Utilize FourCIPP in MeshPy

.github/actions/run_tests/action.yml

@@ -4,7 +4,7 @@ inputs:
   install-command:
     description: Command to install MeshPy with pip
     required: false
-    default: ".[dev]"
+    default: ".[dev,fourc]"
   source-command:
     description: Command to source the virtual environment
     required: false

.github/workflows/testing.yml

@@ -37,7 +37,7 @@ jobs:
           # non-editable installation and turn of coverage, because the coverage
           # only works in editable mode.
           install-command: >-
-            ${{ matrix.python-version == '3.10' && '-e .[dev]' || '.[dev]'}}
+            ${{ matrix.python-version == '3.10' && '-e .[dev,fourc]' || '.[dev,fourc]'}}
           # The single space in the empty string is required, otherwise GitHub
           # evaluates the if clause wrong.
           additional-pytest-flags: >-
@@ -65,7 +65,7 @@ jobs:
       - name: Run the test suite
         uses: ./.github/actions/run_tests
         with:
-          install-command: ".[cubitpy,dev]"
+          install-command: ".[cubitpy,dev,fourc]"
           source-command: "source python-workflow-venv/bin/activate"
           additional-pytest-flags: "--CubitPy --no-cov"
       - name: Upload test results on failure
@@ -96,7 +96,7 @@ jobs:
         uses: ./.github/actions/run_tests
         with:
           source-command: "source python-workflow-venv/bin/activate"
-          install-command: "-e .[dev]"
+          install-command: "-e .[dev,fourc]"
           additional-pytest-flags: "--4C --ArborX --cov-fail-under=92"
       - name: Upload test results on failure
         if: failure()
@@ -124,7 +124,7 @@ jobs:
       - name: Run the test suite
         uses: ./.github/actions/run_tests
         with:
-          install-command: ".[cubitpy,dev]"
+          install-command: ".[cubitpy,dev,fourc]"
           source-command: "source python-workflow-venv/bin/activate"
           additional-pytest-flags: "--performance-tests --exclude-standard-tests -s --no-cov"
       - name: Upload test results on failure

pyproject.toml

@@ -30,7 +30,7 @@ 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"]
+fourc = ["fourcipp@git+https://github.com/4C-multiphysics/fourcipp.git@main"]
 dev = [
   "coverage-badge",
   "coverage",

src/meshpy/core/element_volume.py

@@ -36,21 +36,21 @@ class VolumeElement(_Element):
     vtk_cell_type = None
     vtk_topology: list = []
 
-    def __init__(self, nodes=None, string_pre_nodes="", string_post_nodes="", **kwargs):
+    def __init__(self, nodes=None, data={}, **kwargs):
         super().__init__(nodes=nodes, material=None, **kwargs)
-        self.string_pre_nodes = string_pre_nodes
-        self.string_post_nodes = string_post_nodes
+        self.data = data
 
     def dump_to_list(self):
-        """Return a list with the items representing this object (usually a
-        single item)."""
+        """Return a dict with the items representing this object."""
 
-        # String with the node ids.
-        nodes_string = " ".join(str(node.i_global) for node in self.nodes)
-
-        return [
-            f"{self.i_global} {self.string_pre_nodes} {nodes_string} {self.string_post_nodes}"
-        ]
+        return {
+            "id": self.i_global,
+            "cell": {
+                "type": element_type_to_four_c_string[type(self)],
+                "connectivity": [node.i_global for node in self.nodes],
+            },
+            "data": self.data,
+        }
 
     def get_vtk(self, vtk_writer_beam, vtk_writer_solid, **kwargs):
         """Add the representation of this element to the VTK writer as a
@@ -170,3 +170,13 @@ class VolumeHEX27(VolumeElement):
         25,
         26,
     ]
+
+
+element_type_to_four_c_string = {
+    VolumeHEX8: "HEX8",
+    VolumeHEX20: "HEX20",
+    VolumeHEX27: "HEX27",
+    VolumeTET4: "TET4",
+    VolumeTET10: "TET10",
+    VolumeWEDGE6: "WEDGE6",
+}

src/meshpy/core/geometry_set.py

@@ -22,14 +22,11 @@
 """This module implements a basic class to manage geometry in the input
 file."""
 
-import numpy as _np
-
 from meshpy.core.base_mesh_item import BaseMeshItem as _BaseMeshItem
 from meshpy.core.conf import mpy as _mpy
 from meshpy.core.container import ContainerBase as _ContainerBase
 from meshpy.core.element_beam import Beam as _Beam
 from meshpy.core.node import Node as _Node
-from meshpy.utils.environment import fourcipp_is_available as _fourcipp_is_available
 
 
 class GeometrySetBase(_BaseMeshItem):
@@ -123,21 +120,19 @@ def get_all_nodes(self):
     def dump_to_list(self):
         """Return a list with the legacy strings of this geometry set."""
 
