Merge pull request ESCOMP#50 from jedwards4b/neon_streams

### Description of changes Adds support for NEON tower data in datm. ### Specific notes Contributors other than yourself, if any: CMEPS Issues Fixed (include github issue #): Are there dependencies on other component PRs - [X] CIME (list) Requires branch neon_data_mode (PR ESMCI/cime#3850) - [ ] CMEPS (list) Are changes expected to change answers? - [X] bit for bit - [ ] different at roundoff level - [ ] more substantial Any User Interface Changes (namelist or namelist defaults changes)? - [ ] Yes - [X] No Testing performed: - [X] (required) aux_cdeps - machines and compilers: cheyenne intel - details (e.g. failed tests): SMS_Vnuopc_Ld5.TL319_t061.2000_DATM%JRA-1p4-2018_SLND_SICE_SOCN_SROF_SGLC_SWAV_SESP.cheyenne_intel fails in build with Invalid values ['CORE_IAF_JRA_1p4_2018'] - [ ] (optional) CESM prealpha test - machines and compilers - details (e.g. failed tests): Hashes used for testing: - [ ] CIME - repository to check out: https://github.com/ESCOMP/CESM.git - branch: master - hash:8b48a2e - [ ] CMEPS - repository to check out: https://github.com/ESCOMP/CESM.git - branch: master - hash: v0.9.0 - [ ] CESM - repository to check out: https://github.com/ESCOMP/CESM.git - branch: master - hash:
samsrabin · Apr 23, 2021 · eceb024 · eceb024
2 parents 5be2b5b + 6dc9e76
commit eceb024
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Showing 6 changed files with 84 additions and 28 deletions.
diff --git a/cime_config/stream_cdeps.py b/cime_config/stream_cdeps.py
@@ -42,7 +42,7 @@
  </stream_info>
 
 """
-        
+
 class StreamCDEPS(GenericXML):
 
     def __init__(self, infile, schema):
@@ -64,8 +64,12 @@ def create_stream_xml(self, stream_names, case, streams_xml_file, data_list_file
             stream_file.write('<file id="stream" version="2.0">\n')
         # write contents of stream file
         for stream_name in stream_names:
-            if stream_name:
-                self.stream_nodes = super(StreamCDEPS,self).get_child("stream_entry", {"name" : stream_name}, 
+            if stream_name.startswith("NEON."):
+                self.stream_nodes = super(StreamCDEPS,self).get_child("stream_entry", {"name" : "NEON.$NEONSITE"},
+                                                                     err_msg="No stream_entry {} found".format(stream_name))
+
+            elif stream_name:
+                self.stream_nodes = super(StreamCDEPS,self).get_child("stream_entry", {"name" : stream_name},
                                                                      err_msg="No stream_entry {} found".format(stream_name))
 
             # determine stream_year_first and stream_year_list
@@ -99,26 +103,26 @@ def create_stream_xml(self, stream_names, case, streams_xml_file, data_list_file
                         stream_datafiles = child.xml_element.text
                         stream_datafiles = self._resolve_values(case, stream_datafiles)
                         if 'first_year' in child.xml_element.attrib and 'last_year' in child.xml_element.attrib:
-                            value = child.xml_element.get('first_year') 
+                            value = child.xml_element.get('first_year')
                             value = self._resolve_values(case, value)
                             stream_year_first= int(value)
-                            value = child.xml_element.get('last_year') 
+                            value = child.xml_element.get('last_year')
                             value = self._resolve_values(case, value)
                             stream_year_last = int(value)
                             year_first = max(stream_year_first, data_year_first)
                             year_last = min(stream_year_last, data_year_last)
                             stream_datafiles = self._sub_paths(stream_datafiles, year_first, year_last)
                             stream_datafiles = stream_datafiles.strip()
                         #endif
-                        if stream_vars[node_name]: 
+                        if stream_vars[node_name]:
                             stream_vars[node_name] += "\n      " + self._add_xml_delimiter(stream_datafiles.split("\n"), "file")
                         else:
                             stream_vars[node_name] = self._add_xml_delimiter(stream_datafiles.split("\n"), "file")
 
