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Add Fish HSI
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@matthipsey
matthipsey committed May 5, 2021
1 parent 4e9ed3a commit dc774f9
Showing 1 changed file with 98 additions and 82 deletions.
180 changes: 98 additions & 82 deletions src/aed_habitat_water.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
!# #
!# http:https://aquatic.science.uwa.edu.au/ #
!# #
!# Copyright 2016 - 2020 - The University of Western Australia #
!# Copyright 2016 - 2021 - The University of Western Australia #
!# #
!# GLM is free software: you can redistribute it and/or modify #
!# it under the terms of the GNU General Public License as published by #
Expand Down Expand Up @@ -50,50 +50,34 @@ MODULE aed_habitat_water
TYPE,extends(aed_model_data_t) :: aed_habitat_water_data_t
INTEGER :: num_habitats
!# Variable identifiers
INTEGER :: id_bird, id_mtox
INTEGER :: id_chsi, id_chpl, id_chfl, id_chsd
INTEGER :: id_fssi, id_fsdp, id_fssd, id_fsst, id_fsls, id_fsdw, id_fsmt
INTEGER :: id_rhsi, id_rhpl, id_rhfl, id_rhsd, id_rhtr, id_rhsp
INTEGER :: id_chhsi, id_chhpl, id_chhfl, id_chhsd, id_chhtr, id_chhsp
INTEGER :: id_crhsi, id_crhpl, id_crhfl, id_crhsd, id_crhtr
INTEGER :: id_pshsi, id_pshsd, id_pshpl, id_pshfl
INTEGER :: id_wettime, id_drytime
INTEGER, ALLOCATABLE :: id_d_rupfs(:),id_d_rupft(:),id_d_rupfl(:),id_d_rupfa(:),id_d_rupfd(:)
INTEGER, ALLOCATABLE :: id_d_chafs(:),id_d_chaft(:),id_d_chafl(:),id_d_chafa(:),id_d_chafd(:),id_d_chafv(:)
INTEGER, ALLOCATABLE :: id_d_crcfm(:),id_d_crcft(:),id_d_crcfv(:),id_d_crcfs(:),id_d_crcfd(:),id_d_crcfp(:)
INTEGER, ALLOCATABLE :: id_d_pssfm(:), id_d_pssft(:),id_d_pssfv(:),id_d_pssfs(:),id_d_pssfd(:), id_d_pssfu(:)
INTEGER :: id_mtox
INTEGER, ALLOCATABLE :: id_fish(:)

!# Dependencies
INTEGER :: id_l_ph, id_l_hab, id_l_aass, id_l_rveg, id_l_bveg
INTEGER :: id_l_salg, id_l_falg, id_d_turb, id_l_ncs1, id_l_ncs2, id_l_tau0
INTEGER :: id_l_oxys
INTEGER :: id_l_otrc, id_l_oxy, id_l_sav
INTEGER :: id_l_svwc, id_l_stmp25, id_l_stmp, id_l_veg1, id_l_veg2, id_l_pass
INTEGER, ALLOCATABLE :: id_l_mtox(:)

!# Environment variables
INTEGER :: id_E_temp, id_E_salt, id_E_bathy, id_E_matz, id_E_depth
INTEGER :: id_E_nearlevel, id_E_extc, id_E_Io, id_E_stress, id_E_airtemp

!# Model switches
LOGICAL :: simBirdForaging,simBenthicProd,simFishTolerance,simGalaxiidSpawning
LOGICAL :: simCrabHabitat,simRuppiaHabitat,simCharaHabitat
LOGICAL :: simFishTolerance
LOGICAL :: simMosquitoRisk,simCyanoRisk
LOGICAL :: simMetalTox,simClearWater
LOGICAL :: simCrocEggs,simPassiflora

!# Model parameters
AED_REAL, ALLOCATABLE :: mtox_lims(:)
INTEGER :: num_mtox, n_zones_chara, n_zones_fishspawn
INTEGER :: n_zones_crocs, n_zones_pass
AED_REAL,ALLOCATABLE :: active_zones_chara(:), active_zones_fishspawn(:)
AED_REAL,ALLOCATABLE :: active_zones_crocs(:), active_zones_pass(:)

