emerge 0.4.7__py3-none-any.whl → 0.4.8__py3-none-any.whl

emerge/_emerge/mesher.py

@@ -0,0 +1,339 @@
+# 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/>.
+
+import gmsh
+from .geometry import GeoVolume, GeoObject, GeoSurface
+from .selection import Selection, FaceSelection
+from .periodic import PeriodicCell
+import numpy as np
+from typing import Iterable, Callable
+from loguru import logger
+from enum import Enum
+from .bc import Periodic
+
+class MeshError(Exception):
+    pass
+
+class Algorithm2D(Enum):
+    MESHADAPT = 1
+    AUTOMATIC = 2
+    INITIAL_MESH_ONLY = 3
+    DELAUNAY = 5
+    FRONTAL_DELAUNAY = 6
+    BAMG = 7
+    FRONTAL_DELAUNAY_QUADS = 8
+    PACKING_PARALLELOGRAMS = 9
+    QUASI_STRUCTURED_QUAD = 11
+
+#(1: Delaunay, 3: Initial mesh only, 4: Frontal, 7: MMG3D, 9: R-tree, 10: HXT)
+
+class Algorithm3D(Enum):
+    DELAUNAY = 1
+    INITIAL_MESH_ONLY = 3
+    FRONTAL = 4
+    MMG3D = 7
+    RTREE = 9
+    HXT = 10
+
+_DOM_TO_STR = {
+    0: "point",
+    1: "edge",
+    2: "face",
+    3: "volume",
+}
+def unpack_lists(_list: list[list], collector: list = None) -> list:
+    '''Unpack a recursive list of lists'''
+    if collector is None:
+        collector = []
+    for item in _list:
+        if isinstance(item, list):
+            unpack_lists(item, collector)
+        else:
+            collector.append(item)
+    
+    return collector
+
+class Mesher:
+
+    def __init__(self):
+        self.objects: list[GeoObject] = []
+        self.size_definitions: list[tuple[int, float]] = []
+        self.mesh_fields: list[int] = []
+        self.min_size: float = None
+        self.max_size: float = None
+        self.periodic_cell: PeriodicCell = None
+
+    @property
+    def edge_tags(self) -> list[int]:
+        return [tag[1] for tag in gmsh.model.getEntities(1)]
+    
+    @property
+    def face_tags(self) -> list[int]:
+        return [tag[1] for tag in gmsh.model.getEntities(2)]
+    
+    @property
+    def node_tags(self) -> list[int]:
+        return [tag[1] for tag in gmsh.model.getEntities(0)]
+    
+    @property
+    def volumes(self) -> list[GeoVolume]:
+        return [obj for obj in self.objects if isinstance(obj, GeoVolume)]
+    
+    @property
+    def domain_boundary_face_tags(self) -> list[int]:
+        '''Get the face tags of the domain boundaries'''
+        domain_tags = gmsh.model.getEntities(3)
+        tags = gmsh.model.getBoundary(domain_tags, combined=True, oriented=False)
+        return [int(tag[1]) for tag in tags]
+    
+    @property
+    def domain_internal_face_tags(self) -> list[int]:
+        alltags = self.face_tags
+        boundary = self.domain_boundary_face_tags
+        return [tag for tag in alltags if tag not in boundary]
+    
+    def _get_periodic_bcs(self) -> list[Periodic]:
+        if self.periodic_cell is None:
+            return []
+        return self.periodic_cell._bcs
+    
+    def _check_ready(self) -> None:
+        if self.max_size is None or self.min_size is None:
+            raise MeshError('Either maximum or minimum mesh size is undefined. Make sure \
+                            to set the simulation frequency range before calling mesh instructions.')
+    
+    def submit_objects(self, objects: list[GeoObject]) -> None:
+        """Takes al ist of GeoObjects and computes the fragment. 
