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aed_bio_particles.F90
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aed_bio_particles.F90
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!###############################################################################
!# #
!# aed_bio_particles.F90 #
!# #
!# Developed by : #
!# AquaticEcoDynamics (AED) Group #
!# School of Agriculture and Environment #
!# The University of Western Australia #
!# #
!# http:https://aquatic.science.uwa.edu.au/ #
!# #
!# Copyright 2018 - 2024 - The University of Western Australia #
!# #
!# AED is free software: you can redistribute it and/or modify #
!# it under the terms of the GNU General Public License as published by #
!# the Free Software Foundation, either version 3 of the License, or #
!# (at your option) any later version. #
!# #
!# AED is distributed in the hope that it will be useful, #
!# but WITHOUT ANY WARRANTY; without even the implied warranty of #
!# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
!# GNU General Public License for more details. #
!# #
!# You should have received a copy of the GNU General Public License #
!# along with this program. If not, see <http:https://www.gnu.org/licenses/>. #
!# #
!# ----------------------------------------------------------------------- #
!# #
!# Created Jul 2018 #
!# #
!###############################################################################
#include "aed.h"
!
MODULE aed_bio_particles
!-------------------------------------------------------------------------------
! aed_bio_particles --- test particle model
!
! The AED module test contains basic equations that have no dependencies
!-------------------------------------------------------------------------------
USE aed_core
IMPLICIT NONE
PRIVATE
!
PUBLIC aed_bio_particles_data_t
!
TYPE,extends(aed_model_data_t) :: aed_bio_particles_data_t
!# Variable identifiers
INTEGER :: id_ptm_01, id_ptm_02, id_ptm_03, id_ptm_04, &
id_ptm_05, id_ptm_06, id_ptm_07, id_ptm_08, &
id_ptm_09, id_ptm_10, id_ptm_11, id_ptm_12, &
id_ptm_13, id_ptm_14, id_ptm_15, id_ptm_16, &
id_ptm_17, id_ptm_18
INTEGER :: id_ptm101, id_ptm102, id_ptm103, id_ptm104, &
id_ptm105, id_ptm106, id_ptm107, id_ptm108, &
id_ptm109, id_ptm110, id_ptm111, id_ptm112, &
id_ptm113, id_ptm114, id_ptm115, id_ptm116, &
id_ptm117, id_ptm118
INTEGER :: id_ptm_00
INTEGER :: id_d_oxy, id_d_dc, id_d_dn, id_d_dp
INTEGER :: id_oxy,id_amm,id_nit,id_frp,id_doc,id_don,id_dop
INTEGER :: id_lht, id_larea
AED_REAL :: vvel_new, vvel_old, decay_rate_new, decay_rate_old
AED_REAL :: X_dwww, X_cdw, X_nc, X_pc, mass_limit
CONTAINS
PROCEDURE :: define => aed_define_bio_particles
! PROCEDURE :: calculate => aed_calculate_bio_particles
! PROCEDURE :: calculate_benthic => aed_calculate_benthic_bio_particles
! PROCEDURE :: calculate_riparian => aed_calculate_riparian_bio_particles
! PROCEDURE :: calculate_dry => aed_calculate_dry_bio_particles
! PROCEDURE :: equilibrate => aed_equilibrate_bio_particles
! PROCEDURE :: mobility => aed_mobility_bio_particles
! PROCEDURE :: light_extinction => aed_light_extinction_bio_particles
! PROCEDURE :: delete => aed_delete_bio_particles
PROCEDURE :: particle_bgc => aed_particle_bgc_bio_particles
END TYPE
INTEGER, PARAMETER :: PTM_MASS = 15
INTEGER, PARAMETER :: PTM_VVEL = 14
INTEGER, PARAMETER :: PTM_BIRTH = 17
INTEGER, PARAMETER :: PTM_AGE = 18
INTEGER, PARAMETER :: PTM_STATUS = 19
LOGICAL :: extra_diag = .false.
INTEGER :: diag_level = 10 ! 0 = no diagnostic outputs
! 1 = basic diagnostic outputs
! 2 = flux rates, and supporitng
! 3 = other metrics
!10 = all debug & checking outputs
!===============================================================================
CONTAINS
!###############################################################################
SUBROUTINE aed_define_bio_particles(data, namlst)
!-------------------------------------------------------------------------------
! Initialise the AED model
!
