# Cloud Files¶

## File Structure¶

DESPOTIC cloud files contain descriptions of clouds that can be read by the cloud or zonedcloud classes, using either the class constructor or the read method; see cloud for details. This section contains a description of the format for these files. It is recommended but not required that cloud files have names that end in the extension .desp.

Each line of a cloud file must be blank, contain a comment starting with the character #, or contain a key-value pair formatted as:

key = value


The line may also contain comments after value, again beginning with #. Any content after # is treated as a comment and is ignored. DESPOTIC keys are case-insensitive, and whitespace around keys and values are ignored. For the full list of keys, see Cloud file keys and their meanings. All quantities must be in CGS units. Key-value pairs may be placed in any order, with the exception of the key H2opr, which provides a means of specify the ratio of ortho-to-para-$$\mathrm{H}_2$$, instead of directly setting the ortho-and para-$$\mathrm{H}_2$$ abundances. If this key is specified, it must precede the key xH2, which gives the total $$\mathrm{H}_2$$ abundance including both ortho- and para- species. Not all keys are required to be present. If left unspecified, most quantities default to a fiducial Milky Way value (if a reasonable one exists, e.g., for the gas-dust coupling constant and ISRF strength) or to 0 (if it does not, e.g., for densities and chemical abundances).

Cloud file keys and their meanings
Key Units Description

Physical Properties
nH $$\mathrm{cm}^{-3}$$ Volume density of H nuclei
colDen $$\mathrm{cm}^{-2}$$ Column density of H nuclei, averaged over area
sigmaNT cm $$\mathrm{s}^{-1}$$ Non-thermal velocity dispersion
Tg K Gas temperature
Td K Dust temperature

Dust Properties
alphaGD erg $$\mathrm{cm}^3$$ $$\mathrm{K}^{-3/2}$$ Gas-dust collisional coupling coefficient
sigmaD10 $$\mathrm{cm}^2$$ $$\mathrm{H}^{-1}$$ Dust cross section per H to 10 K thermal radiation
sigmaDPE $$\mathrm{cm}^2$$ $$\mathrm{H}^{-1}$$ Dust cross section per H to 8-13.6 eV photons
sigmaDISRF $$\mathrm{cm}^2$$ $$\mathrm{H}^{-1}$$ Dust cross section per H averaged over ISRF
betaDust Dimensionless Dust IR spectral index
Zdust Dimensionless Dust abundance normalized to Milky Way value

TCMB K CMB temperature
ionRate $$\mathrm{s}^{-1}$$ Primary cosmic ray / x-ray ionization rate
chi Dimensionless ISRF strength, normalized to Solar neighborhood

Chemical composition
emitter   See Emitters

## Emitters¶

The emitter key is more complex than most, and requires special mention. Lines describing emitters follow the format:

emitter = name abundance [noextrap] [energySkip] [file:FILE] [url:URL]


Here the brackets indicate optional items, and the optional items may appear in any order, but must be after the two mandatory ones.

The first mandatory item, name, gives name of the emitting molecule or atom. Note that molecule and atom names are case sensitive, in the sense that DESPOTIC will not assume that co and CO describe the same species. Any string is acceptable for name, but if the file or URL containing the data for that species is not explicitly specified, the name is used to guess the corresponding file name in the Leiden Atomic and Molecular Database (LAMDA) – see Atomic and Molecular Data. It is therefore generally advisable to name a species following LAMDA convention, which is that molecules are specified by their chemical formula, with a number specifying the atomic weight preceding the if the species is not the most common isotope. Thus LAMDA refers to $$^{28}\mathrm{Si}^{16}\mathrm{O}$$ (the molecule composed of the most common isotopes) as sio, $$^{29}\mathrm{Si}^{16}\mathrm{O}$$ as 29sio, and $$^{12}\mathrm{C}^{18}\mathrm{O}$$ as c18o. The automatic search for files in LAMDA also includes common variants of the file name used in LAMDA. The actual file name from which DESPOTIC reads data for a given emitter is stored in the emitterData class – see emitterData.

The second mandatory item, abundance, gives the abundance of that species relative to H nuclei. For example, an abundance of 0.1 would indicate that there is 1 of that species per 10 H nuclei.

The optional items noextrap and energySkip change how DESPOTIC performs computations with that species. If noextrap is set, DESPOTIC will raise an error if any attempt is made to calculate a collision rate coefficient between that species and one of the bulk components (H, He, etc.) that is outside the range tabulated in the data file. If not, DESPOTIC will instead handle temperatures outside the tabulated range by substituting the closest temperature inside the tabulated range. Note that this behavior can be altered within a DESPOTIC program by using the extrap property of the emitterData class – see Full Documentation of All DESPOTIC Classes and Functions.

The optional item energySkip specifies that a species should be ignored when computing heating and cooling rates via the cloud.dEdt method, and by extension whenever thermal equilibria or thermal evolution are computed for that cloud. However, line emission from that species can still be computed using the cloud.lineLum method. This option is therefore useful for including species for which the line emission is an interesting observable, but which are irrelevant to the thermal balance and thus can be omitted when calculating cloud thermal properties in order to save computational time.

Finally, the optional items file:FILE and url:URL specify locations of atomic and molecular data files, either on the local file system or on the web. This capability is useful in part because some LAMDA files do not follow the usual naming convention, or because for some species LAMDA provides more than one version of the data for that species (e.g., two versions of the data file for atomic C exist, one with only the low-lying IR levels, and another including the higher-energy UV levels). File specifications must be of the form file:FILE with FILE replaced by a file name, which can include both absolute and relative paths. If no path or a relative path is given, DESPOTIC searches for the file first in the current directory, and then in the directory $DESPOTIC_HOME/LAMDA, where $DESPOTIC_HOME is an environment variable. If it is not specified, DESPOTIC just looks for a directory called LAMDA relative to the current directory.

The url:URL option can be used to specify the location of a file on the web, usually somewhere on the LAMDA website. It must be specified as url:URL, where URL is replaced by an absolute or relative URL. If an absolute URL is given, DESPOTIC attempts to download the file from that location. If a relative URL is given, DESPOTIC attempts to download the file from at http://$DESPOTIC_LAMDAURL/datafiles/URL, where $DESPOTIC_LAMDAURL is an environment variable. If this environment variable is not specified, DESPOTIC searches for the file at http://home.strw.leidenuniv.nl/~moldata/URL.