Merge pull request #2845 from olyson/b4b-dev_PPE2830-2831

PPE parameter work -Addresses issues 2830 and 2831
ESCOMP · Oct 28, 2024 · f0566a6 · f0566a6
2 parents 9f44365 + 0fd1a04
commit f0566a6
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Showing 12 changed files with 121 additions and 156 deletions.
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -3602,17 +3602,6 @@ sub setup_logic_luna {
   if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) {
      $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" );
   }
-  my $var = "jmaxb1";
-  if ( &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'use_luna'=>$nl_flags->{'use_luna'} );
-  }
-  my $val = $nl->get_value($var);
-  if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     if ( defined($val) ) {
-        $log->fatal_error("Cannot set $var when use_luna is NOT on" );
-     }
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4526,8 +4515,6 @@ sub setup_logic_canopyhydrology {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
 }
 
@@ -4546,7 +4533,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -413,11 +413,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Canopy hydrology namelist defaults -->
 <use_clm5_fpi                               >.true.</use_clm5_fpi>
-<interception_fraction                      >1.0</interception_fraction>
-<maximum_leaf_wetted_fraction               >0.05</maximum_leaf_wetted_fraction>
 <use_clm5_fpi                 phys="clm4_5" >.false.</use_clm5_fpi>
-<interception_fraction        phys="clm4_5" >0.25</interception_fraction>
-<maximum_leaf_wetted_fraction phys="clm4_5" >1.0</maximum_leaf_wetted_fraction>
 
 <!-- Soilwater movement namelist defaults -->
 <soilwater_movement_method               >1</soilwater_movement_method>
@@ -493,9 +489,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <lotmp_snowdensity_method               >'Slater2017'</lotmp_snowdensity_method>
 <lotmp_snowdensity_method phys="clm4_5" >'TruncatedAnderson1976'</lotmp_snowdensity_method>
 
-<upplim_destruct_metamorph                 >175.d00</upplim_destruct_metamorph>
-<upplim_destruct_metamorph   phys="clm4_5" >100.d00</upplim_destruct_metamorph>
-
 <overburden_compress_tfactor>0.08d00</overburden_compress_tfactor>
 
 <reset_snow>.false.</reset_snow>
@@ -551,10 +544,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240822.nc</paramfile>
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -606,9 +599,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_fertilizer                   >.false.</use_fertilizer>
 <use_fertilizer use_crop=".true." >.true.</use_fertilizer>
 
-<!-- Could depend on physics version -->
-<jmaxb1 use_luna=".true." >0.17</jmaxb1>
-
 <!-- o3_veg_stress_method-->
 <o3_veg_stress_method>unset</o3_veg_stress_method>
 

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -404,21 +404,11 @@ Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the
 <default>Default: 40</default>
 </entry>
 
-<entry id="interception_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Fraction of intercepted precipitation
-</entry>
-
 <entry id="use_clm5_fpi" type="logical" category="clm_physics"
        group="clm_canopyhydrology_inparm" valid_values="" >
 If TRUE use clm5 equation for fraction of intercepted precipitation
 </entry>
 
-<entry id="maximum_leaf_wetted_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Maximum fraction of leaf that may be wet prior to drip occuring
-</entry>
-
 <entry id="baseflow_scalar" type="real" category="clm_physics"
        group="soilhydrology_inparm" valid_values="" >
 Scalar multiplier for base flow rate
@@ -712,11 +702,6 @@ Scalar of leaf respiration to vcmax
 The maximum value to use for zeta under stable conditions
 </entry>
 
-<entry id="Jmaxb1" type="real" category="clm_physics"
-       group="luna" >
-baseline proportion of nitrogen allocated for electron transport (J)
-</entry>
-
 <entry id="use_fates" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the FATES model
@@ -2844,11 +2829,6 @@ TruncatedAnderson1976 -- Truncate the Anderson-1976 equation at the value for -1
 Slater2017 ------------- Use equation from Slater that increases snow density for very cold temperatures  (Arctic, Antarctic)
 </entry>
 
-<entry id="upplim_destruct_metamorph" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Upper Limit on Destructive Metamorphism Compaction [kg/m3]
-</entry>
-
 <entry id="overburden_compress_Tfactor" type="real" category="clm_physics"
        group="clm_snowhydrology_inparm"   >
 Snow compaction overburden exponential factor (1/K)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -1235,10 +1235,6 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_luna=.true., lnc_opt=.true.",
                                      phys=>"clm5_0",
                                    },
-     "NOlunabutsetJmaxb1"        =>{ options=>"-envxml_dir . -bgc sp",
-                                     namelst=>"use_luna=.false., jmaxb1=1.0",
-                                     phys=>"clm5_0",
-                                   },
      "envxml_not_dir"            =>{ options=>"-envxml_dir myuser_nl_clm",
                                      namelst=>"",
                                      phys=>"clm5_0",

