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Cnp phosphorus #158

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GiorgiaLine Aug 25, 2026
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14 changes: 14 additions & 0 deletions doc/source/namelists/jules_vegetation.nml.rst
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Expand Up @@ -115,6 +115,20 @@ This file sets the vegetation options. It contains one namelist called :nml:lst:
FALSE
No Nitrogen limitation. Nitrogen fluxes are calculated as diagnostics only.

.. nml:member:: l_phosphorus
:type: logical
:default: F

Only used if :nml:mem:`l_triffid` = TRUE.

TRUE
Enable Phosphorus limitation of carbon uptake. A phosphorus
deposition field should be provided otherwise no P deposition is
assumed.

FALSE
No Phosphorus limitation. Phosphorus fluxes are calculated as diagnostics only.

.. nml:member:: l_trif_eq

:type: logical
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4 changes: 4 additions & 0 deletions doc/source/overview/key-switches.rst
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Expand Up @@ -18,6 +18,10 @@ When TRIFFID is on, competition between tiles is switched on with
:nml:mem:`JULES_VEGETATION::l_veg_compete` and the effect of nitrogen on
vegetation growth is enabled via :nml:mem:`JULES_VEGETATION::l_nitrogen`.

:nml:mem:`JULES_VEGETATION::l_veg_compete`, the effect of nitrogen on
vegetation growth is enabled via :nml:mem:`JULES_VEGETATION::l_nitrogen`, and the effect of phosphorus on
vegetation growth is enabled via :nml:mem:`JULES_VEGETATION::l_phosphorus`.

The crop model, which is simulates phenology and carbon stocks in crops, can be
switched on by setting the number of crop tiles
:nml:mem:`JULES_SURFACE_TYPES::ncpft` to a non-zero value.
Expand Down
7 changes: 7 additions & 0 deletions rose-meta/jules-standalone/HEAD/rose-meta.conf
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Expand Up @@ -2395,6 +2395,13 @@ fail-if=len(this) != namelist:jules_initial=nvars;
= namelist:jules_vegetation=l_landuse == '.true.' and not any(this == "'wood_prod_slow'"); # must be given if l_landuse = TRUE
= namelist:jules_vegetation=l_nitrogen == '.true.' and not any(this == "'ns'"); # must be given if l_nitrogen = TRUE
= namelist:jules_vegetation=l_nitrogen == '.true.' and not any(this == "'n_inorg'"); # must be given if l_nitrogen = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'ps_occ'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'ps_org'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'ps_par'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'ps_in_sorbed'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'ps_or_sorbed'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'p_inorg'"); # must be given if l_phosphorus = TRUE
= namelist:jules_vegetation=l_phosphorus == '.true.' and not any(this == "'plant_p_pool'"); # must be given if l_phosphorus = TRUE
= namelist:jules_surface_types=ncpft > 0 and not any(this == "'cropdvi'"); # cropdvi must be given if ncpft > 0
= namelist:jules_surface_types=ncpft > 0 and not any(this == "'croprootc'"); # croprootc must be given if ncpft > 0
= namelist:jules_surface_types=ncpft > 0 and not any(this == "'cropharvc'"); # cropharvc must be given if ncpft > 0
Expand Down
13 changes: 7 additions & 6 deletions rose-meta/jules-standalone/versions.py
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Expand Up @@ -45,15 +45,16 @@
from .version81_82 import *


class vnYY_txxxx(MacroUpgrade):
class vn81_tphos(MacroUpgrade):

"""Upgrade macro from JULES by Author"""
"""Upgrade macro from JULES by Carolina Duran Rojas"""

BEFORE_TAG = "vnY.Y"
AFTER_TAG = "vnY.Y_txxxx"
BEFORE_TAG = "vn8.2"
AFTER_TAG = "vn8.2_tphos"

def upgrade(self, config, meta_config=None):
"""Upgrade a JULES runtime app configuration."""

# Add settings
return config, self.reports
# Adding logical and real to the jules biogeochemical namelist
self.add_setting(config,
["namelist:jules_vegetation", "l_phosphorus"], ".false.")
60 changes: 55 additions & 5 deletions src/control/shared/CN_utils_mod.F90
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Expand Up @@ -30,8 +30,8 @@ MODULE CN_utils_mod
!-----------------------------------------------------------------------------
CONTAINS

SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &
n_root, n_stem, dvi_cpft)
SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, leaf, wood, root, n_leaf, &
n_root, n_stem, p_leaf, p_root, p_stem, dvi_cpft)

USE jules_vegetation_mod, ONLY: &
! imported scalars that are not altered
Expand All @@ -45,6 +45,10 @@ SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &
! imported arrays that are not altered
retran_l

