Merge pull request #58 from derpycode/_Sulf

Sulf

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/biogem_force_restore_atm_pCO2_13C_sig.dat

@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999999.0 1.0
+-END-OF-DATA-

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/biogem_force_restore_atm_pCO2_sig.dat

@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999999.0 1.0
+-END-OF-DATA-

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/biogem_force_restore_atm_pO2_sig.dat

@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999999.0 1.0
+-END-OF-DATA-

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/configure_forcings_atm.dat

@@ -0,0 +1,25 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+ 06 t 0.1 f t F 2 01 01 '[oxygen (O2) partial pressure (atm)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/configure_forcings_ocn.dat

@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-forcings/pyyyyz.RpCO2_Rp13CO2_RpO2.DOM/configure_forcings_sed.dat

@@ -0,0 +1,20 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-forcings/pyyyyz.RpO2.DOM/biogem_force_restore_atm_pO2_sig.dat

@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999999.0 1.0
+-END-OF-DATA-

genie-forcings/pyyyyz.RpO2.DOM/configure_forcings_atm.dat

@@ -0,0 +1,23 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 06 t 0.1 f t F 2 01 01 '[oxygen (O2) partial pressure (atm)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-forcings/pyyyyz.RpO2.DOM/configure_forcings_ocn.dat

@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-forcings/pyyyyz.RpO2.DOM/configure_forcings_sed.dat