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -875,6 +875,15 @@
       <option name="comment"  >Run matrix solution fast spinup for restart beyond a year (to trigger next year logic) turning off extra options to make faster (so without crop or isotopes). This test would've caught a previous bug.</option>
     </options>
   </test>
+  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/clm60_monthly_matrixcn_soilCN30">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:20:00</option>
+      <option name="comment"  >Smoke test of soil CN-matrix on with soil CN ratio set to 30</option>
+    </options>
+  </test>
   <test name="ERS_D" grid="f19_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240814.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c241017.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240822.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241017.nc'
diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90
@@ -9,9 +9,11 @@ module CNGapMortalityMod
   !
   ! !USES:
   use shr_kind_mod                   , only : r8 => shr_kind_r8
+  use shr_infnan_mod                 , only : nan => shr_infnan_nan, assignment(=)
   use decompMod                      , only : bounds_type
   use abortutils                     , only : endrun
   use shr_log_mod                    , only : errMsg => shr_log_errMsg
+  use clm_varpar                     , only : mxpft
   use pftconMod                      , only : pftcon
   use CNDVType                       , only : dgvs_type
   use CNVegCarbonStateType           , only : cnveg_carbonstate_type, spinup_factor_deadwood
@@ -34,8 +36,10 @@ module CNGapMortalityMod
   public :: CNGapMortality
 
   type, private :: params_type
-     real(r8):: am     ! mortality rate based on annual rate, fractional mortality (1/yr)
      real(r8):: k_mort ! coeff. of growth efficiency in mortality equation
+     real(r8), allocatable :: r_mort(:)  ! Mortality rate (1/year)
+  contains
+     procedure, private :: allocParams    ! Allocate the parameters
   end type params_type
   !
   type(params_type), private :: params_inst
@@ -49,6 +53,24 @@ module CNGapMortalityMod
 
 contains
 
+  !-----------------------------------------------------------------------
+  subroutine allocParams ( this )
+    !
+    implicit none
+
+    ! !ARGUMENTS:
+    class(params_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    character(len=32)  :: subname = 'allocParams'
+    !-----------------------------------------------------------------------
+
+    ! allocate parameters
+
+    allocate( this%r_mort    (0:mxpft) )          ; this%r_mort(:)   = nan
+
+  end subroutine allocParams
+
   !-----------------------------------------------------------------------
   subroutine readParams ( ncid )
     !
@@ -67,18 +89,21 @@ subroutine readParams ( ncid )
     character(len=100) :: errCode = '-Error reading in parameters file:'
     logical            :: readv ! has variable been read in or not
     real(r8)           :: tempr ! temporary to read in constant
+    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
     character(len=100) :: tString ! temp. var for reading
     !-----------------------------------------------------------------------
 
-    tString='r_mort'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%am=tempr
-
     tString='k_mort'
     call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
     params_inst%k_mort=tempr   
+
+    call params_inst%allocParams()
+
+    tString='r_mort'
+    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+    params_inst%r_mort=temp1d
 
   end subroutine readParams
 
@@ -183,8 +208,6 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
          )
 
       dt = real( get_step_size(), r8 )
-      ! set the mortality rate based on annual rate
-      am = params_inst%am
       ! set coeff of growth efficiency in mortality equation 
       k_mort = params_inst%k_mort
 
@@ -216,9 +239,11 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
                am = min(1._r8, am + heatstress(p))
             else ! lpj didn't set this for grasses; cn does
                ! set the mortality rate based on annual rate
-               am = params_inst%am
+               am = params_inst%r_mort(ivt(p))
             end if
 
+         else
+            am = params_inst%r_mort(ivt(p)) 
          end if
 
          m  = am/(get_average_days_per_year() * secspday)

