emerge 0.4.7__py3-none-any.whl → 0.4.9__py3-none-any.whl

emerge/_emerge/mesh3d.py

@@ -0,0 +1,730 @@
+# EMerge is an open source Python based FEM EM simulation module.
+# Copyright (C) 2025  Robert Fennis.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see
+# <https://www.gnu.org/licenses/>.
+
+from __future__ import annotations
+import gmsh
+import numpy as np
+from numba import njit, f8
+from .mesher import Mesher
+from typing import Union, List, Tuple, Callable
+from collections import defaultdict
+from .geometry import GeoVolume
+from .mth.optimized import outward_normal
+from loguru import logger
+from functools import cache
+from .bc import Periodic
+
+@njit(f8(f8[:], f8[:], f8[:]), cache=True, nogil=True)
+def area(x1: np.ndarray, x2: np.ndarray, x3: np.ndarray):
+    e1 = x2 - x1
+    e2 = x3 - x1
+    av = np.array([e1[1]*e2[2] - e1[2]*e2[1], e1[2]*e2[0] - e1[0]*e2[2], e1[0]*e2[1] - e1[1]*e2[0]])
+    return np.sqrt(av[0]**2 + av[1]**2 + av[2]**2)/2
+
+def shortest_distance(point_cloud):
+    """
+    Compute the shortest distance between any two points in a 3D point cloud.
+
+    Parameters:
+    - point_cloud: np.ndarray of shape (3, N)
+
+    Returns:
+    - min_dist: float, the shortest distance
+    """
+    # Transpose to shape (N, 3)
+    points = point_cloud.T  # Shape (N, 3)
+
+    # Compute pairwise squared distances (broadcasting)
+    diff = points[:, np.newaxis, :] - points[np.newaxis, :, :]  # Shape (N, N, 3)
+    dist_sq = np.einsum('ijk,ijk->ij', diff, diff)  # Shape (N, N)
+
+    # Avoid zero on diagonal (distance to self), set to np.inf
+    np.fill_diagonal(dist_sq, np.inf)
+
+    # Return minimum distance
+    return np.sqrt(np.min(dist_sq))
+
+def tri_ordering(i1: int, i2: int, i3: int) -> int:
+    ''' Takes two integer indices of triangle verticces and determines if they are in increasing order or decreasing order.
+    It ignores cyclic shifts of the indices. so (4,10,21) == (10,21,4) == (21,4,10)
+
+    for triangle (4,10,20) (for example)
+    (4,10,20): In co-ordering of phase = 0: i1 < i2, i2 < i3, i3 > i1: 4-10-20-4 diffs = +6 +10 -16
+    (10,20,4): In co-order shift 1: i1 < i2, i2 > i3, i3 < i1: 10-20-4-10 diffs = 10 -16 - (6)
+    (20,4,10): In co-order shift 2: i1 > i2, i2 < i3, i3 < i1: 
+
+    For triangle (20,10,4) 
+    (20,10,3): i1 > i2, i2 > i3
+    (10,3,20): i1 > i2, i2 < i3
+    (3,20,10): i1 < i2, i2 > i3
+    '''
+    return np.sign(np.sign(i2-1) + np.sign(i3-i2) + np.sign(i1-i3))
+
+
+class Mesh3D:
+    """A Mesh managing all 3D mesh related properties.
+
+    Relevant mesh data such as mappings between nodes(vertices), edges, triangles and tetrahedra
+    are managed by the Mesh3D class. Specific information regarding to how actual field values
+    are mapped to mesh elements is managed by the FEMBasis class.
