Hide navigation sidebar

Hide table of contents sidebar

Skip to content

Toggle site navigation sidebar

HOOMD-blue 5.2.0 documentation

Toggle table of contents sidebar

Guides

Getting started
Toggle navigation of Getting started
Tutorials
Toggle navigation of Tutorials
- Introducing HOOMD-blue
  Toggle navigation of Introducing HOOMD-blue
- Introducing Molecular Dynamics
  Toggle navigation of Introducing Molecular Dynamics
- Logging
  Toggle navigation of Logging
- Parallel Simulation With MPI
  Toggle navigation of Parallel Simulation With MPI
- Custom Actions in Python
  Toggle navigation of Custom Actions in Python
- Organizing and Executing Simulations
  Toggle navigation of Organizing and Executing Simulations
- Modelling Rigid Bodies
  Toggle navigation of Modelling Rigid Bodies
- Modelling Patchy Particles
  Toggle navigation of Modelling Patchy Particles
  - The Kern–Frenkel Model
  - Simulating a System of Patchy Particles with HPMC
- Placing barriers in the simulation box
  Toggle navigation of Placing barriers in the simulation box
- Introducing Multiparticle Collison Dynamics
  Toggle navigation of Introducing Multiparticle Collison Dynamics
  - Pressure-Driven Flow Between Parallel Plates
  - Diffusion of a Solution of Nearly-Hard Spheres
- Modelling Flexible Active Interfaces
  Toggle navigation of Modelling Flexible Active Interfaces
  - Describing Membranes as Meshes
  - Simulating a Vesicle with MD
How-to
Toggle navigation of How-to

