emerge 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

emerge/_emerge/physics/microwave/adaptive_mesh.py

@@ -0,0 +1,576 @@
+# 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 .microwave_data import MWField
+import numpy as np
+from ...mth.optimized import matmul, outward_normal, cross_c
+from numba import njit, f8, c16, i8, types # type: ignore
+
+def compute_convergence(Sold: np.ndarray, Snew: np.ndarray) -> float:
+    """
+    Return a single scalar: max |Snew - Sold|.
+    Works for shapes (N,N) or (..., N, N); reduces over all axes.
+    """
+    Sold = np.asarray(Sold)
+    Snew = np.asarray(Snew)
+    if Sold.shape != Snew.shape:
+        raise ValueError("Sold and Snew must have identical shapes")
+    return float(np.abs(Snew - Sold).max())
+
+def select_refinement_indices(errors: np.ndarray, refine: float) -> np.ndarray:
+    """
+    Pick indices to refine based on two rules, then take the smaller set:
+      (A) All indices with |error| >= (1 - refine) * max(|error|)
+      (B) The top ceil(refine * N) indices by |error|
+    Returns indices sorted from largest to smallest |error|.
+    """
+    errs = np.abs(np.ravel(errors))
+    N = errs.size
+    if N == 0:
+        return np.array([], dtype=int)
+    refine = float(np.clip(refine, 0.0, 1.0))
+    if refine == 0.0:
+        return np.array([], dtype=int)
+
+    # Sorted indices by decreasing amplitude
+    sorted_desc = np.argsort(errs)[::-1]
+
+    # Rule A: threshold by amplitude
+    thresh = (1.0 - refine) * errs[sorted_desc[0]]
+    A = np.flatnonzero(errs >= thresh)
+
+    # Rule B: top-k by count
+    k = int(np.ceil(refine * N))
+    B = sorted_desc[:k]
+
+    # Choose the smaller set (tie-breaker: use B)
+    chosen = A if A.size < B.size else B
+    chosen = B
+    # Return chosen indices sorted from largest to smallest amplitude
+    mask = np.zeros(N, dtype=bool)
+    mask[chosen] = True
+    return sorted_desc[mask[sorted_desc]]
+
+
+def compute_size(id: int, coords: np.ndarray, q: float, dss: np.ndarray) -> float:
+    N = len(dss)
+    sizes = []
+    x, y, z = coords[:,id]
+    for n in range(N):
+        if n == id:
+            continue
+        nsize = dss[n]/q - (1-q)/q * ((x-coords[0,n])**2 + (y-coords[1,n])**2 + (z-coords[2,n])**2)**0.5
+        sizes.append(nsize)
+    return np.min(sizes)
+
+def reduce_point_set(coords: np.ndarray, q: float, dss: np.ndarray, scaler: float) -> list[int]:
+    N = len(dss)
+    candidates = []
+    for n in range(N):
+        nsize = compute_size(n, coords, q, dss)
+        if dss[n]*scaler*q**(0.4)< nsize:
+            candidates.append(0)
+        else:
+            candidates.append(1)
+    return [i for i in range(N) if candidates[i]==1]
+
+
+@njit(i8[:, :](i8[:], i8[:, :]), cache=True, nogil=True)
+def local_mapping(vertex_ids, triangle_ids):
+    """
+    Parameters
+    ----------
+    vertex_ids   : 1-D int64 array (length 4)
+        Global vertex 0.1005964238ers of one tetrahedron, in *its* order
+        (v0, v1, v2, v3).
+
+    triangle_ids : 2-D int64 array (nTri × 3)
+        Each row is a global-ID triple of one face that belongs to this tet.
+
+    Returns
+    -------
+    local_tris   : 2-D int64 array (nTri × 3)
+        Same triangles, but every entry replaced by the local index
+        0,1,2,3 that the vertex has inside this tetrahedron.
+        (Guaranteed to be ∈{0,1,2,3}; no -1 ever appears if the input
+        really belongs to the tet.)
