From 1cd7caacd41be5ab22ffd8e67d5268a9cfeb4c88 Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Mon, 17 Aug 2026 11:44:27 +0100 Subject: [PATCH 1/6] adding dim_cslayer as dimension --- src/science/soil/soil_htc_jls_mod.F90 | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/science/soil/soil_htc_jls_mod.F90 b/src/science/soil/soil_htc_jls_mod.F90 index 475e1175..c6a331a3 100644 --- a/src/science/soil/soil_htc_jls_mod.F90 +++ b/src/science/soil/soil_htc_jls_mod.F90 @@ -36,6 +36,7 @@ SUBROUTINE soil_htc ( npnts, nshyd, nsurft, soil_pts, timestep, soil_index, & USE jules_soil_mod, ONLY: facur, gamma_t, mmax, tacur, l_bedrock, & ns_deep USE jules_soil_biogeochem_mod, ONLY: heat_of_respiration, l_bgc_heat +USE ancil_info, ONLY: dim_cslayer USE jules_surface_mod, ONLY: l_flake_model USE jules_surface_types_mod, ONLY: lake USE jules_irrig_mod, ONLY: l_irrig_dmd @@ -104,7 +105,7 @@ SUBROUTINE soil_htc ( npnts, nshyd, nsurft, soil_pts, timestep, soil_index, & ! Volumetric soil moisture concentration at saturation (m3 H2O/m3 soil). w_flux(npnts,0:nshyd), & ! The fluxes of water between layers (kg/m2/s). - resp_s_soilt(npnts,nshyd,dim_cs1) + resp_s_soilt(npnts,dim_cslayer,dim_cs1) ! Soil respiration in pools (kg C/m2/s) in each layer ! The fluxes of water between layers (kg/m2/s). @@ -384,7 +385,7 @@ SUBROUTINE soil_htc ( npnts, nshyd, nsurft, soil_pts, timestep, soil_index, & !$OMP w_flux, dhadv_dtsl0, dhadv_dtsl1, dhadv_dtsl2, v_sat, & !$OMP tiny_0, smcl, small_value, work1, smclsat, bexp, tmax, sathh, & !$OMP dhsl0, timestep, dhsl, resp_s_soilt, l_bgc_heat, dim_cs1, & -!$OMP heat_of_respiration) +!$OMP dim_cslayer, heat_of_respiration) ! Blocking is needed as the nshyd dimension has a spatial ! dependence (n +/-1). Blocking enables parallelising over the @@ -490,7 +491,7 @@ SUBROUTINE soil_htc ( npnts, nshyd, nsurft, soil_pts, timestep, soil_index, & IF (l_bgc_heat) THEN !$OMP DO SCHEDULE(STATIC) DO j = 1, soil_pts - DO n = 1, nshyd + DO n = 1, dim_cslayer !DIR$ IVDEP !CDIR NODEP i = soil_index(j) From 26378cb48d6a1a0b59170ef2da44ff9e9fe3f8be Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Fri, 28 Aug 2026 09:37:32 +0100 Subject: [PATCH 2/6] l_bgc_heat can be used in um and for one layer soil carbon --- rose-meta/jules-standalone/HEAD/rose-meta.conf | 3 --- src/control/shared/jules_soil_biogeochem_mod.F90 | 14 -------------- src/control/um/check_unavailable_options_mod.F90 | 12 +----------- 3 files changed, 1 insertion(+), 28 deletions(-) diff --git a/rose-meta/jules-standalone/HEAD/rose-meta.conf b/rose-meta/jules-standalone/HEAD/rose-meta.conf index e30a27c5..f17daa04 100644 --- a/rose-meta/jules-standalone/HEAD/rose-meta.conf +++ b/rose-meta/jules-standalone/HEAD/rose-meta.conf @@ -4942,8 +4942,6 @@ url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml [namelist:jules_soil_biogeochem=l_bgc_heat] compulsory=true description=Switch for release of biogeochemical heat into the soil. - =Not available to the UM. -fail-if=this == '.true.' and namelist:jules_model_environment=l_jules_parent == 1; #Biogenic heating scheme is not available to the UM sort-key=c1 trigger=namelist:jules_soil_biogeochem=heat_of_respiration: .true.; type=logical @@ -5015,7 +5013,6 @@ sort-key=c url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_q10 value-titles=Q10 temperature function,Clark et al. (2011) temperature function values=.true.,.false. -warn-if=this == '.false.' and namelist:jules_soil_biogeochem=l_bgc_heat == '.true.' widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget [namelist:jules_soil_biogeochem=l_soil_resp_lev2] diff --git a/src/control/shared/jules_soil_biogeochem_mod.F90 b/src/control/shared/jules_soil_biogeochem_mod.F90 index 4b6588f6..358a8ae4 100644 --- a/src/control/shared/jules_soil_biogeochem_mod.F90 +++ b/src/control/shared/jules_soil_biogeochem_mod.F90 @@ -333,20 +333,6 @@ SUBROUTINE check_jules_soil_biogeochem() 'the layered soil temperature calculation (l_ch4_tlayered)' ) END IF -! Check if l_q10=T to use l_bgc_heat -IF ( .NOT. l_q10 .AND. l_bgc_heat ) THEN - CALL ereport( TRIM(RoutineName), warningstatus, & - 'To use the biogenic heating of soil carbon decomposition' // & - 'you must use l_q10=.true. and l_bgc_heat=.true.' ) -END IF - -! Check