                 elif (   node_name == 'stream_meshfile'
-                      or node_name == 'stream_mapalgo' 
-                      or node_name == 'stream_tintalgo' 
-                      or node_name == 'stream_taxmode' 
+                      or node_name == 'stream_mapalgo'
+                      or node_name == 'stream_tintalgo'
+                      or node_name == 'stream_taxmode'
                       or node_name == 'stream_dtlimit'):
                     attributes['model_grid'] = case.get_value("GRID")
                     attributes['compset'] = case.get_value("COMPSET")
@@ -130,7 +134,7 @@ def create_stream_xml(self, stream_names, case, streams_xml_file, data_list_file
                 elif node_name.strip():
                     # Get the other dependencies
                     stream_dict = self._add_value_to_dict(stream_vars, case, node)
-                        
+
             # append to stream xml file
             stream_file_text = _stream_nuopc_file_template.format(**stream_vars)
             with open(streams_xml_file, 'a') as stream_file:
@@ -193,7 +197,7 @@ def _get_input_file_hash(self, data_list_file):
 
     def _get_value_match(self, node, child_name, attributes=None, exact_match=False):
         '''
-        Get the first best match for multiple tags in child_name based on the 
+        Get the first best match for multiple tags in child_name based on the
         attributes input
 
         <values...>
@@ -396,5 +400,3 @@ def _add_xml_delimiter(list_to_deliminate, delimiter):
             #endif
         #endfor
         return "\n      ".join(list_to_deliminate)
-
-
diff --git a/datm/cime_config/buildnml b/datm/cime_config/buildnml
@@ -69,14 +69,20 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
 
     # Initialize namelist defaults
     config = {}
-    config['model_grid'] = model_grid
+    if 'CLM_USRDAT' in model_grid:
+        config['model_grid'] = 'CLM_USRDAT'
+        if case.get_value("NEONSITE"):
+            config['neon'] = "True"
+    else:
+        config['model_grid'] = model_grid
+
     config['datm_mode'] = datm_mode
     config['datm_co2_tseries'] = datm_co2_tseries
     config['datm_presaero'] = datm_presaero
 
     if case.get_value('PTS_LON'):
         scol_lon = float(case.get_value('PTS_LON'))
-    else: 
+    else:
         scol_lon = -999.
     if case.get_value('PTS_LAT'):
         scol_lat = float(case.get_value('PTS_LAT'))

diff --git a/datm/cime_config/namelist_definition_datm.xml b/datm/cime_config/namelist_definition_datm.xml
@@ -37,6 +37,9 @@
       <value datm_mode="1PT" model_grid="1x1_urbanc_alpha">
         1PT.urbanc_alpha
       </value>
+      <value datm_mode="1PT" model_grid="CLM_USRDAT" neon="True">
+        NEON.$NEONSITE
+      </value>
       <value datm_mode="CORE2_NYF" >
         CORE2_NYF.GISS,CORE2_NYF.GXGXS,CORE2_NYF.NCEP
       </value>
@@ -65,7 +68,7 @@
     <type>char</type>
     <category>datm</category>
     <group>datm_nml</group>
-    <valid_values>CLMNCEP,CORE2_NYF,CORE2_IAF,CORE_IAF_JRA,ERA5,CPLHIST</valid_values>
+    <valid_values>CLMNCEP,CORE2_NYF,CORE2_IAF,CORE_IAF_JRA,ERA5,CPLHIST,1PT</valid_values>
     <desc>
       general method that operates on the data.
       ----datamode = "CPLHIST"----
@@ -99,6 +102,7 @@
       active-land-only simulations.
       ----datamode = "ERA5"----
       Fifth generation ECMWF atmospheric reanalysis of the global climate
+      ----datamode = "CPLHIST" ----
     </desc>
     <values>
       <value datm_mode="CLM">
@@ -107,13 +111,10 @@
       <value datm_mode="1PT">
         CLMNCEP
       </value>
-      <value datm_mode="CORE2_NYF">
-        CORE2_NYF
-      </value>
       <value datm_mode="CORE2_IAF">
         CORE2_IAF
       </value>
-      <value datm_mode="CORE_IAF_JRA" >
+      <value datm_mode="CORE_IAF_JRA">
         CORE_IAF_JRA
       </value>
       <value datm_mode="ERA5">
@@ -122,6 +123,9 @@
       <value datm_mode="CPLHIST">
         CPLHIST
       </value>
+      <value>
+        $DATM_MODE
+      </value>
     </values>
   </entry>
 
