clm4_5_16_r262

Rename atm2lnd history fields for downscaled fields, properly turn on vic for clm45, and other minor fixes

bld/namelist_files/namelist_defaults_clm4_5.xml

@@ -312,21 +312,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
-     Greenland periphery: virtual
+     Greenland - inside CISM grid but outside Greenland itself: virtual
      Greenland itself: virtual
      Antarctica: multiple -->
 <glacier_region_behavior>'single_at_atm_topo','virtual','virtual','multiple'</glacier_region_behavior>
 
 <!-- Default glacier melt behavior is:
      Mountain glaciers: remains_in_place
-     Greenland periphery: replaced_by_ice
+     Greenland - inside CISM grid but outside Greenland itself: replaced_by_ice
      Greenland itself: replaced_by_ice
      Antarctica: replaced_by_ice -->
 <glacier_region_melt_behavior>'remains_in_place','replaced_by_ice','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
 
 <!-- Default glacier ice runoff behavior is:
      Mountain glaciers: melted
-     Greenland periphery: melted
+     Greenland - inside CISM grid but outside Greenland itself: melted
      Greenland itself: remains_ice
      Antarctica: remains_ice -->
 <glacier_region_ice_runoff_behavior>'melted','melted','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>

cime_config/config_component.xml

@@ -134,6 +134,7 @@
       <value compset="_CLM45%[^_]*BGCDV"	 >-bgc bgc -dynamic_vegetation</value>
       <value compset="_CLM45%[^_]*CNDV-CROP"	 >-bgc cn -dynamic_vegetation -crop</value>
       <value compset="_CLM45%[^_]*BGCDV-CROP"	 >-bgc bgc -dynamic_vegetation -crop</value>
+      <value compset="_CLM45%[^_]*SP-VIC"	 >-bgc sp -vichydro </value>
       <value compset="_CLM45%[^_]*FATES"	 >-bgc fates -no-megan</value>
 
       <value compset="_CLM50%[^_]*SP"		 >-bgc sp</value>

cime_config/config_pes.xml

@@ -784,4 +784,19 @@
     </mach>
   </grid>
 
+  <overrides>
+    <grid name="any" >
+      <mach name="any" >
+        <pes pesize="any" compset="CISM1">
+          <ntasks>
+            <ntasks_glc>1</ntasks_glc>
+          </ntasks>
+          <nthrds>
+            <nthrds_glc>1</nthrds_glc>
+          </nthrds>
+        </pes>
+      </mach>
+    </grid>
+  </overrides>
+
 </config_pes>

