# hoomd¶

Overview

 hoomd.get_step Get the current simulation time step. hoomd.run Runs the simulation for a given number of time steps. hoomd.run_upto Runs the simulation up to a given time step number.

Details

HOOMD-blue python API

hoomd provides a high level user interface for executing simulations using HOOMD:

import hoomd
from hoomd import md
hoomd.context.initialize()

# create a 10x10x10 square lattice of particles with name A
hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0, type_name='A'), n=10)
# specify Lennard-Jones interactions between particle pairs
nl = md.nlist.cell()
lj = md.pair.lj(r_cut=3.0, nlist=nl)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
# integrate at constant temperature
all = hoomd.group.all();
md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.langevin(group=all, kT=1.2, seed=4)
# run 10,000 time steps
hoomd.run(10e3)


Stability

hoomd is stable. When upgrading from version 2.x to 2.y (y > x), existing job scripts that follow documented interfaces for functions and classes will not require any modifications. Maintainer: Joshua A. Anderson

Attention

This stability guarantee only applies to modules in the hoomd package. Subpackages (hoomd.hpmc, hoomd.md, etc…) may or may not have a stable API. The documentation for each subpackage specifies the level of API stability it provides.

hoomd.get_step()

Get the current simulation time step.

Returns: The current simulation time step.

Example:

print(hoomd.get_step())

hoomd.run(tsteps, profile=False, limit_hours=None, limit_multiple=1, callback_period=0, callback=None, quiet=False)

Runs the simulation for a given number of time steps.

Parameters: tsteps (int) – Number of time steps to advance the simulation. profile (bool) – Set to True to enable high level profiling output at the end of the run. limit_hours (float) – If not None, limit this run to a given number of hours. limit_multiple (int) – When stopping the run due to walltime limits, only stop when the time step is a multiple of limit_multiple. callback (callable) – Sets a Python function to be called regularly during a run. callback_period (int) – Sets the period, in time steps, between calls made to callback. quiet (bool) – Set to True to disable the status information printed to the screen by the run.

Example:

hoomd.run(10)
hoomd.run(10e6, limit_hours=1.0/3600.0, limit_multiple=10)
hoomd.run(10, profile=True)
hoomd.run(10, quiet=True)
hoomd.run(10, callback_period=2, callback=lambda step: print(step))


Execute the run() command to advance the simulation forward in time. During the run, all previously specified analyzers, updaters and the integrator are executed at the specified regular periods.

After run() completes, you may change parameters of the simulation and continue the simulation by executing run() again. Time steps are added cumulatively, so calling run(1000) and then run(2000) would run the simulation up to time step 3000.

run() cannot be executed before the system is initialized. In most cases, run() should only be called after after pair forces, bond forces, and an integrator are specified.

When profile is True, a detailed breakdown of how much time was spent in each portion of the calculation is printed at the end of the run. Collecting this timing information slows the simulation.

Wallclock limited runs:

There are a number of mechanisms to limit the time of a running hoomd script. Use these in a job queuing environment to allow your script to cleanly exit before reaching the system enforced walltime limit.

Force run() to end only on time steps that are a multiple of limit_multiple. Set this to the period at which you dump restart files so that you always end a run() cleanly at a point where you can restart from. Use phase=0 on logs, file dumps, and other periodic tasks. With phase=0, these tasks will continue on the same sequence regardless of the restart period.

Set the environment variable HOOMD_WALLTIME_STOP prior to starting a hoomd script to stop the run() at a given wall clock time. run() monitors performance and tries to ensure that it will end before HOOMD_WALLTIME_STOP. This environment variable works even with multiple stages of runs in a script (use run_upto(). Set the variable to a unix epoch time. For example in a job script that should run 12 hours, set HOOMD_WALLTIME_STOP to 12 hours from now, minus 10 minutes to allow for job cleanup:

export HOOMD_WALLTIME_STOP=\$((date +%s + 12 * 3600 - 10 * 60))


When using HOOMD_WALLTIME_STOP, run() will throw the exception WalltimeLimitReached if it exits due to the walltime limit.

limit_hours is another way to limit the length of a run(). Set it to a number of hours (use fractional values for minutes) to limit this particular run() to that length of time. This is less useful than HOOMD_WALLTIME_STOP in a job queuing environment.

Callbacks:

If callback is set to a Python function then this function will be called regularly at callback_period intervals. The callback function must receive one integer as argument and can return an integer. The argument passed to the callback is the current time step number. If the callback function returns a negative number, the run is immediately aborted.

If callback_period is set to 0 (the default) then the callback is only called once at the end of the run. Otherwise the callback is executed whenever the current time step number is a multiple of callback_period.

hoomd.run_upto(step, **keywords)

Runs the simulation up to a given time step number.

Parameters: step (int) – Final time step of the simulation which to run keywords – Catch for all keyword arguments to pass on to run()

run_upto() runs the simulation, but only until it reaches the given time step. If the simulation has already reached the specified step, a message is printed and no simulation steps are run.

It accepts all keyword options that run() does.

Examples:

run_upto(1000)
run_upto(10000, profile=True)
run_upto(1e9, limit_hours=11)


Modules