+    
+    """
+    def __init__(self, mesher: Mesher):
+        
+        self.geometry: Mesher = mesher
+
+        # All spatial objects
+        self.nodes: np.ndarray = None
+        self.n_i2t: dict = None
+        self.n_t2i: dict = None
+
+        # tets colletions
+        self.tets: np.ndarray = None
+        self.tet_i2t: dict = None
+        self.tet_t2i: dict = None
+        self.centers: np.ndarray = None
+
+        # triangles
+        self.tris: np.ndarray = None
+        self.tri_i2t: dict = None
+        self.tri_t2i: dict = None
+        self.areas: np.ndarray = None
+        self.tri_centers: np.ndarray = None
+
+        # edges
+        self.edges: np.ndarray = None
+        self.edge_i2t: dict = None
+        self.edge_t2i: dict = None
+        self.edge_centers: np.ndarray = None
+        self.edge_lengths: np.ndarray = None
+        
+        # Inverse mappings
+        self.inv_edges: dict = None
+        self.inv_tris: dict = None
+        self.inv_tets: dict = None
+
+        # Mappings
+
+        self.tet_to_edge: np.ndarray = None
+        self.tet_to_edge_sign: np.ndarray = None
+        self.tet_to_tri: np.ndarray = None
+        self.tri_to_tet: np.ndarray = None
+        self.tri_to_edge: np.ndarray = None
+        self.tri_to_edge_sign: np.ndarray = None
+        self.edge_to_tri: defaultdict = None
+        self.node_to_edge: defaultdict = None
+
+        # Physics mappings
+
+        self.tet_to_field: np.ndarray = None
+        self.edge_to_field: np.ndarray = None
+        self.tri_to_field: np.ndarray = None
+
+        ## States
+        self.defined = False
+
+
+        ## Memory
+        self.ftag_to_tri: dict[int, list[int]] = dict()
+        self.ftag_to_node: dict[int, list[int]] = dict()
+        self.vtag_to_tet:  dict[int, list[int]] = dict()
+    
+    @property
+    def n_edges(self) -> int:
+        '''Return the number of edges'''
+        return self.edges.shape[1]
+    
+    @property
+    def n_tets(self) -> int:
+        '''Return the number of tets'''
+        return self.tets.shape[1]
+    
+    @property
+    def n_tris(self) -> int:
+        '''Return the number of triangles'''
+        return self.tris.shape[1]
+    
+    @property
+    def n_nodes(self) -> int:
+        '''Return the number of nodes'''
+        return self.nodes.shape[1]
+
+    def get_edge(self, i1: int, i2: int) -> int:
+        '''Return the edge index given the two node indices'''
+        if i1==i2:
+            raise ValueError("Edge cannot be formed by the same node.")
+        search = (min(int(i1),int(i2)), max(int(i1),int(i2)))
+        result =  self.inv_edges.get(search, None)
+        return result
+    
+    def get_edge_sign(self, i1: int, i2: int) -> int:
+        '''Return the edge index given the two node indices'''
+        if i1==i2:
+            raise ValueError("Edge cannot be formed by the same node.")
+        if i1 > i2:
+            return -1
+        return 1
+        
+    def get_tri(self, i1, i2, i3) -> int:
+        '''Return the triangle index given the three node indices'''
+        return self.inv_tris.get(tuple(sorted((int(i1), int(i2), int(i3)))), None)
+    
+    def get_tet(self, i1, i2, i3, i4) -> int:
+        '''Return the tetrahedron index given the four node indices'''
+        return self.inv_tets.get(tuple(sorted((int(i1), int(i2), int(i3), int(i4)))), None)
+    
+    def boundary_triangles(self, dimtags: list[tuple[int, int]] = None) -> np.ndarray:
+        if dimtags is None:
+            outputtags = []
+            for tags in self.ftag_to_tri.values():
+                outputtags.extend(tags)
+            return np.array(outputtags)
+        else:
+            dts = []
+            for dimtag in dimtags:
+                if dimtag[0]==2:
+                    dts.append(dimtag)
+                elif dimtag[0]==3:
+                    dts.extend(gmsh.model.get_boundary(dimtags))
+            return self.get_triangles([tag[1] for tag in dts])
+        
+
+    def get_tetrahedra(self, vol_tags: Union[int, list[int]]) -> np.ndarray:
+        if isinstance(vol_tags, int):
+            vol_tags = [vol_tags,]
+        
+        indices = []
+        for voltag in vol_tags:
+            indices.extend(self.vtag_to_tet[voltag])
+        return np.array(indices)
+    
+    def get_triangles(self, face_tags: Union[int, list[int]]) -> np.ndarray:
+        '''Returns a numpyarray of all the triangles that belong to the given face tags'''
+        if isinstance(face_tags, int):
+            face_tags = [face_tags,]
+        indices = []
+        for facetag in face_tags:
+            indices.extend(self.ftag_to_tri[facetag])
+        if any([(i is None) for i in indices]):
+            logger.error('Clearing None indices: ', [i for i, ind in enumerate(indices) if ind is None])
+            logger.error('This is usually a sign of boundaries sticking out of domains. Please check your Geometry.')
