From 7abe0e0054c27fce8f1722e22dd659bcf206811e Mon Sep 17 00:00:00 2001
From: jmaerz <92309038+jmaerz@users.noreply.github.com>
Date: Fri, 25 Oct 2024 11:43:39 +0200
Subject: [PATCH] Apply patch of latest commit in master for the dustflux
output PR #420 (#423)
Introduction of dustflux output and of a xml-switch HAMOCC_SINKING_SCHEME with options WLIN, AGG, M4AGO and CONST, default is WLIN, to select a sinking scheme in iHAMOCC.
---
cime_config/buildnml | 29 +++-
cime_config/config_component.xml | 15 +-
cime_config/namelist_definition_blom.xml | 178 ++++++++++++++++-------
cime_config/ocn_in.readme | 1 +
hamocc/mo_accfields.F90 | 10 ++
hamocc/mo_bgcmean.F90 | 35 ++++-
hamocc/mo_biomod.F90 | 28 +++-
hamocc/mo_ncout_hamocc.F90 | 40 ++++-
hamocc/mo_ocprod.F90 | 103 +++++++++----
9 files changed, 338 insertions(+), 101 deletions(-)
diff --git a/cime_config/buildnml b/cime_config/buildnml
index 6ef0f906..89952579 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -83,7 +83,7 @@ def buildnml(case, caseroot, compname):
hamocc_extncycle = case.get_value("HAMOCC_EXTNCYCLE")
hamocc_n2oc = case.get_value("HAMOCC_N2OC")
hamocc_atmndepc = case.get_value("HAMOCC_ATMNDEPC")
- hamocc_m4ago = case.get_value("HAMOCC_M4AGO")
+ hamocc_sinking_scheme = case.get_value("HAMOCC_SINKING_SCHEME")
hamocc_sedbypass = case.get_value("HAMOCC_SEDBYPASS")
hamocc_sedspinup = case.get_value("HAMOCC_SEDSPINUP")
hamocc_sedspinup_yr_start = case.get_value("HAMOCC_SEDSPINUP_YR_START")
@@ -192,7 +192,6 @@ def buildnml(case, caseroot, compname):
config["hamocc_extncycle"] = "yes" if hamocc_extncycle else "no"
config["hamocc_n2oc"] = "yes" if hamocc_n2oc else "no"
config["hamocc_atmndepc"] = "yes" if hamocc_atmndepc else "no"
- config["hamocc_m4ago"] = "yes" if hamocc_m4ago else "no"
config["hamocc_sedbypass"] = "yes" if hamocc_sedbypass else "no"
config["hamocc_sedspinup"] = "yes" if hamocc_sedspinup else "no"
config["hamocc_sedspinup_yr_start"] = hamocc_sedspinup_yr_start
@@ -201,9 +200,29 @@ def buildnml(case, caseroot, compname):
config["is_test"] = "yes" if is_test else "no"
config["comp_interface"] = comp_interface
- # TODO: the following needs to have new ways to turn this to "yes"
- config["use_agg"] = "no"
- config["use_wlin"] = "yes"
+ # Set the sinking scheme in iHAMOCC
+ # Note: the following part requires to have set options for no/yes
+ # in the namelist_definition_blom.xml for the 'use_XXX' switches
+ if hamocc_sinking_scheme == 'WLIN': # current default
+ config['use_wlin'] = 'yes'
+ config['use_agg'] = 'no'
+ config['use_m4ago'] = 'no'
+ elif hamocc_sinking_scheme == 'M4AGO':
+ config['use_wlin'] = 'no'
+ config['use_agg'] = 'no'
+ config['use_m4ago'] = 'yes'
+ elif hamocc_sinking_scheme == 'AGG':
+ config['use_wlin'] = 'no'
+ config['use_agg'] = 'yes'
+ config['use_m4ago'] = 'no'
+ elif hamocc_sinking_scheme == 'CONST':
+ # if all options are 'no' iHAMOCC falls back to constant sinking velocities
+ config['use_wlin'] = 'no'
+ config['use_agg'] = 'no'
+ config['use_m4ago'] = 'no'
+ else: # likely doesn't enter here due to previous cime checkings for available options
+ print('Unknown sinking scheme option in BLOM buildnml- exit now')
+ exit
if is_test:
testcase = case.get_value("TESTCASE")
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 3d462ee0..b13c8542 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -178,13 +178,14 @@
N2O and NH3 fluxes coupled from atmosphere. Requires module ecosys and extncycle
-
- logical
- TRUE,FALSE
- FALSE
- run_component_blom
- env_run.xml
- Set preprocessor option to activate the M4AGO sinking scheme. Requires module ecosys
+
+ char
+ WLIN,M4AGO,AGG,CONST
+ WLIN
+ run_component_blom
+ env_run.xml
+ Set namelist option to activate the M4AGO sinking scheme. Requires module ecosys
+ Namelist option to set sinking scheme. Requires module ecosys
diff --git a/cime_config/namelist_definition_blom.xml b/cime_config/namelist_definition_blom.xml
index 395f9d3b..03ec0732 100644
--- a/cime_config/namelist_definition_blom.xml
+++ b/cime_config/namelist_definition_blom.xml
@@ -3632,13 +3632,13 @@
Switch to couple N2O and NH3 fluxes
-
+
logical
bgcnml
bgcnml
.false.
- .true.
+ .true.
Switch for M4AGO settling scheme
@@ -3813,7 +3813,7 @@
.false.
- add desc
+ Switch to use variable sediment porosity
@@ -3846,6 +3846,7 @@
config_bgc
.true.
+ .false.
