How to use
git clone https://github.com/fjdu/chem_reduce.git
cd chem_reduce
make
./reduce config_reduce_20140223.dat
Edit the ReduceParameters section of the configuration file as needed. You can also change other parameters.
Example config file
! Filename: configure.dat
! Usage
! Just modify this file and run ./reduce.
! The default name of this file is config.dat.
! You can use another name, e.g., XXX.dat, then
! run the program like this: ./reduce XXX.dat
!
&PhysicalParameters
!Av = 3.0D0 ! NHtotal / 1.6D21; obsolete: changed into AV_s now
omega_Albedo = 0.5D0
rateCosIon = 3.0D-17
rateHHH2 = 3.003953e-18 !3.002221e-18 !
!stickCoeffHH = 1D0
!stickCoeffChargeGrain = 0.8D0 !0.5D0
ratioDustGasMass = 1.3D-30
!ratioHDust = 2.857143E11 ! 1D0/3.5D-12
GrainDensity = 2.0D0 ! g/cm^3
GrainRadius = 1.0D-1 ! micron !for gas-to-dust ratio, coulomb correction, rate correction
GrainRadiusBase = 0.02 !0.0202 ! micron ! for rate correction
aGrainMin = 1.0D-5 ! 1D-6 !cm ! only used for calculating the H+H->H2 rate
aGrainMax = 1.0D-5 ! 3D-5 !cm ! only used for calculating the H+H->H2 rate
timeUnit = 1.0D2 ! in years
nSpecies_Est = 1024
rateThreshold = 0D0
/
&ODEParameters
nIteration = 650
RTOL = 1.0D-6 ! relative tolerance
ATOL = 1.0D-30 ! absolute tolerance
/
&Paths
path = "./"
fReactions = "rate06_dipole_reformated_again.dat" ! Reaction network to be reduced
fInitialCondition = "initial_condition_low_metal.dat" ! Initial condition
fSaveFinalResult = "final_abundance_20130528.txt" ! Save final abundances into this file
/
&ReduceParameters
nPhyPar = 3 ! Number of the groups of physical parameters
! The following means we care about three different physical conditions:
! 1. T = 10 K, n = 1D11 cm-3, Av = 20
! 2. T = 30 K, n = 1D9 cm-3, Av = 5
! 3. T = 100 K, n = 1D2 cm-3, Av = 1
Temperature_s = 10.0 30.0 1D2
n_H_s = 1D11 1D9 1D8
Av_s = 20.0 5D0 1D0
file_imp_species_in = "species_we_care_about.dat"
file_imp_reacs_out = "rate06_dipole_reduced_20140223.dat"
! The time steps we care about
n_time_care = 10
time_care = 1E-3 1E-2 1E-1 1E0 1E1 1E2 1E3 1E4 1E5 1E6 ! The time intervals we care about
allow_dead_end = .FALSE.
! The code recursively finds out the important reactions and species at each
! time step we care about. The ratio_tobe_imp parameter specifies the threshold for
! a reaction to be considered important at each recursion.
! The actual ratio_tobe_imp array will be longer than this; the remaining
! elements are padded with the minval of those specified below.
! The use_acum_threshold = .TRUE. means the thresholds are based on accumulated
! contribution of the reactions, hence 0.95 means the reactions that collectively
! contribute to 95% of the reaction rates are kept.
ratio_tobe_imp = 0.99 0.95 0.95 0.9 0.9 0.5 0.5 0.3 0.1
use_acum_threshold = .TRUE.
! A reaction with time scale longer than tScaleMax will be discarded.
tScaleMax = 1.0E15
nHeavyEleMax = 5 ! Max number of elements beyond He in species to be kept
nMaxD = 4 ! Max number of deuterium atoms in species to be kept
nMaxC = 5 ! ... of carbon
abundMaxHeavy = 1E-50 ! A species will not be removed unless its abundance is lower than this.
abundMaxSecondary = 1E-50 ! For similar purpose
abundMaxC = 1D-50
prio_reac_threshold = 0.001 ! Reactions with relative importance lower than
! this will be removed. The importance of a reaction is different for
! different species; it is simply the rate of that reaction devided by the total
! rate of the production or destruction of a species (at a given time).
prio_spe_threshold = 0.001 ! Similar
fLog = "Log.dat"
/