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!$Id: m3d.F90,v 1.46 2009-09-04 11:50:33 bjb Exp $
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#include "cppdefs.h"
!-----------------------------------------------------------------------
!BOP
!
! !MODULE: m3d - 3D model component
!
! !INTERFACE:
   module m3d
!
! !DESCRIPTION:
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!  This module contains declarations for all variables related to 3D
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!  hydrodynamical calculations. Information about the calculation domain
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!  is included from the {\tt domain} module.
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!  The module contains public subroutines for initialisation, integration
!  and clean up of the 3D model component.
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!  The {\tt m3d} module is initialised in the routine {\tt init\_3d}, see
!  section \ref{sec-init-3d} described on page
!  \pageref{sec-init-3d}.
!  The actual calculation routines are called in {\tt integrate\_3d}
!  (see section \ref{sec-integrate-3d} on page \pageref{sec-integrate-3d}).
!  and are linked in from the library {\tt lib3d.a}.
!  After the simulation, the module is closed in {\tt clean\_3d}, see
!  section \ref{sec-clean-3d} on page \pageref{sec-clean-3d}.
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!
! !USES:
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   use exceptions
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   use parameters, only: avmmol
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   use domain, only: openbdy,maxdepth,vert_cord,az
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   use m2d, only: Am
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   use variables_2d, only: D,z,UEx,VEx
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#ifndef NO_BAROCLINIC
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   use temperature,only: init_temperature, do_temperature
   use salinity,   only: init_salinity, do_salinity
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   use eqstate,    only: init_eqstate, do_eqstate
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   use internal_pressure, only: init_internal_pressure, do_internal_pressure
   use internal_pressure, only: ip_method
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#endif
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#ifdef GETM_BIO
   use bio, only: bio_calc
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   use getm_bio, only: do_getm_bio
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#endif
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   use variables_3d
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   use advection_3d, only: init_advection_3d
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   use bdy_3d, only: init_bdy_3d, do_bdy_3d
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   use bdy_3d, only: bdy3d_tmrlx, bdy3d_tmrlx_ucut, bdy3d_tmrlx_max, bdy3d_tmrlx_min
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!  Necessary to use halo_zones because update_3d_halos() have been moved out 
!  temperature.F90 and salinity.F90 - should be changed at a later stage
   use halo_zones, only: update_3d_halo,wait_halo,D_TAG
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   IMPLICIT NONE
!
! !PUBLIC DATA MEMBERS:
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   integer                             :: M=1
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   REALTYPE                            :: cord_relax=_ZERO_
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   logical                             :: calc_temp=.true.
   logical                             :: calc_salt=.true.
   logical                             :: bdy3d=.false.
   integer                             :: bdyfmt_3d,bdyramp_3d
   character(len=PATH_MAX)             :: bdyfile_3d
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   REALTYPE                            :: ip_fac=_ONE_
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   integer                             :: vel_check=0
   REALTYPE                            :: min_vel=-4.,max_vel=4.
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!
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! !REVISION HISTORY:
!  Original author(s): Karsten Bolding & Hans Burchard
!
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! !LOCAL VARIABLES:
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   integer         :: vel_hor_adv=1,vel_ver_adv=1,vel_adv_split=0
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#ifdef NO_BAROCLINIC
   integer         :: ip_method
#endif
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   integer         :: ip_ramp=-1
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!EOP
!-----------------------------------------------------------------------