! Here, the aed namelist is read and the variables exported
! by the model are registered with AED.
!-------------------------------------------------------------------------------
!ARGUMENTS
INTEGER,INTENT(in) :: namlst
CLASS (aed_bio_particles_data_t),INTENT(inout) :: data
!
!LOCALS
INTEGER :: status
! %% NAMELIST %% /aed_bio_particles/
! %% Last Checked 20/08/2021
AED_REAL :: vvel_new = 0.
AED_REAL :: vvel_old = 0.
AED_REAL :: decay_rate_new = 0.
AED_REAL :: decay_rate_old = 0.
AED_REAL :: mass_limit = 10.
AED_REAL :: X_cdw = 0.5
AED_REAL :: X_nc = 0.1
AED_REAL :: X_pc = 0.01
AED_REAL :: X_dwww = 1.0
! From Module Globals
! LOGICAL :: extra_diag = .false. !## Obsolete Use diag_level = 10
! INTEGER :: diag_level = 10 ! 0 = no diagnostic outputs
! ! 1 = basic diagnostic outputs
! ! 2 = flux rates, and supporitng
! ! 3 = other metrics
! !10 = all debug & checking outputs
! %% END NAMELIST %% /aed_bio_particles/
NAMELIST /aed_bio_particles/ vvel_new, vvel_old, &
decay_rate_new, decay_rate_old, &
mass_limit, extra_diag, diag_level, &
X_dwww, X_cdw, X_nc, X_pc
!
!-------------------------------------------------------------------------------
!BEGIN
! Initialise
! Read the namelist
read(namlst,nml=aed_bio_particles,iostat=status)
IF (status /= 0) STOP 'Error reading namelist aed_bio_particles'
print *," aed_bio_particles initialization"
IF ( extra_diag ) diag_level = 10
! Set module parameters
data%vvel_new = vvel_new/secs_per_day
data%vvel_old = vvel_old/secs_per_day
data%decay_rate_new = decay_rate_new/secs_per_day
data%decay_rate_old = decay_rate_old/secs_per_day
data%mass_limit = mass_limit
data%X_dwww = X_dwww
data%X_cdw = X_cdw
data%X_nc = X_nc
data%X_pc = X_pc
! Diagnostic outputs for particle properties
data%id_ptm_00 = aed_define_diag_variable('total_count', '#', 'particle count')
data%id_ptm_14 = aed_define_diag_variable('total_vvel', 'm/s', 'sum of particle vvel')
data%id_ptm_15 = aed_define_diag_variable('total_mass', 'g', 'sum of particle mass')
data%id_ptm_17 = aed_define_diag_variable('total_birth', 'day', 'sum of birth date')
data%id_ptm_18 = aed_define_diag_variable('total_age', 'days', 'sum of particle age')
data%id_ptm114 = aed_define_diag_variable('vvel', 'm/s', 'last particle vvel')
data%id_ptm115 = aed_define_diag_variable('mass', 'g', 'last particle mass')
data%id_ptm117 = aed_define_diag_variable('birth', 'day', 'last particle birth time')
data%id_ptm118 = aed_define_diag_variable('age', 'days', 'last particle age')
! Junk properties
IF( diag_level >= 10 ) THEN
data%id_ptm_01 = aed_define_diag_variable('bioptm01', '', 'bio_particles 01')
data%id_ptm_02 = aed_define_diag_variable('bioptm02', '', 'bio_particles 02')
data%id_ptm_03 = aed_define_diag_variable('bioptm03', '', 'bio_particles 03')
data%id_ptm_04 = aed_define_diag_variable('bioptm04', '', 'bio_particles 04')
data%id_ptm_05 = aed_define_diag_variable('bioptm05', '', 'bio_particles 05')
data%id_ptm_06 = aed_define_diag_variable('bioptm06', '', 'bio_particles 06')
data%id_ptm_07 = aed_define_diag_variable('bioptm07', '', 'bio_particles 07')
data%id_ptm_08 = aed_define_diag_variable('bioptm08', '', 'bio_particles 08')