-        if _fourcipp_is_available():
-            raise ValueError(
-                "Port this functionality to dump the geometry set to a suitable data format"
-            )
+        # Sort nodes based on their global index
+        nodes = sorted(self.get_all_nodes(), key=lambda n: n.i_global)
 
-        # Sort the nodes based on the node GID.
-        nodes = self.get_all_nodes()
-        if len(nodes) == 0:
+        if not nodes:
             raise ValueError("Writing empty geometry sets is not supported")
-        nodes_id = [node.i_global for node in nodes]
-        sort_indices = _np.argsort(nodes_id)
-        nodes = [nodes[i] for i in sort_indices]
 
         return [
-            f"NODE {node.i_global} {self.geometry_set_names[self.geometry_type]} {self.i_global}"
+            {
+                "type": "NODE",
+                "node_id": node.i_global,
+                "d_type": self.geometry_set_names[self.geometry_type],
+                "d_id": self.i_global,
+            }
             for node in nodes
         ]
 

src/meshpy/core/node.py

@@ -24,8 +24,6 @@
 import numpy as _np
 
 from meshpy.core.base_mesh_item import BaseMeshItem as _BaseMeshItem
-from meshpy.core.conf import mpy as _mpy
-from meshpy.utils.environment import fourcipp_is_available as _fourcipp_is_available
 
 
 class Node(_BaseMeshItem):
@@ -53,22 +51,6 @@ def __init__(self, coordinates, *, is_middle_node=False, **kwargs):
         # If this node is replaced, store a link to the remaining node.
         self.master_node = None
 
-    @classmethod
-    def from_legacy_string(cls, input_line):
-        """Create the Node object from a legacy string."""
-
-        if _fourcipp_is_available():
-            raise ValueError(
-                "Port this functionality to create the node from the dict "
-                "representing the node, not the legacy string."
-            )
-
-        # Split up the input line.
-        line_split = input_line.split()
-
-        # Convert the node coordinates into a Node object.
-        return cls([float(line_split[i]) for i in range(3, 6)])
-
     def get_master_node(self):
         """Return the master node of this node.
 
@@ -114,13 +96,11 @@ def rotate(self, *args, **kwargs):
     def dump_to_list(self):
         """Return a list with the legacy string representing this node."""
 
-        if _fourcipp_is_available():
-            raise ValueError(
-                "Port this functionality to create a dict, not the legacy string."
-            )
-
-        coordinate_string = " ".join([str(item) for item in self.coordinates])
-        return [f"NODE {self.i_global} COORD {coordinate_string}"]
+        return {
+            "id": self.i_global,
+            "COORD": self.coordinates,
+            "data": {"type": "NODE"},
+        }
 
 
 class NodeCosserat(Node):
@@ -169,10 +149,8 @@ def dump_to_list(self):
         """Return a list with the legacy string representing this control
         point."""
 
-        if _fourcipp_is_available():
-            raise ValueError(
-                "Port this functionality to create a dict, not the legacy string."
-            )
-
-        coordinate_string = " ".join([str(item) for item in self.coordinates])
-        return [f"CP {self.i_global} COORD {coordinate_string} {self.weight}"]
+        return {
+            "id": self.i_global,
+            "COORD": self.coordinates,
+            "data": {"type": "CP", "weight": self.weight},
+        }

src/meshpy/core/nurbs_patch.py

@@ -28,7 +28,6 @@
 from meshpy.core.material import (
     MaterialSolidBase as _MaterialSolidBase,
 )
-from meshpy.utils.environment import fourcipp_is_available as _fourcipp_is_available
 
 
 class NURBSPatch(_Element):
@@ -72,26 +71,15 @@ def get_nurbs_dimension(self):
             )
         return n_knots
 
-    def dump_element_specific_section(self, yaml_dict):
+    def dump_element_specific_section(self, input_file):
         """Set the knot vectors of the NURBS patch in the input file."""
 
-        if _fourcipp_is_available():
-            raise ValueError("Port this functionality to not use the legacy format.")
-
-        knotvectors_section = "STRUCTURE KNOTVECTORS"
-
-        if knotvectors_section not in yaml_dict.keys():
-            yaml_dict[knotvectors_section] = []
-
-        section = yaml_dict[knotvectors_section]
-        section.append(f"NURBS_DIMENSION {self.get_nurbs_dimension()}")
-        section.append("BEGIN NURBSPATCH")
-        section.append(f"ID {self.n_nurbs_patch}")
+        patch_data = {
+            "knot_vectors": [],
+        }
 
         for dir_manifold in range(len(self.knot_vectors)):
             num_knotvectors = len(self.knot_vectors[dir_manifold])
-            section.append(f"NUMKNOTS {num_knotvectors}")
-            section.append(f"DEGREE {self.polynomial_orders[dir_manifold]}")
 