Use POC sinking scheme with increasing sinking velocity with depth
@@ -3955,6 +3956,7 @@
config_bgc
.false.
+ .true.
Use aggregation scheme for sinking of particles
@@ -3966,7 +3968,7 @@
.false.
- add desc
+ Activate interactive phytoplankton absorption
@@ -5022,7 +5024,7 @@
'hbgcd','hbgcm','hbgcy'
- add desc
+ File name extension for BGC output frequencies
@@ -5032,7 +5034,7 @@
1,30,365
- add desc
+ Averaging period for BGC diagnostic output
@@ -5044,7 +5046,7 @@
1,30,365
0,0,0
- add desc
+ Frequency for writing the BGC output
@@ -5054,7 +5056,7 @@
0,0,0
- add desc
+ switch for compressed/uncompressed output
@@ -5065,7 +5067,7 @@
0,0,0
1,1,1
- add desc
+ netcdf format (valid arguments are 0 for classic, 1 for 64-bit offset and 2 for netcdf4/hdf5 format)
@@ -5075,7 +5077,7 @@
0,1,0
- add desc
+ Writing the BGC inventory files at BGC frequencies
@@ -5171,7 +5173,7 @@
4,2,2
0,0,0
- add desc
+ Surface silicate concentration [mol Si m-3]
@@ -5699,7 +5701,7 @@
4,2,2
0,0,0
- add desc
+ Surface bromoform concentration [mol CHBr3 m-3]
@@ -5711,7 +5713,7 @@
4,2,2
0,0,0
- add desc
+ Surface bromoform flux [mol CHBr3 -m2 s-1]
@@ -5723,7 +5725,7 @@
4,2,2
0,0,0
- add desc
+ Integrated bromoform production [mol CHBr3 m-2 s-1]
@@ -5735,7 +5737,7 @@
4,2,2
0,0,0
- add desc
+ Integrated bromoform loss to photolysis [mol CHBr m-2 s-1]
@@ -5819,7 +5821,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux at 100m [mol C m-2 s-1]
@@ -5831,7 +5833,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux at 500m [mol C m-2 s-1]
@@ -5843,7 +5845,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux at 1000m [mol C m-2 s-1]
@@ -5855,7 +5857,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux at 2000m [mol C m-2 s-1]
@@ -5867,7 +5869,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux at 4000m [mol C m-2 s-1]
@@ -5879,7 +5881,79 @@
4,2,2
0,0,0
- add desc
+ Gravitational POC flux to the sediment [mol C m-2 s-1]
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes at 100m
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes at 500m
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes at 1000m
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes at 2000m
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes at 4000m
+
+
+
+ integer(3)
+ diabgc
+ diabgc
+
+ 0,2,2
+ 4,2,2
+ 0,0,0
+
+ Gravitational dust fluxes to sediment
@@ -5891,7 +5965,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux at 100m [mol Si m-2 s-1]
@@ -5903,7 +5977,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux at 500m [mol Si m-2 s-1]
@@ -5915,7 +5989,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux at 1000m [mol Si m-2 s-1]
@@ -5927,7 +6001,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux at 2000m [mol Si m-2 s-1]
@@ -5939,7 +6013,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux at 4000m [mol Si m-2 s-1]
@@ -5951,7 +6025,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational opal flux to the sediment [mol Si m-2 s-1]
@@ -5963,7 +6037,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux at 100m [mol Ca m-2 s-1]
@@ -5975,7 +6049,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux at 500m [mol Ca m-2 s-1]
@@ -5987,7 +6061,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux at 1000m [mol Ca m-2 s-1]
@@ -5999,7 +6073,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux at 2000m [mol Ca m-2 s-1]
@@ -6011,7 +6085,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux at 4000m [mol Ca m-2 s-1]
@@ -6023,7 +6097,7 @@
4,2,2
0,0,0
- add desc
