Merge pull request #1259 from jedwards4b/index_in_namelist

Index in namelist
Adds support for namelist entries of the form foo(3) = 'a'

Test suite: scripts_regression_tests.py, --namelist-only tests for cesm prealpha and aux_clm45
Note there are some expected failures here due to bugs found in the process. One bug was that
for multi-instance cases all namelists were using the 0001 stream file and they each should have
a separate file. Another bug was that only changes in user_nl_d***_0001 were being used in all
instances (user_nl_d***_000n where n>1 was being ignored)
Test baseline: cesm2_0_alpha06g
Test namelist changes:
Test status: bit for bit

Fixes #1248
Fixes #1274

User interface changes?:

Code review: @jgfouca @mvertens @gold2718

scripts/lib/CIME/XML/namelist_definition.py

@@ -11,10 +11,11 @@
 # pylint:disable=wildcard-import,unused-wildcard-import
 
 import re
+import collections
 
 from CIME.namelist import fortran_namelist_base_value, \
     is_valid_fortran_namelist_literal, character_literal_to_string, \
-    expand_literal_list, Namelist
+    expand_literal_list, Namelist, get_fortran_name_only
 
 from CIME.XML.standard_module_setup import *
 from CIME.XML.entry_id import EntryID
@@ -306,7 +307,7 @@ def is_valid_value(self, name, value):
 
         # Check size of input array.
         if len(expand_literal_list(value)) > size:
-            return False
+            expect(False, "Value index exceeds variable size for variable %s, allowed array length is %s value array size is %s"%(name, size, len(expand_literal_list(value))))
         return True
 
     def _expect_variable_in_definition(self, name, variable_template):
@@ -342,21 +343,22 @@ def validate(self, namelist,filename=None):
         for group_name in namelist.get_group_names():
             for variable_name in namelist.get_variable_names(group_name):
                 # Check that the variable is defined...
-                self._expect_variable_in_definition(variable_name, variable_template)
+                qualified_variable_name = get_fortran_name_only(variable_name)
+                self._expect_variable_in_definition(qualified_variable_name, variable_template)
 
                 # Check if can actually change this variable via filename change
                 if filename is not None:
-                    self._user_modifiable_in_variable_definition(variable_name)
+                    self._user_modifiable_in_variable_definition(qualified_variable_name)
 
                 # and has the right group name...
-                var_group = self.get_group(variable_name)
+                var_group = self.get_group(qualified_variable_name)
                 expect(var_group == group_name,
                        (variable_template + " is in a group named %r, but should be in %r.") %
                        (str(variable_name), str(group_name), str(var_group)))
 
                 # and has a valid value.
                 value = namelist.get_variable_value(group_name, variable_name)
-                expect(self.is_valid_value(variable_name, value),
+                expect(self.is_valid_value(qualified_variable_name, value),
                        (variable_template + " has invalid value %r.") %
                        (str(variable_name), [str(scalar) for scalar in value]))
 
@@ -379,11 +381,12 @@ def dict_to_namelist(self, dict_, filename=None):
         groups = {}
         for variable_name in dict_:
             variable_lc = variable_name.lower()
-            self._expect_variable_in_definition(variable_lc, variable_template)
-            group_name = self.get_group(variable_lc)
+            qualified_varname = get_fortran_name_only(variable_lc)
+            self._expect_variable_in_definition(qualified_varname, variable_template)
+            group_name = self.get_group(qualified_varname)
             expect (group_name is not None, "No group found for var %s"%variable_lc)
             if group_name not in groups:
-                groups[group_name] = {}
+                groups[group_name] = collections.OrderedDict()
             groups[group_name][variable_lc] = dict_[variable_name]
         return Namelist(groups)
 

scripts/lib/CIME/buildnml.py

@@ -118,6 +118,5 @@ def create_namelist_infile(case, user_nl_file, namelist_infile, infile_text=""):
             lines_output.append(line)
 
     lines_output.append("/ \n")
-
     with open(namelist_infile, "w") as file_infile:
         file_infile.write("\n".join(lines_output))