Move some hardcoded parameters to the paramsfile

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -393,8 +393,8 @@ 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="clm5_0">lnd/clm2/paramdata/clm5_params.c200519.nc</paramfile>
-<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c200519.nc</paramfile>
+<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c200614.nc</paramfile>
+<paramfile phys="clm4_5">lnd/clm2/paramdata/clm45_params.c200614.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->

doc/ChangeLog

@@ -1,9 +1,116 @@
 ===============================================================
+Tag name:  ctsm1.0.dev101
+Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326), oleson (Keith Oleson)
+Date: Wed Jun 17 23:51:22 MDT 2020
+One-line Summary: Changes from Keith to bring a list of variables to the parameter file
+
+Purpose of changes
+------------------
+
+Change some hardcoded parameters to go on the parameter files. This is needed in preparation 
+of running the Perturbed Parameter Ensemble.
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #): #995 #138, #206
+
+Fixes #995 -- Soil turnover times are on paramfile and hardcoded
+Fixes #138 -- use tau_ values on paramfile
+Fixes #206 -- add prh30 to paramfile
+Some work on #290 -- LUNA refactoring
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations? No
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): None
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None
+
+Changes made to namelist defaults (e.g., changed parameter values): None
+
+Changes to the datasets (e.g., parameter, surface or initial files): paramfile for both clm4_5 and clm5_0
+   Add 51 new parameters to the paramsfile:
+       bsw_adjustfactor,cpha,csol_clay,csol_om,csol_sand,denitrif_nitrateconc_coefficient,denitrif_nitrateconc_exponent,
+       denitrif_respiration_coefficient,denitrif_respiration_exponent,drift_gs,e_ice,enzyme_turnover_daily,eta0_anderson,
+       eta0_vionnet,fnps,hksat_adjustfactor,ignition_efficiency,jmaxb0,jmaxha,jmaxhd,kcha,koha,kp25ratio,lmrha,lmrhd,
+       lmrse,luna_theta_cj,minrelh,n_baseflow,pd,perched_baseflow_scalar,prh30,relhExp,ssi,sucsat_adjustfactor,theta_cj,
+       theta_ip,theta_psii,tpuha,tpuhd,tkd_clay,tkd_om,tkd_sand,tkm_om,tpu25ratio,vcmaxha,vcmaxhd,watsat_adjustfactor,
+       wc2wjb0,wimp,wind_min
+    k_nitr_max removed and replaced with k_nitr_max_perday
+    meta-data for the tau_* variables changed, and a roundoff difference in the clm4_5 paramfile
+
+Substantial timing or memory changes: None
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): prh30 not used for clm4_5
+   prh30 was added in but won't be used for the CNFireLi2014 formulation. 
+   It's only used for the clm5_0 and following formulations
+
+Changes to tests or testing: None
+
+Code reviewed by: self, oleson
+
+
+CTSM testing: regular
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS (170 tests differ from baseline because of new paramfiles)
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+  regular tests (aux_clm):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None
+
+Pull Requests that document the changes (include PR ids): #1039
+(https://github.com/ESCOMP/ctsm/pull)
+    #1039 -- move hardcoded parameters to paramfile
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev100
 Originator(s):  sacks (Bill Sacks)
 Date:  Tue Jun  9 06:15:15 MDT 2020
 One-line Summary: Deallocate memory after running init_interp
-
+ 
 Purpose of changes
 ------------------
 

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev101 ole/erik 06/17/2020 Changes from Keith to bring a list of variables to the parameter file
   ctsm1.0.dev100    sacks 06/09/2020 Deallocate memory after running init_interp
   ctsm1.0.dev099    sacks 06/08/2020 Update cime, needed for izumi machine updates
   ctsm1.0.dev098 jet/erik 05/28/2020 Bring in GFDL fv3 cubed sphere grids C24, C48, C96, C192, C384

src/biogeochem/CNFireBaseMod.F90

@@ -73,6 +73,11 @@ module CNFireBaseMod
       real(r8) :: cmb_cmplt_fact(num_fp) = (/ 0.5_r8, 0.25_r8 /) ! combustion completion factor (unitless)
   end type
 