doc/ChangeLog

@@ -1,4 +1,241 @@
 ===============================================================
+Tag name:  clm4_5_16_r262
+Originator(s):  sacks (Bill Sacks)
+Date: Fri Oct 27 10:17:54 MDT 2017
+One-line Summary: Rename atm2lnd history fields for downscaled fields, properly turn on vic for clm45, and other minor fixes
+
+Purpose of changes
+------------------
+
+(1) Rename atm2lnd history fields for downscaled fields. The downscaled
+    version is now the default. Non-downscaled history fields are now
+    noted explicitly with a "_FROM_ATM" suffix. A detailed list of
+    changes is given below.
+
+(2) Properly turn on VIC for CLM45 compsets (fixes bug 2465)
+
+(3) Use correct PE layouts for CISM1
+
+(4) Remove CWDC_HR diagnostic field, which was always 0 (fixes bug 2502)
+
+(5) Turn on U10_DUST diagnostic field by default (fixes bug 2246)
+
+(6) Fix documentation of some variables
+
+Detailed list of changes related to (1):
+
+  Rain and snow:
+
+    Old:
+    - RAIN: "atmospheric rain" - NOT downscaled
+    - Rainf: "atmospheric rain" - NOT downscaled
+    - SNOW: "atmospheric snow" - NOT downscaled
+    - RAIN_REPARTITIONED: "atmospheric rain, after rain/snow repartitioning based on temperature" - DOWNSCALED
+    - SNOW_REPARTITIONED: "atmospheric snow, after rain/snow repartitioning based on temperature" - DOWNSCALED
+
+    New:
+    - RAIN: "atmospheric rain, after rain/snow repartitioning based on temperature" - DOWNSCALED
+    - Rainf: "atmospheric rain, after rain/snow repartitioning based on temperature" - DOWNSCALED
+    - SNOW: "atmospheric snow, after rain/snow repartitioning based on temperature" - DOWNSCALED
+    - RAIN_FROM_ATM: "atmospheric rain received from atmosphere (pre-repartitioning)" - NOT downscaled
+    - SNOW_FROM_ATM: "atmospheric snow received from atmosphere (pre-repartitioning)" - NOT downscaled
+
+  Air temperature:
+
+    Old:
+    - TBOT: "atmospheric air temperature" - NOT downscaled
+    - Tair: "atmospheric air temperature" - NOT downscaled
+    - Tair_downscaled: "atmospheric air temperature downscaled to columns" - DOWNSCALED
+
+    New:
+    - TBOT: "atmospheric air temperature (downscaled to columns in glacier regions)" - DOWNSCALED
+    - Tair: "atmospheric air temperature (downscaled to columns in glacier regions)" - DOWNSCALED
+    - Tair_from_atm: "atmospheric air temperature received from atmosphere (pre-downscaling)" - NOT downscaled
+
+  Atmospheric pressure:
+
+    Old:
+    - PBOT: "atmospheric pressure" - NOT downscaled
+    - Psurf: "surface pressure" - NOT downscaled
+
+    New:
+    - PBOT: "atmospheric pressure at surface (downscaled to columns in glacier regions)" - DOWNSCALED
+    - Psurf: "atmospheric pressure at surface (downscaled to columns in glacier regions)" - DOWNSCALED
+
+  Atmospheric longwave radiation:
+
+    Old:
+    - FLDS: "atmospheric longwave radiation" - NOT downscaled
+    - LWdown: "atmospheric longwave radiation" - NOT downscaled
+
+    New:
+    - FLDS: "atmospheric longwave radiation (downscaled to columns in glacier regions)" - DOWNSCALED
+    - LWdown: "atmospheric longwave radiation (downscaled to columns in glacier regions)" - DOWNSCALED
+
+  Potential temperature:
+
+    Old:
+    - THBOT: "atmospheric air potential temperature" - NOT downscaled
+
+    New
+    - THBOT: "atmospheric air potential temperature (downscaled to columns in glacier regions)" - DOWNSCALED
+
+  Specific humidity:
+
+    Old:
+    - QBOT: "atmospheric specific humidity" - NOT downscaled
+    - Qair: "atmospheric specific humidity" - NOT downscaled
+
+    New:
+    - QBOT: "atmospheric specific humidity (downscaled to columns in glacier regions)" - DOWNSCALED
