Merge tag 'rtm1_0_67' into buildlib_update

basetype wasn't declared and needed to be. Also add more "implicit none"
statements in. Remove the deletion of "rtm.input_data_list" file, as cime
now does this. Remove the option of setting single-precision
history output, as it sometimes has numerical conversion issues. The
real solution for it should be to keep a single-precision history
buffer that then outputs at the same precision as stored, rather than
converting just before. This would trigger issues with the conversion
earlier.

Changes ported from mosart/ESCOMP#15 to rtm. Run pylint through buildlib/buildnml,
changes for fill value needed for pio2. Also use the floor operator
for a specific integer divide as python3 turns it into reals.

Add CODE_OF_CONDUCT.md

cime_config/buildlib

@@ -1,6 +1,10 @@
 #!/usr/bin/env python
-
-import os, shutil, sys, glob
+"""
+Build the mosart component library
+"""
+#pylint: disable=unused-wildcard-import, wildcard-import, multiple-imports
+#pylint: disable=wrong-import-position, invalid-name, too-many-locals
+import os, sys
 
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
@@ -23,25 +27,25 @@ def _build_rtm():
 
     with Case(caseroot) as case:
         casetools = case.get_value("CASETOOLS")
-        gmake_j   = case.get_value("GMAKE_J")
-        gmake     = case.get_value("GMAKE")
+        gmake_j = case.get_value("GMAKE_J")
+        gmake = case.get_value("GMAKE")
 
         # create Filepath file
         objroot = case.get_value("OBJROOT")
-        filepath_file = os.path.join(objroot,"rof","obj","Filepath")
+        filepath_file = os.path.join(objroot, "rof", "obj", "Filepath")
         if not os.path.isfile(filepath_file):
             srcroot = case.get_value("SRCROOT")
             caseroot = case.get_value("CASEROOT")
-            paths = [ os.path.join(caseroot,"SourceMods","src.rtm"),
-                      os.path.join(srcroot,"components","rtm","src","riverroute"),
-                      os.path.join(srcroot,"components","rtm","src","cpl")]
+            paths = [os.path.join(caseroot, "SourceMods", "src.rtm"),
+                     os.path.join(srcroot, "components", "rtm", "src", "riverroute"),
+                     os.path.join(srcroot, "components", "rtm", "src", "cpl")]
 
             with open(filepath_file, "w") as filepath:
                 filepath.write("\n".join(paths))
                 filepath.write("\n")
 
         # build the library
-        complib = os.path.join(libroot,"librof.a")
+        complib = os.path.join(libroot, "librof.a")
         makefile = os.path.join(casetools, "Makefile")
 
         cmd = "{} complib -j {} MODEL=rtm COMPLIB={} -f {} {}" \
@@ -50,7 +54,7 @@ def _build_rtm():
         rc, out, err = run_cmd(cmd, from_dir=bldroot)
         expect(rc == 0, "Command %s failed rc=%d\nout=%s\nerr=%s" % (cmd, rc, out, err))
 
-        logger.info("Command %s completed with output %s\nerr %s" ,cmd, out, err)
+        logger.info("Command %s completed with output %s\nerr %s", cmd, out, err)
 
 ###############################################################################
 

cime_config/buildnml

@@ -8,8 +8,8 @@
 
 # Disable these because this is our standard setup
 # pylint: disable=wildcard-import,unused-wildcard-import,wrong-import-position
-
-import os, shutil, sys, glob
+# pylint: disable=multiple-imports
+import os, shutil, sys
 
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
@@ -20,13 +20,13 @@ from standard_script_setup import *
 from CIME.case import Case
 from CIME.nmlgen import NamelistGenerator
 from CIME.utils import expect
-from CIME.buildnml import create_namelist_infile
+from CIME.buildnml import create_namelist_infile, parse_input
 
 logger = logging.getLogger(__name__)
 
 # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
 ####################################################################################
-def _create_namelist(case, confdir, inst_string, infile, nmlgen):
+def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path):
 ####################################################################################
     """Write out the namelist for this component.
 
