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Add connectivity computation (#197)
* Add connectivity computation * Add identity computations of connectivity * Fix gmsh import * Fix create connectivity
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-130
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10 files changed

+48
-130
lines changed

‎chapter1/complex_mode.ipynb

Lines changed: 13 additions & 114 deletions
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@@ -39,19 +39,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"id": "b52b39d9-260d-4c54-b62a-7440c3b92e5a",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"float64\n",
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"complex128\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"from mpi4py import MPI\n",
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"import dolfinx\n",
@@ -80,18 +71,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"id": "4d5b03e3-4d7f-45b7-95eb-9130a5141f34",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<class 'numpy.complex128'>\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"from petsc4py import PETSc\n",
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"from dolfinx.fem.petsc import assemble_vector\n",
@@ -110,7 +93,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"id": "be8461a0-a089-4ff3-8bc8-61b016407e70",
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"metadata": {},
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"outputs": [],
@@ -137,19 +120,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"id": "779ab267-4609-4628-9577-a280b9c18b6d",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"{ c_0 * (conj((v_0))) } * dx(<Mesh #0>[everywhere], {})\n",
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"{ c_0 * (conj((v_0))) } * dx(<Mesh #0>[everywhere], {})\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"L2 = f * ufl.conj(v) * ufl.dx\n",
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"print(L)\n",
@@ -166,78 +140,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"id": "d61c477a-d364-4a81-9362-42f1eb4cd8ee",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[4.21666667e-03+3.33333333e-05j 1.58750000e-03+8.33333333e-06j\n",
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" 4.68333333e-03+1.00000000e-04j 8.13333333e-03+2.66666667e-04j\n",
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" 3.35000000e-03+3.33333333e-05j 4.68333333e-03+3.66666667e-04j\n",
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" 6.43333333e-03+2.66666667e-04j 8.13333333e-03+8.66666667e-04j\n",
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" 2.58333333e-03+3.33333333e-05j 4.68333333e-03+8.33333333e-04j\n",
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" 4.93333333e-03+2.66666667e-04j 6.43333333e-03+8.66666667e-04j\n",
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" 8.13333333e-03+1.86666667e-03j 1.91666667e-03+3.33333333e-05j\n",
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" 4.68333333e-03+1.50000000e-03j 3.63333333e-03+2.66666667e-04j\n",
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" 4.93333333e-03+8.66666667e-04j 6.43333333e-03+1.86666667e-03j\n",
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" 8.13333333e-03+3.26666667e-03j 1.35000000e-03+3.33333333e-05j\n",
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" 4.68333333e-03+2.36666667e-03j 2.53333333e-03+2.66666667e-04j\n",
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" 3.63333333e-03+8.66666667e-04j 4.93333333e-03+1.86666667e-03j\n",
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" 6.43333333e-03+3.26666667e-03j 8.13333333e-03+5.06666667e-03j\n",
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" 8.83333333e-04+3.33333333e-05j 4.68333333e-03+3.43333333e-03j\n",
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" 1.63333333e-03+2.66666667e-04j 2.53333333e-03+8.66666667e-04j\n",
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" 3.63333333e-03+1.86666667e-03j 4.93333333e-03+3.26666667e-03j\n",
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" 6.43333333e-03+5.06666667e-03j 8.13333333e-03+7.26666667e-03j\n",
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" 5.16666667e-04+3.33333333e-05j 4.68333333e-03+4.70000000e-03j\n",
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" 9.33333333e-04+2.66666667e-04j 1.63333333e-03+8.66666667e-04j\n",
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" 2.53333333e-03+1.86666667e-03j 3.63333333e-03+3.26666667e-03j\n",
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" 4.93333333e-03+5.06666667e-03j 6.43333333e-03+7.26666667e-03j\n",
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" 8.13333333e-03+9.86666667e-03j 2.50000000e-04+3.33333333e-05j\n",
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" 4.68333333e-03+6.16666667e-03j 4.33333333e-04+2.66666667e-04j\n",
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" 9.33333333e-04+8.66666667e-04j 1.63333333e-03+1.86666667e-03j\n",
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" 2.53333333e-03+3.26666667e-03j 3.63333333e-03+5.06666667e-03j\n",
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" 4.93333333e-03+7.26666667e-03j 6.43333333e-03+9.86666667e-03j\n",
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" 8.13333333e-03+1.28666667e-02j 8.33333333e-05+3.33333333e-05j\n",
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" 4.68333333e-03+7.83333333e-03j 1.33333333e-04+2.66666667e-04j\n",
