Merge pull request ESCOMP#468 from billsacks/simple_bfb

Minor bug fixes, cleanup, documentation and enhancements

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)