+
+        Args:
+            objects (list[GeoObject]): The set of GeoObjects
+        """
+        if not isinstance(objects, list):
+            objects = [objects,]
+
+        objects = unpack_lists(objects)
+        embeddings = []
+
+        gmsh.model.occ.synchronize()
+
+        final_dimtags = unpack_lists([domain.dimtags for domain in objects])
+
+        dom_mapping = dict()
+        for dom in objects:
+            embeddings.extend(dom._embeddings)
+            for dt in dom.dimtags:
+                dom_mapping[dt] = dom
+        
+
+        embedding_dimtags = unpack_lists([emb.dimtags for emb in embeddings])
+
+        tag_mapping: dict[int, dict] = {0: dict(),
+                                        1: dict(),
+                                        2: dict(),
+                                        3: dict()}
+        if len(objects) > 0:
+            dimtags, output_mapping = gmsh.model.occ.fragment(final_dimtags, embedding_dimtags)
+
+            for domain, mapping in zip(final_dimtags + embedding_dimtags, output_mapping):
+                tag_mapping[domain[0]][domain[1]] = [o[1] for o in mapping]
+            for dom in objects:
+                dom.update_tags(tag_mapping)
+        else:
+            dimtags = final_dimtags
+        
+        self.objects = objects
+        
+        gmsh.model.occ.synchronize()
+
+    def _set_mesh_periodicity(self, 
+                     face1: FaceSelection,
+                     face2: FaceSelection,
+                     lattice: tuple[float,float,float]):
+        translation = [1,0,0,lattice[0],
+                       0,1,0,lattice[1],
+                       0,0,1,lattice[2],
+                       0,0,0,1]
+        gmsh.model.mesh.set_periodic(2, face2.tags, face1.tags, translation)
+
+    def set_algorithm(self,
+                      obj: GeoObject,
+                      algorithm: Algorithm3D) -> None:
+        for tag in obj.tags:
+            gmsh.model.mesh.setAlgorithm(obj.dim, tag, algorithm.value)
+            
+    def set_periodic_cell(self, cell: PeriodicCell, excluded_faces: list[FaceSelection] = None):
+        """Sets the periodic cell information based on the PeriodicCell class object"""
+        if excluded_faces is None:
+            for f1, f2, lat in cell.cell_data():
+                self._set_mesh_periodicity(f1, f2, lat)
+        else:
+            for f1, f2, lat in cell.cell_data():
+                self._set_mesh_periodicity(f1 - excluded_faces, f2 - excluded_faces, lat)
+        self.periodic_cell = cell
+
+    def _set_size_in_domain(self, tags: list[int], max_size: float) -> None:
+        """Define the size of the mesh inside a domain
+
+        Args:
+            tags (list[int]): The tags of the geometry
+            max_size (float): The maximum size (in meters)
+        """
+        ctag = gmsh.model.mesh.field.add("Constant")
+        gmsh.model.mesh.field.set_numbers(ctag, "VolumesList", tags)
+        gmsh.model.mesh.field.set_number(ctag, "VIn", max_size)
+        self.mesh_fields.append(ctag)
+
+    def _set_size_on_face(self, tags: list[int], max_size: float) -> None:
+        """Define the size of the mesh on a face
+
+        Args:
+            tags (list[int]): The tags of the geometry
+            max_size (float): The maximum size (in meters)
+        """
+        ctag = gmsh.model.mesh.field.add("Constant")
+        gmsh.model.mesh.field.set_numbers(ctag, "SurfacesList", tags)
+        gmsh.model.mesh.field.set_number(ctag, "VIn", max_size)
+        self.mesh_fields.append(ctag)
+
+    def set_mesh_size(self, discretizer: Callable, resolution: float):
+        
+        dimtags = gmsh.model.occ.get_entities(2)
+
+        for dim, tag in dimtags:
+            gmsh.model.mesh.setSizeFromBoundary(2, tag, 0)
+
+        mintag = gmsh.model.mesh.field.add("Min")
+        size_mapping = dict()
+
+        for obj in sorted(self.objects, key=lambda x: x._priority):
+            if obj._unset_constraints:
+                self.unset_constraints(obj.dimtags)
+
+            size = discretizer(obj.material)*resolution*obj.mesh_multiplier
+            size = min(size, obj.max_meshsize)
+            logger.info(f'Setting mesh size for {_DOM_TO_STR[obj.dim]} domain with tags {obj.tags} to {1000*size:.3f}mm')
+            for tag in obj.tags:
+                size_mapping[tag] = size
+        
+        for tag, size in size_mapping.items():
+            self._set_size_in_domain([tag,], size)
+
+        gmsh.model.mesh.field.setNumbers(mintag, "FieldsList", self.mesh_fields)
+        gmsh.model.mesh.field.setAsBackgroundMesh(mintag)
+
+        for tag, size in self.size_definitions:
+            gmsh.model.mesh.setSize([tag,], size)
+
+    def unset_constraints(self, dimtags: list[tuple[int,int]]):
+        '''Unset the mesh constraints for the given dimension tags.'''
