Merge pull request #320 from imcs-compsim/migrate_dat_to_yaml

Migrate MeshPy from dat to yaml

Author: davidrudlstorfer

.github/workflows/testing.yml

@@ -97,7 +97,7 @@ jobs:
         with:
           source-command: "source python-workflow-venv/bin/activate"
           install-command: "-e .[dev]"
-          additional-pytest-flags: "--4C --ArborX --cov-fail-under=93"
+          additional-pytest-flags: "--4C --ArborX --cov-fail-under=92"
       - name: Upload test results on failure
         if: failure()
         uses: actions/upload-artifact@v4

pyproject.toml

@@ -29,6 +29,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 cubitpy = ["cubitpy@git+https://github.com/imcs-compsim/cubitpy.git@main"]
+fourc = ["fourcipp@git+https://github.com/4c-multiphysics/fourcipp.git@main"]
 dev = [
   "coverage-badge",
   "coverage",
@@ -50,7 +51,7 @@ Issues = "https://github.com/imcs-compsim/meshpy/issues/"
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=90 --cov=src/meshpy/"
+addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=89 --cov=src/meshpy/"
 markers = [
   "fourc: tests in combination with 4C",
   "arborx: tests in combination with ArborX",

src/meshpy/abaqus/beam.py

@@ -25,7 +25,6 @@
 import numpy as _np
 
 from meshpy.core.element_beam import Beam as _Beam
-from meshpy.core.material import MaterialBeam as _MaterialBeam
 
 
 def generate_abaqus_beam(beam_type: str):
@@ -69,19 +68,3 @@ def generate_abaqus_beam(beam_type: str):
             "n_dim": n_dim,
         },
     )
-
-
-class AbaqusBeamMaterial(_MaterialBeam):
-    """A class representing an Abaqus beam material."""
-
-    def __init__(self, name: str):
-        """Initialize the material. For now it is only supported to state the
-        name of the resulting element set here. The material and cross-section
-        lines in the input file have to be defined manually.
-
-        Args
-        ----
-        name: str
-            Name of the material, this will be the name of the resulting element set
-        """
-        super().__init__(data=name)

src/meshpy/abaqus/input_file.py

@@ -308,7 +308,7 @@ def get_material_lines(self):
         # Create the element sets for the different materials.
         input_file_lines = []
         for material, elements in materials.items():
-            material_name = material.get_dat_lines()[0]
+            material_name = material.dump_to_list()[0]
             input_file_lines.extend(get_set_lines("Elset", elements, material_name))
         return input_file_lines
 

src/meshpy/abaqus/material.py

@@ -0,0 +1,45 @@
+# The MIT License (MIT)
+#
+# Copyright (c) 2018-2025 MeshPy Authors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+"""This file provides functions to create Abaqus beam element classes to be
+used with MeshPy."""
+
+from meshpy.core.material import MaterialBeam as _MaterialBeam
+
+
+class AbaqusBeamMaterial(_MaterialBeam):
+    """A class representing an Abaqus beam material."""
+
+    def __init__(self, name: str):
+        """Initialize the material. For now it is only supported to state the
+        name of the resulting element set here. The material and cross-section
+        lines in the input file have to be defined manually.
+
+        Args
+        ----
+        name: str
+            Name of the material, this will be the name of the resulting element set
+        """
+        super().__init__(data=name)
+
+    def dump_to_list(self):
+        """Return a list with the (single) item representing this material."""
+        return [self.data]

src/meshpy/core/base_mesh_item.py

@@ -47,36 +47,12 @@ def __init__(self, data=None, comments=None):
         else:
             self.comments = comments
 
-    def get_dat_lines(self):
-        """Return the content of this object as a list.
-
-        If comments exist, also add those.
-        """
-
-        # Get data of object.
-        data = self._get_dat()
-        if isinstance(data, str):
-            data = [data]
-
-        # Get comments if given.
-        return_list = []
-        if not len(self.comments) == 0:
-            return_list.extend(self.comments)
-
-        # Return final list.
-        return_list.extend(data)
-        return return_list
-
-    def _get_dat(self):
-        """Return the content of this object as either a list or a str."""
-        return self.data
-
 
 class BaseMeshItemFull(BaseMeshItem):
     """Base class for all objects that are related to a mesh and are fully
     created in MeshPy."""
 
 
 class BaseMeshItemString(BaseMeshItem):
-    """Base class for all objects that are imported from a dat file as a plain
-    string."""
+    """Base class for all objects that are imported from an input file as a
+    plain string."""

src/meshpy/core/boundary_condition.py

@@ -37,10 +37,8 @@ def __init__(self, geometry_set, bc_type=None, **kwargs):
 
         Args
         ----
-        geometry_set: GeometrySet, int
-            Geometry that this boundary condition acts on. An integer can be
-            given, in the case a dat file is imported. This integer is only
-            temporary and will be replaced with the GeometrySet object.
+        geometry_set: GeometrySet
+            Geometry that this boundary condition acts on.
         bc_type: mpy.bc
             Type of the boundary condition.
         """
@@ -50,16 +48,13 @@ def __init__(self, geometry_set, bc_type=None, **kwargs):
         self.geometry_set = geometry_set
 
     @classmethod
-    def from_dat(cls, bc_key, line, **kwargs):
+    def from_dict(cls, geometry_sets, bc_key, bc_dict):
         """This function acts as a factory and creates the correct boundary
-        condition object from a line in the dat file.
+        condition object from a dictionary parsed from an input file."""
 
