add thesis depth map application

examples/depth_map_part/input.yaml

@@ -0,0 +1,18 @@
+steps:
+- 3dthesis:
+    class: depth_map_part
+    application: thesis
+    configure:
+      res: 250.0e-6
+    execute:
+      np: 1
+data:
+  build:
+    datatype: Peregrine
+    name: myna_output
+    path: ..
+    parts:
+      P5:
+        layers: [51]
+myna:
+  workspace: ../example-workspace.yaml

examples/example-workspace.yaml

@@ -11,6 +11,12 @@ thesis:
          res: 25e-6
       execute:
          batch: True
+   depth_map_part:
+      executable: 3DThesis
+      configure:
+         res: 25e-6
+      execute:
+         batch: True
 exaca:
    microstructure_region:
       executable: ExaCA

src/myna/application/thesis/depth_map_part/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright (c) Oak Ridge National Laboratory.
+#
+# This file is part of Myna. For details, see the top-level license
+# at https://github.com/ORNL-MDF/Myna/LICENSE.md.
+#
+# License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause.
+#
+"""Application to use 3DThesis to generate a 2D map of the melt pool depth
+given the laser path and process conditions for a layer.
+"""
+
+from .app import ThesisDepthMapPart
+
+__all__ = ["ThesisDepthMapPart"]

src/myna/application/thesis/depth_map_part/app.py

@@ -0,0 +1,139 @@
+#
+# Copyright (c) Oak Ridge National Laboratory.
+#
+# This file is part of Myna. For details, see the top-level license
+# at https://github.com/ORNL-MDF/Myna/LICENSE.md.
+#
+# License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause.
+#
+"""Defines application behavior for the thesis/depth_map_part
+simulation type
+"""
+
+import os
+import glob
+import polars as pl
+from myna.application.thesis import Thesis, adjust_parameter, read_parameter
+
+
+class ThesisDepthMapPart(Thesis):
+    """Simulation type to simulate a map of the melt pool depth for layers of a part"""
+
+    def __init__(self):
+        super().__init__(output_suffix=".Solidification")
+        self.class_name = "depth_map_part"
+
+    def parse_mynafile_path_to_dict(self, mynafile):
+        """Parses the path of the output Myna file into a dictionary containing the
+        build, part, and layer names.
+
+        Path to the Myna file is expected to be in the format:
+            `working_dir/build/part/layer/stepname/mynafile`
+        """
+        dir_parts = os.path.dirname(mynafile).split(os.path.sep)
+        case_dict = {
+            "build": dir_parts[-4],
+            "part": dir_parts[-3],
+            "layer": dir_parts[-2],
+            "case_dir": os.path.dirname(mynafile),
+            "mynafile": mynafile,
+        }
+        return case_dict
+
+    def configure_case(self, myna_file):
+        """Configure a valid 3DThesis case from Myna data"""
+        # Load case information
+        case_info = self.parse_mynafile_path_to_dict(myna_file)
+
+        # Copy template case
+        self.copy_template_to_case(case_info["case_dir"])
+
+        # Update case parameters
+        self.update_case_parameters(
+            case_info["case_dir"], part=case_info["part"], layer=case_info["layer"]
+        )
+
+    def configure(self):
+        """Configure all simulations associated with the Myna step"""
+
+        # Get expected Myna output files
+        myna_files = self.settings["data"]["output_paths"][self.step_name]
+
+        # Run each case
+        for myna_file in myna_files:
+            self.configure_case(myna_file)
+
+    def execute_case(
+        self,
+        case_directory,
+        proc_list,
+        check_for_existing_results=True,
+    ):
+        """Run the individual 3DThesis case"""
+        # Update simulation threads
+        settings_file = os.path.join(case_directory, self.case_files["settings"])
+        adjust_parameter(settings_file, "MaxThreads", self.args.np)
+
+        # Check if output file exists
+        if check_for_existing_results:
+            output_files = glob.glob(os.path.join(case_directory, "Data", "*.csv"))
+            if (len(output_files) > 0) and not self.args.overwrite:
+                print(f"{case_directory} has already been simulated. Skipping.")
+                return proc_list or []
+
+        # Run Simulation
+        procs = proc_list or []
+        procs = self.run_thesis_case(case_directory, procs)
+
+        return procs or []
+
+    def execute(self):
+        """Execute all cases for the Myna step"""
+        # Get expected Myna output files
+        myna_files = self.settings["data"]["output_paths"][self.step_name]
+
+        # Run each case
+        proc_list = []
+        for case_dir in [os.path.dirname(x) for x in myna_files]:
+            proc_list = self.execute_case(case_dir, proc_list)
+
+        # Wait for any remaining processes
+        for proc in proc_list:
+            pid = proc.pid
+            print(f"- {pid=}: Waiting for simulation to complete")
+            proc.wait()
+            print(f"- {pid=}: Simulation complete")
+
+    def postprocess(self):
+        """Postprocess files from the executed 3DThesis cases for the Myna step"""
+
+        # Get expected Myna output files
+        myna_files = self.settings["data"]["output_paths"][self.step_name]
+
+        # Post-process results to convert to Myna format
+        for mynafile in myna_files:
+            # Get list of result file(s), accounting for MPI ranks
+            case_directory = os.path.dirname(mynafile)
+            case_input_file = os.path.join(case_directory, "ParamInput.txt")
+            output_name = read_parameter(case_input_file, "Name")[0]
+            result_file_pattern = os.path.join(
+                case_directory, "Data", f"{output_name}{self.output_suffix}.Final*.csv"
+            )
+            output_files = sorted(glob.glob(result_file_pattern))
+            if len(output_files) == 0:
+                print(
+                    "Warning: No depth map result files found for "
+                    f"{case_directory} with pattern {result_file_pattern}"
+                )
+                continue
+            for i, filepath in enumerate(output_files):
+                print(i, ":", filepath)
+                df = pl.read_csv(filepath)
+                df = df.filter(pl.col("z") == df["z"].max())
+                df = df.rename({"x": "x (m)", "y": "y (m)", "depth": "depth (m)"})
+                df = df.select(["x (m)", "y (m)", "depth (m)"])
+                if i == 0:
+                    df_all = df.clone()
+                else:
+                    df_all = pl.concat([df_all, df])
+            df_all.write_csv(mynafile)

