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Commit 2f2ec880 authored by florez's avatar florez
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wall with rips

parent 973adb6c
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.ipynb_checkpoints/cyl_02-checkpoint.ipynb
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cyl_03.geo → .ipynb_checkpoints/cyl_03_mohit-checkpoint.geo
View file @ 2f2ec880
...@@ -3,9 +3,10 @@ SetFactory("OpenCASCADE"); ...@@ -3,9 +3,10 @@ SetFactory("OpenCASCADE");
//+ //+
Cylinder(1) = {0, 0, 0, 0, 0, 1, 0.5, 2*Pi}; Cylinder(1) = {0, 0, 0, 0, 0, 1, 0.5, 2*Pi};
//+ //+
Surface Loop(2) = {1, 2, 3}; //Surface Loop(2) = {1, 2, 3};
//+ //+
Volume(2) = {2}; //Volume(2) = {2};
Physical Surface("bottom") = {3}; Physical Surface("bottom") = {3};
Physical Surface("top") = {2}; Physical Surface("top") = {2};
Physical Volume("steel") = {1};
\ No newline at end of file
01/.ipynb_checkpoints/notebook01-checkpoint.ipynb 0 → 100644
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sq_01.geo → 01/cube.geo
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//+
SetFactory("OpenCASCADE"); SetFactory("OpenCASCADE");
Box(1) = {0, 0, 0, 1, 1, 1}; Box(1) = {0, 0, 0, 1, 1, 1};
//+
Physical Surface("top") = {6};
//+
Physical Surface("bottom") = {5}; Physical Surface("bottom") = {5};
Physical Surface("top") = {6};
Physical Volume("cube") = {1};
box1[] = Point{1};
Printf("this is text %g", box1[2]);
Mesh.MeshSizeMin = 1;
Mesh.MeshSizeMax = 1;
Mesh.SaveAll = 1;
Mesh.ElementOrder = 1;
Mesh 3;
Save "cube.msh";
01/cube.msh 0 → 100644
View file @ 2f2ec880
$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
3
2 1 "bottom"
2 2 "top"
3 3 "cube"
$EndPhysicalNames
$Entities
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2 0.9999999000000001 -9.999999994736442e-08 -9.999999994736442e-08 1.0000001 1.0000001 1.0000001 0 4 5 6 -7 -8
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6 -9.999999994736442e-08 -9.999999994736442e-08 0.9999999000000001 1.0000001 1.0000001 1.0000001 1 2 4 2 12 -6 -10
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0.5 0 0.5
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$EndNodes
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01/material.dat 0 → 100644
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material elastic [
name = steel
rho = 7800 # density
E = 210e6 # young's modulus
nu = 0.3 # poisson's ratio
]
\ No newline at end of file
test_01_cylinder.ipynb → 01/notebook01.ipynb
View file @ 2f2ec880
...@@ -3,191 +3,200 @@ ...@@ -3,191 +3,200 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 1, "execution_count": 1,
"id": "1dbbab78-6ef1-4e97-8440-f6db326755e9", "id": "3a4b7e63-10d0-4af2-bc97-5360ea402ff5",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"import akantu as aka\n",
"import numpy as np\n", "import numpy as np\n",
"import pygmsh\n", "import akantu as aka"
"\n",
"# import the pyplot submodule to draw figures\n",
"import matplotlib.pyplot as plt\n",
"# import triangluation routine to plot meshes\n",
"import matplotlib.tri as tri\n",
"# setting a default image size large enough\n",
"plt.rcParams['figure.figsize'] = [10, 10]"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 2, "execution_count": 2,
"id": "4f3b63d5-abe9-43ce-9eca-80cd47fb4d49", "id": "91261137-56d5-49b9-b386-dfb54d40da2a",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"# reading the mesh\n", "# import subprocess\n",
"spatial_dimension = 3 \n", "\n",
"mesh_file = 'shell_cyl_2.msh'\n", "# ret = subprocess.run(\"gmsh -3 -order 1 -o out.msh in.geo\", shell=True)\n",
"mesh = aka.Mesh(spatial_dimension)\n", "# if ret.returncode:\n",
"mesh.read(mesh_file)\n" "# print(\"Beware, gmsh could not run: mesh is not regenerated\")\n",
"# else:\n",
"# print(\"Mesh generated\")"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 3, "execution_count": 3,