+ Gravitational CaCO3 flux to the sediment [mol Ca m-2 s-1]
@@ -6035,7 +6109,7 @@
4,2,2
0,0,0
- add desc
+ Phytoplankton [mol P m-3]
@@ -6047,7 +6121,7 @@
4,2,2
0,0,0
- add desc
+ Zooplankton [mol P m-3]
@@ -6059,7 +6133,7 @@
4,2,2
0,0,0
- add desc
+ Dissolved organic carbon [mol P m-3]
@@ -6071,7 +6145,7 @@
4,2,2
0,0,0
- add desc
+ Primary production [mol C m-3]
@@ -6119,7 +6193,7 @@
2,0,2
0,0,0
- add desc
+ Nitrate concentration [mol NO3 m-3]
@@ -6479,7 +6553,7 @@
2,0,2
0,0,0
- add desc
+ Alkalinity [eq m-3]
@@ -6491,7 +6565,7 @@
2,0,2
0,0,0
- add desc
+ Silicate [mol Si m-3]
@@ -6503,7 +6577,7 @@
2,0,2
0,0,0
- add desc
+ Dissolved inorganic carbon [mol C m-3]
@@ -6515,7 +6589,7 @@
2,0,2
0,0,0
- add desc
+ Detritus [mol P m-3]
@@ -6575,7 +6649,7 @@
2,0,2
0,0,0
- add desc
+ pH [-log10([H+])]
@@ -6635,7 +6709,7 @@
2,0,2
0,0,0
- add desc
+ Preformed phosphorus [mol P m-3]
@@ -6647,7 +6721,7 @@
4,2,2
0,0,0
- Pre-formed silica [mol m-3]
+ Pre-formed silica [mol Si m-3]
@@ -6993,7 +7067,7 @@
0,0,2
- add desc
+ Bromoform [mol CHBr3 m-3]
@@ -7005,7 +7079,7 @@
0,2,2
0,0,0
- add desc
+ Layer thickness [m]
@@ -7557,7 +7631,7 @@
4,2,2
0,0,0
- add desc
+ pH [-log10(H+)]
@@ -7951,7 +8025,7 @@
4,2,2
0,0,0
- add desc
+ Bromoform [mol CHBr3 m-3]
@@ -7963,7 +8037,7 @@
2,0,2
0,0,0
- add desc
+ Diffusive DIC flux to sediment (positive downward) [mol C m-2 s-1]
@@ -7975,7 +8049,7 @@
2,0,2
0,0,0
- add desc
+ Diffusive alkalinity flux to sediment (positive downward) [mol eq m-2 s-1]
@@ -7987,7 +8061,7 @@
2,0,2
0,0,0
- add desc
+ Diffusive phosphate flux to sediment (positive downward) [mol P m-2 s-1]
diff --git a/cime_config/ocn_in.readme b/cime_config/ocn_in.readme
index 891e8785..1f09825d 100644
--- a/cime_config/ocn_in.readme
+++ b/cime_config/ocn_in.readme
@@ -572,6 +572,7 @@
! CARFLX**** - POC flux at **** metres depth [mol C m-2 s-1]
! BSIFLX**** - Biogenic silica flux at **** metres depth [mol Si m-2 s-1]
! CALFLX**** - Calcium carbonate flux at **** metres depth [mol C m-2 s-1]
+! DUSTFLX**** - Dust flux at **** metres depth [g m-2 s-1]
! SEDIFFIC - sediment - water-column diffusive flux of DIC [mol C m-2 s-1]
! SEDIFFAL - sediment - water-column diffusive flux of alkalinity [mol m-2 s-1]
! SEDIFFPH - sediment - water-column diffusive flux of phosphate [mol PO3 m-2 s-1]
diff --git a/hamocc/mo_accfields.F90 b/hamocc/mo_accfields.F90
index d214ea92..679ded85 100644
--- a/hamocc/mo_accfields.F90
+++ b/hamocc/mo_accfields.F90
@@ -50,6 +50,8 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
bsiflx2000,bsiflx4000,calflx_bot,calflx0100,calflx0500, &
calflx1000,calflx2000,calflx4000,carflx_bot,carflx0100, &
carflx0500,carflx1000,carflx2000,carflx4000, &
+ dustflx_bot,dustflx0100, &
+ dustflx0500,dustflx1000,dustflx2000,dustflx4000, &
expoca,expoor,exposi,intdms_bac,intdms_uv,intdmsprod, &
intdnit,intnfix,intphosy,phosy3d, &
int_chbr3_prod,int_chbr3_uv,asize3d,eps3d,wnumb,wmass, &
@@ -63,6 +65,8 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
jcalflx1000,jcalflx2000,jcalflx4000, &
jcalflx_bot,jcarflx0100,jcarflx0500, &
jcarflx1000,jcarflx2000,jcarflx4000,jcarflx_bot, &
+ jdustflx0100,jdustflx0500, &
+ jdustflx1000,jdustflx2000,jdustflx4000,jdustflx_bot, &
jsediffic,jsediffal,jsediffph,jsediffox, &
jburflxsso12,jburflxsssc12,jburflxssssil,jburflxssster, &
jsediffn2,jsediffno3,jsediffsi,jco2flux, &
@@ -335,21 +339,27 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call accsrf(jcarflx0100,carflx0100,omask,0)
call accsrf(jbsiflx0100,bsiflx0100,omask,0)
call accsrf(jcalflx0100,calflx0100,omask,0)