+    """
+    ndim = triangle_ids.shape[0]
+    ntri = triangle_ids.shape[1]
+    out  = np.zeros(triangle_ids.shape, dtype=np.int64)
+
+    for t in range(ntri):                 # each triangle
+        for j in range(ndim):                # each vertex in that triangle
+            gid = triangle_ids[j, t]      # global ID to look up
+
+            # linear search over the four tet vertices
+            for k in range(4):
+                if vertex_ids[k] == gid:
+                    out[j, t] = k         # store local index 0-3
+                    break                 # stop the k-loop
+
+    return out
+
+@njit(f8(f8[:], f8[:], f8[:]), cache = True, nogil=True)
+def compute_volume(xs, ys, zs):
+    x1, x2, x3, x4 = xs
+    y1, y2, y3, y4 = ys
+    z1, z2, z3, z4 = zs
+
+    return np.abs(-x1*y2*z3/6 + x1*y2*z4/6 + x1*y3*z2/6 - x1*y3*z4/6 - x1*y4*z2/6 + x1*y4*z3/6 + x2*y1*z3/6 - x2*y1*z4/6 - x2*y3*z1/6 + x2*y3*z4/6 + x2*y4*z1/6 - x2*y4*z3/6 - x3*y1*z2/6 + x3*y1*z4/6 + x3*y2*z1/6 - x3*y2*z4/6 - x3*y4*z1/6 + x3*y4*z2/6 + x4*y1*z2/6 - x4*y1*z3/6 - x4*y2*z1/6 + x4*y2*z3/6 + x4*y3*z1/6 - x4*y3*z2/6)
+
+@njit(types.Tuple((f8[:], f8[:], f8[:], f8[:], f8))(f8[:], f8[:], f8[:]), cache = True, nogil=True)
+def tet_coefficients(xs, ys, zs):
+    ## THIS FUNCTION WORKS
+    x1, x2, x3, x4 = xs
+    y1, y2, y3, y4 = ys
+    z1, z2, z3, z4 = zs
+
+    aas = np.empty((4,), dtype=np.float64)
+    bbs = np.empty((4,), dtype=np.float64)
+    ccs = np.empty((4,), dtype=np.float64)
+    dds = np.empty((4,), dtype=np.float64)
+
+    V = np.abs(-x1*y2*z3/6 + x1*y2*z4/6 + x1*y3*z2/6 - x1*y3*z4/6 - x1*y4*z2/6 + x1*y4*z3/6 + x2*y1*z3/6 - x2*y1*z4/6 - x2*y3*z1/6 + x2*y3*z4/6 + x2*y4*z1/6 - x2*y4*z3/6 - x3*y1*z2/6 + x3*y1*z4/6 + x3*y2*z1/6 - x3*y2*z4/6 - x3*y4*z1/6 + x3*y4*z2/6 + x4*y1*z2/6 - x4*y1*z3/6 - x4*y2*z1/6 + x4*y2*z3/6 + x4*y3*z1/6 - x4*y3*z2/6)
+    
+    aas[0] = x2*y3*z4 - x2*y4*z3 - x3*y2*z4 + x3*y4*z2 + x4*y2*z3 - x4*y3*z2
+    aas[1] = -x1*y3*z4 + x1*y4*z3 + x3*y1*z4 - x3*y4*z1 - x4*y1*z3 + x4*y3*z1
+    aas[2] = x1*y2*z4 - x1*y4*z2 - x2*y1*z4 + x2*y4*z1 + x4*y1*z2 - x4*y2*z1
+    aas[3] = -x1*y2*z3 + x1*y3*z2 + x2*y1*z3 - x2*y3*z1 - x3*y1*z2 + x3*y2*z1
+    bbs[0] = -y2*z3 + y2*z4 + y3*z2 - y3*z4 - y4*z2 + y4*z3
+    bbs[1] = y1*z3 - y1*z4 - y3*z1 + y3*z4 + y4*z1 - y4*z3
+    bbs[2] = -y1*z2 + y1*z4 + y2*z1 - y2*z4 - y4*z1 + y4*z2
+    bbs[3] = y1*z2 - y1*z3 - y2*z1 + y2*z3 + y3*z1 - y3*z2
+    ccs[0] = x2*z3 - x2*z4 - x3*z2 + x3*z4 + x4*z2 - x4*z3
+    ccs[1] = -x1*z3 + x1*z4 + x3*z1 - x3*z4 - x4*z1 + x4*z3
+    ccs[2] = x1*z2 - x1*z4 - x2*z1 + x2*z4 + x4*z1 - x4*z2
+    ccs[3] = -x1*z2 + x1*z3 + x2*z1 - x2*z3 - x3*z1 + x3*z2
+    dds[0] = -x2*y3 + x2*y4 + x3*y2 - x3*y4 - x4*y2 + x4*y3
+    dds[1] = x1*y3 - x1*y4 - x3*y1 + x3*y4 + x4*y1 - x4*y3
+    dds[2] = -x1*y2 + x1*y4 + x2*y1 - x2*y4 - x4*y1 + x4*y2