   contains

!-----------------------------------------------------------------------
!BOP
!
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! !IROUTINE: init_3d - initialise 3D related stuff \label{sec-init-3d}
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!
! !INTERFACE:
   subroutine init_3d(runtype,timestep,hotstart)
   IMPLICIT NONE
!
! !INPUT PARAMETERS:
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   integer, intent(in)                 :: runtype
   REALTYPE, intent(in)                :: timestep
   logical, intent(in)                 :: hotstart
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!
! !INPUT/OUTPUT PARAMETERS:
!
! !OUTPUT PARAMETERS:
!
! !DESCRIPTION:
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!  Here, the {\tt m3d} namelist is read from {\tt getm.inp}, and the
!  initialisation of variables is called (see routine {\tt init\_variables}
!  described on page \pageref{sec-init-variables}).
!  Furthermore, a number of consistency checks are made for the choices
!  of the momentum advection schemes. When higher-order advection schemes
!  are chosen for the momentum advection, the compiler option {\tt UV\_TVD}
!  has to be set. Here, the macro time step $\Delta t$ is calculated 
!  from the micro time step $\Delta t_m$ and the split factor {\tt M}.
!  Then, in order to have the vertical coordinate system present already here,
!  {\tt coordinates} (see page \pageref{sec-coordinates}) needs to be called,
!  in order to enable proper interpolation of initial values for 
!  potential temperature $\theta$ and salinity $S$ for cold starts. 
!  Those initial values are afterwards read in via the routines
!  {\tt init\_temperature} (page \pageref{sec-init-temperature}) and
!  {\tt init\_salinity} (page \pageref{sec-init-salinity}).
!  Finally, in order to prepare for the first time step, the momentum advection
!  and internal pressure gradient routines are initialised and the
!  internal pressure gradient routine is called.
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!
! !LOCAL VARIABLES:
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   integer         :: rc
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   NAMELIST /m3d/ &
             M,cnpar,cord_relax,                        &
             bdy3d,bdyfmt_3d,bdyramp_3d,bdyfile_3d,     &
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	     bdy3d_tmrlx,bdy3d_tmrlx_ucut,              &
             bdy3d_tmrlx_max,bdy3d_tmrlx_min,           &
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             vel_hor_adv,vel_ver_adv,vel_adv_split,     &
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             calc_temp,calc_salt,                       &
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             avmback,avhback,ip_method,ip_ramp,         &
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             vel_check,min_vel,max_vel
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!
!EOP
!-------------------------------------------------------------------------
!BOC
#ifdef DEBUG
   integer, save :: Ncall = 0
   Ncall = Ncall+1
   write(debug,*) 'init_3d() # ',Ncall
#endif

   LEVEL1 'init_3d'
!  Read 3D-model specific things from the namelist.
   read(NAMLST,m3d)
!   rewind(NAMLST)

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   if (avmback .lt. _ZERO_) then
      LEVEL2 "setting avmback to 0."
      avmback = _ZERO_
   end if
   if (avhback .lt. _ZERO_) then
      LEVEL2 "setting avhback to 0."
      avhback = _ZERO_
   end if

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! Allocates memory for the public data members - if not static
   call init_variables_3d(runtype)

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!  Sanity checks for advection specifications
   LEVEL2 'vel_hor_adv=   ',vel_hor_adv
   LEVEL2 'vel_ver_adv=   ',vel_ver_adv
   LEVEL2 'vel_adv_split= ',vel_adv_split
   if(vel_hor_adv .gt. 1) then
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#ifndef UV_TVD
      STDERR 'To run the model with higher order advection for momentum'
      STDERR 'you need to re-compile the model with the option -DUV_TVD.'
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      call getm_error("init_3d()","GETM needs recompilation")
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#endif
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   else
      vel_adv_split=-1
      if(vel_ver_adv .ne. 1) then
         LEVEL2 "setting vel_ver_adv to 1 - since vel_hor_adv is 1"
         vel_ver_adv=1
      end if
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   end if
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   LEVEL2 "horizontal: ",trim(adv_schemes(vel_hor_adv))," of momentum"
   LEVEL2 "vertical:   ",trim(adv_schemes(vel_ver_adv))," of momentum"

   select case (vel_adv_split)
      case (-1)
      case (0)
         select case (vel_hor_adv)
            case (2,3,4,5,6)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=0: vel_hor_adv not valid (2-6)")
         end select
         select case (vel_ver_adv)
            case (2,3,4,5,6)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=0: vel_ver_adv not valid (2-6)")
         end select
         LEVEL2 "1D split --> full u, full v, full w"
      case (1)
         select case (vel_hor_adv)
            case (2,3,4,5,6)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=1: vel_hor_adv not valid (2-6)")
         end select
         select case (vel_ver_adv)
            case (2,3,4,5,6)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=1: vel_ver_adv not valid (2-6)")
         end select
         LEVEL2 "1D split --> half u, half v, full w, half v, half u"
      case (2)
         select case (vel_hor_adv)
            case (2,7)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=2: vel_hor_adv not valid (2,7)")
         end select
         select case (vel_ver_adv)
            case (2,3,4,5,6)
            case default
               call getm_error("init_3d()", &
                    "vel_adv_split=2: vel_ver_adv not valid (2-6)")
         end select
         LEVEL2 "2D-hor, 1D-vert split --> full uv, full w"
      case default
   end select