-        The geometry set is passed as integer (0 based index) and will
-        be connected after the whole input file is parsed.
-        """
-
-        # Split up the input line.
-        split = line.split()
+        geometry_set_id = int(bc_dict["E"]) - 1
+        geometry_set = geometry_sets[geometry_set_id]
+        del bc_dict["E"]
 
         if bc_key in (
             _mpy.bc.dirichlet,
@@ -74,22 +69,25 @@ def from_dat(cls, bc_key, line, **kwargs):
                 BoundaryCondition as _BoundaryCondition,
             )
 
-            return _BoundaryCondition(
-                int(split[1]) - 1, " ".join(split[2:]), bc_type=bc_key, **kwargs
+            boundary_condition = _BoundaryCondition(
+                geometry_set, bc_dict, bc_type=bc_key
             )
         elif bc_key is _mpy.bc.point_coupling:
             # Coupling condition.
             from meshpy.core.coupling import Coupling as _Coupling
 
-            return _Coupling(
-                int(split[1]) - 1,
+            boundary_condition = _Coupling(
+                geometry_set,
                 bc_key,
-                " ".join(split[2:]),
+                bc_dict,
                 check_overlapping_nodes=False,
                 check_at_init=False,
-                **kwargs,
             )
-        raise ValueError("Got unexpected boundary condition!")
+        else:
+            raise ValueError("Got unexpected boundary condition!")
+
+        boundary_condition.check()
+        return boundary_condition
 
 
 class BoundaryConditionContainer(_ContainerBase):

src/meshpy/core/conf.py

@@ -151,7 +151,7 @@ def set_default_values(self):
         self.git_date = None
 
         # Precision for floats in output.
-        self.dat_precision = "{:.12g}"
+        self.output_precision = "{:.12g}"
 
         # Set the epsilons for comparison of different types of values.
         self.eps_quaternion = 1e-10
@@ -166,10 +166,7 @@ def set_default_values(self):
         self.geometric_search_max_nodes_brute_force = 1000
         self.geometric_search_binning_n_bin = 10
 
-        # Values for the formatting of the input file.
-        self.dat_len_section = 80
-
-        # Import meshes as pure dat or import the geometry.
+        # Import meshes as pure dict or import the geometry.
         self.import_mesh_full = False
 
         # Number of digits for node set output (this will be set in the
@@ -179,19 +176,16 @@ def set_default_values(self):
         self.vtk_nan_int = -1
         self.vtk_nan_float = 0.0
 
-        # Check for overlapping elements when creating a dat file.
+        # Check for overlapping elements when creating an input file.
         self.check_overlapping_elements = True
 
         # Lines to be added to each created input file
         self.input_file_meshpy_header = [
-            "-" * 77,
+            "-" * 40,
             "This input file was created with MeshPy.",
-            "Copyright (c) 2018-2025",
-            "    Ivo Steinbrecher",
-            "    Institute for Mathematics and Computer-Based Simulation",
-            "    Universitaet der Bundeswehr Muenchen",
-            "    https://www.unibw.de/imcs-en",
-            "-" * 77,
+            "Copyright (c) 2018-2025 MeshPy Authors",
+            "https://imcs-compsim.github.io/meshpy/",
+            "-" * 40,
         ]
 
 

src/meshpy/core/coupling.py

@@ -60,12 +60,12 @@ def __init__(
             physical position.
         check_at_init: bool
             If the previous check should be performed at initialization. This is required
-            when importing a coupling from a dat file as the nodes themselves are not build
+            when importing a coupling from an input file as the nodes themselves are not build
             up when the coupling is read.
         """
 
         if isinstance(geometry, int):
-            # This is the case if the boundary condition is read from an existing dat file
+            # This is the case if the boundary condition is read from an existing input file
             pass
         elif isinstance(geometry, _GeometrySetBase):
             pass
@@ -108,15 +108,12 @@ def check(self):
                 "The nodes given to Coupling do not have the same position."
             )
 
-    def _get_dat(self):
-        """Return the dat line for this object.
+    def dump_to_list(self):
+        """Return a list with a single item representing this coupling
+        condition."""
 
-        If no explicit string was given, it depends on the coupling type
-        as well as the beam type.
-        """
-
-        if isinstance(self.coupling_dof_type, str):
-            string = self.coupling_dof_type
+        if isinstance(self.coupling_dof_type, dict):
+            bc_dict = self.coupling_dof_type
         else:
             # In this case we have to check which beams are connected to the node.
             # TODO: Coupling also makes sense for different beam types, this can
@@ -150,9 +147,9 @@ def _get_dat(self):
                             "Coupling beams of different types is not yet possible!"
                         )
 
-            string = beam_four_c_type.get_coupling_string(self.coupling_dof_type)
+            bc_dict = beam_four_c_type.get_coupling_dict(self.coupling_dof_type)
 
-        return f"E {self.geometry_set.i_global} {string}"
+        return [{"E": self.geometry_set.i_global, **bc_dict}]
 
 
 def coupling_factory(geometry, coupling_type, coupling_dof_type, **kwargs):