Getting started

Program parameters

HALMD has three ways of accepting program parameters:

• pass directly as command line options
• read from parameter config file [RC format]
• read from HDF5 data file, optionally resuming from a prior trajectory

Options are described in the command line help:

halmd --help

The group of global options must precede module-specific options, which are introduced by their respective module name.

A first example: Lennard-Jones fluids

Many simulation scenarios can be controlled by command line options, there is no need to setup a separate simulation script. Let us consider a simple fluid with 20,000 Lennard-Jones particles at density . Equilibration is done with the Andersen thermostat at a temperature over 10,000 steps

halmd -v \
  --force=lennard_jones --integrator=verlet_nvt_andersen \
  --timestep 0.005 --time 50 \
  box --density 0.8 --particles 20000 \
  verlet_nvt_andersen --temperature 2 \
  trajectory --every 10000

Many parameters have sensible default values and may be omitted, e.g, the collision rate of the Andersen thermostat (10), or the cutoff radius of the potential (). The option -v makes the output more verbose, check that your CUDA device has beed detected properly.

The equivalent parameter configuration file would look like this

# file example.rc
force=lennard_jones
integrator=verlet_nvt_andersen
timestep=0.005
time=50

[box]
density=0.8
particles=20000

[verlet_nvt_andersen]
temperature=2

[trajectory]
every=10000

It is passed directly to HALMD, while parameters may be overwritten:

halmd -v -c example.rc --time 10

The trajectory is written every 10,000 steps, i.e., at the beginning and the end of the simulation. The initial configuration of the particles is a fcc lattice. The default output settings yield an HDF5 file with a time stamp in its name, halmd_%Y%m%d_%H%M%S.h5 and a corresponding log file.

We may now continue the simulation at constant energy by resuming from the trajectory file and selecting a different integrator

halmd -v \
  --integrator=verlet --timestep 0.001 --time 100 \
  trajectory --file halmd_20110715_160545.h5 \
  thermodynamics --every 100

This will continue the simulation over 10⁵ steps and write observables like thermodynamic state variables every 100 steps (potential energy, instantaneous “temperature”, pressure, ...

If the HDF5 tools are properly installed, we may have a quick overview of the output file

h5ls halmd_20110715_160920.h5

or look at a specific data set

h5dump -d observables/potential_energy halmd_20110713_161511.h5 | less

For a more advanced inspection and analysis of the HDF5 output files, see Plotting the results. You may try the exemplary script

halmd/examples/plotting/plot_h5md.py halmd_20110713_161511.h5