+    - Qair: "atmospheric specific humidity (downscaled to columns in glacier regions)" - DOWNSCALED
+
+
+Bugs fixed or introduced
+------------------------
+
+Bugs fixed (include bugzilla ID):
+- 2192: wrong units in comment for variables qflx_ev_snow, qflx_ev_soil,
+  qflx_ev_h2osfc
+- 2246: Turn on U10_DUST history field variable by default
+- 2363: inline documentation is wrong in SoilTemperatureMod.F90
+- 2401: Need to put in an "override" for PE layouts for CISM1
+- 2465: ICLM45VIC compset doesn't actually turn VIC on
+- 2502: CWDC_HR is identically zero
+- 2503: Wrong units for FAREA_BURNED
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+- Changed meaning of some atm2lnd history fields: see above
+
+Changes to CLM'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): none
+
+Substantial timing or memory changes: none
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): none
+
+Changes to tests or testing: none
+
+Code reviewed by: self; Sean Swenson did a conceptual review of the
+changes in atm2lnd diagnostic fields
+
+Did you follow the steps in .CLMTrunkChecklist: yes
+
+CLM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  unit-tests (components/clm/src):
+
+    cheyenne - pass
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - not run
+
+  regular tests (aux_clm):
+
+    yellowstone_intel - ok 
+    yellowstone_pgi --- ok
+    yellowstone_gnu --- ok
+    cheyenne_intel ---- ok
+    cheyenne_gnu ------ ok
+    hobart_nag -------- ok
+    hobart_pgi -------- ok
+    hobart_intel ------ ok
+
+    ok means tests pass, answers change for some atm2lnd diagnostic
+    fields as noted below
+
+CLM tag used for the baseline comparisons: clm4_5_16_r261
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES
+
+  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: all
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): 
+      - For most configurations: Changes diagnostic fields only (see
+        below for list)
+      - Changes CLM45 compsets with VIC: actually turns on VIC (there
+        are no CLM45 tests with VIC in the test suite)
+
+      Changes the following fields: FLDS, PBOT, QBOT, RAIN, SNOW, TBOT,
+      THBOT: These now give downscaled versions of these fields.
+
+   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 svn externals directories updated (cime, rtm, mosart, cism, etc.): none
+
+List all files eliminated: none
+
+List all files added and what they do: none
+
+List all existing files that have been modified, and describe the changes:
+
+========= Rename atm2lnd history fields for downscaled fields
+M       components/clm/src/main/atm2lndType.F90
+
+========= Properly turn on VIC for CLM45 compsets
+M       components/clm/cime_config/config_component.xml
+
+========= Use correct PE layouts for cism1
+M       components/clm/cime_config/config_pes.xml
+
+========= Remove CWDC_HR diagnostic field
+M       components/clm/src/biogeochem/CNVegCarbonFluxType.F90
+
+========= Turn on U10_DUST by default
+M       components/clm/src/biogeophys/FrictionVelocityMod.F90
+
+========= Fix various documentation
+M       components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
+M       components/clm/src/biogeophys/BareGroundFluxesMod.F90
+M       components/clm/src/biogeophys/WaterfluxType.F90
+M       components/clm/src/biogeophys/SoilTemperatureMod.F90
+M       components/clm/src/biogeophys/SoilFluxesMod.F90
+M       components/clm/src/biogeophys/CanopyFluxesMod.F90
+M       components/clm/src/biogeophys/SoilHydrologyMod.F90
+M       components/clm/src/biogeochem/CNVegStateType.F90
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_16_r261
 Originator(s):  sacks (Bill Sacks)
 Date: Wed Oct 25 07:37:24 MDT 2017

