File Conversion Scripts

A number of file conversion scripts for converting between HOOMD's XML format and other formats are provided in the hoomd/bin directory. These scripts should already be in your PATH and executable from the command line.

HOOMD XML -> LAMMPS input

hoomd2lammps_input.py converts a HOOMD XML file to the LAMMPS input format. It handles positions, velocities, and bonds (if present in the XML file). To run, execute the script on the command line:

hoomd2lammps_input.py input_file.xml output_file.data

Here is the output of the above command when run on share/hoomd/demos/micelle.xml:

Found 9500  particles
Mapped particle types:
{'A': 1, 'B': 2}
Found 9000 bonds
Mapped bond types:
{'polymer': 1}

The script notifies you how many particles, velocities and bonds it reads. Types must be handled in a special way: HOOMD reads types by name, but LAMMPS requires a positive integer from 1 to the number of types. hoomd2lammps_input.py scans the input XML and automatically assigns an integer to every type in the order in which they first appear. The output

Mapped particle types:
{'A': 1, 'B': 2}

is telling you that type A is labeled 1 in the LAMMPS file and type B is labeled 2. The bond type name to integer id conversion is performed in the same manner as the particle types.

HOOMD XML -> LAMMPS dump

hoomd2lammps_dump.py converts a series of HOOMD XML files into the LAMMPS dump format. The output file will be formatted as if generated from the LAMMPS command dump 1 all atom. The use of scaled coordinates in the output can be disabled on the command line by specifying the option --noscale.

Say you have an entire series of dump files from dump.xml in the current working directory. Then

hoomd2lammps_dump.py -o dump.lammpstrj *.xml

will read them all in and write the LAMMPS dump file dump.lammpstrj. HOOMD writes dump files with the time step zero-padded in the file name, so *.xml will list all dump files in time step order. Any number of files can be specified on the command line.

The particle type name to type id handling is the same as in hoomd2lammps_input.py: HOOMD XML -> LAMMPS input

Other formats

If you need to convert to a different format, open one of the existing scripts and see if it can be modified for your needs. The scripts are written in python and the code is easy to read and modify.