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ChemFunctions_mod.f90
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ChemFunctions_mod.f90
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! <ChemFunctions_mod.f90 - the EMEP MSC-W Chemical transport Model>
!*****************************************************************************!
module ChemFunctions_mod
!____________________________________________________________________
! Miscellaneous collection of "standard" functions for chemical
! calculations. Includes Troe, sine and cosine curves, and some
! from KPP system.
!
! Where possible, reference to the EMEP documentation paper, Simpson
! et al., ACP, 2012, are given, indicated by ACP:
!
!____________________________________________________________________
!
!** includes
! troe - standard chemical function
!____________________________________________________________________
use AeroConstants_mod, only: AERO
use AeroFunctions_mod, only: UptakeRate, GammaN2O5_EJSS, GammaN2O5
use CheckStop_mod, only: StopAll
use ChemSpecs_mod, only : SO4, NO3_f, NH4_f, NO3_c
! use Config_module, only : DebugCell, DEBUG ! set with DEBUG%RUNCHEM
use LocalVariables_mod, only : Grid ! => izen, is_mainlysea
use Config_module, only : K1 => KCHEMTOP, K2 => KMAX_MID, USES
use PhysicalConstants_mod, only : AVOG, RGAS_J, DAY_ZEN
use ZchemData_mod, only : itemp, tinv, rh, x=> xn_2d, M, &
aero_fom,aero_fss,aero_fdust, aero_fbc, &
gamN2O5, cN2O5, temp, DpgNw, S_m2m3 ! for gammas & surface area
use ChemSpecs_mod, only : SO4, NO3_f, NH4_f, NO3_c
implicit none
private
public :: troe
public :: troeInLog ! When log(Fc) provided
public :: IUPAC_troe ! Using the approximate expression for F from
! Atkinson et al., 2006 (ACP6, 3625)
public :: xkaero
public :: kaero2 ! for testing
public :: RiemerN2O5
public :: S_RiemerN2O5 !TES
public :: HydrolysisN2O5
public :: ec_ageing_rate
public :: kmt3 ! For 3-body reactions, from Robert OCt 2009
! weighting factor for N2O5 hydrolysis. OLD SCHEME! NOT USED
! Some help factors (VOLFAC) pre-defined here. 0.068e-6 is
! number median radius, assumed for fine aerosol
! 1.2648 is the term 3* exp( -2.5 * (log(sig=1.8))**2 ) used below
! We also assume generic aerosol median number radius of 0.068um
real, parameter, public :: VOLFACSO4 = 96.0/(AVOG) * 1.2648 *0.02/0.068e-6
real, parameter, public :: VOLFACNO3 = 62.0/(AVOG) * 1.2648 *0.02/0.068e-6
real, parameter, public :: VOLFACNH4 = 18.0/(AVOG) * 1.2648 *0.02/0.068e-6
!========================================
contains
!========================================
!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
! KMT3 uses air concenrtation (M) and inverse Temp (tinv) from Zmet
!
function kmt3(a1,c1,a3,c3,a4,c4) result (rckmt3)
real, intent(in) :: a1,c1,a3,c3,a4,c4
real, dimension(size(M)) :: rckmt3
real, dimension(size(M)) :: k1, k3, k4
k1 = a1 * EXP(C1*tinv)
k3 = a3 * EXP(C3*tinv)
k4 = a4 * EXP(C4*tinv)
rckmt3 = k1 + (k3*M)/(1.0+(k3*M)/k4)
end function kmt3
!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
elemental function troe(k0,kinf,Fc,M) result (rctroe)
!+ Calculates Troe expression
! -----------------------------------------------------------
! ds note - this isn't checked or optimised yet. Taken from
! Seinfeld+Pandis, 1998, pp 283, eqn. 5.98.
! Input arguments are intended to represent:
! M may be O2+N2 or just N2 or just O2.
real, intent(in) :: k0,kinf,Fc,M
real :: rctroe
!-- local
real :: x,y, K0M ! temp variable
k0M = k0 * M
!- use the power function replacament, m**n == exp(n*log m)
!-k0M = a*(T/300.0)**(-2.3) * M
!-kinf = p*(T/300.0)**(-1.4)
! k0M = a * exp( b*log(t/300.0) ) * M
! kinf = p * exp( q*log(t/300.0) )
! factors for Fc:
y = k0M/kinf ! used also below
x = log10(y)
x = 1.0/( 1.0 + x*x )
!- F**x == exp(x*logF)
! could have Fc already as log(Fc) to save CPU, but for now
! keep as proper Fc. Slower but less confusing
! rctroe = k0M / ( 1.0 + k0M/kinf) * exp(x*log(Fc))
rctroe = k0M / ( 1.0 + y) * exp(x*log(Fc))
end function troe
!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
elemental function troeInLog(k0,kinf,LogFc,M) result (rctroe)
!+ Calculates Troe expression
! -----------------------------------------------------------
! note - this isn't optimised yet. Taken from
! Seinfeld+Pandis, 1998, pp 283, eqn. 5.98.
