adding regressiont ests

Author: delcmo

regression_test/exodiff_file.txt

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+DEFAULT TOLERANCE relative 1.E-8 absolute 1.E-7 floor 1.E-14
+COORDINATES absolute 1.E-12
+TIME STEPS absolute 1.E-14
+NODAL VARIABLES absolute 1.E-8

regression_test/pytest.ini

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+[pytest]
+markers =
+    push: marks tests that are to be run after pushing to branch (deselect with '-m "not push"')
+    daily: marks tests that are to be run daily (deselect with '-m "not daily"')
+    weekly: marks tests that are to be run weekly (deselect with '-m "not weekly"')
+    incompressible: marks tests for incompressible model.
+    mhd: marks for mhd model.
+    gpu: marks for regression tests to run on GPU node.

regression_test/rename_variables_exodus.py.in

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+# Import Python modules
+import sys
+import glob
+import argparse
+import os
+from os import path
+
+# Description:
+# This Python script implements logic to rename nodal and element variables
+# in Exodus files. The values remain un-changed. The changes in the Exodus
+# files are performed in place. Files to update are to be specified at the
+# command line. See documentation in the Wiki page under Software quality
+# assurance for further details.
+
+# Adding trilinos folder to the system path and import exodus3
+sys.path.insert(
+    0, '@TRILINOS_LIB@')
+import exodus3 as exodus
+
+# Argument parser
+parser = argparse.ArgumentParser(
+    description='Replace field names in Exodus files')
+parser.add_argument('-v',
+                    '--verbose',
+                    action='store_true',
+                    help='more verbose output')
+parser.add_argument('files',
+                    nargs='+',
+                    help='exodus file(s) to modify',
+                    metavar='file')
+parser.add_argument('-n',
+                    '--node',
+                    nargs=2,
+                    action='append',
+                    help='node variable',
+                    metavar=('old-name', 'new-name'))
+parser.add_argument('-e',
+                    '--element',
+                    nargs=2,
+                    action='append',
+                    help='element variable',
+                    metavar=('old-name', 'new-name'))
+args = parser.parse_args()
+
+# Assign variable based on parsed arguments
+nodal_list = args.node
+elem_list = args.element
+if nodal_list is None and elem_list is None:
+    print("\nPlease provide a list of node or element fields to replace.\n")
+    parser.print_help()
+    sys.exit()
+filename_list = args.files
+
+# Collect all Exodus files specified at the command line
+for f in filename_list:
+    if not os.path.isfile(f):
+        sys.exit(f"ERROR: The file '{f}' is not found.")
+
+
+# Verbose function (used when --verbose flag is passed to command line)
+def print_verbose(msg):
+    if args.verbose:
+        print(msg)
+
+
+# Funtion to replace fields
+def replace_field(exo, field_list, field_type):
+    print_verbose(f"\n\tLoop over {field_type} fields to replace:")
+    # Set `exo_put_node` function and field type
+    exo_put_node = lambda: None
+    if field_type == "nodal":
+        exo_put_node = exo.put_node_variable_name
+        field_type = "EX_NODAL"
+    elif field_type == "element":
+        exo_put_node = exo.put_element_variable_name
+        field_type = "EX_ELEM_BLOCK"
+    else:
+        exo.close()
+        sys.exit(
+            f"\t\tError: Current field type '{field_type}' is not supported. Field type options are 'nodal' or 'element'."
+        )
+
+    # Loop over fields to replace
+    exo_field_list = exo.get_variable_names(field_type)
+    field_not_found = []
+    for old_field, new_field in field_list:
+        print_verbose(f"\n\t\t\tField to replace: {old_field}...")
+        found = False
+        # Look for exact match
+        if old_field in exo_field_list:
+            index = exo_field_list.index(old_field) + 1
+            exo_put_node(new_field, index)
+            found = True
+            print_verbose(
+                f"\t\t\t...Field {old_field} found with index {index} and replaced with {new_field}."
+            )
+        if not found:
+            field_not_found.append(old_field)
+            print_verbose(f"\t\t\t...WARNING: field {old_field} not found.")
+    if field_not_found:
+        print_verbose(
+            f"\n\t\tWARNING: List of field(s) not found in the Exodus file {exo.fileName}:"
+        )
+        for old_field in field_not_found:
+            print_verbose(f"\t\t- {old_field}")
+
+    # Return list of fields not found
+    return field_not_found
+
+
+# Loop over file list
+full_report = {}
+sep = 100 * "*"
+for filename in filename_list:
+    print("\n" + sep)
+
+    # Create exodus object from file
+    exo = exodus.exodus(filename, mode='a')
+
+    nodal_field_not_found = None
+    elem_field_not_found = None
+
+    try:
+        # Nodal fields
+        if nodal_list is not None:
+            nodal_field_not_found = replace_field(exo, nodal_list, "nodal")
+
+        # Element fields
+        if elem_list is not None:
+            elem_field_not_found = replace_field(exo, elem_list, "element")
+    finally:
+        # Close exodus object
+        exo.close()
+
+    # Store data in report (dictionary)
+    full_report[filename] = {}
+    if nodal_field_not_found is not None:
+        full_report[filename]["nodal"] = nodal_field_not_found
+    if elem_field_not_found is not None:
+        full_report[filename]["element"] = elem_field_not_found
+
+# Print full report
+print("\n" + sep)
+print("Full report:")
+for filename in filename_list:
+    print(f"\tFile name: {filename}")
+    for key, values in full_report[filename].items():
+        if values:
+            print("\t\t" + key + " variables not updated:")
+            for v in values:
+                print(f"\t\t - {v}")
+        else:
+            print("\t\tall " + key + " variables updated.")