+ call accsrf(jdustflx0100,dustflx0100,omask,0)
call accsrf(jcarflx0500,carflx0500,omask,0)
call accsrf(jbsiflx0500,bsiflx0500,omask,0)
call accsrf(jcalflx0500,calflx0500,omask,0)
+ call accsrf(jdustflx0500,dustflx0500,omask,0)
call accsrf(jcarflx1000,carflx1000,omask,0)
call accsrf(jbsiflx1000,bsiflx1000,omask,0)
call accsrf(jcalflx1000,calflx1000,omask,0)
+ call accsrf(jdustflx1000,dustflx1000,omask,0)
call accsrf(jcarflx2000,carflx2000,omask,0)
call accsrf(jbsiflx2000,bsiflx2000,omask,0)
call accsrf(jcalflx2000,calflx2000,omask,0)
+ call accsrf(jdustflx2000,dustflx2000,omask,0)
call accsrf(jcarflx4000,carflx4000,omask,0)
call accsrf(jbsiflx4000,bsiflx4000,omask,0)
call accsrf(jcalflx4000,calflx4000,omask,0)
+ call accsrf(jdustflx4000,dustflx4000,omask,0)
call accsrf(jcarflx_bot,carflx_bot,omask,0)
call accsrf(jbsiflx_bot,bsiflx_bot,omask,0)
call accsrf(jcalflx_bot,calflx_bot,omask,0)
+ call accsrf(jdustflx_bot,dustflx_bot,omask,0)
endif
if (.not. use_sedbypass) then
diff --git a/hamocc/mo_bgcmean.F90 b/hamocc/mo_bgcmean.F90
index d4b0b74e..5eb4f542 100644
--- a/hamocc/mo_bgcmean.F90
+++ b/hamocc/mo_bgcmean.F90
@@ -123,6 +123,8 @@ module mo_bgcmean
& FLX_BSI2000 =0 ,FLX_BSI4000 =0 ,FLX_BSI_BOT =0 , &
& FLX_CAL0100 =0 ,FLX_CAL0500 =0 ,FLX_CAL1000 =0 , &
& FLX_CAL2000 =0 ,FLX_CAL4000 =0 ,FLX_CAL_BOT =0 , &
+ & FLX_DUST0100 =0 ,FLX_DUST0500 =0 ,FLX_DUST1000 =0 , &
+ & FLX_DUST2000 =0 ,FLX_DUST4000 =0 ,FLX_DUST_BOT =0 , &
& FLX_SEDIFFIC =0 ,FLX_SEDIFFAL =0 ,FLX_SEDIFFPH =0 , &
& FLX_SEDIFFOX =0 ,FLX_SEDIFFN2 =0 ,FLX_SEDIFFNO3 =0 , &
& FLX_SEDIFFSI =0 ,FLX_SEDIFFNH4 =0 ,FLX_SEDIFFN2O =0 , &
@@ -242,6 +244,8 @@ module mo_bgcmean
& FLX_BSI2000 ,FLX_BSI4000 ,FLX_BSI_BOT , &
& FLX_CAL0100 ,FLX_CAL0500 ,FLX_CAL1000 , &
& FLX_CAL2000 ,FLX_CAL4000 ,FLX_CAL_BOT , &
+ & FLX_DUST0100 ,FLX_DUST0500 ,FLX_DUST1000 , &
+ & FLX_DUST2000 ,FLX_DUST4000 ,FLX_DUST_BOT , &
& FLX_SEDIFFIC ,FLX_SEDIFFAL ,FLX_SEDIFFPH , &
& FLX_SEDIFFOX ,FLX_SEDIFFN2 ,FLX_SEDIFFNO3 , &
& FLX_SEDIFFSI ,FLX_SEDIFFNH4 ,FLX_SEDIFFN2O , &
@@ -273,7 +277,7 @@ module mo_bgcmean
& LYR_nitr_NH4_OM ,LYR_nitr_NO2_OM ,LYR_denit_NO3 , &
& LYR_denit_NO2 ,LYR_denit_N2O ,LYR_DNRA_NO2 , &
& LYR_anmx_N2_prod ,LYR_anmx_OM_prod ,LYR_phosy_NH4 , &
- & LYR_phosy_NO3 ,LYR_remin_aerob ,LYR_remin_sulf , &
+ & LYR_phosy_NO3 ,LYR_remin_aerob ,LYR_remin_sulf , &
& LYR_agg_ws ,LYR_dynvis ,LYR_agg_stick , &
& LYR_agg_stickf ,LYR_agg_dmax ,LYR_agg_avdp , &
& LYR_agg_avrhop ,LYR_agg_avdC ,LYR_agg_df , &
@@ -303,11 +307,11 @@ module mo_bgcmean
& LVL_nitr_NH4_OM ,LVL_nitr_NO2_OM ,LVL_denit_NO3 , &
& LVL_denit_NO2 ,LVL_denit_N2O ,LVL_DNRA_NO2 , &
& LVL_anmx_N2_prod ,LVL_anmx_OM_prod ,LVL_phosy_NH4 , &
- & LVL_phosy_NO3 ,LVL_remin_aerob ,LVL_remin_sulf , &
+ & LVL_phosy_NO3 ,LVL_remin_aerob ,LVL_remin_sulf , &
& LVL_agg_ws ,LVL_dynvis ,LVL_agg_stick , &
& LVL_agg_stickf ,LVL_agg_dmax ,LVL_agg_avdp , &
& LVL_agg_avrhop ,LVL_agg_avdC ,LVL_agg_df , &
- & LVL_agg_b ,LVL_agg_Vrhof ,LVL_agg_Vpor , &
+ & LVL_agg_b ,LVL_agg_Vrhof ,LVL_agg_Vpor , &
& SDM_POWAIC ,SDM_POWAAL ,SDM_POWAPH , &
& SDM_POWAOX ,SDM_POWN2 ,SDM_POWNO3 , &
& SDM_POWASI ,SDM_SSSO12 ,SDM_SSSSIL , &
@@ -416,7 +420,13 @@ module mo_bgcmean
& jcalflx1000= 0 , &
& jcalflx2000= 0 , &
& jcalflx4000= 0 , &
- & jcalflx_bot= 0
+ & jcalflx_bot= 0 , &
+ & jdustflx0100= 0 , &
+ & jdustflx0500= 0 , &
+ & jdustflx1000= 0 , &
+ & jdustflx2000= 0 , &
+ & jdustflx4000= 0 , &
+ & jdustflx_bot= 0
integer, dimension(nbgcmax) :: &
& jsediffic = 0 , &
