New soiltex for ctsm5.2.mksurfdata

tools/mksurfdata_esmf/README

@@ -2,9 +2,10 @@
 Build Requirements:
 ===================
 
-mksurfdata_esmf is an distributed memory parallel program (using Message Passing Interface -- MPI) that utilizes
-both ESMF (Earth System Modelling Framework) for regridding as well as PIO (Parallel I/O) and NetCDF output. As
-such libraries must be built for the following:
+mksurfdata_esmf is a distributed memory parallel program (using Message Passing
+Interface -- MPI) that utilizes both ESMF (Earth System Modelling Framework)
+for regridding as well as PIO (Parallel I/O) and NetCDF output. As
+such, libraries must be built for the following:
 
 1) MPI
 2) NetCDF
@@ -13,42 +14,43 @@ such libraries must be built for the following:
 
 In addition for the build: python, bash-shell, CMake and GNU-Make are required
 
-These libraries need to be built such that they can all work together in the same executable. Hence, the above
-order may be required in building them.
+These libraries need to be built such that they can all work together in the
+same executable. Hence, the above order may be required in building them.
 
 =========================================
 Use cime to manage the build requirements
 =========================================
 
-For users working on cime machines you can use the build
-script to build the tool for you. On other machines you'll need to do a port to cime
-and tell how to build for that machine. That's talked about in the cime documentation.
+For users working on cime machines you can use the build script to build the
+tool. On other machines you'll need to do a port to cime and tell how to build
+for that machine. That's talked about in the cime documentation.
 And you'll have to make some modifications to the build script.
 
 https://github.com/ESMCI/cime/wiki/Porting-Overview
 
-Machines that already run CTSM or CESM have been ported to cime. So if you can run the model
-on your machine you will be able to build the tool there.
+Machines that already run CTSM or CESM have been ported to cime. So if you can
+run the model on your machine, you will be able to build the tool there.
 
 To get a list of the machines that have been ported to cime: 
 
 cd ../../cime/scripts
 ./query_config --machines
 
 NOTE:
-In addition to having a port to cime, the machine also needs to have PIO built and able
-to be referenced with the env variable PIO which will need to be in the porting instructions
-for the machine. Currently an independent PIO library is not available on cime ported machines.
+In addition to having a port to cime, the machine also needs to have PIO built
+and able to be referenced with the env variable PIO which will need to be in
+the porting instructions for the machine. Currently an independent PIO library
+is not available on cime ported machines.
 
 =======================
-building the executable
+Building the executable
 =======================
 
 > cd tools/mksurfdata_esmf
 > ./gen_mksurfdata_build.sh      # For machines with a cime build
 
 =======================
-running for a single submission:
+Running for a single submission:
 =======================
 > cd ../
 # to generate your target namelist:
@@ -60,7 +62,7 @@ running for a single submission:
 > qsub mksurfdata_jobscript_single
 
 =======================
-running for the generation of multiple datasets
+Running for the generation of multiple datasets
 =======================
 # Note that gen_mksurfdata_jobscript_multi.py runs ./gen_mksurfdata_namelist.py
 > ./gen_mksurfdata_jobscript_multi.py --help
@@ -76,6 +78,7 @@ slevis HAS RUN THESE CASES and HAS LISTED ISSUES ENCOUNTERED
 ------------------------------------------------------------
 REMEMBER TO compare against existing fsurdat files in
 /glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18
+0) New 30-sec raw data for soil texture fails. Try requesting more mem.
 1) Soil color & texture and ag fire peak month outputs too high in .log
    TODO? Change frac_o from always 1.
 2) Pct lake has chged in the .log bc the old diagnostic omitted mask_i frac_o

