoomd.device.Device 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)
(class in hoomd.md.methods.rattle)
NVT (class in hoomd.md.alchemy.methods)
(class in hoomd.md.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.md.pair)
Or (class in hoomd.trigger)
order (hoomd.md.long_range.pppm.Coulomb attribute)
orientation (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.Snapshot.particles attribute)
orientations (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
origin (hoomd.wall.Cylinder attribute)
(hoomd.wall.Plane attribute)
(hoomd.wall.Sphere attribute)
output (hoomd.write.Table attribute)
OverdampedViscous (class in hoomd.md.methods)
(class in hoomd.md.methods.rattle)
overlaps (hoomd.hpmc.external.wall.WallPotential property)
(hoomd.hpmc.integrate.HPMCIntegrator property)
overwrite (hoomd.write.DCD attribute)
P
Pair (class in hoomd.md.pair)
pair (hoomd.logging.LoggerCategories attribute)
pair_potential (hoomd.hpmc.integrate.HPMCIntegrator property)
PairLocalAccessBase (class in hoomd.data)
pairs (hoomd.data.LocalSnapshot property)
(hoomd.data.LocalSnapshotGPU property)
(hoomd.Snapshot property)
param_array (hoomd.hpmc.pair.user.CPPPotential attribute)
param_array_constituent (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
param_array_isotropic (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
param_move_probability (hoomd.hpmc.shape_move.ShapeSpace attribute)
params (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.Harmonic attribute)
(hoomd.md.dihedral.OPLS attribute)
(hoomd.md.dihedral.Table attribute)
(hoomd.md.external.field.Periodic attribute)
(hoomd.md.external.wall.ForceShiftedLJ attribute)
(hoomd.md.external.wall.Gauss 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.many_body.RevCross attribute)
(hoomd.md.many_body.SquareDensity attribute)
(hoomd.md.many_body.Tersoff 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.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.ExpandedLJ attribute)
(hoomd.md.pair.ExpandedMie attribute)
(hoomd.md.pair.ForceShiftedLJ attribute)
(hoomd.md.pair.Fourier attribute)
(hoomd.md.pair.Gauss 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.HPMCNECIntegrator property)
ParticleSorter (class in hoomd.tune)
partition (hoomd.communicator.Communicator property)
period (hoomd.md.alchemy.methods.NVT attribute)
(hoomd.trigger.Periodic attribute)
Periodic (class in hoomd.md.external.field)
(class in hoomd.trigger)
periodic (hoomd.Box property)
phase (hoomd.trigger.Periodic attribute)
pivot_move_probability (hoomd.hpmc.update.Clusters attribute)
Plane (class in hoomd.md.manifold)
(class in hoomd.wall)
Polyhedron (class in hoomd.hpmc.integrate)
position (hoomd.data.ParticleLocalAccessBase attribute)
(hoomd.Snapshot.particles attribute)
positions (hoomd.hpmc.pair.user.CPPPotentialUnion 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.long_range.pppm.Coulomb attribute)
(hoomd.md.many_body.Triplet attribute)
(hoomd.md.pair.Pair attribute)
(hoomd.md.special_pair.Coulomb attribute)
(hoomd.md.special_pair.LJ attribute)
r_on (hoomd.md.pair.Pair attribute)
radius (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.NeighborList attribute)
reference_orientations (hoomd.hpmc.external.field.Harmonic attribute)
reference_positions (hoomd.hpmc.external.field.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)
replicate() (hoomd.Snapshot method)
(hoomd.State method)
rescale_all (hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT attribute)
reset() (hoomd.md.minimize.FIRE 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)
rotate_moves (hoomd.hpmc.integrate.HPMCIntegrator property)
rotational_degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property)
rotational_diffusion (hoomd.md.update.ActiveRotationalDiffusion attribute)
rotational_kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property)
rotational_thermostat_dof (hoomd.md.methods.NPT attribute)
(hoomd.md.methods.NVT attribute)
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.NPH attribute)
(hoomd.md.methods.NPT 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 (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)
sequence (hoomd.logging.LoggerCategories attribute)
set_box() (hoomd.State method)
set_forces() (hoomd.md.force.Custom method)
set_snapshot() (hoomd.State 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)
sigma (hoomd.md.alchemy.pair.LJGauss attribute)
SimplePolygon (class in hoomd.hpmc.integrate)
Simulation (class in hoomd)
slab_direction (hoomd.md.update.ReversePerturbationFlow attribute)
Snapshot (class in hoomd)
solve() (hoomd.tune.SolverStep method)
solve_one() (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)
SolverStep (class in hoomd.tune)
source_dir (in module hoomd.version)
special_pair_types (hoomd.State property)
SpecialPair (class in hoomd.md.special_pair)
Sphere (class in hoomd.hpmc.integrate)
(class in hoomd.hpmc.nec.integrate)
