ecosim_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                                               !
!=======================================================================
!                                                                      !
!  Ecosim tracer parameters:                                           !
!                                                                      !
!  NBands         Number of spectral irradiance bands.                 !
!  NDbands        Number of spectral irrandiance bands to process for  !
!                   the diagnostics terms. It is possible to reduce    !
!                   its number for the analysis of few selected        !
!                   spectral bands (TODO).                             !
!  Nbac           Number of bacteria constituents.                     !
!  Ndom           Number of dissolved matter constituents.             !
!  Nfec           Number of fecal matter constituents.                 !
!  Nphy           Number of phytoplankton constituents.                !
!  Npig           Number of pigment constituents.                      !
!  PHY            Indices of phytoplankton species considered.         !
!  PIG            Phytoplankton-pigment matrix.                        !
!                                                                      !
!  EcoSim Model Phytoplaknton Parameters:                              !
!                                                                      !
!  HsNO3          Half-saturation for phytoplankton NO3 uptake         !
!                   (micromole_NO3/liter).                             !
!  HsNH4          Half-saturation for phytoplankton NH4 uptake         !
!                   (micromole_NH4/liter).                             !
!  HsSiO          Half-saturation for phytoplankton SiO uptake         !
!                   (micromole_SiO/liter).                             !
!  HsPO4          Half-saturation for phytoplankton PO4 uptake         !
!                   (micromole_PO4/liter).                             !
!  HsFe           Half-saturation for phytoplankton Fe uptake          !
!                  (micromole_Fe/liter).                               !
!  GtALG_max      Maximum 24 hour growth rate (1/day).                 !
!  PhyTbase       Phytoplankton temperature base for exponential       !
!                   response to temperature (Celsius).                 !
!  PhyTfac        Phytoplankton exponential temperature factor         !
!                   (1/Celsius).                                       !
!  BET_           Nitrate uptake inhibition for NH4 (l/micromole).     !
!  maxC2nALG      Maximum phytoplankton C:N ratio                      !
!                   (micromole_C/micromole_N).                         !
!  minC2nALG      Balanced phytoplankton C:N ratio                     !
!                   (micromole_C/micromole_N).                         !
!  C2nALGminABS   Absolute minimum phytoplankton C:N ratio             !
!                   (micromole_C/micromole_N).                         !
!  maxC2SiALG     Maximum phytoplankton C:Si ratio                     !
!                   (micromole_C/micromole_Si).                        !
!  minC2SiALG     Balanced phytoplankton C:Si ratio                    !
!                   (micromole_C/micromole_Si).                        !
!  C2SiALGminABS  Absolute minimum phytoplankton C:Si ratio            !
!                  (micromole_C/micromole_Si).                         !
!  maxC2pALG      Maximum phytoplankton C:P ratio                      !
!                   (micromole_C/micromole_P).                         !
!  minC2pALG      Balanced phytoplankton C:P ratio                     !
!                   (micromole_C/micromole_P).                         !
!  C2pALGminABS   Absolute minimum phytoplankton C:P ratio             !
!                   (micromole_C/micromole_P).                         !
!  maxC2FeALG     Maximum phytoplankton C:Fe ratio                     !
!                   (micromole_C/micromole_Fe).                        !
!  minC2FeALG     Balanced phytoplankton C:Fe ratio                    !
!                   (micromole_C/micromole_Fe).                        !
!  C2FeALGminABS  Absolute minimum phytoplankton C:Fe ratio            !
!                   (micromole_C/micromole_Fe).                        !
!  qu_yld         Maximum quantum yield                                !
!                   (micromole_C/micromole_quanta).                    !
!  E0_comp        Compensation light level (micromole_quanta).         !
!  E0_inhib       Light level for onset of photoinhibition             !
!                   (micromole_quanta).                                !
!  inhib_fac      Exponential decay factor for light limited growth    !
!                   (1/micromole_quanta).                              !
!  C2Chl_max      Maximum lighted limited (nutrient replete) C:Chl     !
!                   ratio (microgram_C/microgram_Chl).                 !
!  mxC2Cl         Rate of change in the lighted limited C:Chl ratio    !
!                   (microgram_C/microgram_Chl/micromole_quanta).      !
!  b_C2Cl         Minimum lighted limited (nutrient replete) C:Chl     !
!                   ratio (microgram_C/microgram_Chl).                 !
!  mxC2Cn         Rate of change in the nutrient limited C:Chl ratio   !
!                   [(ug_C/ug_Chl)/(umole_C/umole_N)].                 !
!  b_C2Cn         Minimum nutrient limited C:Chl ratio                 !
!                   (microgram_C/microgram_Chl).                       !