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" 4.33333333e-04+8.66666667e-04j 9.33333333e-04+1.86666667e-03j\n",
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" 1.63333333e-03+3.26666667e-03j 2.53333333e-03+5.06666667e-03j\n",
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" 3.63333333e-03+7.26666667e-03j 4.93333333e-03+9.86666667e-03j\n",
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" 6.43333333e-03+1.28666667e-02j 8.13333333e-03+1.62666667e-02j\n",
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" 1.25000000e-05+2.50000000e-05j 3.09583333e-03+6.19166667e-03j\n",
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" 1.66666667e-05+1.66666667e-04j 1.33333333e-04+8.66666667e-04j\n",
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" 4.33333333e-04+1.86666667e-03j 9.33333333e-04+3.26666667e-03j\n",
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" 1.63333333e-03+5.06666667e-03j 2.53333333e-03+7.26666667e-03j\n",
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" 3.63333333e-03+9.86666667e-03j 4.93333333e-03+1.28666667e-02j\n",
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" 6.43333333e-03+1.62666667e-02j 3.91666667e-03+9.36666667e-03j\n",
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" 1.66666667e-05+5.00000000e-04j 1.33333333e-04+1.86666667e-03j\n",
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" 4.33333333e-04+3.26666667e-03j 9.33333333e-04+5.06666667e-03j\n",
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" 1.63333333e-03+7.26666667e-03j 2.53333333e-03+9.86666667e-03j\n",
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" 3.63333333e-03+1.28666667e-02j 4.93333333e-03+1.62666667e-02j\n",
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" 3.08333333e-03+9.36666667e-03j 1.66666667e-05+1.03333333e-03j\n",
220-
" 1.33333333e-04+3.26666667e-03j 4.33333333e-04+5.06666667e-03j\n",
221-
" 9.33333333e-04+7.26666667e-03j 1.63333333e-03+9.86666667e-03j\n",
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" 2.53333333e-03+1.28666667e-02j 3.63333333e-03+1.62666667e-02j\n",
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" 2.35000000e-03+9.36666667e-03j 1.66666667e-05+1.76666667e-03j\n",
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" 1.33333333e-04+5.06666667e-03j 4.33333333e-04+7.26666667e-03j\n",
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" 9.33333333e-04+9.86666667e-03j 1.63333333e-03+1.28666667e-02j\n",
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" 2.53333333e-03+1.62666667e-02j 1.71666667e-03+9.36666667e-03j\n",
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" 1.66666667e-05+2.70000000e-03j 1.33333333e-04+7.26666667e-03j\n",
228-
" 4.33333333e-04+9.86666667e-03j 9.33333333e-04+1.28666667e-02j\n",
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" 1.63333333e-03+1.62666667e-02j 1.18333333e-03+9.36666667e-03j\n",
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" 1.66666667e-05+3.83333333e-03j 1.33333333e-04+9.86666667e-03j\n",
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" 4.33333333e-04+1.28666667e-02j 9.33333333e-04+1.62666667e-02j\n",
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" 7.50000000e-04+9.36666667e-03j 1.66666667e-05+5.16666667e-03j\n",
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" 1.33333333e-04+1.28666667e-02j 4.33333333e-04+1.62666667e-02j\n",
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" 4.16666667e-04+9.36666667e-03j 1.66666667e-05+6.70000000e-03j\n",
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" 1.33333333e-04+1.62666667e-02j 1.83333333e-04+9.36666667e-03j\n",
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" 1.66666667e-05+8.43333333e-03j 5.00000000e-05+9.36666667e-03j\n",
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" 4.16666667e-06+3.17500000e-03j]\n"
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]
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}
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],
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"outputs": [],
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"source": [
242148
"J = u_c**2 * ufl.dx\n",
243149
"F = ufl.derivative(J, u_c, ufl.conj(v))\n",
@@ -256,7 +162,7 @@
256162
},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": null,
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"id": "eb2357ae-ac71-4407-bf37-432f1b1e31d0",
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"metadata": {},
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"outputs": [],
@@ -281,18 +187,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"id": "f51d9a7a-2cde-4d0f-8606-91f91c372c4b",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"(0.0007865435216227239+0.0017660156338113711j) 3.553078358632328e-06\n"
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]
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}
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],
193+
"outputs": [],
296194
"source": [
297195
"x = ufl.SpatialCoordinate(mesh)\n",
298196
"u_ex = 0.5 * x[0]**2 + 1j*x[1]**2\n",
@@ -322,6 +220,7 @@
322220
"source": [
323221
"import pyvista\n",
324222
"pyvista.start_xvfb()\n",
223+
"mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
325224
"p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))\n",
326225
"pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)\n",
327226
"grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, geometry)\n",

