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3.1 The complete list of the KROME Options

-h, --help show this help message and exit

-ATOL ATOL set solver absolute tolerance to the float or double value ATOL, e.g. -atol 1d-40 Default is ATOL=1d-20, see also -RTOL and -customATOL

-C create a simple C wrapper

-compact creates a single fortran file with all the modules instead of various file with the different modules. Solver files remain stand-alone (see example make in test/MakefileCompact)

-checkConserv check mass conservation during integration (slower)

-checkReverse check network for reverse reactions. Write warning on screen if any. -checkThermochem print a warning when thermochemistry data are not found for a given species.

-clean clean all in /build (including krome_user_commons.f90 that is normally kept by default) before creating new f90 files.

-columnDensityMethod method use an alternative method to N=1.8e21(n1e-3)*(2./3.) for column density calculation (N) from number density (n). Option available JEANS, which employs Jeans length (l) as N=nl.

-compressFluxes in the ODE fluxes are stored in a single variable

-conserve conserves the species total number and charge global neutrality. Works with some limitations, please read the manual.

-conserveE conserves the charge global neutrality only.

-coolFile FILENAME select the filename to be used to load external cooling. See also tools/lamda2.py script for a LAMDA<->KROME converter. Default FILENAME is data/coolZ.dat, which contains fine-strucutre atomic metal cooling for C,O,Si,Fe, and their first ions. It can also be a list of files comma-separated.

-cooling TERMS cooling options, TERMS can be ATOMIC, H2, HD, Z, DH, DUST, H2GP98, COMPTON, EXPANSION, CIE, DISS, CI, CII, SiI, SiII, OI, OII, FeI, FeII, CHEM (e.g. -cooling=ATOMIC,CII,OI,FeI). Note that further cooling options can be added when reading cooling function from file. If you want a complete list of the available cooling options type -cooling=?

-coolLevels MAXLEV use only the levels up to MAXLEV (included), e.g. -coolLevels=3 Note that levels are zero-based (i.e. ground state is zero).

-coolingQuench TCRIT quenches the cooling when T<TCRIT with a tanh function.

-customATOL filename file with the list of the individual ATOLs in the form SPECIES ATOL in each line, e.g. H2 1d-20, see also -ATOL -customODE FILENAME file with the list of custom ODEs

-customRTOL filename file with the list of the individual RTOLs in the form SPECIES RTOL in each line, e.g. H3+ 1d-4, see also -RTOL

-dry dry pre-compilation: does not write anything in the build directory

-dust DUST include dust ODE using N bins for each TYPE, e.g. -dust 10,C,Si set 10 dust carbon bins and 10 dust silicon dust bins. Note: requires a call to the krome_init_dust subroutine. See -test=dust for an example.

-dustOptions OPTIONS activate dust options: (GROWTH) dust growth, (SPUTTER) sputtering, (H2) molecular hydrogen formation on dust, and (T) dust temperature. The last option provide a template for the FEX routine.

-enzo create patches for ENZO

-flash create patches for FLASH

-forceMF21 force explicit sparsity and Jacobian

-forceMF222 force internal-generated sparsity and Jacobian

-forceRWORK N force the size of RWORK to N

-gamma OPTION define the adiabatic index according to OPTION that can be FULL for employing Grassi et al. 2011, i.e. a density dependent but temperature independent adiabatic index, VIB to keep into account the vibrational paritition function, ROT to keep into account the rotational partition function, EXACT to evaluate the adiabatic index accurately taking into account both contributions, or REDUCED to use only H2 and CO as diatomic molecules (faster). Finally a custom F90 expression e.g. -gamma="1d0" can also be used. Default value is 5/3.

-H2opacity TYPE use H2 opacity for H2 cooling, TYPE can be RIPAMONTI or OMUKAI

-heating TERMS heating options, TERMS can be COMPRESS, PHOTO, CHEM, DH, CR, PHOTOAV. If you want a complete list of the available heating options type -heating=?

-ierr same as -useIERR

-interfaceC generate interface between Fortran and C so one can call KROME from C.

-interfacePy generate interface between Fortran and Python so one can call KROME from Python.

-iRHS implicit loop-based RHS (suggested for large systems)

-listAutomatics list all the automatic reactions available

-maxord MAXORD max order of the BDF solver. Default (and maximum values) is 5.

-mergeTlimits use the same reaction index for equivalent reactions (same reactants and products) that have different temperature limits

-n FILENAME reaction network file

-network FILENAME same as -n

-nochargeCheck skip reaction charge check

-noCheck skip reaction charge and mass check. Equivalent to -nomassCheck -nochargeCheck options.

-noExample do not write test.f90 and Makefile in the build directory

-nomassCheck skip reaction mass check

-noTlimits ignore rate coefficient temperature limits.

-nuclearMult keep into account reactants multeplicity, and modify fluxes according to this. Intended for nuclear networks.