data%id_ptm_09 = aed_define_diag_variable('bioptm09', '', 'bio_particles 09')
data%id_ptm_10 = aed_define_diag_variable('bioptm10', '', 'bio_particles 10')
data%id_ptm_11 = aed_define_diag_variable('bioptm11', '', 'bio_particles 11')
data%id_ptm_12 = aed_define_diag_variable('bioptm12', '', 'bio_particles 12')
data%id_ptm_13 = aed_define_diag_variable('bioptm13', '', 'bio_particles 13')
data%id_ptm_16 = aed_define_diag_variable('bioptm16', '', 'bio_particles 16')
data%id_ptm101 = aed_define_diag_variable('bioptm101', '', 'bio_particles101')
data%id_ptm102 = aed_define_diag_variable('bioptm102', '', 'bio_particles102')
data%id_ptm103 = aed_define_diag_variable('bioptm103', '', 'bio_particles103')
data%id_ptm104 = aed_define_diag_variable('bioptm104', '', 'bio_particles104')
data%id_ptm105 = aed_define_diag_variable('bioptm105', '', 'bio_particles105')
data%id_ptm106 = aed_define_diag_variable('bioptm106', '', 'bio_particles106')
data%id_ptm107 = aed_define_diag_variable('bioptm107', '', 'bio_particles107')
data%id_ptm108 = aed_define_diag_variable('bioptm108', '', 'bio_particles108')
data%id_ptm109 = aed_define_diag_variable('bioptm109', '', 'bio_particles109')
data%id_ptm110 = aed_define_diag_variable('bioptm110', '', 'bio_particles110')
data%id_ptm111 = aed_define_diag_variable('bioptm111', '', 'bio_particles111')
data%id_ptm112 = aed_define_diag_variable('bioptm112', '', 'bio_particles112')
data%id_ptm113 = aed_define_diag_variable('bioptm113', '', 'bio_particles113')
data%id_ptm116 = aed_define_diag_variable('bioptm116', '', 'bio_particles116')
ENDIF
! Diagnostic outputs for fluxes into cell
data%id_d_oxy = aed_define_diag_variable('oxy_flux', 'mmol O2/m3/day','oxygen consumption')
data%id_d_dc = aed_define_diag_variable('dc_flux', 'mmol DOC/m3/day','dissolved C release')
data%id_d_dn = aed_define_diag_variable('dn_flux', 'mmol N/m3/day','dissolved N release')
data%id_d_dp = aed_define_diag_variable('dp_flux', 'mmol P/m3/day','dissolved P release')
! Linked state variables
data%id_oxy = aed_locate_variable('OXY_oxy')
data%id_amm = aed_locate_variable('NIT_amm')
data%id_nit = aed_locate_variable('NIT_nit')
data%id_frp = aed_locate_variable('PHS_frp')
data%id_doc = aed_locate_variable('OGM_doc')
data%id_don = aed_locate_variable('OGM_don')
data%id_dop = aed_locate_variable('OGM_dop')
! Environment variables
data%id_larea = aed_locate_sheet_global('layer_area')
data%id_lht = aed_locate_global('layer_ht')
END SUBROUTINE aed_define_bio_particles
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
SUBROUTINE aed_particle_bgc_bio_particles(data,column,layer_idx,ppid,partcl)
!ARGUMENTS
CLASS (aed_bio_particles_data_t),INTENT(in) :: data
TYPE (aed_column_t),INTENT(inout) :: column(:)
INTEGER,INTENT(in) :: layer_idx
INTEGER,INTENT(inout) :: ppid
AED_REAL,DIMENSION(:),INTENT(inout) :: partcl
!
!LOCALS
INTEGER :: n
AED_REAL :: oxy_flux
AED_REAL :: decay, area, thickness
AED_REAL, PARAMETER :: buoyancy_age = 86400.
AED_REAL, PARAMETER :: DT = 15.*60.
AED_REAL, PARAMETER :: decay_rate = 0.15
AED_REAL, PARAMETER :: fres = 0.7
!
