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HOOMD-blue 5.2.0 documentation
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Guides

  • Getting started
    • Features
    • Installing binaries
    • Building from source
    • Extending HOOMD-blue
    • Citing HOOMD-blue
  • Tutorials
    • Introducing HOOMD-blue
      • The Simulation Object
      • Performing Hard Particle Monte Carlo Simulations
      • Initializing the System State
      • Randomizing the System
      • Compressing the System
      • Equilibrating the System
      • Analyzing Trajectories
    • Introducing Molecular Dynamics
      • Molecular Dynamics Simulations
      • Initializing a Random System
      • Compressing the System
    • Logging
      • Logging to a file
      • Saving Array Quantities
      • Storing Particle Shape
      • Writing Formatted Output
    • Parallel Simulation With MPI
      • Introduction to MPI
      • Domain Decomposition
      • Accessing System Configurations With MPI
      • Running Multiple Simulations With Partitions
    • Custom Actions in Python
      • What are Actions?
      • An Initial Custom Action
      • Custom Action Features
      • Custom Updater
      • Custom Writer
      • Improving Performance
    • Organizing and Executing Simulations
      • Organizing Data
      • Executing Simulations
      • Continuing Simulations
      • Submitting Cluster Jobs
    • Modelling Rigid Bodies
      • Introduction to Rigid Bodies
      • Running Rigid Body Simulations
      • Preparing a General Body
    • Modelling Patchy Particles
      • The Kern–Frenkel Model
      • Simulating a System of Patchy Particles with HPMC
    • Placing barriers in the simulation box
      • Barriers
      • Fixed particles
      • Wall geometries
      • Wall potential (MD)
      • Wall potential (HPMC)
    • Introducing Multiparticle Collison Dynamics
      • Pressure-Driven Flow Between Parallel Plates
      • Diffusion of a Solution of Nearly-Hard Spheres
    • Modelling Flexible Active Interfaces
      • Describing Membranes as Meshes
      • Simulating a Vesicle with MD
  • How-to
    • How to determine the most efficient device
    • How to choose the neighbor list buffer distance
    • How to model molecular systems
    • How to continuously vary potential parameters
    • How to apply arbitrary forces in MD
    • How to minimize the potential energy of a system
    • How to prevent particles from moving
    • How to compute the free energy of solids
    • How to apply arbitrary pair potentials in HPMC
    • How to tune move sizes in multicomponent HPMC systems

