fea: add support for sets export to sesam and auto-clean duplicate no…

…des upon meshing finalization. And significantly improve auto-merge coincident nodes method

src/ada/api/containers.py

@@ -1048,13 +1048,14 @@ def insert_node(n, i):
     def remove(self, nodes: Union[Node, Iterable[Node]]):
         """Remove node(s) from the nodes container"""
         nodes = list(nodes) if isinstance(nodes, Iterable) else [nodes]
-        for node in nodes:
-            if node in self._nodes:
-                logger.debug(f"Removing {node}")
-                self._nodes.pop(self._nodes.index(node))
-                self.renumber()
+        ids = [node.id for node in nodes]
+        for node_id in ids:
+            if node_id in self._idmap.keys():
+                self._idmap.pop(node_id)
             else:
-                logger.error(f"'{node}' not found in node-container.")
+                logger.error(f"'{node_id}' not found in node-container.")
+        self._nodes = list(self._idmap.values())
+        self.renumber()
 
     def remove_standalones(self) -> None:
         """Remove nodes that are without any usage references"""

src/ada/api/spatial/part.py

@@ -720,6 +720,7 @@ def to_fem_obj(
         experimental_pl_splitting=True,
         name=None,
         debug_mode=False,
+            merge_coincident_nodes=True,
     ) -> FEM:
         from ada import Beam, Plate, Shape
         from ada.fem.elements import Mass
@@ -769,6 +770,12 @@ def to_fem_obj(
             n = fem.nodes.add(Node(cog_absolute))
             fem.add_mass(Mass(f"{mass_shape.name}_mass", [n], mass_shape.mass))
 
+        if merge_coincident_nodes:
+            n_before = len(fem.nodes)
+            fem.nodes.remove_standalones()
+            n_after = len(fem.nodes)
+            logger.info(f"Removed {n_before - n_after} standalone nodes")
+
         return fem
 
     def to_gltf(self, gltf_file: str | pathlib.Path, **kwargs):

src/ada/fem/containers.py

@@ -613,7 +613,7 @@ def remove(self, fs_in: Union[List[FemSection], FemSection]):
 
 
 class FemSets:
-    def __init__(self, sets: List[FemSet] = None, parent: FEM = None):
+    def __init__(self, sets: list[FemSet] = None, parent: FEM = None):
         self._fem_obj = parent
         self._sets = sorted(sets, key=attrgetter("type", "name")) if sets is not None else []
         # Merge same name sets

src/ada/fem/formats/sesam/read/read_sets.py

@@ -16,7 +16,7 @@
 
 def get_sets(bulk_str: str, parent: "FEM") -> FemSets:
     set_reader = SetReader(bulk_str, parent)
-    return FemSets(list(set_reader.run()), parent=parent)
+    return FemSets(set_reader.run(), parent=parent)
 
 
 @dataclass
@@ -26,7 +26,7 @@ class SetReader:
 
     _set_type_map: dict = field(default_factory=dict)
 
-    def run(self) -> Iterable[FemSet]:
+    def iter_sets(self) -> Iterable[FemSet]:
         set_map = dict()
         set_groups = (self.get_setmap(m, self.parent) for m in cards.re_setmembs.finditer(self.bulk_str))
 
@@ -45,7 +45,11 @@ def run(self) -> Iterable[FemSet]:
             for fs in self.get_femsets(m, set_map, self.parent):
                 yield fs
 
-    def get_setmap(self, m, parent):
+    def run(self) -> list[FemSet]:
+        return list(self.iter_sets())
+
+    @staticmethod
+    def get_setmap(m, parent):
         d = m.groupdict()
         set_type = "nset" if str_to_int(d["istype"]) == 1 else "elset"
         mem_list = d["members"].split()