+            indices = [i for i in indices if i is not None]
+
+        return np.array(indices)
+    
+    def get_face_tets(self, *taglist: list[int]) -> np.ndarray:
+        ''' Return a list of a tetrahedrons that share a node with any of the nodes in the provided face.'''
+        nodes = set()
+        for tags in taglist:
+            nodes.update(self.get_nodes(tags))
+        return np.array([i for i, tet in enumerate(self.tets.T) if not set(tet).isdisjoint(nodes)])
+
+    def get_nodes(self, face_tags: Union[int, list[int]]) -> np.ndarray:
+        '''Returns a numpyarray of all the nodes that belong to the given face tags'''
+        if isinstance(face_tags, int):
+            face_tags = [face_tags,]
+        
+        nodes = []
+        for facetag in face_tags:
+            nodes.extend(self.ftag_to_node[facetag])
+        
+        return np.array(sorted(list(set(nodes))))
+    
+    
+    def update(self, periodic_bcs: list[Periodic] = None):
+        if periodic_bcs is None:
+            periodic_bcs = []
+            
+        nodes, lin_coords, _  = gmsh.model.mesh.get_nodes()
+        
+        coords = lin_coords.reshape(-1, 3).T
+        
+        ## Vertices
+        self.nodes = coords
+        self.n_i2t = {i: int(t) for i, t in enumerate(nodes)}
+        self.n_t2i = {t: i for i, t in self.n_i2t.items()}
+
+        ## Tetrahedras
+
+        _, tet_tags, tet_node_tags = gmsh.model.mesh.get_elements(3)
+        
+        # The algorithm assumes that only one domain tag is returned in this function. 
+        # Hence the use of tri_node_tags[0] in the next line. If domains are missing.
+        # Make sure to combine all the entries in the tri-node-tags list
+        
+        tet_node_tags = [self.n_t2i[int(t)] for t in tet_node_tags[0]]
+        tet_tags = np.squeeze(np.array(tet_tags))
+
+        self.tets = np.array(tet_node_tags).reshape(-1,4).T
+        self.tet_i2t = {i: int(t) for i, t in enumerate(tet_tags)}
+        self.tet_t2i = {t: i for i, t in self.tet_i2t.items()}
+
+        self.centers = (self.nodes[:,self.tets[0,:]] + self.nodes[:,self.tets[1,:]] + self.nodes[:,self.tets[2,:]] + self.nodes[:,self.tets[3,:]]) / 4
+        
+        # Resort node indices to be sorted on all periodic conditions
+        # This sorting makes sure that each edge and triangle on a source face is 
+        # sorted in the same order as the corresponding target face triangle or edge.
+        # In other words, if a source face triangle or edge index i1, i2, i3 is mapped to j1, j2, j3 respectively
+        # Then this ensures that if i1>i2>i3 then j1>j2>j3
+    
+        for bc in periodic_bcs:
+            nodemap, ids1, ids2 = self._derive_node_map(bc)
+            nodemap = {int(a): int(b) for a,b in nodemap.items()}
+            self.nodes[:,ids2] = self.nodes[:,ids1]
+            for itet in range(self.tets.shape[1]):
+                self.tets[:,itet] = [nodemap.get(i, i) for i in self.tets[:,itet]]
+            self.n_t2i = {t: nodemap.get(i,i) for t,i in self.n_t2i.items()}
+            self.n_i2t = {t: i for i, t in self.n_t2i.items()}
+
+        # Extract unique edges and triangles
+        edgeset = set()
+        triset = set()
+        for itet in range(self.tets.shape[1]):
+            i1, i2, i3, i4 = sorted([int(ind) for ind in self.tets[:, itet]])
+            edgeset.add((i1, i2))
+            edgeset.add((i1, i3))
+            edgeset.add((i1, i4))
+            edgeset.add((i2, i3))
+            edgeset.add((i2, i4))
+            edgeset.add((i3, i4))
+            triset.add((i1,i2,i3))
+            triset.add((i1,i2,i4))
+            triset.add((i1,i3,i4))
+            triset.add((i2,i3,i4))
+
+        # Edges are effectively Randomly sorted
+        # It contains index pairs of vertices edge 1 = (ev1, ev2) etc.