USE jules_fields_mod, ONLY: psparms

USE jules_soil_biogeochem_mod, ONLY: l_cp_r, w_cp_r, r_cp_r

IMPLICIT NONE

!-----------------------------------------------------------------------------
Expand All @@ -57,6 +61,8 @@ SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &
REAL(KIND=real_jlslsm), INTENT(IN) :: &
lai_bal &
! Balanced LAI
, leaf &
! Leaf carbon (kg C m-2)
, wood &
! Wood carbon (kg C m-2)
, root &
Expand All @@ -74,28 +80,65 @@ SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &
! Leaf N content (kg N m-2)
, n_root &
! Root N content (kg N m-2)
, n_stem
, n_stem &
! Wood N content (kg N m-2)
, p_leaf &
! Leaf P content (kg P m-2)
, p_root &
! Root P content (kg P m-2)
, p_stem
! Wood P content (kg P m-2)

!-----------------------------------------------------------------------------
! Local scalar variables.
!-----------------------------------------------------------------------------
INTEGER :: &
errcode
errcode &
! Error code to pass to ereport.
, st_int

REAL(KIND=real_jlslsm) :: &
fstem &
! Ratio of respiring stem wood to total wood
, nl_ave &
! Leaf nitrogen per unit LAI, averaged over the canopy (kg m-2).
, x_tmp
, x_tmp &
! Temporary factor used in calculation of canopy average.
, l_cp &
! Ratio of leaf C to P
, r_cp &
! Ratio of root C to P
, w_cp &
! Ratio of wood C to P
, st_real

CHARACTER(LEN=*), PARAMETER :: RoutineName = 'CALC_N_COMPS_TRIFFID'

!-----------------------------------------------------------------------------
!end of header
!!! GL CNP_PHOS Something is missing here
st_real = psparms%stype_soilt(l,1,1)
st_int = INT(st_real)
!!! GL CNP_PHOS This should be a warning but doing it to check everything else
IF (st_int < 1) THEN
st_int = 1
END IF
! Need the index to be an integer not a real?
l_cp = l_cp_r(st_int)
r_cp = r_cp_r(st_int)
w_cp = w_cp_r(st_int)
Comment on lines +119 to +129

!values for veg P coming from Iain Hartley and Beto (the values are total
!leaf, stem and root P. Now we are using C:P and C pools
! for C values: Leaf (Fyllas 2009, BGS- BNT site), Stem and root: from AFEX
! project)
!P concentrations (g kg-1): Leaf 0.5; Stem and branch 0.06; Fine root 0.4;
!coarseroot 0.1
!C concnetrations (mg g-1): Leaf 491; Stem and branch 440; Fine root 450;
!coarseroot 0.1
! p_leaf= 0.00192
! p_root = 0.00105
! p_stem = 0.00029

IF ( l_leaf_n_resp_fix ) THEN

Expand Down Expand Up @@ -151,6 +194,9 @@ SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &

END IF

! Eq. 1 in CNP GMD paper:
p_leaf = leaf / l_cp

Comment on lines +197 to +199
!------------------------------------------------------------------------------
! Calculate root and stem N.
!------------------------------------------------------------------------------
Expand All @@ -163,6 +209,10 @@ SUBROUTINE calc_n_comps_triffid(l, n, phen, lai_bal, wood, root, n_leaf, &
n_stem = ns_nl(n) * nl0(n) * wood
END IF

! Eqs. 2-3 in CNP GMD paper:
p_root = root / r_cp
p_stem = wood / w_cp

END SUBROUTINE calc_n_comps_triffid

!#############################################################################
Expand Down
33 changes: 31 additions & 2 deletions src/control/shared/jules_soil_biogeochem_mod.F90
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Expand Up @@ -153,7 +153,7 @@ MODULE jules_soil_biogeochem_mod
! Namelist variables used only by the 4-pool soil C model.
!-----------------------------------------------------------------------------
REAL(KIND=real_jlslsm) :: &
bio_hum_CN = rmdi, &
bio_hum_CN= rmdi, &
! Soil Bio and Hum CN ratio parameter
sorp = rmdi, &
! Soil inorganic N factor in leaching.
Expand All @@ -164,8 +164,37 @@ MODULE jules_soil_biogeochem_mod
! roots after the roots uptake from the soil around them)
! per 360 days. Should be quicker than the turnover rate of inorganic
! N hence choice of value (100 vs 1).
tau_resp = rmdi
tau_resp = rmdi, &
! Parameter controlling decay of respiration with depth (m-1)
! P Vars
bio_hum_CP(18) = rmdi, &
! Soil Bio and Hum CP ratio parameter
l_cp_r(18) = rmdi, &
! Leaf C:P ratio
w_cp_r(18) = rmdi, &
! Wood C:P ratio
r_cp_r(18) = rmdi, &
! Root C:P ratio
ps_in_max(18) = rmdi, &
! Maximum inorganic P
ps_or_max(18) = rmdi, &
! Maximum organic P
npr_soil = rmdi, &
! Soil Bio and Hum NP ratio parameter
a_root = rmdi, &
! Soil Bio and Hum CN ratio parameter
fpl = rmdi, &
! Soil Bio and Hum CN ratio parameter
k_org_sorp = rmdi, &
! Organic P sorbed ratio parameter
k_org_desorp = rmdi, &
! Organic P desorbed ratio parameter
k_in_sorp = rmdi, &
! Inorganic P sorbed ratio parameter
k_in_desorp = rmdi, &
! Inorganic P sorbed ratio parameter
sorp_pl = rmdi
! Soil inorganic P factor in leaching.