!  mxPacEff       Rate of change in package effect                     !
!                   [1/(microgram_C/microgram_Chl)].                   !
!  b_PacEff       Maximum package effect                               !
!                   [1/(microgram_C/microgram_Chl)].                   !
!  mxChlB         Rate of change in the Chl_b:Chl_a ratio              !
!                   [(ug_Chl_b/ug_Chl_a)/(ug_C/ug_Chl_a)].             !
!  b_ChlB         Maximum Chl_b:Chl_a ratio                            !
!                   (microgram_Chl_b/microgram_Chl_a).                 !
!  mxChlC         Rate of change in the Chl_c:Chl_a ratio              !
!                   [(ug_Chl_c/ug_Chl_a)/(ug_C/ug_Chl_a)].             !
!  b_ChlC         Maximum Chl_c:Chl_a ratio                            !
!                   (microgram_Chl_c/microgram_Chl_a).                 !
!  mxPSC          Rate of change in the PSC:Chl_a ratio                !
!                   [(ug_PSC/ug_Chl_a)/(ug_C/ug_Chl_a)].               !
!  b_PSC          Maximum PSC:Chl_a ratio                              !
!                  (microgram_Chl_c/microgram_Chl_a).                  !
!  mxPPC          Rate of change in the PPC:Chl_a ratio                !
!                   [(ug_PPC/ug_Chl_a)/(ug_C/ug_Chl_a)].               !
!  b_PPC          Maximum PPC:Chl_a ratio                              !
!                  (microgram_Chl_c/microgram_Chl_a).                  !
!  mxLPUb         Rate of change in the LPUb:Chl_a ratio               !
!                   [(ug_LPUb/ug_Chl_a)/(ug_C/ug_Chl_a)].              !
!  b_LPUb         Maximum LPUb:Chl_a ratio                             !
!                   (microgram_HPUb/microgram_Chl_a).                  !
!  mxHPUb         Rate of change in the HPUb:Chl_a ratio               !
!                   [(ug_HPUb/ug_Chl_a)/(ug_C/ug_Chl_a)].              !
!  b_HPUb         Maximum HPUb:Chl_a ratio                             !
!                   (microgram_HPUb/microgram_Chl_a).                  !
!  FecDOC         Proportion of grazing stress which is apportioned    !
!                   to DOM (nondimensional).                           !
!  FecPEL         Proportion of grazing stress which is apportioned    !
!                   to fecal pellets (nondimesional).                  !
!  FecCYC         Proportion of grazing stress which is apportioned    !
!                   to direct remineralization (nondimensional).       !
!  ExALG          Proportion of daily production that is lost to       !
!                   excretion (nondimensional).                        !
!  WS             Phytoplankton sinking speed (meters/day).            !
!  HsGRZ          Phytoplankton grazing parameter (nondimensional).    !
!  MinRefuge      Refuge Phytoplankton population (micromole_C/liter). !
!  RefugeDep      Maximum Refuge Phytoplankton depth (meters).         !
!  Norm_Vol       Normalized Volume factor (nondimensional).           !
!  Norm_Surf      Normalized surface area factor (nondimensional).     !
!  HsDOP          Half Saturation Constant for DOP uptake              !
!                   (micromole_DOP/liter).                             !
!  C2pALKPHOS     C:P ratio where DOP uptake begins                    !
!                   (micromole_C/micromole_P).                         !
!  HsDON          Half Saturation Constant for DON uptake              !
!                   (micromole_DON/liter).                             !
!  C2nNupDON      C:N ratio where DON uptake begins                    !
!                   (micromole_C/micromole_N).                         !
!                                                                      !
! Bacteria Parameters:                                                 !
!                                                                      !
!  HsDOC_ba       Half saturation constant for bacteria DOC uptake     !
!                   (micromole_DOC/liter).                             !
!  GtBAC_max      Maximum 24 hour bacterial growth rate (1/day).       !
!  BacTbase       Phytoplankton temperature base for exponential       !
!                   response to temperature, (Celsius).                !
!  BacTfac        Phytoplankton exponential temperature factor         !
!                   (1/Celsius).                                       !
!  C2nBAC         Carbon to Nitrogen ratio of Bacteria                 !
!                   (micromole_C/micromole_N).                         !
!  C2pBAC         Carbon to Phosphorus ratio of Bacteria               !
!                   (micromole_C/micromole_P).                         !
!  C2FeBAC        Carbon to Iron ratio of Bacteria                     !
!                   (micromole_C/micromole_Fe)                         !
!  BacDOC         Proportion of bacterial grazing stress which is      !
!                   apportioned to DOM (nondimensional).               !
!  BacPEL         Proportion of bacterial grazing stress which is      !