+        # Same for traingles
+        self.edges = np.array(sorted(list(edgeset))).T
+        self.tris = np.array(sorted(list(triset))).T
+        
+        self.tri_centers = (self.nodes[:,self.tris[0,:]] + self.nodes[:,self.tris[1,:]] + self.nodes[:,self.tris[2,:]]) / 3
+        def _hash(ints):
+            return tuple(sorted([int(x) for x in ints]))
+        
+        # Map edge index tuples to edge indices
+        # This mapping tells which characteristic index pair (4,3) maps to which edge
+        self.inv_edges = {(int(self.edges[0,i]), int(self.edges[1,i])): i for i in range(self.edges.shape[1])}
+        self.inv_tris = {_hash((self.tris[0,i], self.tris[1,i], self.tris[2,i])): i for i in range(self.tris.shape[1])}
+        self.inv_tets = {_hash((self.tets[0,i], self.tets[1,i], self.tets[2,i], self.tets[3,i])): i for i in range(self.tets.shape[1])}
+        
+        # Tet links
+
+        self.tet_to_edge = np.zeros((6, self.tets.shape[1]), dtype=int)-99999
+        self.tet_to_edge_sign = np.zeros((6, self.tets.shape[1]), dtype=int)-999999
+        self.tet_to_tri = np.zeros((4, self.tets.shape[1]), dtype=int)-99999
+        self.tet_to_tri_sign = np.zeros((4, self.tets.shape[1]), dtype=int)-999999
+
+        tri_to_tet = defaultdict(list)
+        for itet in range(self.tets.shape[1]):
+            edge_ids = [self.get_edge(self.tets[i-1,itet],self.tets[j-1,itet]) for i,j in zip([1, 1, 1, 2, 4, 3], [2, 3, 4, 3, 2, 4])]
+            id_signs = [self.get_edge_sign(self.tets[i-1,itet],self.tets[j-1,itet]) for i,j in zip([1, 1, 1, 2, 4, 3], [2, 3, 4, 3, 2, 4])]
+            self.tet_to_edge[:,itet] = edge_ids
+            self.tet_to_edge_sign[:,itet] = id_signs
+            self.tet_to_tri[:,itet] = [self.get_tri(self.tets[i-1,itet],self.tets[j-1,itet],self.tets[k-1,itet]) for i,j,k in zip([1, 1, 1, 2], [2, 3, 4, 3], [3, 4, 2, 4])]
+            
+            
+            self.tet_to_tri_sign[0,itet] = tri_ordering(self.tets[0,itet], self.tets[1,itet], self.tets[2,itet])
+            self.tet_to_tri_sign[1,itet] = tri_ordering(self.tets[0,itet], self.tets[2,itet], self.tets[3,itet])
+            self.tet_to_tri_sign[2,itet] = tri_ordering(self.tets[0,itet], self.tets[3,itet], self.tets[1,itet])
+            self.tet_to_tri_sign[3,itet] = tri_ordering(self.tets[1,itet], self.tets[2,itet], self.tets[3,itet])
+            
+            tri_to_tet[self.tet_to_tri[0, itet]].append(itet)
+            tri_to_tet[self.tet_to_tri[1, itet]].append(itet)
+            tri_to_tet[self.tet_to_tri[2, itet]].append(itet)
+            tri_to_tet[self.tet_to_tri[3, itet]].append(itet)
+        
+        # Tri links
+        self.tri_to_tet = np.zeros((2, self.tris.shape[1]), dtype=int)-1
+        for itri in range(self.tris.shape[1]):
+            tets = tri_to_tet[itri]
+            self.tri_to_tet[:len(tets), itri] = tets
+        
+        _, tet_tags, tet_node_tags = gmsh.model.mesh.get_elements(2)
+        
+        # The algorithm assumes that only one domain tag is returned in this function. 
+        # Hence the use of tri_node_tags[0] in the next line. If domains are missing.
