#undef GROWTH_ONLY
SUBROUTINE biology_floats (ng, Lstr, Lend, Predictor, my_thread)
!
!svn $Id: oyster_floats.h 889 2018-02-10 03:32:52Z arango $
!************************************************** Hernan G. Arango ***
! Copyright (c) 2002-2019 The ROMS/TOMS Group Diego A. Narvaez !
! Licensed under a MIT/X style license !
! See License_ROMS.txt !
!***********************************************************************
! !
! This routine sets behavior for Lagrangian particles that simulates !
! planktonic larvae. The planktonic behavior is based on the model !
! of Dekshenieks et al. (1993; 1996; 1997). It calculates the size !
! (length) and development of oyster larvae. Results about this model !
! can be found in Narvaez et al. 2012 a,b (in review) !
! !
! The governing equation are: !
! !
! d(Lsize)/d(t) = growth(food,Lsize) * Gfactor(T,S) * turb_ef !
! !
! w_bio = TS * SW - (1 - TS) * SR !
! !
! where !
! !
! turbef = m * turb + c, for turbidity < 0.1 g/l !
! or !
! turbef = b * EXP(-beta*(turb-turb0)), for turbidity > 0.1 g/l !
! !
! TS = c * DS + d, for increasing salinity gradient DS !
! or !
! TS = -e * DS + f, for decreasing salinity gradient DS !
! !
! SR = 2.665 * EXP(0.0058*(Lsize-220)) !
! !
! TS: fraction of active larvae: fractional swimming time !
! SW: larval swimming rate (mm/s) !
! SR: larval sinking rate (mm/s) !
! DS: salinity change rate (1/s) !
! !
! References: !
! !
! Dekshenieks, M.M., E.E. Hofmann, and E.N. Powell, 1993: !
! Environmental effect on the growth and development of !
! Eastern oyster, Crassostrea virginica (Gmelin, 1791), !
! larvae: A modeling study, J. Shelfish Res, 12, 241-254. !
! !
! Dekshenieks, M.M., E.E. Hofmann, J.M. Klinck, and E.N. !
! Powell, 1996: Modeling the vertical distribution of !
! oyster larvae in response to environmental conditions, !
! Mar. Ecol. Prog. Ser., 136, 97-110. !
! !
! Dekshenicks, M.M., E.E. Hofmann, J.M. Klinck, and E.N. !
! Powell, 1997: A modeling study of the effect of size- !
! and depth_dependent predation on larval survival, J. !
! Plankton Res., 19, (11), 1583-1598. !
! !
! Narvaez, D.A, J.M. Klinck, E.N. Powell, E.E. Hofmann, J. Wilkin !
! and D. B. Haidvogel. Modeling the dispersal of Eastern !
! oyster (Crassostrea virginica) larvae in Delaware Bay, J. Mar. !
! Res., in review. !
! !
! Narvaez, D.A, J.M. Klinck, E.N. Powell, E.E. Hofmann, J. Wilkin !
! and D. B. Haidvogel. Circulation and behavior controls on !
! dispersal of Eastern oyster (Crassostrea virginica) larvae in !
! Delaware Bay, J. Mar. Res., in review. !
! !
!***********************************************************************
!
USE mod_param
USE mod_floats
USE mod_stepping
!
! Imported variable declarations.
!
integer, intent(in) :: ng, Lstr, Lend
logical, intent(in) :: Predictor
#ifdef ASSUMED_SHAPE
logical, intent(in) :: my_thread(Lstr:)
#else
logical, intent(in) :: my_thread(Lstr:Lend)
#endif
!
#ifdef PROFILE
CALL wclock_on (ng, iNLM, 10, __LINE__, __FILE__)
#endif
CALL biology_floats_tile (ng, Lstr, Lend, &
& nfm3(ng), nfm2(ng), nfm1(ng), nf(ng), &
& nfp1(ng), &
& Predictor, my_thread, &
& DRIFTER(ng) % bounded, &
& DRIFTER(ng) % Tinfo, &
& DRIFTER(ng) % track)
#ifdef PROFILE
CALL wclock_off (ng, iNLM, 10, __LINE__, __FILE__)
#endif
RETURN
END SUBROUTINE biology_floats
!
!***********************************************************************
SUBROUTINE biology_floats_tile (ng, Lstr, Lend, &
& nfm3, nfm2, nfm1, nf, nfp1, &
& Predictor, my_thread, bounded, &
& Tinfo, track)
!***********************************************************************
!
USE mod_param
USE mod_parallel
USE mod_behavior
#ifdef BIOLOGY
USE mod_biology
#endif
USE mod_floats
USE mod_grid
USE mod_iounits
USE mod_scalars
!