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!  Sanity checks for bdy 3d
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   if (bdy3d .and. bdy3d_tmrlx) then
      LEVEL2 'bdy3d_tmrlx=.true.'
      LEVEL2 'bdy3d_tmrlx_max=   ',bdy3d_tmrlx_max
      LEVEL2 'bdy3d_tmrlx_min=   ',bdy3d_tmrlx_min
      LEVEL2 'bdy3d_tmrlx_ucut=  ',bdy3d_tmrlx_ucut
      if (bdy3d_tmrlx_min<_ZERO_ .or. bdy3d_tmrlx_min>_ONE_)          &
           call getm_error("init_3d()",                               &
           "bdy3d_tmrlx_min is out of valid range [0:1]")
      if (bdy3d_tmrlx_max<bdy3d_tmrlx_min .or. bdy3d_tmrlx_min>_ONE_) &
           call getm_error("init_3d()",                               &
           "bdy3d_tmrlx_max is out of valid range [bdy3d_tmrlx_max:1]")
      if (bdy3d_tmrlx_ucut<_ZERO_)                                    &
           call getm_error("init_3d()",                               &
           "bdy3d_tmrlx_max is out of valid range [0:inf[")
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   end if

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   LEVEL2 'ip_ramp=',ip_ramp

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   LEVEL2 'vel_check=',vel_check
   if (vel_check .ne. 0) then
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      LEVEL3 'doing sanity checks on velocities'
      LEVEL3 'min_vel=',min_vel
      LEVEL3 'max_vel=',max_vel
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      if (vel_check .gt. 0) then
         LEVEL3 'out-of-bound values result in termination of program'
      end if
      if (vel_check .lt. 0) then
         LEVEL3 'out-of-bound values result in warnings only'
      end if
   end if

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   dt = M*timestep
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#ifdef CONSTANT_VISCOSITY
   num=avmback
   nuh=avhback
#else
   num=1.e-15
   nuh=1.e-15
#endif
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!  Needed for interpolation of temperature and salinity
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   if (.not. hotstart) then
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      call start_macro()
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      call coordinates(vert_cord,cord_relax,maxdepth)
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      call hcc_check()
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   end if
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#ifndef NO_BAROCLINIC
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   if (runtype .eq. 3 .or. runtype .eq. 4) then
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      T = _ZERO_ ; S = _ZERO_ ; rho = _ZERO_
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      if(calc_temp) call init_temperature(1)
      if(calc_salt) call init_salinity(1)
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   end if
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#endif
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#ifndef NO_BAROCLINIC
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    if (runtype .eq. 3 .or. runtype .eq. 4) then
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      call init_eqstate()
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#ifndef PECS
      call do_eqstate()
#endif
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      if (runtype .ge. 3) call init_internal_pressure()
      if (runtype .eq. 3) call do_internal_pressure()
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      if (runtype .eq. 4) then
         call init_advection_3d(2)
      end if
   end if
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#endif
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   if (.not. openbdy) bdy3d=.false.
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   if (bdy3d) call init_bdy_3d()

#ifdef DEBUG
   write(debug,*) 'Leaving init_3d()'
   write(debug,*)
#endif
   return
   end subroutine init_3d
!EOC