+        # Make sure to combine all the entries in the tri-node-tags list
+        tet_node_tags = [self.n_t2i[int(t)] for t in tet_node_tags[0]]
+        tet_tags = np.squeeze(np.array(tet_tags))
+
+        self.tri_i2t = {self.get_tri(*self.tris[:,i]): int(t) for i, t in enumerate(tet_tags)}
+        self.tri_t2i = {t: i for i, t in self.tri_i2t.items()}
+
+        self.tri_to_edge = np.ndarray((3, self.tris.shape[1]), dtype=int)
+        self.tri_to_edge_sign = np.ndarray((3, self.tris.shape[1]), dtype=int)
+        self.edge_to_tri = defaultdict(list)
+
+        for itri in range(self.tris.shape[1]):
+            i1, i2, i3 = self.tris[:, itri]
+            ie1 = self.get_edge(i1,i2)
+            ie2 = self.get_edge(i2,i3)
+            ie3 = self.get_edge(i1,i3)
+            self.tri_to_edge[:,itri] = [ie1, ie2, ie3]
+            self.tri_to_edge_sign[:,itri] = [self.get_edge_sign(i1,i2), self.get_edge_sign(i2,i3), self.get_edge_sign(i3,i1)]
+            self.edge_to_tri[ie1].append(itri)
+            self.edge_to_tri[ie2].append(itri)
+            self.edge_to_tri[ie3].append(itri)
+
+        self.node_to_edge = defaultdict(list)
+        for eid in range(self.n_edges):
+            v1, v2 = self.edges[0, eid], self.edges[1, eid]
+            self.node_to_edge[v1].append(eid)
+            self.node_to_edge[v2].append(eid)
+
+        self.node_to_edge = {key: sorted(list(set(val))) for key, val in self.node_to_edge.items()}
+
+        ## Quantities
+
+        self.edge_centers = (self.nodes[:,self.edges[0,:]] + self.nodes[:,self.edges[1,:]]) / 2
+        self.edge_lengths = np.sqrt(np.sum((self.nodes[:,self.edges[0,:]] - self.nodes[:,self.edges[1,:]])**2, axis=0))
+        self.areas = np.array([area(self.nodes[:,self.tris[0,i]], self.nodes[:,self.tris[1,i]], self.nodes[:,self.tris[2,i]]) for i in range(self.tris.shape[1])])
+
+
+        ## Tag bindings
+        face_dimtags = gmsh.model.get_entities(2)
+        for d,t in face_dimtags:
+            domain_tag, f_tags, node_tags = gmsh.model.mesh.get_elements(2, t)
+            node_tags = [self.n_t2i[int(t)] for t in node_tags[0]]
+            self.ftag_to_node[t] = node_tags
+            node_tags = np.squeeze(np.array(node_tags)).reshape(-1,3).T
+            self.ftag_to_tri[t] = [self.get_tri(node_tags[0,i], node_tags[1,i], node_tags[2,i]) for i in range(node_tags.shape[1])]
+
+        vol_dimtags = gmsh.model.get_entities(3)
+        for d,t in vol_dimtags:
+            domain_tag, v_tags, node_tags = gmsh.model.mesh.get_elements(3, t)
+            node_tags = [self.n_t2i[int(t)] for t in node_tags[0]]
+            node_tags = np.squeeze(np.array(node_tags)).reshape(-1,4).T
+            self.vtag_to_tet[t] = [self.get_tet(node_tags[0,i], node_tags[1,i], node_tags[2,i], node_tags[3,i]) for i in range(node_tags.shape[1])]
+
+        self.defined = True
+
+
+    ## Higher order functions
+
+    def _derive_node_map(self, bc: Periodic) -> tuple[dict[int, int], np.ndarray, np.ndarray]:
+        """Computes an old to new node index mapping that preserves global sorting
+
+        Since basis function field direction is based on the order of indices in tetrahedron
+        for periodic boundaries it is important that all triangles and edges in each source
+        face are in the same order as the target face. This method computes the mapping for the
+        secondary face nodes
+
+        Args:
+            bc (Periodic): The Periodic boundary condition
+
+        Returns:
+            tuple[dict[int, int], np.ndarray, np.ndarray]: The node index mapping and the node index arrays
+        """
+
+        def gen_key(coord, mult):