src/ada/fem/formats/sesam/write/write_sets.py

@@ -0,0 +1,51 @@
+from __future__ import annotations
+
+from os import write
+from typing import TYPE_CHECKING
+
+from ada.fem.formats.sesam.write.write_utils import write_ff
+
+if TYPE_CHECKING:
+    from ada import FEM
+
+
+def sets_str(fem: FEM) -> str:
+    out_str = ""
+
+    for i, fs in enumerate(fem.sets.sets):
+        out_str += write_ff("TDSETNAM", [(4, i, 100 + len(fs.name), 0), (fs.name,)])
+        nfield = len(fs.members) + 5
+        mem_ids = [mem.id for mem in fs.members]
+        if fs.type == "elset":
+            istype = 2
+        else:
+            istype = 1
+
+        start = 0
+        card_idx = 0
+        if nfield > 1024:
+            num_cards = int(nfield / 1019)
+            for card_idx in range(1, num_cards + 1):
+                mem_ids_local = mem_ids[start : card_idx * 1019]
+                remainder_mem_ids = []
+                for k in range(3, len(mem_ids_local), 4):
+                    remainder_mem_ids.append(mem_ids_local[k : k + 4])
+                out_str += write_ff(
+                    "GSETMEMB", [(1024, i, card_idx, istype), (0, *mem_ids_local[:3]), *remainder_mem_ids]
+                )
+                start = card_idx * 1019
+
+        card_idx += 1
+        length = nfield - start
+        if length < 4:
+            out_str += write_ff("GSETMEMB", [(length, i, card_idx, istype), (0, *mem_ids[start : start + length])])
+        else:
+            mem_ids_local = mem_ids[start : start + length - 5]
+            remainder_mem_ids = []
+            for k in range(3, len(mem_ids_local), 4):
+                remainder_mem_ids.append(mem_ids_local[k : k + 4])
+            out_str += write_ff(
+                "GSETMEMB", [(len(mem_ids_local) + 5, i, card_idx, istype), (0, *mem_ids_local[:3]), *remainder_mem_ids]
+            )
+
+    return out_str

src/ada/fem/formats/sesam/write/writer.py

@@ -10,6 +10,7 @@
 from ada.fem.exceptions.model_definition import DoesNotSupportMultiPart
 
 from .templates import top_level_fem_str
+from .write_sets import sets_str
 from .write_utils import write_ff
 
 if TYPE_CHECKING:
@@ -69,6 +70,7 @@ def to_fem(assembly, name, analysis_dir=None, metadata=None, model_data_only=Fal
         d.write(univec_str(part.fem))
         d.write(nodes_str(part.fem))
         d.write(mass_str(part.fem))
+        d.write(sets_str(part.fem))
         d.write(bc_str(part.fem) + bc_str(assembly.fem))
         d.write(constraint_str(part.fem) + constraint_str(assembly.fem))
         d.write(hinges_str(part.fem))

src/ada/fem/meshing/concepts.py

@@ -325,7 +325,8 @@ def add_obj_to_elem_ref(el: Elem, obj: Shape | Beam | Plate | Pipe):
             # create a variable for all overlapping element ids
             overlapping_el_ids = existing_el_ids.intersection(el_ids)
             if overlapping_el_ids:
-                logger.warning("Overlapping element ids found")
+                logger.warning(f"Overlapping element ids found for {gmsh_data.obj.name}: {overlapping_el_ids}")
+
             elements.update({el.id: el for el in entity_elements})
 
         fem.elements = FemElements(elements.values(), fem_obj=fem)

src/ada/fem/meshing/partitioning/partition_plates.py

@@ -49,7 +49,7 @@ def partition_intersected_plates(plate_con: PlateConnections, gmsh_session: Gmsh
                     intersecting_plates.add((pl2_dim, pl2_ent))
             try:
                 res, res_map = gmsh_session.model.occ.fragment(
-                    list(intersecting_plates), [(pl1_dim, pl1_ent)], removeTool=False
+                    list(intersecting_plates), [(pl1_dim, pl1_ent)], removeTool=True
                 )
             except Exception as e:
                 logger.error(f"Error while fragmenting plate: {pl1.name} using {pl2.name} {e}")
@@ -114,9 +114,9 @@ def split_plates_by_beams(gmsh_session: GmshSession):
                 bm_gmsh_obj.entities = new_ents
                 for ent in new_ents:
                     int_bm_map[(ent[0], ent[1])] = bm_gmsh_obj
-                # for ent in old_entities:
-                #     if ent not in new_ents:
-                #         int_bm_map.pop((ent[0], ent[1]), None)
+                for ent in old_entities:
+                    if ent not in new_ents:
+                        int_bm_map.pop((ent[0], ent[1]), None)
 