!-----------------------------------------------------------------------
!BOP
!
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! !IROUTINE: integrate_3d - calls to do 3D model integration
! \label{sec-integrate-3d}
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!
! !INTERFACE:
   subroutine integrate_3d(runtype,n)
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   use getm_timers, only: tic, toc, TIM_INTEGR3D
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   IMPLICIT NONE
!
! !INPUT PARAMETERS:
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   integer, intent(in)                 :: runtype,n
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!
! !INPUT/OUTPUT PARAMETERS:
!
! !OUTPUT PARAMETERS:
!
! !DESCRIPTION:
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! This is a wrapper routine to call all 3D related subroutines.
! The call position for the {\tt coordinates} routine depends on 
! the compiler option 
! {\tt MUDFLAT}: If it is defined, then the 
! call to {\tt coordinates} construction is made such that drying and flooding
! is stable. If {\tt MUDFLAT} is not defined, then the adaptive grids with
! Lagrangian component which are currently under development are supported. 
! Both, drying and flooding and
! Lagrangian coordinates does not go together yet.
! The call sequence is as follows:
!
! \vspace{0.5cm}
! 
! \begin{tabular}{lll}
! {\tt start\_macro}           & initialising a 3d step & see page
! \pageref{sec-start-macro} \\
! {\tt do\_bdy\_3d}            & boundary conditions for $\theta$ and $S$ & see
! page \pageref{sec-do-bdy-3d} \\
! {\tt coordinates}            & layer heights ({\tt MUTFLAT} defined) & see
! page \pageref{sec-coordinates} \\
! {\tt bottom\_friction\_3d}   & bottom friction & see page
! \pageref{sec-bottom-friction-3d} \\
! {\tt do\_internal\_pressure} & internal pressure gradient & see page
! \pageref{sec-do-internal-pressure} \\
! {\tt uu\_momentum\_3d}       & layer-integrated $u$-velocity & see page
! \pageref{sec-uu-momentum-3d} \\
! {\tt vv\_momentum\_3d}       & layer-integrated $v$-velocity & see page
! \pageref{sec-vv-momentum-3d} \\
! {\tt coordinates}            & layer heights ({\tt MUTFLAT} not defined) & see
! page \pageref{sec-coordinates} \\
! {\tt ww\_momentum\_3d}       & grid-related vertical velocity & see page
! \pageref{sec-ww-momentum-3d} \\
! {\tt uv\_advect\_3d}         & momentum advection & see page
! \pageref{sec-uv-advect-3d} \\
! {\tt uv\_diffusion\_3d}      & momentum diffusion & see page
! \pageref{sec-uv-diffusion-3d} \\
! {\tt stresses\_3d}           & stresses (for GOTM) & see page
! \pageref{sec-stresses-3d} \\
! {\tt ss\_nn}                 & shear and stratification (for GOTM) & see page
! \pageref{sec-ss-nn} \\
! {\tt gotm}                   & interface and call to GOTM & see page
! \pageref{sec-gotm} \\
! {\tt do\_temperature}        & potential temperature equation & see page
! \pageref{sec-do-temperature} \\
! {\tt do\_salinity}           & salinity equation & see page
! \pageref{sec-do-salinity} \\
! {\tt do\_eqstate}            & equation of state & see page
! \pageref{sec-do-eqstate} \\
! {\tt do\_spm}                & suspended matter equation & see page 
! \pageref{sec-do-spm} \\
! {\tt do\_getm\_bio}          & call to GOTM-BIO (not yet released) & \\
! {\tt slow\_bottom\_friction} & slow bottom friction & see page
! \pageref{sec-slow-bottom-friction} \\
! {\tt slow\_advection}        & slow advection terms & see page
! \pageref{sec-slow-advection} \\
! {\tt slow\_diffusion}        & slow diffusion terms & see page
! \pageref{sec-slow-diffusion} \\
! {\tt slow\_terms}            & sum of slow terms & see page
! \pageref{sec-slow-terms} \\
! {\tt stop\_macro}            & finishing a 3d step & see page
! \pageref{sec-stop-macro}
! \end{tabular}
! 
! \vspace{0.5cm}
!
! Several calls are only executed for certain compiler options. At each
! time step the call sequence for the horizontal momentum equations is
! changed in order to allow for higher order accuracy for the Coriolis
! rotation.
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!
! !LOCAL VARIABLES:
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  logical, save              :: ufirst=.true.
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!
!EOP
!-------------------------------------------------------------------------
!BOC
#ifdef DEBUG
   integer, save :: Ncall = 0
   Ncall = Ncall+1
   write(debug,*) 'integrate_3d() # ',Ncall
#endif
   call start_macro()
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#ifndef NO_BAROCLINIC
#endif
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#ifdef MUDFLAT
   call coordinates(vert_cord,cord_relax,maxdepth)
#endif
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#ifndef NO_BOTTFRIC
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   if (kmax .gt. 1) then
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      call bottom_friction_3d()
   end if
#endif
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   call tic(TIM_INTEGR3D)
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   SS = _ZERO_
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   call toc(TIM_INTEGR3D)
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#ifndef NO_BAROCLINIC
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   call tic(TIM_INTEGR3D)
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   NN = _ZERO_
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   call toc(TIM_INTEGR3D)
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   if (runtype .eq. 4) call do_internal_pressure()
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#endif
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   call tic(TIM_INTEGR3D)
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   huo=hun
   hvo=hvn
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   ip_fac=_ONE_
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   if (ip_ramp .gt. 0) ip_fac=min( _ONE_ , n*_ONE_/ip_ramp)
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   call toc(TIM_INTEGR3D)
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#ifdef STRUCTURE_FRICTION
   call structure_friction_3d
#endif
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   if (ufirst) then
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      call uu_momentum_3d(n,bdy3d)
      call vv_momentum_3d(n,bdy3d)
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      ufirst=.false.
   else
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      call vv_momentum_3d(n,bdy3d)
      call uu_momentum_3d(n,bdy3d)
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      ufirst=.true.
   end if
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#ifndef MUDFLAT
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   call coordinates(vert_cord,cord_relax,maxdepth)
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#endif
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   if (kmax .gt. 1) then
      call ww_momentum_3d()
   end if
#ifndef NO_ADVECT
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   if (kmax .gt. 1) then
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      call uv_advect_3d(vel_hor_adv,vel_ver_adv,vel_adv_split)
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      if (Am .gt. _ZERO_) then
         call uv_diffusion_3d(Am)  ! Must be called after uv_advect_3d
      end if
   end if
#else
   STDERR 'NO_ADVECT 3D'
#endif
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   if (kmax .gt. 1) then
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#ifndef NO_BOTTFRIC
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      call stresses_3d()
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#endif
#ifndef CONSTANT_VISCOSITY
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#ifndef PARABOLIC_VISCOSITY
      call ss_nn()
#endif
      call gotm()
#endif
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   end if
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#ifndef NO_BAROCLINIC
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   if(runtype .eq. 4) then        ! prognostic T and S
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      if (calc_temp) call do_temperature(n)
      if (calc_salt) call do_salinity(n)
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!     The following is a bit clumpsy and should be changed when do_bdy_3d()
!     operates on individual fields and not as is the case now - on both
!     T and S.
#ifndef NO_BAROCLINIC
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      call tic(TIM_INTEGR3D)
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      if (bdy3d) call do_bdy_3d(0,T)
      if (calc_temp) then
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         call update_3d_halo(T,T,az,imin,jmin,imax,jmax,kmax,D_TAG)
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         call wait_halo(D_TAG)
         call mirror_bdy_3d(T,D_TAG)
      end if
      if (calc_salt) then
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         call update_3d_halo(S,S,az,imin,jmin,imax,jmax,kmax,D_TAG)
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         call wait_halo(D_TAG)
         call mirror_bdy_3d(S,D_TAG)
      end if
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      call toc(TIM_INTEGR3D)
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#endif
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   end if
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#endif
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#ifndef NO_BAROCLINIC
   if(runtype .eq. 4) then
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#ifndef PECS
      call do_eqstate()
#endif
   end if
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#endif
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#ifdef GETM_BIO
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   call tic(TIM_INTEGR3D)
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   if (bio_calc) call do_getm_bio(dt)
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   call toc(TIM_INTEGR3D)
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#endif

