options_example

#THIS IS AN OPTION FILE FOR KROME
############# NOTES ###################
#Note that this file is an alternative to call the options from command line, e.g. -cooling=H2,HD
#You can call this file by using -options=FILENAME, where FILENAME is the path of this file.
#The options can be (un)selected in several ways:
#if the option do not requires any argument (e.g. -conserve) you can write one of the following
# conserve
# conserve YES
# conserve TRUE
# conserve T
# conserve 1
#or to exclude the command
# conserve NO
# conserve FALSE
# conserve F
# conserve 0
#When the option requires a parameter (e.g. -ATOL=1d-10)
# you must specify the parameter as
# ATOL 1d-10
# ATOL=1d-10
#note that you can prepend "-" character before the option, e.g.
# -ATOL 1d-10
# -conserve
#comments are allowed via hash (#) and C-like comments (//)
############# END NOTES ###################

#absolute tolerance, the default is 1d-20
#ATOL 1d-10

#create a C wrapper to call KROME from a C program, see wrapC example in tests, or call it using -test=wrapC
# -C

#prepare a single file that stores all the KROME modules in one. Less intelligible, but more compact. See -test=compact for an example
# -compact

#check mass conservation during integration (slower). Returns an error if the mass conservation relative error is larger than 0.001
# intended for debugging purposes
# -checkConserv

#check network for reverse reactions. Write warning on screen if missing.
# -checkReverse

#print a warning when thermochemistry data are not found for a given species. Intended for reverse reactions.
# -checkThermochem

#clean the build directory before write, including krome_user_commons.f90. Warning, you cannot undo this action.
# -clean

#in the ODE the fluxes are stored in a single variable instead of explicitly written. For old compilers.
# -compressFluxes


#conserves the species total number and charge global neutrality. Works with some limitations, please read the manual before using,
# especially for non-primordial environments with heteronuclear molecules.
# -conserve

#conserves the charge global neutrality by changing the electrons number density in order to balance the ions
# -conserveE

#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-structure atomic metal cooling for C,O,Si,Fe, and their first ions. 
# It can also be a list of files comma-separated.
# -coolFile=your/cooling/file

#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=?
-cooling=H2,HD


#quenching cooling using a multiplication factor of (tanh(T-Tcrit)+1)/2, where Tcrit in K is the critical temperature
# around where the factor starts to have effect. You can modify this function in the cooling() function in the krome_cooling module
# -coolingQuench=Tcrit

#a file with the list of the individual ATOLs in the form SPECIES ATOL in each line, e.g. 
# H2 1d-20
# HD 1d-6
# See also -ATOL. Note that comments (#) are allowed
# -customATOL=your/custom/atol/file

#file with the list of custom ODEs to extend the ODEs employed by the chemistry. See -test=lotkav for an example and the
# file tests/lotkav/lotkav
# -customODE=custom/ODE/file

#a file with the list of the individual RTOLs in the form SPECIES RTOL in each line, e.g. 
# H2 1d-4
# HD 1d-2
# See also -RTOL. Note that comments (#) are allowed
# -customRTOL=your/custom/rtol/file


#dry pre-compilation: does not write anything in the build directory. Employed To test and debug the python pre-processor.
# -dry

#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.
# -dust=10,C,Si

#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.
# -dustOptions=GROWTH,SPUTTER,H2

#create patches for ENZO code in the build folder
# -enzo

#create patches for FLASH code in the build folder
# -flash

#force explicit sparsity and Jacobian
# -forceMF21

#force internal generated sparsity and Jacobian (default)
# -forceMF222

#force RWORK size to N. Use this option in case of solver error.
# -foceRWORK=3000

#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 calculate the vibrational
# partition function and keeping the rotational part constant to 2, ROT to keep into account the rotational partition function and the 
# vibrational part to zero, or EXACT to evaluate the adiabatic index accurately taking into account both contributions. 
# Finally a custom F90 expression e.g. -gamma="1.5d0" can also be used, as well as any fortran expression. Default value is 5/3 (ideal atomic gas).
-gamma=FULL

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

#see useIERR
# -ierr

#implicit loop-based RHS (suggested for large systems, e.g. >1000 reactions). This option compacts the FEX construction into a loop instead of 
# writing explicit equations. It's faster during compilation, but slower at running time, even if depends on the solver employed.
# -iRHS 

#max order of the BDF solver. Default (and maximum values) is 5. Reducing the order to 2 can be helpful to increase the stability in some
# cases.
# -maxord=2

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

#reaction network file path
-n networks/react_primordialZ2

#same as -n
# -network networks/react_primordialZ2

#skip reaction charge check. Helpful with nuclear networks
# -nochargeCheck

#skip reaction charge and mass check. Equivalent to -nomassCheck -nochargeCheck options (see).
# -noCheck

#do not write test.f90 and Makefile in the build directory. Ignored if -test option is enabled.
# -noExample

#skip reaction mass check
# -nomassCheck

#ignore rate coefficient temperature limits.
# -noTlimits

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

#uses a pedantic Makefile from tests\ folder. Slow at run-time but traps errors. 
# -pedantic

#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.
# -project=myProject

#print a quote and exit. All other options are ignored.
# -quote

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

#add an offset to the array of the passive scalar. The default is 3.
# -ramsesOffset=5

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

#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!
# -report

#create reverse reaction from the current network using NASA polynomials and thermochemistry data.
# -reverse

#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
# -RTOL=1d-4

#write a shorter header in the f90 files
# -sh

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

#skip duplicate reactions, e.g. same reactants and products, but not same temperature range. Use with caution!
# -skipDup

#do not write Jacobian in krome_ode.f90 file. Useful to reduce compilation time when Jacobian is not needed (MF=222).
# Note that Jacobian is written also if not used. If it is very large this could increase the compilation time.
# -skipJacobian

#do not compute dT/dt in the ODE RHS function
# -skipODEthermo

#use FOLDER as source directory instead of the default folder src\
# -source=source/directory

#use star module for nuclear reactions.
# -stars

#create a test model in /build . Type make and ./krome in build/ folder to run it
#tests are listed in the folder tests/
# -test=collapseZ

#et 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. Noe that in the reaction file you can
#indicate the limits for individual reactions. The latter override the default.
# -Tlimit=GE,LT

#skip to check if the build folder is empty or not and replace everything
# -unsafe

#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.
#You can also use an array also defined in the krome_user_commons module
# -useCustomCoe=mycoe(:)

#use Dvode implementation in F90 (slower and not fully maintained)
# -useDvodeF90


#check if the solver has reached the equilibrium. 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!
# -useEquilibrium

#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)
# -useFileIdx


#use H2 opacity for H2 cooling using Ripamonti+Abel2004
#-useH2opacity


#use ierr in the interface with KROME to return errors instead of stopping the execution, see also -ierr.
# -useIERR

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

#postpone an expression to each ODE. EXPRESSION must be a valid f90 expression starting with an operator (e.g. *3.d0 or +1.d-10)
# -useODEConstant="+1d-2"

#include photochemistry
# -usePhIoniz

#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.
# -usePlainIsotopes

#use tabulated rate coefficients. Note that if your rates depend on a parameter other than the temperature
#you may incur on errors. For this reason KROME has the possibility to add some statement in the reaction
#file to prevent tabulation: for a single reaction just add in the line before @noTab_next or @noTabNext
#while for blocks of reactions use @noTab_start / @noTab_stop or @noTab_begin / @noTab_end. Note that these
#statements are case insensitive
-useTabs

#print the current version of KROME
# -v
# -ver
# -version