if l_layeredC=T to use l_bgc_heat -IF ( .NOT. l_layeredc .AND. l_bgc_heat ) THEN - CALL ereport( TRIM(RoutineName), errorstatus, & - 'To use the biogenic heating of soil carbon decomposition' // & - 'you must use l_layeredc=.true. and l_bgc_heat=.true.' ) -END IF - ! Check if l_bgc_heat = T, heat_of_respiration is 3.7e09 IF ( l_bgc_heat ) THEN IF ( ABS( heat_of_respiration - rmdi ) < EPSILON(1.0) ) THEN diff --git a/src/control/um/check_unavailable_options_mod.F90 b/src/control/um/check_unavailable_options_mod.F90 index 5c39b56f..e044bd7f 100644 --- a/src/control/um/check_unavailable_options_mod.F90 +++ b/src/control/um/check_unavailable_options_mod.F90 @@ -24,8 +24,7 @@ SUBROUTINE check_unavailable_options() USE jules_urban_mod, ONLY: l_urban_empirical USE jules_rivers_mod, ONLY: l_riv_overbank, l_rivers, i_river_vn, & rivers_um_trip, rivers_rfm -USE jules_soil_biogeochem_mod, ONLY: l_ch4_microbe, l_label_frac_cs, & - l_bgc_heat +USE jules_soil_biogeochem_mod, ONLY: l_ch4_microbe, l_label_frac_cs USE jules_soil_mod, ONLY: l_tile_soil, l_bedrock USE jules_surface_types_mod, ONLY: ncpft USE jules_water_resources_mod, ONLY: l_water_resources @@ -71,15 +70,6 @@ SUBROUTINE check_unavailable_options() END IF END IF -! jules_soil_biogeochem_mod -IF ( l_bgc_heat ) THEN - error_sum = error_sum + 1 - WRITE(jules_message,'(I0,A,L1)') error_sum, & - ": Biogenic heating scheme is only available to standalone JULES. " // & - "l_bgc_heat = ", l_bgc_heat - CALL jules_print(RoutineName, jules_message, level = PrNorm) -END IF - ! jules_soil_biogeochem_mod IF ( l_ch4_microbe ) THEN error_sum = error_sum + 1 From f78d8287853d689815d64d2607d6d88ab841e73a Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Fri, 28 Aug 2026 10:04:13 +0100 Subject: [PATCH 3/6] adding cla --- CONTRIBUTORS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index db1cc110..5c9e382f 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -5,3 +5,4 @@ | yaswant | Yaswant Pradhan | Met Office | 2026-06-30 | | doucla | Douglas Clark | UKCEH | 2026-07-03 | | james-bruten-mo | James Bruten | Met Office | 2026-07-09 | +| eleanorgb | Eleanor Burke | Met Office | 2026-08-24 | From f7a0f7ab500b888cc816ab29271322a870ddbcc6 Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Fri, 28 Aug 2026 13:07:46 +0100 Subject: [PATCH 4/6] fixing resp_s_soilt call --- src/science/soil/hydrol_jls_mod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/science/soil/hydrol_jls_mod.F90 b/src/science/soil/hydrol_jls_mod.F90 index d86095c2..0572457d 100644 --- a/src/science/soil/hydrol_jls_mod.F90 +++ b/src/science/soil/hydrol_jls_mod.F90 @@ -1126,7 +1126,7 @@ SUBROUTINE hydrol ( & sathh_soilt(:,m,:), smcl_soilt(:,m,:), snowdepth_surft, & surf_ht_flux_ld, smvcst_soilt(:,m,:), w_flux_soilt(:,m,:), & sthf_soilt(:,m,:), sthu_soilt(:,m,:), sthu_irr_soilt(:,m,:), & - t_soil_soilt(:,m,:), tsoil_deep_gb, dim_cs1, resp_s_soilt ) + t_soil_soilt(:,m,:), tsoil_deep_gb, dim_cs1, resp_s_soilt(:,m,:,:) ) ELSE ! Surface and soil tiles map directly on to each other. DO m = 1, nsoilt @@ -1139,7 +1139,7 @@ SUBROUTINE hydrol ( & sathh_soilt(:,m,:), smcl_soilt(:,m,:), snowdepth_surft, & snow_soil_htf(:,n), smvcst_soilt(:,m,:), w_flux_soilt(:,m,:), & sthf_soilt(:,m,:), sthu_soilt(:,m,:), sthu_irr_soilt(:,m,:), & - t_soil_soilt(:,m,:), tsoil_deep_gb, dim_cs1, resp_s_soilt ) + t_soil_soilt(:,m,:), tsoil_deep_gb, dim_cs1, resp_s_soilt(:,m,:,:) ) END DO END IF From 83fd7a4b7e55cd7cff2c24f7c262fda16fe5cb6c Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Tue, 15 Sep 2026 12:08:38 +0100 Subject: [PATCH 5/6] better merging into main --- .../jules-standalone/HEAD/rose-meta.conf | 702 ------------------ 1 file changed, 702 deletions(-) diff --git a/rose-meta/jules-standalone/HEAD/rose-meta.conf b/rose-meta/jules-standalone/HEAD/rose-meta.conf index b72002f7..32948207 100644 --- a/rose-meta/jules-standalone/HEAD/rose-meta.conf +++ b/rose-meta/jules-standalone/HEAD/rose-meta.conf @@ -4033,708 +4033,6 @@ sort-key=Panel-E09 type=real url=https://metoffice.github.io/jules/latest/namelists/jules_soil.nml.html#JULES_SOIL::zst -[namelist:jules_soil_biogeochem] -compulsory=true -ns=namelist/JULES Science Settings/jules_soil_biogeochem -sort-key=07 -title=Soil biogeochemistry