Updates based on bug fixes and feedback.

Externals_CAM.cfg

@@ -17,7 +17,7 @@ required = True
 local_path = src/physics/ncar_ccpp
 protocol = git
 repo_url = https://github.com/mwaxmonsky/atmospheric_physics
-tag = 9705c32c2c2e9b47655a3a057d25b5acbed20210
+tag = 8e04841df78634fd38b6826af893485e0ecdbf8f
 required = True
 
 [externals_description]

src/data/generate_input_to_stdnames_update.py

@@ -0,0 +1,60 @@
+import argparse
+from collections import defaultdict
+from pathlib import Path
+from bs4 import BeautifulSoup
+import csv
+import re
+
+
+def parse_csv(csv_filepath):
+  datamap = defaultdict(set)
+  pattern = re.compile("\w+")
+  print(f"Opening {csv_filepath}")
+  with open(csv_filepath) as csvfile:
+    csvdata = csv.reader(csvfile)
+    for row in csvdata:
+      inputname = row[0].split(" ")[0]
+      standardnameMatch = pattern.fullmatch(row[5].split(" ")[0])
+      if csvdata.line_num < 432 and standardnameMatch and inputname and "Skipping" not in row[5] and "CCPP" not in row[5]:
+        print(f"Adding {inputname} under {standardnameMatch.string}")
+        # if standardnameMatch.string in datamap:
+        #   raise Exception(f"Found duplicate standard name {standardnameMatch.string} on line {csvdata.line_num}")
+        datamap[standardnameMatch.string].add(inputname)
+  return datamap
+
+
+
+def generate_stdname_xml(current_dict, output_filename):
+  xmltree = BeautifulSoup(features="xml")
+
+  entries = xmltree.new_tag("entries")
+  for k, v in current_dict.items():
+    entry = xmltree.new_tag("entry")
+    entry["stdname"] = k
+    names = xmltree.new_tag("ic_file_input_names")
+    for name in v:
+      namenode = xmltree.new_tag("ic_file_input_name")
+      namenode.string = name
+      names.append(namenode)
+    entry.append(names)
+    entries.append(entry)
+  xmltree.append(entries)
+  with open(output_filename, "w") as xmlout:
+    print(f"Creating new xml file : {output_filename}")
+    xmlout.write(xmltree.prettify())
+
+
+def main():
+  parser = argparse.ArgumentParser(description='')
+  parser.add_argument('--csv-file', type=str, default='CCPP Standard Names - Sheet1.csv', help='')
+  parser.add_argument('--current-map', type=str, default='stdnames_to_inputnames_dictionary.xml', help='')
+  parser.add_argument('--output-map', type=str, default='stdnames_to_inputnames_dictionary_new.xml', help='')
+
+  args = parser.parse_args()
+
+  current_csv_entries = parse_csv(args.csv_file)
+  generate_stdname_xml(current_csv_entries, args.output_map)
+
+
+if __name__=="__main__": 
+    main()

src/data/inputnames_to_stdnames.py

@@ -18,7 +18,7 @@ def write_new_ncdata_file(input_filename, output_filename, inputname_dict):
     base_cmd += f' {input_filename}'
     os.system(base_cmd)
 
-def parse_stdname_file(file_to_parse):
+def parse_stdname_file(file_to_parse, tphys):
     """Parse XML standard name dictionary"""
     with open(file_to_parse, encoding='utf-8') as fh1:
         try:
@@ -35,15 +35,17 @@ def parse_stdname_file(file_to_parse):
         for sub_element in entry:
             if sub_element.tag == "ic_file_input_names":
                 for input_name in sub_element:
-                    inputname_dict[input_name.text.strip()] = stdname
+                    if not input_name.text.startswith(tphys):
+                        inputname_dict[input_name.text.strip()] = stdname
+                    # end if startswith
                 # end for input_name
             # end if sub_element.tag
         # end if for sub_element in entry
     # end if for entry in root
     return inputname_dict
 
 
-def main(input_file, output_filename, stdname_file):
+def main(input_file, output_filename, stdname_file, tphys):
     """Parse standard name dictionary and then replace input name variables with stdnames"""
     if not os.path.isfile(input_file):
         print(f"Input file {input_file} does not exist")
@@ -74,7 +76,7 @@ def main(input_file, output_filename, stdname_file):
         #end if os.path.isdir(output_dir)
     #end if len(output_dir.strip())) == 0
     # Parse the standard name dictionary
-    inputname_dict = parse_stdname_file(stdname_file)
+    inputname_dict = parse_stdname_file(stdname_file, tphys)
     if not inputname_dict:
         print(f"Standard name dictionary {stdname_file} empty or not parse-able")
         return 6
@@ -97,9 +99,12 @@ def parse_command_line(arguments, description):
     parser.add_argument("--stdnames", type=str, required=True,
                         metavar='stdname file',
                         help="Full path to the standard names dictionary (e.g. stdnames_to_inputnames_dictionary.xml)")
+    parser.add_argument('--tphys', type=str, required=True,
+                        metavar='tphysac or tphybs group - REQUIRED',
+                        help='Group to convert to stdandard names')
     pargs = parser.parse_args(arguments)
     return pargs
 
 if __name__ == "__main__":
     ARGS = parse_command_line(sys.argv[1:], __doc__)
-    sys.exit(main(ARGS.input, ARGS.output, ARGS.stdnames))
+    sys.exit(main(ARGS.input, ARGS.output, ARGS.stdnames, ARGS.tphys))