Python API

hoomd
Toggle navigation of hoomd
- box
  Toggle navigation of box
  - BoxInterface
- communicator
  Toggle navigation of communicator
  - Communicator
- custom
  Toggle navigation of custom
  - Action
  - CustomOperation
- data
  Toggle navigation of data
- device
  Toggle navigation of device
  - CPU
  - Device
  - GPU
  - NoticeFile
  - auto_select
- error
  Toggle navigation of error
- filter
  Toggle navigation of filter
  - All
  - CustomFilter
  - Intersection
  - Null
  - ParticleFilter
  - Rigid
  - SetDifference
  - Tags
  - Type
  - Union
- logging
  Toggle navigation of logging
- mesh
  Toggle navigation of mesh
  - Mesh
- operation
  Toggle navigation of operation
  - AutotunedObject
  - Compute
  - Integrator
  - Operation
  - TriggeredOperation
  - Tuner
  - Updater
  - Writer
- trigger
  Toggle navigation of trigger
  - After
  - And
  - Before
  - Not
  - On
  - Or
  - Periodic
  - Trigger
- tune
  Toggle navigation of tune
- update
  Toggle navigation of update
- util
  Toggle navigation of util
  - make_example_simulation
- variant
  Toggle navigation of variant
  - box
    Toggle navigation of box
  - Constant
  - Cycle
  - Power
  - Ramp
  - Variant
- version
- wall
  Toggle navigation of wall
  - Cylinder
  - Plane
  - Sphere
  - WallGeometry
- write
  Toggle navigation of write
  - Burst
  - CustomWriter
  - DCD
  - GSD
  - HDF5Log
  - Table
- Box
- Operations
- Simulation
- Snapshot
- State
hpmc
Toggle navigation of hpmc
- compute
  Toggle navigation of compute
  - FreeVolume
  - SDF
- external
  Toggle navigation of external
- integrate
  Toggle navigation of integrate
- nec
  Toggle navigation of nec
  - integrate
    Toggle navigation of integrate
  - tune
    Toggle navigation of tune
    - ChainTime
- pair
  Toggle navigation of pair
  - AngularStep
  - ExpandedGaussian
  - LJGauss
  - LennardJones
  - OPP
  - Pair
  - Step
  - Union
- shape_move
  Toggle navigation of shape_move
  - Elastic
  - ShapeMove
  - ShapeSpace
  - Vertex
- tune
  Toggle navigation of tune
  - BoxMCMoveSize
  - MoveSize
- update
  Toggle navigation of update
  - BoxMC
  - GCA
  - MuVT
  - QuickCompress
  - Shape
md
Toggle navigation of md
- alchemy
  Toggle navigation of alchemy
  - methods
    Toggle navigation of methods
    - Alchemostat
    - NVT
  - pair
    Toggle navigation of pair
- angle
  Toggle navigation of angle
  - Angle
  - CosineSquared
  - Harmonic
  - Table
- bond
  Toggle navigation of bond
  - Bond
  - FENEWCA
  - Harmonic
  - Table
  - Tether
- compute
  Toggle navigation of compute
  - HarmonicAveragedThermodynamicQuantities
  - ThermodynamicQuantities
- constrain
  Toggle navigation of constrain
- data
  Toggle navigation of data
- dihedral
  Toggle navigation of dihedral
  - Dihedral
  - OPLS
  - Periodic
  - Table
- external
  Toggle navigation of external
  - field
    Toggle navigation of field
    - Electric
    - Field
    - Magnetic
    - Periodic
  - wall
    Toggle navigation of wall
    - ForceShiftedLJ
    - Gaussian
    - LJ
    - Mie
    - Morse
    - WallPotential
    - Yukawa
- force
  Toggle navigation of force
  - Active
  - ActiveOnManifold
  - Constant
  - Custom
  - Force
- improper
  Toggle navigation of improper
- long_range
  Toggle navigation of long_range
  - pppm
    Toggle navigation of pppm
    - Coulomb
    - make_pppm_coulomb_forces
- manifold
  Toggle navigation of manifold
  - Cylinder
  - Diamond
  - Ellipsoid
  - Gyroid
  - Manifold
  - Plane
  - Primitive
  - Sphere
- many_body
  Toggle navigation of many_body
- mesh
  Toggle navigation of mesh
  - bending
    Toggle navigation of bending
    - BendingRigidity
    - Helfrich
  - bond
    Toggle navigation of bond
    - FENEWCA
    - Harmonic
    - Tether
  - conservation
    Toggle navigation of conservation
  - MeshPotential
- methods
  Toggle navigation of methods
  - rattle
    Toggle navigation of rattle
  - thermostats
    Toggle navigation of thermostats
    - Berendsen
    - Bussi
    - MTTK
    - Thermostat
  - Brownian
  - ConstantPressure
  - ConstantVolume
  - DisplacementCapped
  - Langevin
  - Method
  - OverdampedViscous
  - Thermostatted
- minimize
  Toggle navigation of minimize
  - FIRE
- nlist
  Toggle navigation of nlist
  - Cell
  - NeighborList
  - Stencil
  - Tree
- pair
  Toggle navigation of pair
  - aniso
    Toggle navigation of aniso
  - 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
  Toggle navigation of special_pair
  - Coulomb
  - LJ
  - SpecialPair
- tune
  Toggle navigation of tune
  - NeighborListBuffer
- update
  Toggle navigation of update
- HalfStepHook
- Integrator
mpcd
Toggle navigation of mpcd
- collide
  Toggle navigation of collide
- fill
  Toggle navigation of fill
  - GeometryFiller
  - VirtualParticleFiller
- force
  Toggle navigation of force
- geometry
  Toggle navigation of geometry
- methods
  Toggle navigation of methods
  - BounceBack
- stream
  Toggle navigation of stream
- tune
  Toggle navigation of tune
  - ParticleSorter
- update
  Toggle navigation of update
  - ReverseNonequilibriumShearFlow
- Integrator

Reference

Documentation
Toggle navigation of Documentation
- Notation
- Units
- Logo
Changes
Toggle navigation of Changes
For developers
Toggle navigation of For developers
Open source
Toggle navigation of Open source
- License
- Credits
Index

Toggle table of contents sidebar

Tutorials¶

Introducing HOOMD-blue
Introducing Molecular Dynamics
Logging
Parallel Simulation With MPI
Custom Actions in Python
Organizing and Executing Simulations
Modelling Rigid Bodies
Modelling Patchy Particles
Placing barriers in the simulation box
Introducing Multiparticle Collison Dynamics
Modelling Flexible Active Interfaces

Introducing HOOMD-blue

Citing HOOMD-blue

Development of HOOMD-blue is led by the Glotzer Group at the University of Michigan (supported by NSF DMR 1808342) with many external contributions.

Copyright © 2009-2025 The Regents of the University of Michigan

Made with Sphinx and @pradyunsg's Furo