options -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#namelist-JULES_SOIL_BIOGEOCHEM - -[namelist:jules_soil_biogeochem=alpha_ch4] -compulsory=true -description=Ratio between maintenance and growth respiration rates for methanogens -range=0.00001:0.1 -sort-key=8i -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::alpha_ch4 - -[namelist:jules_soil_biogeochem=bio_hum_cn] -compulsory=true -description=Bio and Hum Soil Carbon pools CN ratio -range=1:301 -sort-key=g -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::bio_hum_cn - -[namelist:jules_soil_biogeochem=ch4_cpow] -compulsory=true -description=Power of soil carbon used for anaerobic decomposition (default 1, could be 2/3 for organic soils) -range=0.01:5 -sort-key=r -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::ch4_cpow - -[namelist:jules_soil_biogeochem=ch4_substrate] -compulsory=true -description=Choose substrate for interactive methane -sort-key=o -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::ch4_substrate -value-titles=Soil carbon,NPP,Soil respiration -values=1,2,3 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=const_ch4_cs] -compulsory=true -description=Scale factor for soil carbon substrate CH4 emissions -range=1.0e-14:1.0e-6 -sort-key=2c -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::const_ch4_cs - -[namelist:jules_soil_biogeochem=const_ch4_npp] -compulsory=true -description=Scale factor for NPP substrate CH4 emissions -range=1.0e-5:0.01 -sort-key=2d -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::const_ch4_npp - -[namelist:jules_soil_biogeochem=const_ch4_resps] -compulsory=true -description=Scale factor for soil respiration substrate CH4 emissions -range=1.0e-5:0.01 -sort-key=2e -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::const_ch4_resps - -[namelist:jules_soil_biogeochem=cs_decomp_soil_moist_func] -compulsory=true -description=Switch for moisture function for soil decomposition -sort-key=m1 -trigger=namelist:jules_soil_biogeochem=fsthsat_cs_decomp_opt1: 1; -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::cs_decomp_soil_moist_func -value-titles=Clark (2011) function, Modified Chadburn (2022) function -values=0,1 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=cue_ch4] -compulsory=true -description=Carbon use efficiency of methanogenic growth -range=0.001:0.5 -sort-key=8f -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::cue_ch4 - -[namelist:jules_soil_biogeochem=diff_n_pft] -compulsory=true -description=Inorganic N diffusion in soil (360 days-1) -range=0.1:1500 -sort-key=b2 -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::diff_n_pft - -[namelist:jules_soil_biogeochem=ev_ch4] -compulsory=true -description=Timescale over which methanogenic traits adapt to temperature change (yr) -range=0.1:10.0 -sort-key=8j -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::ev_ch4 - -[namelist:jules_soil_biogeochem=frz_ch4] -compulsory=true -description=Factor to reduce CH4 substrate production when soil is sufficiently frozen (only in microbial scheme) -range=0:1 -sort-key=8h -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::frz_ch4 - -[namelist:jules_soil_biogeochem=fsthsat_cs_decomp_opt1] -compulsory=true -description=Soil decomposition factor when soil is saturated (proportion of maximum) -range=0.0:1.0 -sort-key=m1a -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::fsthsat_cs_decomp_opt1 - -[namelist:jules_soil_biogeochem=heat_of_respiration] -compulsory=true -description=The heat released during respiration (J/kg C) -range=0: -sort-key=c1a -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::heat_of_respiration - -[namelist:jules_soil_biogeochem=k2_ch4] -compulsory=true -description=Scale factor for methanogenic respiration rate (hr-1) -range=0.001:0.5 -sort-key=8b -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::k2_ch4 - -[namelist:jules_soil_biogeochem=kaps] -compulsory=true -description=Specific soil respiration rate at 25 degC and optimum soil moisture (s-1) for 1-pool model -range=1.0e-12:1.0e-4 -sort-key=e -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::kaps - -[namelist:jules_soil_biogeochem=kaps_4pool] -compulsory=true -description=Specific soil respiration rates for the