!                   apportioned to fecal pellets (nondimensional).     !
!  BacCYC         Proportion of bacterial grazing stress which is      !
!                   apportioned to direct remineralization             !
!                   (nondimensional).                                  !
!  ExBAC_c        Bacterial recalcitrant carbon excretion as a         !
!                   proportion of uptake (nondimensional)              !
!  ExBacC2N       Bacterial recalcitrant excretion carbon to nitrogen  !
!                   ratio (micromole_C/micromole_N).                   !
!  Bac_Ceff       Bacterial gross growth carbon efficiency             !
!                   (nondimensional).                                  !
!  RtNIT          Maximum bacterial nitrification rate (1/day).        !
!  HsNIT          Half saturation constant for bacterial nitrification !
!                   (micromole NH4/liter)                              !
!                                                                      !
! Dissolved Organic Matter Parameters:                                 !
!                                                                      !
!  cDOCfrac_c     Colored fraction of DOC production from              !
!                   phytoplankton and bacterial losses                 !
!                   (nondimensional).                                  !
!  RtUVR_DIC      UV degradation of DOC into DIC at 410 nanometers     !
!                   (micromole/meter/liter/hour).                      !
!  RtUVR_DIC      UV degradation of DOC into colorless labile DOC at   !
!                   410 nanometers (micromole/meter/liter/hour).       !
!                                                                      !
! Fecal and detritus Parameters:                                       !
!                                                                      !
!  WF             Fecal sinking flux (meters/day).                     !
!  RegTbase       Fecal regeneration temperature base for exponential  !
!                   response to temperature (Celsius).                 !
!  RegTfac        Fecal regeneration exponential temperature factor    !
!                   (1/Celsius).                                       !
!  RegCR          Fecal carbon regeneration rate (1/day).              !
!  RegNR          Fecal nitrogen regeneration rate (1/day).            !
!  RegSR          Fecal silica regeneration rate (1/day).              !
!  RegPR          Fecal phosphorus regeneration rate (1/day).          !
!  RegFR          Fecal iron regeneration rate (1/day).                !
!                                                                      !
!======================================================================!
!
      USE mod_param
      USE mod_scalars
!
      implicit none
!
!-----------------------------------------------------------------------
!  Bio-optical EcoSim parameters.
!-----------------------------------------------------------------------
!
      integer, parameter :: nbands = 60      ! spectral bands
      integer, parameter :: nbac = 1         ! bacteria constituents
      integer, parameter :: ndom = 2         ! DOM constituents
      integer, parameter :: nfec = 2         ! Fecal constituents
      integer, parameter :: nphy = 4         ! Phytoplankton groups
      integer, parameter :: npig = 7         ! Pigments
!
!  Set number of spectral irrandiance bands to process for the
!  diagnostics terms. It is possible to reduce its number for the
!  analysis of few selected spectral bands (TODO).
!
      integer :: ndbands = nbands
!
!  Determine number of EcoSim biological tracer. Currently, there is a
!  maximum of seven phytoplankton species and seven different pigments:
!
! [1] small diatom           [1] chlorophyll-a
! [2] large diatom           [2] chlorophyll-b
! [3] small dinoflagellate   [3] chlorophyll-c
! [4] large dinoflagellate   [4] photosythetic carotenoids
! [5] synechococcus          [5] photoprotective carotenoids
! [6] small prochlorococcus  [6] low  urobilin phycoeurythin carotenoids
! [7] large prochlorococcus  [7] high urobilin phycoeurythin carotenoids
!
!  The phytoplankton/pigment matrix is as follows:
!
!               P h y t o p l a n k t o n
!              [1]   [2]   [3]   [4]   [5]   [6]   [7]
!
!       t [7]   0     0     0     0     1     0     0
!       n [6]   0     0     0     0     0     0     0
!       e [5]   1     1     1     1     1     1     1
!       m [4]   1     1     1     1     0     0     0
!       g [3]   1     1     1     1     0     0     0
!       i [2]   0     0     0     0     0     1     1
!       P [1]   1     1     1     1     1     1     1
!
      integer, parameter, dimension(7,7) :: pig = reshape (             &
     &                                      (/ 1, 1, 1, 1, 1, 1, 1,     &
     &                                         0, 0, 0, 0, 0, 1, 1,     &
     &                                         1, 1, 1, 1, 0, 0, 0,     &
     &                                         1, 1, 1, 1, 0, 0, 0,     &
     &                                         1, 1, 1, 1, 1, 1, 1,     &
     &                                         0, 0, 0, 0, 0, 0, 0,     &
     &                                         0, 0, 0, 0, 1, 0, 0 /),  &
     &                                      (/ 7, 7 /) )
!
