diff --git a/Makefile b/Makefile
index 1f4a169aa2532e6b58ddf5bcde556f789704e9c4..28623501b0b09b47ad3acb725996b18ee68750f6 100644
--- a/Makefile
+++ b/Makefile
@@ -1,8 +1,8 @@
# Makefile for LAKE model
exec = lake.out
- FC=ifort#mpif90
- #FC=gfortran
+ #FC=ifort#mpif90
+ FC=gfortran
check_keys = # -check bounds -check pointers
debug_keys = #-g # debugger
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diff --git a/docs/users_guide.pdf b/docs/users_guide.pdf
index 0d3dbbb3e9974cc9b19b94f5b950c120a41dbd7f..2e48b49a3e3c283b72edaaabe95638d87dc10af3 100644
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diff --git a/docs/users_guide.synctex.gz b/docs/users_guide.synctex.gz
index 3ee64cefc80bcd2fd41b4556742e93e1b34971fc..b9d79467542bf77353acb749211e8685ca2f871a 100644
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diff --git a/docs/users_guide.tex b/docs/users_guide.tex
index fd7664dcbc8d788c30e9acbbf8c839d25ba6ce1a..7e023877a8f2623c95d94328580133bf074c8602 100644
--- a/docs/users_guide.tex
+++ b/docs/users_guide.tex
@@ -381,6 +381,8 @@ give significant speedup \\
\hline
\emph{backdiff} & Switch for background diffusivity by Hondzo and Stefan (1993); 1 -- off, 1 -- on \\
\hline
+\emph{backdiff0} & A multiplier in background diffusivity expression by Hondzo and Stefan (1993), relevant if \emph{backdiff}=1; if \emph{backdiff0}$<$0., then a reference value from original paper is used \\
+\hline
\emph{nManning} & Manning's coefficient, relevant for \emph{dyn\_pgrad}=5 \\
\hline
\emph{zero\_model} & Switch for zero-dimensional model: 0 -off, 1 - on \\
@@ -389,6 +391,14 @@ give significant speedup \\
\hline
\emph{soil\_meth\_prod} & Switch for new organics methane production under lakes: 1. - on, 0. - off \\
\hline
+\emph{VmaxCH4aeroboxid} & Maximal methane aerobic oxidation rate in Monod equation throughout water column; if \emph{VmaxCH4aeroboxid}$<$0., then a reference value is used\\
+\hline
+\emph{khsCH4} & Methane half-saturation constant in methane aerobic oxidation rate in Monod equation throughout water column; if \emph{khsCH4}$<$0., then a reference value is used \\
+\hline
+\emph{khsO2} & Oxygen half-saturation constant in methane aerobic oxidation rate in Monod equation throughout water column; if \emph{khsO2}$<$0., then a reference value is used \\
+\hline
+\emph{r0methprod} & A constant multiplier in the expression for methane production in sediments; if \emph{r0methprod}$<$0., then a reference value is used \\
+\hline
\emph{outflpar} & The treatment of effluent temperature: 0 - value at the outflow = cross-section mean; 1 - the cross-section mean = 0.5*(inflow value + outflow value); 2 - variables at the outflow are calculated using Lagrangian approach \\
\hline
\emph{sensflux0} & Sensible heat flux upwards, constant in time (relevant if PBLpar = 0), $W/m^2$ \\
diff --git a/driver_file.dat b/driver_file.dat
index 52a0fb23ee8285881047d0d01a947e2a66687b1e..91087485f9302313245b9d845fb213f6765400a5 100644
--- a/driver_file.dat
+++ b/driver_file.dat
@@ -1,2 +1,2 @@
# The file with parameters for driver of the Lake model
-setup/Mojai2016-2017_driver.dat
+setup/testlake_driver.dat
\ No newline at end of file
diff --git a/setup/testlake_setup.dat b/setup/testlake_setup.dat
index d96166daaf21952fbb039d519c93a54fe2a21d84..3612db5da2c28c6d56d8bffade3404ba2d60961f 100644
--- a/setup/testlake_setup.dat
+++ b/setup/testlake_setup.dat
@@ -150,10 +150,15 @@ pgrad 0.
nManning 5.E-2
horvisc 0.
backdiff 0
+backdiff0 8.17E-4
botfric 1
zero_model 0
thermokarst_meth_prod 0.
soil_meth_prod 1.
