diff --git a/src/bvpy/domains/abstract.py b/src/bvpy/domains/abstract.py
index c284b621833bd94f30fba53336ff3ab75b3ccf3e..2aa00aca77bc40f636248e39be97f2640e9218c0 100644
--- a/src/bvpy/domains/abstract.py
+++ b/src/bvpy/domains/abstract.py
@@ -391,6 +391,11 @@ class AbstractDomain(ABC):
if self.mesh is not None:
self.model.mesh.clear()
+ if not self.volumes:
+ self.model.addPhysicalGroup(dim, [self.surfaces[0]])
+ else:
+ self.model.addPhysicalGroup(dim, [self.volumes[0]])
+
self.model.mesh.generate(dim)
self.mesh, cell_markers, facet_markers = gmshio.model_to_mesh(self.model, MPI.COMM_SELF, 0)
# self.bdata = _generate_default_boundary_data(self.mesh)
diff --git a/src/bvpy/domains/primitives.py b/src/bvpy/domains/primitives.py
index 52e751c225627247c6ae8a91b068a6d161fb3d5b..b8c73901870f24aa1d0beb202b4b6a2c9e393e64 100644
--- a/src/bvpy/domains/primitives.py
+++ b/src/bvpy/domains/primitives.py
@@ -150,10 +150,8 @@ class Rectangle(AbstractDomain, OccModel):
None
"""
- _dim = 2
self.surfaces[0] = self.factory.addRectangle(x, y, 0, length, width)
self.synchronize()
- self.model.addPhysicalGroup(_dim, [self.surfaces[0]])
class Disk(AbstractDomain, OccModel):
"""Instanciates a circular domain.
@@ -277,14 +275,10 @@ class Disk(AbstractDomain, OccModel):
None
"""
- _dim = 2
- _tag = [1]
-
circle = self.factory.addCircle(*center, radius)
curve_loop = self.factory.addCurveLoop([circle], circle)
self.surfaces[0] = self.factory.addPlaneSurface([curve_loop])
self.synchronize()
- self.model.addPhysicalGroup(_dim, [self.surfaces[0]])
class HemiSphere(AbstractDomain, BuiltInModel):
@@ -486,6 +480,7 @@ class Cube(AbstractDomain, OccModel):
def __init__(self, x=0, y=0, z=0, dx=1, dy=1, dz=1, **kwargs):
super(Cube, self).__init__(**kwargs)
self._characteristic_size = {}
+ self._cell_type = 'tetra'
self.geometry(x, y, z, dx, dy, dz)
def geometry(self, x, y, z, dx, dy, dz):
@@ -498,6 +493,7 @@ class Cylinder(AbstractDomain, OccModel):
dx=0, dy=0, dz=1, r=0.5, open=False, **kwargs):
super(Cylinder, self).__init__(**kwargs)
self._characteristic_size = {}
+ self._cell_type = 'tetra'
self.geometry(x, y, z, dx, dy, dz, r, open)
def geometry(self, x, y, z, dx, dy, dz, r, open):
@@ -604,6 +600,7 @@ class Sphere(AbstractDomain, OccModel):
"""
super(Sphere, self).__init__(**kwargs)
self._characteristic_size = {'Radius': radius}
+ self._cell_type = 'tetra'
self.geometry(radius, center)
def geometry(self, radius, center):
@@ -622,17 +619,9 @@ class Sphere(AbstractDomain, OccModel):
None
"""
- # self.volumes[0] = self.factory.addSphere(*center, radius)
- # self.synchronize()
-
- _dim = 2
- _tag = [1]
- self.surfaces[0] = self.factory.addSphere(*center, radius)
+ self.volumes[0] = self.factory.addSphere(*center, radius)
self.synchronize()
- self.model.addPhysicalGroup(_dim, [self.surfaces[0]])
- # self.model.mesh.generate(_dim)
-
-
+
class Ellipsoid(AbstractDomain, OccModel):
"""Instanciates an Ellispoid domain.