!  Set phytoplankton species to consider (see above classification):
!
      integer, parameter, dimension(Nphy) :: phy = (/ 1, 2, 4, 5 /)
!
!-----------------------------------------------------------------------
!  Set biological tracer identification indices.
!-----------------------------------------------------------------------
!
      integer, allocatable :: idbio(:)  ! Biological tracers
 
      integer :: ibacc(nbac)        ! Bacteria, Carbon group
      integer :: ibacn(nbac)        ! Bacteria, Nitrogen group
      integer :: ibacp(nbac)        ! Bacteria, Phosphorous group
      integer :: ibacf(nbac)        ! Bacteria, Iron group
      integer :: icdmc(ndom)        ! Color degradational matter
      integer :: idomc(ndom)        ! DOM, Carbon group
      integer :: idomn(ndom)        ! DOM, Nitrogen group
      integer :: idomp(ndom)        ! DOM, Phosphorous group
      integer :: ifecc(nfec)        ! Fecal matter, Carbon group
      integer :: ifecn(nfec)        ! Fecal matter, Nitrogen group
      integer :: ifecp(nfec)        ! Fecal matter, Phosphorous group
      integer :: ifecf(nfec)        ! Fecal matter, Iron group
      integer :: ifecs(nfec)        ! Fecal matter, Silica group
      integer :: iphyc(nphy)        ! Phytoplankton, Carbon group
      integer :: iphyn(nphy)        ! Phytoplankton, Nitrogen group
      integer :: iphyp(nphy)        ! Phytoplankton, Phosphorous group
      integer :: iphyf(nphy)        ! Phytoplankton, Iron group
      integer :: iphys(nphy)        ! Phytoplankton, Silica group
      integer :: ipigs(nphy,npig)   ! Phytoplankton, pigment group
      integer :: ino3_              ! Nitrate concentration
      integer :: inh4_              ! Ammonium concentration
      integer :: ipo4_              ! Phosphate concentration
      integer :: ifeo_              ! Iron concentration
      integer :: isio_              ! Silica concentration
      integer :: idic_              ! Dissolved inorganic Carbon
      integer :: firstpig           ! Index of first tracer pigment
 
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!-----------------------------------------------------------------------
!  Set biological diagnostic identification indices.
!-----------------------------------------------------------------------
!
!  Center wavelenght of spectral irradiance bands for diagnostic
!  terms.
!
      real(r8), allocatable :: dia_light(:)
!
!  3D diagnostic variable IDs.
!
      integer, allocatable :: idbio3(:)
!
      integer  :: idspir = 1        ! surface spectral irradiance
!
!  4D diagnostic variable IDs.
!
      integer, allocatable :: idbio4(:)
!
      integer  :: iddirr = 1        ! downward irradiance (Ed)
      integer  :: idsirr = 2        ! scalar irradiance (E0)
      integer  :: idlatt = 3        ! light attenuation (Kd)
      integer  :: idaphy = 4        ! PHY absorption (aPHYN_at)
      integer  :: idadet = 5        ! detrital absorption (aDET)
      integer  :: idacdc = 6        ! CDC absorption (aCDC)
      integer  :: idacos = 7        ! avg cosine zenith angle (avgcos)
      integer  :: idbphy = 8        ! PHY backscattering (bb_phy)
      integer  :: idsphy = 9        ! PHY scattering (b_phy)
      integer  :: idbtot = 10       ! total backscattering (bb_tot)
      integer  :: idstot = 11       ! total scattering (b_tot)
#endif
!
!-----------------------------------------------------------------------
!  EcoSim group names used on standard output.
!-----------------------------------------------------------------------
!
      character (len=16), dimension(Nbac) :: bacname
      character (len=11), dimension(Ndom) :: domname
      character (len=13), dimension(Nfec) :: fecname
      character (len=21), dimension(Nphy) :: phyname
 
      character (len=39), dimension(7) :: pigname =                     &
     &          (/ 'chlorophyll-a                          ',           &
     &             'chlorophyll-b                          ',           &
     &             'chlorophyll-c                          ',           &
     &             'photosynthetic carotenoids             ',           &
     &             'photoprotective carotenoids            ',           &
     &             'low urobilin phycoeurythin carotenoids ',           &
     &             'high urobilin phycoeurythin carotenoids' /)
!
!-----------------------------------------------------------------------
!  Standard input parameters.
!-----------------------------------------------------------------------
!
!  Number of biological iterations.
!
      integer, allocatable :: bioiter(:)
!
!  Control flags.
!
      logical, allocatable :: rtuvr_flag(:)
      logical, allocatable :: nfix_flag(:)
      logical, allocatable :: regen_flag(:)
!
!  Phytoplankton parameters.