+VmaxCH4aeroboxid 1.15E-7
+khsCH4 3.75E-2
+khsO2 2.1E-2
+r0methprod 6.E-8
outflpar 0
#
sensflux0 100.
diff --git a/setup_file.dat b/setup_file.dat
index 0d70e77af85f4b9d218abc1500326efbad128192..077f3395b9568848c03cdadb82971a34dd727779 100644
--- a/setup_file.dat
+++ b/setup_file.dat
@@ -1,2 +1,2 @@
# The file with parameters for setup of the experiment
-setup/Mojai2016-2017_setup.dat
+setup/testlake_setup.dat
\ No newline at end of file
diff --git a/source/Makefile b/source/Makefile
index d0a1ff6a73d776b5538d341636f08c7a1e59df16..097572a9e06b5940d96a88f2103f10e70532f005 100644
--- a/source/Makefile
+++ b/source/Makefile
@@ -1,7 +1,7 @@
# Compiling source files of LAKE model
- FC=ifort#mpif90
- #FC=gfortran
+ #FC=ifort#mpif90
+ FC=gfortran
EXEC = lake.out
INCLPATHS =
@@ -25,9 +25,9 @@
#opt_keys = -fopenmp -O3 #-fp-model source
#check_keys = -g -Wall -Warray-temporaries -Wconversion -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow -finit-real=nan
#check_keys = -g -ffpe-trap=invalid,zero,overflow,denormal -fcheck=all -fbacktrace
- check_keys = -g -ffpe-trap=invalid,zero,overflow -fcheck=all -fbacktrace
+ check_keys = #-g -ffpe-trap=invalid,zero,overflow -fcheck=all -fbacktrace
#check_keys = -g -fcheck=all -fbacktrace
- #check_keys = -fbacktrace
+ check_keys = -fopenmp -O3 -fbacktrace
endif
objfiles_path = ../objfiles/
diff --git a/source/model/driving_params_mod.f90 b/source/model/driving_params_mod.f90
index b12b43fa355f82c75672416b8671e46f3458034f..060e5461748e14b3ba1a287b832c4cafd3be82e5 100644
--- a/source/model/driving_params_mod.f90
+++ b/source/model/driving_params_mod.f90
@@ -25,7 +25,7 @@ type, public :: intpar
end type
integer(kind=iintegers), parameter :: numder = 42 ! Number derived-type model integer controls handled in unified manner
-integer(kind=iintegers), parameter :: numder_real = 17 ! The same, but real controls
+integer(kind=iintegers), parameter :: numder_real = 22 ! The same, but real controls
real(kind=ireals), parameter :: missing_value = -999.
@@ -63,6 +63,11 @@ type(realpar), target :: nManning
type(realpar), target :: horvisc
type(realpar), target :: zserout
type(realpar), target :: pgrad
+type(realpar), target :: backdiff0
+type(realpar), target :: VmaxCH4aeroboxid
+type(realpar), target :: khsCH4
+type(realpar), target :: khsO2
+type(realpar), target :: r0methprod
real(kind=ireals) :: dttribupdate = missing_value
@@ -230,6 +235,11 @@ if (firstcall) then
dertypepar_real(15)%p => horvisc
dertypepar_real(16)%p => zserout
dertypepar_real(17)%p => pgrad
+ dertypepar_real(18)%p => backdiff0
+ dertypepar_real(19)%p => VmaxCH4aeroboxid
+ dertypepar_real(20)%p => khsCH4
+ dertypepar_real(21)%p => khsO2
+ dertypepar_real(22)%p => r0methprod
dertypepar(1)%p => stabfunc
dertypepar(2)%p => tribheat
@@ -292,6 +302,11 @@ if (firstcall) then
horvisc%name = 'horvisc'