+    dds[3] = x1*y2 - x1*y3 - x2*y1 + x2*y3 + x3*y1 - x3*y2
+
+    return aas, bbs, ccs, dds, V
+
+@njit(c16[:](f8[:], f8[:,:], c16[:], i8[:,:], i8[:,:]), cache=True, nogil=True)
+def compute_field(coords: np.ndarray, 
+                 vertices: np.ndarray,
+                 Etet: np.ndarray, 
+                 l_edge_ids: np.ndarray, 
+                 l_tri_ids: np.ndarray):
+    
+    x = coords[0]
+    y = coords[1]
+    z = coords[2]
+    
+    xvs = vertices[0,:]
+    yvs = vertices[1,:]
+    zvs = vertices[2,:]
+    
+    a_s, b_s, c_s, d_s, V = tet_coefficients(xvs, yvs, zvs)
+    
+    Em1s = Etet[0:6]
+    Ef1s = Etet[6:10]
+    Em2s = Etet[10:16]
+    Ef2s = Etet[16:20]
+    
+    Exl = 0.0 + 0.0j
+    Eyl = 0.0 + 0.0j
+    Ezl = 0.0 + 0.0j
+    
+    V1 = (216*V**3)
+    for ie in range(6):
+        Em1, Em2 = Em1s[ie], Em2s[ie]
+        edgeids = l_edge_ids[:, ie]
+        a1, a2 = a_s[edgeids]
+        b1, b2 = b_s[edgeids]
+        c1, c2 = c_s[edgeids]
+        d1, d2 = d_s[edgeids]
+        x1, x2 = xvs[edgeids]
+        y1, y2 = yvs[edgeids]
+        z1, z2 = zvs[edgeids]
+        F1 = (a1 + b1*x + c1*y + d1*z)
+        F2 = (a2 + b2*x + c2*y + d2*z)
+        L = np.sqrt((x1 - x2)**2 + (y1 - y2)**2 + (z1 - z2)**2)
+        ex =  L*(Em1*F1 + Em2*F2)*(b1*F2 - b2*F1)/V1
+        ey =  L*(Em1*F1 + Em2*F2)*(c1*F2 - c2*F1)/V1
+        ez =  L*(Em1*F1 + Em2*F2)*(d1*F2 - d2*F1)/V1
+
+        Exl += ex
+        Eyl += ey
+        Ezl += ez
+    
+    for ie in range(4):
+        Em1, Em2 = Ef1s[ie], Ef2s[ie]
+        triids = l_tri_ids[:, ie]
+        a1, a2, a3 = a_s[triids]
+        b1, b2, b3 = b_s[triids]
+        c1, c2, c3 = c_s[triids]
+        d1, d2, d3 = d_s[triids]
+
+        x1, x2, x3 = xvs[l_tri_ids[:, ie]]
+        y1, y2, y3 = yvs[l_tri_ids[:, ie]]
+        z1, z2, z3 = zvs[l_tri_ids[:, ie]]
+
+        L1 = np.sqrt((x1-x3)**2 + (y1-y3)**2 + (z1-z3)**2)
+        L2 = np.sqrt((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)
+        
+        F1 = (a1 + b1*x + c1*y + d1*z)
+        F2 = (a2 + b2*x + c2*y + d2*z)
+        F3 = (a3 + b3*x + c3*y + d3*z)
+        
+        Q1 = Em1*L1*F2
+        Q2 = Em2*L2*F3
+        ex =  (-Q1*(b1*F3 - b3*F1) + Q2*(b1*F2 - b2*F1))/V1
+        ey =  (-Q1*(c1*F3 - c3*F1) + Q2*(c1*F2 - c2*F1))/V1
+        ez =  (-Q1*(d1*F3 - d3*F1) + Q2*(d1*F2 - d2*F1))/V1
+        
+        Exl += ex
+        Eyl += ey
+        Ezl += ez
+
+    out = np.zeros((3,), dtype=np.complex128)
+    out[0] = Exl
+    out[1] = Eyl
+    out[2] = Ezl
+    return out
+
+@njit(c16[:,:](f8[:,:], f8[:,:], c16[:], i8[:,:], i8[:,:]), cache=True, nogil=True)
+def compute_curl(coords: np.ndarray, 
+                 vertices: np.ndarray,
+                 Etet: np.ndarray, 
+                 l_edge_ids: np.ndarray, 
