! Copyright 2014 College of William and Mary
!
! Licensed under the Apache License, Version 2.0 (the "License");
! you may not use this file except in compliance with the License.
! You may obtain a copy of the License at
!
! http://www.apache.org/licenses/LICENSE-2.0
!
! Unless required by applicable law or agreed to in writing, software
! distributed under the License is distributed on an "AS IS" BASIS,
! WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
! See the License for the specific language governing permissions and
! limitations under the License.
SUBROUTINE bio_init
!!======================================================================
!! April/May, 2007 - Original code !
!!======================================================Marta Rodrigues=
!! !
!! This subroutine is from ROMS (where is called ana_biology.h): !
!! !
!! February, 2009 - Extended for oxygen cycle !
!!======================================================================
!!
!!======================================================================
!! Copyright (c) 2002-2007 The ROMS/TOMS Group !
!! Licensed under a MIT/X style license !
!! See License_ROMS.txt !
!! !
!=======================================================================
! !
! This routine sets initial conditions for biological tracer fields !
! using analytical expressions. !
! !
!=======================================================================
!
USE bio_param
! USE schism_glbl, only : trel0,nvrt,nea,tr_el,idry_e
USE schism_glbl, only : tr_nd,nvrt,npa,irange_tr
USE biology
IMPLICIT NONE
! Imported variable declarations.
! real(r8), dimension(ntracers,nvrt,nea), intent(out) :: trel0
!
! Local variable declarations.
!
integer :: i, iseco, itrc, j, k, tmp00, tmp1, tmp2, tmp3
real(r8) :: cff1, cff2, cff3, cff4, cff5, cff6, cff7, cff8, cff9
real(r8) :: cff10, cff11, cff12, cff13, cff14, cff15
real(r8) :: salt, sftm, temp
!
!---------------------------------------------------------------------
! EcoSim initial fields.
!---------------------------------------------------------------------
!
! Assumed maximum temperature gradient.
!
cff3=1.0_r8/14.0_r8
cff4=1.0_r8/16.0_r8
cff5=32.0_r8
cff7=1.0_r8/0.0157_r8
cff8=1.0_r8/6.625_r8
cff9=1.0_r8/16.0_r8
cff10=1.0_r8/15.0_r8
cff11=1.0_r8/8.0_r8
cff12=1.0_r8/128.0_r8
cff13=1.0_r8/1000.0_r8
cff14=1.0_r8/12.0_r8
cff15=cff5*cff8*cff14 ! mole N : gram Chl
!Marta Rodrigues - For vertical and node
DO k= nvrt, 1, -1
DO i=1, npa
!if(idry_e(i)==1) cycle
! Initialization of surface chlorophyll.
!
!Marta Rodrigues - temperature and salinity values
sftm=tr_nd(1,nvrt,i) !tsel(1,nvrt,i) !sea surface temperature
temp=tr_nd(1,k,i) !tsel(1,k,i)
salt=tr_nd(2,k,i) !tsel(2,k,i)
cff1=-0.0827_r8*sftm+2.6386_r8
cff2=MAX(0.00001_r8,cff1*(1.0_r8-(sftm-temp)*cff3))
!
! Initialization of nutrients.
!
tmp00 = irange_tr(1,6)-1
tmp1 = tmp00+iNH4_
tr_nd(tmp1,k,i)=0.053_r8*temp+0.7990_r8 !NH4
tmp2 = tmp00+iNO3_
tr_nd(tmp2,k,i)=8.5_r8-cff2*cff15-tr_nd(tmp1,k,i) !NO3
tmp3 = tmp00+iPO4_
tr_nd(tmp3,k,i)=(tr_nd(tmp1,k,i)+tr_nd(tmp2,k,i))*cff4 !PO4
IF(IRON==1)THEN
tmp1 = tmp00+iFeO_
tr_nd(tmp1,k,i)=1.0_r8 !MFR
ENDIF
!
! Assuming diatoms are 75% of initialized chlorophyll.
!
tmp1 = tmp00+iSiO_
tr_nd(tmp1,k,i)=5.5_r8-(cff2*0.75_r8)*cff15*1.20_r8
tmp1 = tmp00+iDIC_
tr_nd(tmp1,k,i)=2000.0_r8
! Marta Rodrigues - Initialization of DO and COD (oxygen)
tmp1 = tmp00+iDO_
tr_nd(tmp1,k,i)=150.0_r8
tmp1 = tmp00+iCOD_
tr_nd(tmp1,k,i)=0.0_r8
!
! Bacteria Initialization.
!
DO iseco=1,Nbac
tmp1 = tmp00+iBacC(iseco)
tr_nd(tmp1,k,i)=0.85_r8
tmp2 = tmp00+iBacN(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*N2cBAC
tmp2 = tmp00+iBacP(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*P2cBAC
IF(IRON==1)THEN
tmp2 = tmp00+iBacF(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*Fe2cBAC !MFR
ENDIF
END DO
!
