clm4_5_17_r263

Keep the hydraulic conductivity for organic soil higher than it is for mineral soil. This was found to be an issue and fixed by
Sean Swenson, Dave Lawrence, and Keith Oleson. Double dry deposition velocity for SO2 (Jean-Francois Lamaruque) for both clm4_5
and clm5_0.  Fix bug for value of NACTIVE at first time-step. Partial fix so that max daylengh isn't hardwired to present day at least
at initialization (see caveat below). Move the sample files for the mkprocdata_map tool (for mapping between unstructured grids
and regular lat lon grids) out of CLM and into $CSMDATA. Update the c13/c14 timeseries files to the 2.0 version as per Keith Lindsay.

bld/namelist_files/namelist_defaults_clm4_5.xml

@@ -86,8 +86,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <stomatalcond_method phys="clm4_5"                         >Ball-Berry1987</stomatalcond_method>
 
 <!-- Carbon isotope concentration files -->
-<atm_c13_filename use_c13=".true." use_c13_timeseries=".true." >lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_c170429.nc</atm_c13_filename>
-<atm_c14_filename use_c14=".true." use_c14_bombspike =".true." >lnd/clm2/isotopes/atm_delta_C14_CMIP6_3x1_global_1850-2015_yearly_c170429.nc</atm_c14_filename>
+<atm_c13_filename use_c13=".true." use_c13_timeseries=".true." >lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_v2.0_c171012.nc</atm_c13_filename>
+<atm_c14_filename use_c14=".true." use_c14_bombspike =".true." >lnd/clm2/isotopes/atm_delta_C14_CMIP6_3x1_global_1850-2015_yearly_v2.0_c171012.nc</atm_c14_filename>
 
