Merge pull request #21 from tpgillam/tg/sif_header

Add ability to configure Header section

pyelmer/elmer.py

@@ -7,6 +7,7 @@
 of a dictionary called data.
 """
 
+import os
 import yaml
 
 
@@ -21,6 +22,10 @@ class Simulation:
 
     def __init__(self):
         self.intro_text = ""
+        self.header = {
+            "CHECK KEYWORDS": '"Warn"',
+            "Mesh DB": '"." "."',
+        }
         self.materials = {}
         self.bodies = {}
         self.boundaries = {}
@@ -30,6 +35,7 @@ def __init__(self):
         self.equations = {}
         self.constants = {"Stefan Boltzmann": 5.6704e-08}
         self.settings = {}
+        self.sif_filename = "case.sif"
 
     def write_sif(self, simulation_dir):
         """Write sif file.
@@ -38,11 +44,13 @@ def write_sif(self, simulation_dir):
             simulation_dir (str): Path of simulation directory
         """
         self._set_ids()
-        with open(simulation_dir + "/case.sif", "w") as f:
+        with open(os.path.join(simulation_dir, self.sif_filename), "w") as f:
             if self.intro_text != "":
                 f.write(self.intro_text)
                 f.write("\n\n")
-            f.write("""Header\n  CHECK KEYWORDS "Warn"\n  Mesh DB "." "."\nEnd\n\n""")
+            f.write("Header\n")
+            f.write(self._dict_to_str(self.header, key_value_separator=" "))
+            f.write("End\n\n")
             f.write("Simulation\n")
             f.write(self._dict_to_str(self.settings))
             f.write("End\n\n")
@@ -101,8 +109,9 @@ def write_startinfo(self, simulation_dir):
         Args:
             simulation_dir (str): simulation directory
         """
-        with open(simulation_dir + "/ELMERSOLVER_STARTINFO", "w") as f:
-            f.write("case.sif\n")
+        with open(os.path.join(simulation_dir, "ELMERSOLVER_STARTINFO"), "w") as f:
+            f.write(self.sif_filename)
+            f.write("\n")
 
     def write_boundary_ids(self, simulation_dir):
         """Write yaml-file containing the boundary names and the
@@ -115,10 +124,10 @@ def write_boundary_ids(self, simulation_dir):
         with open(simulation_dir + "/boundaries.yml", "w") as f:
             yaml.dump(data, f, sort_keys=False)
 
-    def _dict_to_str(self, dictionary):
+    def _dict_to_str(self, dictionary, *, key_value_separator=" = "):
         text = ""
         for key, value in dictionary.items():
-            text = "".join([text, "  ", key, " = ", str(value), "\n"])
+            text = "".join([text, "  ", key, key_value_separator, str(value), "\n"])
         return text
 
     def _set_ids(self):
@@ -508,7 +517,7 @@ def load_body_force(name, simulation, setup_file=""):
         BodyForce object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/body_forces.yml"
+        setup_file = os.path.join(data_dir, "body_forces.yml")
     with open(setup_file) as f:
         data = yaml.safe_load(f)[name]
     return BodyForce(simulation, name, data)

pyelmer/test/test_elmer.py

@@ -1,8 +1,10 @@
 import pytest
 import yaml
+import filecmp
 import gmsh
 import os
 import re
+import tempfile
 from objectgmsh import add_physical_group, get_boundaries_in_box
 from pyelmer import elmer
 
@@ -282,8 +284,16 @@ def test_write_sif():
     test_boundary = elmer.Boundary(sim, "test_boundary", [ph_test_boundary])
     test_boundary.data.update({"test_parameter": "1.0"})
 
-    sim.write_startinfo(sim_dir)
-    sim.write_sif(sim_dir)
+    with tempfile.TemporaryDirectory() as tempdir:
+        sim.write_startinfo(tempdir)
+        sim.write_sif(tempdir)
+
+        files = os.listdir(tempdir)
+        # Ensure that we have generated the same files as stored in git.
+        assert os.listdir(sim_dir) == files
+        for file in files:
+            # Check that the contents of each file agrees with the reference.
+            assert filecmp.cmp(os.path.join(sim_dir, file), os.path.join(tempdir, file))
 
     # check format of sif file
     simulation = {}
@@ -318,7 +328,9 @@ def test_write_sif():
         initial_conditions,
     ]
 
-    with open(sim_dir + "/case.sif", "r") as f:
+    # We already know that the reference sif file is equal to that which we generated,
+    # so read the reference sif file here.
+    with open(os.path.join(sim_dir, "case.sif"), "r") as f:
         read_object = False
         write_index = None
         write_name = None
@@ -367,6 +379,7 @@ def test_write_sif():
                 else:
                     objects[write_index].update({key: value})
 
+    assert simulation == sim.settings
     assert equations["test_equation"] == test_eqn.get_data()
     assert solvers["test_solver"] == test_solver.get_data()
     assert solvers["test_post_solver"] == test_post_solver.get_data()