tools/mksurfdata_esmf/gen_mksurfdata_namelist.py

@@ -176,7 +176,19 @@ def get_parser():
             [default: %(default)s]
             """,
         action="store_true",
-        dest="hres_flag",
+        dest="hres_pft",
+        default=False,
+    )
+    parser.add_argument(
+        "--hires_soitex",
+        help="""
+            If you want to use the high-resolution soil texture dataset rather
+            than the default lower resolution dataset.
+            (Low resolution is 5x5min, high resolution 30-second)
+            [default: %(default)s]
+            """,
+        action="store_true",
+        dest="hres_soitex",
         default=False,
     )
     parser.add_argument(
@@ -245,7 +257,8 @@ def main ():
     potveg = args.potveg_flag
     glc_nec = args.glc_nec
     merge_gis = args.merge_gis
-    if args.hres_flag:
+
+    if args.hres_pft:
         if (start_year == 1850 and end_year == 1850) or \
            (start_year == 2005 and end_year == 2005):
             hires_pft = 'on'
@@ -254,6 +267,12 @@ def main ():
             sys.exit(5)
     else:
         hires_pft = 'off'
+
+    if args.hres_soitex:
+        hires_soitex = 'on'
+    else:
+        hires_soitex = 'off'
+
     verbose = args.verbose
 
     if force_model_mesh_file != 'none':
@@ -319,6 +338,7 @@ def main ():
 
     # create attribute list for parsing xml file
     attribute_list = {'hires_pft':hires_pft,
+                      'hires_soitex':hires_soitex,
                       'pft_years':pft_years,
                       'pft_years_ssp':pft_years_ssp,
                       'ssp_rcp':ssp_rcp,
@@ -390,6 +410,10 @@ def main ():
                 new_key = f"{child1.tag}_urban"
                 rawdata_files[new_key] = os.path.join(input_path, item.text)
 
+            if item.tag == 'lookup_filename':
+                new_key = f"{child1.tag}_lookup"
+                rawdata_files[new_key] = os.path.join(input_path, item.text)
+
     # determine output mesh
     tree2 = ET.parse('../../ccs_config/component_grids_nuopc.xml')
     root = tree2.getroot()

tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml

@@ -20,16 +20,9 @@
   </mksrf_flai>
 
   <!-- ======================== -->
-  <!-- soil properties: forganic, fmax, soil-texture and soil color-->
+  <!-- soil properties: fmax, soil-texture (sand/clay, orgc), and soil color-->
   <!-- ======================== -->
 
-  <mksrf_forganic>
-    <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_organic_10level_5x5min_ISRIC-WISE-NCSCD_nlev7_c120830.nc</data_filename>
-      <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_5x5min_nomask_c200129.nc</mesh_filename>
-    </entry>
-  </mksrf_forganic>
-
   <!-- <mksrf_firrig> -->
   <!--   <entry> -->
   <!--     <data_filename>lnd/clm2/rawdata/mksrf_irrig_2160x4320_simyr2000.c110527.nc</data_filename> -->
@@ -50,9 +43,15 @@
 
   <mksrf_fsoitex>
     <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_soitex.10level.c010119.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/mksrf_soil_mapunits_5x5min_WISE.c220330.nc</data_filename>
+      <lookup_filename>lnd/clm2/rawdata/mksrf_soil_lookup.10level.WISE.c220330.nc</lookup_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_5x5min_nomask_c200129.nc</mesh_filename>
     </entry>
+    <entry hires_soitex='on'>
+      <data_filename>lnd/clm2/rawdata/mksrf_soil_mapunits_30sec_WISE.c220330.nc</data_filename>
+      <lookup_filename>lnd/clm2/rawdata/mksrf_soil_lookup.10level.WISE.c220330.nc</lookup_filename>
+      <mesh_filename>lnd/clm2/rawdata/mksrf_soil_mapunits_30sec_WISE.c220330.nc</mesh_filename>
+    </entry>
   </mksrf_fsoitex>
 
