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HOOMD-blue 5.2.0 documentation

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Guides

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

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

Reference

Documentation
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- Notation
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Changes
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For developers
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Open source
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- License
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Index

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Index¶

Index
Module Index

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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