!-------------------------------------------------------------------------------
!BEGIN
! Check if we are in a new cell, to reset cumulative counters
IF (ppid == 0) THEN
_DIAG_VAR_(data%id_ptm_14) = zero_
_DIAG_VAR_(data%id_ptm_15) = zero_
_DIAG_VAR_(data%id_ptm_17) = zero_
_DIAG_VAR_(data%id_ptm_18) = zero_
_DIAG_VAR_(data%id_d_oxy) = zero_
_DIAG_VAR_(data%id_d_dc) = zero_
_DIAG_VAR_(data%id_d_dn) = zero_
_DIAG_VAR_(data%id_d_dp) = zero_
IF( diag_level >= 10 ) THEN
_DIAG_VAR_(data%id_ptm_01) = zero_
_DIAG_VAR_(data%id_ptm_02) = zero_
_DIAG_VAR_(data%id_ptm_03) = zero_
_DIAG_VAR_(data%id_ptm_04) = zero_
_DIAG_VAR_(data%id_ptm_05) = zero_
_DIAG_VAR_(data%id_ptm_06) = zero_
_DIAG_VAR_(data%id_ptm_07) = zero_
_DIAG_VAR_(data%id_ptm_08) = zero_
_DIAG_VAR_(data%id_ptm_09) = zero_
_DIAG_VAR_(data%id_ptm_10) = zero_
_DIAG_VAR_(data%id_ptm_11) = zero_
_DIAG_VAR_(data%id_ptm_12) = zero_
_DIAG_VAR_(data%id_ptm_13) = zero_
_DIAG_VAR_(data%id_ptm_16) = zero_
ENDIF
ENDIF
! Increment the particle count for this cell and set to diagnostic
ppid = ppid + 1
_DIAG_VAR_(data%id_ptm_00) = ppid !,AED_REAL) ! total number of particles within a cell
! Particle decay, changing with age
thickness = _STATE_VAR_(data%id_lht)
area = _STATE_VAR_S_(data%id_larea)
IF((partcl(PTM_AGE)-partcl(PTM_BIRTH))<buoyancy_age) THEN
decay = partcl(PTM_MASS) * (DT*data%decay_rate_new) ! g / timestep
ELSE
decay = partcl(PTM_MASS) * (DT*data%decay_rate_old) ! g / timestep
ENDIF
partcl(PTM_MASS) = partcl(PTM_MASS) - decay
IF ( partcl(PTM_MASS) <= data%mass_limit ) partcl(PTM_STATUS) = -1
oxy_flux = data%X_dwww * (1e3/12.) * (decay/DT) * data%X_cdw / (area*thickness) ! mmol C / m3/ s
! Respiration of decaying particles
_FLUX_VAR_(data%id_oxy) = _FLUX_VAR_(data%id_oxy) - fres * oxy_flux
_FLUX_VAR_(data%id_amm) = _FLUX_VAR_(data%id_amm) + fres * oxy_flux * data%X_nc
_FLUX_VAR_(data%id_frp) = _FLUX_VAR_(data%id_frp) + fres * oxy_flux * data%X_pc
_FLUX_VAR_(data%id_nit) = _FLUX_VAR_(data%id_nit) + zero_
! DOM leakage from particles during decay
_FLUX_VAR_(data%id_doc) = _FLUX_VAR_(data%id_doc) + (1.-fres) * oxy_flux
_FLUX_VAR_(data%id_don) = _FLUX_VAR_(data%id_don) + (1.-fres) * oxy_flux * data%X_nc
_FLUX_VAR_(data%id_dop) = _FLUX_VAR_(data%id_dop) + (1.-fres) * oxy_flux * data%X_pc
! Cumulative oxygen and nutrient fluxes into a cell
_DIAG_VAR_(data%id_d_oxy) = _DIAG_VAR_(data%id_d_oxy) - fres * oxy_flux * secs_per_day ! O2
_DIAG_VAR_(data%id_d_dc) = _DIAG_VAR_(data%id_d_dc) - (1.-fres)* oxy_flux * secs_per_day ! DOC
_DIAG_VAR_(data%id_d_dn) = &
_DIAG_VAR_(data%id_d_dn) - oxy_flux * data%X_nc * secs_per_day ! DON + NH4 + NO3
_DIAG_VAR_(data%id_d_dp) = _DIAG_VAR_(data%id_d_dp) - oxy_flux * data%X_pc * secs_per_day ! DOP + FRP
! Particle bouyancy, changing with age
