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.

Commands controlling the running of simulations:

• run - Runs the simulation for a given number of time steps.

Initialization commands (init):

• init.read_xml - Reads initial system state from an XML file.
• 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.reset - Resets all hoomd_script variables.

Pair forces (pair):

• pair.lj - Lennard-Jones pair force.
• pair.gauss - Gaussian pair force.
• nlist - Interface for controlling neighbor list parameters.

Bond forces (bond):

• bond.harmonic - Harmonic bond forces.
• bond.fene - FENE bond forces.

Wall forces (wall):

• wall.lj - Lennard-Jones wall force.

Other forces (force):

• force.constant - Constant force.

Integration methods (integrate):

• integrate.nve - NVE Integration via Velocity-Verlet.
• integrate.nvt - NVT Integration via the Nosé-Hoover thermostat.
• integrate.bdnvt - NVT integration via Brownian dynamics.
• integrate.npt - NPT Integration via the Nosé-Hoover thermostat, Anderson barostat.

Change particle or system properties during each time step (update):

• update.rescale_temp - Rescales particle velocities.
• update.zero_momentum - Zeroes system momentum.
• update.sort - Sorts particles in memory to improve cache coherency.

Real time analysis of data (analyze):

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

File output for offline analysis (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.xml - Writes simulation snapshots in the HOOMD XML format.

Define groups of particles (group):

• group.all - Groups all particles.
• group.tags - Groups particles by tag.
• group.type - Groups particles by type.