! Input arguments are intended to represent:
! M may be O2+N2 or just N2 or just O2.
real, intent(in) :: k0,kinf,LogFc,M
real :: rctroe
!-- local
real :: x,y, K0M ! temp variable
k0M = k0 * M
!- use the power function replacament, m**n == exp(n*log m)
!-k0M = a*(T/300.0)**(-2.3) * M
!-kinf = p*(T/300.0)**(-1.4)
! k0M = a * exp( b*log(t/300.0) ) * M
! kinf = p * exp( q*log(t/300.0) )
! factors for Fc:
y = k0M/kinf ! used also below
x = log10(y)
x = 1.0/( 1.0 + x*x )
!- F**x == exp(x*logF)
! give Fc already as log(Fc)
! rctroe = k0M / ( 1.0 + k0M/kinf) * exp(x*log(Fc))
rctroe = k0M / ( 1.0 + y) * exp(x*LogFc)
end function troeInLog
!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
elemental function IUPAC_troe(k0,kinf,Fc,M,N) result (rctroe)
!+ Calculates Troe expression
! -----------------------------------------------------------
! note - this isn't optimised yet. Taken from
! Atkinson et al. ACP 2006, 6, 3625-4055.
! Input arguments are intended to represent:
! M may be O2+N2 or just N2 or just O2.
! NOTE that in the IUPAC nomenclature k0 already contains [M] so
! the k0(IUPAC)=k0*M here
! N=[0.75-1.27*log10(Fc)]
real, intent(in) :: k0,kinf,Fc,M,N
real :: rctroe
!-- local
real :: x,y, K0M ! temp variable
k0M = k0 * M
!- use the power function replacement, m**n == exp(n*log m)
!-k0M = a*(T/300.0)**(-2.3) * M
!-kinf = p*(T/300.0)**(-1.4)
! k0M = a * exp( b*log(t/300.0) ) * M
! kinf = p * exp( q*log(t/300.0) )
! factors for Fc:
y = k0M/kinf ! used also below
x = log10(y)/N
x = 1.0/( 1.0 + x*x )
!- F**x == exp(x*logF)
rctroe = k0M / ( 1.0 + y) * exp(x*log(Fc))
end function IUPAC_troe
!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
!OLD VOLFAC SYSTEM - WILL SOON BE DELETED FROM ALL CODE
! N2O5 -> nitrate calculation
!===========================================================================
! N2O5 -> nitrate calculation. Some constants for
! calculation of volume fraction of sulphate aerosol, and rate of uptake
! Mass of sulfate relative to sulfate+nitrate according to Riemer N,
! Vogel H, Vogel B, Schell B, Ackermann I, Kessler C, Hass H
! JGR 108 (D4): FEB 27 2003
!
!
! The first order reaction coefficient K (corrected for gas phase diffusion,
! Schwartz, 1986) is given by
!
! K= S* alpha* v/4 ACP:44
! alpha=sticking coeff. for N2O5 =0.02
! v=mean molecular speed for N2O5
! S=aerosol surfac
!
! The surface area of the aerosols can be calculated as
!
! S = V * surface/volume of aerosols
! V=volume fraction of sulphate (cm3 aerosol/cm3 air)
! (similar for nitrate and ammonium):
!
! e.g. simplest form (not used) would be:
! V = (so4 in moleculescm-3) x atw sulphate
! ---------------------------------------------------------
! AVOG X specific density of aerosols (assumed 2g/cm3*rh correction)
!
! Or, shorter, V = C x M0/(AVOG*rho)
!
! where C is conc. e.g. sulphate (molecule/cm3), M0 is molwt.
! We do not want to include concentrations or rho yet, so:
!
! Let VOL = M0/AVOG
!
! E12:47
! The surface/volume ratio is calculated using Whitby particle distribution
! with number mean radius rgn=0.068 and standard deviation (Sigma)=2.