+  type, public :: params_type
+     real(r8) :: prh30                ! Factor related to dependence of fuel combustibility on 30-day running mean of relative humidity (unitless)
+     real(r8) :: ignition_efficiency  ! Ignition efficiency of cloud-to-ground lightning (unitless)
+  end type params_type
+
   !
   type, abstract, extends(cnfire_method_type) :: cnfire_base_type
     private
@@ -89,6 +94,7 @@ module CNFireBaseMod
       !
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: CNFireInit        ! Initialization of CNFire
+      procedure, public :: CNFireReadParams  ! Read in constant parameters from the paramsfile
       procedure, public :: CNFireReadNML     ! Read in namelist for CNFire
       procedure, public :: CNFireInterp      ! Interpolate fire data
       procedure, public :: CNFireArea        ! Calculate fire area
@@ -122,6 +128,7 @@ end function need_lightning_and_popdens_interface
   end interface
 
   type(cnfire_const_type), public, protected :: cnfire_const          ! Fire constants shared by Li versons
+  type(params_type)      , public, protected :: cnfire_params         ! Fire parameters shared by Li versions
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -975,6 +982,30 @@ subroutine CNFireFluxes (this, bounds, num_soilc, filter_soilc, num_soilp, filte
 
   end subroutine CNFireFluxes
 
+  !-----------------------------------------------------------------------
+  subroutine CNFireReadParams( this, ncid )
+    !
+    ! Read in the constant parameters from the input NetCDF parameter file
+    ! !USES:
+    use ncdio_pio   , only: file_desc_t
+    use paramUtilMod, only: readNcdioScalar
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(cnfire_base_type)         :: this
+    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
+    !
+    ! !LOCAL VARIABLES:
+    character(len=*), parameter :: subname = 'CNFireReadParams'
+    !--------------------------------------------------------------------
+
+    ! Factor related to dependence of fuel combustibility on 30-day running mean of relative humidity (unitless)
+    call readNcdioScalar(ncid, 'prh30', subname, cnfire_params%prh30)
+    ! Ignition efficiency of cloud-to-ground lightning (unitless)
+    call readNcdioScalar(ncid, 'ignition_efficiency', subname, cnfire_params%ignition_efficiency)
+
+  end subroutine CNFireReadParams
+
   !-----------------------------------------------------------------------
   subroutine hdm_init( this, bounds, NLFilename )
    !

src/biogeochem/CNFireLi2014Mod.F90

@@ -40,7 +40,7 @@ module CNFireLi2014Mod
   use ColumnType                         , only : col                
   use PatchType                          , only : patch                
   use CNFireMethodMod                    , only : cnfire_method_type
-  use CNFireBaseMod                      , only : cnfire_base_type, cnfire_const
+  use CNFireBaseMod                      , only : cnfire_base_type, cnfire_const, cnfire_params
   !
   implicit none
   private
@@ -570,7 +570,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                    min(1._r8,exp(SHR_CONST_PI*(forc_t(c)-SHR_CONST_TKFRZ)/10._r8))
               lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
               fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
-              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8*cos(3._r8*grc%lat(g)))*0.25_r8)*(1._r8-fs)*(1._r8-cropf_col(c)) 
+              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8*cos(3._r8*grc%lat(g)))* &
+                         cnfire_params%ignition_efficiency)*(1._r8-fs)*(1._r8-cropf_col(c)) 
               nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
               Lb_lf    = 1._r8+10.0_r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
               if ( wtlf(c) > 0.0_r8 )then

src/biogeochem/CNFireLi2016Mod.F90

@@ -41,7 +41,7 @@ module CNFireLi2016Mod
   use PatchType                          , only : patch                
   use SoilBiogeochemStateType            , only : get_spinup_latitude_term
   use CNFireMethodMod                    , only : cnfire_method_type
-  use CNFireBaseMod                      , only : cnfire_base_type, cnfire_const
+  use CNFireBaseMod                      , only : cnfire_base_type, cnfire_const, cnfire_params
   !
   implicit none
   private
@@ -58,6 +58,10 @@ module CNFireLi2016Mod
     procedure, public :: CNFireArea    ! Calculate fire area
   end type cnfire_li2016_type
 