AED_REAL, ALLOCATABLE :: fish_alpha(:), fish_Tmax(:), fish_Taccl(:), fish_Ocrit(:), fish_KO(:)
INTEGER :: num_mtox, num_fish

CONTAINS
PROCEDURE :: define => aed_define_habitat_water
! PROCEDURE :: calculate => aed_calculate_habitat_water
PROCEDURE :: calculate => aed_calculate_habitat_water
! PROCEDURE :: calculate_benthic => aed_calculate_benthic_habitat_water
PROCEDURE :: calculate_riparian => aed_calculate_riparian_habitat_water
! PROCEDURE :: calculate_riparian => aed_calculate_riparian_habitat_water
! PROCEDURE :: mobility => aed_mobility_habitat_water
! PROCEDURE :: light_extinction => aed_light_extinction_habitat_water
! PROCEDURE :: delete => aed_delete_habitat_water
Expand All @@ -103,7 +87,6 @@ MODULE aed_habitat_water
!-------------------------------------------------------------------------------
!MODULE VARIABLES
AED_REAL, PARAMETER :: DDT = 0.25/24. ! Currently assuming 15 min timestep
LOGICAL :: extra_diag
INTEGER :: diag_level = 10

!===============================================================================
Expand All @@ -124,48 +107,42 @@ SUBROUTINE aed_define_habitat_water(data, namlst)
CLASS (aed_habitat_water_data_t),INTENT(inout) :: data
!
!LOCALS
INTEGER :: i, z, status, num_mtox
INTEGER :: n_zones_chara = 0, active_zones_chara(MAX_ZONES)
INTEGER :: n_zones_fishspawn = 0,active_zones_fishspawn(MAX_ZONES)
LOGICAL :: simFishTolerance, simGalaxiidSpawning, simBenthicProd, &
simCyanoRisk, simMosquitoRisk, simCrabHabitat, simClearWater, &
simRuppiaHabitat, simCharaHabitat, simMetalTox
INTEGER :: i, f, z, status, num_mtox, num_fish
LOGICAL :: simFishTolerance,simCyanoRisk,simMosquitoRisk,simClearWater,simMetalTox
AED_REAL :: mtox_lims(10)
CHARACTER(len=64) :: bird_acid_link, bird_habs_link, bird_aass_link, bird_rveg_link, bird_bveg_link
CHARACTER(len=64) :: fshsi_veg_link, fshsi_oxy_link, fshsi_otrc_link
CHARACTER(len=64) :: chsi_otrc_link, chsi_oxy_link, chsi_veg_link
CHARACTER(len=64) :: chhsi_salg_link,chhsi_falg_link
CHARACTER(len=64) :: chhsi_ncs1_link,chhsi_ncs2_link,chhsi_tau0_link
CHARACTER(len=64) :: crhsi_ncs1_link,crhsi_ncs2_link
CHARACTER(len=64) :: crhsi_stmp_link,crhsi_svwc_link,crhsi_pass_link
CHARACTER(len=64) :: pshsi_stmp_link,pshsi_svwc_link,pshsi_veg1_link,pshsi_veg2_link
CHARACTER(len=64) :: pshsi_ncs1_link, pshsi_ncs2_link
CHARACTER(len=64) :: rhsi_salg_link, rhsi_falg_link
CHARACTER(len=40) :: mtox_acid_link, mtox_aass_link
AED_REAL :: fish_alpha(20),fish_Tmax(20),fish_Taccl(20),fish_Ocrit(20),fish_KO(20)
CHARACTER(len=40) :: mtox_acid_link, mtox_aass_link, fish_oxy_link
CHARACTER(len=40) :: mtox_vars(10)

NAMELIST /aed_habitat_water/ &
simFishTolerance, &
simClearWater, &
simCyanoRisk, &
simMetalTox, mtox_vars, mtox_lims, &
CHARACTER(6) :: fish_name

