Merge clm4_5_8_r178, commit '17ae361c', into andre-ed-clm-16x

ChangeLog

@@ -1,4 +1,151 @@
 ===============================================================
+Tag name:  clm4_5_8_r178
+Originator(s):  sacks (Bill Sacks)
+Date: Sun Apr 17 19:28:55 MDT 2016
+One-line Summary: Remove some consistency checks, and merge crop_prog with use_crop in code
+
+Purpose of changes
+------------------
+
+(1) Remove some consistency checks that were doing more harm than good:
+
+    (a) Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+        and crop output points. This is mainly to support the common use case of
+        interpolating from non-crop to crop, without requiring the user to set
+        this flag.
+
+    (b) Remove check_finidat_fsurdat_consistency - now never do this check. This
+        consistency check was causing more problems than it solved, both for
+        users and developers (e.g., requiring us to change initial conditions
+        files whenever we made new versions of the surface dataset).
+
+(2) Remove crop_prog logical variable from the code. This was identical to
+    use_crop, and so it was confusing to have these two separate variables. Uses
+    of crop_prog have been replaced by uses of use_crop.
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CLM's user interface (e.g., new/renamed XML or namelist variables):
+- No longer need to set init_interp_fill_missing_with_natveg when interpolating
+from non-crop to crop
+
+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
+
+
+Code reviews and testing
+------------------------
+
+Code reviewed by: self
+
+CLM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    yellowstone - pass (ran bld/unit_testers tests)
+
+  unit-tests (components/clm/src):
+
+    yellowstone - pass
+
+  tools-tests (components/clm/test/tools):
+
+    yellowstone - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     yellowstone - not run
+
+  regular tests (aux_clm40, aux_clm45):
+
+    yellowstone_intel - pass
+    yellowstone_pgi - pass
+    yellowstone_gnu (clm45 only) - pass
+    hobart_nag - pass
+
+CLM tag used for the baseline comparisons: clm4_5_8_r177
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, cism, etc.): none
+
+List all files eliminated:
+
+========= Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+          and crop output points
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/user_nl_clm
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/include_user_mods
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/README
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop
+
+List all files added and what they do:
+
+List all existing files that have been modified, and describe the changes:
+
+========= Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+          and crop output points
+M       components/clm/src/init_interp/initInterpMindist.F90
+M       components/clm/src/init_interp/test/initInterpMindist_test/test_init_interp_mindist.pf
+M       components/clm/cime_config/testdefs/testmods_dirs/clm/clm50KitchenSink/user_nl_clm
+M       components/clm/cime_config/testdefs/testlist_clm.xml
+
+========= Remove check_finidat_fsurdat_consistency - now never do this check
+M       components/clm/src/main/restFileMod.F90
+M       components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
+
+========= Remove crop_prog - use use_crop in its place
+M       components/clm/src/ED/main/EDCLMLinkMod.F90
+M       components/clm/src/biogeophys/EnergyFluxType.F90
+M       components/clm/src/biogeophys/TemperatureType.F90
+M       components/clm/src/biogeophys/WaterStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
+M       components/clm/src/dyn_subgrid/dynSubgridControlMod.F90
+M       components/clm/src/unit_test_stubs/main/histFileMod_stub.F90
+M       components/clm/src/biogeochem/CNFUNMod.F90
+M       components/clm/src/biogeochem/CNVegNitrogenStateType.F90
+M       components/clm/src/biogeochem/CNPrecisionControlMod.F90
+M       components/clm/src/biogeochem/CNPhenologyMod.F90
+M       components/clm/src/biogeochem/CropType.F90
+M       components/clm/src/biogeochem/CNVegNitrogenFluxType.F90
+M       components/clm/src/biogeochem/CNDriverMod.F90
+M       components/clm/src/biogeochem/CNVegCarbonFluxType.F90
+M       components/clm/src/biogeochem/CNVegCarbonStateType.F90
+M       components/clm/src/biogeochem/CNNStateUpdate1Mod.F90
+M       components/clm/src/biogeochem/CNBalanceCheckMod.F90
+M       components/clm/src/biogeochem/CNVegStateType.F90
+M       components/clm/src/main/clm_varctl.F90
+M       components/clm/src/main/clm_driver.F90
+M       components/clm/src/main/clm_initializeMod.F90
+M       components/clm/src/main/initGridCellsMod.F90
+M       components/clm/src/main/histFileMod.F90
+M       components/clm/src/main/clm_varpar.F90
+M       components/clm/src/main/pftconMod.F90
+M       components/clm/src/main/surfrdMod.F90
+M       components/clm/src/main/clm_instMod.F90
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_8_r177
 Originator(s):  sacks (Bill Sacks)
 Date: Thu Apr 14 14:00:25 MDT 2016

components/clm/bld/namelist_files/namelist_definition_clm4_5.xml

@@ -1792,12 +1792,6 @@ If TRUE, apply harvest from flanduse_timeseries file.
 <!-- Namelist options related to finidat consistency checks                                    -->
 <!-- ========================================================================================  -->
 
