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HOOMD-blue 5.0.0 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
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
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- data
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- device
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  - CPU
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- error
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- filter
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  - All
  - CustomFilter
  - Intersection
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  - Rigid
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  - Tags
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- logging
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- mesh
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  - Mesh
- operation
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  - AutotunedObject
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  - Integrator
  - Operation
  - TriggeredOperation
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  - After
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- util
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  - make_example_simulation
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- write
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  - Burst
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hpmc
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  - FreeVolume
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- external
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- integrate
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- nec
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  - tune
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    - ChainTime
- pair
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  - AngularStep
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- shape_move
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  - Elastic
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- tune
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  - BoxMCMoveSize
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- update
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  - BoxMC
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md
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- alchemy
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  - methods
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    - Alchemostat
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  - pair
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- angle
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  - Angle
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- bond
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  - HarmonicAveragedThermodynamicQuantities
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- constrain
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    - ForceShiftedLJ
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  - bending
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  - conservation
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  - MeshPotential
- methods
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    - Berendsen
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- minimize
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  - FIRE
- nlist
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  - Cell
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- pair
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  - aniso
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  - Buckingham
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  - DPDLJ
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  - NeighborListBuffer
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- HalfStepHook
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mpcd
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- fill
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- geometry
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- methods
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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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Index

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mesh¶

Mesh potentials for molecular dynamics.

Modules

bending
bond
conservation

Classes

MeshPotential

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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