zserout%name = 'zserout'
pgrad%name = 'pgrad'
+ backdiff0%name = 'backdiff0'
+ VmaxCH4aeroboxid%name = 'VmaxCH4aeroboxid'
+ khsCH4%name = 'khsCH4'
+ khsO2%name = 'khsO2'
+ r0methprod%name = 'r0methprod'
stabfunc%name = 'stabfunc' ;
diff --git a/source/model/lake_modules.f90 b/source/model/lake_modules.f90
index abc6914e0c9b031d17b2b34095baabe57c2e9b9e..1fde2a0ec85e27c5201305d8f8da1fd776b71745 100644
--- a/source/model/lake_modules.f90
+++ b/source/model/lake_modules.f90
@@ -1702,7 +1702,7 @@ real(kind=ireals), protected :: delta_Eq ! activation energy for methane oxidati
real(kind=ireals), protected :: Vmaxw ! reaction potential in oxygen-saturated Michaelis-Menten kinetics,
! after (Liikanen et al., 2002)
real(kind=ireals), protected :: k_ch40 ! half-saturation constant in oxygen-saturated Michaelis-Menten kinetics,
- ! after (Liikanen et al., 2002)
+ ! after (Liikanen et al., 2002)
real(kind=ireals), protected :: koxyg ! Methane oxidation constant in 1-st order kinetics, (Striegl et al., 1998)
@@ -1844,7 +1844,7 @@ real(kind=ireals), protected :: Chla_to_extinct !linear dependence coefficient o
contains
SUBROUTINE SET_METH_OXYG_CONSTANTS
-use DRIVING_PARAMS, only : nsoilcols_
+use DRIVING_PARAMS, only : nsoilcols_, r0methprod
implicit none
pH = 6. !The pH of the water in a lake, assumed to be constant
@@ -1967,6 +1967,10 @@ allocate(r0_methprod_phot (1:nsoilcols_%par))
allocate(r0_methprod_nonphot(1:nsoilcols_%par))
r0_methprod_phot (:) = 6.d-8 ! the constant for CH_4 production in photic zone, mol/(m**3*s)
r0_methprod_nonphot(:) = 6.d-8 ! the constant for CH_4 production below photic zone, mol/(m**3*s)
+if (r0methprod%par >= 0.) then
+ r0_methprod_phot (:) = r0methprod%par
+ r0_methprod_nonphot(:) = r0methprod%par
+endif
forg0 = 0.857 ! the constant in depth dependence of methane production rate
lambda_new_org = 3. !5. in Walter & Heimann model,
diff --git a/source/model/methane_mod.f90 b/source/model/methane_mod.f90
index 5d20cb9b62b147b1d5760195a8161bea5f51286a..b71925ae567380f036139e3d3bc1a75918c5fd07 100644
--- a/source/model/methane_mod.f90
+++ b/source/model/methane_mod.f90
@@ -1097,7 +1097,8 @@ endif ifdeep
SUBROUTINE METHANE_OXIDATION &
& (M, i_maxN, dt, ddz, h1, bathymwater, oxyg, qwater, DIC, Tw, qwateroxidtot, qwateroxidML)
- use METH_OXYG_CONSTANTS
+ use METH_OXYG_CONSTANTS, only : Vmaxw, k_ch4, k_ch40, k_o2, koxyg
+ use DRIVING_PARAMS, only : VmaxCH4aeroboxid, khsCH4, khsO2
use ARRAYS_BATHYM, only : bathym
use PHYS_FUNC, only : &
& REACPOT_ARRHEN
@@ -1130,8 +1131,20 @@ endif ifdeep
integer(kind=iintegers) :: i
real(kind=ireals) :: x, xo2, xch4, exc, D, temp_K ! Work variables
real(kind=ireals) :: qwater_old, oxyg_old
+ real(kind=ireals), save :: Vmax_CH4aeroboxid, khs_CH4, khs_O2
real(kind=ireals), allocatable :: qwaterold(:)
+ logical, save :: firstcall = .true.