+            return tuple([int(round(c*mult)) for c in coord])
+        
+        ftag_to_node = dict()
+        face_dimtags = gmsh.model.get_entities(2)
+
+        node_ids_1 = []
+        node_ids_2 = []
+        
+        for d,t in face_dimtags:
+            domain_tag, f_tags, node_tags = gmsh.model.mesh.get_elements(2, t)
+            node_tags = [self.n_t2i[int(t)] for t in node_tags[0]]
+            if t in bc.face1.tags:
+                node_ids_1.extend(node_tags)
+            if t in bc.face2.tags:
+                node_ids_2.extend(node_tags)
+            ftag_to_node[t] = node_tags
+        
+        all_node_ids = np.unique(np.array(node_ids_1 + node_ids_2))
+        dsmin = shortest_distance(self.nodes[:,all_node_ids])
+
+        node_ids_1 = sorted(list(set(node_ids_1)))
+        node_ids_2 = sorted(list(set(node_ids_2)))
+        dv = np.array(bc.dv)
+        nodemapdict = defaultdict(lambda: [None, None])
+        
+        mult = int(10**(-np.round(np.log10(dsmin))+2))
+        
+        for i1, i2 in zip(node_ids_1, node_ids_2):
+            nodemapdict[gen_key(self.nodes[:,i1], mult)][0] = i1
+            nodemapdict[gen_key(self.nodes[:,i2]-dv, mult)][1] = i2
+
+        nodemap = {i1: i2 for i1, i2 in nodemapdict.values()}
+
+        node_ids_2_unsorted = [nodemap[i] for i in sorted(node_ids_1)]
+        node_ids_2_sorted = sorted(node_ids_2_unsorted)
+        conv_map = {i1: i2 for i1, i2 in zip(node_ids_2_unsorted, node_ids_2_sorted)}
+        return conv_map, np.array(node_ids_2_unsorted), np.array(node_ids_2_sorted)
+
+
+    def retreive(self, material_selector: Callable, volumes: list[GeoVolume]) -> np.ndarray:
+        '''Retrieve the material properties of the geometry'''
+        arry = np.zeros((3,3,self.n_tets,), dtype=np.complex128)
+
+        xs = self.centers[0,:]
+        ys = self.centers[1,:]
+        zs = self.centers[2,:]
+        
+        for volume in sorted(volumes, key=lambda x: x._priority):
+        
+            for dimtag in volume.dimtags:
+                etype, etag_list, ntags = gmsh.model.mesh.get_elements(*dimtag)
+                for etags in etag_list:
+                    tet_ids = [self.tet_t2i[t] for t in etags]
+
+                    value = material_selector(volume.material, xs[tet_ids], ys[tet_ids], zs[tet_ids])
+                    arry[:,:,tet_ids] = value
+        return arry
+    
+    def plot_gmsh(self) -> None:
+        gmsh.fltk.run()
+
+    def find_edge_groups(self, edge_ids: np.ndarray) -> dict:
+        """
+        Find the groups of edges in the mesh.
+
+        Split an edge list into sets (islands) whose vertices are mutually connected.
+
+        Parameters
+        ----------
+        edges : np.ndarray, shape (2, N)
+            edges[0, i] and edges[1, i] are the two vertex indices of edge *i*.
+            The array may contain any (hashable) integer vertex labels, in any order.
+
+        Returns
+        -------
+        List[Tuple[int, ...]]
+            A list whose *k*‑th element is a `tuple` with the (zero‑based) **edge IDs**
+            that belong to the *k*‑th connected component.  Ordering is:
+            • components appear in the order in which their first edge is met,  
+            • edge IDs inside each tuple are sorted increasingly.
+
+        Notes
+        -----
+        * Only the connectivity of the supplied edges is considered.  
+        In particular, vertices that never occur in `edges` do **not** create extra
+        components.
+        * Runtime is *O*(N + V), with N = number of edges, V = number of
+        distinct vertices.  No external libraries are needed.