!
      real(r8), allocatable :: hsno3(:,:)
      real(r8), allocatable :: hsnh4(:,:)
      real(r8), allocatable :: hssio(:,:)
      real(r8), allocatable :: hspo4(:,:)
      real(r8), allocatable :: hsfe(:,:)
      real(r8), allocatable :: gtalg_max(:,:)
      real(r8), allocatable :: phytbase(:,:)
      real(r8), allocatable :: phytfac(:,:)
      real(r8), allocatable :: bet_(:,:)
      real(r8), allocatable :: maxc2nalg(:,:)
      real(r8), allocatable :: minc2nalg(:,:)
      real(r8), allocatable :: c2nalgminabs(:,:)
      real(r8), allocatable :: maxc2sialg(:,:)
      real(r8), allocatable :: minc2sialg(:,:)
      real(r8), allocatable :: c2sialgminabs(:,:)
      real(r8), allocatable :: maxc2palg(:,:)
      real(r8), allocatable :: minc2palg(:,:)
      real(r8), allocatable :: c2palgminabs(:,:)
      real(r8), allocatable :: maxc2fealg(:,:)
      real(r8), allocatable :: minc2fealg(:,:)
      real(r8), allocatable :: c2fealgminabs(:,:)
      real(r8), allocatable :: qu_yld(:,:)
      real(r8), allocatable :: e0_comp(:,:)
      real(r8), allocatable :: e0_inhib(:,:)
      real(r8), allocatable :: inhib_fac(:,:)
      real(r8), allocatable :: c2chl_max(:,:)
      real(r8), allocatable :: mxc2cl(:,:)
      real(r8), allocatable :: b_c2cl(:,:)
      real(r8), allocatable :: mxc2cn(:,:)
      real(r8), allocatable :: b_c2cn(:,:)
      real(r8), allocatable :: mxpaceff(:,:)
      real(r8), allocatable :: b_paceff(:,:)
      real(r8), allocatable :: mxchlb(:,:)
      real(r8), allocatable :: b_chlb(:,:)
      real(r8), allocatable :: mxchlc(:,:)
      real(r8), allocatable :: b_chlc(:,:)
      real(r8), allocatable :: mxpsc(:,:)
      real(r8), allocatable :: b_psc(:,:)
      real(r8), allocatable :: mxppc(:,:)
      real(r8), allocatable :: b_ppc(:,:)
      real(r8), allocatable :: mxlpub(:,:)
      real(r8), allocatable :: b_lpub(:,:)
      real(r8), allocatable :: mxhpub(:,:)
      real(r8), allocatable :: b_hpub(:,:)
      real(r8), allocatable :: fecdoc(:,:)
      real(r8), allocatable :: fecpel(:,:,:)
      real(r8), allocatable :: feccyc(:,:)
      real(r8), allocatable :: exalg(:,:)
      real(r8), allocatable :: ws(:,:)
      real(r8), allocatable :: hsgrz(:,:)
      real(r8), allocatable :: minrefuge(:,:)
      real(r8), allocatable :: refugedep(:,:)
      real(r8), allocatable :: norm_vol(:,:)
      real(r8), allocatable :: norm_surf(:,:)
      real(r8), allocatable :: hsdop(:,:)
      real(r8), allocatable :: c2palkphos(:,:)
      real(r8), allocatable :: hsdon(:,:)
      real(r8), allocatable :: c2nnupdon(:,:)
!
!  Bacteria parameters.
!
      real(r8), allocatable :: hsdoc_ba(:,:)
      real(r8), allocatable :: gtbac_max(:,:)
      real(r8), allocatable :: bactbase(:,:)
      real(r8), allocatable :: bactfac(:,:)
      real(r8), allocatable :: c2nbac(:)
      real(r8), allocatable :: c2pbac(:)
      real(r8), allocatable :: c2febac(:)
      real(r8), allocatable :: bacdoc(:)
      real(r8), allocatable :: bacpel(:)
      real(r8), allocatable :: baccyc(:)
      real(r8), allocatable :: exbac_c(:)
      real(r8), allocatable :: exbacc2n(:)
      real(r8), allocatable :: bac_ceff(:)
      real(r8), allocatable :: rtnit(:)
      real(r8), allocatable :: hsnit(:)
!
!  DOM parameters.
!
      real(r8), allocatable :: cdocfrac_c(:,:)
      real(r8), allocatable :: rtuvr_dic(:)
      real(r8), allocatable :: rtuvr_doc(:)
!
!  Fecal parameters.