+                 l_tri_ids: np.ndarray):
+    
+    x = coords[0,:]
+    y = coords[1,:]
+    z = coords[2,:]
+    
+    xvs = vertices[0,:]
+    yvs = vertices[1,:]
+    zvs = vertices[2,:]
+    
+    a_s, b_s, c_s, d_s, V = tet_coefficients(xvs, yvs, zvs)
+    
+    Em1s = Etet[0:6]
+    Ef1s = Etet[6:10]
+    Em2s = Etet[10:16]
+    Ef2s = Etet[16:20]
+    
+    Exl = np.zeros((x.shape[0],), dtype=np.complex128)
+    Eyl = np.zeros((x.shape[0],), dtype=np.complex128)
+    Ezl = np.zeros((x.shape[0],), dtype=np.complex128)
+    
+    V1 = (216*V**3)
+    V2 = (72*V**3)
+    
+    for ie in range(6):
+        Em1, Em2 = Em1s[ie], Em2s[ie]
+        edgeids = l_edge_ids[:, ie]
+        a1, a2 = a_s[edgeids]
+        b1, b2 = b_s[edgeids]
+        c1, c2 = c_s[edgeids]
+        d1, d2 = d_s[edgeids]
+        x1, x2 = xvs[edgeids]
+        y1, y2 = yvs[edgeids]
+        z1, z2 = zvs[edgeids]
+
+        L = np.sqrt((x1 - x2)**2 + (y1 - y2)**2 + (z1 - z2)**2)
+        C1 = Em1*a1
+        C2 = Em1*b1
+        C3 = Em1*c1
+        C4 = Em1*c2
+        C5 = Em2*a2
+        C6 = Em2*b2
+        C7 = Em2*c1
+        C8 = Em2*c2
+        C9 = Em1*b2
+        C10 = Em2*b1
+        D1 = c1*d2
+        D2 = c2*d1
+        D3 = d1*d2
+        D4 = d1*d1
+        D5 = c2*d2
+        D6 = d2*d2
+        D7 = b1*d2
+        D8 = b2*d1
+        D9 = c1*d1
+        D10 = b2*d2
+        D11 = b1*c2
+        D12 = b2*c1
+        D13 = c1*c2
+        D14 = c1*c1
+        D15 = b2*c2
+        
+        ex =  L*(-C1*D1 + C1*D2 - C2*D1*x + C2*D2*x - C3*D1*y + C3*D2*y - C3*D3*z + C4*D4*z - C5*D1 + C5*D2 - C6*D1*x + C6*D2*x - C7*D5*y - C7*D6*z + C8*D2*y + C8*D3*z)/V2
+        ey =  L*(C1*D7 - C1*D8 + C2*D7*x - C2*D8*x + C2*D1*y + C2*D3*z - C9*D9*y - C9*D4*z + C5*D7 - C5*D8 + C10*D10*x + C10*D5*y + C10*D6*z - C6*D8*x - C6*D2*y - C6*D3*z)/V2
+        ez =  L*(-C1*D11 + C1*D12 - C2*D11*x + C2*D12*x - C2*D13*y - C2*D2*z + C9*D14*y + C9*D9*z - C5*D11 + C5*D12 - C10*D15*x - C10*c2*c2*y - C10*D5*z + C6*D12*x + C6*D13*y + C6*D1*z)/V2
+        Exl += ex
+        Eyl += ey
+        Ezl += ez
+    
+    for ie in range(4):
+        Em1, Em2 = Ef1s[ie], Ef2s[ie]
+        triids = l_tri_ids[:, ie]
+        a1, a2, a3 = a_s[triids]
+        b1, b2, b3 = b_s[triids]
+        c1, c2, c3 = c_s[triids]
+        d1, d2, d3 = d_s[triids]
+
+        x1, x2, x3 = xvs[l_tri_ids[:, ie]]
+        y1, y2, y3 = yvs[l_tri_ids[:, ie]]
+        z1, z2, z3 = zvs[l_tri_ids[:, ie]]
+
+        L1 = np.sqrt((x1-x3)**2 + (y1-y3)**2 + (z1-z3)**2)
+        L2 = np.sqrt((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)
+        F1 = (a3 + b3*x + c3*y + d3*z)
+        F2 = (a1 + b1*x + c1*y + d1*z)
+        F3 = (a2 + b2*x + c2*y + d2*z)
+        N1 = (d1*F1 - d3*F2)
+        N2 = (c1*F1 - c3*F2)
+        N3 = (c1*d3 - c3*d1)
+        N4 = (d1*F3 - d2*F2)