+  !
+  ! !PRIVATE MEMBER DATA:
+  !-----------------------------------------------------------------------
+
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
 
@@ -593,7 +597,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then  
               afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
               arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
-              arh30=1._r8-max(0.7_r8, min(1._r8,rh30_col(c)/90._r8))
+              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
               if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
                 fire_m   = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8)*((1._r8 -max(0._r8,&
                     min(1._r8,(btran_col(c)/wtlf(c)-bt_min)/(bt_max-bt_min))))**0.5_r8)
@@ -602,8 +606,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
               end if
               lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
               fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
-              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8*cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))*0.22_r8)  &
-                         *(1._r8-fs)*(1._r8-cropf_col(c))
+              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8*cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                         cnfire_params%ignition_efficiency)*(1._r8-fs)*(1._r8-cropf_col(c))
               nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
               Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
               spread_m = fire_m**0.5_r8

src/biogeochem/CNFireMethodMod.F90

@@ -21,6 +21,9 @@ module CNFireMethodMod
      ! Read namelist for the fire datasets
      procedure(CNFireReadNML_interface), public, deferred :: CNFireReadNML
 
+     ! Read parameters  for the fire datasets
+     procedure(CNFireReadParams_interface), public, deferred :: CNFireReadParams
+
      ! Interpolate the fire datasets
      procedure(CNFireInterp_interface) , public, deferred :: CNFireInterp
 
@@ -78,6 +81,21 @@ subroutine CNFireReadNML_interface(this, NLFilename )
 
   end subroutine CNFireReadNML_interface
 
+  subroutine CNFireReadParams_interface( this, ncid )
+    !
+    ! !DESCRIPTION:
+    ! Read parameters from parameter file
+    !
+    ! USES
+    use ncdio_pio   , only: file_desc_t
+    import :: cnfire_method_type
+    ! !ARGUMENTS:
+    implicit none
+    class(cnfire_method_type)     :: this
+    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
+
+  end subroutine CNFireReadParams_interface
+
   subroutine CNFireInterp_interface(this, bounds)
     !
     ! !DESCRIPTION:

src/biogeochem/CNVegetationFacade.F90

@@ -193,7 +193,7 @@ module CNVegetationFacade
 contains
 
   !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename, nskip_steps)
+  subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid)
     !
     ! !DESCRIPTION:
     ! Initialize a CNVeg object.
@@ -203,12 +203,14 @@ subroutine Init(this, bounds, NLFilename, nskip_steps)
     ! !USES:
     use CNFireFactoryMod , only : create_cnfire_method
     use clm_varcon       , only : c13ratio, c14ratio
+    use ncdio_pio        , only : file_desc_t
     !
     ! !ARGUMENTS:
     class(cn_vegetation_type), intent(inout) :: this
     type(bounds_type), intent(in)    :: bounds
     character(len=*) , intent(in)    :: NLFilename  ! namelist filename
     integer          , intent(in)    :: nskip_steps ! Number of steps to skip at startup
+    type(file_desc_t), intent(inout) :: params_ncid ! NetCDF handle to parameter file
     !
     ! !LOCAL VARIABLES:
     integer :: begp, endp
@@ -274,6 +276,7 @@ subroutine Init(this, bounds, NLFilename, nskip_steps)
     end if
 
     call create_cnfire_method(NLFilename, this%cnfire_method)
+    call this%cnfire_method%CNFireReadParams( params_ncid )
 
   end subroutine Init
 

src/biogeophys/BareGroundFluxesMod.F90

@@ -33,8 +33,9 @@ module BareGroundFluxesMod
   public :: readParams
 
   type, private :: params_type
-      real(r8) :: a_coef  ! Drag coefficient under less dense canopy (unitless)
-      real(r8) :: a_exp  ! Drag exponent under less dense canopy (unitless)
+      real(r8) :: a_coef   ! Drag coefficient under less dense canopy (unitless)
+      real(r8) :: a_exp    ! Drag exponent under less dense canopy (unitless)
+      real(r8) :: wind_min ! Minimum wind speed at the atmospheric forcing height (m/s)
   end type params_type
   type(params_type), private ::  params_inst
   !------------------------------------------------------------------------------
@@ -60,6 +61,8 @@ subroutine readParams( ncid )
     call readNcdioScalar(ncid, 'a_coef', subname, params_inst%a_coef)
     ! Drag exponent under less dense canopy (unitless)
     call readNcdioScalar(ncid, 'a_exp', subname, params_inst%a_exp)
+    ! Minimum wind speed at the atmospheric forcing height (m/s)
+    call readNcdioScalar(ncid, 'wind_min', subname, params_inst%wind_min)
 