+        """
+        edges = self.edges[:,edge_ids]
+        if edges.ndim != 2 or edges.shape[0] != 2:
+            raise ValueError("`edges` must have shape (2, N)")
+
+        #n_edges: int = edges.shape[1]
+
+        # --- build “vertex ⇒ incident edge IDs” map ------------------------------
+        vert2edges = defaultdict(list)
+        for eid in edge_ids:
+            v1, v2 = self.edges[0, eid], self.edges[1, eid]
+            vert2edges[v1].append(eid)
+            vert2edges[v2].append(eid)
+        
+        groups = []
+
+        ungrouped = set(edge_ids)
+
+        group = [edge_ids[0],]
+        ungrouped.remove(edge_ids[0])
+
+        while True:
+            new_edges = set()
+            for edge in group:
+                v1, v2 = self.edges[0, edge], self.edges[1, edge]
+                new_edges.update(set(vert2edges[v1]))
+                new_edges.update(set(vert2edges[v2]))
+
+            new_edges = new_edges.intersection(ungrouped)
+            if len(new_edges) == 0:
+                groups.append(tuple(sorted(group)))
+                if len(ungrouped) == 0:
+                    break
+                group = [ungrouped.pop(),]
+            else:
+                group += list(new_edges)
+                ungrouped.difference_update(new_edges)
+
+        return groups
+
+    def boundary_surface(self, 
+                         face_tags: Union[int, list[int]], 
+                         origin: tuple[float, float, float] = None) -> SurfaceMesh:
+        tri_ids = self.get_triangles(face_tags)
+        if origin is None:
+            nodes = self.nodes[:,self.get_nodes(face_tags)]
+            x0 = np.mean(nodes[0,:])
+            y0 = np.mean(nodes[1,:])
+            z0 = np.mean(nodes[2,:])
+            origin = (x0, y0, z0)
+
+        return SurfaceMesh(self, tri_ids, origin)
+    
+class SurfaceMesh:
+
+    def __init__(self,
+                 original: Mesh3D,
+                 tri_ids: np.ndarray,
+                 origin: tuple[float, float, float]):
+        
+        ## Compute derived mesh properties
+        tris = original.tris[:, tri_ids]
+        unique_nodes = np.sort(np.unique(tris.flatten()))
+        new_ids = np.arange(unique_nodes.shape[0])
+        old_to_new_node_id_map = {a: b for a,b in zip(unique_nodes, new_ids)}
+        new_tris = np.array([[old_to_new_node_id_map[tris[i,j]] for i in range(3)] for j in range(tris.shape[1])]).T
+
+
+        ### Store information
+        self._tri_ids = tri_ids
+        self._origin = origin
+
+        self.original_tris: np.ndarray = original.tris
+
+        self.old_new_node_map: dict[int,int] = old_to_new_node_id_map
+        self.original: Mesh3D = original
+        self._alignment_origin: np.ndarray = np.array(origin).astype(np.float64)
+        self.nodes: np.ndarray = original.nodes[:, unique_nodes]
+        self.tris: np.ndarray = new_tris
+
+        ## initialize derived
+        self.edge_centers: np.ndarray = None
+        self.edge_tris: np.ndarray = None
+        self.n_nodes = self.nodes.shape[1]
+        self.n_tris = self.tris.shape[1]
+        self.n_edges = None
+        self.areas: np.ndarray = None
+        self.normals: np.ndarray = None
+
+        # Generate derived
+        self.update()
+
+    def copy(self) -> SurfaceMesh:
+        return SurfaceMesh(self.original, self._tri_ids, self._origin)
+    
+    def flip(self, ax: str) -> SurfaceMesh:
+        if ax.lower()=='x':
+            self.flipX()
+        if ax.lower()=='y':
+            self.flipY()
+        if ax.lower()=='z':
+            self.flipZ()
+        #self.tris[(0,1),:] = self.tris[(1,0),:]
+
+    def flipX(self) -> SurfaceMesh:
+        self.nodes[0,:] = -self.nodes[0,:]
+        self.normals[0,:] = -self.normals[0,:]
+        self.edge_centers[0,:] = -self.edge_centers[0,:]
+    
+    def flipY(self) -> SurfaceMesh:
+        self.nodes[1,:] = -self.nodes[1,:]
+        self.normals[1,:] = -self.normals[1,:]
+        self.edge_centers[1,:] = -self.edge_centers[1,:]
+    
+    def flipZ(self) -> SurfaceMesh:
+        self.nodes[2,:] = -self.nodes[2,:]
+        self.normals[2,:] = -self.normals[2,:]
+        self.edge_centers[2,:] = -self.edge_centers[2,:]
+
+    def from_source_tri(self, triid: int) -> int | None:
+        ''' Returns a triangle index from the old mesh to the new mesh.'''