REAL(KIND=real_jlslsm) :: &
kaps_4pool(4) = rmdi
Expand Down
10 changes: 10 additions & 0 deletions src/control/shared/p_s_parms.F90
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Expand Up @@ -96,6 +96,9 @@ MODULE p_s_parms
! thaw depth calculation based on unfrozen water content fraction.
REAL(KIND=real_jlslsm), ALLOCATABLE :: soil_ph_soilt(:,:,:)
! Soil pH, defined on soil layers.
! P Vars
REAL(KIND=real_jlslsm), ALLOCATABLE :: stype_soilt(:,:,:)
! Soil pH, defined on soil layers. - ported from CNP_FAR
Comment on lines +99 to +101
END TYPE

!================================
Expand Down Expand Up @@ -127,6 +130,7 @@ MODULE p_s_parms
REAL(KIND=real_jlslsm), POINTER :: sthf_soilt(:,:,:)
REAL(KIND=real_jlslsm), POINTER :: sthu_min_soilt(:,:,:)
REAL(KIND=real_jlslsm), POINTER :: soil_ph_soilt(:,:,:)
REAL(KIND=real_jlslsm), POINTER :: stype_soilt(:,:,:)
END TYPE

CHARACTER(LEN=*), PARAMETER, PRIVATE :: ModuleName='P_S_PARMS'
Expand Down Expand Up @@ -173,6 +177,7 @@ SUBROUTINE psparms_alloc(land_pts,t_i_length,t_j_length, &
ALLOCATE(psparms_data%smvcwt_soilt(land_pts,nsoilt,sm_levels))
ALLOCATE(psparms_data%smvcst_soilt(land_pts,nsoilt,sm_levels))
ALLOCATE(psparms_data%clay_soilt(land_pts,nsoilt,dim_cslayer))
ALLOCATE(psparms_data%stype_soilt(land_pts,nsoilt,dim_cslayer))

psparms_data%bexp_soilt(:,:,:) = 0.0
psparms_data%sathh_soilt(:,:,:) = 0.0
Expand All @@ -183,6 +188,7 @@ SUBROUTINE psparms_alloc(land_pts,t_i_length,t_j_length, &
psparms_data%smvcwt_soilt(:,:,:) = 0.0
psparms_data%smvcst_soilt(:,:,:) = 0.0
psparms_data%clay_soilt(:,:,:) = 0.0
psparms_data%stype_soilt(:,:,:) = 0.0

! Plant and soil parameters
ALLOCATE(psparms_data%albsoil_soilt(land_pts,nsoilt))
Expand Down Expand Up @@ -286,6 +292,7 @@ SUBROUTINE psparms_dealloc(psparms_data)
DEALLOCATE(psparms_data%soil_ph_soilt)
DEALLOCATE(psparms_data%v_close_pft)
DEALLOCATE(psparms_data%v_open_pft)
DEALLOCATE(psparms_data%stype_soilt)

IF (lhook) CALL dr_hook(ModuleName//':'//RoutineName,zhook_out,zhook_handle)
RETURN
Expand Down Expand Up @@ -345,6 +352,7 @@ SUBROUTINE psparms_assoc(psparms,psparms_data)
psparms%soil_ph_soilt => psparms_data%soil_ph_soilt
psparms%v_close_pft => psparms_data%v_close_pft
psparms%v_open_pft => psparms_data%v_open_pft
psparms%stype_soilt => psparms_data%stype_soilt

IF (lhook) CALL dr_hook(ModuleName//':'//RoutineName,zhook_out,zhook_handle)
RETURN
Expand Down Expand Up @@ -400,6 +408,8 @@ SUBROUTINE psparms_nullify(psparms)
NULLIFY(psparms%soil_ph_soilt)
NULLIFY(psparms%v_close_pft)
NULLIFY(psparms%v_open_pft)
NULLIFY(psparms%stype_soilt)
!!! GL CNP_PHOS: DO I need to put the the other soilt vars here?

IF (lhook) CALL dr_hook(ModuleName//':'//RoutineName,zhook_out,zhook_handle)
RETURN
Expand Down
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