@@ -865,6 +875,19 @@ subroutine alloc_mem_bgcmean(kpie,kpje,kpke)
jcalflx4000(n)=i_bsc_m2d*min(1,FLX_CAL4000(n))
if (FLX_CAL_BOT(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jcalflx_bot(n)=i_bsc_m2d*min(1,FLX_CAL_BOT(n))
+ if (FLX_DUST0100(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx0100(n)=i_bsc_m2d*min(1,FLX_DUST0100(n))
+ if (FLX_DUST0500(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx0500(n)=i_bsc_m2d*min(1,FLX_DUST0500(n))
+ if (FLX_DUST1000(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx1000(n)=i_bsc_m2d*min(1,FLX_DUST1000(n))
+ if (FLX_DUST2000(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx2000(n)=i_bsc_m2d*min(1,FLX_DUST2000(n))
+ if (FLX_DUST4000(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx4000(n)=i_bsc_m2d*min(1,FLX_DUST4000(n))
+ if (FLX_DUST_BOT(n) > 0) i_bsc_m2d=i_bsc_m2d+1
+ jdustflx_bot(n)=i_bsc_m2d*min(1,FLX_DUST_BOT(n))
+
if (.not. use_sedbypass) then
if (FLX_SEDIFFIC(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jsediffic(n)=i_bsc_m2d*min(1,FLX_SEDIFFIC(n))
@@ -957,7 +980,9 @@ subroutine alloc_mem_bgcmean(kpie,kpje,kpke)
jbsiflx0100+jbsiflx0500+jbsiflx1000+ &
jbsiflx2000+jbsiflx4000+jbsiflx_bot+ &
jcalflx0100+jcalflx0500+jcalflx1000+ &
- jcalflx2000+jcalflx4000+jcalflx_bot > 0)
+ jcalflx2000+jcalflx4000+jcalflx_bot+ &
+ jdustflx0100+jdustflx0500+jdustflx1000+ &
+ jdustflx2000+jdustflx4000+jdustflx_bot > 0)
i_atm_m2d=i_bsc_m2d
do n=1,nbgc
diff --git a/hamocc/mo_biomod.F90 b/hamocc/mo_biomod.F90
index 56bea1c0..cbe6fedd 100644
--- a/hamocc/mo_biomod.F90
+++ b/hamocc/mo_biomod.F90
@@ -69,6 +69,12 @@ module mo_biomod
real, dimension (:,:), allocatable, public :: calflx2000
real, dimension (:,:), allocatable, public :: calflx4000
real, dimension (:,:), allocatable, public :: calflx_bot
+ real, dimension (:,:), allocatable, public :: dustflx0100
+ real, dimension (:,:), allocatable, public :: dustflx0500
+ real, dimension (:,:), allocatable, public :: dustflx1000
+ real, dimension (:,:), allocatable, public :: dustflx2000
+ real, dimension (:,:), allocatable, public :: dustflx4000
+ real, dimension (:,:), allocatable, public :: dustflx_bot
real, dimension (:,:,:), allocatable, public :: phosy3d
! Variables for interactive phytoplanktion absorption (use_FB_BGC_OCE=.true.)
@@ -277,7 +283,7 @@ subroutine alloc_mem_biomod(kpie,kpje,kpke)
allocate (calflx2000(kpie,kpje),stat=errstat)
allocate (calflx4000(kpie,kpje),stat=errstat)
allocate (calflx_bot(kpie,kpje),stat=errstat)
- if(errstat.ne.0) stop 'not enough memory bsiflx*'
+ if(errstat.ne.0) stop 'not enough memory calflx*'
calflx0100(:,:) = 0.0
calflx0500(:,:) = 0.0
calflx1000(:,:) = 0.0
@@ -285,6 +291,26 @@ subroutine alloc_mem_biomod(kpie,kpje,kpke)
calflx4000(:,:) = 0.0
calflx_bot(:,:) = 0.0
+ if (mnproc.eq.1) then
+ write(io_stdo_bgc,*)'Memory allocation for variable dustflx* ...'
+ write(io_stdo_bgc,*)'First dimension : ',kpie
+ write(io_stdo_bgc,*)'Second dimension : ',kpje
+ endif
+
+ allocate (dustflx0100(kpie,kpje),stat=errstat)
+ allocate (dustflx0500(kpie,kpje),stat=errstat)
+ allocate (dustflx1000(kpie,kpje),stat=errstat)
+ allocate (dustflx2000(kpie,kpje),stat=errstat)
+ allocate (dustflx4000(kpie,kpje),stat=errstat)
+ allocate (dustflx_bot(kpie,kpje),stat=errstat)
+ if(errstat.ne.0) stop 'not enough memory dustflx*'
+ dustflx0100(:,:) = 0.0
+ dustflx0500(:,:) = 0.0
+ dustflx1000(:,:) = 0.0
+ dustflx2000(:,:) = 0.0
+ dustflx4000(:,:) = 0.0
+ dustflx_bot(:,:) = 0.0
+
if (mnproc.eq.1) then
write(io_stdo_bgc,*)'Memory allocation for variable phosy3d ...'
