MODULE mod_biology
!
!git $Id$
!svn $Id: hypoxia_srm_mod.h 1151 2023-02-09 03:08:53Z arango $
!================================================== Hernan G. Arango ===
!  Copyright (c) 2002-2023 The ROMS/TOMS Group                         !
!    Licensed under a MIT/X style license                              !
!    See License_ROMS.md                                               !
!=======================================================================
!                                                                      !
!  Parameters for Hypoxia Simple Respiration Model:                    !
!                                                                      !
!  BioIter        Maximum number of iterations to achieve convergence  !
!                   of the nonlinear solution.                         !
!  ResRate        Total biological respiration rate (1/day).           !
!                                                                      !
!=======================================================================
!
      USE mod_param
!
      implicit none
!
!  Set biological tracer identification indices.
!
      integer, allocatable :: idbio(:)  ! Biological tracers

      integer :: iOxyg                  ! Dissolved oxygen concentration
      integer :: idResR                 ! total respiration rate
!
!  Biological parameters.
!
      integer, allocatable :: BioIter(:)

      real(r8), allocatable :: ResRate(:)   ! repiration rate (1/day)
!
      CONTAINS
!
      SUBROUTINE initialize_biology
!
!=======================================================================
!                                                                      !
!  This routine sets several variables needed by the biology model.    !
!  It allocates and assigns biological tracers indices.                !
!                                                                      !
!=======================================================================
!
!  Local variable declarations
!
      integer :: i, ic
!
!-----------------------------------------------------------------------
!  Set number of biological tracers.
!-----------------------------------------------------------------------
!
      NBT=1

#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!-----------------------------------------------------------------------
!  Set sources and sinks biology diagnostic parameters.
!-----------------------------------------------------------------------
!
!  Set number of diagnostics terms.
!
      NDbio2d=1
      NDbio3d=0
!
!  Initialize biology diagnostic indices.
!
      iO2fx=1
#endif
!
!-----------------------------------------------------------------------
!  Allocate various module variables.
!-----------------------------------------------------------------------
!
      IF (.not.allocated(BioIter)) THEN
        allocate ( BioIter(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(ResRate)) THEN
        allocate ( ResRate(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF
!
!  Allocate biological tracer vector.
!
      IF (.not.allocated(idbio)) THEN
        allocate ( idbio(NBT) )
        Dmem(1)=Dmem(1)+REAL(NBT,r8)
      END IF

#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!  Allocate biological diagnostics vectors
!
      IF (.not.allocated(iDbio2)) THEN
        allocate ( iDbio2(NDbio2d) )
        Dmem(1)=Dmem(1)+REAL(NDbio2d,r8)
      END IF
#endif
!
!-----------------------------------------------------------------------
!  Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
      ic=NAT+NPT+NCS+NNS
      DO i=1,NBT
        idbio(i)=ic+i
      END DO
      ic=ic+1
      iOxyg=ic
!
      RETURN
      END SUBROUTINE initialize_biology

      END MODULE mod_biology