             # Check the type of knot vector, in case that the multiplicity of the first and last
             # knot vectors is not p + 1, then it is a closed (periodic) knot vector, otherwise it
@@ -115,12 +103,24 @@ def dump_element_specific_section(self, yaml_dict):
                     knotvector_type = "Periodic"
                     break
 
-            section.append(f"TYPE {knotvector_type}")
+            patch_data["knot_vectors"].append(
+                {
+                    "DEGREE": self.polynomial_orders[dir_manifold],
+                    "TYPE": knotvector_type,
+                    "knots": [
+                        knot_vector_val
+                        for knot_vector_val in self.knot_vectors[dir_manifold]
+                    ],
+                }
+            )
 
-            for knot_vector_val in self.knot_vectors[dir_manifold]:
-                section.append(knot_vector_val)
+        if "STRUCTURE KNOTVECTORS" not in input_file:
+            input_file.add({"STRUCTURE KNOTVECTORS": []})
+            input_file["STRUCTURE KNOTVECTORS"] = []
 
-        section.append("END NURBSPATCH")
+        patches = input_file["STRUCTURE KNOTVECTORS"]
+        patch_data["ID"] = len(patches) + 1
+        patches.append(patch_data)
 
     def get_number_elements(self):
         """Get the number of elements in this patch by checking the amount of
@@ -167,9 +167,6 @@ def dump_to_list(self):
         """Return a list with all the element definitions contained in this
         patch."""
 
-        if _fourcipp_is_available():
-            raise ValueError("Port this functionality to not use the legacy format.")
-
         # Check the material
         self._check_material()
 
@@ -211,20 +208,29 @@ def get_ids_ctrlpts_surface(knot_span_u, knot_span_v):
             ):
                 element_cps_ids = get_ids_ctrlpts_surface(knot_span_u, knot_span_v)
 
-                string_cps = " ".join(
-                    [str(self.nodes[i].i_global) for i in element_cps_ids]
+                connectivity = [self.nodes[i].i_global for i in element_cps_ids]
+
+                num_cp_in_element = (self.polynomial_orders[0] + 1) * (
+                    self.polynomial_orders[1] + 1
                 )
 
                 patch_elements.append(
-                    "{} {} NURBS{} {} MAT {} {}".format(
-                        self.i_global + j,
-                        self.element_string,
-                        (self.polynomial_orders[0] + 1)
-                        * (self.polynomial_orders[1] + 1),
-                        string_cps,
-                        self.material.i_global,
-                        self.element_description,
-                    )
+                    {
+                        "id": self.i_global + j,
+                        "cell": {
+                            "type": f"NURBS{num_cp_in_element}",
+                            "connectivity": connectivity,
+                        },
+                        "data": {
+                            "type": "WALLNURBS",
+                            "MAT": self.material.i_global,
+                            **(
+                                self.element_description
+                                if self.element_description
+                                else {}
+                            ),
+                        },
+                    }
                 )
                 j += 1
 
@@ -243,9 +249,6 @@ def dump_to_list(self):
         """Return a list with all the element definitions contained in this
         patch."""
 
-        if _fourcipp_is_available():
-            raise ValueError("Port this functionality to not use the legacy format.")
-
         # Check the material
         self._check_material()
 
@@ -302,9 +305,7 @@ def get_ids_ctrlpts_volume(knot_span_u, knot_span_v, knot_span_w):
                         knot_span_u, knot_span_v, knot_span_w
                     )
 
-                    string_cps = " ".join(
-                        [str(self.nodes[i].i_global) for i in element_cps_ids]
-                    )
+                    connectivity = [self.nodes[i].i_global for i in element_cps_ids]
 
                     num_cp_in_element = (
                         (self.polynomial_orders[0] + 1)
@@ -313,13 +314,22 @@ def get_ids_ctrlpts_volume(knot_span_u, knot_span_v, knot_span_w):
                     )
 
                     patch_elements.append(
-                        "{} SOLID NURBS{} {} MAT {} {}".format(
-                            self.i_global + increment_ele,
-                            num_cp_in_element,
-                            string_cps,
-                            self.material.i_global,
-                            self.element_description,
-                        )
+                        {
+                            "id": self.i_global + increment_ele,
+                            "cell": {
+                                "type": f"NURBS{num_cp_in_element}",
+                                "connectivity": connectivity,
+                            },
+                            "data": {
+                                "type": "SOLID",
+                                "MAT": self.material.i_global,
+                                **(
+                                    self.element_description
+                                    if self.element_description
+                                    else {}
+                                ),
+                            },
+                        }
                     )
                     increment_ele += 1