diff --git a/src/biogeophys/CanopyHydrologyMod.F90 b/src/biogeophys/CanopyHydrologyMod.F90
@@ -49,6 +49,8 @@ module CanopyHydrologyMod
      real(r8) :: snow_canopy_storage_scalar ! Canopy-storage-of-snow parameter (kg/m2)
      real(r8) :: snowcan_unload_temp_fact   ! Temperature canopy snow unload scaling (C2 in Eq. 14, Roesch et al. 2001) (K*s)
      real(r8) :: snowcan_unload_wind_fact   ! Wind canopy snow unload scaling (modifies 1.56e5, where 1.56e5 is C3 in Eq. 15, Roesch et al. 2001) (-)
+     real(r8) :: interception_fraction      ! Fraction of intercepted precipitation (-)
+     real(r8) :: maximum_leaf_wetted_fraction ! Maximum fraction of leaf that may be wet (-)
   end type params_type
   type(params_type), private ::  params_inst
   !
@@ -67,8 +69,6 @@ module CanopyHydrologyMod
   private :: BulkDiag_FracWet                            ! Determine fraction of vegetated surface that is wet
   !
   ! !PRIVATE DATA MEMBERS:
-  real(r8) :: interception_fraction ! Fraction of intercepted precipitation
-  real(r8) :: maximum_leaf_wetted_fraction ! Maximum fraction of leaf that may be wet
   logical, private :: use_clm5_fpi    = .false. ! use clm5 fpi equation
 
   character(len=*), parameter, private :: sourcefile = &
@@ -99,8 +99,6 @@ subroutine CanopyHydrology_readnl( NLFilename )
     character(len=32) :: subname = 'CanopyHydrology_readnl'  ! subroutine name
     !-----------------------------------------------------------------------
     namelist /clm_canopyhydrology_inparm/ &
-         interception_fraction, &
-         maximum_leaf_wetted_fraction, &
          use_clm5_fpi
 
     ! ----------------------------------------------------------------------
@@ -125,15 +123,11 @@ subroutine CanopyHydrology_readnl( NLFilename )
     end if
 
     ! Broadcast namelist variables read in
-    call shr_mpi_bcast(interception_fraction, mpicom)
-    call shr_mpi_bcast(maximum_leaf_wetted_fraction, mpicom)
     call shr_mpi_bcast(use_clm5_fpi, mpicom)
 
     if (masterproc) then
        write(iulog,*) ' '
        write(iulog,*) 'canopyhydrology settings:'
-       write(iulog,*) '  interception_fraction        = ',interception_fraction
-       write(iulog,*) '  maximum_leaf_wetted_fraction = ',maximum_leaf_wetted_fraction
        write(iulog,*) '  use_clm5_fpi                 = ',use_clm5_fpi
     endif
 
@@ -162,6 +156,10 @@ subroutine readParams( ncid )
     call readNcdioScalar(ncid, 'snowcan_unload_temp_fact', subname, params_inst%snowcan_unload_temp_fact)
     ! Wind canopy snow unload scaling (modifies 1.56e5, where 1.56e5 is C3 in Eq. 15, Roesch et al. 2001) (-)
     call readNcdioScalar(ncid, 'snowcan_unload_wind_fact', subname, params_inst%snowcan_unload_wind_fact)
+    ! Fraction of intercepted precipitation (-)
+    call readNcdioScalar(ncid, 'interception_fraction', subname, params_inst%interception_fraction)
+    ! Maximum fraction of leaf that may be wet (-)
+    call readNcdioScalar(ncid, 'maximum_leaf_wetted_fraction', subname, params_inst%maximum_leaf_wetted_fraction)
 
    end subroutine readParams
 
@@ -535,7 +533,7 @@ subroutine BulkFlux_CanopyInterceptionAndThroughfall(bounds, num_nolakep, filter
         if (check_point_for_interception_and_excess(p)) then
            ! Coefficient of interception
            if (use_clm5_fpi) then
-              fpiliq = interception_fraction * tanh(elai(p) + esai(p))
+              fpiliq = params_inst%interception_fraction * tanh(elai(p) + esai(p))
            else
               fpiliq = 0.25_r8*(1._r8 - exp(-0.5_r8*(elai(p) + esai(p))))
            end if
@@ -1170,7 +1168,7 @@ subroutine BulkDiag_FracWet(bounds, num_soilp, filter_soilp, &
            if (h2ocan > 0._r8) then
               vegt    = frac_veg_nosno(p)*(elai(p) + esai(p))
               fwet(p) = (h2ocan / (vegt * params_inst%liq_canopy_storage_scalar))**0.666666666666_r8
-              fwet(p) = min (fwet(p),maximum_leaf_wetted_fraction)   ! Check for maximum limit of fwet
+              fwet(p) = min (fwet(p),params_inst%maximum_leaf_wetted_fraction)   ! Check for maximum limit of fwet
               if (snocan(p) > 0._r8) then
                  fcansno(p) = (snocan(p) / (vegt * params_inst%snow_canopy_storage_scalar))**0.15_r8 ! must match snocanmx 
                  fcansno(p) = min (fcansno(p),1.0_r8)