write(io_stdo_bgc,*)'First dimension : ',kpie
diff --git a/hamocc/mo_ncout_hamocc.F90 b/hamocc/mo_ncout_hamocc.F90
index 4e794472..d867384f 100644
--- a/hamocc/mo_ncout_hamocc.F90
+++ b/hamocc/mo_ncout_hamocc.F90
@@ -46,6 +46,8 @@ subroutine ncwrt_bgc(iogrp)
flx_car2000,flx_car4000,flx_car_bot, &
flx_bsi0100,flx_bsi0500,flx_bsi1000, &
flx_bsi2000,flx_bsi4000,flx_bsi_bot, &
+ flx_dust0100,flx_dust0500,flx_dust1000, &
+ flx_dust2000,flx_dust4000,flx_dust_bot, &
flx_sediffic,flx_sediffal,flx_sediffph, &
flx_sediffox,flx_sediffn2,flx_sediffno3,flx_sediffsi, &
flx_bursso12,flx_bursssc12,flx_burssssil, &
@@ -61,6 +63,8 @@ subroutine ncwrt_bgc(iogrp)
jcalflx2000,jcalflx4000,jcalflx_bot, &
jcarflx0100,jcarflx0500,jcarflx1000, &
jcarflx2000,jcarflx4000,jcarflx_bot, &
+ jdustflx0100,jdustflx0500,jdustflx1000, &
+ jdustflx2000,jdustflx4000,jdustflx_bot, &
jco2fxd,jco2fxu,jco3,jdic,jdicsat, &
jdms,jdms_bac,jdms_uv,jdmsflux,jdmsprod, &
jdoc,jdp,jeps,jexpoca,jexport,jexposi,jgrazer, &
@@ -418,6 +422,11 @@ subroutine ncwrt_bgc(iogrp)
call msksrf(jcalflx1000(iogrp),k1000)
call msksrf(jcalflx2000(iogrp),k2000)
call msksrf(jcalflx4000(iogrp),k4000)
+ call msksrf(jdustflx0100(iogrp),k0100)
+ call msksrf(jdustflx0500(iogrp),k0500)
+ call msksrf(jdustflx1000(iogrp),k1000)
+ call msksrf(jdustflx2000(iogrp),k2000)
+ call msksrf(jdustflx4000(iogrp),k4000)
! --- Mask sea floor in level data
call msklvl(jlvlphyto(iogrp),depths)
@@ -580,6 +589,12 @@ subroutine ncwrt_bgc(iogrp)
call wrtsrf(jcalflx2000(iogrp), FLX_CAL2000(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'calflx2000')
call wrtsrf(jcalflx4000(iogrp), FLX_CAL4000(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'calflx4000')
call wrtsrf(jcalflx_bot(iogrp), FLX_CAL_BOT(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'calflx_bot')
+ call wrtsrf(jdustflx0100(iogrp), FLX_DUST0100(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx0100')
+ call wrtsrf(jdustflx0500(iogrp), FLX_DUST0500(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx0500')
+ call wrtsrf(jdustflx1000(iogrp), FLX_DUST1000(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx1000')
+ call wrtsrf(jdustflx2000(iogrp), FLX_DUST2000(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx2000')
+ call wrtsrf(jdustflx4000(iogrp), FLX_DUST4000(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx4000')
+ call wrtsrf(jdustflx_bot(iogrp), FLX_DUST_BOT(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'dustflx_bot')
if (.not. use_sedbypass) then
call wrtsrf(jsediffic(iogrp), FLX_SEDIFFIC(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'sedfdic')
call wrtsrf(jsediffal(iogrp), FLX_SEDIFFAL(iogrp), rnacc*1e3/dtbgc,0.,cmpflg,'sedfalk')
@@ -934,6 +949,12 @@ subroutine ncwrt_bgc(iogrp)
call inisrf(jcalflx2000(iogrp),0.)
call inisrf(jcalflx4000(iogrp),0.)
call inisrf(jcalflx_bot(iogrp),0.)
+ call inisrf(jdustflx0100(iogrp),0.)
+ call inisrf(jdustflx0500(iogrp),0.)
+ call inisrf(jdustflx1000(iogrp),0.)
+ call inisrf(jdustflx2000(iogrp),0.)
+ call inisrf(jdustflx4000(iogrp),0.)
+ call inisrf(jdustflx_bot(iogrp),0.)
if (.not. use_sedbypass) then
call inisrf(jsediffic(iogrp),0.)
call inisrf(jsediffal(iogrp),0.)
@@ -1251,6 +1272,8 @@ subroutine hamoccvardef(iogrp,timeunits,calendar,cmpflg)
flx_bsi0100,flx_bsi0500,flx_bsi1000,flx_bsi2000,flx_bsi4000, &
flx_bsi_bot,flx_cal0100,flx_cal0500,flx_cal1000,flx_cal2000, &
flx_cal4000,flx_cal_bot,flx_sediffic,flx_sediffal, &
+ flx_dust0100,flx_dust0500,flx_dust1000,flx_dust2000,flx_dust4000, &
+ flx_dust_bot, &
flx_sediffph,flx_sediffox,flx_sediffn2,flx_sediffno3, &
flx_sediffsi,flx_bursso12,flx_bursssc12,flx_burssssil,flx_burssster, &
srf_n2ofx,srf_atmco2,lyr_dp,lyr_dic, &
@@ -1475,6 +1498,19 @@ subroutine hamoccvardef(iogrp,timeunits,calendar,cmpflg)
& 'CaCO3 flux at 4000m',' ','mol Ca m-2 s-1',0)
call ncdefvar3d(FLX_CAL_BOT(iogrp),cmpflg,'p','calflx_bot', &
& 'CaCO3 flux to sediment',' ','mol Ca m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST0100(iogrp),cmpflg,'p','dustflx0100', &