    end subroutine readParams
 
@@ -287,7 +290,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
          dlrad(p)  = 0._r8
          ulrad(p)  = 0._r8
 
-         ur(p)    = max(1.0_r8,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g)))
+         ur(p)    = max(params_inst%wind_min,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g)))
          dth(p)   = thm(p)-t_grnd(c)
          dqh(p)   = forc_q(c) - qg(c)
          dthv     = dth(p)*(1._r8+0.61_r8*forc_q(c))+0.61_r8*forc_th(c)*dqh(p)

src/biogeophys/CanopyFluxesMod.F90

@@ -58,12 +58,13 @@ module CanopyFluxesMod
   public :: readParams
 
   type, private :: params_type
-     real(r8) :: lai_dl  ! Plant litter area index (m2/m2)
-     real(r8) :: z_dl  ! Litter layer thickness (m)
-     real(r8) :: a_coef  ! Drag coefficient under less dense canopy (unitless)
-     real(r8) :: a_exp  ! Drag exponent under less dense canopy (unitless)
-     real(r8) :: csoilc  ! Soil drag coefficient under dense canopy (unitless)
-     real(r8) :: cv  ! Turbulent transfer coeff. between canopy surface and canopy air (m/s^(1/2))
+     real(r8) :: lai_dl   ! Plant litter area index (m2/m2)
+     real(r8) :: z_dl     ! Litter layer thickness (m)
+     real(r8) :: a_coef   ! Drag coefficient under less dense canopy (unitless)
+     real(r8) :: a_exp    ! Drag exponent under less dense canopy (unitless)
+     real(r8) :: csoilc   ! Soil drag coefficient under dense canopy (unitless)
+     real(r8) :: cv       ! Turbulent transfer coeff. between canopy surface and canopy air (m/s^(1/2))
+     real(r8) :: wind_min ! Minimum wind speed at the atmospheric forcing height (m/s)
   end type params_type
   type(params_type), private ::  params_inst
   !
@@ -176,6 +177,8 @@ subroutine readParams( ncid )
     call readNcdioScalar(ncid, 'csoilc', subname, params_inst%csoilc)
     ! Turbulent transfer coeff between canopy surface and canopy air (m/s^(1/2))
     call readNcdioScalar(ncid, 'cv', subname, params_inst%cv)
+    ! Minimum wind speed at the atmospheric forcing height (m/s)
+    call readNcdioScalar(ncid, 'wind_min', subname, params_inst%wind_min)
 
   end subroutine readParams
 
@@ -755,7 +758,7 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
          taf(p) = (t_grnd(c) + thm(p))/2._r8
          qaf(p) = (forc_q(c)+qg(c))/2._r8
 
-         ur(p) = max(1.0_r8,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g)))
+         ur(p) = max(params_inst%wind_min,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g)))
          dth(p) = thm(p)-taf(p)
          dqh(p) = forc_q(c)-qaf(p)
          delq(p) = qg(c) - qaf(p)

src/biogeophys/HydrologyDrainageMod.F90

@@ -8,7 +8,7 @@ module HydrologyDrainageMod
   use shr_log_mod       , only : errMsg => shr_log_errMsg
   use decompMod         , only : bounds_type
   use clm_varctl        , only : iulog, use_vichydro
-  use clm_varcon        , only : e_ice, denh2o, denice, rpi, spval
+  use clm_varcon        , only : denh2o, denice, rpi, spval
   use atm2lndType       , only : atm2lnd_type
   use glc2lndMod        , only : glc2lnd_type
   use SoilHydrologyType , only : soilhydrology_type