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It's either GB or MA
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@TCallaghan2
TCallaghan2 committed Nov 20, 2023
1 parent b2504ff commit 14c030c
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Showing 3 changed files with 70 additions and 67 deletions.
5 changes: 2 additions & 3 deletions SRC/IORoutines.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -234,16 +234,15 @@ integer function Load_Grid(grid, domain_name)
close(63)
num_grids=n

if (domain_name(1:2).eq.'GB')then
if (domain_name .eq. 'GB')then
grid%posn(1:num_grids)%is_closed = .TRUE.
do n=1,num_grids
if( any ((/grid%posn(n)%mgmt_area_index.eq.8, grid%posn(n)%mgmt_area_index.eq.5,&
& grid%posn(n)%mgmt_area_index.eq.10 /)))then
grid%posn(n)%is_closed = .FALSE.
endif
enddo
endif
if (domain_name(1:2).eq.'MA')then
else
grid%posn(1:num_grids)%is_closed = .FALSE.
do n=1,num_grids
if( any ((/ grid%posn(n)%mgmt_area_index.eq.3, grid%posn(n)%mgmt_area_index.eq.4,&
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124 changes: 66 additions & 58 deletions SRC/ScallopGrowth.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -124,13 +124,13 @@
!>----------------------------------------------------------------------------------------------------------------
MODULE Growth_Mod
use globals
implicit none
implicit none
integer, parameter :: growth_param_size = 4

!> @class Growth_Class
!>
!> Subroutines that determine expected growth of scallops
type Growth_Class
type Growth_Class
!> @public @memberof Growth_Class
!> Asymptotic size mean
real(dp) L_inf_mu
Expand Down Expand Up @@ -212,31 +212,23 @@ subroutine Set_Growth(growth, grid, shell_lengths, num_ts, num_sz_classes, dom_n

shell_lengths(1:num_size_classes) = Set_Shell_Heights(dfloat(length_min), dfloat(length_delta))

if(domain_name(1:2).eq.'GB')then
if(domain_name .eq. 'GB')then
do n=1,num_grids
call Get_Growth_GB(grid%posn(n)%z, grid%posn(n)%lat, grid%posn(n)%is_closed, growth(n)%L_inf_mu, growth(n)%K_mu)
growth(n)%L_inf_sd = 14.5D0
growth(n)%K_sd = .12D0
if( grid%posn(n)%mgmt_area_index .eq. 11 ) then
!Peter Pan region Linfity = 110.3 K = 0.423
! TODO: Why are these values held constant
growth(n)%L_inf_mu=110.3D0
growth(n)%K_mu=0.423D0
endif
! TODO Get_Growth_ is expecting is_open, change to .NOT. is_closed?
call Get_Growth_GB(grid%posn(n)%z, grid%posn(n)%lat, grid%posn(n)%is_closed, growth(n)%L_inf_mu, growth(n)%K_mu,&
& growth(n)%L_inf_sd, growth(n)%K_sd, grid%posn(n)%mgmt_area_index)
growth(n)%G = Gen_Size_Trans_Matrix(growth(n)%L_inf_mu, growth(n)%L_inf_sd, &
& growth(n)%K_mu, growth(n)%K_sd, shell_lengths, 'AppxC')
enddo
endif
if(domain_name(1:2).eq.'MA')then
else
do n=1,num_grids
call Get_Growth_MA(grid%posn(n)%z, grid%posn(n)%lat, grid%posn(n)%is_closed, growth(n)%L_inf_mu, growth(n)%K_mu)
! TODO: Why are these values held constant
growth(n)%L_inf_sd = 10.8D0
growth(n)%K_sd = .045D0
! TODO Get_Growth_ is expecting is_open, change to .NOT. is_closed?
call Get_Growth_MA(grid%posn(n)%z, grid%posn(n)%lat, grid%posn(n)%is_closed, growth(n)%L_inf_mu, growth(n)%K_mu,&
& growth(n)%L_inf_sd, growth(n)%K_sd)
growth(n)%G = Gen_Size_Trans_Matrix(growth(n)%L_inf_mu, growth(n)%L_inf_sd, &
& growth(n)%K_mu, growth(n)%K_sd, shell_lengths, 'AppxC')
enddo
endif
do n=1, num_grids
growth(n)%G = Gen_Size_Trans_Matrix(growth(n)%L_inf_mu, growth(n)%L_inf_sd, &
& growth(n)%K_mu, growth(n)%K_sd, shell_lengths, 'AppxC')
enddo

Gpar(1:num_grids,1) = growth(1:num_grids)%L_inf_mu
Gpar(1:num_grids,2) = growth(1:num_grids)%L_inf_sd
Expand Down Expand Up @@ -388,89 +380,105 @@ function Set_Shell_Heights(length_min, length_delta)
return
endfunction Set_Shell_Heights