+        i1in = self.original.tris[0,triid]
+        i2in = self.original.tris[1,triid]
+        i3in = self.original.tris[2,triid]
+        i1 = self.old_new_node_map.get(i1in,None)
+        i2 = self.old_new_node_map.get(i2in,None)
+        i3 = self.old_new_node_map.get(i3in,None)
+        if i1 is None or i2 is None or i3 is None:
+            return None
+        return self.get_tri(i1, i2, i3)
+    
+    def from_source_edge(self, edgeid: int) -> int | None:
+        ''' Returns an edge index form the old mesh to the new mesh.'''
+        i1 = self.old_new_node_map.get(self.original.edges[0,edgeid],None)
+        i2 = self.old_new_node_map.get(self.original.edges[1,edgeid],None)
+        if i1 is None or i2 is None:
+            return None
+        return self.get_edge(i1, i2)
+    
+    def get_edge(self, i1: int, i2: int) -> int:
+        '''Return the edge index given the two node indices'''
+        if i1==i2:
+            raise ValueError("Edge cannot be formed by the same node.")
+        search = (min(int(i1),int(i2)), max(int(i1),int(i2)))
+        result =  self.inv_edges.get(search, None)
+        return result
+    
+    def get_edge_sign(self, i1: int, i2: int) -> int:
+        '''Return the edge index given the two node indices'''
+        if i1==i2:
+            raise ValueError("Edge cannot be formed by the same node.")
+        if i1 > i2:
+            return -1
+        return 1
+        
+    def get_tri(self, i1, i2, i3) -> int:
+        '''Return the triangle index given the three node indices'''
+        return self.inv_tris.get(tuple(sorted((int(i1), int(i2), int(i3)))), None)
+    
+    def update(self) -> None:
+        ## First Edges
+
+        edges = set()
+        for i in range(self.n_tris):
+            i1, i2, i3 = self.tris[:,i]
+            edges.add((i1, i2))
+            edges.add((i2, i3))
+            edges.add((i1, i3))
+
+        edgelist = list(edges)
+
+        self.edges = np.array(edgelist).T
+        self.n_edges = self.edges.shape[1]
+        self.edge_centers = (self.nodes[:,self.edges[0,:]] + self.nodes[:,self.edges[1,:]])/2
+
+        ## Mapping from edge pairs to edge index
+         
+        def _hash(ints):
+            return tuple(sorted([int(x) for x in ints]))
+        
+        self.inv_edges = {(int(self.edges[0,i]), int(self.edges[1,i])): i for i in range(self.edges.shape[1])}
+        self.inv_tris = {_hash((self.tris[0,i], self.tris[1,i], self.tris[2,i])): i for i in range(self.tris.shape[1])}
+        ##
+        origin = self._alignment_origin
+
+        self.areas = np.array([area(self.nodes[:,self.tris[0,i]], 
+                                    self.nodes[:,self.tris[1,i]], 
+                                    self.nodes[:,self.tris[2,i]]) for i in range(self.n_tris)]).T
+        self.normals = np.array([outward_normal(
+                                    self.nodes[:,self.tris[0,i]], 
+                                    self.nodes[:,self.tris[1,i]], 
+                                    self.nodes[:,self.tris[2,i]], 
+                                    origin) for i in range(self.n_tris)]).T
+        
+        self.tri_to_edge = np.ndarray((3, self.tris.shape[1]), dtype=int)
+        self.edge_to_tri = defaultdict(list)
+
+        for itri in range(self.tris.shape[1]):
+            i1, i2, i3 = self.tris[:, itri]
+            ie1 = self.get_edge(i1,i2)
+            ie2 = self.get_edge(i2,i3)
+            ie3 = self.get_edge(i1,i3)
+            self.tri_to_edge[:,itri] = [ie1, ie2, ie3]
+        
+    @property
+    def exyz(self) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
+        return self.edge_centers[0,:], self.edge_centers[1,:], self.edge_centers[2,:]
+