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Version: Develop 🚧

Model Parameters

UCLCHEM will default to these values unless they are overridden by user. Users can override these by adding the variable name as written here in the param_dict argument of any UCLCHEM model function. param_dict is not case sensitive.

Physical Variables​

ParameterDefault ValueDescription
initialTemp10.0Initial gas temperature in Kelvin for all gas parcels in model.
initialDens1.00d2Initial gas density in H nuclei per cmβˆ’3^{-3} for all gas parcels in model.
finalDens1.00d5Final gas density achieved via freefall.
currentTime0.0Time at start of model in years.
finalTime5.0d6Time to stop model in years, if not using endAtFinalDensity below.
radfield1.0Interstellar radiation field in Habing
zeta1.0Cosmic ray ionisation rate as multiple of 1.310βˆ’17sβˆ’11.3 10^{-17} s^{-1}
rout0.05Outer radius of cloud being modelled in pc.
rin0.0Minimum radial distance from cloud centre to consider.
baseAv2.0Extinction at cloud edge, Av of a parcel at rout.
points1Number of gas parcels equally spaced between rin to rout to consider

Behavioural Controls​

The following parameters generally turn on or off features of the model. If a parameter is set to True, then it is turned on. If it is set to False, then it is turned off.

ParameterDefault ValueDescription
freezeFactor1.0Modify freeze out rate of gas parcels by this factor.
endAtFinalDensity.False.Choose to end model at final density, otherwise end at final time.
freefall.False.Controls whether models density increaes following freefall equation.
freefallFactor1.0Modify freefall rate by factor, usually to slow it.
desorb.True.Toggles all non-thermal desoprtion processes on or off.
h2desorb.True.Individually toggle non-thermal desorption due to H2 formation.
crdesorb.True.Individually toggle non-thermal desorption due to cosmic rays.
uvdesorb.True.Individually toggle non-thermal desorption due to uv photons.
thermdesorb.True.Toggle continuous thermal desorption.
instantSublimation.False.Toggle instantaneous sublimation of the ices at t
cosmicRayAttenuation.False.Use column density to attenuate cosmic ray ionisation rate following Padovani et al. 2018.
ionModel'L'L/H model for cosmic ray attenuation Padovani et al. 2018.
improvedH2CRPDissociation.False.Use H2 CRP dissociation rate from Padovani et al. 2018b.

Input and Output​

ParameterDefault ValueDescription
outputFile"output/full.dat"File to write full output of UCLCHEM. This includes physical parameter values and all abundances at every time step.
columnFile"output/column.dat"File to write specific species abundances, see outSpecies.
writeStep1Writing to columnFile only happens every writeStep timesteps.
abundSaveFileNoneFile to store final abundances at the end of the model so future models can use them as the initial abundances. If not provided, no file will be produced.
abundLoadFileNoneFile from which to load initial abundances for the model, created through abundSaveFile. If not provided, the model starts from elemental gas.
outSpeciesNoneA space separated list of species to output to columnFile. Supplied as a separate list argument to most python functions, see python API docs.

Initial Abundances​

Unless otherwise specified, we take all abundances from Jenkins et al. 2009, using the heavily depleted case from Table 4.

ParameterDefault ValueDescription
metallicity1.0Scale the abundances of all elements heavier than He by this factor.
ion2Sets how much elemental C is initially atomic (0
fh0.5Total elemental abundance of H is always 1 by definition because abundances are relative to number of H nuclei. Use fh to set how much to initially put in atomic H, the rest goes to H2.
fhe0.1Total elemental abundance of He.
fc1.77d-04Total elemental abundance of C.
fo3.34d-04Total elemental abundance of O.
fn6.18d-05Total elemental abundance of N.
fs3.51d-6Total elemental abundance of S.
fmg2.256d-06Total elemental abundance of Mg.
fsi1.78d-06Total elemental abundance of Si.
fcl3.39d-08Total elemental abundance of Cl.
fp7.78d-08Total elemental abundance of P.
ffe2.01d-7Total elemental abundance of Fe.
ff3.6d-08fp depleted 1/100 of solar from Asplund 2009.
fd0.0The following elements are not typically used. We do not recommend any particular value.
fli0.0Total elemental abundance of Li.
fna0.0Total elemental abundance of Na.
fpah0.0Total initial abundance of PAHs.
f15n0.0Total initial abundance of 15N.
f13c0.0Total initial abundance of 13C.
f18O0.0Total initial abundance of 18O.

Integration Controls​

ParameterDefault ValueDescription
reltol1d-8Relative tolerance for integration, see integration docs for advice.
abstol_factor1.0d-14Absolute tolerance for integration is calculated by multiplying species abundance by this factor.
abstol_min1.0d-25Minimum value absolute tolerances can take.
MXSTEP10000Maximum steps allowed in integration before warning is thrown.

Here be Dragons​

These are not recommended to be changed unless you know what you are doing

ParameterDefault ValueDescription
ebmaxh21.21d3Maximum binding energy of species desorbed by H2 formation.
ebmaxcr1.21d3Maximum binding energy of species desorbed by cosmic ray ionisation.
ebmaxuvcr1.0d4Maximum binding energy of species desorbed by UV photons.
epsilon0.01Number of molecules desorbed per H2 formation.
uv_yield0.1Number of molecules desorbed per UV photon.
phi1.0d5Number of molecules desorbed per cosmic ray ionisation.
uvcreff1.0d-3Ratio of CR induced UV photons to ISRF UV photons.
omega0.5Dust grain albedo.
alpha{1:0.0,2:0.0}Set alpha coeffecients of reactions using a python dictionary where keys are reaction numbers and values are the coefficients. Once you do this, you cannot return to the default value in the same python script or without restarting the kernel in iPython. See the chemistry docs for how alpha is used for each reaction type.
beta{1:0.0,2:0.0}Set beta coeffecients of reactions using a python dictionary where keys are reaction numbers and values are the coefficients. Once you do this, you cannot return to the default value in the same python script or without restarting the kernel in iPython. See the chemistry docs for how beta is used for each reaction type.
gama{1:0.0,2:0.0}Set gama coeffecients of reactions using a python dictionary where keys are reaction numbers and values are the coefficients. Once you do this, you cannot return to the default value in the same python script or without restarting the kernel in iPython. See the chemistry docs for how gama is used for each reaction type.