@@ -731,6 +720,7 @@ class Ellipsoid(AbstractDomain, OccModel):
super(Ellipsoid, self).__init__(**kwargs)
self._characteristic_size = {'Oxy radius': radius_xy,
'Oz radius': radius_z}
+ self._cell_type = 'tetra'
self.geometry(radius_xy, radius_z, center)
def geometry(self, radius_xy, radius_z, center=[0, 0, 0]):
@@ -756,7 +746,6 @@ class Ellipsoid(AbstractDomain, OccModel):
self.volumes[0] = self.factory.addSphere(*center, radius_z)
self.factory.dilate([(3, self.volumes[0])], *center, ratio, ratio, 1)
self.synchronize()
- self.model.addPhysicalGroup(2, [self.volumes[0]])
class Torus(AbstractDomain, OccModel):
@@ -883,4 +872,3 @@ class Torus(AbstractDomain, OccModel):
"""
self.surfaces[0] = self.factory.addTorus(*center, main_radius, tube_radius)
self.synchronize()
- self.model.addPhysicalGroup(2, [self.surfaces[0]])
diff --git a/tutorials/bvpy_tutorial_2_domains.ipynb b/tutorials/bvpy_tutorial_2_domains.ipynb
index e99e1299a5acce48012b6257b5903b32d1843d34..21223f26862f5f82ca3222de60c257dade1f0782 100644
--- a/tutorials/bvpy_tutorial_2_domains.ipynb
+++ b/tutorials/bvpy_tutorial_2_domains.ipynb
@@ -46,15 +46,7 @@
"cell_type": "code",
"execution_count": 1,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "####### Rectangle\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"from bvpy.domains import Rectangle\n",
"domain = Rectangle()"
@@ -77,7 +69,6 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "####### Rectangle 2\n",
"Number of triangles within the domain AFTER discretization: 4\n"
]
}
@@ -153,7 +144,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "72bb02fedfcd464faa86c5f07de28589",
+ "model_id": "962f1bb475cb45eca0a1228b7b6c41ae",
"version_major": 2,
"version_minor": 0
},
@@ -191,21 +182,13 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 5,
"metadata": {},
"outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Info : Clearing all models and views...\n",
- "Info : Done clearing all models and views\n"
- ]
- },
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "7face6d24f314334a03f15805958abf8",
+ "model_id": "e561ccff5399482eb3d4928de75f32ee",
"version_major": 2,
"version_minor": 0
},
@@ -226,8 +209,7 @@
"\n",
"d1 = Rectangle(length=2, width=3, clear=True)\n",
"\n",
- "# TODO methode pas propre ??\n",
- "d1.set_cell_size(.1)\n",
+ "d1.set_cell_size(.05)\n",
"\n",
"plot(d1)\n"
]
@@ -249,13 +231,13 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "4a3a113f374547749ae6a5a01cdeff4c",
+ "model_id": "b5db0aa22c1945e0b82b57bafae8c249",
"version_major": 2,
"version_minor": 0
},
@@ -281,13 +263,13 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "298b8023f3014b1f811f3a36b17a7765",
+ "model_id": "3d3f14eed8fa4bf4b371dd7395cd9005",
"version_major": 2,
"version_minor": 0
},
@@ -314,7 +296,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 1,
"metadata": {},
"outputs": [
{
@@ -336,6 +318,8 @@
],
"source": [
"from bvpy.domains import HemiSphere\n",
+ "from bvpy.utils.visu import plot, set_renderer\n",
+ "\n",
"hsph = HemiSphere(cell_size=0.1, clear=True)\n",
"plot(hsph)"
]
@@ -349,21 +333,13 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 9,
"metadata": {},
"outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Info : Clearing all models and views...\n",
- "Info : Done clearing all models and views\n"
- ]
- },
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "1013193846f44b1787cc7f3d66354a06",
+ "model_id": "f4c9b9021ef04184b2a14e75c4f45d32",
"version_major": 2,
"version_minor": 0
},
@@ -391,13 +367,13 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "f2c103eabca941508ed07a529681d6c5",
+ "model_id": "f282dc8ea0864d71b137db207b31f06f",
"version_major": 2,
"version_minor": 0
},
@@ -424,13 +400,13 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "67b2c90594e34945a4e117801cd1ae51",
+ "model_id": "47d8a09373f244449677019fb66eafd7",
"version_major": 2,
"version_minor": 0
},
@@ -471,13 +447,13 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "2984515db25541c1b1888b3a3a5ab4fe",
+ "model_id": "890f8e1bdad14aae8149deda32465d1d",
"version_major": 2,
"version_minor": 0
},
@@ -497,14 +473,12 @@
" \n",
"set_renderer('notebook')\n",
"\n",
- "#TODO : how these operations are done\n",
"dsk1 = Disk(center=[0, -.25, 0], clear=True, cell_size=.1)\n",
"dsk2 = Disk(center=[0, .25, 0])\n",
- "# dsk3 = Disk(radius=.3)\n",
- "rec1 = Rectangle(y=-.05, x=-.5, length=10, width=.1)\n",
+ "dsk3 = Disk(radius=.3)\n",
+ "rec1 = Rectangle(y=-.05, x=-.5, length=1, width=.1)\n",
"\n",
- "# cmplx_dom = dsk1 & dsk2 - (dsk3 + rec1)\n",
- "cmplx_dom = rec1 \n",
+ "cmplx_dom = dsk1 & dsk2 - (dsk3 + rec1)\n",
"\n",
"plot(cmplx_dom)"
]
@@ -525,10 +499,28 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 13,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "9acdb0a75a5441a79109755fdb731a71",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "ViewInteractiveWidget(height=768, layout=Layout(height='auto', width='100%'), width=1024)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
+ "from bvpy.domains import Sphere\n",
+ "from bvpy.utils.visu import plot, set_renderer\n",
+ "\n",
"sph1 = Sphere(clear=True)\n",
"sph2 = Sphere(center=[0,1,0], radius=.5)\n",
"\n",
@@ -547,9 +539,24 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 14,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "132ea445eae74e7f836119b4b35da5b6",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "ViewInteractiveWidget(height=768, layout=Layout(height='auto', width='100%'), width=1024)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"big = Sphere(radius=10, cell_type='tetra', clear=True)\n",
"sml = Sphere(radius=9, cell_type='tetra')\n",
@@ -646,7 +653,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3.10.6 ('bvpyx-fenicsx-dev')",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},