Python API

  • hoomd
    • box
      • BoxInterface
    • communicator
      • Communicator
    • custom
      • Action
      • CustomOperation
    • data
      • AngleLocalAccessBase
      • BondLocalAccessBase
      • ConstraintLocalAccessBase
      • DihedralLocalAccessBase
      • HOOMDArray
      • HOOMDGPUArray
      • ImproperLocalAccessBase
      • LocalSnapshot
      • LocalSnapshotGPU
      • PairLocalAccessBase
      • ParticleLocalAccessBase
      • TypeParameter
    • device
      • CPU
      • Device
      • GPU
      • NoticeFile
      • auto_select
    • error
      • DataAccessError
      • GPUNotAvailableError
      • IncompleteSpecificationError
      • IsolationWarning
      • MPINotAvailableError
      • MutabilityError
      • SimulationDefinitionError
      • TypeConversionError
    • filter
      • All
      • CustomFilter
      • Intersection
      • Null
      • ParticleFilter
      • Rigid
      • SetDifference
      • Tags
      • Type
      • Union
    • logging
      • Logger
      • LoggerCategories
      • log
      • modify_namespace
    • mesh
      • Mesh
    • operation
      • AutotunedObject
      • Compute
      • Integrator
      • Operation
      • TriggeredOperation
      • Tuner
      • Updater
      • Writer
    • trigger
      • After
      • And
      • Before
      • Not
      • On
      • Or
      • Periodic
      • Trigger
    • tune
      • CustomTuner
      • GradientDescent
      • GridOptimizer
      • LoadBalancer
      • ManualTuneDefinition
      • Optimizer
      • ParticleSorter
      • RootSolver
      • ScaleSolver
      • SecantSolver
      • SolverStep
    • update
      • BoxResize
      • CustomUpdater
      • FilterUpdater
      • RemoveDrift
    • util
      • make_example_simulation
    • variant
      • box
        • BoxVariant
        • Constant
        • Interpolate
        • InverseVolumeRamp
      • Constant
      • Cycle
      • Power
      • Ramp
      • Variant
    • version
    • wall
      • Cylinder
      • Plane
      • Sphere
      • WallGeometry
    • write
      • Burst
      • CustomWriter
      • DCD
      • GSD
      • HDF5Log
      • Table
    • Box
    • Operations
    • Simulation
    • Snapshot
    • State
  • hpmc
    • compute
      • FreeVolume
      • SDF
    • external
      • External
      • Harmonic
      • Linear
      • WallPotential
    • integrate
      • ConvexPolygon
      • ConvexPolyhedron
      • ConvexSpheropolygon
      • ConvexSpheropolyhedron
      • ConvexSpheropolyhedronUnion
      • Ellipsoid
      • FacetedEllipsoid
      • FacetedEllipsoidUnion
      • HPMCIntegrator
      • Polyhedron
      • SimplePolygon
      • Sphere
      • SphereUnion
      • Sphinx
    • nec
      • integrate
        • ConvexPolyhedron
        • HPMCNECIntegrator
        • Sphere
      • tune
        • ChainTime
    • pair
      • AngularStep
      • ExpandedGaussian
      • LJGauss
      • LennardJones
      • OPP
      • Pair
      • Step
      • Union
    • shape_move
      • Elastic
      • ShapeMove
      • ShapeSpace
      • Vertex
    • tune
      • BoxMCMoveSize
      • MoveSize
    • update
      • BoxMC
      • GCA
      • MuVT
      • QuickCompress
      • Shape
  • md
    • alchemy
      • methods
        • Alchemostat
        • NVT
      • pair
        • AlchemicalDOF
        • AlchemicalDOFStore
        • LJGauss
    • angle
      • Angle
      • CosineSquared
      • Harmonic
      • Table
    • bond
      • Bond
      • FENEWCA
      • Harmonic
      • Table
      • Tether
    • compute
      • HarmonicAveragedThermodynamicQuantities
      • ThermodynamicQuantities
    • constrain
      • Constraint
      • Distance
      • Rigid
    • data
      • ForceLocalAccess
      • ForceLocalAccessGPU
      • NeighborListLocalAccess
      • NeighborListLocalAccessGPU
    • dihedral
      • Dihedral
      • OPLS
      • Periodic
      • Table
    • external
      • field
        • Electric
        • Field
        • Magnetic
        • Periodic
      • wall
        • ForceShiftedLJ
        • Gaussian
        • LJ
        • Mie
        • Morse
        • WallPotential
        • Yukawa
    • force
      • Active
      • ActiveOnManifold
      • Constant
      • Custom
      • Force
    • improper
      • Harmonic
      • Improper
      • Periodic
    • long_range
      • pppm
        • Coulomb
        • make_pppm_coulomb_forces
    • manifold
      • Cylinder
      • Diamond
      • Ellipsoid
      • Gyroid
      • Manifold
      • Plane
      • Primitive
      • Sphere
    • many_body
      • RevCross
      • SquareDensity
      • Tersoff
      • Triplet
    • mesh
      • bending
        • BendingRigidity
        • Helfrich
      • bond
        • FENEWCA
        • Harmonic
        • Tether
      • conservation
        • Area
        • MeshConservationPotential
        • TriangleArea
        • Volume
      • MeshPotential
    • methods
      • rattle
        • Brownian
        • DisplacementCapped
        • Langevin
        • MethodRATTLE
        • NVE
        • OverdampedViscous
      • thermostats
        • Berendsen
        • Bussi
        • MTTK
        • Thermostat
      • Brownian
      • ConstantPressure
      • ConstantVolume
      • DisplacementCapped
      • Langevin
      • Method
      • OverdampedViscous
      • Thermostatted
    • minimize
      • FIRE
    • nlist
      • Cell
      • NeighborList
      • Stencil
      • Tree
    • pair
      • aniso
        • ALJ
        • AnisotropicPair
        • Dipole
        • GayBerne
        • Patchy
        • PatchyExpandedGaussian
        • PatchyExpandedLJ
        • PatchyExpandedMie
        • PatchyGaussian
        • PatchyLJ
        • PatchyMie
        • PatchyYukawa
      • Buckingham
      • DLVO
      • DPD
      • DPDConservative
      • DPDLJ
      • Ewald
      • ExpandedGaussian
      • ExpandedLJ
      • ExpandedMie
      • ForceShiftedLJ
      • Fourier
      • Gaussian
      • LJ
      • LJ0804
      • LJ1208
      • LJGauss
      • Mie
      • Moliere
      • Morse
      • OPP
      • Pair
      • ReactionField
      • TWF
      • Table
      • WangFrenkel
      • Yukawa
      • ZBL
    • special_pair
      • Coulomb
      • LJ
      • SpecialPair
    • tune
      • NeighborListBuffer
    • update
      • ActiveRotationalDiffusion
      • ReversePerturbationFlow
      • ZeroMomentum
    • HalfStepHook
    • Integrator
  • mpcd
    • collide
      • AndersenThermostat
      • CellList
      • CollisionMethod
      • StochasticRotationDynamics
    • fill
      • GeometryFiller
      • VirtualParticleFiller
    • force
      • BlockForce
      • BodyForce
      • ConstantForce
      • SineForce
    • geometry
      • ConcentricCylinders
      • CosineChannel
      • CosineExpansionContraction
      • Geometry
      • ParallelPlates
      • PlanarPore
      • Sphere
    • methods
      • BounceBack
    • stream
      • BounceBack
      • Bulk
      • StreamingMethod
    • tune
      • ParticleSorter
    • update
      • ReverseNonequilibriumShearFlow
    • Integrator

Reference

  • Documentation
    • Notation
    • Units
    • Logo
  • Changes
    • Change Log
    • Migrating to the latest version
    • Deprecated
  • For developers
    • Contributing
    • Code style
    • Testing
  • Open source
    • License
    • Credits
  • Index
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Development of HOOMD-blue is led by the Glotzer Group at the University of Michigan (supported by NSF DMR 1808342) with many external contributions.

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