   <mksrf_fmax>

tools/mksurfdata_esmf/src/CMakeLists.txt

@@ -19,7 +19,6 @@ set(SRCFILES mkagfirepkmonthMod.F90
              mkinputMod.F90
              mklaiMod.F90
              mklanwatMod.F90
-             mkorganicMod.F90
              mkpeatMod.F90
              mkpioMod.F90
              mkpftMod.F90

tools/mksurfdata_esmf/src/mkfileMod.F90

@@ -179,8 +179,6 @@ subroutine mkfile_define_atts(pioid, dynlanduse)
     rcode = pio_put_att(pioid, pio_global, 'mesh_soil_texture_file', trim(str))
     str = get_filename(mksrf_fsoicol_mesh)
     rcode = pio_put_att(pioid, pio_global, 'mesh_soil_color_file', trim(str))
-    str = get_filename(mksrf_forganic_mesh)
-    rcode = pio_put_att(pioid, pio_global, 'mesh_soil_organic_file', trim(str))
     str = get_filename(mksrf_furban_mesh)
     rcode = pio_put_att(pioid, pio_global, 'mesh_urban_file', trim(str))
     str = get_filename(mksrf_fmax_mesh)
@@ -216,11 +214,11 @@ subroutine mkfile_define_atts(pioid, dynlanduse)
        str = get_filename(mksrf_fsoicol)
        rcode = pio_put_att(pioid, pio_global, 'soil_color_raw_data_file_name', trim(str))
        str = get_filename(mksrf_fsoitex)
-       rcode = pio_put_att(pioid, pio_global, 'soil_texture_raw_data_file_name', trim(str))
+       rcode = pio_put_att(pioid, pio_global, 'soil_texture_mapunit_raw_data_file_name', trim(str))
+       str = get_filename(mksrf_fsoitex_lookup)
+       rcode = pio_put_att(pioid, pio_global, 'soil_texture_lookup_raw_data_file_name', trim(str))
        str = get_filename(mksrf_fmax)
        rcode = pio_put_att(pioid, pio_global, 'fmax_raw_data_file_name', trim(str))
-       str = get_filename(mksrf_forganic)
-       rcode = pio_put_att(pioid, pio_global, 'organic_matter_raw_data_file_name', trim(str))
        str = get_filename(mksrf_fvocef)
        rcode = pio_put_att(pioid, pio_global, 'VOC_EF_raw_data_file_name', trim(str))
     end if
@@ -261,18 +259,18 @@ subroutine mkfile_define_vars(pioid, dynlanduse)
        call mkpio_def_spatial_var(pioid=pioid, varname='SOIL_COLOR', xtype=PIO_INT, &
             long_name='soil color', units='unitless')
 
-       call mkpio_def_spatial_var(pioid=pioid, varname='PCT_SAND', xtype=xtype, &
+       call mkpio_def_spatial_var(pioid=pioid, varname='PCT_SAND', xtype=PIO_REAL, &
             lev1name='nlevsoi', &
             long_name='percent sand', units='unitless')
 
-       call mkpio_def_spatial_var(pioid=pioid, varname='PCT_CLAY', xtype=xtype, &
+       call mkpio_def_spatial_var(pioid=pioid, varname='PCT_CLAY', xtype=PIO_REAL, &
             lev1name='nlevsoi', &
             long_name='percent clay', units='unitless')
 
        call mkpio_def_spatial_var(pioid=pioid, varname='mapunits', xtype=PIO_INT, &
             long_name='soil texture map units', units='unitless')
 
-       call mkpio_def_spatial_var(pioid=pioid, varname='ORGANIC', xtype=xtype, &
+       call mkpio_def_spatial_var(pioid=pioid, varname='ORGANIC', xtype=PIO_REAL, &
             lev1name='nlevsoi', &
             long_name='organic matter density at soil levels', &
             units='kg/m3 (assumed carbon content 0.58 gC per gOM)')

tools/mksurfdata_esmf/src/mkinputMod.F90

@@ -44,13 +44,11 @@ module mkinputMod
   character(CX) , public    :: mksrf_fhrvtyp                = ' ' ! harvest data file name
   character(CX) , public    :: mksrf_fhrvtyp_mesh           = ' ' ! harvest mesh file name
 