! Then surface/volume=3/r * exp( -5/2 *(lnSigma)^2)=26.54
! 3* exp( -5/2 *(lnSigma)^2)=1.2648 for sigma=1.8
! (monodisperse aerosols; 4*pi*r^2/(4/3 pi*r^3)= 3/r =88.2)
!
! Then
! A = VOL * C * 1.24648 /(0.068e-6*rho)
! and
! K = VOL * C * 1.24648 /(0.068e-6*rho) * alpha* v/4
! Set
! VOLFAC= VOL*1.24648/0.068e-6 *alpha
! Then
! K = VOLFAC *C *v/(4*rho)
!
! rcmisc k=v/(4*rho)
!
! K = VOLFAC *rcmisc() *C
!
! According to Riemer et al, 2003, we weight the reaction probability
! according to the composition of the aerosol
!
! alpha(N2O5)=f*alpha1 +(1-f)alpha2 ACP:45
! alpha1=0.02
! alpha2=0.002
! f= Mso4/(Mso4+Mno3), M=aerosol mass concentration ACP:46
! N2O5 -> aerosol based upon based on Riemer 2003 and
! In testing, we had also tried a simple acounting for
! results shown in Riemer et al., 2009.
! We did not attempt to model OC, but simply reduce the rate by
! a factor of two to loosely account for this effect.
! June08 - changed from use of more accurate xnew to xn_2d, since
! surface area won't change so much, and anyway the uncertainties
! are large. (and xn_2d leads to fewer dependencies)
function RiemerN2O5() result(rate)
real, dimension(K1:K2) :: rate
real :: rc
real :: f ! Was f_Riemer
real, parameter :: EPSIL = 1.0 ! One mol/cm3 to stop div by zero
integer :: k
real :: xNO3 ! As the partitioning between fine and coarse is so difficult
! we include both in the nitrate used here.
do k = K1, K2
if ( rh(k) > 0.4) then
xNO3 = x(NO3_f,k) + x(NO3_c,k)
!mean molec speed of N2O5 (MW 108), m/s
! with density corrected for rh (moderate approx.)
rc = sqrt(3.0 * RGAS_J * itemp(k) / 0.108) & ! mol.speed (m/s)
/(4*(2.5 - rh(k)*1.25)) ! density
f = 96.0*x(SO4,k)/( 96.*x(SO4,k) + 62.0* xNO3 + EPSIL )
rate(k) = (0.9*f + 0.1) * rc * &
!TEST 0.5 * & ! v. loosely based on Reimer 2009
( VOLFACSO4 * x(SO4,k) + VOLFACNO3 * xNO3 &
+ VOLFACNH4 * x(NH4_f,k) ) !SIA aerosol surface
else
rate(k) = 0.0
end if
end do ! k
end function RiemerN2O5
!---------------------------------------------------------------------
! crude, but rate = xxxx . S , dvs S = rate / xxxx
function S_RiemerN2O5(k) result(S)
integer, intent(in) :: k
real :: S
real :: c, rate, gam, rho
real :: f ! Was f_Riemer
real, parameter :: EPSIL = 1.0 ! One mol/cm3 to stop div by zero
real :: xNO3 ! As the partitioning between fine and coarse is so difficult
! we include both in the nitrate used here.
xNO3 = x(NO3_f,k) + x(NO3_c,k)
!mean molec speed of N2O5 (MW 108), m/s
! with density corrected for rh (moderate approx.)
c = sqrt(3.0 * RGAS_J * itemp(k) / 0.108) ! mol.speed (m/s)
rho= (2.5 - rh(k)*1.25) ! density, g/cm3
f = 96.0*x(SO4,k)/( 96.*x(SO4,k) + 62.0* xNO3 + EPSIL )
rate= (0.9*f + 0.1) * c /(4.0*rho) * &
!TEST 0.5 * & ! v. loosely based on Reimer 2009
( VOLFACSO4 * x(SO4,k) + VOLFACNO3 * xNO3 &
+ VOLFACNH4 * x(NH4_f,k) ) !SIA aerosol surface
!rate = 1/4 . gamma. c . S
!rate in s-1
gam = ( 0.9*f + 0.1 )*0.02
S = 4.0 * rate/(gam * c ) ! will give S in m2
end function S_RiemerN2O5
!---------------------------------------------------------------------
function HydrolysisN2O5(ormethod) result(rate)
character(len=*), intent(in) , optional:: ormethod ! overrides default method if wanted
character(len=30), save :: method
real, dimension(K1:K2) :: rate
real :: rc
real :: f ! Was f_Riemer
real :: gam, gamSS,gamDU, S, S_ss, S_du, Rwet ! for newer methods
real, save :: g1 = 0.02, g2=0.002 ! gammas for 100% SO4, 100% NO3, default
! fixed-value gammas can be specified with e.g. Gamma:0.02. We derive
! the numerical value, gFix, from this string
real, save :: gFix= -999. ! fixed-value, from Gamma:xxxx values
character(len=20) :: gtxt ! for Gamma:xxxx values
real, parameter :: EPSIL = 1.0 ! One mol/cm3 to stop div by zero
integer :: k
real :: xNO3 ! As the partitioning between fine and coarse is so difficult
! we include both in the nitrate used here.
