Merge branch 'find_soil_layer'

Change hard-coded soil layers in phenology to use a target depth Adds infrastructure for finding the soil layer containing a given depth (covered by unit tests). In phenology code, replaces hard-coded level 3 with a target soil depth. This value is read from the parameter file. The default value is set in a way that is bit-for-bit for standard CLM45 and CLM50 configurations, but this will change answers for non-SP configurations using the NWP soil layer structure or non-standard soil layer structures. This is important for the sake of supporting flexible soil layers, as in the NWP configuration. Also, some cleanup of the CNPhenology parameter reading code. Resolves ESCOMP#952
jtruesdal · Apr 6, 2020 · 9e25889 · 9e25889
2 parents 384c726 + 2a48f6b
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diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -372,8 +372,8 @@ 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.c190829.nc</paramfile>
-<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c190829.nc</paramfile>
+<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c200402.nc</paramfile>
+<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c200402.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,152 @@
 ===============================================================
+Tag name:  ctsm1.0.dev087
+Originator(s):  sacks (Bill Sacks)
+Date:  Mon Apr  6 11:23:51 MDT 2020
+One-line Summary: Change hard-coded soil layers in phenology to use a target depth
+
+Purpose of changes
+------------------
+
+Adds infrastructure for finding the soil layer containing a given depth
+(covered by unit tests).
+
+In phenology code, replaces hard-coded level 3 with a target soil
+depth. This value is read from the parameter file. The default value is
+set in a way that is bit-for-bit for standard CLM45 and CLM50
+configurations, but this will change answers for non-SP configurations
+using the NWP soil layer structure or non-standard soil layer
+structures.
+
+This is important for the sake of supporting flexible soil layers, as in
+the NWP configuration.
+
+Also, some cleanup of the CNPhenology parameter reading code.
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/ctsm#952 (Change hard coded soil layers in phenology
+  to use a target depth)
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(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
+
+[X] ctsm5_0-nwp  -- only for non-SP cases
+
+[ ] 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):
+- New parameter added to NetCDF parameter file: phenology_soil_depth
+
+Substantial timing or memory changes: none expected (not checked)
+
+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): none
+
+Changes to tests or testing: none
+
+Code reviewed by: Erik Kluzek
+
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- ok
+    izumi ------- pass
+
+    ok means tests pass, a few answer changes as expected
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  If a tag changes answers relative to baseline comparison the
+  following should be filled in (otherwise remove this section):
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Non-SP cases with NWP or non-standard
+      soil layer structures
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): 
+      larger than roundoff; same vs. new climate not investigated
+
+      Differences in non-SP cases with soil layer structure different
+      from that of standard clm45 or clm50. Differences observed in
+      tests
+      ERS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_intel.clm-deepsoil_bedrock
+      and
+      SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default.
+
+      ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default
+      had no differences; I'm guessing this is just because there didn't
+      happen to be the appropriate PFTs present to show differences in
+      this short, coarse-resolution test.
+
+   If bitwise differences were observed, how did you show they were no worse
+   than roundoff? N/A
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - casename: N/A
+
+   URL for LMWG diagnostics output used to validate new climate: N/A
+
+
+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):
+https://github.com/ESCOMP/CTSM/pull/963
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev086
 Originator(s):  mvertens (Mariana Vertenstein)
 Date:  Thu Mar 19 16:03:26 MDT 2020

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev087    sacks 04/06/2020 Change hard-coded soil layers in phenology to use a target depth
   ctsm1.0.dev086 mvertens 03/19/2020 Updates to NUOPC cap and minor fixes to ncdio_pio
   ctsm1.0.dev085    sacks 03/16/2020 Update cime
   ctsm1.0.dev084   negins 02/19/2020 Bounds assertion for C isotopes when threading is on

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
@@ -29,13 +29,13 @@ module CNPhenologyMod
   use pftconMod                       , only : pftcon
   use SoilStateType                   , only : soilstate_type
   use TemperatureType                 , only : temperature_type
-  use WaterDiagnosticBulkType                  , only : waterdiagnosticbulk_type
-  use Wateratm2lndBulkType                  , only : wateratm2lndbulk_type
-  use ColumnType                      , only : col                
+  use WaterDiagnosticBulkType         , only : waterdiagnosticbulk_type
+  use Wateratm2lndBulkType            , only : wateratm2lndbulk_type
+  use initVerticalMod                 , only : find_soil_layer_containing_depth
+  use ColumnType                      , only : col
   use GridcellType                    , only : grc                
   use PatchType                       , only : patch   
   use atm2lndType                     , only : atm2lnd_type             
-  use atm2lndType                     , only : atm2lnd_type
   !
   implicit none
   private
@@ -59,6 +59,7 @@ module CNPhenologyMod
      real(r8) :: crit_offset_swi ! critical number of water stress days to initiate offset
      real(r8) :: soilpsi_off     ! critical soil water potential for leaf offset
      real(r8) :: lwtop   	 ! live wood turnover proportion (annual fraction)
+     real(r8) :: phenology_soil_depth ! soil depth used for measuring states for phenology triggers
   end type params_type
 
   type(params_type) :: params_inst
@@ -76,6 +77,7 @@ module CNPhenologyMod
   real(r8) :: crit_offset_swi               ! water stress days for offset trigger
   real(r8) :: soilpsi_off                   ! water potential for offset trigger (MPa)
   real(r8) :: lwtop                         ! live wood turnover proportion (annual fraction)
+  integer  :: phenology_soil_layer          ! soil layer used for measuring states for phenology triggers
 