src/data/registry.xml

@@ -356,13 +356,5 @@
       <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
       <initial_value>zvir</initial_value>
     </variable>
-    <variable local_name="heating_rate"
-              standard_name="tendency_of_dry_air_enthalpy_at_constant_pressure"
-              units="J kg-1 s-1" type="real" kind="kind_phys"
-              allocatable="allocatable">
-      <long_name>ff</long_name>
-      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
-      <ic_file_input_names>tendency_of_air_enthalpy</ic_file_input_names>
-    </variable>
   </file>
 </registry>

src/data/stdnames_to_inputnames_dictionary.xml

@@ -288,5 +288,9 @@
       <ic_file_input_name>n2ovmr</ic_file_input_name>
     </ic_file_input_names>
   </entry>
-
+  <entry stdname="standard_gravitational_acceleration">
+    <ic_file_input_names>
+      <ic_file_input_name>gravit</ic_file_input_name>
+    </ic_file_input_names>
+  </entry>
 </entries>

src/dynamics/utils/hycoef.F90

@@ -48,7 +48,7 @@ module hycoef
 
 !> \section arg_table_hycoef  Argument Table
 !! \htmlinclude hycoef.html
-real(kind_phys), public, :: etamid(pver)  ! hybrid coordinate - midpoints
+real(kind_phys), allocatable, public :: etamid(:)  ! hybrid coordinate - midpoints
 
 !=======================================================================
 contains
@@ -59,6 +59,7 @@ subroutine hycoef_init(file, psdry)
 !   use cam_history_support, only: add_hist_coord, add_vert_coord, formula_terms_t
    use physconst,    only: pref
    use string_utils, only: to_str
+   use phys_vars_init_check, only: mark_as_initialized
 
    !-----------------------------------------------------------------------
    !
@@ -126,10 +127,10 @@ subroutine hycoef_init(file, psdry)
       call endrun(subname//': allocate hybm(pver) failed with stat: '//to_str(iret))
    end if
 
-   !allocate(etamid(pver), stat=iret)
-   !if (iret /= 0) then
-   !   call endrun(subname//': allocate etamid(pver) failed with stat: '//to_str(iret))
-   !end if
+   allocate(etamid(pver), stat=iret)
+   if (iret /= 0) then
+      call endrun(subname//': allocate etamid(pver) failed with stat: '//to_str(iret))
+   end if
 
    allocate(hybd(pver), stat=iret)
    if (iret /= 0) then
@@ -329,6 +330,11 @@ subroutine hycoef_init(file, psdry)
       write(iulog,9830) pverp, hypi(pverp)
     end if
 
+    ! Mark etamid (input name) as initialized (by standard name sum_of_sigma_...)
+    call mark_as_initialized( &
+      'sum_of_sigma_pressure_hybrid_coordinate_a_coefficient_and_sigma_pressure_hybrid_coordinate_b_coefficient')
+
+
 9800 format( 1x, i3, 3p, 3(f10.4,10x) )
 9810 format( 1x, 3x, 3p, 3(10x,f10.4) )
 9820 format(1x,'reference pressures (Pa)')
@@ -397,26 +403,68 @@ subroutine hycoef_read(File)
    character(len=*), parameter :: routine = 'hycoef_read'
    !----------------------------------------------------------------------------
 
+   ! Set PIO to return error codes.
+   call pio_seterrorhandling(file, PIO_BCAST_ERROR, pio_errtype)
+
    ! PIO traps errors internally, no need to check ierr
 
    ierr = PIO_Inq_DimID(File, 'lev', lev_dimid)
+   if (ierr /= PIO_NOERR) then
+      ierr = PIO_Inq_DimID(File, 'reference_pressure_in_atmosphere_layer', lev_dimid)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading lev')
+      end if
+   end if
    ierr = PIO_Inq_dimlen(File, lev_dimid, flev)
    if (pver /= flev) then
       write(iulog,*) routine//': ERROR: file lev does not match model. lev (file, model):',flev, pver
       call endrun(routine//': ERROR: file lev does not match model.')
    end if
 
    ierr = PIO_Inq_DimID(File, 'ilev', lev_dimid)
+   if (ierr /= PIO_NOERR) then
+      ierr = PIO_Inq_DimID(File, 'reference_pressure_in_atmosphere_layer_at_interface', lev_dimid)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading ilev')
+      end if
+   end if
    ierr = PIO_Inq_dimlen(File, lev_dimid, filev)
    if (pverp /= filev) then
       write(iulog,*) routine//':ERROR: file ilev does not match model ilev (file, model):',filev, pverp
       call endrun(routine//':ERROR: file ilev does not match model.')
    end if
 
    ierr = pio_inq_varid(File, 'hyai', hyai_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_a_coefficient_at_interface', hyai_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading hyai')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hyam', hyam_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_a_coefficient', hyam_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading hyam')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hybi', hybi_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_b_coefficient_at_interface', hybi_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading hybi')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hybm', hybm_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_b_coefficient', hybm_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': reading hybm')
+      end if
+   end if
 
    ierr = pio_get_var(File, hyai_desc, hyai)
    ierr = pio_get_var(File, hybi_desc, hybi)
@@ -428,11 +476,13 @@ subroutine hycoef_read(File)
    end if
 
    ! Check whether file contains value for P0.  If it does then use it
-
-   ! Set PIO to return error codes.
-   call pio_seterrorhandling(file, PIO_BCAST_ERROR, pio_errtype)
-
    ierr = pio_inq_varid(file, 'P0', p0_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'reference_pressure', p0_desc)
+      !if (ierr /= PIO_NOERR) then
+      !   call endrun(routine//': reading P0')
+      !end if
+   end if
    if (ierr == PIO_NOERR) then
       ierr = pio_get_var(file, p0_desc, ps0)
       if (ierr /= PIO_NOERR) then