!==================================================================================================================
!>
!> @public @memberof Growth_Class
!>
!> Provides growth parameters Linf and K for Georges Bank.
!> Provides growth parameters L and K parameters for Georges Bank.
!> From R code sent by Dvora July 28th 2021
!>
!> @param[in] depth in meters
!> @param[in] lat Geospatial coordinate, Latitude
!> @param[in] is_open Logical that indicates if grid is open for fishing
!> @param[out] Linf von Bertlanaffy asymptotic growth parameter
!> @param[out] K von Bertlanaffy asymptotic growth parameter
!> @param[out] L_inf_mu von Bertlanaffy asymptotic growth parameter
!> @param[out] K_mu von Bertlanaffy asymptotic growth parameter
!> @param[out] L_inf_sd standard deviation von Bertlanaffy asymptotic growth parameter
!> @param[out] K_sd standard deviation von Bertlanaffy asymptotic growth parameter
!> @param[in] area_index index to indicate management area
!==================================================================================================================
subroutine Get_Growth_GB(depth, lat, is_open, Linf, K)
subroutine Get_Growth_GB(depth, lat, is_open, L_inf_mu, K_mu, L_inf_sd, K_sd, area_index)
real(dp), intent(in) :: depth, lat
logical, intent(in) :: is_open
real(dp), intent(out) :: Linf, K
real(dp), intent(out) :: L_inf_mu, K_mu
real(dp), intent(out) :: L_inf_sd, K_sd
integer, intent(in) :: area_index

real(dp) fixed_coef(6), random_eff(3)
real(dp) depth_norm, latitude, intercept, slope, random_intercept, random_slope,randomCov
real(dp) mean_start_shell_height, mean_depth, mean_lat, mean_ring2

parameter(mean_start_shell_height = 94.73, mean_depth = 72.89, mean_lat = 41.04, mean_ring2 = 109.576)
fixed_coef = (/ -34.96, 57.415, -8.51, -17.65, 0.9076, 3.741/) !fixed effects coef
! intercept, slope, coef of depth, latitude, closed/open for intercept term
random_eff = (/ 81.05, 51.38, -60.53 /) !random effects, intercept, slope, cov
depth_norm = depth / mean_depth
latitude = lat/mean_lat
intercept = fixed_coef(1) + fixed_coef(3) * depth_norm + fixed_coef(4)*latitude + fixed_coef(5) &
& * Logic_To_Double(is_open) + mean_ring2
slope = ( fixed_coef(2) + fixed_coef(6)* depth_norm ) / mean_start_shell_height
random_intercept = random_eff(1)
random_slope = random_eff(2) / mean_start_shell_height**2
randomCov = random_eff(3) / mean_start_shell_height
K = -log(slope) + random_slope/2. / slope**2
Linf = (intercept/(1.-slope)) + (intercept * random_slope / (1. - slope) + randomCov) / (1. - slope**2)
if (area_index .eq. 11) then
!Peter Pan region Linfity = 110.3 K = 0.423
L_inf_mu = 110.3D0
K_mu = 0.423D0
else
fixed_coef = (/ -34.96, 57.415, -8.51, -17.65, 0.9076, 3.741/) !fixed effects coef
! intercept, slope, coef of depth, latitude, closed/open for intercept term
random_eff = (/ 81.05, 51.38, -60.53 /) !random effects, intercept, slope, cov
depth_norm = depth / mean_depth
latitude = lat/mean_lat
intercept = fixed_coef(1) + fixed_coef(3) * depth_norm + fixed_coef(4)*latitude + fixed_coef(5) &
& * Logic_To_Double(is_open) + mean_ring2
slope = ( fixed_coef(2) + fixed_coef(6)* depth_norm ) / mean_start_shell_height
random_intercept = random_eff(1)
random_slope = random_eff(2) / mean_start_shell_height**2
randomCov = random_eff(3) / mean_start_shell_height

L_inf_mu = (intercept/(1.-slope)) + (intercept * random_slope / (1. - slope) + randomCov) / (1. - slope**2)
K_mu = -log(slope) + random_slope/2. / slope**2
endif