NAMELIST /aed_habitat_water/ &
simFishTolerance, num_fish, &
fish_alpha,fish_Tmax,fish_Taccl,fish_Ocrit,fish_KO,&
simClearWater, &
simCyanoRisk, &
simMetalTox, mtox_vars, mtox_lims, &
diag_level
!
!-------------------------------------------------------------------------------
!BEGIN
print *," aed_habitat_water initialization"
print *," WARNING! aed_habitat model is currently under development"
print *," WARNING! aed_habitat model is currently under development"

! Default
simFishTolerance = .false.
simClearWater = .false.
simCyanoRisk = .false.
simMetalTox = .false.

simFishTolerance = .false.
fish_alpha(:) = 1.
fish_Tmax(:) = 40.
fish_Taccl(:) = 0.
fish_Ocrit(:) = 10.
fish_KO(:) = 10.

! Read the namelist
read(namlst,nml=aed_habitat_water,iostat=status)
IF (status /= 0) STOP 'Error reading namelist aed_habitat'
IF (status /= 0) STOP 'ERROR reading namelist aed_habitat_water'

! Update module level switches
data%num_habitats = 0
Expand Down Expand Up @@ -198,57 +175,80 @@ SUBROUTINE aed_define_habitat_water(data, namlst)
ENDDO
ENDIF

!-- FISH TOLERANCE
IF( simFishTolerance ) THEN
fish_name = 'fish0'
data%num_fish = MAX(MIN(num_fish,20),0)
ALLOCATE(data%id_fish(num_fish));
DO f=1,num_fish
fish_name(5:5) = CHAR(ICHAR('0') + f)
data%id_fish(f) = aed_define_diag_variable(TRIM(fish_name),'-', 'Fish Habittat Suitability')
ENDDO

fish_oxy_link = 'OXY_sat'
data%id_l_oxys = aed_locate_global(TRIM(fish_oxy_link))

ALLOCATE(data%fish_alpha(num_fish))
ALLOCATE(data%fish_Tmax(num_fish))
ALLOCATE(data%fish_Taccl(num_fish))
ALLOCATE(data%fish_Ocrit(num_fish))
ALLOCATE(data%fish_KO(num_fish))
DO f=1,num_fish
data%fish_alpha(f) = fish_alpha(f)
data%fish_Tmax(f) = fish_Tmax(f)
data%fish_Taccl(f) = fish_Taccl(f)
data%fish_Ocrit(f) = fish_Ocrit(f)
data%fish_KO(f) = fish_KO(f)
ENDDO
print *,'yo'
ENDIF

! !-- GENERAL
! IF( simGalaxiidSpawning .OR. simCharaHabitat .OR. simRuppiaHabitat) THEN
! data%id_wettime = aed_define_sheet_diag_variable('wettime','d','time cell has been innundated')
! data%id_drytime = aed_define_sheet_diag_variable('drytime','d','time cell has been exposed')
! ENDIF

! Register environmental dependencies
data%id_E_salt = aed_locate_global('salinity')
data%id_E_extc = aed_locate_global('extc_coef')
data%id_E_temp = aed_locate_global('temperature')
data%id_E_depth = aed_locate_global('layer_ht')
data%id_E_bathy = aed_locate_global_sheet('bathy')
data%id_E_matz = aed_locate_global_sheet('material')
data%id_E_Io = aed_locate_global_sheet('par_sf')
data%id_E_airtemp = aed_locate_global_sheet('air_temp')
data%id_E_stress = aed_locate_global_sheet('taub')
data%id_E_nearlevel = aed_locate_global_sheet('nearest_depth')
data%id_E_salt = aed_locate_global('salinity')
data%id_E_extc = aed_locate_global('extc_coef')
data%id_E_temp = aed_locate_global('temperature')
data%id_E_depth = aed_locate_global('layer_ht')
! data%id_E_bathy = aed_locate_global_sheet('bathy')
! data%id_E_matz = aed_locate_global_sheet('material')
! data%id_E_Io = aed_locate_global_sheet('par_sf')
! data%id_E_airtemp = aed_locate_global_sheet('air_temp')
! data%id_E_stress = aed_locate_global_sheet('taub')
! data%id_E_nearlevel = aed_locate_global_sheet('nearest_depth')