+ & 'Dust flux at 100m',' ','g m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST0500(iogrp),cmpflg,'p','dustflx0500', &
+ & 'Dust flux at 500m',' ','g m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST1000(iogrp),cmpflg,'p','dustflx1000', &
+ & 'Dust flux at 1000m',' ','g m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST2000(iogrp),cmpflg,'p','dustflx2000', &
+ & 'Dust flux at 2000m',' ','g m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST4000(iogrp),cmpflg,'p','dustflx4000', &
+ & 'Dust flux at 4000m',' ','g m-2 s-1',0)
+ call ncdefvar3d(FLX_DUST_BOT(iogrp),cmpflg,'p','dustflx_bot', &
+ & 'Dust flux to sediment',' ','g m-2 s-1',0)
+
call ncdefvar3d(SRF_N2OFX(iogrp),cmpflg,'p','n2oflux', &
& 'N2O flux',' ','mol N2O m-2 s-1',0)
if (.not. use_sedbypass) then
@@ -1486,7 +1522,7 @@ subroutine hamoccvardef(iogrp,timeunits,calendar,cmpflg)
& ' ','mol m-2 s-1',0)
call ncdefvar3d(FLX_SEDIFFPH(iogrp),cmpflg,'p','sedfpho', &
& 'diffusive phosphate flux to sediment (positive downwards)', &
- & ' ','mol m-2 s-1',0)
+ & ' ','mol P m-2 s-1',0)
call ncdefvar3d(FLX_SEDIFFOX(iogrp),cmpflg,'p','sedfox', &
& 'diffusive oxygen flux to sediment (positive downwards)', &
& ' ','mol O2 m-2 s-1',0)
@@ -1646,7 +1682,7 @@ subroutine hamoccvardef(iogrp,timeunits,calendar,cmpflg)
call ncdefvar3d(LYR_PREFPO4(iogrp),cmpflg,'p', &
& 'p_po4','Preformed phosphorus',' ','mol P m-3',1)
call ncdefvar3d(LYR_PREFSILICA(iogrp),cmpflg,'p', &
- & 'p_silica','Preformed silica',' ','mol N m-3',1)
+ & 'p_silica','Preformed silica',' ','mol Si m-3',1)
call ncdefvar3d(LYR_PREFALK(iogrp),cmpflg,'p', &
& 'p_talk','Preformed alkalinity',' ','eq m-3',1)
call ncdefvar3d(LYR_PREFDIC(iogrp),cmpflg,'p', &
diff --git a/hamocc/mo_ocprod.F90 b/hamocc/mo_ocprod.F90
index 37c5e49b..ab954217 100644
--- a/hamocc/mo_ocprod.F90
+++ b/hamocc/mo_ocprod.F90
@@ -81,6 +81,8 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
use mo_biomod, only: bsiflx0100,bsiflx0500,bsiflx1000,bsiflx2000,bsiflx4000,bsiflx_bot, &
calflx0100,calflx0500,calflx1000,calflx2000,calflx4000,calflx_bot, &
carflx0100,carflx0500,carflx1000,carflx2000,carflx4000,carflx_bot, &
+ dustflx0100,dustflx0500,dustflx1000,dustflx2000,dustflx4000, &
+ dustflx_bot, &
expoor,exposi,expoca,intdnit,intdms_bac,intdmsprod,intdms_uv, &
intphosy,int_chbr3_prod,int_chbr3_uv, &
phosy3d,abs_oce,strahl,asize3d,wmass,wnumb,eps3d,phosy_NH4, &
@@ -1158,6 +1160,16 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wdust = wdust_const
wdustd = wdust_const
dagg = 0.0
+ else if (use_M4AGO) then
+ wpoc = ws_agg(i,j,k)
+ wpocd = ws_agg(i,j,kdonor)
+ wcal = ws_agg(i,j,k)
+ wcald = ws_agg(i,j,kdonor)
+ wopal = ws_agg(i,j,k)
+ wopald = ws_agg(i,j,kdonor)
+ wdust = ws_agg(i,j,k)
+ wdustd = ws_agg(i,j,kdonor)
+ dagg = 0.0
else
wpoc = wpoc_const
wpocd = wpoc_const
@@ -1169,17 +1181,6 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wdustd = wdust_const
dagg = 0.0
endif
- if (use_M4AGO) then ! superseding every other method
- wpoc = ws_agg(i,j,k)
- wpocd = ws_agg(i,j,kdonor)
- wcal = ws_agg(i,j,k)
- wcald = ws_agg(i,j,kdonor)
- wopal = ws_agg(i,j,k)
- wopald = ws_agg(i,j,kdonor)
- wdust = ws_agg(i,j,k)
- wdustd = ws_agg(i,j,kdonor)
- dagg = 0.0
- endif
if( k == 1 ) then
wpocd = 0.0
@@ -1189,11 +1190,9 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
if (use_AGG) then
wnosd = 0.0
else if (use_WLIN) then
- if (use_M4AGO) then
- wpoc = ws_agg(i,j,k)
- else
- wpoc = wmin
- endif
+ wpoc = wmin
+ else if (use_M4AGO) then
+ wpoc = ws_agg(i,j,k)
endif
endif
@@ -1380,19 +1379,28 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wpoc = wmass(i,j,k)
wcal = wmass(i,j,k)
wopal = wmass(i,j,k)
+ wdust = dustsink
else if (use_WLIN) then
wpoc = min(wmin+wlin*ptiestu(i,j,k), wmax)
- endif
- if (use_M4AGO) then
+ wdust = wdust_const
+ else if (use_M4AGO) then
wpoc = ws_agg(i,j,k)
wcal = ws_agg(i,j,k)
wopal = ws_agg(i,j,k)
+ wdust = ws_agg(i,j,k)
+ else
+ wpoc = wpoc_const
+ wcal = wcal_const
+ wopal = wopal_const
+ wdust = wdust_const
endif
if (use_AGG) then