-<entry id="check_finidat_fsurdat_consistency" type="logical" category="clm_restart"
-       group="finidat_consistency_checks" valid_values="" >
-If TRUE (which is the default), check consistency between surface dataset used to create the finidat file
-and the current fsurdat. This check is only done for a transient run.
-</entry>
-
 <entry id="check_finidat_year_consistency" type="logical" category="clm_restart"
        group="finidat_consistency_checks" valid_values="" >
 If TRUE (which is the default), check consistency between year on the finidat file
@@ -1857,6 +1851,11 @@ If FALSE (which is the default): If an output type cannot be found in the input
 code aborts
 If TRUE: If an output type cannot be found in the input, fill with closest natural veg column
 (using bare soil for patch-level variables)
+
+NOTE: Natural vegetation and crop landunits always behave as if this were true. e.g., if
+we can't find a column with the same type as a given crop column in the output, then we
+always fill with the closest natural veg patch / column, regardless of the value of this
+flag. So interpolation from non-crop to crop cases can be done without setting this flag.
 </entry>
 
 </namelist_definition>

components/clm/cime_config/testdefs/testlist_clm.xml

@@ -659,7 +659,7 @@
         <machine compiler="intel" testtype="aux_clm45" testmods="clm/cropMonthOutput">yellowstone</machine>
       </test>
       <test name="SMS_D_Ld3">
-        <machine compiler="gnu" testtype="aux_clm45" testmods="clm/interp_f19_noncrop2crop" comment="test interpolation of non-crop to crop (also change resolution, but that is not an essential part of this test)">yellowstone</machine>
+        <machine compiler="gnu" testtype="aux_clm45" testmods="clm/interp_f19_noncrop" comment="test interpolation of non-crop to crop (also change resolution, but that is not an essential part of this test)">yellowstone</machine>
       </test>
       <test name="SMS_Lm1_D">
         <machine compiler="intel" testtype="aux_clm45" testmods="clm/snowlayers_3_monthly" comment="nlevsno less than 5 is not important scientifically, but is useful for making sure no code assumes that there are 5 snow layers (because this should result in an array bounds exception); this test can be removed once CLM5 is released and most new branches are based off of CLM5 (which will have a runtime-set number of snow layers, rather than assuming 5 snow layers)... until then, I want this test to catch any new code that assumes 5 snow layers">yellowstone</machine>

components/clm/cime_config/testdefs/testmods_dirs/clm/clm50KitchenSink/user_nl_clm

@@ -1,5 +1,4 @@
 finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.IG1850CRUCLM50BGC.0481-01-01.1.9x2.5_g1v6_gl5_simyr1850_c160127.nc'
-init_interp_fill_missing_with_natveg = .true.
 limit_irrigation = .false.
 leaf_mr_vcm = 0.015d00
 use_bedrock = .true.