@@ -135,7 +139,7 @@
     </desc>
     <values>
       <value>$ATM_DOMAIN_MESH</value>
-      <value single_column='true'>null</value> 
+      <value single_column='true'>null</value>
     </values>
   </entry>
 
@@ -149,7 +153,7 @@
     </desc>
     <values>
       <value>$ATM_DOMAIN_MESH</value>
-      <value single_column='true'>null</value> 
+      <value single_column='true'>null</value>
     </values>
   </entry>
 
@@ -162,7 +166,7 @@
     </desc>
     <values>
       <value>$ATM_NX</value>
-      <value single_column='true'>1</value> 
+      <value single_column='true'>1</value>
     </values>
   </entry>
 
@@ -175,7 +179,7 @@
     </desc>
     <values>
       <value>$ATM_NY</value>
-      <value single_column='true'>1</value> 
+      <value single_column='true'>1</value>
     </values>
   </entry>
 

diff --git a/datm/cime_config/stream_definition_datm.xml b/datm/cime_config/stream_definition_datm.xml
@@ -18,10 +18,10 @@
   %ym   => year-month from the range yearfirst to yearlast with all 12 months
   %ymd  => year-month-day from the range yearfirst to yearlast with all 12 months
 
-  ****** 
+  ******
   NOTE:
   any <file></file> entry that has %y, %ym or %ymd MUST have first_year and last_year syntax
-  ****** 
+  ******
 
   Each mode below, except for presaero, has a set of streams associated with it
   The presaero stream, is associated with all modes
@@ -194,6 +194,48 @@
   BC.QIAN.Precip
   -->
 
+  <!-- ===================================  -->
+  <!-- datm_mode 1PT NEON                   -->
+  <!-- ===================================  -->
+
+  <stream_entry name="NEON.$NEONSITE">
+    <stream_meshfile>
+      <meshfile>none</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file first_year="2018" last_year="2019">$DIN_LOC_ROOT/atm/cdeps/v1/$NEONSITE/%ym.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>PRECTmms Faxa_precn</var>
+      <var>FSDS     Faxa_swdn </var>
+      <var>ZBOT     Sa_z    </var>
+      <var>TBOT     Sa_tbot </var>
+      <var>WIND     Sa_wind </var>
+      <var>RH       Sa_rh   </var>
+      <var>PSRF     Sa_pbot </var>
+      <var>FLDS     Faxa_lwdn </var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>none</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>null</stream_vectors>
+    <stream_year_align>2018</stream_year_align>
+    <stream_year_first>2018</stream_year_first>
+    <stream_year_last>2019</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode>extend</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1e30</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
   <!-- ===================================  -->
   <!-- datm_mode CLMGSWP3v1                 -->
   <!-- ===================================  -->
@@ -209,7 +251,7 @@
       <var>FSDS Faxa_swdn</var>
     </stream_datavars>
     <stream_lev_dimname>null</stream_lev_dimname>
-    <stream_mapalgo> 
+    <stream_mapalgo>
       <mapalgo>bilinear</mapalgo>
     </stream_mapalgo>
     <stream_vectors>null</stream_vectors>

diff --git a/datm/datm_datamode_clmncep_mod.F90 b/datm/datm_datamode_clmncep_mod.F90
@@ -349,6 +349,9 @@ subroutine datm_datamode_clmncep_advance(masterproc, logunit, mpicom, rc)
        rtmp = maxval(Sa_tbot(:))
        call shr_mpi_max(rtmp, tbotmax, mpicom, 'datm_tbot', all=.true.)
        write(logunit,*) trim(subname),' tbotmax = ',tbotmax
+       if(tbotmax <= 0) then
+          call shr_sys_abort(subname//'ERROR: bad value in tbotmax')
+       endif
 
        ! determine anidrmax (see below for use)
        if (atm_prognostic) then

diff --git a/streams/dshr_strdata_mod.F90 b/streams/dshr_strdata_mod.F90
@@ -940,7 +940,6 @@ subroutine shr_strdata_advance(sdat, ymd, tod, logunit, istr, timers, rc)
        ! ---------------------------------------------------------
 
        do ns = 1,nstreams
-
           if (trim(sdat%stream(ns)%tinterpalgo) == 'coszen') then
 
              ! Determine stream lower bound index