-options filename read the options from a file instead of command line (in principle you can use both). See options_example file.

-pedantic uses a pedantic Makefile (debug purposes)

-project NAME build everything in a folder called build_NAME instead of building all in the default build folder. It also creates a NAME.kpj file with the krome input used.

-quote print a citation and exit

-quotelist print all the citations and exit

-ramses create patches for RAMSES, see also -enzo and -flash

-ramsesOffset offset add an offset to the array of the passive scalar. The default is 3.

-ramsesTH create patches for RAMSES_TH. This is a private version and probably does not fix your needs.

-report generate report file in the main call to krome as KROME_ERROR_REPORT and when calling the fex as KROME_ODE_REPORT. It also stores abundances evolution in fex as fort.98, and prepares a report.gps gnuplot script file to plot evolutions callable in gnuplot with load 'report.gps'. Warning: it slows the whole system!

-reverse create reverse reaction from the current network using NASA polynomials. -RTOL RTOL set solver relative tolerance to the float double value RTOL, e.g. -RTOL 1e-5 Default is RTOL=1d-4, see also -ATOL and -customRTOL

-photoBins NBINS define the number of frequency bins for the impinging radiation.

-sh write a shorter header in the f90 files

-shielding TYPE use H2 self-shielding, TYPE can be DB96 for Draine+Bertoldi 1996, WG11 for the more accurate Wolcott+Greene 2011

-shieldHabingDust dust shielding for Habing flux (when calculated from photobins). The shielding function is pre-set but the user can change it.

-skipDup skip duplicate reactions

-skipJacobian do not write Jacobian in krome_ode.f90 file. Useful to reduce compilation time when Jacobian is not needed (MF=222).

-skipODEthermo do not compute dT/dt in the ODE RHS function (fex)

-source folder use FOLDER as source directory

-stars use star module for nuclear reactions. NOTE: krome_stars module required in the Makefile

-test TEST Create a test model in /build. TEST can be: atmosphere, auto, chianti, cloud, collapse, collapseCO, collapseUV, collapseUV_Xrays, collapseZ, collapseZ_induced, collapseZ_UV, compact, dust, earlyUniverse, lamda, lotkav, map, reverse, shock1D, shock1Dcool, shock1Dphoto, slowmanifold, stars, Cinterface, Pyinterface.

-Tlimit opLow,opHigh set the operators for all the reaction temperature limits where opLow is the operator for the first temperature value in the reaction file, and opHigh is for the second one. e.g. if the T limits for a given reaction are 10. and 1d4 the option -Tlmit GE,LE will provide (Tgas>=10. AND Tgas<=1d4) as the reaction range of validity. Operators opLow and opHigh must be one of the following: LE, GE, LT, GT.

-unsafe skip to check if the build folder is empty or not

-useCoolCMBFloor include a cooling floor given by the CMB temperature. note that you must define Tcmb by using the subroutine krome_get_Tcmb(your_Tcmb) before calling krome.

-useCustomCoe FUNCTION use a user-defined custom function that returns a real*8 array of size NREA = number of reactions, that replaces the standard rate coefficient calculation function. Note that FUNCTION must be explicitly included in krome_user_commons module.

-useDvodeF90 use Dvode implementation in F90 (slower)

-useEquilibrium check if the solver has reached the equilbirum. If so break the solver's loop and return the values found. It is useful when the system oscillates around a solution (as in some photoheating cases). To be used with caution!

-useFileIdx use the reaction index in the reaction file instead of using the automatic progressive index starting from 1. Useful with rate coefficients that depends on other coefficients, e.g. k(10) = 1d-2*k(3)

-useIERR use ierr in the interface with KROME to return errors instead of stopping the execution

-useN use number densities (1/cm3) as input/ouput instead of fractions (#)

-useODEConstant EXPRESSION postpone an expression to each ODE. EXPRESSION must be a valid f90 expression (e.g. *3.d0 or +1.d-10)

-usePhIoniz includes photochemistry (obsolete)

-usePhotoInduced includes the photo-induced transitions in the calculation of the cooling according to the choosen photon flux.

-usePhotoOpacity computes photorates using opacity as a function of the species densities and the photo cross sections, i.e. exp(-sum_i N_isigma_i). Column densities are computed from density by using the local approximation N = 1.8e21(n/1000)**(2/3) 1/cm2.

-usePlainIsotopes use kA format for isotopes instead of [k]A format, where k is the isotopic number and A is the atom name, e.g. krome looks for 14C instead of [14]C in the reactions file.

-useThermoToggle include thermal calculation control. Use krome_thermo_on and krome_thermo_off to switch on/off the thermal processes (i.e. cooling and heating). Default is on.

-useTabs use tabulated rate coefficients (free parameter: temperature)

-v print the current version of KROME

-ver same as -v

-version same as -v