Merge pull request #846 from ekluzek/relfatesupdate

Update to fates sci.1.30.0_api.8.0.0

Externals.cfg

@@ -7,30 +7,30 @@ required = True
 [cism]
 local_path = components/cism
 protocol = git
-repo_url = https://github.com/ESCOMP/cism-wrapper
-tag = release-cesm2.0.04
+repo_url = https://github.com/ESCOMP/CISM-wrapper
+tag = cism-release-cesm2.1.2_01
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
-repo_url = https://github.com/ESCOMP/rtm
-tag = release-cesm2.0.03
+repo_url = https://github.com/ESCOMP/RTM
+tag = release-cesm2.0.04
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
-repo_url = https://github.com/ESCOMP/mosart
-tag = release-cesm2.0.03
+repo_url = https://github.com/ESCOMP/MOSART
+tag = release-cesm2.0.04
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime5.6.25
+tag = cime5.6.28
 required = True
 
 [externals_description]

Externals_CLM.cfg

@@ -1,15 +1,15 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/ncar/fates-release
-tag = fates_s1.21.0_a7.0.0_br_rev2
+repo_url = https://github.com/NGEET/fates
+tag = sci.1.30.0_api.8.0.0
 required = True
 
 [PTCLM]
 local_path = tools/PTCLM
 protocol = git
-repo_url = https://github.com/ESCOMP/ptclm
-tag = PTCLM2_180611
+repo_url = https://github.com/ESCOMP/PTCLM
+tag = PTCLM2_20200121
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_clm4_5.xml

@@ -378,7 +378,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_default_2trop.c190114.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.8.0.0_12pft_c191216.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

bld/namelist_files/namelist_defaults_overall.xml

@@ -55,9 +55,8 @@ determine default values for namelists.
 <!-- Default simulation year range -->
 <sim_year_range>constant</sim_year_range>
 
-<!-- Check resolution and land/mask before continuing -->
-<chk_res mode="clm_stndln" >1</chk_res>
-<chk_res mode="ext_cesm"   >0</chk_res>
+<!-- Check resolution and land/mask in the local resolution list before continuing - normally turned off -->
+<chk_res>0</chk_res>
 
 <!-- Add note to namelist files documenting the options given to build-namelist -->
 <note mode="clm_stndln" >1</note>

cime_config/testdefs/ExpectedTestFails.xml

@@ -11,10 +11,12 @@
     <entry issue="#840"            >FAIL PEPEM_Ld1.f10_f10_musgs.I2000Clm50BgcCrop.hobart_intel.clm-crop RUN</entry>
   </category>
   <category name="fates">
+    <entry issue="NGEET/fates/#559" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro RUN</entry>
     <entry issue="667"              >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro COMPARE_base_rest</entry>
     <entry issue="667"              >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro RUN</entry>
-    <entry issue="NGEET/fates/#510" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro MEMLEAK</entry>
     <entry issue="667"              >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro RUN</entry>
-    <entry issue="NGEET/fates/#510" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro MEMLEAK</entry>
+    <entry issue="NGEET/fates/#510" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro MEMLEAK</entry>
+    <entry issue="NGEET/fates/#508" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro RUN</entry>
+    <entry issue="NGEET/fates/#508" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro RUN</entry>
   </category>
 </expectedFails> 

cime_config/testdefs/testlist_clm.xml

@@ -1882,22 +1882,14 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5" grid="f19_g16" compset="I2000Clm45BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERS_D_Ld5" grid="f19_g16" compset="I2000Clm50BgcCruGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Run a short non-Fates test (without land-ice model) in the fates test list, to make sure fates changes do not mess up the standard model</option>
     </options>
   </test>
   <test name="ERS_D_Mmpi-serial_Ld5" grid="1x1_brazil" compset="I2000Clm50FatesCruGs" testmods="clm/FatesColdDef">
@@ -1996,7 +1988,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ly2" grid="1x1_brazil" compset="I2000Clm50FatesCruGs" testmods="clm/FatesColdDef">
+  <test name="SMS_Lm13" grid="1x1_brazil" compset="I2000Clm50FatesCruGs" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -2021,7 +2013,7 @@
       <machine name="cheyenne" compiler="intel" category="prebeta"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:60:00</option>
       <option name="comment"  >The main point of this test is simply to make sure that the CMIP6WACCMDECK modifier works for
 2-degree since that resolution turns off Carbon isotopes </option>
     </options>

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -3,9 +3,11 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_spitfire= .true.
-hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
+hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN_ELEM','LITTER_OUT_ELEM',
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF',
-   'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN'
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF',
+   'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN',
+   'LITTER_FINES_AG_ELEM','LITTER_FINES_BG_ELEM','LITTER_CWD_AG_ELEM','LITTER_CWD_BG_ELEM',
+   'SEED_BANK'

cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm

@@ -27,4 +27,6 @@ hist_fincl1       = 'NCL_BY_AGE','NPATCH_BY_AGE','BIOMASS_BY_AGE','NPP_BY_AGE','
                     'NPP_LEAF_UNDERSTORY_SCLS','NPP_FROOT_UNDERSTORY_SCLS','NPP_BSW_UNDERSTORY_SCLS',
                     'NPP_BDEAD_UNDERSTORY_SCLS','NPP_BSEED_UNDERSTORY_SCLS','NPP_STORE_UNDERSTORY_SCLS','RDARK_UNDERSTORY_SCLS',
                     'LIVESTEM_MR_UNDERSTORY_SCLS','LIVECROOT_MR_UNDERSTORY_SCLS','FROOT_MR_UNDERSTORY_SCLS','RESP_G_UNDERSTORY_SCLS',
-                    'RESP_M_UNDERSTORY_SCLS'
+                    'RESP_M_UNDERSTORY_SCLS','LITTER_IN_ELEM','LITTER_OUT_ELEM','SEED_BANK_ELEM','SEEDS_IN_LOCAL_ELEM','SEEDS_IN_EXTERN_ELEM',
+		    'SEED_GERM_ELEM','SEED_DECAY','CBALANCE_ERROR_FATES','ERROR_FATES','LITTER_FINES_AG_ELEM','LITTER_FINES_BG_ELEM','LITTER_CWD_BG_ELEM',
+		    'LITTER_CWD_AG_ELEM','LITTER_CWD'

cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm

@@ -6,5 +6,5 @@ hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT'
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF',
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF',
    'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN'

cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm

@@ -2,4 +2,4 @@ hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT'
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC'
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR'

doc/.ChangeLog_template

@@ -95,9 +95,9 @@ CTSM testing:
 
     cheyenne_intel ---- 
     cheyenne_gnu ------ 
-    hobart_nag -------- 
-    hobart_pgi -------- 
-    hobart_intel ------ 
+    izumi_nag --------- 
+    izumi_pgi --------- 
+    izumi_intel ------- 
 
 Answer changes
 --------------

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+release-clm5.0.30     erik 01/21/2020 Update FATES to sci.1.30.0_api.8.0.0
 release-clm5.0.29     erik 11/19/2019 Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings)
 release-clm5.0.28     erik 11/14/2019 Several bit-for-bit fixes especially around soil-moisture streams
 release-clm5.0.27     erik 08/13/2019 Add presoribed soil moisture streams as an option, and a few fixes

doc/release-clm5.0.ChangeLog

@@ -1,4 +1,98 @@
 ===============================================================
+Tag name:  release-clm5.0.30
+Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Tue Jan 21 13:50:48 MST 2020
+One-line Summary: Update FATES to sci.1.30.0_api.8.0.0
+
+Purpose of this version:
+------------------------
+
+Update FATES to sci.1.30.0_api.8.0.0, and point to the NGEET version, rather
+than NCAR/fates-release version.
+
+One change to soil-moisture (also check if gridcell weight is non-zero, before specifying prescribed soil moisture.
+Also update mosart with cold start bug fix. Update rtm, cism, and cime to versions on cesm2.1.2 release tag. 
+Fix some issues with PTCLM.
+
+CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes)
+
+Summary of changes:
+-------------------
+
+Issues fixed (include CTSM Issue #): #847 #871
+  Fixes #847 -- issues with prescribed soil moisture
+  Fixes #871 -- don't check for valid resolution for CESM cases by default
+
+Science changes since: release-clm5.0.28
+  FATES science update from sci-1.27.1  to sci.1.30.0
+
+Software changes since: release-clm5.0.28
+  FATES API update from api.7.3.0 to api.8.0.0
+
+Changes to User Interface since: release-clm5.0.28
+  fates paramfile is updated
+
+Testing:
+--------
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS (35 tests are different because of fates param file update)
+
+  unit-tests (components/clm/src):
+
+    cheyenne - PASS
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - PASS
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - OK
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- OK
+    cheyenne_gnu ------ OK
+    izumi_nag --------- OK
+    izumi_pgi --------- OK
+    izumi_intel ------- OK
+
+Summary of Answer changes:
+-------------------------
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here: previous
+
+Changes answers relative to baseline: Yes, but only when running with FATES
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: with FATES active
+    - what platforms/compilers: all
+    - nature of change: similar climate
+
+Detailed list of changes:
+------------------------
+
+Externals being used: all externals updated
+
+   cism:   cism-release-cesm2.1.2_01
+   rtm:    release-cesm2.0.04
+   mosart: release-cesm2.0.04
+   cime:   cim5.6.28
+   FATES:  sci.1.30.0_api.8.0.0
+   PTCLM:  PTCLM2_20200121
+
+CTSM Tag versions pulled over from master development branch: None
+
+Pull Requests that document the changes (include PR ids): #846
+(https://github.com/ESCOMP/ctsm/pull)
+   #846 -- Update to fates sci.1.30.0_api.8.0.0
+
+===============================================================
+===============================================================
 Tag name:  release-clm5.0.29
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Tue Nov 19 12:14:02 MST 2019

src/biogeophys/CanopyFluxesMod.F90

@@ -21,7 +21,6 @@ module CanopyFluxesMod
   use decompMod             , only : bounds_type
   use PhotosynthesisMod     , only : Photosynthesis, PhotoSynthesisHydraulicStress, PhotosynthesisTotal, Fractionation
   use EDAccumulateFluxesMod , only : AccumulateFluxes_ED
-  use EDBtranMod            , only : btran_ed
   use SoilMoistStressMod    , only : calc_effective_soilporosity, calc_volumetric_h2oliq
   use SoilMoistStressMod    , only : calc_root_moist_stress, set_perchroot_opt
   use SimpleMathMod         , only : array_div_vector

src/biogeophys/SoilMoistureStreamMod.F90

@@ -358,7 +358,9 @@ subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, &
          g = col%gridcell(c)
          ig = g_to_ig(g)
 
-         if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) ) then
+         ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847)
+         if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. &
+              (col%wtgcell(c) /= 0._r8) ) then
             !       this is a 2d field (gridcell/nlevsoi) !
             do j = 1, nlevsoi