@@ -0,0 +1,20 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION

genie-main/configs/cgenie.eb_go_gs_ac_bg_sg_rg.p0093k.BASESFePOM-S.config

@@ -0,0 +1,166 @@
+# *******************************************************************
+# CONFIGURATION TEMPLATE (EMBM + GOLDSTEIN + GOLDSTEIN SEA-ICE + ATCHEM + BIOGEM + SEDGEM + ROKGEM)
+# *******************************************************************
+
+# *******************************************************************
+# GENIE COMPONENT SELECTION
+# *******************************************************************
+ma_flag_ebatmos=.TRUE.
+ma_flag_goldsteinocean=.TRUE.
+ma_flag_goldsteinseaice=.TRUE.
+ma_flag_atchem=.TRUE.
+ma_flag_biogem=.TRUE.
+ma_flag_sedgem=.TRUE.
+ma_flag_rokgem=.TRUE.
+# *******************************************************************
+
+# *******************************************************************
+# GRID CONFIGURATION
+# *******************************************************************
+# Topography
+ma_fname_topo='p0093k'
+# Grid resolution of climate components
+GENIENXOPTS='$(DEFINE)GENIENX=36'
+GENIENYOPTS='$(DEFINE)GENIENY=36'
+GENIENLOPTS='$(DEFINE)GENIENL=1'
+GOLDSTEINNLONSOPTS='$(DEFINE)GOLDSTEINNLONS=36'
+GOLDSTEINNLATSOPTS='$(DEFINE)GOLDSTEINNLATS=36'
+GOLDSTEINNLEVSOPTS='$(DEFINE)GOLDSTEINNLEVS=16'
+# Topography for climate components
+ea_topo='p0093k'
+go_topo='p0093k'
+gs_topo='p0093k'
+# Wind forcing for climate components
+ea_taux_u="p0093k_taux_u.interp"
+ea_tauy_u="p0093k_tauy_u.interp"
+ea_taux_v="p0093k_taux_v.interp"
+ea_tauy_v="p0093k_tauy_v.interp"
+ea_adv_u="p0093k_uncep.silo"
+ea_adv_v="p0093k_vncep.silo"
+#assumed longitudinal offset of the grid
+gm_par_grid_lon_offset=-180.0
+# Grid resolution of solid Earth components
+SEDGEMNLONSOPTS='$(DEFINE)SEDGEMNLONS=36'
+SEDGEMNLATSOPTS='$(DEFINE)SEDGEMNLATS=36'
+ROKGEMNLONSOPTS='$(DEFINE)ROKGEMNLONS=36'
+ROKGEMNLATSOPTS='$(DEFINE)ROKGEMNLATS=36'
+# Topography for solid Earth components
+rg_topo="p0093k.k1"
+# *******************************************************************
+
+# *******************************************************************
+# TRACER CONFIGURATION
+# *******************************************************************
+# Set number of tracers
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=18'
+# Select tracers
+gm_atm_select_3=.true.
+gm_atm_select_4=.true.
+gm_atm_select_6=.true.
+gm_atm_select_16=.true.
+gm_ocn_select_3=.true.
+gm_ocn_select_4=.true.
+gm_ocn_select_8=.true.
+gm_ocn_select_9=.true.
+gm_ocn_select_10=.true.
+gm_ocn_select_12=.true.
+gm_ocn_select_15=.true.
+gm_ocn_select_16=.true.
+gm_ocn_select_20=.true.
+gm_ocn_select_22=.true.
+gm_ocn_select_23=.true.
+gm_ocn_select_24=.true.
+gm_ocn_select_35=.true.
+gm_ocn_select_38=.true.
+gm_ocn_select_40=.true.
+gm_ocn_select_50=.true.
+gm_sed_select_3=.true.
+gm_sed_select_4=.true.
+gm_sed_select_8=.true.
+gm_sed_select_10=.true.
+gm_sed_select_13=.true.
+gm_sed_select_14=.true.
+gm_sed_select_15=.true.
+gm_sed_select_21=.true.
+gm_sed_select_22=.true.
+gm_sed_select_25=.true.
+gm_sed_select_32=.true.
+gm_sed_select_33=.true.
+gm_sed_select_34=.true.
+gm_sed_select_36=.true.
+gm_sed_select_73=.true.
+# Set tracer initial values
+ac_atm_init_3=278.0E-06
+ac_atm_init_4=-6.5
+ac_atm_init_6=0.2095
+bg_ocn_init_3=2.244E-03
+bg_ocn_init_4=0.4
+bg_ocn_init_8=2.159E-06
+bg_ocn_init_9=0.650E-09
+bg_ocn_init_10=1.696E-04
+bg_ocn_init_12=2.363E-03
+bg_ocn_init_24=1.000E-09
+bg_ocn_init_35=1.025E-02
+bg_ocn_init_38=2.916E-02
+bg_ocn_init_40=0.0
+bg_ocn_init_50=5.282E-02
+# *******************************************************************
+
+# *******************************************************************
+# PHYSICAL CLIMATE CONFIGURATION #1: main goin parameters
+# *******************************************************************
+# temp0
+go_10=10.0
+# temp1
+go_11=10.0
+# rel
+go_12=0.9000000
+# scl_tau / SclTau
+go_13=1.531013488769531300
+# ocean diffusivites iso (or horiz) / OcnHorizDiff
+go_14=1494.438354492187500000
+# ocean diffusivites dia (or vert) / OcnVertDiff
+go_15=0.000025363247914356
+# inverse minimum drag in days / InvDrag
+go_16=2.710164785385131800
+# scl_tau (should be same as GOLDSTEIN's value) / SclTau
+ea_11=1.531013488769531300
+# atm. diff. amp. for T / AtmDiffAmpT
+ea_12=5204945.000000000000000000
+# atm. diff. amp. for q / AtmDiffAmpQ
+ea_13=1173269.250000000000000000
+# dist'n width / AtmDiffWidthT
+ea_14=1.410347938537597700
+# dist'n slope / AtmDiffSlopeT
+ea_15=0.090003050863742828
+# atm. advection factor for T_z / AtmAdvectCoeffTm
+ea_16=0.001037851092405617
+# atm. advection factor for T_m / AtmAdvectCoeffQm
+ea_17=0.0000000E+00
+# atm. advection factor for q_z / AtmAdvectCoeffQz
+ea_18=0.164652019739151000
+# atm. advection factor for q_m / AtmAdvectCoeffQz
+ea_19=0.164652019739151000
+# SclFWF
+ea_28=0.0
+# sea-ice eddy diffusivity / SeaiceDiff
+gs_11=3573.718017578125000000
+# solar constant reduced by 0.56% for end Cretaceous
+ma_genie_solar_constant=1360.33
+# adjusted planetary albedo
+ea_albedop_offs=0.200
+ea_albedop_amp=0.260
+ea_albedop_skew=0.0
+ea_albedop_skewp=0
+ea_albedop_mod2=-0.000
+ea_albedop_mod4=0.000
+ea_albedop_mod6=0.250
+# minus 1 PSU
+go_saln0=33.9
+# set climate feedback
+ea_36=y
+# *******************************************************************
+
+# *******************************************************************
+# USER-APPENDED OPTIONS FOLLOW ...
+# *******************************************************************

genie-main/current_config.dat

@@ -1 +1 @@
-testbiogem
+cgenie.eb_go_gs_ac_bg_sg_rg.p0093k.BASESFePOM-S

genie-main/src/xml-config/xml/definition.xml

@@ -6525,6 +6525,14 @@
  <value datatype="boolean">.false.</value>
  <description>Include explicit P-cycle in OMEN-SED?</description>
  </param>
+ <param name="par_sed_huelse2017_remove_impl_sulALK">
+ <value datatype="boolean">.true.</value>
+ <description>Remove implicit Alk associated with buried sulf-OM?</description>
+ </param>
+ <param name="par_sed_huelse2017_sim_P_loss">
+ <value datatype="boolean">.false.</value>
+ <description>Simulate ocean Porg loss with buried sulf-OM?</description>
+ </param>
  <param name="par_sed_huelse2017_k1">
  <value datatype="real">0.0065</value>
  <description>global labile Corg degradation rate constant, units of 1/yr</description>