+        for dimtag in dimtags:
+            gmsh.model.mesh.setSizeFromBoundary(dimtag[0], dimtag[1], 0)
+            
+    def set_boundary_size(self, object: GeoSurface | FaceSelection, 
+                          size:float,
+                          growth_rate: float = 1.4,
+                          max_size: float = None):
+        """Refine the mesh size along the boundary of a conducting surface
+
+        Args:
+            object (GeoSurface | FaceSelection): _description_
+            size (float): _description_
+            growth_rate (float, optional): _description_. Defaults to 1.1.
+            max_size (float, optional): _description_. Defaults to None.
+        """
+        
+        dimtags = object.dimtags
+
+        if max_size is None:
+            self._check_ready()
+            max_size = self.max_size
+        
+        growth_distance = np.log10(max_size/size)/np.log10(growth_rate)
+        
+        nodes = gmsh.model.getBoundary(dimtags, combined=False, oriented=False, recursive=False)
+
+        disttag = gmsh.model.mesh.field.add("Distance")
+
+        gmsh.model.mesh.field.setNumbers(disttag, "CurvesList", [n[1] for n in nodes])
+        gmsh.model.mesh.field.setNumber(disttag, "Sampling", 100)
+
+        thtag = gmsh.model.mesh.field.add("Threshold")
+        gmsh.model.mesh.field.setNumber(thtag, "InField", disttag)
+        gmsh.model.mesh.field.setNumber(thtag, "SizeMin", size)
+        gmsh.model.mesh.field.setNumber(thtag, "SizeMax", max_size)
+        gmsh.model.mesh.field.setNumber(thtag, "DistMin", size)
+        gmsh.model.mesh.field.setNumber(thtag, "DistMax", growth_distance*size)
+    
+        self.mesh_fields.append(thtag)
+
+    def set_domain_size(self, obj: GeoVolume | Selection, size: float):
+        """Manually set the maximum element size inside a domain
+
+        Args:
+            obj (GeoVolume | Selection): The volumetric domain
+            size (float): The maximum mesh size
+        """
+        self._set_size_in_domain(obj.tags, size)
+
+    def set_face_size(self, obj: GeoSurface | Selection, size: float):
+        """Manually set the maximum element size on a face
+
+        Args:
+            obj (GeoSurface | Selection): The surface domain
+            size (float): The maximum size
+        """
+        self._set_size_on_face(obj.tags, size)
+        
+    def refine_conductor_edge(self, dimtags: list[tuple[int,int]], size):
+        nodes = gmsh.model.getBoundary(dimtags, combined=False, recursive=False)
+
+        # for node in nodes:
+        #     pcoords = np.linspace(0, 0.5, 10)
+        #     gmsh.model.mesh.setSizeAtParametricPoints(node[0], node[1], pcoords, size*np.ones_like(pcoords))
+        #     #self.size_definitions.append((node, size))
+        # gmsh.model.mesh.setSizeFromBoundary(dimtag[0], dimtag[1], 0)
+
+        tag = gmsh.model.mesh.field.add("Distance")
+
+        #gmsh.model.mesh.field.setNumbers(1, "PointsList", [5])
+        gmsh.model.mesh.field.setNumbers(tag, "CurvesList", [n[1] for n in nodes])
+        gmsh.model.mesh.field.setNumber(tag, "Sampling", 100)
+
+        # We then define a `Threshold' field, which uses the return value of the
+        # `Distance' field 1 in order to define a simple change in element size
+        # depending on the computed distances
+        #
+        # SizeMax -                     /------------------
+        #                              /
+        #                             /
+        #                            /
+        # SizeMin -o----------------/
+        #          |                |    |
+        #        Point         DistMin  DistMax
+        thtag = gmsh.model.mesh.field.add("Threshold")
+        gmsh.model.mesh.field.setNumber(thtag, "InField", tag)
+        gmsh.model.mesh.field.setNumber(thtag, "SizeMin", size)
+        gmsh.model.mesh.field.setNumber(thtag, "SizeMax", 100)
+        gmsh.model.mesh.field.setNumber(thtag, "DistMin", 0.2*size)
+        gmsh.model.mesh.field.setNumber(thtag, "DistMax", 5*size)
+
+        self.mesh_fields.append(thtag)
+        
+
+        for dimtag in dimtags:
+            gmsh.model.mesh.setSizeFromBoundary(dimtag[0], dimtag[1], 0)
+

emerge/_emerge/mth/common_functions.py

@@ -0,0 +1,33 @@
+# 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/>.
