UCLCHEM can be compiled and run from the top directory in the following way:
cd src make cd .. ./uclchem
src/Makefile contains a small number of user choices. Namely, the compiler and physics module. UCLCHEM comes with various physical models which can be chosen by setting the variable
PHYSICS in the makefile to the correct fortran file.
All possible input parameters for UCLCHEM can be found in
src/defaultparameters.f90. When the code is compiled, each parameter is set the value given in this file. Any changes to this file require a recompile.
Beyond this, any subset of parameters can be written to a file and the file path given to UCLCHEM at run time. This will modify the parameters for a single run. For example if we create a file called test.inp:
initialDens 1.0d2 finalDens 1.0d4 collapse 1
and then run UCLCHEM:
The code will run using the values in
src/defaultparameters.f90 except for the three parameters listed in test.inp which will take the values from that file.
UCLCHEM has two major outputs. The first is the ”full” output including the major gas properties and the fractional abundance of every single species in the network. This is written to the file given by the
outputFile parameter and is written at every timestep. For those using the full output, a set of python functions to read and plot the abundances from the full output file are provided in
Optionally, a more machine readable output can be created by suppling the
outputSpecies as inputs. This produces columnated file of time, density and temperature along with the abundances of the species in the
outputSpecies array. The parameter
writeStep sets how often this is written.