src/myna/application/thesis/depth_map_part/configure.py

@@ -0,0 +1,25 @@
+#
+# Copyright (c) Oak Ridge National Laboratory.
+#
+# This file is part of Myna. For details, see the top-level license
+# at https://github.com/ORNL-MDF/Myna/LICENSE.md.
+#
+# License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause.
+#
+"""Script to be executed by the configure stage of `myna.core.workflow.run` to set up
+valid 3DThesis cases based on the specified user inputs and template
+"""
+
+from myna.application.thesis.depth_map_part.app import (
+    ThesisDepthMapPart,
+)
+
+
+def configure():
+    """Configure all case directories"""
+    app = ThesisDepthMapPart()
+    app.configure()
+
+
+if __name__ == "__main__":
+    configure()

src/myna/application/thesis/depth_map_part/execute.py

@@ -0,0 +1,25 @@
+#
+# Copyright (c) Oak Ridge National Laboratory.
+#
+# This file is part of Myna. For details, see the top-level license
+# at https://github.com/ORNL-MDF/Myna/LICENSE.md.
+#
+# License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause.
+#
+"""Script to be executed by the configure stage of `myna.core.workflow.run` to set up
+valid 3DThesis cases based on the specified user inputs and template
+"""
+
+from myna.application.thesis.depth_map_part.app import (
+    ThesisDepthMapPart,
+)
+
+
+def execute():
+    """Configure all case directories"""
+    app = ThesisDepthMapPart()
+    app.execute()
+
+
+if __name__ == "__main__":
+    execute()

src/myna/application/thesis/depth_map_part/postprocess.py

@@ -0,0 +1,25 @@
+#
+# Copyright (c) Oak Ridge National Laboratory.
+#
+# This file is part of Myna. For details, see the top-level license
+# at https://github.com/ORNL-MDF/Myna/LICENSE.md.
+#
+# License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause.
+#
+"""Script to be executed by the configure stage of `myna.core.workflow.run` to set up
+valid 3DThesis cases based on the specified user inputs and template
+"""
+
+from myna.application.thesis.depth_map_part.app import (
+    ThesisDepthMapPart,
+)
+
+
+def postprocess():
+    """Configure all case directories"""
+    app = ThesisDepthMapPart()
+    app.postprocess()
+
+
+if __name__ == "__main__":
+    postprocess()

src/myna/application/thesis/depth_map_part/template/Beam.txt

@@ -0,0 +1,11 @@
+Shape
+{
+	Width_X		130.0e-6
+	Width_Y		130.0e-6
+	Depth_Z		10.0e-6
+}
+Intensity
+{
+	Power	350
+	Efficiency	0.40
+}

src/myna/application/thesis/depth_map_part/template/Domain.txt

@@ -0,0 +1,12 @@
+X
+{
+	Res	100e-6
+}
+Y
+{
+	Res	100e-6
+}
+Z
+{
+	Res	10e-6
+}

src/myna/application/thesis/depth_map_part/template/Material.txt

@@ -0,0 +1,8 @@
+Constants
+{
+	T_0	298.15
+	T_L	1733.0
+	k	29.7658
+	c	592.555
+	p	7800.0
+}

src/myna/application/thesis/depth_map_part/template/Mode.txt

@@ -0,0 +1,5 @@
+Solidification
+{
+	Tracking	Surface
+	Timestep	1e-4
+}

src/myna/application/thesis/depth_map_part/template/Output.txt

@@ -0,0 +1,33 @@
+Grid
+{
+	x	1
+	y	1
+	z	1
+}
+Temperature
+{
+	T	0
+	T_hist	0
+}
+Solidification
+{
+	tSol	0
+	G	0
+	Gx	0
+	Gy	0
+	Gz	0
+	V	0
+	dTdt	0
+	eqFrac	0
+	RDF		0
+	numMelt	0
+	depth 	1
+	mpStats 0
+}
+Solidification+
+{
+	H	0
+	Hx	0
+	Hy	0
+	Hz	0
+}

src/myna/application/thesis/depth_map_part/template/ParamInput.txt

@@ -0,0 +1,14 @@
+Simulation
+{
+	Name		thermal_3dthesis
+	Mode		Mode.txt
+	Material	Material.txt
+	Beam		Beam.txt
+	Path		Path.txt
+}
+Options
+{
+	Domain		Domain.txt
+	Output		Output.txt
+	Settings	Settings.txt
+}

src/myna/application/thesis/depth_map_part/template/Settings.txt

@@ -0,0 +1,4 @@
+Compute
+{
+	MaxThreads	4
+}

src/myna/application/thesis/path.py

@@ -71,7 +71,7 @@ def loadData(
             self.setSize()
             self.setEnd()
         else:
-            self.data = pd.read_csv(file, sep="\s+")
+            self.data = pd.read_csv(file, sep=r"\s+")
             self.setSize()
             self.data["time"] = 0.0