+ if (firstcall) then
+ !Reference values of methane oxidation constants
+ Vmax_CH4aeroboxid = Vmaxw
+ khs_CH4 = k_CH4
+ khs_O2 = k_O2
+ if (VmaxCH4aeroboxid%par >= 0.) Vmax_CH4aeroboxid = VmaxCH4aeroboxid%par
+ if (khsCH4%par >= 0.) khs_CH4 = khsCH4%par
+ if (khsO2%par >= 0.) khs_O2 = khsO2%par
+ endif
+
allocate(qwaterold(1:M+1))
qwaterold(:) = qwater(:)
@@ -1141,8 +1154,8 @@ endif ifdeep
case (1)
! Full Michaelis-Menten
temp_K = Tw(i) + Kelvin0
- x = dt*Vmaxw & !REACPOT_ARRHEN(delta_Eq,temp_K,temp0,Vmaxw) &
- & /(k_o2 + oxyg(i))/(k_ch4 + qwater(i))
+ x = dt*Vmax_CH4aeroboxid & !REACPOT_ARRHEN(delta_Eq,temp_K,temp0,Vmaxw) &
+ & /(khs_O2 + oxyg(i))/(khs_CH4 + qwater(i))
D = 1. + 2.*x*(2.*qwater(i) + oxyg(i)) + &
& x*x*(2.*qwater(i) - oxyg(i))*(2.*qwater(i) - oxyg(i))
oxyg_old = oxyg(i)
@@ -1205,14 +1218,9 @@ endif ifdeep
endif
qwateroxidML = qwateroxidML/bathymwater(1)%area_int
-!do i = 1, M+1
-! if (qwater(i) > 1000.) then
-! write(*,*) 'Methane! in oxidation'
-! endif
-!enddo
-
deallocate(qwaterold)
-
+
+ if (firstcall) firstcall = .false.
END SUBROUTINE METHANE_OXIDATION
diff --git a/source/model/phys_func.f90 b/source/model/phys_func.f90
index e047353f4084702b5db9564d862cd98c90b0e06b..317e5ab729a078e3dc09d620da8ca489b58aaa99 100644
--- a/source/model/phys_func.f90
+++ b/source/model/phys_func.f90
@@ -1944,6 +1944,7 @@ END FUNCTION FP_THETA
use ARRAYS_GRID, only : gridspacing_type
use ARRAYS_WATERSTATE, only : waterstate_type
use ARRAYS_BATHYM, only : layers_type
+ use DRIVING_PARAMS, only : backdiff0
implicit none
!Input/output variables
real(kind=ireals) , intent(in) :: area
@@ -1956,6 +1957,16 @@ END FUNCTION FP_THETA
real(kind=ireals) :: x, y
real(kind=ireals), parameter :: C1 = 8.17E-4, C2 = 0.56, C3 = -0.43, xmin = 7.E-5
+ real(kind=ireals), save :: z !A multiplier in expression for background diffusivity
+ logical, save :: firstcall = .true.
+
+ if (firstcall) then
+ if (backdiff0%par >= 0.) then
+ z = backdiff0%par
+ else
+ z = C1 !default value
+ endif
+ endif
do i = 1, M
x = g/row0*(wst%row(i+1)-wst%row(i))/(ls%h1*gsp%ddz(i))
@@ -1968,11 +1979,10 @@ END FUNCTION FP_THETA
wst%lamw_back(i) = wst%lamw_back(i) * 1.E-4 !converting from cm**2/s to m**2/s
wst%lamw_back(i) = wst%lamw_back(i) * cw_m_row0
wst%lamw_back(i) = wst%lamw_back(i) * 5.E-1 !Calibration multiplyer
- !wst%lamw_back(i) = wst%lamw_back(i) * 5.E-1 !Calibration multiplyer, Lake Iseo
endif
enddo
- !print*, maxval(wst%lamw_back(:))
+ if (firstcall) firstcall = .false.
END SUBROUTINE DIFFMIN_HS
diff --git a/tools/plot_contour.py b/tools/plot_contour.py
index 9fde184ff8800af32d31ab95c7e01c1c54dd324c..ab3ae363806a3312bc3515ddbbec36a961ecc896 100644
--- a/tools/plot_contour.py
+++ b/tools/plot_contour.py
@@ -93,7 +93,7 @@ nmod_max = 12 #The last item in the list above, from the modeled data
#Constants
day_sec = 24.*60.*60.
-path = '../results/cuette/time_series/' # path to files
+path = '../results/testlake/time_series/' # path to files
#pathobs = os.path.expanduser('/media/victor/main/Files/main/observdata/Iseo/')
pathobs = os.path.expanduser('/home/victor/Files/main/observdata/Iseo/')
#pathobs = os.path.expanduser('/media/victor/main/Files/main/observdata/Kuivajarvi/Kuiva2014sept_campaign/')