hypoxia_srm_mod.h

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      MODULE mod_biology
!
!git $Id$
!================================================== Hernan G. Arango ===
!  Copyright (c) 2002-2025 The ROMS 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