(class in hoomd.md.manifold)
(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_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)
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.field.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.Power attribute)
(hoomd.variant.Ramp attribute)
t_start (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)
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.NPT attribute)
(hoomd.md.methods.NVT attribute)
tauS (hoomd.md.methods.NPH attribute)
(hoomd.md.methods.NPT attribute)
tbb_enabled (in module hoomd.version)
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.NPH method)
thermalize_particle_momenta() (hoomd.State method)
thermalize_thermostat_and_barostat_dof() (hoomd.md.methods.NPT method)
thermalize_thermostat_dof() (hoomd.md.methods.NVT method)
ThermodynamicQuantities (class in hoomd.md.compute)
thermostat_energy (hoomd.md.methods.NPT property)
(hoomd.md.methods.NVT property)
tilts (hoomd.Box property)
timestep (hoomd.Simulation property)
(hoomd.trigger.After attribute)
(hoomd.trigger.Before attribute)
(hoomd.trigger.On attribute)
to_dict() (hoomd.wall.Cylinder method)
(hoomd.wall.Plane method)
(hoomd.wall.Sphere method)
(hoomd.wall.WallGeometry method)
to_matrix() (hoomd.Box method)
tolerance (hoomd.md.constrain.Distance attribute)
(hoomd.md.methods.rattle.Brownian attribute)
(hoomd.md.methods.rattle.Langevin 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.force.Force property)
tps (hoomd.Simulation property)
transfer_types (hoomd.hpmc.update.MuVT attribute)
translate_moves (hoomd.hpmc.integrate.HPMCIntegrator property)
translation_move_probability (hoomd.hpmc.integrate.HPMCIntegrator attribute)
translational_degrees_of_freedom (hoomd.md.compute.ThermodynamicQuantities property)
translational_kinetic_energy (hoomd.md.compute.ThermodynamicQuantities property)
translational_thermostat_dof (hoomd.md.methods.NPT attribute)
(hoomd.md.methods.NVT attribute)
Tree (class in hoomd.md.nlist)
triangles (hoomd.mesh.Mesh property)
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.Clusters attribute)
(hoomd.hpmc.update.MuVT attribute)
(hoomd.hpmc.update.QuickCompress attribute)
(hoomd.hpmc.update.Shape attribute)
(hoomd.md.update.ActiveRotationalDiffusion attribute)
(hoomd.trigger.Not attribute)
(hoomd.tune.LoadBalancer attribute)
(hoomd.tune.ParticleSorter attribute)
(hoomd.update.BoxResize attribute)
(hoomd.update.FilterUpdater attribute)
(hoomd.update.RemoveDrift attribute)
(hoomd.write.DCD attribute)
(hoomd.write.GSD attribute)
(hoomd.write.Table attribute)
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)
tuned (hoomd.hpmc.tune.BoxMCMoveSize property)
(hoomd.hpmc.tune.MoveSize property)
Tuner (class in hoomd.operation)
tuners (hoomd.Operations property)
TWF (class in hoomd.md.pair)
Type (class in hoomd.filter)
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
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.pairs attribute)
(hoomd.Snapshot.particles attribute)
typeids (hoomd.hpmc.pair.user.CPPPotentialUnion attribute)
TypeParameter (class in hoomd.data.typeparam)
types (hoomd.filter.Type property)
(hoomd.hpmc.tune.MoveSize attribute)
(hoomd.Snapshot.angles attribute)
(hoomd.Snapshot.bonds attribute)
(hoomd.Snapshot.dihedrals attribute)
(hoomd.Snapshot.impropers attribute)
(hoomd.Snapshot.pairs attribute)
(hoomd.Snapshot.particles attribute)
(hoomd.State property)
U
Union (class in hoomd.filter)
unwrap_full (hoomd.write.DCD attribute)
unwrap_rigid (hoomd.write.DCD attribute)
update() (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.update.BoxResize attribute)
velocity (hoomd.data.ParticleLocalAccessBase 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.HPMCNECIntegrator property)
virials (hoomd.md.force.Force property)
volume (hoomd.Box property)
(hoomd.hpmc.shape_move.Vertex attribute)
(hoomd.hpmc.update.BoxMC attribute)
(hoomd.md.compute.ThermodynamicQuantities 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.wall)
(class in hoomd.md.external.wall)
walls (hoomd.hpmc.external.wall.WallPotential property)
(hoomd.md.external.wall.ForceShiftedLJ attribute)
(hoomd.md.external.wall.Gauss 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)
width (hoomd.md.angle.Table attribute)
(hoomd.md.bond.Table attribute)
(hoomd.md.dihedral.Table attribute)
wrap() (hoomd.Snapshot method)
write() (hoomd.write.GSD static method)
(hoomd.write.Table method)
Writer (class in hoomd.operation)
writers (hoomd.Operations property)
X
x (hoomd.tune.LoadBalancer attribute)
(hoomd.tune.ManualTuneDefinition property)
xmax (hoomd.hpmc.compute.SDF attribute)
xy (hoomd.Box property)
xz (hoomd.Box 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)
Z
z (hoomd.tune.LoadBalancer attribute)
ZBL (class in hoomd.md.pair)
ZeroMomentum (class in hoomd.md.update)
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v: v3.2.0
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