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bio_wf.f90
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bio_wf.f90
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!=======================================================================
! Fiscm Biology Example
!
! Description
! - i-state model for a simple creature
! - uses temperature-dependent stage duration
!
! Comments:
! - contains two routines:
! init_bio: read optional namelist to set params
! set initial positions (x,y,s)
! set spawning times
! add global information to NetCDF output
! advance_bio: advance the biological state in time
! e.g. grow, die, settle, reproduce
!
! !REVISION HISTORY:
! Original author(s): G. Cowles
!
!=======================================================================
Module Bio
Use gparms
Use mod_igroup
Implicit none
!parameters
integer,parameter :: nstages = 4
real(sp) :: days_at_liberty = 1.0
real(sp) :: some_other_var = 1.0
!namelist can be read from input to overide parameters
Namelist /NML_WF/ &
& days_at_liberty, &
& some_other_var
contains
!------------------------------------------------------------------
! initialize a group
! - read the control namelist (optional)
! - add state variables and initialize them
! - modify state variables (position, spawn time, initial weight, etc.)
!------------------------------------------------------------------
subroutine init_bio(g,Nind_start)
use output_routines
use utilities
implicit none
type(igroup), intent(inout) :: g
integer, intent(in) :: Nind_start
integer :: iunit,ios
logical :: fexist
real(sp), pointer :: tspawn(:)
real(sp), pointer :: x(:)
real(sp), pointer :: y(:)
real(sp), pointer :: s(:)
real(sp), pointer :: z(:)
integer, pointer :: tid(:)
real(sp) :: ff
integer :: i,ii,nhead
!set current problem size
if(Nind_start < 0)then
write(*,*)'must specify more than 0 individuals in init_bio'
stop
else if(Nind_start > g%Tnind)then
write(*,*)'number of individuals in init_bio (',Nind_start,') exceeds problem size',g%Tnind
stop
endif
g%Nind = Nind_start
!read the namelist (if any)
if(g%paramfile /= "NONE")then
inquire(file=trim(g%paramfile),exist=fexist)
if(.not.fexist)then
write(*,*)'fatal error: namelist file: ',trim(g%paramfile),' does not exist, stopping...'
stop
endif
iunit = 33
open(unit=iunit,file=trim(g%paramfile),form='formatted')
read(unit=iunit,nml=nml_wf,iostat=ios)
if(ios /= 0)then
write(*,*)'fatal error: could not read bs namelist from: ',trim(g%paramfile)
stop
endif
close(iunit)
endif ! file /= NONE
!set the spawning time
call get_state('tspawn',g,tspawn)
tspawn = 0.0
!set the spawning location
!-----------------------------------
! 2D,3D -> initialize x,y
!-----------------------------------
if(g%space_dim == 2)then
call get_state('x',g,x)
call get_state('y',g,y)
call get_state('tid',g,tid)
!gom
!call random_square(g%Nind,8.751e5_sp,9.01e5_sp,-7.55e4_sp,-4.567e4_sp,x,y)
!do i=1,g%Nind
! x(i) = 270000 + float(i-1)*1000.
! y(i) = 154000.
!end do
!fake_forcing
!do i=1,g%Nind
! x(i) = 0.0
! y(i) = 0.0
!end do
!initial condition file
write(*,*)'reading ic file 2d'
open(unit=33,file=trim(g%init_pos_file),form='formatted')
read(33,*)ii,nhead
do i=1,nhead
read(33,*)
end do
do i=1,g%Nind
read(33,*)x(i),y(i),ff,tspawn(i),tid(i)
end do
close(33)
endif
!-----------------------------------
! 3D -> initialize s-coordinate
!-----------------------------------
if(g%space_dim == 3)then
call get_state('s',g,s)
call get_state('z',g,z)
call get_state('x',g,x)
call get_state('y',g,y)
call get_state('tid',g,tid)
s = 0;
z = 0;
allocate(zpini(g%Nind))
!do i=1,g%Nind
! s(i) = -float(i-1)/float(g%Nind-1)
!end do
!initial condition file
write(*,*)'reading ic file'
open(unit=33,file=trim(g%init_pos_file),form='formatted')
read(33,*)ii,nhead
write(*,*)nhead
if(ii /= g%Nind)then
write(*,*)'The number of points are wrong in',g%init_pos_file
stop
endif
do i=1,nhead
read(33,*)
end do
do i=1,g%Nind
read(33,*)x(i),y(i),zpini(i),tspawn(i),tid(i)
if(sz_cor == 0)then
s(i) = zpini(i)
elseif(sz_cor == 1)then
z(i) = zpini(i)
endif
end do
close(33)
endif
write(*,*)'done with ic'
! skagit
! do i=1,g%Nind
! x(i) = 540006 + float(i)*100.
! y(i) = 5.3526256e6 + float(i)*100.
! end do
! test data
! do i=1,g%Nind
! x(i) = float(i-1)*100.
! y(i) = 0.0
! end do
!add parameters to netcdf file header
call add_cdfglobs(g,"info","some kind of info")
call add_cdfglobs(g,"nstages",4)
call add_cdfglobs(g,"days_at_liberty",days_at_liberty)
call add_cdfglobs(g,"some_other_var",some_other_var)
end subroutine init_bio
!------------------------------------------------------------------
! advance the biology (this routine is called from the main loop at
! a time interval of DT_bio )
! use temperature-stage dependence from
!
! Incze, L.S., Naimie, C., 2000. Modeling the transport of lobster
! (homarus americanus) larvae and postlarvae in the Gulf of
! Maine. Fish. Oceanogr. 9, 99-113.
!------------------------------------------------------------------
subroutine advance_bio(g,mtime)
type(igroup), intent(inout) :: g
real(sp), intent(in ) :: mtime
real(sp), pointer :: tspawn(:)
real(sp), pointer :: T(:)
integer , pointer :: stage(:)
integer , pointer :: istatus(:)
integer :: i,N
real(sp) :: deltaT,D
!construct pointers to access and modify state variables for the group
call get_state('status',g,istatus)
call get_state('stage',g,stage)
call get_state('tspawn',g,tspawn)
!set problem size
N = g%nind
deltaT = g%DT_bio*sec_2_day !time step in days
! following interface is cleaner but compiler cannot construct
! generic interface if arguments are the same even if the
! return value is of different type
! PASD => get_state('PASD',g)
! istatus => get_state('status',g)
! stage => get_state('stage',g)
do i=1,N !main loop
if(istatus(i) /= ACTIVE)cycle
if( (mtime - tspawn(i)) > days_at_liberty)then
istatus(i) = SETTLED
endif;
end do !end main loop
end subroutine advance_bio
End Module Bio