! Marta Rodrigues
! Zooplankton initialization.
DO iseco=1,Nzoo
tmp1 = tmp00+iZooC(iseco)
tr_nd(tmp1,k,i)=2_r8
tmp1 = tmp00+iZooN(iseco)
tr_nd(tmp1,k,i)=0.2_r8
tmp1 = tmp00+iZooP(iseco)
tr_nd(tmp1,k,i)=0.02_r8
END DO
! Initialize phytoplankton populations.
!
! tmp1 = tmp00+iPhyC(1)
! tr_nd(tmp1,k,i)=MAX(0.02_r8, &
! & 0.75_r8*0.75_r8*cff5*cff2*cff14)
DO iseco=1,Nphy
tmp1 = tmp00+iPhyC(iseco)
tr_nd(tmp1,k,i)=MAX(0.02_r8, &
& 0.75_r8*0.75_r8*cff5*cff2*cff14)
tmp2 = tmp00+iPhyN(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff8
tmp3 = tmp00+iPhyP(iseco)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)*cff4
IF(IRON==1)THEN
tmp3 = tmp00+iPhyF(iseco)
tr_nd(tmp3,k,i)=tr_nd(tmp1,k,i)*cff13 !MFR
ENDIF
IF (iPhyS(iseco).gt.0) THEN
tmp3 = tmp00+iPhyS(iseco)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)*1.20_r8
END IF
! Initialize Pigments in ugrams/liter (not umole/liter).
!
cff6=12.0_r8/cff5
tmp2 = tmp00+iPigs(iseco,1)
tr_nd(tmp2,k,i)=cff6*tr_nd(tmp1,k,i)
!
! Chlorophyll-b.
!
cff6=cff5-b_C2Cl(iseco)
IF (iPigs(iseco,2).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,2)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_ChlB(iseco)+ &
& mxChlB(iseco)*cff6)
END IF
!
! Chlorophyll-c.
!
IF (iPigs(iseco,3).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,3)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_ChlC(iseco)+ &
& mxChlC(iseco)*cff6)
END IF
!
! Photosynthetic Carotenoids.
!
IF (iPigs(iseco,4).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,4)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_PSC(iseco)+ &
& mxPSC(iseco)*cff6)
END IF
!
! Photoprotective Carotenoids.
!
IF (iPigs(iseco,5).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,5)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_PPC(iseco)+ &
& mxPPC(iseco)*cff6)
END IF
!
! Low Urobilin Phycoeurythin Carotenoids.
!
IF (iPigs(iseco,6).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,6)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_LPUb(iseco)+ &
& mxLPUb(iseco)*cff6)
END IF
!
! High Urobilin Phycoeurythin Carotenoids.
!
IF (iPigs(iseco,7).gt.0) THEN
tmp3 = tmp00+iPigs(iseco,7)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)* &
& (b_HPUb(iseco)+ &
& mxHPUb(iseco)*cff6)
END IF
END DO
!
! DOC initialization.
!
cff6=MAX(0.001_r8,-0.9833_r8*salt+33.411_r8)
tmp1 = tmp00+iDOMC(1)
tr_nd(tmp1,k,i)=0.1_r8
tmp2 = tmp00+iDOMN(1)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff8
tmp3 = tmp00+iDOMP(1)
tr_nd(tmp3,k,i)=tr_nd(tmp2,k,i)*cff9
IF(CDOC==1) THEN
tmp2 = tmp00+iCDMC(1)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cDOCfrac_c(1) !MFR
ENDIF
IF(Ndom==2)THEN !MFR
tmp1 = tmp00+iDOMC(2)
tr_nd(tmp1,k,i)=15.254_r8*cff6+70.0_r8
tmp2 = tmp00+iDOMN(2)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff10
tmp1 = tmp00+iDOMP(2)
tr_nd(tmp1,k,i)=0.0_r8
IF(CDOC==1) THEN
tmp1 = tmp00+iCDMC(2)
tr_nd(tmp1,k,i)=(0.243_r8*cff6+0.055_r8)*cff7 !MFR
ENDIF
ENDIF
!
! Fecal Initialization.
!
DO iseco=1,Nfec
tmp1 = tmp00 + iFecC(iseco)
tr_nd(tmp1,k,i)=0.002_r8
tmp2 = tmp00 + iFecN(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff11
tmp2 = tmp00 + iFecP(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff12
IF(IRON==1) THEN
tmp2 = tmp00 + iFecF(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff13 !MFR
ENDIF
tmp2 = tmp00 + iFecS(iseco)
tr_nd(tmp2,k,i)=tr_nd(tmp1,k,i)*cff11
END DO
END DO
END DO
RETURN
END SUBROUTINE bio_init