@@ -40,7 +40,7 @@ def _create_namelist(case, confdir, inst_string, infile, nmlgen):
     #----------------------------------------------------
     config = {}
     config['rtm_mode'] = case.get_value("RTM_MODE")
-    config['rtm_flood_mode']  = case.get_value("RTM_FLOOD_MODE")
+    config['rtm_flood_mode'] = case.get_value("RTM_FLOOD_MODE")
     config['clm_accelerated_spinup'] = case.get_value("CLM_ACCELERATED_SPINUP")
     config['rof_grid'] = case.get_value("ROF_GRID")
     config['lnd_grid'] = case.get_value("LND_GRID")
@@ -52,14 +52,7 @@ def _create_namelist(case, confdir, inst_string, infile, nmlgen):
     # Check for incompatible options.
     #----------------------------------------------------
     if config["rof_grid"] == "null" and config["rtm_mode"] != "NULL":
-        expect (False, "ROF_GRID is null RTM_MODE not NULL")
-
-    #----------------------------------------------------
-    # Clear out old data.
-    #----------------------------------------------------
-    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "rtm.input_data_list")
-    if os.path.exists(data_list_path):
-        os.remove(data_list_path)
+        expect(False, "ROF_GRID is null RTM_MODE not NULL")
 
     #----------------------------------------------------
     # Initialize namelist defaults
@@ -74,10 +67,10 @@ def _create_namelist(case, confdir, inst_string, infile, nmlgen):
     if run_type == 'branch' or run_type == 'hybrid':
         run_refcase = case.get_value("RUN_REFCASE")
         run_refdate = case.get_value("RUN_REFDATE")
-        run_tod     = case.get_value("RUN_REFTOD")
+        run_tod = case.get_value("RUN_REFTOD")
         filename = "%s.rtm%s.r.%s-%s.nc" %(run_refcase, inst_string, run_refdate, run_tod)
         rundir = case.get_value("RUNDIR")
-        if not os.path.exists(os.path.join(rundir, filename ) ):
+        if not os.path.exists(os.path.join(rundir, filename)):
             filename = "%s.rtm.r.%s-%s.nc" %(run_refcase, run_refdate, run_tod)
 
         if run_type == "hybrid":
@@ -90,7 +83,7 @@ def _create_namelist(case, confdir, inst_string, infile, nmlgen):
         else:
             nmlgen.add_default("finidat_rtm")
 
-    ncpl_base_period  = case.get_value('NCPL_BASE_PERIOD')
+    ncpl_base_period = case.get_value('NCPL_BASE_PERIOD')
     if ncpl_base_period == 'hour':
         basedt = 3600
     elif ncpl_base_period == 'day':
@@ -113,10 +106,10 @@ def _create_namelist(case, confdir, inst_string, infile, nmlgen):
 
     rof_ncpl = case.get_value("ROF_NCPL")
     if basedt % rof_ncpl != 0:
-        expect(False, "rof_ncpl %s doesn't divide evenly into basedt \n" 
+        expect(False, "rof_ncpl %s doesn't divide evenly into basedt %s\n"
                %(rof_ncpl, basedt))
     else:
-        rtm_tstep = basedt / rof_ncpl
+        rtm_tstep = basedt // rof_ncpl
     nmlgen.set_value("rtm_tstep", value=rtm_tstep)
 
     #----------------------------------------------------
@@ -130,26 +123,26 @@ def buildnml(case, caseroot, compname):
 ###############################################################################
     """Build the namelist """
 
-    # Build the component namelist 
+    # Build the component namelist
     if compname != "rtm":
         raise AttributeError
 
-    srcroot = case.get_value("SRCROOT") 
+    srcroot = case.get_value("SRCROOT")
     rundir = case.get_value("RUNDIR")
     ninst = case.get_value("NINST_ROF")
 
     # Determine configuration directory
-    confdir = os.path.join(caseroot,"Buildconf","rtmconf")
+    confdir = os.path.join(caseroot, "Buildconf", "rtmconf")
     if not os.path.isdir(confdir):
         os.makedirs(confdir)
 
     #----------------------------------------------------
-    # Construct the namelist generator 
+    # Construct the namelist generator
     #----------------------------------------------------
     # determine directory for user modified namelist_definitions.xml and namelist_defaults.xml
     user_xml_dir = os.path.join(caseroot, "SourceMods", "src.rtm")
-    expect (os.path.isdir(user_xml_dir),
-            "user_xml_dir %s does not exist " %user_xml_dir)
+    expect(os.path.isdir(user_xml_dir),
+           "user_xml_dir %s does not exist "%user_xml_dir)
 