"id": "ac11734f-f415-43aa-a1a3-92edca236554", "id": "c1339e28-e6b1-4155-b25e-f3b848025838",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"material_file = \"\"\"\n", "material_file = \"\"\"\n",
"material elastic [\n", "material elastic [\n",
" name = steel\n", " name = steel\n",
" rho = 1 # density\n", " rho = 7800 # density\n",
" E = 1 # young's modulus\n", " E = 210e6 # young's modulus\n",
" nu = 0.3 # poisson's ratio\n", " nu = 0.3 # poisson's ratio\n",
"]\"\"\"\n", "]\"\"\"\n",
"\n",
"# writing the material file\n", "# writing the material file\n",
"open('material.dat', 'w').write(material_file)\n", "open('material.dat', 'w').write(material_file)\n",
"#reading the material file\n", "#reading the material file\n",
"material_file = 'material.dat'\n", "material_file = 'material.dat'"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "30c1bb68-80b2-41ea-9aa6-a08daf741c9b",
"metadata": {},
"outputs": [],
"source": [
"aka.parseInput(material_file)\n", "aka.parseInput(material_file)\n",
"\n", "\n",
"# creating the solid mechanics model\n", "spatial_dimension = 3\n",
"model = aka.SolidMechanicsModel(mesh)\n", "mesh = aka.Mesh(spatial_dimension)\n",
"mesh.read('cube.msh')\n",
"\n", "\n",
"# initialize a static solver\n", "model = aka.SolidMechanicsModel(mesh)\n",
"model.initFull(_analysis_method=aka._static)" "model.initFull(_analysis_method=aka._static)"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 4, "execution_count": 5,
"id": "e2379428-0b40-406f-bfed-160eb297f730", "id": "9bb306b5-2e9c-4b3e-aaeb-347e7a1ee5f8",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"# Bottom ring 'bottom', top ring 'top', cylinder surface 'surface'\n",
"\n",
"# set the displacement/Dirichlet boundary conditions\n",
"for dir in [aka._x, aka._y, aka._z]:\n", "for dir in [aka._x, aka._y, aka._z]:\n",
" model.applyBC(aka.FixedValue(0, dir), \"bottom\")\n", " model.applyBC(aka.FixedValue(0.0, dir), \"bottom\")\n",
"\n", "\n",
"\n", "# trac = np.eye(3)\n",
"\n", "trac = [0, 0, 1e8]\n",
"# set the force/Neumann boundary conditions\n", "model.applyBC(aka.FromTraction(trac), \"top\")\n",
"\n", "np.set_printoptions(threshold=10)\n"
"trac = np.eye(3) # Newtons/m^2\n",
"trac = [0,0,1]\n",
"\n",
"model.applyBC(aka.FromTraction(trac), \"top\")\n"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 5, "execution_count": 6,
"id": "6d82b932-ca93-45eb-8e3e-c0ec2c24f381", "id": "4d56ac9e-37db-48d3-8366-f8f8cb000bb6",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [
{ {
"data": { "data": {
"text/plain": [ "text/plain": [
"array([[0., 0., 0.],\n", "<py11_akantu.Material at 0x7f2145e75730>"
" [0., 0., 0.],\n",
" [0., 0., 0.],\n",
" ...,\n",
" [0., 0., 0.],\n",
" [0., 0., 0.],\n",
" [0., 0., 0.]])"
] ]
}, },
"execution_count": 5, "execution_count": 6,
"metadata": {}, "metadata": {},
"output_type": "execute_result" "output_type": "execute_result"
} }
], ],
"source": [ "source": [
"np.set_printoptions(threshold=20)\n", "steel = model.getMaterial('steel')\n",
"steel"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "845b08f6-cda8-4a72-8fa0-f1ba47fb432f",
"metadata": {},
"outputs": [],
"source": [
"solver = model.getNonLinearSolver()\n",
"solver.set(\"max_iterations\", 6)\n",
"solver.set(\"threshold\", 1e-8)\n",
"solver.set(\"convergence_type\", aka.SolveConvergenceCriteria.residual)\n",
"\n", "\n",
"model.getExternalForce()[:]\n", "model.solveStep()"
"# np.size(model.getExternalForce(),0)\n",
"# model.getBlockedDOFs()"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 6, "execution_count": 10,
"id": "09675758-79eb-4314-b23f-f34fe359dc9f", "id": "2a96374a-1ade-42cf-8024-69c1dd27f02e",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [
{ {
"data": { "data": {
"text/plain": [ "text/plain": [
"array([[0., 0., 0.],\n", "24"
" [0., 0., 0.],\n",
" [0., 0., 0.],\n",
" ...,\n",
" [0., 0., 0.],\n",
" [0., 0., 0.],\n",
" [0., 0., 0.]])"