IF((partcl(PTM_AGE)-partcl(PTM_BIRTH))<buoyancy_age) THEN
partcl(PTM_VVEL) = data%vvel_new
ELSE
partcl(PTM_VVEL) = data%vvel_old
ENDIF
! Set diagnostics, summarising particles in this cell
! 1st, Cumulate particle properties (divide by particle number for average)
_DIAG_VAR_(data%id_ptm_14) = _DIAG_VAR_(data%id_ptm_14) + partcl(PTM_VVEL)
_DIAG_VAR_(data%id_ptm_15) = &
_DIAG_VAR_(data%id_ptm_15) + partcl(PTM_MASS) ! total particle mass within a cell
_DIAG_VAR_(data%id_ptm_17) = _DIAG_VAR_(data%id_ptm_17) + partcl(PTM_BIRTH)
_DIAG_VAR_(data%id_ptm_18) = &
_DIAG_VAR_(data%id_ptm_18) + (partcl(PTM_AGE)-partcl(PTM_BIRTH)) /secs_per_day
IF( diag_level >= 10 ) THEN
_DIAG_VAR_(data%id_ptm_01) = _DIAG_VAR_(data%id_ptm_01) + partcl(1)
_DIAG_VAR_(data%id_ptm_02) = _DIAG_VAR_(data%id_ptm_02) + partcl(2)
_DIAG_VAR_(data%id_ptm_03) = _DIAG_VAR_(data%id_ptm_03) + partcl(3)
_DIAG_VAR_(data%id_ptm_04) = _DIAG_VAR_(data%id_ptm_04) + partcl(4)
_DIAG_VAR_(data%id_ptm_05) = _DIAG_VAR_(data%id_ptm_05) + partcl(5)
_DIAG_VAR_(data%id_ptm_06) = _DIAG_VAR_(data%id_ptm_06) + partcl(6)
_DIAG_VAR_(data%id_ptm_07) = _DIAG_VAR_(data%id_ptm_07) + partcl(7)
_DIAG_VAR_(data%id_ptm_08) = _DIAG_VAR_(data%id_ptm_08) + partcl(8)
_DIAG_VAR_(data%id_ptm_09) = _DIAG_VAR_(data%id_ptm_09) + partcl(9)
_DIAG_VAR_(data%id_ptm_10) = _DIAG_VAR_(data%id_ptm_10) + partcl(10)
_DIAG_VAR_(data%id_ptm_11) = _DIAG_VAR_(data%id_ptm_11) + partcl(11)
_DIAG_VAR_(data%id_ptm_12) = _DIAG_VAR_(data%id_ptm_12) + partcl(12)
_DIAG_VAR_(data%id_ptm_13) = _DIAG_VAR_(data%id_ptm_13) + partcl(13)
_DIAG_VAR_(data%id_ptm_16) = _DIAG_VAR_(data%id_ptm_16) + partcl(16)
ENDIF
! 2nd, Set particle property (this will therefore remember last particle only)
_DIAG_VAR_(data%id_ptm114) = partcl(PTM_VVEL)
_DIAG_VAR_(data%id_ptm115) = partcl(PTM_MASS)
_DIAG_VAR_(data%id_ptm117) = partcl(PTM_BIRTH)
_DIAG_VAR_(data%id_ptm118) = (partcl(PTM_AGE)-partcl(PTM_BIRTH))/secs_per_day
IF( diag_level >= 10 ) THEN
_DIAG_VAR_(data%id_ptm101) = partcl(1)
_DIAG_VAR_(data%id_ptm102) = partcl(2)
_DIAG_VAR_(data%id_ptm103) = partcl(3)
_DIAG_VAR_(data%id_ptm104) = partcl(4)
_DIAG_VAR_(data%id_ptm105) = partcl(5)
_DIAG_VAR_(data%id_ptm106) = partcl(6)
_DIAG_VAR_(data%id_ptm107) = partcl(7)
_DIAG_VAR_(data%id_ptm108) = partcl(8)
_DIAG_VAR_(data%id_ptm109) = partcl(9)
_DIAG_VAR_(data%id_ptm110) = partcl(10)
_DIAG_VAR_(data%id_ptm111) = partcl(11)
_DIAG_VAR_(data%id_ptm112) = partcl(12)
_DIAG_VAR_(data%id_ptm113) = partcl(13)
_DIAG_VAR_(data%id_ptm116) = partcl(16)
ENDIF
!print *,'ptm ',ppid,(partcl(PTM_AGE)-partcl(PTM_BIRTH))/secs_per_day,partcl(PTM_MASS), &
! decay,partcl(PTM_VVEL),_DIAG_VAR_(data%id_ptm_15)
END SUBROUTINE aed_particle_bgc_bio_particles
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
END MODULE aed_bio_particles