regression_test/test_incompressible/test_cavity/gold/incompressible_2d_triangular_cavity_Re100_solution.exo

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+version https://git-lfs.github.com/spec/v1
+oid sha256:9291bb12ce740d707a9cab981467d99678af8ff088fe5e3ee007053e9bf53852
+size 1274912

regression_test/test_incompressible/test_cavity/gold/incompressible_2d_triangular_cavity_Re400_solution.exo

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+version https://git-lfs.github.com/spec/v1
+oid sha256:9f58f9193002e8726c3fb3d66bc5d87b0c6f5767f76aa2dff9824f38693a5071
+size 1274912

regression_test/test_incompressible/test_cavity/gold/incompressible_2d_triangular_cavity_Re800_solution.exo

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+version https://git-lfs.github.com/spec/v1
+oid sha256:7077218589ce653a2a0f8f3cc7f3c775c4511c392588bb3890b451097bce68c9
+size 1274912

regression_test/test_incompressible/test_cavity/test_cavity.py

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+import sys
+import os
+import pytest
+
+import vertexcfd_test
+
+
+class TestCavity:
+    # setup method for class
+    @classmethod
+    def setup_class(self):
+        """ setup any state specific to the execution of the
+          given class (which usually contains tests)."""
+        print('\n***************** Setup class method *******************')
+
+        # Class variables (to not change)
+        self.mesh_file_path = vertexcfd_test.mesh_file_path
+        self.input_file_path = vertexcfd_test.input_file_path
+        self.vertexcfd_exec = vertexcfd_test.vertexcfd_exec
+        self.exodiff_exec = vertexcfd_test.exodiff_exec
+        self.main_path = vertexcfd_test.main_path
+        self.no_exodiff_file = None
+
+        # Change working directory to test directory
+        self.test_path = os.path.dirname(os.path.realpath(__file__))
+        os.chdir(self.test_path)
+
+    # teardown method for class
+    @classmethod
+    def teardown_class(self):
+        """ teardown any state that was previously
+          setup with a call to setup_class."""
+        print('\n****************** Teardown class method ******************')
+        # Change working directory back to main directory
+        os.chdir(vertexcfd_test.main_path)
+
+    # setup method for each function
+    def setup_method(self):
+        """ setup test."""
+        print('\nSetup method')
+        # Initialize input file, mesh file and output file names
+        self.input_file = None
+        self.mesh_file = None
+        self.output_file = None
+
+    # teardown method for each function
+    def teardown_method(self):
+        """ teardown test."""
+        print('\nTeardown method')
+        # Delete input file, mesh file and output file
+        vertexcfd_test.clean_working_directory(self)
+
+    #############################################################################
+    #############################################################################
+    #############################################################################
+    @pytest.mark.push
+    @pytest.mark.daily
+    @pytest.mark.weekly
+    @pytest.mark.incompressible
+    def test_2d_triangular_cavity(self, request):
+        # Parameters
+        mark_expr = request.config.option.markexpr
+        vertexcfd_options = ()
+        copy_xml_file = False
+
+        # default parameters to be used on 'push'
+        base_input_file = "incompressible_2d_triangular_cavity"
+        self.input_file = base_input_file + "_Re100.xml"
+        source_input_file = self.input_file
+        output_name = base_input_file + "_Re100_solution.exo"
+        nu = 0.8
+
+        if ("daily" in mark_expr):
+            self.input_file = base_input_file + "_Re400.xml"
+            output_name = base_input_file + "_Re400_solution.exo"
+            nu = 0.2
+        elif ("weekly" in mark_expr):
+            self.input_file = base_input_file + "_Re800.xml"
+            output_name = base_input_file + "_Re800_solution.exo"
+            nu = 0.1
+
+        xml_args_to_replace_list = []
+        xml_args_to_replace_list.append(
+            vertexcfd_test.xml_args_to_replace('Parameter', 'name',
+                                               'Kinematic viscosity', nu))
+        xml_args_to_replace_list.append(
+            vertexcfd_test.xml_args_to_replace('Parameter', 'name',
+                                               'Exodus Output File',
+                                               output_name))
+
+        vertexcfd_test.create_xml_file_from_base_file(
+            self, source_input_file, xml_args_to_replace_list)
+
+        # Parameters for exodiff executables
+        exodiff_options = ()
+
+        #### The following code should not be modified ####
+        # Run VertexCFD and call exodiff to compare to gold file
+        vertexcfd_test.run_test(self, vertexcfd_options, exodiff_options,
+                                copy_xml_file)

regression_test/test_incompressible/test_pipe_flow/exodiff_file.txt

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+DEFAULT TOLERANCE relative 1.E-8 absolute 1.E-7 floor 1.E-14
+COORDINATES absolute 1.E-12
+TIME STEPS absolute 1.E-8
+NODAL VARIABLES absolute 1.E-8

regression_test/test_incompressible/test_pipe_flow/gold/incompressible_2d_channel_periodic_solution.exo

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a4fa171ad1cb4cb9bc294c82c08c75b6642abdf2d0e0dc26d449e92ac23a5827
+size 688136

regression_test/test_incompressible/test_pipe_flow/gold/incompressible_2d_heated_channel_solution.exo

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:829352490118d2033883d361f46406a73f65b7c153dae48d80c9e18f3476cd9b
+size 932072