L_inf_sd = 10.8D0
K_sd = .045D0
return
end subroutine Get_Growth_GB

!==================================================================================================================
!>
!> @public @memberof Growth_Class
!>
!> Provides growth parameters Linf and K for Mid Atlantic
!> Provides growth parameters L and K parameters for Mid Atlantic
!> From R code sent by Dvora July 28th 2021
!>
!> @param[in] depth in meters
!> @param[in] lat Geospatial coordinate, Latitude
!> @param[in] is_open Logical that indicates if grid is open for fishing
!> @param[out] Linf von Bertlanaffy asymptotic growth parameter
!> @param[out] K von Bertlanaffy asymptotic growth parameter
!> @param[out] L_inf_mu von Bertlanaffy asymptotic growth parameter
!> @param[out] K_mu von Bertlanaffy asymptotic growth parameter
!> @param[out] L_inf_sd standard deviation von Bertlanaffy asymptotic growth parameter
!> @param[out] K_sd standard deviation von Bertlanaffy asymptotic growth parameter
!==================================================================================================================
subroutine Get_Growth_MA(depth, lat, is_open, Linf, K)
! Provides growth parameters Linf and K for Mid Atlantic.
! From R code sent by Dvora July 28th 2021
subroutine Get_Growth_MA(depth, lat, is_open, L_inf_mu, K_mu, L_inf_sd, K_sd)
real(dp), intent(in)::depth, lat
logical, intent(in)::is_open
real(dp), intent(out)::Linf,K
real(dp), intent(out)::L_inf_mu,K_mu
real(dp), intent(out) :: L_inf_sd, K_sd

real(dp) fixed_coef(5),random_eff(3)
real(dp) depth_norm, latitude, intercept, slope, random_intercept, random_slope, randomCov
real(dp) mean_start_shell_height, mean_depth, mean_lat, mean_ring2
real(dp) open

parameter(mean_start_shell_height = 85.74, mean_depth = 52.79, mean_lat = 38.99, mean_ring2 = 106.17 )
fixed_coef = (/0.951,48.333,-9.53,-37.51,-2.31 /) !fixed effects coef
! intercept, slope, coef of depth, latitude, closed/open for intercept term
random_eff = (/38.35,13.27,-20.77 /) !random effects, intercept, slope, cov
if (is_open) then
open = 1._dp
else
open = 0._dp
endif
depth_norm = depth / mean_depth
latitude = lat/mean_lat
intercept = fixed_coef(1)+fixed_coef(3) * depth_norm + fixed_coef(4) *latitude + fixed_coef(5) * open + mean_ring2
intercept = fixed_coef(1)+fixed_coef(3) * depth_norm + fixed_coef(4) *latitude &
& + fixed_coef(5) * Logic_To_Double(is_open) + mean_ring2
slope = fixed_coef(2) / mean_start_shell_height
random_intercept = random_eff(1)
random_slope = random_eff(2) / mean_start_shell_height**2
randomCov = random_eff(3) / mean_start_shell_height
K = -log(slope) + random_slope/2./slope**2
Linf = (intercept / (1.-slope)) + (intercept*random_slope / (1.-slope) + randomCov) / (1.-slope**2)
L_inf_mu = (intercept / (1.-slope)) + (intercept*random_slope / (1.-slope) + randomCov) / (1.-slope**2)
K_mu = -log(slope) + random_slope/2./slope**2

L_inf_sd = 10.8D0
K_sd = .045D0
return
end subroutine Get_Growth_MA


!==================================================================================================================
!> @fn MN18_AppxC_Trans_Matrix
Expand Down
8 changes: 2 additions & 6 deletions SRC/ScallopMortality.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -98,12 +98,10 @@ subroutine Set_Mortality(mortality, grid, shell_lengths, num_sz_classes, dom_nam
mortality(1:num_grids)%natural_mort_adult = .25D0
mortality(1:num_grids)%incidental = 0.05D0
h0 = 65._dp
elseif (domain_name .eq. 'GB') then
else
mortality(1:num_grids)%natural_mort_adult = .2D0
mortality(1:num_grids)%incidental = 0.1D0
h0 = 70._dp
else
PRINT *, term_red, 'UNKNOWN DOMAIN NAME', domain_name, term_blk
endif
a = 0.1D0
mortality(1:num_grids)%is_closed = grid%posn(1:num_grids)%is_closed
Expand Down Expand Up @@ -571,9 +569,7 @@ subroutine Mortality_Density_Dependent(max_rec_ind, mortality, state)
if(domain_name(1:2).eq.'MA')then
recruit_density = sum(state(1:max_rec_ind)) * domain_area_sqm/(10.**6)
mortality%natural_mort_juv = max( mortality%natural_mort_adult , exp(-9.701_dp + 1.093_dp * log(recruit_density)) )
endif

if(domain_name(1:2).eq.'GB')then
else
recruit_density = sum(state(1:max_rec_ind)) * domain_area_sqm/(10.**6)
mortality%natural_mort_juv = max( mortality%natural_mort_adult , exp(-10.49_dp + 1.226_dp * log(recruit_density)) )
endif
Expand Down

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