four pools of the 4-pool model (s-1) -length=4 -range=1.0e-12:1.0e-4 -sort-key=f -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::kaps_4pool - -[namelist:jules_soil_biogeochem=kd_ch4] -compulsory=true -description=Scale factor for methanogenic death/turnover rate (hr-1) -range=0.000001:0.01 -sort-key=8c -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::kd_ch4 - -[namelist:jules_soil_biogeochem=l_bgc_heat] -compulsory=true -description=Switch for release of biogeochemical heat into the soil. -sort-key=c1 -trigger=namelist:jules_soil_biogeochem=heat_of_respiration: .true.; -type=logical -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_bgc_heat - -[namelist:jules_soil_biogeochem=l_ch4_interactive] -compulsory=true -description=Switch on interactive methane -fail-if=this == '.true.' and namelist:jules_soil_biogeochem=l_ch4_tlayered == '.false.' -sort-key=n -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_ch4_interactive -value-titles=Methane flux updates soil C, Methane flux does not update soil C -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=l_ch4_microbe] -compulsory=true -description=Use microbial methane model - =NOT AVAILABLE TO UM -sort-key=8a -trigger=namelist:jules_soil_biogeochem=k2_ch4: .true.; - =namelist:jules_soil_biogeochem=kd_ch4: .true.; - =namelist:jules_soil_biogeochem=rho_ch4: .true.; - =namelist:jules_soil_biogeochem=q10_mic_ch4: .true.; - =namelist:jules_soil_biogeochem=cue_ch4: .true.; - =namelist:jules_soil_biogeochem=mu_ch4: .true.; - =namelist:jules_soil_biogeochem=frz_ch4: .true.; - =namelist:jules_soil_biogeochem=alpha_ch4: .true.; - =namelist:jules_soil_biogeochem=ev_ch4: .true.; - =namelist:jules_soil_biogeochem=q10_ev_ch4: .true.; -type=logical -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_ch4_microbe -warn-if=this== '.true.' and namelist:jules_soil_biogeochem=ch4_substrate != 1 # microbial model only tuned for ch4_substrate=1 - -[namelist:jules_soil_biogeochem=l_ch4_tlayered] -compulsory=true -description=Calculate methane emissions from layered soil temperature (vs 1m average) -sort-key=p -trigger=namelist:jules_soil_biogeochem=tau_ch4: .true.; -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_ch4_tlayered -value-titles=Use layered soil temperature, Use depth-averaged soil temperature -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=l_label_frac_cs] -compulsory=true -description=Label and trace a fraction of soil carbon - =NOT AVAILABLE TO UM -sort-key=b1 -type=logical -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_label_frac_cs - -[namelist:jules_soil_biogeochem=l_layeredc] -compulsory=true -description=Use layered soil carbon model -fail-if=this == '.true.' and namelist:jules_soil_biogeochem=soil_bgc_model == 3 -sort-key=b -trigger=namelist:jules_soil_biogeochem=tau_resp: .true.; - =namelist:jules_soil_biogeochem=l_label_frac_cs: .true.; - =namelist:jules_soil_biogeochem=diff_n_pft: .true.; - =namelist:jules_soil_biogeochem=z_burn_max: .true.; -type=logical -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_layeredc - -[namelist:jules_soil_biogeochem=l_q10] -compulsory=true -description=Choose soil decomposition dependence on temperature -sort-key=c -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_q10 -value-titles=Q10 temperature function,Clark et al. (2011) temperature function -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=l_soil_resp_lev2] -compulsory=true -description=Soil respiration calculated using temperature and moisture from layer 2 -sort-key=m -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_soil_resp_lev2 -value-titles=Use 2nd soil layer + total moisture content for respiration, Use top soil layer + unfrozen moisture content for respiration -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=mu_ch4] -compulsory=true -description=Threshold growth rate below which methanogens die (hr-1) -range=0.000001:0.01 -sort-key=8g -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::mu_ch4 - -[namelist:jules_soil_biogeochem=n_inorg_turnover] -compulsory=true -description=Inorganic Nitrogren Turnover rate (360 days-1) -range=0.01:100 -sort-key=i -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::n_inorg_turnover - -[namelist:jules_soil_biogeochem=q10_ch4_cs] -compulsory=true -description=Q10 factor for soil carbon substrate CH4 emissions -range=0.1:10.0 -sort-key=2f -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_ch4_cs - -[namelist:jules_soil_biogeochem=q10_ch4_npp] -compulsory=true -description=Q10 factor for NPP substrate CH4 emissions -range=0.1:10.0 -sort-key=2g -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_ch4_npp - -[namelist:jules_soil_biogeochem=q10_ch4_resps] -compulsory=true -description=Q10 factor for soil respiration substrate CH4 emissions -range=0.1:10.0 -sort-key=2h -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_ch4_resps - -[namelist:jules_soil_biogeochem=q10_ev_ch4] -compulsory=true -description=Q10 for temperature response of methanogenic traits under adaptation -range=0.1:10.0 -sort-key=8k -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_ev_ch4 - -[namelist:jules_soil_biogeochem=q10_mic_ch4] -compulsory=true -description=Q10 factor for methanogens -range=0.1:10.0 -sort-key=8e -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_mic_ch4 - -[namelist:jules_soil_biogeochem=q10_soil] -compulsory=true -description=Q10 factor for soil respiration -range=0.1:10.0 -sort-key=d -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::q10_soil - -[namelist:jules_soil_biogeochem=rho_ch4] -compulsory=true -description=Factor in substrate limitation function (related to half saturation of substrate for methanogenic respiration) -range=1.0:1000.0 -sort-key=8d -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::rho_ch4 - -[namelist:jules_soil_biogeochem=soil_bgc_model] -compulsory=true -description=Choice of soil biogeochemistry model -fail-if=this == 1 and namelist:jules_vegetation=l_triffid == '.true.'; # Can't use 1-pool with TRIFFID - =this == 2 and namelist:jules_vegetation=l_triffid != '.true.'; # Can't use 4-pool soil C without TRIFFID - =this == 3 and namelist:jules_vegetation=l_triffid != '.true.'; # Can't use ECOSSE without TRIFFID -sort-key=a -trigger=namelist:jules_soil_biogeochem=l_q10: 1, 2; - =namelist:jules_soil_biogeochem=q10_soil: 1, 2, 3; - =namelist:jules_soil_biogeochem=l_soil_resp_lev2: 1, 2; - =namelist:jules_soil_biogeochem=cs_decomp_soil_moist_func: 1, 2; - =namelist:jules_soil_biogeochem=kaps: 1; - =namelist:jules_soil_biogeochem=kaps_4pool: 2; - =namelist:jules_soil_biogeochem=sorp: 2; - =namelist:jules_soil_biogeochem=n_inorg_turnover: 2; - =namelist:jules_soil_biogeochem=bio_hum_cn: 2; - =namelist:jules_soil_biogeochem=diff_n_pft: 2; - =namelist:jules_soil_biogeochem=tau_lit: 2, 3; - =namelist:jules_soil_biogeochem=tau_resp: 2; - =namelist:jules_soil_ecosse=l_soil_n: 3; - =namelist:jules_soil_ecosse=depo_nit_frac: 3; - =namelist:jules_soil_ecosse=l_match_layers: 3; - =namelist:jules_soil_ecosse=dt_soilc: 3; - =namelist:jules_soil_ecosse=dz_soilc_io: 3; - =namelist:jules_soil_ecosse=plant_input_profile: 3; - =namelist:jules_soil_ecosse=pi_sfc_depth: 3; - =namelist:jules_soil_ecosse=pi_sfc_frac: 3; - =namelist:jules_soil_ecosse=bacteria_min_frac: 3; - =namelist:jules_soil_ecosse=bacteria_max_frac: 3; - =namelist:jules_soil_ecosse=bacteria_min_frac_ph: 3; - =namelist:jules_soil_ecosse=bacteria_max_frac_ph: 3; - =namelist:jules_soil_ecosse=cn_bacteria: 3; - =namelist:jules_soil_ecosse=cn_fungi: 3; - =namelist:jules_soil_ecosse=decomp_rate: 3; - =namelist:jules_soil_ecosse=decomp_wrate_min_smith: 3; - =namelist:jules_soil_ecosse=decomp_wrate_min_clark: 3; - =namelist:jules_soil_ecosse=decomp_temp_coeff_smith: 3; - =namelist:jules_soil_ecosse=decomp_ph_min: 3; - =namelist:jules_soil_ecosse=decomp_ph_max: 3; - =namelist:jules_soil_ecosse=decomp_ph_rate_min: 3; - =namelist:jules_soil_ecosse=depth_nitrif: 3; - =namelist:jules_soil_ecosse=nitrif_frac_n2o_fc: 3; - =namelist:jules_soil_ecosse=nitrif_frac_gas: 3; - =namelist:jules_soil_ecosse=nitrif_frac_no: 3; - =namelist:jules_soil_ecosse=nitrif_max_factor: 3; - =namelist:jules_soil_ecosse=nitrif_rate: 3; - =namelist:jules_soil_ecosse=nitrif_wrate_min: 3; - =namelist:jules_soil_ecosse=denit50: 3; - =namelist:jules_soil_ecosse=denit_frac_n2_fc: 3; - =namelist:jules_soil_ecosse=denit_nitrate_equal: 3; - =namelist:jules_soil_ecosse=denit_water_coeff: 3; - =namelist:jules_soil_ecosse=denit_bio_factor: 