dump command

Syntax:

dump ID N filename species1-ID species2-ID ...
dump ID delta filename species1-ID species2-ID ... 

• ID = user-assigned name for the dump
• N = dump particles every N timesteps (integer value)
• delta = dump particles every delta seconds (floating point value)
• filename = file to dump to
• speciesN-ID = optional list of species-IDs to dump to file

Examples:

dump 1 100 tmp.dump
dump Ca-dump 0.1 tmp.dump.Ca Ca-cyto Ca-ER 

Description:

Dump a snapshot of particle coordinates and species types to a file every so often as a simulation runs. The species list is optional; if not specified, all particles are dumped.

The ID of a dump can contain alphanumeric characters and underscores.

The frequency of output can be specied in timesteps or elapsed simulation time. Using an integer versus a floating-point value (with a decimal point) determines how the argument is interpreted.

Any species-ID can contain a single wildcard character * which will match species and alias names in the usual way. E.g. a species-ID can be *, ab*, *ab, ab*cd.

Multiple dumps (with different IDs) can be defined. See the undump command for turning off a dump.

The format of the dump file is self-explanatory. For each particle, an ID, its species type (an an integer), and its x,y,z coordinates are printed. Dump files can be visualized with the Pizza.py toolkit or converted into other formats (via Pizza.py) suitable for visualization with other tools, e.g. VMD.

Restrictions:

This command can only be used for spatial simluations.

Related commands:

dump_modify, stats, undump

Default: none