‎chapter1/complex_mode.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.16.1
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# jupytext_version: 1.15.2
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# kernelspec:
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# display_name: Python 3 (DOLFINx complex)
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# language: python
@@ -126,6 +126,7 @@
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127127
import pyvista
128128
pyvista.start_xvfb()
129+
mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
129130
p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))
130131
pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
131132
grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, geometry)

‎chapter1/fundamentals_code.ipynb

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@@ -453,6 +453,7 @@
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"source": [
454454
"from dolfinx import plot\n",
455455
"pyvista.start_xvfb()\n",
456+
"domain.topology.create_connectivity(tdim, tdim)\n",
456457
"topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)\n",
457458
"grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)"
458459
]

‎chapter1/fundamentals_code.py

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@@ -6,7 +6,7 @@
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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.16.1
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# jupytext_version: 1.15.2
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python
@@ -232,6 +232,7 @@
232232
# + vscode={"languageId": "python"}
233233
from dolfinx import plot
234234
pyvista.start_xvfb()
235+
domain.topology.create_connectivity(tdim, tdim)
235236
topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)
236237
grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
237238
# -

‎chapter2/ns_code1.ipynb

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@@ -579,6 +579,7 @@
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"glyphs = function_grid.glyph(orient=\"u\", factor=0.2)\n",
580580
"\n",
581581
"# Create a pyvista-grid for the mesh\n",
582+
"mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
582583
"grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))\n",
583584
"\n",
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"# Create plotter\n",

‎chapter2/ns_code1.py

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@@ -6,7 +6,7 @@
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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.16.1
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# jupytext_version: 1.15.2
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python
@@ -345,6 +345,7 @@ def u_exact(x):
345345
glyphs = function_grid.glyph(orient="u", factor=0.2)
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347347
# Create a pyvista-grid for the mesh
348+
mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
348349
grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))
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# Create plotter

‎chapter3/em.ipynb

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@@ -1077,8 +1077,10 @@
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"source": [
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"pyvista.start_xvfb()\n",
10791079
"plotter = pyvista.Plotter()\n",
1080-
"grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))\n",
1081-
"num_local_cells = mesh.topology.index_map(mesh.topology.dim).size_local\n",
1080+
"tdim = mesh.topology.dim\n",
1081+
"mesh.topology.create_connectivity(tdim, tdim)\n",
1082+
"grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, tdim))\n",
1083+
"num_local_cells = mesh.topology.index_map(tdim).size_local\n",
10821084
"grid.cell_data[\"Marker\"] = ct.values[ct.indices < num_local_cells]\n",
10831085
"grid.set_active_scalars(\"Marker\")\n",
10841086
"actor = plotter.add_mesh(grid, show_edges=True)\n",
@@ -1288,6 +1290,7 @@
12881290
"# We include ghosts cells as we access all degrees of freedom (including ghosts) on each process\n",
12891291
"top_imap = mesh.topology.index_map(mesh.topology.dim)\n",
12901292
"num_cells = top_imap.size_local + top_imap.num_ghosts\n",
1293+
"mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
12911294
"midpoints = compute_midpoints(mesh, mesh.topology.dim, np.arange(num_cells, dtype=np.int32))\n",
12921295
"\n",
12931296
"num_dofs = W.dofmap.index_map.size_local + W.dofmap.index_map.num_ghosts\n",

‎chapter3/em.py

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@@ -6,7 +6,7 @@
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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.16.1
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# jupytext_version: 1.15.2
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python
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pyvista.start_xvfb()
214214
plotter = pyvista.Plotter()
215-
grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))
216-
num_local_cells = mesh.topology.index_map(mesh.topology.dim).size_local
215+
tdim = mesh.topology.dim
216+
mesh.topology.create_connectivity(tdim, tdim)
217+
grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, tdim))
218+
num_local_cells = mesh.topology.index_map(tdim).size_local
217219
grid.cell_data["Marker"] = ct.values[ct.indices < num_local_cells]
218220
grid.set_active_scalars("Marker")
219221
actor = plotter.add_mesh(grid, show_edges=True)
@@ -312,6 +314,7 @@
312314
# We include ghosts cells as we access all degrees of freedom (including ghosts) on each process
313315
top_imap = mesh.topology.index_map(mesh.topology.dim)
314316
num_cells = top_imap.size_local + top_imap.num_ghosts
317+
mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
315318
midpoints = compute_midpoints(mesh, mesh.topology.dim, np.arange(num_cells, dtype=np.int32))
316319