END SUBROUTINE aed_define_habitat_water
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



!###############################################################################
SUBROUTINE aed_calculate_riparian_habitat_water(data,column,layer_idx,pc_wet)
SUBROUTINE aed_calculate_habitat_water(data,column,layer_idx)
!-------------------------------------------------------------------------------
! Calculate pelagic bottom fluxes and benthic sink and source terms of AED habitat.
! Everything in units per surface area (not volume!) per time.
! Calculate pelagic habitat quality metrics.
!-------------------------------------------------------------------------------
!ARGUMENTS
CLASS (aed_habitat_water_data_t),INTENT(in) :: data
TYPE (aed_column_t),INTENT(inout) :: column(:)
INTEGER,INTENT(in) :: layer_idx
AED_REAL,INTENT(in) :: pc_wet
!
!LOCALS
! Environment
AED_REAL :: temp, salt, wlevel, extc, bathy, matz, Io, Ig, vel, stress, tau0, stem05, stem25
AED_REAL :: temp, salt, wlevel, extc, bathy, Io, vel, tau0

! State
AED_REAL :: depth, ph, hab, sdepth, uzaass, aass, conc, mtox, turb, grav, stem, svwc
AED_REAL :: osat

! Temporary variables
INTEGER :: i
INTEGER :: i, f
AED_REAL :: euphotic, drytime, light
AED_REAL :: OPCTmax, Ocrit, alpha, Tmax , HSI_f, Ko

! Parameters
AED_REAL, PARAMETER :: crit_soil_acidity = 100.000
AED_REAL, PARAMETER :: crit_water_ph = 6.0
AED_REAL, PARAMETER :: crit_soil_type = 5.5 ! (matz 6&7 is sand)
AED_REAL, PARAMETER :: crit_rveg_depth = 0.6
AED_REAL, PARAMETER :: sav_height = 0.1 !assume plant are 10cm to middle
AED_REAL, PARAMETER :: crit_salinity = 50.0
AED_REAL, PARAMETER :: crit_leg_depth = 0.12
Expand All @@ -263,24 +263,40 @@ SUBROUTINE aed_calculate_riparian_habitat_water(data,column,layer_idx,pc_wet)

!-------------------------------------------------------------------------------
!BEGIN
matz = 0.0 ; salt = 0.0 ; euphotic = 0.0 ; bathy = 0.0 !## CAB [-Wmaybe-uninitialized]
salt = 0.0 ; euphotic = 0.0 ; bathy = 0.0


!---------------------------------------------------------------------------+
!-- HABITAT TEMPLATE X:
! IF( data%simMosquitoRisk ) THEN
!
! ! _DIAG_VAR_S_(data%id_fish) = mtox
!
! ENDIF
!-- HABITAT TEMPLATE : FISH TOLERANCE
IF( data%simFishTolerance ) THEN

salt = _STATE_VAR_(data%id_E_salt) ! salinity g/L
temp = _STATE_VAR_(data%id_E_temp) ! degC
osat = _STATE_VAR_(data%id_l_oxys) ! oxy %


DO f=1,data%num_fish
Ocrit = data%fish_Ocrit(f)
alpha = data%fish_alpha(f)
Tmax = data%fish_Tmax(f)
Ko = data%fish_Ko(f)

END SUBROUTINE aed_calculate_riparian_habitat_water
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
OPCTmax = Ocrit - MIN(alpha * (Tmax - temp),zero_)
HSI_f = zero_
IF(osat>OPCTmax) THEN
HSI_f = (osat-OPCTmax)/(Ko+osat-OPCTmax)
HSI_f = MIN(HSI_f / ((100.-OPCTmax)/(Ko+100.-OPCTmax)),one_)
ENDIF

_DIAG_VAR_(data%id_fish(f)) = HSI_f
ENDDO

ENDIF



END SUBROUTINE aed_calculate_habitat_water
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


END MODULE aed_habitat_water

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