 <!-- Irrigation default -->
 <irrigate use_crop=".true." >.false.</irrigate>

doc/ChangeLog

@@ -1,4 +1,141 @@
 ===============================================================
+Tag name:  clm4_5_17_r263
+Originator(s):  erik (Erik Kluzek)
+Date: Wed Nov  8 15:36:41 MST 2017
+One-line Summary: Drydep vel. for SO2 doubled, influence of organic mater in soil calmed, max daylength not hardwired to present day
+
+Purpose of changes
+------------------
+
+Keep the hydraulic conductivity for organic soil higher than it is for mineral soil. This was found to be an issue and fixed by 
+Sean Swenson, Dave Lawrence, and Keith Oleson. Double dry deposition velocity for SO2 (Jean-Francois Lamaruque) for both clm4_5
+and clm5_0.  Fix bug for value of NACTIVE at first time-step. Partial fix so that max daylengh isn't hardwired to present day at least
+at initialization (see caveat below). Move the sample files for the mkprocdata_map tool (for mapping between unstructured grids
+and regular lat lon grids) out of CLM and into $CSMDATA. Update the c13/c14 timeseries files to the 2.0 version as per Keith Lindsay.
+
+Bugs fixed or introduced
+------------------------
+
+Bugs fixed (include bugzilla ID): 
+ 2530 -- organic soil influence varies wildly
+ 2304 -- NACTIVE at first time step
+ 1843 -- Max daylength now uses orbital parameters at initialization rather than hardwired to present day (partial)
+
+Known bugs introduced in this tag:
+ 2529 -- SSP case that runs on cheyenne fails on hobart
+
+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): None
+
+Changes made to namelist defaults (e.g., changed parameter values): None
+
+Changes to the datasets (e.g., parameter, surface or initial files): c13/c14 time-series files
+
+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):
+  Max daylength will still be wrong in cases where variable_years is used, where the orbit
+  changes after initializaiton. It'll start out correct and begin to diverge each year.
+  Since, this feature is untested it's not worth going through the additional changes to
+  correct it during the run.
+
+  At the time the tag was made, cheyenne was down, so there are six tests that weren't confirmed to pass:
+     ERS_D_Ld3.f19_f19_mg16.IHistClm40SpCruGs.cheyenne_intel.clm-40default
+     ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput
+     SMS_D_Ld5.f10_f10_musgs.I2000Clm50Fates.cheyenne_intel.clm-fates
+     SMS_D_Ly2.1x1_numaIA.IHistClm50BgcCropGs.cheyenne_intel.clm-ciso_bombspike1963
+     SMS_Ld1.f19_f19_mg16.IHistClm40SpCruGs.cheyenne_intel.clm-40default
+     SMS_Ld1.f19_g17.I2000Clm50Vic.cheyenne_intel.clm-default
+
+Changes to tests or testing: tools testing modified to point to files in CSMDATA
+
+Code reviewed by: self,lamar,oleson,sacks,dlawren
+
+Did you follow the steps in .CLMTrunkChecklist: yes
+
+CLM testing: regular, tools
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS
+
+  unit-tests (components/clm/src):
+
+    cheyenne - PASS
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - PASS
+
+  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
+
+CLM tag used for the baseline comparisons:  clm4_5_16_r262
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes!
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm4_5 and clm5_0
+    - what platforms/compilers: all
+    - nature of change: changes answers with bug fixes in a significant way
+
+   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: oleson/csm/clm50_r243_1deg_GSWP3V2_cropopt_nsc_hksat_hist
+
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, mosart, cism, etc.): none
+
+List all files eliminated:
+
+        Remove sample files, move to CSMDATA, remove sample namelist
+   D components/clm/tools/mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc
+   D components/clm/tools/mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc
+   D components/clm/tools/mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc
+   D components/clm/tools/mkprocdata_map/mkprocdata_map_in
+
+List all files added and what they do:
+
+   A components/clm/tools/mkprocdata_map/README.filedescriptions -- Describe the files in this directory
+
+List all existing files that have been modified, and describe the changes:
+
+   M components/clm/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 - Point to files in CSMDATA rather than mkprocdata_map dir.
+
+   M components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml -- Point to new v2.0 of the c13/c14 timeseries files
+
+   M components/clm/src/biogeophys/SoilStateInitTimeConstMod.F90 -- Fix bug 2530 for organic mater influence in soil
+   M components/clm/src/biogeochem/DryDepVelocity.F90 ------------- Double SO2 dry deposition rate
+   M components/clm/src/biogeochem/CNFUNMod.F90 ------------------- Bug, 2304 for NACTIVE on history for first time-step
+   M components/clm/src/biogeochem/ch4Mod.F90 --------------------- Bug, 2528, floating overflow for methane (doesn't change answers)
+   M components/clm/src/main/clm_initializeMod.F90 ---------------- Bug, 1843, max daylength no longer hardwired to present day at initialization
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_16_r262
 Originator(s):  sacks (Bill Sacks)
 Date: Fri Oct 27 10:17:54 MDT 2017

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  clm4_5_17_r263     erik 11/08/2017 Drydep vel. for SO2 doubled, influence of organic mater in soil calmed, max daylength not hardwired to present day
   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

src/biogeochem/CNFUNMod.F90

@@ -1472,7 +1472,6 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
 
       Nactive_no3(p)            = n_active_no3_acc_total(p)/dt   + n_active_no3_retrans_total(p)/dt
       Nactive_nh4(p)            = n_active_nh4_acc_total(p)/dt   + n_active_nh4_retrans_total(p)/dt  
-      Nactive(p)                = Nactive_no3(p)  + Nactive_nh4(p) + Nnonmyc_no3(p) + Nnonmyc_nh4(p)
 
 
 
@@ -1489,6 +1488,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
       Nuptake(p)                = Nactive_no3(p) + Nactive_nh4(p) + Nnonmyc_no3(p) &
                                   + Nnonmyc_nh4(p) + Nfix(p) + Npassive(p) + &
                                   retransn_to_npool(p)+free_retransn_to_npool(p) 
+      Nactive(p)                = Nactive_no3(p)  + Nactive_nh4(p) + Nnonmyc_no3(p) + Nnonmyc_nh4(p)
 