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  clm4_5_16_r262    sacks 10/27/2017 Rename atm2lnd history fields for downscaled fields, properly turn on vic for clm45, and other minor fixes
   clm4_5_16_r261    sacks 10/25/2017 Add option to reset snow over glacier columns
   clm4_5_16_r260     erik 10/24/2017 Update paramater file for CLM50 as well as fates, fix a few issues
   clm4_5_16_r259     erik 10/17/2017 Update to latest cime from cesm2_0_beta07 and config_components version 3

src/biogeochem/CNVegCarbonFluxType.F90

@@ -2799,11 +2799,6 @@ subroutine InitHistory(this, bounds, carbon_type)
 
     if (carbon_type == 'c12') then
 
-       this%cwdc_hr_col(begc:endc) = spval
-       call hist_addfld1d (fname='CWDC_HR', units='gC/m^2/s', &
-            avgflag='A', long_name='coarse woody debris C heterotrophic respiration', &
-            ptr_col=this%cwdc_hr_col)
-
        this%cwdc_loss_col(begc:endc) = spval
        call hist_addfld1d (fname='CWDC_LOSS', units='gC/m^2/s', &
             avgflag='A', long_name='coarse woody debris C loss', &

src/biogeochem/CNVegStateType.F90

@@ -321,7 +321,7 @@ subroutine InitHistory(this, bounds)
          ptr_col=this%nfire_col)
 
     this%farea_burned_col(begc:endc) = spval
-    call hist_addfld1d (fname='FAREA_BURNED',  units='proportion', &
+    call hist_addfld1d (fname='FAREA_BURNED',  units='proportion/sec', &
          avgflag='A', long_name='timestep fractional area burned', &
          ptr_col=this%farea_burned_col)
 

src/biogeophys/BareGroundFluxesMod.F90

@@ -208,9 +208,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
          ram1                   => frictionvel_inst%ram1_patch                  , & ! Output: [real(r8) (:)   ]  aerodynamical resistance (s/m)                                        
 
          htvp                   => energyflux_inst%htvp_col                     , & ! Input:  [real(r8) (:)   ]  latent heat of evaporation (/sublimation) [J/kg]                      
-         qflx_ev_snow           => waterflux_inst%qflx_ev_snow_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from snow (W/m**2) [+ to atm]                        
-         qflx_ev_soil           => waterflux_inst%qflx_ev_soil_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from soil (W/m**2) [+ to atm]                        
-         qflx_ev_h2osfc         => waterflux_inst%qflx_ev_h2osfc_patch          , & ! Output: [real(r8) (:)   ]  evaporation flux from h2osfc (W/m**2) [+ to atm]                      
+         qflx_ev_snow           => waterflux_inst%qflx_ev_snow_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from snow (mm H2O/s) [+ to atm]                        
+         qflx_ev_soil           => waterflux_inst%qflx_ev_soil_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from soil (mm H2O/s) [+ to atm]                        
+         qflx_ev_h2osfc         => waterflux_inst%qflx_ev_h2osfc_patch          , & ! Output: [real(r8) (:)   ]  evaporation flux from h2osfc (mm H2O/s) [+ to atm]                      
          qflx_evap_soi          => waterflux_inst%qflx_evap_soi_patch           , & ! Output: [real(r8) (:)   ]  soil evaporation (mm H2O/s) (+ = to atm)                              
          qflx_evap_tot          => waterflux_inst%qflx_evap_tot_patch           , & ! Output: [real(r8) (:)   ]  qflx_evap_soi + qflx_evap_can + qflx_tran_veg                         
 

src/biogeophys/CanopyFluxesMod.F90

@@ -480,9 +480,9 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
          qflx_tran_veg          => waterflux_inst%qflx_tran_veg_patch           , & ! Output: [real(r8) (:)   ]  vegetation transpiration (mm H2O/s) (+ = to atm)                      
          qflx_evap_veg          => waterflux_inst%qflx_evap_veg_patch           , & ! Output: [real(r8) (:)   ]  vegetation evaporation (mm H2O/s) (+ = to atm)                        
          qflx_evap_soi          => waterflux_inst%qflx_evap_soi_patch           , & ! Output: [real(r8) (:)   ]  soil evaporation (mm H2O/s) (+ = to atm)                              
-         qflx_ev_snow           => waterflux_inst%qflx_ev_snow_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from snow (W/m**2) [+ to atm]                        
-         qflx_ev_soil           => waterflux_inst%qflx_ev_soil_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from soil (W/m**2) [+ to atm]                        
-         qflx_ev_h2osfc         => waterflux_inst%qflx_ev_h2osfc_patch          , & ! Output: [real(r8) (:)   ]  evaporation flux from h2osfc (W/m**2) [+ to atm]                      
+         qflx_ev_snow           => waterflux_inst%qflx_ev_snow_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from snow (mm H2O/s) [+ to atm]                        
+         qflx_ev_soil           => waterflux_inst%qflx_ev_soil_patch            , & ! Output: [real(r8) (:)   ]  evaporation flux from soil (mm H2O/s) [+ to atm]                        
+         qflx_ev_h2osfc         => waterflux_inst%qflx_ev_h2osfc_patch          , & ! Output: [real(r8) (:)   ]  evaporation flux from h2osfc (mm H2O/s) [+ to atm]                      
 