carflx0100(i,j) = (ocetra(i,j,k,idet)+ocetra(i,j,k,iphy))*rcar*wpoc
+ dustflx0100(i,j)= ocetra(i,j,k,ifdust)*wdust + ocetra(i,j,k,iadust)*wpoc
else
carflx0100(i,j) = ocetra(i,j,k,idet)*rcar*wpoc
+ dustflx0100(i,j)= ocetra(i,j,k,ifdust)*wdust
endif
bsiflx0100(i,j) = ocetra(i,j,k,iopal)*wopal
calflx0100(i,j) = ocetra(i,j,k,icalc)*wcal
@@ -1405,19 +1413,28 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wpoc = wmass(i,j,k)
wcal = wmass(i,j,k)
wopal = wmass(i,j,k)
+ wdust = dustsink
else if (use_WLIN) then
wpoc = min(wmin+wlin*ptiestu(i,j,k), wmax)
+ wdust = wdust_const
+ else if (use_M4AGO) then
+ wpoc = ws_agg(i,j,k)
+ wcal = ws_agg(i,j,k)
+ wopal = ws_agg(i,j,k)
+ wdust = ws_agg(i,j,k)
+ else
+ wpoc = wpoc_const
+ wcal = wcal_const
+ wopal = wopal_const
+ wdust = wdust_const
endif
- if (use_M4AGO) then
- wpoc = ws_agg(i,j,k)
- wcal = ws_agg(i,j,k)
- wopal = ws_agg(i,j,k)
- endif
if (use_AGG) then
carflx0500(i,j) = (ocetra(i,j,k,idet)+ocetra(i,j,k,iphy))*rcar*wpoc
+ dustflx0500(i,j)= ocetra(i,j,k,ifdust)*wdust + ocetra(i,j,k,iadust)*wpoc
else
carflx0500(i,j) = ocetra(i,j,k,idet)*rcar*wpoc
+ dustflx0500(i,j)= ocetra(i,j,k,ifdust)*wdust
endif
bsiflx0500(i,j) = ocetra(i,j,k,iopal)*wopal
calflx0500(i,j) = ocetra(i,j,k,icalc)*wcal
@@ -1430,19 +1447,28 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wpoc = wmass(i,j,k)
wcal = wmass(i,j,k)
wopal = wmass(i,j,k)
+ wdust = dustsink
else if (use_WLIN) then
wpoc = min(wmin+wlin*ptiestu(i,j,k), wmax)
- endif
- if (use_M4AGO) then
+ wdust = wdust_const
+ else if (use_M4AGO) then
wpoc = ws_agg(i,j,k)
wcal = ws_agg(i,j,k)
wopal = ws_agg(i,j,k)
+ wdust = ws_agg(i,j,k)
+ else
+ wpoc = wpoc_const
+ wcal = wcal_const
+ wopal = wopal_const
+ wdust = wdust_const
endif
if (use_AGG) then
carflx1000(i,j) = (ocetra(i,j,k,idet)+ocetra(i,j,k,iphy))*rcar*wpoc
+ dustflx1000(i,j)= ocetra(i,j,k,ifdust)*wdust + ocetra(i,j,k,iadust)*wpoc
else
carflx1000(i,j) = ocetra(i,j,k,idet)*rcar*wpoc
+ dustflx1000(i,j)= ocetra(i,j,k,ifdust)*wdust
endif
bsiflx1000(i,j) = ocetra(i,j,k,iopal)*wopal
calflx1000(i,j) = ocetra(i,j,k,icalc)*wcal
@@ -1455,19 +1481,28 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wpoc = wmass(i,j,k)
wcal = wmass(i,j,k)
wopal = wmass(i,j,k)
+ wdust = dustsink
else if (use_WLIN) then
wpoc = min(wmin+wlin*ptiestu(i,j,k), wmax)
- endif
- if (use_M4AGO) then
+ wdust = wdust_const
+ else if (use_M4AGO) then
wpoc = ws_agg(i,j,k)
wcal = ws_agg(i,j,k)
wopal = ws_agg(i,j,k)
+ wdust = ws_agg(i,j,k)
+ else
+ wpoc = wpoc_const
+ wcal = wcal_const
+ wopal = wopal_const
+ wdust = wdust_const
endif
if (use_AGG) then
carflx2000(i,j) = (ocetra(i,j,k,idet)+ocetra(i,j,k,iphy))*rcar*wpoc
+ dustflx2000(i,j)= ocetra(i,j,k,ifdust)*wdust + ocetra(i,j,k,iadust)*wpoc
else
carflx2000(i,j) = ocetra(i,j,k,idet)*rcar*wpoc
+ dustflx2000(i,j)= ocetra(i,j,k,ifdust)*wdust
endif
bsiflx2000(i,j) = ocetra(i,j,k,iopal)*wopal
calflx2000(i,j) = ocetra(i,j,k,icalc)*wcal
@@ -1480,19 +1515,28 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
wpoc = wmass(i,j,k)
wcal = wmass(i,j,k)
wopal = wmass(i,j,k)
+ wdust = dustsink
else if (use_WLIN) then
wpoc = min(wmin+wlin*ptiestu(i,j,k), wmax)
- endif
- if (use_M4AGO) then
+ wdust = wdust_const
+ else if (use_M4AGO) then
wpoc = ws_agg(i,j,k)
wcal = ws_agg(i,j,k)
wopal = ws_agg(i,j,k)
+ wdust = ws_agg(i,j,k)
+ else
+ wpoc = wpoc_const
+ wcal = wcal_const
+ wopal = wopal_const
+ wdust = wdust_const
endif
if (use_AGG) then
carflx4000(i,j) = (ocetra(i,j,k,idet)+ocetra(i,j,k,iphy))*rcar*wpoc
+ dustflx4000(i,j)= ocetra(i,j,k,ifdust)*wdust + ocetra(i,j,k,iadust)*wpoc
else
carflx4000(i,j) = ocetra(i,j,k,idet)*rcar*wpoc
+ dustflx4000(i,j)= ocetra(i,j,k,ifdust)*wdust
endif
bsiflx4000(i,j) = ocetra(i,j,k,iopal)*wopal
calflx4000(i,j) = ocetra(i,j,k,icalc)*wcal
@@ -1502,6 +1546,7 @@ subroutine ocprod(kpie,kpje,kpke,kbnd,pdlxp,pdlyp,pddpo,omask,ptho,pi_ph,psao,pp
carflx_bot(i,j) = prorca(i,j)*rcar
bsiflx_bot(i,j) = silpro(i,j)
calflx_bot(i,j) = prcaca(i,j)
+ dustflx_bot(i,j)= produs(i,j)
endif ! omask > 0.5
enddo