      ! free N goes straight to the npool, not throught Nuptake...
       sminn_to_plant_fun(p)     = Nactive_no3(p) + Nactive_nh4(p) + Nnonmyc_no3(p) + Nnonmyc_nh4(p) + Nfix(p) + Npassive(p)

src/biogeochem/DryDepVelocity.F90

@@ -611,6 +611,8 @@ subroutine depvel_compute( bounds, &
                   velocity(pi,ispec) = 0.2_r8
                case ( 'CB1', 'CB2', 'OC1', 'OC2', 'SOAM', 'SOAI', 'SOAT', 'SOAB', 'SOAX' )
                   velocity(pi,ispec) = 0.10_r8
+               case ( 'SO2' )
+                  velocity(pi,ispec) = (1._r8/(ram1(pi)+rb1(pi)+rc))*200._r8
                case default
                   velocity(pi,ispec) = (1._r8/(ram1(pi)+rb1(pi)+rc))*100._r8
                end select

src/biogeochem/ch4Mod.F90

@@ -3342,7 +3342,11 @@ subroutine ch4_tran (bounds, &
 
             o2demand = o2_decomp_depth(c,j) + o2_oxid_depth(c,j) ! o2_decomp_depth includes autotrophic root respiration
             if (o2demand > 0._r8) then
-               o2stress(c,j) = min((conc_o2(c,j) / dtime + o2_aere_depth(c,j)) / o2demand, 1._r8)
+               if ( (conc_o2(c,j) / dtime + o2_aere_depth(c,j)) > o2demand )then
+                  o2stress(c,j) = 1._r8
+               else
+                  o2stress(c,j) = (conc_o2(c,j) / dtime + o2_aere_depth(c,j)) / o2demand
+               end if
             else
                o2stress(c,j) = 1._r8
             end if

src/biogeophys/SoilStateInitTimeConstMod.F90

@@ -457,7 +457,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
                 om_watsat         = max(0.93_r8 - 0.1_r8   *(zsoi(lev)/zsapric), 0.83_r8)
                 om_b              = min(2.7_r8  + 9.3_r8   *(zsoi(lev)/zsapric), 12.0_r8)
                 om_sucsat         = min(10.3_r8 - 0.2_r8   *(zsoi(lev)/zsapric), 10.1_r8)
-                om_hksat          = max(0.28_r8 - 0.2799_r8*(zsoi(lev)/zsapric), 0.0001_r8)
+                om_hksat          = max(0.28_r8 - 0.2799_r8*(zsoi(lev)/zsapric), xksat)
 
                 soilstate_inst%bd_col(c,lev)        = (1._r8 - soilstate_inst%watsat_col(c,lev))*2.7e3_r8 
                 soilstate_inst%watsat_col(c,lev)    = (1._r8 - om_frac) * soilstate_inst%watsat_col(c,lev) + om_watsat*om_frac

src/main/clm_initializeMod.F90

@@ -385,11 +385,10 @@ subroutine initialize2( )
     call InitDaylength(bounds_proc, declin=declin, declinm1=declinm1)
 
     ! Initialize maximum daylength, based on latitude and maximum declination
-    ! maximum declination hardwired for present-day orbital parameters, 
-    ! +/- 23.4667 degrees = +/- 0.409571 radians, use negative value for S. Hem
+    ! given by the obliquity use negative value for S. Hem
 
     do g = bounds_proc%begg,bounds_proc%endg
-       max_decl = 0.409571
+       max_decl = obliqr
        if (grc%lat(g) < 0._r8) max_decl = -max_decl
        grc%max_dayl(g) = daylength(grc%lat(g), max_decl)
     end do

test/tools/nl_files/mkprocdata_ne30_to_f19_I2000

@@ -1 +1 @@
--i CFGDIR/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc -o ne30output_onf19grid.nc -m CFGDIR/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc -t CFGDIR/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc -e EXEDIR
+-i CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc -o ne30output_onf19grid.nc -m CSMDATA/lnd/clm2/test_mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc -t CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc -e EXEDIR

tools/mkprocdata_map/README.filedescriptions

@@ -0,0 +1,25 @@
+README.filedescriptions                        Erik Kluzek
+                                               11/7/2017
+
+mkprocdata_map_all ------------ Script to run over a list of files
+mkprocdata_map_wrap ----------- Main script to actually use
+mkprocdata_map_functions.bash - Bash shell functions to use in other scripts
+README ------------------------ Description and how to run
+src --------------------------- Directory with FORTRAN source code
+
+Also there are some sample files that can be used for testing under inputdata in 
+
+$DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map
+
+See how this is done by looking at the file for testing mkprocdata_map: 
+
+../../test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 
+
+Which does something like the following:
+
+./mkprocdata_map_wrap \
+-i $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc \
+-o ne30output_onf19grid.nc \
+-m $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc \
+-t $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc
+