3; - =namelist:jules_soil_ecosse=amm_leach_min: 3; - =namelist:jules_soil_ecosse=n_inorg_max_conc: 3; - =namelist:jules_soil_ecosse=l_driver_ave: 3; - =namelist:jules_soil_ecosse=l_decomp_slow: 3; - =namelist:jules_soil_ecosse=temp_modifier: 3; - =namelist:jules_soil_ecosse=water_modifier: 3; - =namelist:jules_soil_ecosse=dim_cslayer: 3; -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::soil_bgc_model -value-titles=Single pool model,4-pool model,ECOSSE -values=1,2,3 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_biogeochem=sorp] -compulsory=true -description=Soil leaching N Retention factor -range=0.01:100.0 -sort-key=h -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::sorp - -[namelist:jules_soil_biogeochem=t0_ch4] -compulsory=true -description=Reference temperature for Q10 function CH4 emissions -range=250:320 -sort-key=2b -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::t0_ch4 - -[namelist:jules_soil_biogeochem=tau_ch4] -compulsory=true -description=Decay factor with depth representing methane oxidation -range=0.01:100.0 -sort-key=q -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::tau_ch4 - -[namelist:jules_soil_biogeochem=tau_lit] -compulsory=true -description=Exponential decay constant for reduction of litter inputs with depth -range=0.01:100.0 -sort-key=b2 -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::tau_lit - -[namelist:jules_soil_biogeochem=tau_resp] -compulsory=true -description=Exponential decay constant for reduction of respiration with depth -range=0.01:100.0 -sort-key=b2 -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::tau_resp - -[namelist:jules_soil_biogeochem=z_burn_max] -compulsory=true -description=Maximum burn depth for soil - soil carbon is burned above this level -range=0.0:10.0 -sort-key=b2 -type=real -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::z_burn_max - -[namelist:jules_soil_ecosse] -compulsory=true -ns=namelist/JULES Science Settings/jules_soil_ecosse -sort-key=07 -title=Soil ECOSSE model options - -[namelist:jules_soil_ecosse=amm_leach_min] -compulsory=true -description=Minimum allowed amount of N in NH4 after leaching (kg m-3) -range=0: -type=real - -[namelist:jules_soil_ecosse=bacteria_max_frac] -compulsory=true -description=Maximum fraction of decomposer community that are bacteria -range=0:1 -type=real - -[namelist:jules_soil_ecosse=bacteria_max_frac_ph] -compulsory=true -description=Soil pH at or above which the fraction of bacteria is at a maximum -range=0:14 -type=real - -[namelist:jules_soil_ecosse=bacteria_min_frac] -compulsory=true -description=Minimum fraction of decomposer community that are bacteria -range=0:1 -type=real - -[namelist:jules_soil_ecosse=bacteria_min_frac_ph] -compulsory=true -description=Soil pH at or below which the fraction of bacteria is at a minimum -range=0:14 -type=real - -[namelist:jules_soil_ecosse=cn_bacteria] -compulsory=true -description=C:N ratio of soil bacteria -range=0.1: -type=real - -[namelist:jules_soil_ecosse=cn_fungi] -compulsory=true -description=C:N ratio of soil fungi -range=0.1: -type=real - -[namelist:jules_soil_ecosse=decomp_ph_max] -compulsory=true -description=pH above which rate of decomposition is maximum -range=0:14 -type=real - -[namelist:jules_soil_ecosse=decomp_ph_min] -compulsory=true -description=pH below which rate of decomposition is minimum -range=0:14 -type=real - -[namelist:jules_soil_ecosse=decomp_ph_rate_min] -compulsory=true -description=Minimum allowed value of pH rate modifier for decomposition -range=0:1 -type=real - -[namelist:jules_soil_ecosse=decomp_rate] -compulsory=true -description=Rate constants for decomposition of each pool (s-1) -length=4 -type=real - -[namelist:jules_soil_ecosse=decomp_temp_coeff_smith] -compulsory=true -description=Constants in Smith et al. (2010) soil C decomposition rate temperature modifier -length=3 -type=real - -[namelist:jules_soil_ecosse=decomp_wrate_min_clark] -compulsory=true -description=Minimum allowed value of the JULES form for water rate modifier for decomposition -range=0:1 -type=real - -[namelist:jules_soil_ecosse=decomp_wrate_min_smith] -compulsory=true -description=Minimum allowed value of the Smith et al. (2010) water rate modifier for decomposition -range=0:1 -type=real - -[namelist:jules_soil_ecosse=denit50] -compulsory=true -description=Amount of nitrate at which denitrification rate is 50% of the potential rate (kg m-3) -range=0: -type=real - -[namelist:jules_soil_ecosse=denit_bio_factor] -compulsory=true -description=Factor in denitrification calculation to convert C flux into a representation of biological activity -range=0: -type=real - -[namelist:jules_soil_ecosse=denit_frac_n2_fc] -compulsory=true -description=Fraction of denitrified N that becomes N2 when soil moisture is at field capacity -range=0:1 -type=real - -[namelist:jules_soil_ecosse=denit_nitrate_equal] -compulsory=true -description=Amount of N in soil nitrate at which denitrified N is released as equal amounts of N2 and N2O (kg m-3) -range=0: -type=real - -[namelist:jules_soil_ecosse=denit_water_coeff] -compulsory=true -description=Fitted constants describing water modifier for denitrification -length=3 -type=real - -[namelist:jules_soil_ecosse=depo_nit_frac] -compulsory=true -description=Fraction of total N deposition that is added to soil nitrate -range=0:1 -type=real - -[namelist:jules_soil_ecosse=depth_nitrif] -compulsory=true -description=Greatest depth at which nitrification and denitrification are allowed (m) -range=0: -type=real - -[namelist:jules_soil_ecosse=dim_cslayer] -compulsory=true -description=Number of soil carbon layers -range=1: -type=integer - -[namelist:jules_soil_ecosse=dt_soilc] -compulsory=true -description=Timestep length for soil biogeochemistry model (s) -type=real - -[namelist:jules_soil_ecosse=dz_soilc_io] -compulsory=true -description=Thicknesses of the soil biogeochemistry layers (m) -fail-if=len(this) != dim_cslayer; # Must have a value for each layer -length=: -type=real - -[namelist:jules_soil_ecosse=l_decomp_slow] -compulsory=true -description=Switch to slow decomposition when N is limiting -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_ecosse.nml.html#JULES_SOIL_ECOSSE::l_decomp_slow -value-titles=Decomposition slowed, Decomposition less efficient -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_ecosse=l_driver_ave] -compulsory=true -description=Switch for time-averaging of ECOSSE driving variables -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_ecosse.nml.html#JULES_SOIL_ECOSSE::l_driver_ave -value-titles=Time average, Instantaneous values -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_ecosse=l_match_layers] -compulsory=true -description=Switch to match soil C and N layers to soil moisture layers -trigger=namelist:jules_soil_ecosse=dim_cslayer: .false.; - =namelist:jules_soil_ecosse=dz_soilc_io: .false.; -url=https://metoffice.github.io/jules/latest/namelists/jules_soil_ecosse.nml.html#JULES_SOIL_ECOSSE::l_match_layers -value-titles=Match to soil moisture layers, Specify layers -values=.true.,.false. -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_ecosse=l_soil_n] -compulsory=true -description=Switch for a prognostic model of soil Nitrogen -trigger=namelist:jules_soil_ecosse=depo_nit_frac: .true.; - =namelist:jules_soil_ecosse=l_decomp_slow: .true.; - =namelist:jules_soil_ecosse=bacteria_min_frac: .true.; - =namelist:jules_soil_ecosse=bacteria_max_frac: .true.; - =namelist:jules_soil_ecosse=bacteria_min_frac_ph: .true.; - =namelist:jules_soil_ecosse=bacteria_max_frac_ph: .true.; - =namelist:jules_soil_ecosse=cn_bacteria: .true.; - =namelist:jules_soil_ecosse=cn_fungi: .true.; - =namelist:jules_soil_ecosse=depth_nitrif: .true.; - =namelist:jules_soil_ecosse=nitrif_frac_n2o_fc: .true.; - =namelist:jules_soil_ecosse=nitrif_rate: .true.; - =namelist:jules_soil_ecosse=nitrif_frac_gas: .true.; - =namelist:jules_soil_ecosse=nitrif_frac_no: .true.; - =namelist:jules_soil_ecosse=nitrif_max_factor: .true.; - =namelist:jules_soil_ecosse=nitrif_wrate_min: .true.; - =namelist:jules_soil_ecosse=denit50: .true.; - =namelist:jules_soil_ecosse=denit_frac_n2_fc: .true.; - =namelist:jules_soil_ecosse=denit_nitrate_equal: .true.; - =namelist:jules_soil_ecosse=denit_water_coeff: .true.; - =namelist:jules_soil_ecosse=denit_bio_factor: .true.; - =namelist:jules_soil_ecosse=amm_leach_min: .true.; - =namelist:jules_soil_ecosse=n_inorg_max_conc: .true.; -type=logical - -[namelist:jules_soil_ecosse=n_inorg_max_conc] -compulsory=true -description=Maximum-allowed concentration of inorganic N in a layer (kg m-3) -type=real - -[namelist:jules_soil_ecosse=nitrif_frac_gas] -compulsory=true -description=Fraction of nitrification lost as gas through full nitrification -range=0:1 -type=real - -[namelist:jules_soil_ecosse=nitrif_frac_n2o_fc] -compulsory=true -description=Fraction of nitrification lost as N2O by partial nitrification at field capacity -range=0:1 -type=real - -[namelist:jules_soil_ecosse=nitrif_frac_no] -compulsory=true -description=Fraction of nitrification gas loss through full nitrification that is NO -range=0:1 -type=real - -[namelist:jules_soil_ecosse=nitrif_max_factor] -compulsory=true -description=Shape factor in rate modifier for nitrification (kg m-3) -range=0:1 -type=real - -[namelist:jules_soil_ecosse=nitrif_rate] -compulsory=true -description=Rate constant for nitrification (s-1) -range=0: -type=real - -[namelist:jules_soil_ecosse=nitrif_wrate_min] -compulsory=true -description=Minimum allowed value of water rate modifier for nitrification when Smith et al., 2010 form is used -range=0: -type=real - -[namelist:jules_soil_ecosse=pi_sfc_depth] -compulsory=true -description=Depth of soil over which fraction pi_sfc_frac of plant litterfall is added (m). -type=real - -[namelist:jules_soil_ecosse=pi_sfc_frac] -compulsory=true -description=Fraction of plant litterfall that is added to the surface soil layer (of depth pi_sfc_depth). -range=0:1 -type=real - -[namelist:jules_soil_ecosse=plant_input_profile] -compulsory=true -description=Switch for distribution of litterfall inputs to the soil. -trigger=namelist:jules_soil_ecosse=pi_sfc_depth: 1; - =namelist:jules_soil_ecosse=pi_sfc_frac: 1; -value-titles=RootProfile,Exponential -values=1,2 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_ecosse=temp_modifier] -compulsory=true -description=Switch for form of temperature rate modifier for decomposition -value-titles=Q10,Smith -values=1,2 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - -[namelist:jules_soil_ecosse=water_modifier] -compulsory=true -description=Switch for form of water rate modifier for decomposition -value-titles=Clark,Smith -values=1,2 -widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget - [namelist:jules_soil_props] compulsory=true description=Configuration of spatially varying soil properties From 069ca9a185354627b6e4086bd5d09dd089e7c0db Mon Sep 17 00:00:00 2001 From: eleanorgb <38913404+eleanorgb@users.noreply.github.com> Date: Tue, 15 Sep 2026 13:16:04 +0100 Subject: [PATCH 6/6] updating metadata in jules-shared --- .../jules-shared/jules-model-environment/HEAD/rose-meta.conf | 1 - rose-meta/jules-shared/jules-soil-biogeochem/HEAD/rose-meta.conf | 1 - 2 files changed, 2 deletions(-) diff --git a/rose-meta/jules-shared/jules-model-environment/HEAD/rose-meta.conf b/rose-meta/jules-shared/jules-model-environment/HEAD/rose-meta.conf index adc29f7c..ec2d7520 100644 --- a/rose-meta/jules-shared/jules-model-environment/HEAD/rose-meta.conf +++ b/rose-meta/jules-shared/jules-model-environment/HEAD/rose-meta.conf @@ -32,7 +32,6 @@ trigger=namelist:jules_deposition=l_deposition_from_ukca: 1; =namelist:jules_soil=l_bedrock: 0; =namelist:jules_soil=l_tile_soil: 0; =namelist:jules_soil_biogeochem=l_label_frac_cs: 0; - =namelist:jules_soil_biogeochem=l_bgc_heat: 0; =namelist:jules_surface=l_vary_z0m_soil: 1; =namelist:jules_surface=formdrag: 1; =namelist:jules_surface=i_modiscopt: 1; diff --git a/rose-meta/jules-shared/jules-soil-biogeochem/HEAD/rose-meta.conf b/rose-meta/jules-shared/jules-soil-biogeochem/HEAD/rose-meta.conf index 785c4782..ecd04a6c 100644 --- a/rose-meta/jules-shared/jules-soil-biogeochem/HEAD/rose-meta.conf +++ b/rose-meta/jules-shared/jules-soil-biogeochem/HEAD/rose-meta.conf @@ -227,7 +227,6 @@ sort-key=c url=https://metoffice.github.io/jules/latest/namelists/jules_soil_biogeochem.nml.html#JULES_SOIL_BIOGEOCHEM::l_q10 value-titles=Q10 temperature function,Clark et al. (2011) temperature function values=.true.,.false. -warn-if=this == '.false.' and namelist:jules_soil_biogeochem=l_bgc_heat == '.true.' widget[rose-config-edit]=cylc8_compat.ComboBoxValueWidget [namelist:jules_soil_biogeochem=l_soil_resp_lev2]