             pl_gmsh_obj.entities = replaced_pl_entities
             gmsh_session.model.occ.synchronize()

src/ada/fem/meshing/utils.py

@@ -242,7 +242,7 @@ def get_elements_from_entity(model: gmsh.model, ent, fem: FEM, dim) -> list[Elem
 
 def get_elements_from_entities(model: gmsh.model, entities, fem: FEM) -> list[Elem]:
     elements = []
-    for dim, ent in entities:
+    for dim, ent in set(entities):
         try:
             elements += get_elements_from_entity(model, ent, fem, dim)
         except BaseException as e:

src/ada/fem/sets.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, List, Union
+from typing import TYPE_CHECKING, List, Union, Literal
 
 from ada.api.nodes import Node
 
@@ -29,7 +29,14 @@ class FemSet(FemBase):
 
     TYPES = SetTypes
 
-    def __init__(self, name, members: None | list[Elem | Node], set_type=None, metadata=None, parent=None):
+    def __init__(
+        self,
+        name,
+        members: None | list[Elem | Node],
+        set_type: Literal["nset", "elset"] = None,
+        metadata=None,
+        parent=None,
+    ):
         super().__init__(name, metadata, parent)
         from ada.fem import Elem
 
@@ -66,7 +73,7 @@ def add_members(self, members: List[Union[Elem, Node]]):
         self._members += members
 
     @property
-    def type(self):
+    def type(self) -> str:
         return self._set_type.lower()
 
     @property

src/frontend/src/components/viewer/DynamicGridHelper.tsx

@@ -13,9 +13,8 @@ const DynamicGridHelper: React.FC = () => {
 
     if (boundingBox) {
       const size = calculateGridSize(boundingBox);
-      const divisions = size;
+      const divisions = Math.max(10, Math.floor(size / 10));
       grid = new ThreeGridHelper(size, divisions, 'white', 'gray');
-      //grid.position.y = boundingBox.min.y - (size * 0.05); // Adjust grid position if needed
     } else {
       // Default grid if no bounding box is available
       grid = new ThreeGridHelper(10, 10, 'white', 'gray');

src/frontend/src/components/viewer/OrientationGizmo.tsx

@@ -8,7 +8,7 @@ const OrientationGizmo = () => {
             // Rotate the gizmo so that Z is treated as up
             matrix={[1, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1]}
         >
-            {/*<GizmoViewport axisColors={['red', 'green', 'blue']} labelColor="black" labels={["x", "z", "y"]}/>*/}
+            {/*<GizmoViewport axisColors={['red', 'blue', 'green']} labelColor="black" labels={["x", "z", "y"]}/>*/}
             <GizmoViewcube color={"blue"} textColor={"white"}/>
         </GizmoHelper>
     );

tests/core/fem/formats/sesam/test_fem_sesam.py

@@ -1,4 +1,9 @@
+import ada
+from ada.fem.containers import FemElements
+from ada.fem.formats.sesam.read.read_sets import SetReader
+from ada.fem.formats.sesam.write.write_sets import sets_str
 from ada.fem.formats.sesam.write.writer import write_ff
+from ada.fem.shapes.definitions import LineShapes
 
 
 def test_write_ff():
@@ -17,3 +22,22 @@ def test_write_ff():
     ]
     test_str += write_ff(fflag, ddata)
     # print(test_str)
+
+
+def test_write_sets():
+
+    elements = [
+        ada.fem.Elem(el_id, [ada.Node((el_id, 0, 0), el_id), ada.Node((el_id + 1, 0, 0), el_id + 1)], LineShapes.LINE)
+        for el_id in range(1, 2000)
+    ]
+    fem = ada.FEM("MyFem", elements=FemElements(elements))
+    original_set = fem.add_set(ada.fem.FemSet("MySet", elements))
+    result_str = sets_str(fem)
+
+    return_fem = ada.FEM("MyFem", elements=fem.elements)
+    sr = SetReader(result_str, return_fem)
+    roundtripped_sets = sr.run()
+    assert len(roundtripped_sets) == 1
+
+    roundtripped_set = roundtripped_sets[0]
+    assert len(original_set.members) == len(roundtripped_set.members)