     # NOTE: User definition *replaces* existing definition.
     namelist_xml_dir = os.path.join(srcroot, "components", "rtm", "cime_config")
@@ -163,6 +156,12 @@ def buildnml(case, caseroot, compname):
     # Create the namelist generator object - independent of instance
     nmlgen = NamelistGenerator(case, definition_file)
 
+    #----------------------------------------------------
+    # Clear out old data.
+    #----------------------------------------------------
+    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "mosart.input_data_list")
+    if os.path.exists(data_list_path):
+        os.remove(data_list_path)
     #----------------------------------------------------
     # Loop over instances
     #----------------------------------------------------
@@ -175,9 +174,9 @@ def buildnml(case, caseroot, compname):
 
         # If multi-instance case does not have restart file, use
         # single-case restart for each instance
-        rpointer = "rpointer.rof" 
-        if (os.path.isfile(os.path.join(rundir,rpointer)) and
-            (not os.path.isfile(os.path.join(rundir,rpointer + inst_string)))):
+        rpointer = "rpointer.rof"
+        if (os.path.isfile(os.path.join(rundir, rpointer)) and
+                (not os.path.isfile(os.path.join(rundir, rpointer + inst_string)))):
             shutil.copy(os.path.join(rundir, rpointer),
                         os.path.join(rundir, rpointer + inst_string))
 
@@ -193,20 +192,20 @@ def buildnml(case, caseroot, compname):
         create_namelist_infile(case, user_nl_file, infile)
         namelist_infile = [infile]
 
-        # create namelist 
-        _create_namelist(case, confdir, inst_string, namelist_infile, nmlgen)
+        # create namelist
+        _create_namelists(case, confdir, inst_string, namelist_infile, nmlgen, data_list_path)
 
         # copy namelist files and stream text files, to rundir
         if os.path.isdir(rundir):
-            file_src  = os.path.join(confdir, 'rof_in')
+            file_src = os.path.join(confdir, 'rof_in')
             file_dest = os.path.join(rundir, 'rof_in')
             if inst_string:
                 file_dest += inst_string
             shutil.copy(file_src, file_dest)
-            
+
             for txtfile in glob.glob(os.path.join(confdir, "*txt*")):
                 shutil.copy(txtfile, rundir)
-                
+
 ###############################################################################
 def _main_func():
 

cime_config/namelist_definition_rtm.xml

@@ -205,13 +205,13 @@
     <type>integer(6)</type>
     <category>history</category>
     <group>rtm_inparm</group>
-    <valid_values>1,2</valid_values>
+    <valid_values>1</valid_values>
     <desc>
       Per tape series  history file density (i.e. output precision) 
-      1=double precision, 2=single precision
+      1=double precision, 2=single precision (NOT functional)
     </desc>
     <values>
-      <value>2</value>
+      <value>1</value>
     </values>
   </entry>
 

docs/ChangeLog

@@ -1,3 +1,27 @@
+===============================================================
+Tag name:  rtm1_0_67
+Originator(s): erik
+Date: May 07, 2019
+One-line Summary: Move release-cesm2.0.02 to master
+
+basetype wasn't declared and needed to be. Also add more "implicit none"
+statements in. Remove the deletion of "rtm.input_data_list" file, as cime
+now does this. Remove the option of setting single-precision
+history output, as it sometimes has numerical conversion issues. The
+real solution for it should be to keep a single-precision history
+buffer that then outputs at the same precision as stored, rather than
+converting just before. This would trigger issues with the conversion
+earlier.
+
+Changes ported from mosart/#15 to rtm. Run pylint through buildlib/buildnml,
+changes for fill value needed for pio2. Also use the floor operator
+for a specific integer divide as python3 turns it into reals.
+
+Add CODE_OF_CONDUCT.md
+
+Testing:
+   rtm testlist on hobart and cheyenne (PASS)
+
 ===============================================================
 Tag name:  rtm1_0_66
 Originator(s): erik