+        N5 = (c1*F3 - c2*F2)
+        D1 = c1*d2
+        D2 = c2*d1
+        N6 = (D1 - D2)
+        N7 = (b1*F1 - b3*F2)
+        N8 = (b1*d3 - b3*d1)
+        N9 = (b1*F3 - b2*F2)
+        D7 = b1*d2
+        D8 = b2*d1
+        N10 = (D7 - D8)
+        D11 = b1*c2
+        D12 = b2*c1
+        ex =  (Em1*L1*(-c2*N1 + d2*N2 + 2*N3*F3) - Em2*L2*(-c3*N4 + d3*N5 + 2*N6*F1))/V1
+        ey =  (-Em1*L1*(-b2*N1 + d2*N7 + 2*N8*F3) + Em2*L2*(-b3*N4 + d3*N9 + 2*N10*F1))/V1
+        ez =  (Em1*L1*(-b2*N2 + c2*N7 + 2*(b1*c3 - b3*c1)*F3) - Em2*L2*(-b3*N5 + c3*N9 + 2*(D11 - D12)*F1))/V1
+        
+        Exl += ex
+        Eyl += ey
+        Ezl += ez
+
+    out = np.zeros((3,x.shape[0]), dtype=np.complex128)
+    out[0,:] = Exl
+    out[1,:] = Eyl
+    out[2,:] = Ezl
+    return out
+
+@njit(c16[:](f8[:], f8[:,:], c16[:], i8[:,:], i8[:,:], c16[:,:]), cache=True, nogil=True)
+def compute_curl_curl(coords: np.ndarray, 
+                    vertices: np.ndarray,
+                    Etet: np.ndarray, 
+                    l_edge_ids: np.ndarray, 
+                    l_tri_ids: np.ndarray,
+                    Um: np.ndarray):
+    
+    uxx, uxy, uxz = Um[0,0], Um[0,1], Um[0,2]
+    uyx, uyy, uyz = Um[1,0], Um[1,1], Um[1,2]
+    uzx, uzy, uzz = Um[2,0], Um[2,1], Um[2,2]
+    
+    x = coords[0]
+    y = coords[1]
+    z = coords[2]
+    
+    xvs = vertices[0,:]
+    yvs = vertices[1,:]
+    zvs = vertices[2,:]
+    
+    Exl = 0.0 + 0.0j
+    Eyl = 0.0 + 0.0j
+    Ezl = 0.0 + 0.0j
+    
+    a_s, b_s, c_s, d_s, V = tet_coefficients(xvs, yvs, zvs)
+    
+    Em1s = Etet[0:6]
+    Ef1s = Etet[6:10]
+    Em2s = Etet[10:16]
+    Ef2s = Etet[16:20]
+    
+    V1 = (216*V**3)
+    
+    for ie in range(6):
+        Em1, Em2 = Em1s[ie], Em2s[ie]
+        edgeids = l_edge_ids[:, ie]
+        a1, a2 = a_s[edgeids]
+        b1, b2 = b_s[edgeids]
+        c1, c2 = c_s[edgeids]
+        d1, d2 = d_s[edgeids]
+        x1, x2 = xvs[edgeids]
+        y1, y2 = yvs[edgeids]
+        z1, z2 = zvs[edgeids]
+
+        L1 = np.sqrt((x1 - x2)**2 + (y1 - y2)**2 + (z1 - z2)**2)
+        ex = -3*L1*(Em1*(b1*c1*c2*uzz - b1*c1*d2*uzy - b1*c2*d1*uyz + b1*d1*d2*uyy - b2*c1**2*uzz + b2*c1*d1*uyz + b2*c1*d1*uzy - b2*d1**2*uyy + c1**2*d2*uzx - c1*c2*d1*uzx - c1*d1*d2*uyx + c2*d1**2*uyx) + Em2*(b1*c2**2*uzz - b1*c2*d2*uyz - b1*c2*d2*uzy + b1*d2**2*uyy - b2*c1*c2*uzz + b2*c1*d2*uyz + b2*c2*d1*uzy - b2*d1*d2*uyy + c1*c2*d2*uzx - c1*d2**2*uyx - c2**2*d1*uzx + c2*d1*d2*uyx))
+        ey = 3*L1*(Em1*(b1**2*c2*uzz - b1**2*d2*uzy - b1*b2*c1*uzz + b1*b2*d1*uzy + b1*c1*d2*uzx - b1*c2*d1*uxz - b1*c2*d1*uzx + b1*d1*d2*uxy + b2*c1*d1*uxz - b2*d1**2*uxy - c1*d1*d2*uxx + c2*d1**2*uxx) + Em2*(b1*b2*c2*uzz - b1*b2*d2*uzy - b1*c2*d2*uxz + b1*d2**2*uxy - b2**2*c1*uzz + b2**2*d1*uzy + b2*c1*d2*uxz + b2*c1*d2*uzx - b2*c2*d1*uzx - b2*d1*d2*uxy - c1*d2**2*uxx + c2*d1*d2*uxx))