+
+import numpy as np
+
+def  norm(Field: np.ndarray) -> np.ndarray:
+    ''' Computes the complex norm of a field (3,N)'''
+    return np.sqrt(np.abs(Field[0,:])**2 + np.abs(Field[1,:])**2 + np.abs(Field[2,:])**2)
+
+def coax_rout(rin: float,
+              eps_r: float = 1,
+              Z0: float = 50) -> float:
+    return rin*10**(Z0*np.sqrt(eps_r)/138)
+
+def coax_rin(rout: float,
+              eps_r: float = 1,
+              Z0: float = 50) -> float:
+    return rout/10**(Z0*np.sqrt(eps_r)/138)
+

emerge/_emerge/mth/integrals.py

@@ -0,0 +1,71 @@
+# 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/>.
+
+import numpy as np
+from typing import Callable
+from numba import njit, f8, i8, types, c16
+from .optimized import gaus_quad_tri, generate_int_points_tri, calc_area
+
+
+@njit(c16(f8[:,:], i8[:,:], c16[:], f8[:,:], c16[:,:]), cache=True, nogil=True)
+def _fast_integral_c(nodes, triangles, constants, DPTs, field_values):
+    tot = np.complex128(0.0)
+
+    for it in range(triangles.shape[1]):
+        vertex_ids = triangles[:, it]
+        v1 = nodes[:,vertex_ids[0]]
+        v2 = nodes[:,vertex_ids[1]]
+        v3 = nodes[:,vertex_ids[2]]
+        A = calc_area(v1, v2, v3)
+        field = np.sum(DPTs[0,:]*field_values[:,it])
+        tot = tot + constants[it] * field * A
+    return tot
+
+@njit(f8(f8[:,:], i8[:,:], f8[:], f8[:,:], f8[:,:]), cache=True, nogil=True)
+def _fast_integral_f(nodes, triangles, constants, DPTs, field_values):
+    tot = np.float64(0.0)
+    for it in range(triangles.shape[1]):
+        vertex_ids = triangles[:, it]
+        v1 = nodes[:,vertex_ids[0]]
+        v2 = nodes[:,vertex_ids[1]]
+        v3 = nodes[:,vertex_ids[2]]
+        A = calc_area(v1, v2, v3)
+        field = np.sum(DPTs[0,:]*field_values[:,it])
+        tot = tot + constants[it] * field * A
+    return tot
+
+def surface_integral(nodes: np.ndarray, 
+                     triangles: np.ndarray, 
+                     function: Callable, 
+                     constants: np.ndarray = None,
+                     ndpts: int = 4):
+
+    if constants is None:
+        constants = np.ones(triangles.shape[1])
+        
+    DPTs = gaus_quad_tri(ndpts)
+    xall_flat, yall_flat, zall_flat, shape = generate_int_points_tri(nodes, triangles, DPTs)
+
+    fvals = function(xall_flat, yall_flat, zall_flat)
+
+    fA = fvals.reshape(shape)
+
+    if np.iscomplexobj(fA) or np.iscomplexobj(constants):
+        return _fast_integral_c(nodes, triangles, constants.astype(np.complex128), DPTs, fA.astype(np.complex128))
+    else:
+        return _fast_integral_f(nodes, triangles, constants, DPTs, fA)
+