Merge branch 'minor_fixes_release' into release-clm5.0

History fields for vertically-resolved sums of soil C/N, and minor fixes Main change is from Keith Oleson: Add history fields for vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. Also minor fixes: - Output cpl hist files in SSP test (resolves #61) - Remove FATES-related commented-out code in OzoneMod (this has been moved to #618) - Minor tweak to run_sys_tests
ESCOMP · Jan 23, 2019 · f65c9c4 · f65c9c4
2 parents 02f0af2 + e4054b4
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diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
@@ -63,6 +63,9 @@ SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
     <RUN_TYPE>startup</RUN_TYPE>
     <STOP_N>4</STOP_N>
     <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
   </test>
 
 </config_test>
diff --git a/cime_config/usermods_dirs/_includes/cmip6_carbon_isotopes/user_nl_clm b/cime_config/usermods_dirs/_includes/cmip6_carbon_isotopes/user_nl_clm
@@ -7,6 +7,8 @@ use_c14 = .true.
 use_c13_timeseries = .true.
 use_c14_bombspike = .true.
 
+! h0 stream (monthly average, gridcell-level)
+hist_fexcl1 += 'C14_SOILC_vr'
 ! h3 stream (yearly average, gridcell-level)
-hist_fincl4 += 'C14_SOIL1C_vr', 'C14_SOIL2C_vr', 'C14_SOIL3C_vr'
+hist_fincl4 += 'C14_SOILC_vr'
 
diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm
@@ -3,7 +3,7 @@
 !----------------------------------------------------------------------------------
 
 ! h0 stream (monthly average, gridcell-level)
-hist_fexcl1 += 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
+hist_fexcl1 += 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
 hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LITR1C_TO_SOIL1C','LITR1N_TO_SOIL1N','LITR2C_TO_SOIL1C', 'LITR2N_TO_SOIL1N','LITR3C_TO_SOIL2C','LITR3N_TO_SOIL2N','DWT_WOOD_PRODUCTC_GAIN_PATCH'
 
 ! h1 stream (monthly average, finest sub-grid)
@@ -14,7 +14,7 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO
 hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP'
 
 ! h3 stream (yearly average, gridcell-level)
-hist_fincl4 += 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I'
+hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I'
 
 ! h4 stream (yearly average, landunit-level)
 hist_fincl5 += 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I'

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,110 @@
 ===============================================================
+Tag name:  ctsm1.0.dev025
+Originator(s): Keith Oleson, Bill Sacks
+Date: Wed Jan 23 10:48:01 MST 2019
+One-line Summary: History fields for vertically-resolved sums of soil C and N, and minor fixes
+
+Purpose of changes
+------------------
+
+Main change is from Keith Oleson: Add history fields for
+vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13,
+C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and
+C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods,
+including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr',
+'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output
+'SOILC_vr', 'SOILN_vr', and similarly for C isotopes.
+
+Also minor fixes:
+- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61)
+- Remove FATES-related commented-out code in OzoneMod (this has been
+  moved to https://github.com/ESCOMP/ctsm/issues/618)
+- Minor tweak to run_sys_tests
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/ctsm#61
+
+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
+
+[ ] 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):
+- For runs that use the output_bgc usermods, including cmip6 runs, we no
+  longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr',
+  'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr',
+  and similarly for C isotopes.
+
+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)
+---------------------------------------------
+NOTE: Be sure to review the steps in ../CTSMMasterChecklist 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: Bill Sacks; Erik Kluzek reviewed the changes to the SSP test
+
+
+CTSM testing:
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+     cheyenne - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- pass
+    hobart ------ pass
+
+CTSM tag used for the baseline comparisons: ctsm1.0.dev024
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+
+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/551
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev015
 Originator(s):  sacks (Bill Sacks)
 Date: Sun Oct 28 14:29:30 MDT 2018

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+release-clm5.0.17    sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes
+  ctsm1.0.dev025     sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes
 release-clm5.0.16     erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere
 release-clm5.0.15    sacks 12/06/2018 Option for rain-to-snow to immediately run off in some regions
 release-clm5.0.14     erik 11/29/2018 Update cime and fix surface dataset for f05 1850 non-crop case