logical, save :: first_call = .true.
character(len=*), parameter :: dtxt = 'HydrolN2O5:'
if( first_call ) then
method = USES%n2o5HydrolysisMethod
if ( present(ormethod) ) method = ormethod ! WHEN is this used?
if( method(1:6)=="Gamma:" ) then
gtxt=method(7:)
read(gtxt,*) gFix
method='gFixed'
end if
end if
select case ( method )
case ( "ORIGRIEMER","OrigRiemer")
do k = K1, K2
if ( rh(k) > 0.4) then
xNO3 = x(NO3_f,k) + x(NO3_c,k)
!mean molec speed of N2O5 (MW 108), m/s
! with density corrected for rh (moderate approx.)
rc = sqrt(3.0 * RGAS_J * itemp(k) / 0.108) & ! mol.speed (m/s)
/(4*(2.5 - rh(k)*1.25)) ! density
f = 96.0*x(SO4,k)/( 96.*x(SO4,k) + 62.0* xNO3 + EPSIL )
rate(k) = (0.9*f + 0.1) * rc * &
!TEST 0.5 * & ! v. loosely based on Reimer 2009
( VOLFACSO4 * x(SO4,k) + VOLFACNO3 * xNO3 &
+ VOLFACNH4 * x(NH4_f,k) ) !SIA aerosol surface
else
rate(k) = 0.0
end if
end do ! k
!---------------------------------------
case ( "Smix", "SmixTen" )
!if ( DEBUG%RUNCHEM .and. DebugCell ) then
! write(*,*) dtxt//trim(method), rh(K2), S_m2m3(AERO%PM_F,K2) , S_m2m3(AERO%DU_C,K2)
!end if
do k = K1, K2
if ( rh(k) > 0.4) then ! QUERY???
xNO3 = x(NO3_f,k) + 0.27 * x(NO3_c,k) ! fracPM25, crude...
f = 96*x(SO4,k)/( 96*x(SO4,k) + 62* xNO3 + EPSIL )
S = S_m2m3(AERO%PM_F,k) !NOW all fine PM
gam = GammaN2O5(temp(k),rh(k),&
f,aero_fom(k),aero_fss(k),aero_fdust(k),aero_fbc(k))
rate(k) = UptakeRate(cN2O5(k),gam,S) !1=fine SIA ! +OM
!Add coarse model ! was SmixC
S_ss = S_m2m3(AERO%SS_C,k)
gamSS=GammaN2O5_EJSS(rh(k))
S_du = S_m2m3(AERO%DU_C,k)
! gamDU=0.01 ! for dust
! same as UptakeRate(cN2O5,gam,S), but easier to code here:
rate(k) = rate(k) + cN2O5(k)*(gamSS*S_ss+0.01*S_du)/4
! ToDo update gam for export. Currently at fine-mod only
!Coarse end
if( method == "SmixTen") then
gam = 0.1 * gam ! cf Brown et al, 2009!
rate(k) = 0.1 * rate(k)
end if
else
gam = 0.0 ! just for export
rate(k) = 0.0
end if
gamN2O5(k) = gam ! just for export
end do
!---------------------------------------
case ( "RiemerSIA", "RiemerSIAc3", "RiemerPMF", "mixedPMF" )
do k = K1, K2
if ( rh(k) > 0.4) then ! QUERY???
