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species command

Syntax:

species file ID1 ID2 ... keyword value ... 

Examples:

species air.species air
species ar.species Ar
species air.species air CO2 CO vibfile co2.species.vib
species myfile H+ Cl- HCl 

Description:

Define one or more particle species to use in the simulation. This command can be used as many times as desired to add species to the list of species that the simulation recognizes.

The specified file is the name of a file containing definitions for a list of species, not all of which need to specified in this command, or used in a simulation. Only those requested by ID will be extracted from the file and they must be present in the file. The format of the species file is discussed below. The data directory in the SPARTA distribution contains several species files, all with the suffix ".species".

Each ID is a character string used to identify the species, such as N or O2 or NO or D or Fe-. The string can be any combination of alphanumeric characters or "+", "-", or underscore.

Instead of specifying IDs for single species, one of several pre-defined multi-species names can be used, each of which is expanded into a list of several individual species IDs. The list of currently recognized abbreviations is as follows:

These abbreviations can be used in combination with single-species IDs as in the 3rd example above.


The format of a species file is as follows. Comments or blank lines are allowed in the file. Comment lines start with a "#" character. All other lines must have the following format with values separated by whitespace:

species-ID prop1 prop2 ... prop9 prop10 

The species-ID is a string that will be matched against the requested species-ID, as described above. The properties are as follows:

The allowed values for rotational degrees of freedom (rotdof = prop3) are 0,2,3. Typically, 0 = monatomic species, 2 = diatomic, 3 = anything else.

The allowed values for vibrational degrees of freedom (vibdof = prop5) are 0,2,4,6,8. The associated number of vibrational modes is vibdof divided by 2. Typically, 0 modes = monatomic species, 1 mode = diatomic, 2/3/4 modes = triatomic or larger molecules.

Note that all the listed rotational and vibrational values must be specified for each species, but in cases where they are not used by SPARTA, they can simply be specified as 0.0. Whether or not the values are used for a species depends on the value of rotdof and vibdof. Whether the values are used in a simulation also depends on the settings specified for the rotation and vibration keywords of the collide_modify command.

Specifically, if prop3 for rotdof = 0, then prop4 is ignored. If prop5 for vibdof = 0, then prop6 and prop7 are ignored.

If vibdof = 4,6,8, then information for 2,3,4 vibrational modes can be specified for the species in a separate file using the optional vibfile keyword, as discussed below. If the collide_modify vibration command is used with a setting of discrete, then this vibrational mode info must be specified for each species with a vibdof = 4,6,8. Note that the fix vibmode command must also be used to allocate per-particle storage for these additional modes.


The optional vibfile keyword can be used to specify additional vibrational information in the specified vfile. If this option is used, then an entry must appear in vfile for every species in this command with a vibdof value = 4,6,8. Note that even if this vibrational info is read, it is ignored by SPARTA unless the collide_modify vibrate setting is specified as discrete.

The format of a species vibrational file is as follows. See data/co2.species.vib for an example. Comments or blank lines are allowed in the file. Comment lines start with a "#" character. All other lines must have the following format with values separated by whitespace:

species-ID N temp1 relax1 degen1 temp2 relax2 degen2 ... tempN relaxN degenN 

The species-ID is a string that will be matched against the requested species-ID, as described above. N is the number of vibrational modes that follow, which must be either 2,3,4, and must match the corresponding vibdof value = 4,6,8 (divided by two) used in the species file.

For each of the N modes, 3 values are listed:

These quantities are used during collisions if vibrational energy is modeled in discrete levels.

Note that the values for temp1 and relax1 override the same values defined in the species file (prop7 and prop6) when they are listed for the same species in the vibfile.


Restrictions: none

Related commands: none

Default: none