! Imported variable declarations.
!
integer, intent(in) :: ng, Lstr, Lend
integer, intent(in) :: nfm3, nfm2, nfm1, nf, nfp1
logical, intent(in) :: Predictor
!
#ifdef ASSUMED_SHAPE
logical, intent(in) :: bounded(:)
logical, intent(in) :: my_thread(Lstr:)
real(r8), intent(in) :: Tinfo(0:,:)
real(r8), intent(inout) :: track(:,0:,:)
#else
logical, intent(in) :: bounded(Nfloats(ng))
logical, intent(in) :: my_thread(Lstr:Lend)
real(r8), intent(in) :: Tinfo(0:izrhs,Nfloats(ng))
real(r8), intent(inout) :: track(NFV(ng),0:NFT,Nfloats(ng))
#endif
!
! Local variable declarations.
!
integer :: i, i1, i2, j1, j2, l
real(r8) :: dsalt, temp, salt
real(r8) :: Lfood, Lturb, Lsize, LsizeNew
real(r8) :: Grate, Gfactor, turb_ef
real(r8) :: SwimRate, SwimTime, SwimTimeNew
real(r8) :: bottom, brhs, sink, w_bio
real(r8) :: cff1, cff2, cff3, cff4
real(r8) :: p1, p2, q1, q2
real(r8) :: my_food, my_salt, my_size, my_temp
real(r8) :: oGfactor_DS, oGfactor_DT
real(r8) :: oGrate_DF, oGrate_DL
real(r8) :: oswim_DL, oswim_DT
real(r8) :: HalfDT
!
!-----------------------------------------------------4-----------------
! Estimate larval growth, as length (um), based on food, salinity,
! temperature and turbidity. Then, estimate swimming time (s),
! larvae sinking velocity (m/s) and larvae vertical velocity (m/s).
!-----------------------------------------------------------------------
!
! Compute look tables inverse axis increments to avoid repetitive
! divisions.
!
oGrate_DF=1.0_r8/Grate_DF
oGrate_DL=1.0_r8/Grate_DL
oGfactor_DS=1.0_r8/Gfactor_DS
oGfactor_DT=1.0_r8/Gfactor_DT
oswim_DT=1.0_r8/swim_DT
oswim_DL=1.0_r8/swim_DL
!
! Assign predictor/corrector weights.
!
IF (Predictor) THEN
cff1=8.0_r8/3.0_r8
cff2=4.0_r8/3.0_r8
ELSE
cff1=9.0_r8/8.0_r8
cff2=1.0_r8/8.0_r8
cff3=3.0_r8/8.0_r8
cff4=6.0_r8/8.0_r8
END IF
!
! Compute biological behavior fields.
!
HalfDT=0.5_r8*dt(ng)
DO l=Lstr,Lend
IF (my_thread(l).and.bounded(l)) THEN
!
! If newly relased float, initialize biological behavior fields. Note
! that since we need temperature and salinity, we need to initialize
! their values to all time levels. Otherwise, we will have a parallel
! bug.
!
IF (time(ng)-HalfDT.le.Tinfo(itstr,l).and. &
& time(ng)+HalfDT.gt.Tinfo(itstr,l)) THEN
temp=track(ifTvar(itemp),nfp1,l)
salt=track(ifTvar(isalt),nfp1,l)
DO i=0,NFT
track(isizf,i,l)=Larvae_size0(ng)
track(iswim,i,l)=0.5_r8*(swim_Tmin(ng)+swim_Tmax(ng))
track(ifTvar(itemp),i,l)=temp
track(ifTvar(isalt),i,l)=salt
END DO
END IF
!
! Get temperature, salinity, larvae size (length), swimming time, and
! food supply. For now, assume constant food and turbidity. This
! can be changed in the future with spatial and temporal variability
! for food and/or turbidity. If this is the case, we need to have
! something like:
!
! IF (Predictor) THEN
! Lfood=track(ifood,nf,l)
! Lturb=track(iturb,nf,l)
! ...
! ELSE
! Lfood=track(ifood,nfp1,l)
! Lturb=track(iturb,nfp1,l)
! ...
! END IF
!
! The food variability may be from data, ecosystem model, or analytical
! functions. Similarly, the turbidity may be from data, sediment model,
! or analytical functions.
!
temp=track(ifTvar(itemp),nfp1,l)
salt=track(ifTvar(isalt),nfp1,l)
dsalt=track(ifTvar(isalt),nfp1,l)- &
& track(ifTvar(isalt),nf ,l)
IF (Predictor) THEN
Lsize=track(isizf,nf,l)
SwimTime=track(iswim,nf,l)
Lfood=food_supply(ng)
Lturb=turb_ambi(ng)
ELSE
Lsize=track(isizf,nfp1,l)
SwimTime=track(iswim,nfp1,l)
Lfood=food_supply(ng)
Lturb=turb_ambi(ng)
END IF
!
