Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition
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:

Miscellaneous

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

Initialize

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

Integrate

Update

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

Bond potentials

Angle potentials

Dihedral potentials

Improper potentials

Electrostatic potentials

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

Wall potentials

  • wall.lj - Lennard-Jones wall force

Constraint forces

External forces

Other forces

Helpers

Group

Variants

Miscellaneous commands

Tune

Benchmark

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

Documentation for HOOMD-blue v0.11.3
Generated on Wed Apr 10 2013 12:15:22 for HOOMD-blue by doxygen 1.8.0