!
      real(r8), allocatable :: wf(:,:)
      real(r8), allocatable :: regtbase(:,:)
      real(r8), allocatable :: regtfac(:,:)
      real(r8), allocatable :: regcr(:,:)
      real(r8), allocatable :: regnr(:,:)
      real(r8), allocatable :: regsr(:,:)
      real(r8), allocatable :: regpr(:,:)
      real(r8), allocatable :: regfr(:,:)
!
!-----------------------------------------------------------------------
!  Internal parameters.
!-----------------------------------------------------------------------
!
!  Spectral band width used in light calculations.
!
      real(r8), parameter :: dlam  = 5.0_r8
!
!  Flags used for testing purposes.
!
      real(r8), parameter :: small  = 1.0e-6_r8
      real(r8), parameter :: vsmall = 1.0e-14_r8
      real(r8), parameter :: larger = 1.0e+10_r8
      real(r8), parameter :: vlarge = 1.0e+50_r8
!
!  Array indexes for frequently used constituents.
!
      integer, parameter :: ilab=1    ! labile index for DOC.
      integer, parameter :: irct=2    ! relict index for DOC.
      integer, parameter :: ichl=1    ! pigment index for chlorophyll-a
      integer, parameter :: isfc=1    ! slow fecal pellet index
      integer, parameter :: iffc=2    ! fast fecal pellet index
!
!  Phytoplankton calculated paramters.
!
      real(r8), allocatable :: imaxc2nalg(:,:)   ! inverse C2nALG
      real(r8), allocatable :: imaxc2sialg(:,:)  ! inverse C2SiALG
      real(r8), allocatable :: imaxc2palg(:,:)   ! inverse C2pALG
      real(r8), allocatable :: imaxc2fealg(:,:)  ! inverse C2FeALG
!
!  Bacteria calculated parameters.
!
      real(r8), allocatable :: n2cbac(:)
      real(r8), allocatable :: p2cbac(:)
      real(r8), allocatable :: fe2cbac(:)
      real(r8), allocatable :: hsnh4_ba(:,:)
      real(r8), allocatable :: hspo4_ba(:,:)
      real(r8), allocatable :: hsfe_ba(:,:)
      real(r8), allocatable :: r_exbac_c(:)
      real(r8), allocatable :: exbac_n(:)
      real(r8), allocatable :: frac_exbac_n(:)
      real(r8), allocatable :: i_bac_ceff(:)
!
!  Absorption parameters.
!
      real(r8), dimension(NBands) :: wavedp   ! a and b factor
      real(r8), dimension(Ndom) :: adoc410    ! CDM absorption at 410
      real(r8), dimension(Ndom) :: adoc300    ! CDM absorption at 300
!
      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, j, ng
 
      character (len=21), dimension(7) :: PhyGroups =                   &
     &                                 (/ 'small diatom         ',      &
     &                                    'large diatom         ',      &
     &                                    'small dinoflagellate ',      &
     &                                    'large dinoflagellate ',      &
     &                                    'synechococcus        ',      &
     &                                    'small prochlorococcus',      &
     &                                    'large prochlorococcus' /)
!
!-----------------------------------------------------------------------
!  Determine number of biological tracers.
!-----------------------------------------------------------------------
!
!       Nutrients: NO3, NO4, PO4, FeO, SiO, DIC  (6)
!        Bacteria: C, Fe, N, P                   (Nbac*4)
!             DOM: CDM, C, N, P                  (Ndom*4)
!           Fecal: C, Fe, N, P, Si               (Nfec*5)
!    Phytoplakton: C, Fe, N, P                   (Nphy*4 + Si)
!        Pigments: look table
!
      nbt=6+(nbac*4)+(ndom*4)+(nfec*5)+(nphy*4)
!
!  Add phytoplankton silica constituents.
!
      DO i=1,nphy
        IF (phy(i).le.2) nbt=nbt+1
      END DO
!
!  Add pigments.  Check phytoplankton-pigment table for values greater
!  than zero.
!
      DO j=1,npig
        DO i=1,nphy
          IF (pig(phy(i),j).eq.1) nbt=nbt+1
        END DO
      END DO
 
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!-----------------------------------------------------------------------
!  Set sources and sinks biology number of diagnostic terms.
!-----------------------------------------------------------------------
!
      ndbio3d=1
      ndbio4d=11
#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(rtuvr_flag)) THEN
        allocate ( rtuvr_flag(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(nfix_flag)) THEN
        allocate ( nfix_flag(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(regen_flag)) THEN
        allocate ( regen_flag(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
!