! Determine larval growth rate (um/day) contribution as function of
! food supply (mg_Carbon/l) and larval size (um). Linearly interpolate
! growth rate from the look table of food concentration versus larval
! size. Notice that extrapolation is suppresed by bounding "Lfood" and
! "Lsize" to the range values in the look table.
!
my_food=MIN(MAX(Grate_F0,Lfood), &
& Grate_F0+Grate_DF*REAL(Grate_Im-1,r8))
my_size=MIN(MAX(Grate_L0,Lsize), &
& Grate_L0+Grate_DL*REAL(Grate_Jm-1,r8))
i1=INT(1.0_r8+(my_food-Grate_F0)*oGrate_DF)
i2=MIN(i1+1,Grate_Im)
j1=INT(1.0_r8+(my_size-Grate_L0)*oGrate_DL)
j2=MIN(j1+1,Grate_Jm)
p2=(my_food-(Grate_F0+REAL(i1-1,r8)*Grate_DF))*oGrate_DF
q2=(my_size-(Grate_L0+REAL(j1-1,r8)*Grate_DL))*oGrate_DL
p1=1.0_r8-p2
q1=1.0_r8-q2
Grate=p1*q1*Grate_table(i1,j1)+ &
& p2*q1*Grate_table(i2,j1)+ &
& p1*q2*Grate_table(i1,j2)+ &
& p2*q2*Grate_table(i2,j2)
!
! Determine larval growth rate factor (nondimensional) as function of
! salinity and temperature (Celsius). Linearly interpolate growth rate
! factor from the look table of salinity versus temperature. Notice
! that extrapolation is suppresed by bounding "salt" and "temp" to the
! range values in the look table.
!
IF (temp.lt.Gfactor_T0) THEN
Gfactor=0.0_r8
ELSE
my_salt=MIN(MAX(Gfactor_S0,salt), &
& Gfactor_S0+Gfactor_DS*REAL(Gfactor_Im-1,r8))
my_temp=MIN(MAX(Gfactor_T0,temp), &
& Gfactor_T0+Gfactor_DT*REAL(Gfactor_Jm-1,r8))
i1=INT(1.0_r8+(my_salt-Gfactor_S0)*oGfactor_DS)
i2=MIN(i1+1,Gfactor_Im)
j1=INT(1.0_r8+(my_temp-Gfactor_T0)*oGfactor_DT)
j2=MIN(j1+1,Gfactor_Jm)
p2=(my_salt-(Gfactor_S0+REAL(i1-1,r8)*Gfactor_DS))* &
& oGfactor_DS
q2=(my_temp-(Gfactor_T0+REAL(j1-1,r8)*Gfactor_DT))* &
& oGfactor_DT
p1=1.0_r8-p2
q1=1.0_r8-q2
Gfactor=p1*q1*Gfactor_table(i1,j1)+ &
& p2*q1*Gfactor_table(i2,j1)+ &
& p1*q2*Gfactor_table(i1,j2)+ &
& p2*q2*Gfactor_table(i2,j2)
END IF
!
! Determine turbidity effect (linear or exponential) on larval growth.
! Then, compute new larvae size (um) as function of growth rate (um/s)
! which is loaded in track(ibrhs,:,:).
!
IF (Lsize.gt.turb_size(ng)) THEN
IF (Lturb.gt.turb_crit(ng)) THEN
turb_ef=turb_base(ng)* &
& EXP(-turb_rate(ng)*(Lturb-turb_mean(ng)))
ELSE
turb_ef=turb_slop(ng)*Lturb+turb_axis(ng)
END IF
track(ibrhs,nfp1,l)=Grate*Gfactor*turb_ef*sec2day
ELSE
track(ibrhs,nfp1,l)=Larvae_GR0(ng)*Gfactor*sec2day
END IF
IF (Predictor) THEN
track(isizf,nfp1,l)=track(isizf,nfm3,l)+ &
& dt(ng)*(cff1*track(ibrhs,nf ,l)- &
& cff2*track(ibrhs,nfm1,l)+ &
& cff1*track(ibrhs,nfm2,l))
ELSE
track(isizf,nfp1,l)=cff1*track(isizf,nf ,l)- &
& cff2*track(isizf,nfm2,l)+ &
& dt(ng)*(cff3*track(ibrhs,nfp1,l)+ &
& cff4*track(ibrhs,nf ,l)- &
& cff3*track(ibrhs,nfm1,l))
END IF
Lsize=track(isizf,nfp1,l)
!
