Merge pull request #3 from CoryMartin-NOAA/feature/diff_parm

Added tasks to construct aero_diffparm.yaml from template.

parm/config/gfs/config.aeroanlgenb

@@ -9,5 +9,9 @@ echo "BEGIN: config.aeroanlgenb"
 source "${EXPDIR}/config.resources" aeroanlgenb
 
 export BMATYAML="${PARMgfs}/gdas/aero/berror/aero_diagb.yaml.j2"
+export DIFFUSIONYAML="${PARMgfs}/gdas/aero/berror/aero_diffusionparm.yaml.j2"
+export iterations=10
+export fixed value=1.0
+
 
 echo "END: config.aeroanlgenb"

ush/python/pygfs/task/aero_bmatrix.py

@@ -25,6 +25,7 @@ def __init__(self, config: Dict[str, Any]) -> None:
         _res_anl = int(self.config['CASE_ANL'][1:])
 
         _bmat_yaml = os.path.join(self.runtime_config.DATA, f"{self.runtime_config.CDUMP}.t{self.runtime_config['cyc']:02d}z.chem_diagb.yaml")
+        _diffusion_yaml = os.path.join(self.runtime_config.DATA, f"{self.runtime_config.CDUMP}.t{self.runtime_config['cyc']:02d}z.chem_diffusion.yaml")
 
         # Create a local dictionary that is repeatedly used across this class
         local_dict = AttrDict(
@@ -41,6 +42,7 @@ def __init__(self, config: Dict[str, Any]) -> None:
                 'APREFIX': f"{self.runtime_config.CDUMP}.t{self.runtime_config.cyc:02d}z.",  # TODO: CDUMP is being replaced by RUN
                 'GPREFIX': f"gdas.t{self.runtime_config.previous_cycle.hour:02d}z.",
                 'bmat_yaml': _bmat_yaml,
+                'diffusion_yaml': _diffusion_yaml,
             }
         )
 
@@ -63,6 +65,11 @@ def initialize(self: BMatrix) -> None:
         save_as_yaml(self.task_config.bmat_config, self.task_config.bmat_yaml)
         logger.info(f"Wrote bmat YAML to: {self.task_config.bmat_yaml}")
 
+        # generate diffusion parameters YAML file
+        logger.debug(f"Generate diffusion YAML file: {self.task_config.diffusion_yaml}")
+        save_as_yaml(self.task_config.diffusion_config, self.task_config.diffusion_yaml)
+        logger.info(f"Wrote diffusion YAML to: {self.task_config.diffusion_yaml}")
+
         # create output directory
         FileHandler({'mkdir': [os.path.join(self.task_config['DATA'], 'stddev')]}).sync()
 
@@ -95,9 +102,12 @@ def finalize(self) -> None:
         # copy full YAML from executable to ROTDIR
         src = os.path.join(self.task_config['DATA'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.chem_diagb.yaml")
         dest = os.path.join(self.task_config.COM_CHEM_ANALYSIS, f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.chem_diagb.yaml")
+        src_diffusion = os.path.join(self.task_config['DATA'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.chem_diffusion.yaml")
+        dest_diffusion = os.path.join(self.task_config.COM_CHEM_ANALYSIS, f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.chem_diffusion.yaml")
         yaml_copy = {
             'mkdir': [self.task_config.COM_CHEM_ANALYSIS],
-            'copy': [[src, dest]]
+            'copy': [[src, dest]],
+            'copy': [[src_diffusion, dest_diffusion]]
         }
         FileHandler(yaml_copy).sync()
 

ush/python/pygfs/task/bmatrix.py

@@ -27,6 +27,7 @@ def initialize(self) -> None:
         super().initialize()
         # all BMatrix tasks need a config
         self.task_config.bmat_config = self.get_bmat_config()
+        self.task_config.diffusion_config = self.get_diffusion_config()
 
     def finalize(self) -> None:
         super().finalize()
@@ -44,9 +45,31 @@ def get_bmat_config(self) -> Dict[str, Any]:
             a dictionary containing the fully rendered B matrix yaml configuration
         """
 
-        # generate JEDI YAML file
+        # generate JEDI YAML file for stddev
         logger.info(f"Generate B Matrix YAML config: {self.task_config.bmat_yaml}")
         bmat_config = parse_j2yaml(self.task_config.BMATYAML, self.task_config, searchpath=self.gdasapp_j2tmpl_dir)
         logger.debug(f"BMAT config:\n{pformat(bmat_config)}")
 
         return bmat_config
+
+    def get_diffusion_config(self) -> Dict[str, Any]:
+        """Compile a dictionary of diffusion operator configuration from DIFFUSIONYAML template file
+
+        Parameters
+        ----------
+        diffusion_iter
+        fixed_val
+        horiz_len
+
+        Returns
+        ----------
+        diffusion_config : Dict
+            a dictionary containing the fully rendered diffusion operator yaml configuration
+        """
+
+        # generate JEDI YAML file for diffusion parameters
+        logger.info(f"Generate Diff Parmameter YAML config: {self.task_config.diffusion_yaml}")
+        diffusion_config = parse_j2yaml(self.task_config.DIFFUSIONYAML, self.task_config, searchpath=self.gdasapp_j2tmpl_dir)
+        logger.debug(f"DIFFUSION config:\n{pformat(diffusion_config)}")
+
+        return diffusion_config