          rssun                  => photosyns_inst%rssun_patch                   , & ! Output: [real(r8) (:)   ]  leaf sunlit stomatal resistance (s/m) (output from Photosynthesis)
          rssha                  => photosyns_inst%rssha_patch                   , & ! Output: [real(r8) (:)   ]  leaf shaded stomatal resistance (s/m) (output from Photosynthesis)

src/biogeophys/FrictionVelocityMod.F90

@@ -182,12 +182,10 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='10-m wind (ice landunits only)', &
          ptr_patch=this%u10_clm_patch, l2g_scale_type='ice', default='inactive')
 
-    if (use_cn) then
-       this%u10_patch(begp:endp) = spval
-       call hist_addfld1d (fname='U10_DUST', units='m/s', &
-            avgflag='A', long_name='10-m wind for dust model', &
-            ptr_patch=this%u10_patch, default='inactive')
-    end if
+    this%u10_patch(begp:endp) = spval
+    call hist_addfld1d (fname='U10_DUST', units='m/s', &
+         avgflag='A', long_name='10-m wind for dust model', &
+         ptr_patch=this%u10_patch)
 
     if (use_cn) then
        this%ram1_patch(begp:endp) = spval

src/biogeophys/SoilFluxesMod.F90

@@ -126,9 +126,9 @@ subroutine SoilFluxes (bounds, num_urbanl, filter_urbanl, &
          qflx_sub_snow           => waterflux_inst%qflx_sub_snow_patch      , & ! Output: [real(r8) (:)   ]  sublimation rate from snow pack (mm H2O /s) [+]
          qflx_dew_snow           => waterflux_inst%qflx_dew_snow_patch      , & ! Output: [real(r8) (:)   ]  surface dew added to snow pack (mm H2O /s) [+]
          qflx_dew_grnd           => waterflux_inst%qflx_dew_grnd_patch      , & ! Output: [real(r8) (:)   ]  ground surface dew formation (mm H2O /s) [+]
-         qflx_ev_snow            => waterflux_inst%qflx_ev_snow_patch       , & ! In/Out: [real(r8) (:)   ]  evaporation flux from snow (W/m**2) [+ to atm]
-         qflx_ev_soil            => waterflux_inst%qflx_ev_soil_patch       , & ! In/Out: [real(r8) (:)   ]  evaporation flux from soil (W/m**2) [+ to atm]
-         qflx_ev_h2osfc          => waterflux_inst%qflx_ev_h2osfc_patch     , & ! In/Out: [real(r8) (:)   ]  evaporation flux from soil (W/m**2) [+ to atm]
+         qflx_ev_snow            => waterflux_inst%qflx_ev_snow_patch       , & ! In/Out: [real(r8) (:)   ]  evaporation flux from snow (mm H2O/s) [+ to atm]
+         qflx_ev_soil            => waterflux_inst%qflx_ev_soil_patch       , & ! In/Out: [real(r8) (:)   ]  evaporation flux from soil (mm H2O/s) [+ to atm]
+         qflx_ev_h2osfc          => waterflux_inst%qflx_ev_h2osfc_patch     , & ! In/Out: [real(r8) (:)   ]  evaporation flux from soil (mm H2O/s) [+ to atm]
 
          eflx_sh_grnd            => energyflux_inst%eflx_sh_grnd_patch      , & ! Output: [real(r8) (:)   ]  sensible heat flux from ground (W/m**2) [+ to atm]
          eflx_sh_veg             => energyflux_inst%eflx_sh_veg_patch       , & ! Output: [real(r8) (:)   ]  sensible heat flux from leaves (W/m**2) [+ to atm]