Merge pull request #468 from billsacks/simple_bfb

Minor bug fixes, cleanup, documentation and enhancements

.gitignore

@@ -1,10 +1,10 @@
 # directories checked out by manage_externals, and other files created
 # by manage_externals
 manage_externals.log
-src/fates/
-tools/PTCLM/
-cime/
-components/
+/src/fates/
+/tools/PTCLM/
+/cime/
+/components/
 
 # ignore svn directories
 **/.svn/**
@@ -26,28 +26,35 @@ CMakeFiles/
 
 
 # unit testing directories
-src/unit_tests.*
+/src/unit_tests.*
+
+# files generated by the unit test build
+/src/dyn_subgrid/dynVarMod.F90
+/src/dyn_subgrid/dynVarTimeInterpMod.F90
+/src/dyn_subgrid/dynVarTimeUninterpMod.F90
+/src/utils/array_utils.F90
+/src/unit_test_stubs/utils/restUtilMod_stub.F90
+/src/unit_test_stubs/main/ncdio_pio_fake.F90
+/src/unit_test_stubs/main/ncdio_var.F90
+/src/unit_test_shr/unittestArrayMod.F90
 
 # cime_config
 buildnmlc
 buildcppc
 
-# don't ignore cism build utilities directory
-!components/cism/**/build
-
 # configure / build files
-bld/**/CESM_cppdefs
-bld/**/Filepath
-bld/**/config_cache.xml
-bld/**/lnd_in
-bld/**/drv_flds_in
+/bld/**/CESM_cppdefs
+/bld/**/Filepath
+/bld/**/config_cache.xml
+/bld/**/lnd_in
+/bld/**/drv_flds_in
 
 # build-naemlist testing
-bld/unit_testers/lnd_in*
-bld/unit_testers/drv_flds_in*
-bld/unit_testers/temp_file.txt*
-bld/unit_testers/user_nl_clm_real_parameters*
-bld/unit_testers/env_run.xml
+/bld/unit_testers/lnd_in*
+/bld/unit_testers/drv_flds_in*
+/bld/unit_testers/temp_file.txt*
+/bld/unit_testers/user_nl_clm_real_parameters*
+/bld/unit_testers/env_run.xml
 
 # tools testing output
 td.*.status
@@ -66,19 +73,19 @@ clm.input_data_list.previous
 *.stdout.txt.o*
 
 # Tools executables
-tools/mksurfdata_map/mksurfdata_map
-tools/mkprocdata_map/mkprocdata_map
+/tools/mksurfdata_map/mksurfdata_map
+/tools/mkprocdata_map/mkprocdata_map
 
 # mksurfdata output files
-tools/mksurfdata_map/surfdata_*.nc
-tools/mksurfdata_map/landuse.timeseries_*.nc
+/tools/mksurfdata_map/surfdata_*.nc
+/tools/mksurfdata_map/landuse.timeseries_*.nc
 
 # mkmapdata output files
-tools/mkmapdata/PET*.RegridWeightGen.Log
-tools/mkmapdata/regrid.*.out
-tools/mkmapdata/regrid.*.err
-tools/mkmapdata/regrid.o*
-tools/mkmapdata/map*.nc
+/tools/mkmapdata/PET*.RegridWeightGen.Log
+/tools/mkmapdata/regrid.*.out
+/tools/mkmapdata/regrid.*.err
+/tools/mkmapdata/regrid.o*
+/tools/mkmapdata/map*.nc
 
 # build output
 *.o

bld/namelist_files/namelist_definition_clm4_5.xml

@@ -2432,20 +2432,24 @@ to the atmosphere) (but using the 'general' method will typically have
 only a very minor impact on results in this case). For this method to
 work, the input finidat file needs to be at the same resolution as the
 current configuration. So this is a less general form of
-init_interp. However, it can be used when transitioning from a spinup
-run to a transient run, or in other cases where the only difference is
-in internal memory allocation. In order to catch possible problems, this
-uses a different algorithm for finding the input point for each output
-point, which ensures that each active output point is associated with
-exactly one input point with the same latitude, longitude and type. This
-method requires (a) the same grid for input and output, within roundoff;
-(b) any non-zero-weight point in the input must have memory allocated
-for it in this grid cell in the output (this will be satisfied if the
-point is non-zero-weight on the surface dataset or if it's a point for
-which we allocate memory even for zero-weight points); (c) any active
-point in the output (based on the surface dataset and rules for
-determining active points) must have a matching point in this grid cell
-in the input.
+init_interp. However, it can be used in cases where the only difference
+is in internal memory allocation. In order to catch possible problems,
+this uses a different algorithm for finding the input point for each
+output point, which ensures that each active output point is associated
+with exactly one input point with the same latitude, longitude and
+type. This method requires (a) the same grid for input and output,
+within roundoff; (b) any non-zero-weight point in the input must have
+memory allocated for it in this grid cell in the output (this will be
+satisfied if the point is non-zero-weight on the surface dataset or if
+it's a point for which we allocate memory even for zero-weight points);
+(c) any active point in the output (based on the surface dataset and
+rules for determining active points) must have a matching point in this
+grid cell in the input. (Note that this generally can NOT be used when
+transitioning from a spinup run to a transient run, because spinup runs
+typically have irrigation off and transient runs have irrigation on, and
+the presence/absence of irrigation affects the subgrid structure; if it
+weren't for that difference, then this option would be useful for this
+use case.)
 