      IF (.not.allocated(hsno3)) THEN
        allocate ( hsno3(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsnh4)) THEN
        allocate ( hsnh4(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hssio)) THEN
        allocate ( hssio(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hspo4)) THEN
        allocate ( hspo4(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsfe)) THEN
        allocate ( hsfe(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(gtalg_max)) THEN
        allocate ( gtalg_max(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(phytbase)) THEN
        allocate ( phytbase(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(phytfac)) THEN
        allocate ( phytfac(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(bet_)) THEN
        allocate ( bet_(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(maxc2nalg)) THEN
        allocate ( maxc2nalg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(minc2nalg)) THEN
        allocate ( minc2nalg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2nalgminabs)) THEN
        allocate ( c2nalgminabs(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(maxc2sialg)) THEN
        allocate ( maxc2sialg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(minc2sialg)) THEN
        allocate ( minc2sialg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2sialgminabs)) THEN
        allocate ( c2sialgminabs(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(maxc2palg)) THEN
        allocate ( maxc2palg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(minc2palg)) THEN
        allocate ( minc2palg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2palgminabs)) THEN
        allocate ( c2palgminabs(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(maxc2fealg)) THEN
        allocate ( maxc2fealg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(minc2fealg)) THEN
        allocate ( minc2fealg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2fealgminabs)) THEN
        allocate ( c2fealgminabs(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(qu_yld)) THEN
        allocate ( qu_yld(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(e0_comp)) THEN
        allocate ( e0_comp(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(e0_inhib)) THEN
        allocate ( e0_inhib(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(inhib_fac)) THEN
        allocate ( inhib_fac(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2chl_max)) THEN
        allocate ( c2chl_max(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxc2cl)) THEN
        allocate ( mxc2cl(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_c2cl)) THEN
        allocate ( b_c2cl(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxc2cn)) THEN
        allocate ( mxc2cn(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_c2cn)) THEN
        allocate ( b_c2cn(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxpaceff)) THEN
        allocate ( mxpaceff(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_paceff)) THEN
        allocate ( b_paceff(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxchlb)) THEN
        allocate ( mxchlb(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_chlb)) THEN
        allocate ( b_chlb(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxchlc)) THEN
        allocate ( mxchlc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_chlc)) THEN
        allocate ( b_chlc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxpsc)) THEN
        allocate ( mxpsc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_psc)) THEN
        allocate ( b_psc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxppc)) THEN
        allocate ( mxppc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_ppc)) THEN
        allocate ( b_ppc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxlpub)) THEN
        allocate ( mxlpub(nphy,ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(b_lpub)) THEN
        allocate ( b_lpub(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(mxhpub)) THEN
        allocate ( mxhpub(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(b_hpub)) THEN
        allocate ( b_hpub(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(fecdoc)) THEN
        allocate ( fecdoc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(fecpel)) THEN
        allocate ( fecpel(nphy,nfec,ngrids) )
        dmem(1)=dmem(1)+real(nphy*nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(feccyc)) THEN
        allocate ( feccyc(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(exalg)) THEN
        allocate ( exalg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(ws)) THEN
        allocate ( ws(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsgrz)) THEN
        allocate ( hsgrz(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(minrefuge)) THEN
        allocate ( minrefuge(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(refugedep)) THEN
        allocate ( refugedep(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(norm_vol)) THEN
        allocate ( norm_vol(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(norm_surf)) THEN
        allocate ( norm_surf(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsdop)) THEN
        allocate ( hsdop(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2palkphos)) THEN
        allocate ( c2palkphos(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsdon)) THEN
        allocate ( hsdon(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2nnupdon)) THEN
        allocate ( c2nnupdon(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
!
      IF (.not.allocated(hsdoc_ba)) THEN
        allocate ( hsdoc_ba(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(gtbac_max)) THEN
        allocate ( gtbac_max(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(bactbase)) THEN
        allocate ( bactbase(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(bactfac)) THEN
        allocate ( bactfac(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(c2nbac)) THEN
        allocate ( c2nbac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(c2pbac)) THEN
        allocate ( c2pbac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(c2febac)) THEN
        allocate ( c2febac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(bacdoc)) THEN
        allocate ( bacdoc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(bacpel)) THEN
        allocate ( bacpel(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(baccyc)) THEN
        allocate ( baccyc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(exbac_c)) THEN
        allocate ( exbac_c(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(exbacc2n)) THEN
        allocate ( exbacc2n(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(bac_ceff)) THEN
        allocate ( bac_ceff(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(rtnit)) THEN
        allocate ( rtnit(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(hsnit)) THEN
        allocate ( hsnit(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
!
      IF (.not.allocated(cdocfrac_c)) THEN
        allocate ( cdocfrac_c(ndom,ngrids) )
        dmem(1)=dmem(1)+real(ndom*ngrids,r8)
      END IF
 
      IF (.not.allocated(rtuvr_dic)) THEN
        allocate ( rtuvr_dic(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(rtuvr_doc)) THEN
        allocate ( rtuvr_doc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
!