] ]
}, },
"execution_count": 6, "execution_count": 10,
"metadata": {}, "metadata": {},
"output_type": "execute_result" "output_type": "execute_result"
} }
], ],
"source": [ "source": [
"# configure the linear algebra solver\n", "mesh.getConnectivity(aka._tetrahedron_4)\n",
"solver = model.getNonLinearSolver()\n", "stress_field = model.getMaterial(0).getStress(aka._tetrahedron_4)\n",
"solver.set(\"max_iterations\", 3)\n", "np.set_printoptions(threshold=100)\n",
"solver.set(\"threshold\", 1e-8)\n", "stress_field\n",
"solver.set(\"convergence_type\", aka.SolveConvergenceCriteria.residual)\n", "mesh.getNbElement()"
"\n",
"# compute the solution\n",
"model.solveStep()\n",
"\n",
"u = model.getDisplacement()\n",
"np.set_printoptions(threshold=120)\n",
"u"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 7, "execution_count": null,
"id": "a81b557e-7adb-452a-9982-efeef3070962", "id": "23e23201-534c-4b3b-8121-6f8504b57243",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [],
{ "source": [
"ename": "Exception", "np.argmax(stress_field,0)\n",
"evalue": "akantu::debug::Exception : No element of type (not_ghost:_cohesive_2d_4) in this const ElementTypeMapArray<unsigned int> class(\"mesh:connectivities\") [/tmp/app/spack-stage/spack-stage-akantu-master-t5tv2fws2j5an4dr4sqytng27g7b3fyr/spack-src/src/mesh/element_type_map_tmpl.hh:293]", "np.size(stress_field,0)\n",
"output_type": "error", "stress_normal = stress_field[:,(0,4,8)]\n",
"traceback": [ "np.size(stress_normal,0)"
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mException\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-7-254e5de967ab>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0;31m# generate paraview files\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 10\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdump\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mException\u001b[0m: akantu::debug::Exception : No element of type (not_ghost:_cohesive_2d_4) in this const ElementTypeMapArray<unsigned int> class(\"mesh:connectivities\") [/tmp/app/spack-stage/spack-stage-akantu-master-t5tv2fws2j5an4dr4sqytng27g7b3fyr/spack-src/src/mesh/element_type_map_tmpl.hh:293]"
] ]
} },
], {
"cell_type": "code",
"execution_count": null,
"id": "60a70c37-31bf-48bf-a4ac-8333abd62e93",
"metadata": {},
"outputs": [],
"source": [ "source": [
"# specify what field to output into paraview files\n", "# specify what field to output into paraview files\n",
"model.setBaseName(\"shell_cyl\")\n", "model.setBaseName(\"cube\")\n",
"model.addDumpFieldVector(\"displacement\")\n", "model.addDumpFieldVector(\"displacement\")\n",
"model.addDumpFieldVector(\"external_force\")\n", "model.addDumpFieldVector(\"external_force\")\n",
"model.addDumpField(\"strain\")\n", "model.addDumpField(\"strain\")\n",
"model.addDumpField(\"stress\")\n", "model.addDumpField(\"stress\")\n",
"model.addDumpField(\"blocked_dofs\")\n", "model.addDumpField(\"blocked_dofs\")\n",
"\n", "\n",
"# generate paraview files\n",
"model.dump()" "model.dump()"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"id": "b9caba6a-e863-495b-989c-fd3bc3cf44ab", "id": "ac9c3e33-7117-4809-a433-3e7fef3a3344",
"metadata": {},
"outputs": [],
"source": [
"import pyvista as pv\n",
"\n",
"p = pv.Plotter(off_screen=False, notebook=False)\n",
"p.background_color = 'white'\n",
"\n",
"cyl_msh = pv.read(f'paraview/cube_{0:04d}.pvtu')\n",
"cyl_msh.set_active_scalars('displacement')\n",
"cyl_warped = cyl_msh.warp_by_vector('displacement')\n",
"cyl_warped.set_active_scalars('displacement')\n",
"\n",
"cyl_warped.plot()\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "738e4f52-bea5-4ae3-9454-2456af57c208",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [] "source": []
......
%% Cell type:code id:1dbbab78-6ef1-4e97-8440-f6db326755e9 tags: %% Cell type:code id:3a4b7e63-10d0-4af2-bc97-5360ea402ff5 tags:
``` python ``` python
import akantu as aka
import numpy as np import numpy as np
import pygmsh import akantu as aka
# import the pyplot submodule to draw figures
import matplotlib.pyplot as plt
# import triangluation routine to plot meshes
import matplotlib.tri as tri
# setting a default image size large enough
plt.rcParams['figure.figsize'] = [10, 10]
``` ```
%% Cell type:code id:4f3b63d5-abe9-43ce-9eca-80cd47fb4d49 tags: %% Cell type:code id:91261137-56d5-49b9-b386-dfb54d40da2a tags:
``` python ``` python
# reading the mesh # import subprocess
spatial_dimension = 3
mesh_file = 'shell_cyl_2.msh' # ret = subprocess.run("gmsh -3 -order 1 -o out.msh in.geo", shell=True)
mesh = aka.Mesh(spatial_dimension) # if ret.returncode:
mesh.read(mesh_file) # print("Beware, gmsh could not run: mesh is not regenerated")
# else:
# print("Mesh generated")
``` ```
%% Cell type:code id:ac11734f-f415-43aa-a1a3-92edca236554 tags: %% Cell type:code id:c1339e28-e6b1-4155-b25e-f3b848025838 tags:
``` python ``` python
material_file = """ material_file = """
material elastic [ material elastic [
name = steel