 </entry>
 

cime_config/testdefs/testlist_clm.xml

@@ -657,14 +657,6 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P36x2_Lm36" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/irrigOn_reduceOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:60:00</option>
-    </options>
-  </test>
   <test name="ERP_P180x2_D" grid="f19_g17" compset="I2000Clm50SpRtmFl" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -753,6 +745,7 @@
   <test name="ERP_P72x2_Lm36" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/clm50cropIrrigMonth_interp">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="cheyenne" compiler="intel" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1350,10 +1343,10 @@
   </test>
   <test name="SMS_D_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm45BgcCropQianGs" testmods="clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">02:00:00</option>
       <option name="comment"  >Want a debug test that tests a number of aspects of transient crops, including a new crop landunit and shifting PCT_CFT; move to CLM50 once we can get it fast enough (see bug 2391)</option>
     </options>
   </test>

cime_config/usermods_dirs/cmip6_output/user_nl_cpl

@@ -0,0 +1 @@
+histaux_l2x1yrg = .true.

src/biogeochem/CNDriverMod.F90

@@ -754,7 +754,7 @@ subroutine CNDriverNoLeaching(bounds,
          dgvs_inst, cnveg_state_inst,                                                                                              &
          cnveg_carbonstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst,                         &
          leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full),                                  &
-         froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full),                                & 
+         froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full),                                &
          croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full),                                &
          stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full),                                  &
          totsomc_col=soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc),                                                       &

src/biogeochem/CNFUNMod.F90

@@ -1236,7 +1236,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
                      frac_ideal_C_use = max(0.0_r8,1.0_r8 - (total_N_resistance-fun_cn_flex_a(ivt(p)))/fun_cn_flex_b(ivt(p)) )
                      ! then, if the plant is very much in need of N, the C used for uptake is increased accordingly.                  
                      if(delta_CN .gt.0.and. frac_ideal_C_use.lt.1.0)then           
-                       frac_ideal_C_use = frac_ideal_C_use + (1.0_r8-frac_ideal_C_use)*min(1.0_r8, delta_CN/fun_cn_flex_c(ivt(p)));                       
+                       frac_ideal_C_use = frac_ideal_C_use + (1.0_r8-frac_ideal_C_use)*min(1.0_r8, delta_CN/fun_cn_flex_c(ivt(p)))
                      end if    
                      ! If we have too much N (e.g. from free N retranslocation) then make frac_ideal_c_use even lower.    
                      ! For a CN delta of fun_cn_flex_c, then we reduce C expendiure to the minimum of 0.5. 

src/biogeochem/CNGapMortalityMod.F90

@@ -193,7 +193,7 @@ subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_so
          cnveg_carbonflux_inst%m_livecrootc_to_litter_patch(p)          = cnveg_carbonstate_inst%livecrootc_patch(p)          * m
          if (spinup_state == 2 .and. .not. use_cndv) then   !accelerate mortality of dead woody pools 
            cnveg_carbonflux_inst%m_deadstemc_to_litter_patch(p)         = cnveg_carbonstate_inst%deadstemc_patch(p)  * m * 10._r8
-           cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch(p)        = cnveg_carbonstate_inst%deadcrootc_patch(p) * m * 10._r8        
+           cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch(p)        = cnveg_carbonstate_inst%deadcrootc_patch(p) * m * 10._r8
          else
            cnveg_carbonflux_inst%m_deadstemc_to_litter_patch(p)         = cnveg_carbonstate_inst%deadstemc_patch(p)           * m
            cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch(p)        = cnveg_carbonstate_inst%deadcrootc_patch(p)          * m

src/biogeochem/CNVegNitrogenFluxType.F90

@@ -950,7 +950,7 @@ subroutine InitHistory(this, bounds)
             ptr_patch=this%fert_patch)
     end if
 
