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HOOMD-blue 4.3.0 documentation
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Guides

  • Getting started
    • Features
    • Installing binaries
    • Building from source
    • 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
      • Kern–Frenkel Model
      • Simulating a System of Patchy Particles
  • 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

Python API

  • hoomd
    • hoomd.box
    • hoomd.communicator
    • hoomd.custom
    • hoomd.data
      • hoomd.data.array
    • hoomd.device
    • hoomd.error
    • hoomd.filter
    • hoomd.logging
    • hoomd.mesh
    • hoomd.operation
    • hoomd.trigger
    • hoomd.tune
    • hoomd.update
    • hoomd.util
    • hoomd.variant
    • hoomd.version
    • hoomd.wall
    • hoomd.write
  • hoomd.hpmc
    • hoomd.hpmc.compute
    • hoomd.hpmc.integrate
    • hoomd.hpmc.nec
      • hoomd.hpmc.nec.integrate
      • hoomd.hpmc.nec.tune
    • hoomd.hpmc.tune
    • hoomd.hpmc.update
    • hoomd.hpmc.pair
      • hoomd.hpmc.pair.user
    • hoomd.hpmc.external
      • hoomd.hpmc.external.user
      • hoomd.hpmc.external.field
      • hoomd.hpmc.external.wall
    • hoomd.hpmc.shape_move
  • hoomd.md
    • md.alchemy
      • md.alchemy.pair
      • md.alchemy.methods
    • md.angle
    • md.bond
    • md.constrain
    • md.compute
    • md.data
    • md.dihedral
    • md.external
      • md.external.field
      • md.external.wall
    • md.force
    • md.improper
    • md.long_range
      • md.long_range.pppm
    • md.manifold
    • md.many_body
    • md.methods
      • md.methods.thermostats
      • md.methods.rattle
    • md.mesh
      • md.mesh.bond
    • md.minimize
    • md.nlist
    • md.pair
      • md.pair.aniso
    • md.special_pair
    • md.tune
    • md.update

Reference

  • Documentation
    • Notation
    • Units
    • Logo
  • Changes
    • Change Log
    • Migrating to the latest version
    • Deprecated
  • For developers
    • Contributing
    • Code style
    • Testing
    • Components
  • Open source
    • License
    • Credits
  • Index
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Index#

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  • Module Index

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Credits

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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