RUNTIME
coordinate
coordinate option
Default: Rectangular
The user may also choose cylindrical, rotational (=axisymetric), or spherical coordinates.
correction_max
correction_max value
Default: 2
Absolute magnitude of the maximum correction to the natural logarithm of a component species in any one Newton step. This is an optional parameter which controls the absolute magnitude of the maximum allowable correction to a component species in any particular Newton step. The correction is in units of the natural logarithm of the species molality. The limitation of the correction is a form of damping of the Newton step which prevents overflows in many cases. Correction factors over 10 are not recommended. Excessively small correction factors (< 1) will slow the rate of convergence of the Newton method significantly.
database
database FileName
Default: database.dbs
Option to specify a database file.
database_sweep
database_sweep
Default: false
THIS OPTION IS NOT AVAILABLE AT THE MOMENT.
The keyword parameter database_sweep is followed by true or false and is used to select, when true, the option to sweep the entire thermodynamic database so as to load all possible species and minerals. In this case, the user’s choice of secondary species and minerals listed in the input file is ignored. After the sweep, each of the geochemical conditions is speciated and the code stops. User’s who want to use these species and minerals in an actual reactive transport run need to copy the list of secondary species and/or minerals over to the keyword blocks for these categories within the input file and then deselect the database_sweep option. This option supersedes whatever is set with the speciate_only keyword described below.
data_processing
data_processing true/false
Default: false
This option makes it possible to post-treat the results of previous simulations to plot profiles and color maps.
debye-huckel
debye-huckel true/false
Default: true
The keyword parameter debye-huckel is followed by true or false and is used to select the model to compute activity coefficients. Currently, the only two options are the extended Debye-Huckel model (Helgeson) or activity coefficients equal to 1 (no activity corrections).
DO NOT USE THIS OPTION. IT MUST BE FIXED
density_module
density_module name
Default: temperature
The default is to calculate the fluid density only as a function of temperature. No other options are available at the moment.
fix_saturation
fix_saturation value
THIS OPTION IS NOT AVAILABLE AT THE MOMENT.
Default: 1
This is an optional parameter that can be used to set a constant, uniform liquid saturation for a problem. The value must be greater than 0.0 and less than or equal to 1.0.
ksprelativetolerance
ksprelativetolerance value
Default is $10^{-5}$.
KSPGMRESSetRestart
KSPGMRESSetRestart value
Default is 100. Lower values yield to poor convergence.
See: https://petsc.org/release/manualpages/KSP/KSPGMRESSetRestart/
later_inputfiles
later_inputfiles FileName1 FileName2 ...
This option allows additional input files to be read automatically restart. Normally this option is used in conjunction with the keywords save_restart and restart, which generate and read respectively restart of “pickup” files that can be used to read in the spatial distribution of species and minerals from a previous run, and to change boundary or inner-grid conditions. There is no a a priori restriction on the number of files. The later_inputfiles option should be specified only in the first input file in the series to be read (later specifications will be ignored).
masterspecies
masterspecies primary species name
Default: H+
The maximum change in masterspecies concentration is printed at each screen_output together with the location of the grid cell where the maximum change occured.
max_ksp_iterations
max_ksp_iterations value
max_ksp_iterations_first_timesteps
max_ksp_iterations_first_timesteps value
max_newton_iteration
max_newton_iteration value
min_newton_iteration
min_newton_iteration value
ompthreads
ompthreads value
Default: 1
The value indicates the number of threads used by each processor in OpenMP offload regions in the code. The number of processor used for the calculation is indicated with the -n option in the command line that launched the calculations:
In the above example the calculation is run with MPI using 8 processors. With an ompthreads value of 2, each of the 8 processors will use 2 threads. Your computer must have 16 available processors to run in these conditions. If there are not enough available processors, the number of ompthreads will be automatically reduced to the maximum number of available processors.
o2h2production
o2h2production true/false
read_saturationfile
read_saturationfile FileName
THIS OPTION IS NOT AVAILABLE AT THE MOMENT.
This provides the name of a file containing liquid saturations distributed in space to be read. This option overrides the fix_saturation keyword. The format of the file depends on the optional format specified. singlecolumn, SingleColumn, ContinuousRead, Unformatted, distanceplusvariable, fullform, full
restart
restart FileName
This keyword parameter specifies that the code should be restarted. If restart is not followed by anything, the default restart file name of crunch.rst is used. Alternatively, the user may specify an optional restart file name (this can be useful, since the default file name will be overwritten with a new run). This optional restart file, however, must have been created in an earlier run with the save_restart keyword. Binary restart files will be created each time a set of spatial profiles are written (see keyword spatial_profile in the OUTPUT keyword block). With a normal successful termination of the code, the restart file will be updated at the end of the run. Subsequent output to the “breakthrough” files (see keyword time_series) can be appended by adding the optional append keyword after the filename.
save_restart
save_restart FileName
This keyword parameter specifies that the code should create a restart file with the name provided. If the keyword save_restart is not provided, restart information will be saved to the default restart file name of crunch.rst.
screen_output
screen_output value
This gives the interval at which run time output (time, time step size, number of Newton iterations required…) is written to the screen. This is useful where the code is taking a large number of time steps to complete a run and only periodic information is needed. This number should be a minimum of 1 (output every time step).
preconditionner
preconditionner option
Options include: bjacobi, asm.
Default is bjacobi.
speciate_only
speciate_only true/false
The keyword parameter speciate_only is followed by true or false and is used to select, when true, the option to speciate the geochemical conditions and then to stop without carrying out any reactive transport calculations. This option is contrasted with database_sweep which, in addition to stopping after the speciation calculations, also sweeps the database to load all of the possible species and minerals. Using speciate_only, the user’s list of secondary species and minerals given in the input file is used.
timestep_init
timestep_init value
This indicates the initial time step to be used in simulation. The default units are seconds, with the option to reset the time units to one of those discussed under Space and Time Units (e.g., seconds, days, etc.) using the time_units parameter keyword.
timestep_max
timestep_max value
This indicates the maximum time step allowed in problem. The default units are seconds, with the option to reset the time units to one of those discussed under Space and Time Units (e.g., seconds, days, etc.) using the time_units parameter keyword.
time_unit
time_unit option
This indicates the time units to be used in the input file.
The default units are seconds.
Options include: years (365 days), days, hours, minutes, seconds.
verbose
verbose true/false
none, minimal, minimum, medium, all