diff --git a/doc/release-clm5.0.ChangeLog b/doc/release-clm5.0.ChangeLog
@@ -1,4 +1,113 @@
 ===============================================================
+Tag name:  release-clm5.0.17
+Originator(s): Keith Oleson, Bill Sacks
+Date: Wed Jan 23 11:03:22 MST 2019
+One-line Summary: History fields for vertically-resolved sums of soil C and N, and minor fixes
+
+Purpose of this version:
+------------------------
+
+Main change is from Keith Oleson: Add history fields for
+vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13,
+C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and
+C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods,
+including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr',
+'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output
+'SOILC_vr', 'SOILN_vr', and similarly for C isotopes.
+
+Also minor fixes:
+- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61)
+- Remove FATES-related commented-out code in OzoneMod (this has been
+  moved to https://github.com/ESCOMP/ctsm/issues/618)
+- Minor tweak to run_sys_tests
+
+
+CTSM Master Tag This Corresponds To: ctsm1.0.dev025
+
+Summary of changes:
+-------------------
+
+Issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/ctsm#61
+
+Science changes since: release-clm5.0.16
+   None
+
+Software changes since: release-clm5.0.16
+   See above
+
+Changes to User Interface since: release-clm5.0.16
+   None
+
+Testing:
+--------
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  unit-tests (components/clm/src):
+
+    cheyenne - pass
+    hobart --- not run
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - not run
+    hobart --- not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - not run
+     hobart --- not run
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- pass
+    cheyenne_gnu ------ pass
+    hobart_nag -------- pass
+    hobart_pgi -------- pass
+    hobart_intel ------ pass
+
+  regular tests (prealpha):
+
+    cheyenne_intel - not run
+    cheyenne_gnu --- not run
+    hobart_nag ----- not run
+
+  regular tests (prebeta):
+
+    cheyenne_intel - not run
+    cheyenne_gnu --- not run
+    hobart_nag ----- not run
+
+Summary of Answer changes:
+-------------------------
+
+Baseline version for comparison: release-clm5.0.16
+
+Changes answers relative to baseline: NO
+
+
+Detailed list of changes:
+------------------------
+
+Externals being used:
+
+   cism:   release-cesm2.0.04
+   rtm:    release-cesm2.0.02
+   mosart: release-cesm2.0.03
+   cime:   cime_cesm2_1_rel_06
+   FATES:  fates_s1.8.1_a3.0.0
+   PTCLM:  PTCLM2_180611
+
+CTSM Tag versions pulled over from master development branch: ctsm1.0.dev025
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/ctsm/pull/551
+
+===============================================================
+===============================================================
 Tag name:  release-clm5.0.16
 Originator(s):  erik (Erik Kluzek)
 Date: Tue Jan 15 15:13:43 MST 2019

diff --git a/src/biogeophys/OzoneMod.F90 b/src/biogeophys/OzoneMod.F90
@@ -361,51 +361,21 @@ subroutine CalcOzoneStress(this, bounds, num_exposedvegp, filter_exposedvegp, &
        p = filter_exposedvegp(fp)
        c = patch%column(p)
 
-!       if (.not.patch%is_fates(p)) then   ! When FATES coexists with other vegetation,
-                                     ! or when it has an ozone compatible module,  this
-                                     ! logic will likely come into play
-
-          ! Ozone stress for shaded leaves
-          call CalcOzoneStressOnePoint( &
-               forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
-               rs=rssha(p), rb=rb(p), ram=ram(p), &
-               tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
-               o3uptake=o3uptakesha(p), o3coefv=o3coefvsha(p), o3coefg=o3coefgsha(p))
-
-          ! Ozone stress for sunlit leaves
-          call CalcOzoneStressOnePoint( &
-               forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
-               rs=rssun(p), rb=rb(p), ram=ram(p), &
-               tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
-               o3uptake=o3uptakesun(p), o3coefv=o3coefvsun(p), o3coefg=o3coefgsun(p))
-
-          tlai_old(p) = tlai(p)
-
-!       else
-!          ! FATES is fundamentlaly incompatible with this type of patch-level
-!          ! association with plant functional type, so for the time
-!          ! being, fates patches will just push these values to invalid
-!          o3uptakesha(p) = spval
-!          o3coefvsha(p)  = spval
-!          o3coefgsha(p)  = spval
-!          o3uptakesun(p) = spval
-!          o3coefvsun(p)  = spval
-!          o3coefgsun(p)  = spval 
-!
-!       end if
-
-!       else
-!          ! FATES is fundamentlaly incompatible with this type of patch-level
-!          ! association with plant functional type, so for the time
-!          ! being, fates patches will just push these values to invalid
-!          o3uptakesha(p) = spval
-!          o3coefvsha(p)  = spval
-!          o3coefgsha(p)  = spval
-!          o3uptakesun(p) = spval
-!          o3coefvsun(p)  = spval
-!          o3coefgsun(p)  = spval 
-!
-!       end if
+       ! Ozone stress for shaded leaves
+       call CalcOzoneStressOnePoint( &
+            forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
+            rs=rssha(p), rb=rb(p), ram=ram(p), &
+            tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
+            o3uptake=o3uptakesha(p), o3coefv=o3coefvsha(p), o3coefg=o3coefgsha(p))
+
+       ! Ozone stress for sunlit leaves
+       call CalcOzoneStressOnePoint( &
+            forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
+            rs=rssun(p), rb=rb(p), ram=ram(p), &
+            tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
+            o3uptake=o3uptakesun(p), o3coefv=o3coefvsun(p), o3coefg=o3coefgsun(p))
+
+       tlai_old(p) = tlai(p)
 
     end do