! Estimate the fraction of time that the larvae spend swimming.
!
IF (ABS(dsalt).lt.0.00001_r8) THEN
dsalt=0.0_r8
END IF
IF (dsalt.gt.0.0_r8) THEN
SwimTimeNew=MIN(SwimTime+dsalt*slope_Sinc(ng),swim_Tmax(ng))
ELSE
SwimTimeNew=MAX(SwimTime+dsalt*slope_Sdec(ng),swim_Tmin(ng))
END IF
!
! Compute swim behavior as function of larval size and temperature.
! Linearly interpolate swimming rate (mm/s) from the look table of
! larval size (um) versus temperature (Celsius). Notice that
! extrapolation is suppresed by bounding "Lsize" and "temp" to
! the range values in the look table.
!
IF ((temp.lt.swim_T0).or.(Lsize.lt.swim_L0)) THEN
SwimRate=0.0_r8
ELSE
my_size=MIN(MAX(swim_L0,Lsize), &
& swim_L0+swim_DL*REAL(swim_Im-1,r8))
my_temp=MIN(MAX(swim_T0,temp), &
& swim_T0+swim_DT*REAL(swim_Jm-1,r8))
i1=INT(1.0_r8+(my_size-swim_L0)*oswim_DL)
i2=MIN(i1+1,swim_Im)
j1=INT(1.0_r8+(my_temp-swim_T0)*oswim_DT)
j2=MIN(j1+1,swim_Jm)
p2=(my_size-(swim_L0+REAL(i1-1,r8)*swim_DL))*oswim_DL
q2=(my_temp-(swim_T0+REAL(j1-1,r8)*swim_DT))*oswim_DT
p1=1.0_r8-p2
q1=1.0_r8-q2
SwimRate=p1*q1*swim_table(i1,j1)+ &
& p2*q1*swim_table(i2,j1)+ &
& p1*q2*swim_table(i1,j2)+ &
& p2*q2*swim_table(i2,j2)
SwimRate=SwimRate*0.001_r8 ! convert from mm/s to m/s
END IF
!
! Compute larvae sinking velocity (m/s).
!
sink=sink_base(ng)*(EXP(sink_rate(ng)*(Lsize-sink_size(ng))))
sink=sink*0.001_r8 ! convert from mm/s to m/s
!
! Compute larvae vertical velocity (m/s).
!
#ifdef GROWTH_ONLY
w_bio=0.0_r8
#else
w_bio=SwimTime*SwimRate-(1.0_r8-SwimTime)*sink
#endif
!
! Load behavior into track array. Apply settlement condition: larvae
! greater or equal than SETTLE_SIZE, settle on the bottom.
!
IF (track(isizf,nfp1,l).lt.settle_size(ng)) THEN
track(iwbio,nfp1,l)=w_bio
track(iwsin,nfp1,l)=sink
track(iswim,nfp1,l)=SwimTimeNew
ELSE
i1=MIN(MAX(0,INT(track(ixgrd,nfp1,l))),Lm(ng)+1)
i2=MIN(i1+1,Lm(ng)+1)
j1=MIN(MAX(0,INT(track(iygrd,nfp1,l))),Mm(ng)+1)
j2=MIN(j1+1,Mm(ng)+1)
p2=REAL(i2-i1,r8)*(track(ixgrd,nfp1,l)-REAL(i1,r8))
q2=REAL(j2-j1,r8)*(track(iygrd,nfp1,l)-REAL(j1,r8))
p1=1.0_r8-p2
q1=1.0_r8-q2
bottom=p1*q1*GRID(ng)%h(i1,j1)+ &
& p2*q1*GRID(ng)%h(i2,j1)+ &
& p1*q2*GRID(ng)%h(i1,j2)+ &
& p2*q2*GRID(ng)%h(i2,j2)
track(idpth,nfp1,l)=-bottom
track(isizf,nfp1,l)=track(isizf,nf,l)
track(iwbio,nfp1,l)=0.0_r8
track(iwsin,nfp1,l)=0.0_r8
track(iswim,nfp1,l)=0.0_r8
END IF
!
! If newly relased float, set vertical migration fields for all time
! levels.
!
IF (time(ng)-HalfDT.le.Tinfo(itstr,l).and. &
& time(ng)+HalfDT.gt.Tinfo(itstr,l)) THEN
brhs=track(ibrhs,nfp1,l)
sink=track(iwsin,nfp1,l)
w_bio=track(iwbio,nfp1,l)
DO i=0,NFT
track(ibrhs,i,l)=brhs
track(iwsin,i,l)=sink
track(iwbio,i,l)=w_bio
END DO
END IF
END IF
END DO
RETURN
END SUBROUTINE biology_floats_tile