-    if (use_crop) then
+    if (use_crop .and. .not. use_fun) then
        this%soyfixn_patch(begp:endp) = spval
        call hist_addfld1d (fname='SOYFIXN', units='gN/m^2/s', &
             avgflag='A', long_name='soybean fixation', &

src/biogeophys/CanopyTemperatureMod.F90

@@ -110,8 +110,8 @@ subroutine CanopyTemperature(bounds, &
     real(r8) :: qsatgdT      ! d(qsatg)/dT
     real(r8) :: fac          ! soil wetness of surface layer
     real(r8) :: psit         ! negative potential of soil
-    real(r8) :: hr           ! relative humidity
-    real(r8) :: hr_road_perv ! relative humidity for urban pervious road
+    real(r8) :: hr           ! alpha soil
+    real(r8) :: hr_road_perv ! alpha soil for urban pervious road
     real(r8) :: wx           ! partial volume of ice and water of surface layer
     real(r8) :: fac_fc       ! soil wetness of surface layer relative to field capacity
     real(r8) :: eff_porosity ! effective porosity in layer

src/biogeophys/SurfaceAlbedoMod.F90

@@ -112,13 +112,14 @@ subroutine SurfaceAlbedoInitTimeConst(bounds)
     allocate(isoicol(bounds%begc:bounds%endc)) 
 
     ! Determine soil color and number of soil color classes 
-    ! if number of soil color classes is not on input dataset set it to 8
 
     call getfil (fsurdat, locfn, 0)
     call ncd_pio_openfile (ncid, locfn, 0)
 
     call ncd_io(ncid=ncid, varname='mxsoil_color', flag='read', data=mxsoil_color, readvar=readvar)
-    if ( .not. readvar ) mxsoil_color = 8  
+    if ( .not. readvar ) then
+       call endrun(msg=' ERROR: mxsoil_color NOT on surfdata file '//errMsg(sourcefile, __LINE__))
+    end if
 
     allocate(soic2d(bounds%begg:bounds%endg)) 
     call ncd_io(ncid=ncid, varname='SOIL_COLOR', flag='read', data=soic2d, dim1name=grlnd, readvar=readvar)

src/main/ncdio_pio.F90.in

@@ -104,7 +104,7 @@ module ncdio_pio
   interface ncd_io
      module procedure ncd_io_char_var0_start_glob
 
-     !DIMS 0,1
+     !DIMS 0
      module procedure ncd_io_{DIMS}d_log_glob
 
      !DIMS 0,1,2,3
@@ -1192,11 +1192,11 @@ contains
   end subroutine ncd_io_char_var0_start_glob
 
   !------------------------------------------------------------------------
-  !DIMS 0,1
+  !DIMS 0
   subroutine ncd_io_{DIMS}d_log_glob(varname, data, flag, ncid, readvar, nt, posNOTonfile)
     !
     ! !DESCRIPTION:
-    ! netcdf I/O of global integer variable
+    ! netcdf I/O of global logical variable
     !
     ! !ARGUMENTS:
     class(file_desc_t) , intent(inout) :: ncid      ! netcdf file id
@@ -1242,12 +1242,7 @@ contains
              call shr_sys_abort(' ERROR: bad integer value for logical data'//errMsg(sourcefile, __LINE__))
           end if
 #else
-          allocate(idata1d(size(data)))
-          data = (idata1d == 1)
-          if ( any(idata1d /= 0 .and. idata1d /= 1) )then
-             call shr_sys_abort(' ERROR: read in bad integer value(s) for logical data'//errMsg(sourcefile, __LINE__))
-          end if
-          deallocate(idata1d)
+          call shr_sys_abort('ncd_io_*_log_glob not implemented for DIMS > 0')
 #endif
        endif
        if (present(readvar)) readvar = varpresent
@@ -1267,18 +1262,7 @@ contains
        status = pio_put_var(ncid, varid, start, count, idata1d)
        deallocate(idata1d)
 #else
-       start(1) = 1 ; count(1) = size(data)
-       start(2) = 1 ; count(2) = 1
-       if (present(nt)) start(2) = nt
-       allocate(idata1d(size(data)))
-       where( data )
-          idata1d = 1
-       elsewhere
-          idata1d = 0
-       end where
-       call ncd_inqvid  (ncid, varname, varid, vardesc)
-       status = pio_put_var(ncid, varid, start, count, idata1d)
-       deallocate( idata1d )
+       call shr_sys_abort('ncd_io_*_log_glob not implemented for DIMS > 0')
 #endif
 
     endif   ! flag

src/main/restFileMod.F90

@@ -714,10 +714,10 @@ subroutine restFile_dimcheck( ncid )
        call check_dim(ncid, namep, nump, msg=msg)
        if ( use_fates ) call check_dim(ncid, nameCohort  , numCohort, msg=msg)
     end if
-    call check_dim(ncid, 'levsno'  , nlevsno, &
-         msg = 'You can deal with this mismatch by rerunning with ' // &
-               'use_init_interp = .true. in user_nl_clm')
-    call check_dim(ncid, 'levgrnd' , nlevgrnd)
+    msg = 'You can deal with this mismatch by rerunning with ' // &
+         'use_init_interp = .true. in user_nl_clm'
+    call check_dim(ncid, 'levsno'  , nlevsno, msg=msg)
+    call check_dim(ncid, 'levgrnd' , nlevgrnd, msg=msg)
     call check_dim(ncid, 'levurb'  , nlevurb)
     call check_dim(ncid, 'levlak'  , nlevlak)