The Tools:HoomdConfigReader and Tools::HoomdConfigWriter classes each require an auxiliary type map file that contains a mapping between the integer atom and group type identifiers used in all of the simpatico programs and string identifiers used in the Hoomd XML configuration file format.

Commands

The name of the auxiliary type map file must be given as the first of two string parameters of the READ_CONFIG or WRITE_CONFIG commands in the command script for the mdPp postprocessor. The syntax for both commands is

READ_CONFIG typeMapFile configFile

WRITE_CONFIG typeMapFile configFile

where typeMapFile is the path to auxiliary type map file and configFile is the nameo of the Hoomd XML configuration file to be read from or written to.

Type File Format

Here is an example of the format of a type map file for a system with two types of atom and one type of bond, with no angles or dihedrals:

ATOM TYPES:
  nType 2
  Types 0 A
        1 B
BOND TYPES:
  nType 1
  Types 0 polymer

In this example, the atom types with indexes 0 and 1 in simpatico are referred to by labels 'A' and 'B' in the Hoomd XML file, while the single bond type is type 0 in simpatico and type 'polymer' in the Hoomd file.