components/clm/doc/ChangeLog

@@ -1,4 +1,151 @@
 ===============================================================
+Tag name:  clm4_5_8_r178
+Originator(s):  sacks (Bill Sacks)
+Date: Sun Apr 17 19:28:55 MDT 2016
+One-line Summary: Remove some consistency checks, and merge crop_prog with use_crop in code
+
+Purpose of changes
+------------------
+
+(1) Remove some consistency checks that were doing more harm than good:
+
+    (a) Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+        and crop output points. This is mainly to support the common use case of
+        interpolating from non-crop to crop, without requiring the user to set
+        this flag.
+
+    (b) Remove check_finidat_fsurdat_consistency - now never do this check. This
+        consistency check was causing more problems than it solved, both for
+        users and developers (e.g., requiring us to change initial conditions
+        files whenever we made new versions of the surface dataset).
+
+(2) Remove crop_prog logical variable from the code. This was identical to
+    use_crop, and so it was confusing to have these two separate variables. Uses
+    of crop_prog have been replaced by uses of use_crop.
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CLM's user interface (e.g., new/renamed XML or namelist variables):
+- No longer need to set init_interp_fill_missing_with_natveg when interpolating
+from non-crop to crop
+
+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
+
+
+Code reviews and testing
+------------------------
+
+Code reviewed by: self
+
+CLM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    yellowstone - pass (ran bld/unit_testers tests)
+
+  unit-tests (components/clm/src):
+
+    yellowstone - pass
+
+  tools-tests (components/clm/test/tools):
+
+    yellowstone - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     yellowstone - not run
+
+  regular tests (aux_clm40, aux_clm45):
+
+    yellowstone_intel - pass
+    yellowstone_pgi - pass
+    yellowstone_gnu (clm45 only) - pass
+    hobart_nag - pass
+
+CLM tag used for the baseline comparisons: clm4_5_8_r177
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, cism, etc.): none
+
+List all files eliminated:
+
+========= Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+          and crop output points
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/user_nl_clm
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/include_user_mods
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop/README
+D       components/clm/cime_config/testdefs/testmods_dirs/clm/interp_f19_noncrop2crop
+
+List all files added and what they do:
+
+List all existing files that have been modified, and describe the changes:
+
+========= Make init_interp_fill_missing_with_natveg unnecessary for natural veg
+          and crop output points
+M       components/clm/src/init_interp/initInterpMindist.F90
+M       components/clm/src/init_interp/test/initInterpMindist_test/test_init_interp_mindist.pf
+M       components/clm/cime_config/testdefs/testmods_dirs/clm/clm50KitchenSink/user_nl_clm
+M       components/clm/cime_config/testdefs/testlist_clm.xml
+
+========= Remove check_finidat_fsurdat_consistency - now never do this check
+M       components/clm/src/main/restFileMod.F90
+M       components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
+
+========= Remove crop_prog - use use_crop in its place
+M       components/clm/src/ED/main/EDCLMLinkMod.F90
+M       components/clm/src/biogeophys/EnergyFluxType.F90
+M       components/clm/src/biogeophys/TemperatureType.F90
+M       components/clm/src/biogeophys/WaterStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
+M       components/clm/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
+M       components/clm/src/dyn_subgrid/dynSubgridControlMod.F90
+M       components/clm/src/unit_test_stubs/main/histFileMod_stub.F90
+M       components/clm/src/biogeochem/CNFUNMod.F90
+M       components/clm/src/biogeochem/CNVegNitrogenStateType.F90
+M       components/clm/src/biogeochem/CNPrecisionControlMod.F90
+M       components/clm/src/biogeochem/CNPhenologyMod.F90
+M       components/clm/src/biogeochem/CropType.F90
+M       components/clm/src/biogeochem/CNVegNitrogenFluxType.F90
+M       components/clm/src/biogeochem/CNDriverMod.F90
+M       components/clm/src/biogeochem/CNVegCarbonFluxType.F90
+M       components/clm/src/biogeochem/CNVegCarbonStateType.F90
+M       components/clm/src/biogeochem/CNNStateUpdate1Mod.F90
+M       components/clm/src/biogeochem/CNBalanceCheckMod.F90
+M       components/clm/src/biogeochem/CNVegStateType.F90
+M       components/clm/src/main/clm_varctl.F90
+M       components/clm/src/main/clm_driver.F90
+M       components/clm/src/main/clm_initializeMod.F90
+M       components/clm/src/main/initGridCellsMod.F90
+M       components/clm/src/main/histFileMod.F90
+M       components/clm/src/main/clm_varpar.F90
+M       components/clm/src/main/pftconMod.F90
+M       components/clm/src/main/surfrdMod.F90
+M       components/clm/src/main/clm_instMod.F90
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_8_r177
 Originator(s):  sacks (Bill Sacks)
 Date: Thu Apr 14 14:00:25 MDT 2016

components/clm/doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+   clm4_5_8_r178    sacks 04/17/2016 Remove some consistency checks, and merge crop_prog with use_crop in code
    clm4_5_8_r177    sacks 04/14/2016 Move CN product pools to gridcell level
    clm4_5_8_r176    sacks 04/13/2016 Calculate active flags and filters earlier in initialization
    clm4_5_8_r175    sacks 04/09/2016 For glc_mec, change downscaling and where SMB is computed

components/clm/doc/UsersGuide/clm_ug.xml

@@ -162,7 +162,7 @@ The purpose of this guide is to instruct both the novice and experienced user, a
 </para>
 </abstract>
 
-<releaseinfo>$URL: https://svn-ccsm-models.cgd.ucar.edu/clm2/trunk_tags/clm4_5_8_r177/components/clm/doc/UsersGuide/clm_ug.xml $</releaseinfo>
+<releaseinfo>$URL: https://svn-ccsm-models.cgd.ucar.edu/clm2/trunk_tags/clm4_5_8_r178/components/clm/doc/UsersGuide/clm_ug.xml $</releaseinfo>
 
 <date>&build_date;</date>
 

components/clm/src/ED/main/EDCLMLinkMod.F90

@@ -250,7 +250,7 @@ subroutine InitHistory(this, bounds)
     !
     ! !USES:
     use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools
-    use clm_varpar , only : nlevdecomp, nlevdecomp_full, crop_prog
+    use clm_varpar , only : nlevdecomp, nlevdecomp_full
     use clm_varcon , only : spval
     use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
     !