+        ez = -3*L1*(Em1*(b1**2*c2*uyz - b1**2*d2*uyy - b1*b2*c1*uyz + b1*b2*d1*uyy - b1*c1*c2*uxz + b1*c1*d2*uxy + b1*c1*d2*uyx - b1*c2*d1*uyx + b2*c1**2*uxz - b2*c1*d1*uxy - c1**2*d2*uxx + c1*c2*d1*uxx) + Em2*(b1*b2*c2*uyz - b1*b2*d2*uyy - b1*c2**2*uxz + b1*c2*d2*uxy - b2**2*c1*uyz + b2**2*d1*uyy + b2*c1*c2*uxz + b2*c1*d2*uyx - b2*c2*d1*uxy - b2*c2*d1*uyx - c1*c2*d2*uxx + c2**2*d1*uxx))
+        
+        Exl += ex*V1
+        Eyl += ey*V1
+        Ezl += ez*V1
+    
+    for ie in range(4):
+        Em1, Em2 = Ef1s[ie], Ef2s[ie]
+        triids = l_tri_ids[:, ie]
+        a1, a2, a3 = a_s[triids]
+        b1, b2, b3 = b_s[triids]
+        c1, c2, c3 = c_s[triids]
+        d1, d2, d3 = d_s[triids]
+
+        x1, x2, x3 = xvs[l_tri_ids[:, ie]]
+        y1, y2, y3 = yvs[l_tri_ids[:, ie]]
+        z1, z2, z3 = zvs[l_tri_ids[:, ie]]
+
+        L1 = np.sqrt((x1-x3)**2 + (y1-y3)**2 + (z1-z3)**2)
+        L2 = np.sqrt((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)
+        
+        ex = L1*(Em1*L1*(3*c2*uzx*(c1*d3 - c3*d1) + 3*c2*uzz*(b1*c3 - b3*c1) - 3*d2*uyx*(c1*d3 - c3*d1) + 3*d2*uyy*(b1*d3 - b3*d1) - uyz*(-b2*(c1*d3 - c3*d1) + c2*(b1*d3 - b3*d1) + 2*d2*(b1*c3 - b3*c1)) - uzy*(b2*(c1*d3 - c3*d1) + 2*c2*(b1*d3 - b3*d1) + d2*(b1*c3 - b3*c1))) - Em2*L2*(3*c3*uzx*(c1*d2 - c2*d1) + 3*c3*uzz*(b1*c2 - b2*c1) - 3*d3*uyx*(c1*d2 - c2*d1) + 3*d3*uyy*(b1*d2 - b2*d1) - uyz*(-b3*(c1*d2 - c2*d1) + c3*(b1*d2 - b2*d1) + 2*d3*(b1*c2 - b2*c1)) - uzy*(b3*(c1*d2 - c2*d1) + 2*c3*(b1*d2 - b2*d1) + d3*(b1*c2 - b2*c1))))
+        ey = L1*(Em1*L1*(3*b2*uzy*(b1*d3 - b3*d1) - 3*b2*uzz*(b1*c3 - b3*c1) + 3*d2*uxx*(c1*d3 - c3*d1) - 3*d2*uxy*(b1*d3 - b3*d1) + uxz*(-b2*(c1*d3 - c3*d1) + c2*(b1*d3 - b3*d1) + 2*d2*(b1*c3 - b3*c1)) - uzx*(2*b2*(c1*d3 - c3*d1) + c2*(b1*d3 - b3*d1) - d2*(b1*c3 - b3*c1))) - Em2*L2*(3*b3*uzy*(b1*d2 - b2*d1) - 3*b3*uzz*(b1*c2 - b2*c1) + 3*d3*uxx*(c1*d2 - c2*d1) - 3*d3*uxy*(b1*d2 - b2*d1) + uxz*(-b3*(c1*d2 - c2*d1) + c3*(b1*d2 - b2*d1) + 2*d3*(b1*c2 - b2*c1)) - uzx*(2*b3*(c1*d2 - c2*d1) + c3*(b1*d2 - b2*d1) - d3*(b1*c2 - b2*c1))))
+        ez = -L1*(Em1*L1*(3*b2*uyy*(b1*d3 - b3*d1) - 3*b2*uyz*(b1*c3 - b3*c1) + 3*c2*uxx*(c1*d3 - c3*d1) + 3*c2*uxz*(b1*c3 - b3*c1) - uxy*(b2*(c1*d3 - c3*d1) + 2*c2*(b1*d3 - b3*d1) + d2*(b1*c3 - b3*c1)) - uyx*(2*b2*(c1*d3 - c3*d1) + c2*(b1*d3 - b3*d1) - d2*(b1*c3 - b3*c1))) - Em2*L2*(3*b3*uyy*(b1*d2 - b2*d1) - 3*b3*uyz*(b1*c2 - b2*c1) + 3*c3*uxx*(c1*d2 - c2*d1) + 3*c3*uxz*(b1*c2 - b2*c1) - uxy*(b3*(c1*d2 - c2*d1) + 2*c3*(b1*d2 - b2*d1) + d3*(b1*c2 - b2*c1)) - uyx*(2*b3*(c1*d2 - c2*d1) + c3*(b1*d2 - b2*d1) - d3*(b1*c2 - b2*c1)))) 
+        
+        Exl += ex*V1
+        Eyl += ey*V1
+        Ezl += ez*V1
+
+    out = np.zeros((3,), dtype=np.complex128)
+    out[0] = Exl
+    out[1] = Eyl
+    out[2] = Ezl