317320
num_dofs = W.dofmap.index_map.size_local + W.dofmap.index_map.num_ghosts

‎chapter3/subdomains.ipynb

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@@ -169,13 +169,15 @@
169169
"uh = problem.solve()\n",
170170
"\n",
171171
"# Filter out ghosted cells\n",
172-
"num_cells_local = mesh.topology.index_map(mesh.topology.dim).size_local\n",
172+
"tdim = mesh.topology.dim\n",
173+
"num_cells_local = mesh.topology.index_map(tdim).size_local\n",
173174
"marker = np.zeros(num_cells_local, dtype=np.int32)\n",
174175
"cells_0 = cells_0[cells_0 < num_cells_local]\n",
175176
"cells_1 = cells_1[cells_1 < num_cells_local]\n",
176177
"marker[cells_0] = 1\n",
177178
"marker[cells_1] = 2\n",
178-
"topology, cell_types, x = vtk_mesh(mesh, mesh.topology.dim, np.arange(num_cells_local, dtype=np.int32))\n",
179+
"mesh.topology.create_connectivity(tdim, tdim)\n",
180+
"topology, cell_types, x = vtk_mesh(mesh, tdim, np.arange(num_cells_local, dtype=np.int32))\n",
179181
"\n",
180182
"p = pyvista.Plotter(window_size=[800, 800])\n",
181183
"grid = pyvista.UnstructuredGrid(topology, cell_types, x)\n",
@@ -552,9 +554,11 @@
552554
"# As the dolfinx.MeshTag contains a value for every cell in the\n",
553555
"# geometry, we can attach it directly to the grid\n",
554556
"\n",
555-
"topology, cell_types, x = vtk_mesh(mesh, mesh.topology.dim)\n",
557+
"tdim = mesh.topology.dim\n",
558+
"mesh.topology.create_connectivity(tdim, tdim)\n",
559+
"topology, cell_types, x = vtk_mesh(mesh, tdim)\n",
556560
"grid = pyvista.UnstructuredGrid(topology, cell_types, x)\n",
557-
"num_local_cells = mesh.topology.index_map(mesh.topology.dim).size_local\n",
561+
"num_local_cells = mesh.topology.index_map(tdim).size_local\n",
558562
"grid.cell_data[\"Marker\"] = ct.values[ct.indices < num_local_cells]\n",
559563
"grid.set_active_scalars(\"Marker\")\n",
560564
"\n",

‎chapter3/subdomains.py

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -106,13 +106,15 @@ def Omega_1(x):
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uh = problem.solve()
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# Filter out ghosted cells
109-
num_cells_local = mesh.topology.index_map(mesh.topology.dim).size_local
109+
tdim = mesh.topology.dim
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num_cells_local = mesh.topology.index_map(tdim).size_local
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marker = np.zeros(num_cells_local, dtype=np.int32)
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cells_0 = cells_0[cells_0 < num_cells_local]
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cells_1 = cells_1[cells_1 < num_cells_local]
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marker[cells_0] = 1
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marker[cells_1] = 2
115-
topology, cell_types, x = vtk_mesh(mesh, mesh.topology.dim, np.arange(num_cells_local, dtype=np.int32))
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mesh.topology.create_connectivity(tdim, tdim)
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topology, cell_types, x = vtk_mesh(mesh, tdim, np.arange(num_cells_local, dtype=np.int32))
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p = pyvista.Plotter(window_size=[800, 800])
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grid = pyvista.UnstructuredGrid(topology, cell_types, x)
@@ -277,9 +279,11 @@ def create_mesh(mesh, cell_type, prune_z=False):
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# As the dolfinx.MeshTag contains a value for every cell in the
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# geometry, we can attach it directly to the grid
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280-
topology, cell_types, x = vtk_mesh(mesh, mesh.topology.dim)
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tdim = mesh.topology.dim
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mesh.topology.create_connectivity(tdim, tdim)
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topology, cell_types, x = vtk_mesh(mesh, tdim)
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grid = pyvista.UnstructuredGrid(topology, cell_types, x)
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num_local_cells = mesh.topology.index_map(mesh.topology.dim).size_local
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num_local_cells = mesh.topology.index_map(tdim).size_local
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grid.cell_data["Marker"] = ct.values[ct.indices < num_local_cells]
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grid.set_active_scalars("Marker")
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