docs/release-cesm2.0.ChangeLog

@@ -0,0 +1,111 @@
+===============================================================
+Tag name:  release-cesm2.0.02
+Originator(s): erik
+Date: Oct 19, 2018
+One-line Summary: Fix some issues with nag compiler, remove rtmhist_ndens==2 option
+
+basetype wasn't declared and needed to be. Also add more "implicit none"
+statements in. Remove the deletion of "rtm.input_data_list" file, as cime
+now does this. Remove the option of setting single-precision
+history output, as it sometimes has numerical conversion issues. The
+real solution for it should be to keep a single-precision history
+buffer that then outputs at the same precision as stored, rather than
+converting just before. This would trigger issues with the conversion
+earlier.
+
+RTM Master Tag This Corresponds To: rtm1_0_66 (with changes)
+
+Software Changes since last release: release-cesm2.0.01
+  * Fix issues with nag compiler
+  * Remove single precision output option
+
+Science Changes since last release: release-cesm2.0.00
+  * None
+
+Changes to User Interface since: release-cesm2.0.00
+  * rtmhist_ndens can no longer equal 2.
+
+Pull Requests that document the changes (include PR ids):
+   #10 -- Fix some issues with nag compiler
+
+Testing:
+   rtm testlist on hobart and cheyenne (PASS)
+
+
+===============================================================
+Tag name:  release-cesm2.0.01
+Originator(s): erik
+Date: Oct 10, 2018
+One-line Summary: pylint cleanup, and fill value changes for pio2
+
+Changes ported from mosart/#15 to rtm. Run pylint through buildlib/buildnml,
+changes for fill value needed for pio2. Also use the floor operator
+for a specific integer divide as python3 turns it into reals.
+
+RTM Master Tag This Corresponds To: rtm1_0_66 (with changes)
+
+Purpose:
+
+Software Changes since last release: release-cesm2.0.00
+  * pylint on buildlib/buildnml
+  * fill value changes needed for pio2 from the mosart changes
+  * Use floor operator in buildnml for an integer division
+
+Science Changes since last release: release-cesm2.0.00
+  * None
+
+Changes to User Interface since: release-cesm2.0.00
+  * None
+
+Pull Requests that document the changes (include PR ids):
+   #9 -- Same changes on mosart fill-value and pylint cleanup on rtm enhancement
+
+Testing:
+   rtm testlist on hobart and cheyenne (PASS)
+
+===============================================================
+Tag name:  release-cesm2.0.00
+Originator(s): erik
+Date: May 21, 2018
+One-line Summary: First CESM2.0 release version, identical to rtm1_0_66
+
+Purpose:
+
+First RTM version for the CESM2.0 release. This tag is identical to rtm1_0_66
+
+RTM Master Tag This Corresponds To: rtm1_0_66
+
+Software Changes since last release: rtm1_0_30
+
+  * Add in model_doi_url read in from infodata from coupler.
+  * RTM own's version of config_archive.xml
+  * Remove old rof_comp_esmf
+  * Remove revision_id from output files
+  * Convert testlist format to version 2, and use new Clm5 compset names.
+  * Remove yellowstone tests.
+  * Update config_component.xml to version 3 format.
+  * if NINST_RTM > 1, will check if REFCASE has instance name and use it, otherwise without it.
+  * I/O fixes from Jim Edwards
+  * Update buildnamelist to cime5 python namelist infrastructure
+  * Add time period frequency to output history file
+  * Remove ESMF top level coupler interface and tests
+  * Have RTM react to CLM_ACCELERATED_SPINUP setting from CLM and turn itself off
+  * Update to newer cime versions
+  * Move tests from goldbach to hobart
+  * Don't assume that direction files are global
+  * NAG6.0 requires additional pointers to be nullified
+  * readnamelist on mastertask only
+  * PIO2 Compatibility changes
+  * address valgrind errors
+  * add SHR_ASSERT macros
+  * migration of cpl_share/, cpl_esmf/ and cpl_mct code into new cpl/ and introduction of rof_import_export.F90
+
+Science Changes since last release: rtm1_0_30
+
+  * Treat irrigation as a seperate flux
+  * Remove directo to ocean runnoff
+  * fix fthresh bug and refactor RtmFloodInit
+  * convert volr coupling field from state to flux
+  * RTM Master Tag this corresponds to: rtm1_0_66
+
+===============================================================