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   UEx=_ZERO_ ; VEx=_ZERO_
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#ifndef NO_BAROTROPIC
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   if (kmax .gt. 1) then
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#ifndef NO_BOTTFRIC
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      call slow_bottom_friction()
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#endif
#ifndef NO_ADVECT
#ifndef UV_ADV_DIRECT
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      call slow_advection()
      if (Am .gt. _ZERO_) then
         call slow_diffusion(Am) ! Has to be called after slow_advection.
      end if
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#endif
#endif
   end if
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   call slow_terms()
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#endif
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   call tic(TIM_INTEGR3D)
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   call stop_macro()
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   call toc(TIM_INTEGR3D)
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#ifdef DEBUG
     write(debug,*) 'Leaving integrate_3d()'
     write(debug,*)
#endif
   return
   end subroutine integrate_3d
!EOC

!-----------------------------------------------------------------------
!BOP
!
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! !IROUTINE: clean_3d - cleanup after 3D run \label{sec-clean-3d}
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!
! !INTERFACE:
   subroutine clean_3d()
   IMPLICIT NONE
!
! !INPUT PARAMETERS:
!
! !INPUT/OUTPUT PARAMETERS:
!
! !OUTPUT PARAMETERS:
!
! !DESCRIPTION:
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! Here, a call to the routine {\tt clean\_variables\_3d} which howewer
! does not do anything yet.
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!
! !LOCAL VARIABLES:
!
!EOP
!-----------------------------------------------------------------------
!BOC
#ifdef DEBUG
   integer, save :: Ncall = 0
   Ncall = Ncall+1
   write(debug,*) 'clean_3d() # ',Ncall
#endif

   call clean_variables_3d()

#ifdef DEBUG
     write(debug,*) 'Leaving clean_3d()'
     write(debug,*)
#endif
   return
   end subroutine clean_3d
!EOC

!-----------------------------------------------------------------------

   end module m3d

!-----------------------------------------------------------------------
! Copyright (C) 2000 - Hans Burchard and Karsten Bolding (BBH)         !
!-----------------------------------------------------------------------