   ! CropPhenology variables and constants
   real(r8) :: p1d, p1v                      ! photoperiod factor constants for crop vernalization
@@ -164,77 +166,29 @@ subroutine readParams ( ncid )
     ! !DESCRIPTION:
     !
     ! !USES:
-    use ncdio_pio    , only: file_desc_t,ncd_io
+    use ncdio_pio    , only: file_desc_t
+    use paramUtilMod , only : readNcdioScalar
 
     ! !ARGUMENTS:
     implicit none
     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
     !
     ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNPhenolParamsType'
-    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 parameter
-    character(len=100) :: tString ! temp. var for reading
+    character(len=*), parameter  :: subname = 'readParams_CNPhenology'
     !-----------------------------------------------------------------------
 
-    !
-    ! read in parameters
-    !   
-    tString='crit_dayl'
-    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%crit_dayl=tempr
-
-    tString='ndays_on'
-    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%ndays_on=tempr
-
-    tString='ndays_off'
-    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%ndays_off=tempr
-
-    tString='fstor2tran'
-    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%fstor2tran=tempr
-
-    tString='crit_onset_fdd'
-    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%crit_onset_fdd=tempr
-
-    tString='crit_onset_swi'
-    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%crit_onset_swi=tempr
-
-    tString='soilpsi_on'
-    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%soilpsi_on=tempr
-
-    tString='crit_offset_fdd'
-    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%crit_offset_fdd=tempr
-
-    tString='crit_offset_swi'
-    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%crit_offset_swi=tempr
-
-    tString='soilpsi_off'
-    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%soilpsi_off=tempr
-
-    tString='lwtop_ann'
-    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%lwtop=tempr   
+    call readNcdioScalar(ncid, 'crit_dayl', subname, params_inst%crit_dayl)
+    call readNcdioScalar(ncid, 'ndays_on', subname, params_inst%ndays_on)
+    call readNcdioScalar(ncid, 'ndays_off', subname, params_inst%ndays_off)
+    call readNcdioScalar(ncid, 'fstor2tran', subname, params_inst%fstor2tran)
+    call readNcdioScalar(ncid, 'crit_onset_fdd', subname, params_inst%crit_onset_fdd)
+    call readNcdioScalar(ncid, 'crit_onset_swi', subname, params_inst%crit_onset_swi)
+    call readNcdioScalar(ncid, 'soilpsi_on', subname, params_inst%soilpsi_on)
+    call readNcdioScalar(ncid, 'crit_offset_fdd', subname, params_inst%crit_offset_fdd)
+    call readNcdioScalar(ncid, 'crit_offset_swi', subname, params_inst%crit_offset_swi)
+    call readNcdioScalar(ncid, 'soilpsi_off', subname, params_inst%soilpsi_off)
+    call readNcdioScalar(ncid, 'lwtop_ann', subname, params_inst%lwtop)
+    call readNcdioScalar(ncid, 'phenology_soil_depth', subname, params_inst%phenology_soil_depth)
 
   end subroutine readParams
 
@@ -376,6 +330,10 @@ subroutine CNPhenologyInit(bounds)
     ! set transfer parameters
     fstor2tran=params_inst%fstor2tran
 
+    call find_soil_layer_containing_depth( &
+         depth = params_inst%phenology_soil_depth, &
+         layer = phenology_soil_layer)
+
     ! -----------------------------------------
     ! Constants for CNStressDecidPhenology
     ! -----------------------------------------
@@ -903,7 +861,7 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
                ! if the gdd flag is set, and if the soil is above freezing
                ! then accumulate growing degree days for onset trigger
 
-               soilt = t_soisno(c,3)
+               soilt = t_soisno(c, phenology_soil_layer)
                if (onset_gddflag(p) == 1.0_r8 .and. soilt > SHR_CONST_TKFRZ) then
                   onset_gdd(p) = onset_gdd(p) + (soilt-SHR_CONST_TKFRZ)*fracday
                end if
@@ -1120,8 +1078,8 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
          g = patch%gridcell(p)
 
          if (stress_decid(ivt(p)) == 1._r8) then
-            soilt = t_soisno(c,3)
-            psi = soilpsi(c,3)
+            soilt = t_soisno(c, phenology_soil_layer)
+            psi = soilpsi(c, phenology_soil_layer)
 
             ! onset gdd sum from Biome-BGC, v4.1.2
             crit_onset_gdd = exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) - SHR_CONST_TKFRZ))

diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt
@@ -23,6 +23,7 @@ list(APPEND clm_sources
   glc2lndMod.F90
   glcBehaviorMod.F90
   initSubgridMod.F90
+  initVerticalMod.F90
   landunit_varcon.F90
   lnd2glcMod.F90
   ncdio_utils.F90