!Unfortunate hard-coding. Will fix in later stages
if( method == "RiemerSIA" ) then
!M24 S = S_m2m3(AERO%SIA_F,k)
!M24 Rwet = 0.5*DpgNw(AERO%SIA_F,k)
call StopAll(dtxt//'Deprecated:'//method)
else if( method == "RiemerSIAc3" ) then
!M24 S = S_m2m3(AERO%SIA_F,k)
!M24 Rwet = 0.5*DpgNw(AERO%SIA_F,k)
call StopAll(dtxt//'Deprecated:'//method)
if( first_call ) g2=g1/3.0 ! Chang notes that the factor of ten
! reduction was too high
! use whole aerosol area, but Riemer nitrate (factor 3 though):
else ! if( USES%n2o5HydrolysisMethod == "RiemerPMF" ) then
!.or. USES%n2o5HydrolysisMethod == "mixedPMF" ) then
S = S_m2m3(AERO%PM_F,k)
!Rwet = 0.5*DpgNw(AERO%PM_F,k)
! Chang notes that the factor of ten reduction was too high, and
! in PMF we also have EC, OM, etc.
if( first_call ) g2=g1/3.0
end if
xNO3 = x(NO3_f,k) + x(NO3_c,k)
!mean molec speed of N2O5 (MW 108), m/s
!c=cMolSpeed(temp(k),108.0)
f = 96.0*x(SO4,k)/( 96.*x(SO4,k) + 62.0* xNO3 + EPSIL )
gam = g1 * f + g2 * (1-f)
!rate(k) = UptakeRate(c,gam,S,Rwet) !1=fine SIA ! +OM
rate(k) = UptakeRate(cN2O5(k),gam,S) !1=fine SIA ! +OM
if( method == "mixedPMF" ) then
! 2) Add fine sea-salt
S = S_m2m3(AERO%SS_F,k)
!Rwet = 0.5*DpgNw(AERO%SS_F,k)
gam = GammaN2O5_EJSS(rh(k))
rate(k) = rate(k) + UptakeRate(cN2O5(k),gam,S) !1=fine SIA ! +OM
! 3) Add fine dust
S = S_m2m3(AERO%DU_F,k)
!Rwet = 0.5*DpgNw(AERO%DU_F,k)
gam = 0.01 ! Evans & Jacob, 2005
rate(k) = rate(k) + UptakeRate(cN2O5(k),gam,S) !1=fine SIA ! +OM
end if
else
rate(k) = 0.0
end if
end do ! k
!case ( "Gamma:0.002", "Gamma:0.05", "Gamma:0.005") ! Inspired by Brown et al. 2009
case ( "gFixed") ! Fixed gammas
do k = K1, K2
if ( rh(k) > 0.4) then ! QUERY???
gam = gFix ! Found above
S = S_m2m3(AERO%PM_F,k) !fine SIA +OM + ...
rate(k) = UptakeRate(cN2O5(k),gam,S)
else
rate(k) = 0.0
gam = 0.0 ! just for export
end if
gamN2O5(k) = gam ! just for export
end do ! k
case default
call StopAll("Unknown N2O5 hydrolysis"//method )
end select
first_call = .false.
end function HydrolysisN2O5
!---------------------------------------------------------------------
function xkaero() result(rate)
! Former rate for HNO3 -> NO3_c, not now used
real, dimension(K1:K2) :: rate
integer :: k
do k = K1, K2
if ( rh(k) > 0.9) then
rate(k) = 1.0e-4
else
rate(k) = 5.0e-6
end if
end do !k
end function xkaero
!---------------------------------------------------------------------
function kaero2() result(rate)
! New rate for HNO3 -> NO3_c, used only over sea squares
! as very crude simulation of sea-salt HNO3 interactions
! near surface (layer 16 ca. 600m).
real, dimension(K1:K2) :: rate
integer :: k
if ( Grid%is_mainlysea) then
rate(K1:15) = 0.0
do k = 16, K2
if ( rh(k) > 0.9) then
rate(k) = 1.0e-4
else
rate(k) = 5.0e-6
end if
end do !k
else ! over land
rate(K1:K2) = 0.0
end if
end function kaero2
!---------------------------------------------------------------------
function ec_ageing_rate() result(rate)
!.. Sets ageing rates for fresh EC [1/s] loosely based on Riemer etal. ACP(2004)
! See also Tsyro et al, JGR, 112, D23S19, 2007
! ---------------------------------
real, dimension(K1:K2) :: rate
if ( Grid%izen <= DAY_ZEN ) then ! daytime
rate (K2-2 : K2) = 3.5e-5 ! half-lifetime ~ 8h
rate (K1 : K2-3) = 1.4e-4 ! ~ 2h
else
rate (K1 : K2 ) = 9.2e-6 ! ~ 30h
end if
end function ec_ageing_rate
end module ChemFunctions_mod