+    return out
+
+@njit(types.Tuple((f8[:], f8[:]))(f8[:,:], i8[:,:], i8[:,:], i8[:,:], f8[:,:],
+                                  c16[:], f8[:], f8[:], i8[:,:], i8[:,:],
+                                  f8[:,:], i8[:,:], i8[:,:], c16[:], c16[:], f8), cache=True, nogil=True)
+def compute_error_single(nodes, tets, tris, edges, centers, 
+                         Efield, 
+                         edge_lengths,
+                         areas,
+                         tet_to_edge, 
+                         tet_to_tri, 
+                         tri_centers, 
+                         tri_to_tet,
+                         tet_to_field, 
+                         er, 
+                         ur,
+                         k0,) -> np.ndarray:
+
+
+    # UNPACK DATA
+    ntet = tets.shape[1]
+    nedges = edges.shape[1]
+    
+    
+    # INIT POSTERIORI ERROR ESTIMATE
+    error = np.zeros((ntet,), dtype=np.float64)
+    max_elem_size = np.zeros((ntet,), dtype=np.float64)
+    
+    hks = np.zeros((ntet,), dtype=np.float64)
+    hfs = np.zeros((4,ntet), dtype=np.float64)
+    face_error1 = np.zeros((4,3,ntet), dtype=np.complex128)
+    face_error2 = np.zeros((4,3,ntet), dtype=np.complex128)
+    
+
+    # Compute Error estimate
+    for itet in range(ntet):
+        uinv = (1/ur[itet])*np.eye(3)
+        ermat = er[itet]*np.eye(3)
+        
+        vertices = nodes[:,tets[:, itet]]
+        
+        g_node_ids = tets[:, itet]
+        g_edge_ids = edges[:, tet_to_field[:6, itet]]
+        g_tri_ids = tris[:, tet_to_field[6:10, itet]-nedges]
+
+        l_edge_ids = local_mapping(g_node_ids, g_edge_ids)
+        l_tri_ids = local_mapping(g_node_ids, g_tri_ids)
+
+        coords = centers[:,itet]
+        Ef = Efield[tet_to_field[:,itet]]
+        Rv1 = -compute_curl_curl(coords, vertices, Ef, l_edge_ids, l_tri_ids, uinv)
+        Rv2 = k0**2*(ermat @ compute_field(coords, vertices, Ef, l_edge_ids, l_tri_ids))
+        
+        triids = tet_to_tri[:,itet]
+        facecoords = tri_centers[:, triids]
+        
+        Volume = compute_volume(vertices[0,:], vertices[1,:], vertices[2,:])
+        hks[itet] = Volume**(1/3)
+        Rf = matmul(uinv, compute_curl(facecoords, vertices, Ef, l_edge_ids, l_tri_ids))
+        tetc = centers[:,itet].flatten()
+        
+        max_elem_size[itet] = np.mean(edge_lengths[tet_to_edge[:,itet]])
+        
+        for iface in range(4):
+            i1, i2, i3 = tris[:, triids[iface]]
+            normal = outward_normal(nodes[:,i1], nodes[:,i2], nodes[:,i3], tetc).astype(np.complex128)
+            
+            adj_tets = [int(tri_to_tet[j,triids[iface]]) for j in range(2)]
+            adj_tets = [num for num in adj_tets if num not in (itet, -1234)]
+            
+            if len(adj_tets) == 0:
+                continue