-  character(CX) , public    :: mksrf_forganic               = ' ' ! organic matter data file name
-  character(CX) , public    :: mksrf_forganic_mesh          = ' ' ! organic matter mesh file name
-
   character(CX) , public    :: mksrf_fsoicol                = ' ' ! soil color data file name
   character(CX) , public    :: mksrf_fsoicol_mesh           = ' ' ! soil color mesh file name
 
-  character(CX) , public    :: mksrf_fsoitex                = ' ' ! soil texture data file name
+  character(CX) , public    :: mksrf_fsoitex                = ' ' ! soil texture mapunit data file name
+  character(CX) , public    :: mksrf_fsoitex_lookup         = ' ' ! soil texture lookup data file name
   character(CX) , public    :: mksrf_fsoitex_mesh           = ' ' ! soil texture mesh file name
 
   character(CX) , public    :: mksrf_fmax                   = ' ' ! fmax data file name
@@ -136,9 +134,8 @@ subroutine read_namelist_input()
          mksrf_fhrvtyp,             &
          mksrf_fhrvtyp_mesh,        &
          mksrf_fsoitex,             &
+         mksrf_fsoitex_lookup,      &
          mksrf_fsoitex_mesh,        &
-         mksrf_forganic,            &
-         mksrf_forganic_mesh,       &
          mksrf_fsoicol,             &
          mksrf_fsoicol_mesh,        &
          mksrf_fvocef,              &
@@ -224,14 +221,12 @@ subroutine read_namelist_input()
     call mpi_bcast (mksrf_fhrvtyp_mesh, len(mksrf_fhrvtyp_mesh), MPI_CHARACTER, 0, mpicom, ier)
 
     call mpi_bcast (mksrf_fsoitex, len(mksrf_fsoitex), MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (mksrf_fsoitex_lookup, len(mksrf_fsoitex_lookup), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (mksrf_fsoitex_mesh, len(mksrf_fsoitex_mesh), MPI_CHARACTER, 0, mpicom, ier)
 
     call mpi_bcast (mksrf_fmax, len(mksrf_fmax), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (mksrf_fmax_mesh, len(mksrf_fmax_mesh), MPI_CHARACTER, 0, mpicom, ier)
 
-    call mpi_bcast (mksrf_forganic, len(mksrf_forganic), MPI_CHARACTER, 0, mpicom, ier)
-    call mpi_bcast (mksrf_forganic_mesh, len(mksrf_forganic_mesh), MPI_CHARACTER, 0, mpicom, ier)
-
     call mpi_bcast (mksrf_fsoicol, len(mksrf_fsoicol), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (mksrf_fsoicol_mesh, len(mksrf_fsoicol_mesh), MPI_CHARACTER, 0, mpicom, ier)
 
@@ -347,12 +342,10 @@ subroutine write_namelist_input()
        write(ndiag,'(a)')' inland wetland from:        '//trim(mksrf_fwetlnd)
        write(ndiag,'(a)')' mesh for wetland            '//trim(mksrf_fwetlnd_mesh)
        write(ndiag,*)
-       write(ndiag,'(a)')' soil texture from:          '//trim(mksrf_fsoitex)
+       write(ndiag,'(a)')' soil texture mapunits from: '//trim(mksrf_fsoitex)
+       write(ndiag,'(a)')' soil texture (sand/clay, orgc) lookup: '//trim(mksrf_fsoitex_lookup)
        write(ndiag,'(a)')' mesh for soil texture       '//trim(mksrf_fsoitex_mesh)
        write(ndiag,*)
-       write(ndiag,'(a)')' soil organic from:          '//trim(mksrf_forganic)
-       write(ndiag,'(a)')' mesh for soil organic       '//trim(mksrf_forganic_mesh)
-       write(ndiag,*)
        write(ndiag,'(a)')' soil color from:            '//trim(mksrf_fsoicol)
        write(ndiag,'(a)')' mesh for soil color         '//trim(mksrf_fsoicol_mesh)
        write(ndiag,*)