      IF (.not.allocated(wf)) THEN
        allocate ( wf(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regtbase)) THEN
        allocate ( regtbase(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regtfac)) THEN
        allocate ( regtfac(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regcr)) THEN
        allocate ( regcr(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regnr)) THEN
        allocate ( regnr(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regsr)) THEN
        allocate ( regsr(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regpr)) THEN
        allocate ( regpr(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
 
      IF (.not.allocated(regfr)) THEN
        allocate ( regfr(nfec,ngrids) )
        dmem(1)=dmem(1)+real(nfec*ngrids,r8)
      END IF
!
      IF (.not.allocated(imaxc2nalg)) THEN
        allocate ( imaxc2nalg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(imaxc2sialg)) THEN
        allocate ( imaxc2sialg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(imaxc2palg)) THEN
        allocate ( imaxc2palg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
 
      IF (.not.allocated(imaxc2fealg)) THEN
        allocate ( imaxc2fealg(nphy,ngrids) )
        dmem(1)=dmem(1)+real(nphy*ngrids,r8)
      END IF
!
      IF (.not.allocated(n2cbac)) THEN
        allocate ( n2cbac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(p2cbac)) THEN
        allocate ( p2cbac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(fe2cbac)) THEN
        allocate ( fe2cbac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(hsnh4_ba)) THEN
        allocate ( hsnh4_ba(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(hspo4_ba)) THEN
        allocate ( hspo4_ba(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(hsfe_ba)) THEN
        allocate ( hsfe_ba(nbac,ngrids) )
        dmem(1)=dmem(1)+real(nbac*ngrids,r8)
      END IF
 
      IF (.not.allocated(r_exbac_c)) THEN
        allocate ( r_exbac_c(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(exbac_n)) THEN
        allocate ( exbac_n(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(frac_exbac_n)) THEN
        allocate ( frac_exbac_n(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(i_bac_ceff)) THEN
        allocate ( i_bac_ceff(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(idbio3)) THEN
        allocate ( idbio3(ndbio3d) )
        dmem(1)=dmem(1)+real(ndbio3d,r8)
      END IF
 
      IF (.not.allocated(idbio4)) THEN
        allocate ( idbio4(ndbio4d) )
        dmem(1)=dmem(1)+real(ndbio4d,r8)
      END IF
#endif
!
!-----------------------------------------------------------------------
!  Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
      ic=nat+npt+ncs+nns
      DO i=1,nbt
        idbio(i)=ic+i
      END DO
      idic_=ic+1
      ifeo_=ic+2
      inh4_=ic+3
      ino3_=ic+4
      ipo4_=ic+5
      isio_=ic+6
      ic=ic+6
      DO i=1,nbac
        ibacc(i)=ic+1
        ibacf(i)=ic+2
        ibacn(i)=ic+3
        ibacp(i)=ic+4
        ic=ic+4
      END DO
      DO i=1,ndom
        icdmc(i)=ic+1
        idomc(i)=ic+2
        idomn(i)=ic+3
        idomp(i)=ic+4
        ic=ic+4
      END DO
      DO i=1,nfec
        ifecc(i)=ic+1
        ifecf(i)=ic+2
        ifecn(i)=ic+3
        ifecp(i)=ic+4
        ifecs(i)=ic+5
        ic=ic+5
      END DO
      DO i=1,nphy
        iphyc(i)=ic+1
        iphyf(i)=ic+2
        iphyn(i)=ic+3
        iphyp(i)=ic+4
        ic=ic+4
      END DO
      DO i=1,nphy
        IF (phy(i).le.2) THEN
          ic=ic+1
          iphys(i)=ic
        ELSE
          iphys(i)=0
        END IF
      END DO
      firstpig=ic+1
      DO j=1,npig
        DO i=1,nphy
          ipigs(i,j)=0
          IF (pig(phy(i),j).eq.1) THEN
            ic=ic+1
            ipigs(i,j)=ic
          END IF
        END DO
      END DO
!
!-----------------------------------------------------------------------
!  Set EcoSim group variable names.
!-----------------------------------------------------------------------
!
      DO i=1,nphy
        phyname(i)=phygroups(phy(i))
      END DO
      DO i=1,nbac
        WRITE (bacname(i),'(a,1x,i1)') 'Bacteria Group', i
      END DO
      DO i=1,ndom
        WRITE (domname(i),'(a,1x,i1)') 'DOM Group', i
      END DO
      DO i=1,nfec
        WRITE (fecname(i),'(a,1x,i1)') 'Fecal Group', i
      END DO
!
      RETURN
      END SUBROUTINE initialize_biology
 
      END MODULE mod_biology