Index of Script Commands

Click on an individual command in the list to go to its documentation. Click on the package link at the beginning of each list to get a general overview of all commands in that package.

Table of contents:

• Run
• Option
• Initialize
• Integrate
• Update
• Compute
• Analyze
• Dump
• Potentials
  • Pair potentials
  • Bond potentials
  • Angle potentials
  • Dihedral potentials
  • Improper potentials
  • Electrostatic potentials
  • Wall potentials
  • Constraint forces
  • External forces
  • Other forces

• Helpers
  • Group
  • Variants

Miscellaneous

• Tune
• Benchmark

Run

• run - Runs the simulation for a given number of time steps
• run_upto - Runs the simulation up to a given time step number

Option

• Command line
  • Command line options
• In script
  • option.set_mode - Set the execution mode
  • option.set_gpu - Set the gpu
  • option.set_ncpu - Set the number of CPU threads
  • option.set_gpu_error_checking - Set the error checking flag
  • option.set_min_cpu - Set the minimize CPU usage flag
  • option.set_ignore_display - Set the ignore display GPU flag
  • option.get_user - Get user options

Initialize

• init.create_empty - Create an empty system
• init.create_random - Generates N randomly positioned particles of the same type
• init.create_random_polymers - Generates any number of randomly positioned polymers of configurable types
• init.read_bin - Reads initial system state from a binary file
• init.read_xml - Reads initial system state from an XML file

• init.reset - Resets all hoomd_script variables
  • init.is_initialized - Tests if the system has been initialized

• data access - Access particles, bonds, and other state information inside scripts

Integrate

• integrate.mode_minimize_fire - Energy Minimizer (FIRE)
• integrate.mode_minimize_rigid_fire - Energy Minimizer (rigid bodies) (FIRE)
• integrate.mode_standard - Enables a variety of standard integration methods
  • integrate.berendsen - NVT integration via the Berendsen thermostat
  • integrate.bdnvt - NVT integration via Brownian dynamics
  • integrate.bdnvt_rigid - NVT integration of rigid bodies via Brownian Dynamics
  • integrate.nph - NPH integration via the Andersen / modified Parrinello-Rahman barostat
  • integrate.npt - NPT Integration via the Nosé-Hoover thermostat, Andersen barostat
  • integrate.npt_rigid - NPT Integration of rigid bodies
  • integrate.nve - NVE Integration via Velocity-Verlet
  • integrate.nve_rigid - NVE integration of rigid bodies
  • integrate.nvt - NVT Integration via the Nosé-Hoover thermostat
  • integrate.nvt_rigid - NVT integration of rigid bodies

Update

• update.box_resize - Rescales the system box size
• update.enforce2d - Enforces 2D simulation
• update.rescale_temp - Rescales particle velocities
• update.sort - Sorts particles in memory to improve cache coherency
• update.zero_momentum - Zeroes system momentum

Compute

• compute.thermo - Compute thermodynamic properties of a group of particles

Analyze

• analyze.imd - Sends simulation snapshots to VMD in real-time
• analyze.log - Logs a number of calculated quantities to a file
• analyze.msd - Calculates the mean-squared displacement of groups of particles and logs the values to a file

Dump

• dump.dcd - Writes simulation snapshots in the DCD format
• dump.mol2 - Writes a simulation snapshot in the MOL2 format
• dump.pdb - Writes simulation snapshots in the PBD format
• dump.bin - Writes simulation snapshots in a binary format
• dump.xml - Writes simulation snapshots in the HOOMD XML format

Potentials

Pair potentials

• pair.cgcmm - CMM coarse-grain model pair force
• pair.dpd - NVT Integration via Dissipative Particle Dynamics pair force
• pair.dpdlj - NVT Integration via Dissipative Particle Dynamics and LJ Force pair force
• pair.dpd_conservative - DPD Conservative pair force
• pair.eam - EAM pair force
• pair.ewald - Short range ewald pair force
• pair.gauss - Gaussian pair force
• pair.lj - Lennard-Jones pair force
• pair.morse - Morse pair force
• pair.table - Tabulated pair force
• pair.slj - Shifted Lennard-Jones pair force
• pair.yukawa - Yukawa pair force
• pair.force_shifted_lj - Force shifted Lennard-Jones pair force
• nlist - Interface for controlling neighbor list parameters

Bond potentials

• bond.harmonic - Harmonic bond force
• bond.fene - FENE bond force
• bond.table - Tabulated bond force

Angle potentials

• angle.harmonic - Harmonic angle force
• angle.cgcmm - CGCMM angle force

Dihedral potentials

• dihedral.harmonic - Harmonic dihedral force

Improper potentials

• improper.harmonic - Harmonic improper force

Electrostatic potentials

• charge.pppm - Long-range electrostatics computed with the PPPM method

Wall potentials

• wall.lj - Lennard-Jones wall force

Constraint forces

• constrain.sphere - Constrain particles to the surface of a sphere

External forces

• external.periodic - One-dimension periodic potential

Other forces

• force.constant - Constant force

Helpers

Group

• Create groups
  • group.all - Groups all particles
  • group.charged - Groups particles that are charged
  • group.cuboid - Groups particles in a cuboid
  • group.nonrigid - Groups particles that do not belong to rigid bodies
  • group.rigid - Groups particles that belong to rigid bodies
  • group.tag_list - Groups particles by tag list
  • group.tags - Groups particles by tag
  • group.type - Groups particles by type
• Combine groups
  • group.difference - Create a new group from the set difference or complement of two existing groups
  • group.intersection - Create a new group from the set intersection of two existing groups
  • group.union - Create a new group from the set union of two existing groups

Variants

• variant.linear_interp - Linearly interpolated variant

Miscellaneous commands

Tune

• tune.find_optimal_block_sizes - Determine optimal block size tuning parameters
• tune.r_buff() - Make a series of short runs to determine the fastest performing r_buff setting

Benchmark

• benchmark.series - Perform a series of short runs to benchmark overall simulation performance