+            area = areas[triids[iface]]
+            
+            hfs[iface,itet] = area**0.5
+            
+            itet_adj = adj_tets[0]
+            iface_adj = np.argwhere(tet_to_tri[:,itet_adj]==triids[iface])[0][0]
+            
+            face_error2[iface_adj, :, itet_adj] = -area*cross_c(normal, uinv @ Rf[:, iface])
+            face_error1[iface, :, itet] = area*cross_c(normal, uinv @ Rf[:,iface])
+        
+
+        error[itet] = np.linalg.norm(np.abs(Volume*(Rv1 + Rv2)))**2
+    
+    fdiff = np.abs(face_error1 - face_error2)
+    fnorm = fdiff[:,0,:]**2 + fdiff[:,1,:]**2 + fdiff[:,2,:]**2
+    ferror = np.sum(fnorm*hfs, axis=0)
+    error = hks**2*error + 0.5*ferror
+
+    return error, max_elem_size
+
+def compute_error_estimate(field: MWField) -> np.ndarray:
+    mesh = field.mesh
+
+    nodes = mesh.nodes
+    tris = mesh.tris
+    tets = mesh.tets
+    edges = mesh.edges
+    centers = mesh.centers
+    
+    As = mesh.areas
+    tet_to_edge = mesh.tet_to_edge
+    tet_to_tri = mesh.tet_to_tri
+    tri_centers = mesh.tri_centers
+    tri_to_tet = mesh.tri_to_tet
+    tet_to_field = field.basis.tet_to_field
+    er = field._der
+    ur = field._dur
+    Ls = mesh.edge_lengths
+    
+    errors = []
+    for key in field._fields.keys():
+        excitation = field._fields[key]
+        
+        error, sizes = compute_error_single(nodes, tets, tris, edges,
+                             centers, excitation, Ls, As, 
+                             tet_to_edge, tet_to_tri, tri_centers,
+                             tri_to_tet, tet_to_field, er, ur, field.k0)
+        
+        errors.append(error)
+    
+    error = np.max(np.array(errors), axis=0)
+    return error, sizes

emerge/_emerge/physics/microwave/assembly/assembler.py

@@ -105,7 +105,7 @@ class Assembler:
     def __init__(self, settings: Settings):
         
         self.cached_matrices = None
-        self.settings = settings
+        self.settings: Settings = settings
     
     def assemble_bma_matrices(self,
                               field: Nedelec2,
@@ -186,11 +186,12 @@ class Assembler:
 
         return E, B, np.array(solve_ids), nedlegfield
 
-    def assemble_freq_matrix(self, field: Nedelec2, 
-                        materials: list[Material],
-                        bcs: list[BoundaryCondition],
-                        frequency: float,
-                        cache_matrices: bool = False) -> SimJob:
+    def assemble_freq_matrix(self, 
+                             field: Nedelec2, 
+                            materials: list[Material],
+                            bcs: list[BoundaryCondition],
+                            frequency: float,
+                            cache_matrices: bool = False) -> SimJob:
         """Assembles the frequency domain FEM matrix
 
         Args: