Les routines nitrate.F90 et ammonium.F90 ont ete transportees de /meanflow a...

Les routines nitrate.F90 et ammonium.F90 ont ete transportees de /meanflow a extras/bio afin de simplifier la prise en compte des dependences (voir Makefile respectifs). Il n'est donc plus necessaire de modifier le code avant de changer de modele biologique.

src/extras/bio/Makefile

@@ -7,22 +7,31 @@ include ../../Rules.make
 
 LIB	= $(LIBDIR)/libbio$(buildtype).a
 
-DOCSRC	=  bio.F90 \
-bio_var.F90 bio_template.F90 bio_npzd.F90 bio_iow.F90 \
-          bio_sed.F90 bio_fasham.F90 bio_ismer.F90\
-          bio_save.F90
+DOCSRC	=  bio.F90	\
+bio_var.F90		\
+bio_template.F90	\
+bio_npzd.F90		\
+bio_iow.F90		\
+bio_sed.F90		\
+bio_fasham.F90		\
+bio_ismer.F90		\
+bio_save.F90		\
+nitrate.F90		\
+ammonium.F90
 
 OBJ   = \
-${LIB}(bio_var.o)		\
-${LIB}(bio_fluxes.o)		\
-${LIB}(bio_template.o)		\
-${LIB}(bio_npzd.o)		\
-${LIB}(bio_iow.o)		\
-${LIB}(bio_mab.o)		\
-${LIB}(bio_ismer.o)		\
-${LIB}(bio_fasham.o)		\
-${LIB}(bio_sed.o)		\
-${LIB}(bio_save.o)		\
+${LIB}(bio_var.o)	\
+${LIB}(bio_fluxes.o)	\
+${LIB}(bio_template.o)	\
+${LIB}(bio_npzd.o)	\
+${LIB}(bio_iow.o)	\
+${LIB}(bio_mab.o)	\
+${LIB}(bio_ismer.o)	\
+${LIB}(bio_fasham.o)	\
+${LIB}(bio_sed.o)	\
+${LIB}(bio_save.o)	\
+${LIB}(nitrate.o)	\
+${LIB}(ammonium.o)	\
 ${LIB}(bio.o)
 
 all: ${OBJ}

src/extras/bio/ammonium.F90

+!$Id: nitrate.F90,v 1.11 2007-01-06 11:49:15 kbk Exp $
+#include"cppdefs.h"
+!-----------------------------------------------------------------------
+!BOP
+!
+! !ROUTINE: The nitrate equation \label{sec:nitrate}
+!
+! !INTERFACE:
+   subroutine ammonium(nlev,dt,cnpar,nus,gams,cc)
+!
+! !DESCRIPTION:
+! This subroutine computes the balance of ammonium in the form
+!  \begin{equation}
+!   \label{SEq}
+!    \dot{S}
+!    = {\cal D}_S
+!    - \frac{1}{\tau^S_R}(S-S_{obs})
+!    \comma
+!  \end{equation}
+!  where $\dot{S}$ denotes the material derivative of the nitrate $N$, and
+!  ${\cal D}_N$ is the sum of the turbulent and viscous transport
+!  terms modelled according to
+!  \begin{equation}
+!   \label{DN}
+!    {\cal D}_N
+!    = \frstder{z}
+!     \left(
+!        \left( \nu^N_t + \nu^N \right) \partder{N}{z} - \tilde{\Gamma}_N
+!        \right)
+!    \point
+!  \end{equation}
+!  In this equation, $\nu^N_t$ and $\nu^N$ are the turbulent and
+!  molecular diffusivities of nitrate, respectively,
+!  and $\tilde{\Gamma}_N$
+!  denotes the non-local flux of nitrate, see
+!  \sect{sec:turbulenceIntro}. In the current version of GOTM,
+!  we set $\nu^N_t = \nu^\N$ for simplicity.
+!
+!  Horizontal advection is optionally
+!  included  (see {\tt obs.nml}) by means of prescribed
+!  horizontal gradients $\partial_xN$ and $\partial_yN$ and
+!  calculated horizontal mean velocities $U$ and $V$.
+!  Relaxation with the time scale $\tau^N_R$
+!  towards a precribed (changing in time)
+!  profile $N_{obs}$ is possible.
+
+!  Inner sources or sinks are not considered.
+!  The surface freshwater flux is given by means of the precipitation
+!  - evaporation data read in as $P-E$ through the {\tt airsea.nml} namelist:
+!  \begin{equation}
+!     \label{S_sbc}
+!    {\cal D}_S =  S (P-E),
+!    \qquad \mbox{at } z=\zeta,
+!  \end{equation}
+!  with $P-E$ given as a velocity (note that ${\cal D}_S$ is the flux in the
+!  direction of $z$, and thus positive for a \emph{loss} of nitrate) .
+!  Diffusion is numerically treated implicitly,
+!  see equations (\ref{sigmafirst})-(\ref{sigmalast}).
+!  The tri-diagonal matrix is solved then by a simplified Gauss elimination.
+!  Vertical advection is included, and it must be non-conservative,
+!  which is ensured by setting the local variable {\tt adv\_mode=0},
+!  see section \ref{sec:advectionMean} on page \pageref{sec:advectionMean}.
+!
+! !USES:
+
+   use meanflow,     only: avmola                       !CHG5
+   use meanflow,     only: h,u,v,w,amm,avh              !CHG5
+   use observations, only: dadx,dady,a_adv              !CHG5
+   use observations, only: w_adv_discr,w_adv_method
+   use observations, only: aprof,ARelaxTau              !CHG5
+   use airsea,       only: p_e
+   use util,         only: Dirichlet,Neumann
+   use util,         only: oneSided,zeroDivergence
+   use bio_var,      only: bio_model,numc
+
+   IMPLICIT NONE
+!
+
+! !INPUT PARAMETERS:
+
+
+!  number of vertical layers
+   integer, intent(in)                 :: nlev
+
+!   time step (s)
+   REALTYPE, intent(in)                :: dt
+
+!  numerical "implicitness" parameter
+   REALTYPE, intent(in)                :: cnpar
+
+!  diffusivity of nitrate (m^2/s) (!CHG3 same as salinity)
+   REALTYPE, intent(in)                :: nus(0:nlev)
+
+!  non-local salinity flux (psu m/s)
+   REALTYPE, intent(in)                :: gams(0:nlev)
+
+!  nitrate concentration after bio loop
+   REALTYPE, intent(in), optional      :: cc(1:numc,0:nlev)   !CHG3
+!
+! !REVISION HISTORY:
+!  Original author(s): Dany Dumont (dany_dumont@ete.inrs.ca)
+!
+!  $Log: nitrate.F90,v $
+!  Creation 1.0  2008-06-11 14:27:00  dd
+!  based on salinity.F90
+!
+!EOP
+!
+! !LOCAL VARIABLES:
+   integer                   :: adv_mode=0
+   integer                   :: posconc=1
+   integer                   :: i
+   integer                   :: DiffBcup,DiffBcdw
+   integer                   :: AdvBcup,AdvBcdw
+   REALTYPE                  :: DiffSup,DiffSdw
+   REALTYPE                  :: AdvSup,AdvSdw
+   REALTYPE                  :: Lsour(0:nlev)
+   REALTYPE                  :: Qsour(0:nlev)
+!
+!-----------------------------------------------------------------------
+!BOC
+!
+!  set boundary conditions
+   DiffBcup       = Neumann
+   DiffBcdw       = Neumann
+   DiffSup        = -1.*amm(nlev)*p_e     !CHG5
+   DiffSdw        = _ZERO_
+
+   AdvBcup       = zeroDivergence
+   AdvBcdw       = oneSided
+   AdvSup        = _ZERO_
+   AdvSdw        = _ZERO_
+
+!  compute total diffusivity
+   do i=0,nlev
+      avh(i)=nus(i)+avmola            !CHG5
+   end do
+
+!  add contributions to source term
+   Lsour=_ZERO_
+   Qsour=_ZERO_
+
+   do i=1,nlev
+!     from non-local turbulence
+#ifdef NONLOCAL
+      Qsour(i) = Qsour(i) - ( gams(i) - gams(i-1) )/h(i)
+#endif
+   end do
+
+!  ... and from lateral advection
+   if (a_adv) then
+      do i=1,nlev
+         Qsour(i) = Qsour(i) - u(i)*dadx(i) - v(i)*dady(i)        !CHG5
+      end do
+   end if
+
+! redefinir amm apres un cyle bio
+#ifdef BIO
+!do i=1,nlev
+!   !amm(i) = cc(6,i)     ! bio_model=2,4
+!   amm(i) = cc(9,i)     ! bio_model=6
+!end do
+   if (bio_model.eq.2) then
+      do i=1,nlev
+         amm(i) = cc(6,i)
+      end do
+   else if (bio_model.eq.4) then
+      do i=1,nlev
+         amm(i) = cc(6,i)
+      end do
+   else if (bio_model.eq.6) then
+      do i=1,nlev
+         amm(i) = cc(9,i)
+      end do
+   end if
+#endif
+
+!  do advection step
+   if (w_adv_method .ne. 0) then
+      call adv_center(nlev,dt,h,h,w,AdvBcup,AdvBcdw,                    &
+                          AdvSup,AdvSdw,w_adv_discr,adv_mode,amm)         !CHG5
+   end if
+
+!  do diffusion step
+   call diff_center(nlev,dt,cnpar,posconc,h,DiffBcup,DiffBcdw,          &
+                    DiffSup,DiffSdw,avh,LSour,Qsour,ARelaxTau,aprof,amm)   !CHG5
+
+   return
+   end subroutine ammonium
+!EOC
+
+!-----------------------------------------------------------------------
+! Copyright by the GOTM-team under the GNU Public License - www.gnu.org
+!-----------------------------------------------------------------------

src/extras/bio/nitrate.F90

+!$Id: nitrate.F90,v 1.11 2007-01-06 11:49:15 kbk Exp $
+#include"cppdefs.h"
+!-----------------------------------------------------------------------
+!BOP
+!
+! !ROUTINE: The nitrate equation \label{sec:nitrate}
+!
+! !INTERFACE:
+   subroutine nitrate(nlev,dt,cnpar,nus,gams,cc)
+!
+! !DESCRIPTION:
+! This subroutine computes the balance of nitrate in the form
+!  \begin{equation}
+!   \label{SEq}
+!    \dot{S}
+!    = {\cal D}_S
+!    - \frac{1}{\tau^S_R}(S-S_{obs})
+!    \comma
+!  \end{equation}
+!  where $\dot{S}$ denotes the material derivative of the nitrate $N$, and
+!  ${\cal D}_N$ is the sum of the turbulent and viscous transport
+!  terms modelled according to
+!  \begin{equation}
+!   \label{DN}
+!    {\cal D}_N
+!    = \frstder{z}
+!     \left(
+!        \left( \nu^N_t + \nu^N \right) \partder{N}{z} - \tilde{\Gamma}_N
+!        \right)
+!    \point
+!  \end{equation}
+!  In this equation, $\nu^N_t$ and $\nu^N$ are the turbulent and
+!  molecular diffusivities of nitrate, respectively,
+!  and $\tilde{\Gamma}_N$
+!  denotes the non-local flux of nitrate, see
+!  \sect{sec:turbulenceIntro}. In the current version of GOTM,
+!  we set $\nu^N_t = \nu^\N$ for simplicity.
+!
+!  Horizontal advection is optionally
+!  included  (see {\tt obs.nml}) by means of prescribed
+!  horizontal gradients $\partial_xN$ and $\partial_yN$ and
+!  calculated horizontal mean velocities $U$ and $V$.
+!  Relaxation with the time scale $\tau^N_R$
+!  towards a precribed (changing in time)
+!  profile $N_{obs}$ is possible.
+
+!  Inner sources or sinks are not considered.
+!  The surface freshwater flux is given by means of the precipitation
+!  - evaporation data read in as $P-E$ through the {\tt airsea.nml} namelist:
+!  \begin{equation}
+!     \label{S_sbc}
+!    {\cal D}_S =  S (P-E),
+!    \qquad \mbox{at } z=\zeta,
+!  \end{equation}
+!  with $P-E$ given as a velocity (note that ${\cal D}_S$ is the flux in the
+!  direction of $z$, and thus positive for a \emph{loss} of nitrate) .
+!  Diffusion is numerically treated implicitly,
+!  see equations (\ref{sigmafirst})-(\ref{sigmalast}).
+!  The tri-diagonal matrix is solved then by a simplified Gauss elimination.
+!  Vertical advection is included, and it must be non-conservative,
+!  which is ensured by setting the local variable {\tt adv\_mode=0},
+!  see section \ref{sec:advectionMean} on page \pageref{sec:advectionMean}.
+!
+! !USES:
+
+   use meanflow,     only: avmoln                       !CHG3
+   use meanflow,     only: h,u,v,w,nit,avh              !CHG3
+   use observations, only: dndx,dndy,n_adv              !CHG3
+   use observations, only: w_adv_discr,w_adv_method
+   use observations, only: nprof,NRelaxTau              !CHG3
+   use airsea,       only: p_e
+   use util,         only: Dirichlet,Neumann
+   use util,         only: oneSided,zeroDivergence
+   use bio_var,      only: bio_model,numc
+
+   IMPLICIT NONE
+!
+
+! !INPUT PARAMETERS:
+
+
+!  number of vertical layers
+   integer, intent(in)                 :: nlev
+
+!   time step (s)
+   REALTYPE, intent(in)                :: dt
+
+!  numerical "implicitness" parameter
+   REALTYPE, intent(in)                :: cnpar
+
+!  diffusivity of nitrate (m^2/s) (!CHG3 same as salinity)
+   REALTYPE, intent(in)                :: nus(0:nlev)
+
+!  non-local salinity flux (psu m/s)
+   REALTYPE, intent(in)                :: gams(0:nlev)
+
+!  nitrate concentration after bio loop
+!DD Not independent of the bio model, only works with 7 compartments model (Fasham)
+!   REALTYPE, intent(in), optional      :: cc(1:10,0:nlev)   !CHG3
+   REALTYPE, intent(in), optional      :: cc(1:numc,0:nlev)   !CHG3
+!
+! !REVISION HISTORY:
+!  Original author(s): Dany Dumont (dany_dumont@ete.inrs.ca)
+!
+!  $Log: nitrate.F90,v $
+!  Creation 1.0  2008-06-11 14:27:00  dd
+!  based on salinity.F90
+!
+!EOP
+!
+! !LOCAL VARIABLES:
+   integer                   :: adv_mode=0
+   integer                   :: posconc=1
+   integer                   :: i
+   integer                   :: DiffBcup,DiffBcdw
+   integer                   :: AdvBcup,AdvBcdw
+   REALTYPE                  :: DiffSup,DiffSdw
+   REALTYPE                  :: AdvSup,AdvSdw
+   REALTYPE                  :: Lsour(0:nlev)
+   REALTYPE                  :: Qsour(0:nlev)
+!
+!-----------------------------------------------------------------------
+!BOC
+!
+!  set boundary conditions
+   DiffBcup       = Neumann
+   DiffBcdw       = Neumann
+   DiffSup        = -1.*nit(nlev)*p_e     !CHG3
+   DiffSdw        = _ZERO_
+
+   AdvBcup       = zeroDivergence
+   AdvBcdw       = oneSided
+   AdvSup        = _ZERO_
+   AdvSdw        = _ZERO_
+
+!  compute total diffusivity
+   do i=0,nlev
+      avh(i)=nus(i)+avmoln            !CHG3
+   end do
+
+!  add contributions to source term
+   Lsour=_ZERO_
+   Qsour=_ZERO_
+
+   do i=1,nlev
+!     from non-local turbulence
+#ifdef NONLOCAL
+      Qsour(i) = Qsour(i) - ( gams(i) - gams(i-1) )/h(i)
+#endif
+   end do
+
+!  ... and from lateral advection
+   if (n_adv) then
+      do i=1,nlev
+         Qsour(i) = Qsour(i) - u(i)*dndx(i) - v(i)*dndy(i)        !CHG3
+      end do
+   end if
+
+! redefinir nit apres un cyle bio
+#ifdef BIO
+!do i=1,nlev
+!   !nit(i) = cc(7,i)    ! bio_model=2,4
+!   nit(i) =  cc(1,i)   ! bio_model=1,6
+!end do
+   if (bio_model.eq.1) then
+      do i=1,nlev
+         nit(i) = cc(1,i)
+      end do
+   else if (bio_model.eq.2) then
+      do i=1,nlev
+         nit(i) = cc(7,i)
+      end do
+   else if (bio_model.eq.4) then
+      do i=1,nlev
+         nit(i) = cc(7,i)
+      end do
+  else if (bio_model.eq.6) then
+      do i=1,nlev
+         nit(i) = cc(1,i)
+      end do
+   end if
+#endif
+
+!  do advection step
+   if (w_adv_method .ne. 0) then
+      call adv_center(nlev,dt,h,h,w,AdvBcup,AdvBcdw,                    &
+                          AdvSup,AdvSdw,w_adv_discr,adv_mode,nit) !CHG3
+   end if
+
+!  do diffusion step
+   call diff_center(nlev,dt,cnpar,posconc,h,DiffBcup,DiffBcdw,          &
+                    DiffSup,DiffSdw,avh,LSour,Qsour,NRelaxTau,nprof,nit)     !CHG3
+
+   return
+   end subroutine nitrate
+!EOC
+
+!-----------------------------------------------------------------------
+! Copyright by the GOTM-team under the GNU Public License - www.gnu.org
+!-----------------------------------------------------------------------

src/meanflow/Makefile

@@ -18,8 +18,6 @@ intpressure.F90		\
 friction.F90		\
 temperature.F90		\
 salinity.F90		\
-nitrate.F90		\
-ammonium.F90		\
 buoyancy.F90		\
 shear.F90	\
 stratification.F90	\
@@ -38,8 +36,6 @@ ${LIB}(intpressure.o)		\
 ${LIB}(friction.o)		\
 ${LIB}(temperature.o)		\
 ${LIB}(salinity.o)		\
-${LIB}(nitrate.o)		\
-${LIB}(ammonium.o)		\
 ${LIB}(stratification.o)	\
 ${LIB}(shear.o)	\
 ${LIB}(buoyancy.o)		\