fixup missed issues from #130 and #137

src/myna/application/additivefoam/additivefoam.py

@@ -35,13 +35,6 @@ def __init__(self):
         if self.args.exec is None:
             self.args.exec = "additiveFoam"
 
-    def copy_template_to_dir(self, target_dir):
-        """Copies the specified template directory to the specified target directory"""
-        # Ensure directory structure to target exists
-        os.makedirs(os.path.dirname(target_dir), exist_ok=True)
-        if self.args.template is not None:
-            shutil.copytree(self.args.template, target_dir, dirs_exist_ok=True)
-
     def has_matching_template_mesh_dict(self, mesh_path, mesh_dict):
         """Checks if there is a usable mesh dictionary in the case directory
 

src/myna/application/additivefoam/solidification_region_reduced/app.py

@@ -410,7 +410,7 @@ def generate_resource_mesh(self, case_dict):
         """
 
         # Copy app template to the resource directory
-        self.copy_template_to_dir(case_dict["resource_template_dir"])
+        self.copy_template_to_case(case_dict["resource_template_dir"])
 
         # Generate coarse background mesh
         self.create_coarse_mesh(case_dict)
@@ -478,7 +478,7 @@ def execute_case(self, mynafile):
 
     def postprocess(self):
         """Postprocesses all cases"""
-        _, _, files_are_valid = self.sim_class_obj.get_output_files()
+        _, _, files_are_valid = self.component.get_output_files()
         if not all(files_are_valid):
             mynafiles = self.settings["data"]["output_paths"][self.step_name]
             for mynafile in mynafiles:
@@ -521,7 +521,7 @@ def postprocess_case(self, mynafile):
                     if len(datafiles) > 0:
                         # Header
                         process = self.start_subprocess(
-                            ["echo", "x,y,z,tm,ts,cr"],
+                            ["echo", "x (m),y (m),z (m),tm (s),ts (s),cr (k/s)"],
                             stdout=mf,
                             stderr=f,
                         )

src/myna/application/additivefoam/solidification_region_reduced/template/system/ExaCA

@@ -7,7 +7,7 @@
 ExaCA
 {
     type ExaCA;
-    libs ("libExaCAFunctionObject.so");
+    libs ("libadditiveFoamFunctionObjects.so");
 
     box         ( 0.0495 -0.0495 -0.0003 ) ( 0.0505 -0.0485 0 );
     dx          2.5e-6;

src/myna/application/additivefoam/solidification_region_reduced_stl/app.py

@@ -115,7 +115,7 @@ def generate_resource_mesh(self, case_dict):
         ]["file_local"]
 
         # Copy app template to the resource directory
-        self.copy_template_to_dir(case_dict["resource_template_dir"])
+        self.copy_template_to_case(case_dict["resource_template_dir"])
 
         # Generate coarse background mesh
         self.create_coarse_mesh(case_dict)

src/myna/application/additivefoam/solidification_region_reduced_stl/template/system/ExaCA

@@ -7,7 +7,7 @@
 ExaCA
 {
     type ExaCA;
-    libs ("libExaCAFunctionObject.so");
+    libs ("libadditiveFoamFunctionObjects.so");
 
     box         ( 0.172 0.072 -0.0003 ) ( 0.173 0.073 0 );
     dx          2.5e-6;

src/myna/application/cubit/cubit.py

@@ -10,7 +10,6 @@
 inherited by all Myna Component applications in this module."""
 
 import os
-import shutil
 from myna.core.app.base import MynaApp
 
 
@@ -50,10 +49,3 @@ def __init__(self):
             )
         else:
             self.args.exec = original_executable_arg
-
-    def copy_template_to_dir(self, target_dir):
-        """Copies the specified template directory to the specified target directory"""
-        # Ensure directory structure to target exists
-        os.makedirs(os.path.dirname(target_dir), exist_ok=True)
-        if self.args.template is not None:
-            shutil.copytree(self.args.template, target_dir, dirs_exist_ok=True)

src/myna/application/deer/creep_timeseries_region/app.py

@@ -68,7 +68,7 @@ def configure_case(self, case_dir, exodus_file):
         Args:
             case_dir: directory to configure into a valid Deer case
             exodus_file: Exodus mesh file associated with the case"""
-        self.copy_template_to_dir(case_dir)
+        self.copy_template_to_case(case_dir)
         self.generate_orientation_file(case_dir, exodus_file)
         self.update_case_loading_parameters(case_dir, exodus_file)
 

src/myna/application/deer/deer.py

@@ -9,8 +9,6 @@
 """Define the application functionality for the base `DeerApp`, which should be
 inherited by all Myna Component applications in this module."""
 
-import os
-import shutil
 from myna.core.app.base import MynaApp
 
 
@@ -28,10 +26,3 @@ def __init__(self):
             help="Path to the root Moose install directory",
         )
         self.parse_known_args()
-
-    def copy_template_to_dir(self, target_dir):
-        """Copies the specified template directory to the specified target directory"""
-        # Ensure directory structure to target exists
-        os.makedirs(os.path.dirname(target_dir), exist_ok=True)
-        if self.args.template is not None:
-            shutil.copytree(self.args.template, target_dir, dirs_exist_ok=True)

src/myna/core/app/base.py

@@ -56,20 +56,6 @@ def __init__(self):
                 list(x.keys())[0] for x in self.settings["steps"]
             ].index(self.step_name)
 
-        # Check if there is a corresponding component class. This will be None if
-        # class name is not in the Component lookup dictionary
-        if self.class_name is not None:
-            self.sim_class_obj = None
-            try:
-                self.sim_class_obj = return_step_class(self.class_name, verbose=False)
-                self.sim_class_obj.apply_settings(
-                    self.settings["steps"][self.step_number],
-                    self.settings.get("data"),
-                    self.settings.get("myna"),
-                )
-            except KeyError:
-                pass
-
         # Set up argparse
         self.parser = argparse.ArgumentParser(
             description="Configure input files for specified Myna cases"
@@ -183,6 +169,23 @@ def template(self):
             return Path(self.path) / "template"
         return Path(self.args.template)
 
+    @property
+    def component(self):
+        """Return the corresponding component class. This will be None if
+        class name is not in the Component lookup dictionary"""
+        if self.class_name is not None:
+            obj = None
+            try:
+                obj = return_step_class(self.class_name, verbose=False)
+                obj.apply_settings(
+                    self.settings["steps"][self.step_number],
+                    self.settings.get("data"),
+                    self.settings.get("myna"),
+                )
+                return obj
+            except KeyError:
+                return obj
+
     def parse_known_args(self):
         """Parse known command line arguments to update self.args and apply
         any corrections"""
@@ -291,7 +294,7 @@ def copy_template_to_case(self, case_dir):
         try:
             case_dir_files = os.listdir(case_dir)
             case_dir_files.remove("myna_data.yaml")
-        except ValueError:
+        except (ValueError, FileNotFoundError):
             case_dir_files = []
 
         # Copy if there are no existing files in the case directory or overwrite is specified