From 9db1eacd80415b6ef55d3d22244cf2f36eccf8cc Mon Sep 17 00:00:00 2001
From: Dmitri Naumov <dmitri.naumov@ufz.de>
Date: Tue, 19 Sep 2023 19:08:27 +0200
Subject: [PATCH] [T/M] Automatic formatting of the notebook
---
.../Mechanics/Linear/SimpleMechanics.ipynb | 243 +++++++++++-------
1 file changed, 150 insertions(+), 93 deletions(-)
diff --git a/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb b/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
index 784f8c366c3..bce8e212961 100644
--- a/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
+++ b/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
@@ -29,7 +29,7 @@
"source": [
"import os\n",
"\n",
- "out_dir = os.environ.get('OGS_TESTRUNNER_OUT_DIR', '_out')\n",
+ "out_dir = os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\")\n",
"if not os.path.exists(out_dir):\n",
" os.makedirs(out_dir)"
]
@@ -57,97 +57,121 @@
"model = ogs.OGS(PROJECT_FILE=os.path.join(out_dir, f\"{prj_name}.prj\"))\n",
"model.geo.add_geom(filename=f\"./square_1x1.gml\")\n",
"model.mesh.add_mesh(filename=f\"./square_1x1_quad_1e2.vtu\")\n",
- "model.processes.set_process(name=\"SD\",\n",
- " type=\"SMALL_DEFORMATION\",\n",
- " integration_order=\"2\",\n",
- " specific_body_force=\"0 0\")\n",
- "model.processes.set_constitutive_relation(type=\"LinearElasticIsotropic\",\n",
- " youngs_modulus=\"E\",\n",
- " poissons_ratio=\"nu\")\n",
- "model.processes.add_process_variable(process_variable=\"process_variable\",\n",
- " process_variable_name=\"displacement\")\n",
- "model.processes.add_process_variable(secondary_variable=\"sigma\",\n",
- " output_name=\"sigma\")\n",
- "model.timeloop.add_process(process=\"SD\",\n",
- " nonlinear_solver_name=\"basic_newton\",\n",
- " convergence_type=\"DeltaX\",\n",
- " norm_type=\"NORM2\",\n",
- " abstol=\"1e-15\",\n",
- " time_discretization=\"BackwardEuler\")\n",
- "model.timeloop.set_stepping(process=\"SD\", type=\"FixedTimeStepping\",\n",
- " t_initial=\"0\",\n",
- " t_end=\"1\",\n",
- " repeat=\"4\",\n",
- " delta_t=\"0.25\")\n",
- "model.timeloop.add_output(type=\"VTK\",\n",
- " prefix=prj_name,\n",
- " repeat=\"1\",\n",
- " each_steps=\"4\",\n",
- " variables=[\"displacement\", \"sigma\"])\n",
- "model.media.add_property(medium_id=\"0\",\n",
- " phase_type=\"Solid\",\n",
- " name=\"density\",\n",
- " type=\"Constant\",\n",
- " value=\"1\")\n",
+ "model.processes.set_process(\n",
+ " name=\"SD\",\n",
+ " type=\"SMALL_DEFORMATION\",\n",
+ " integration_order=\"2\",\n",
+ " specific_body_force=\"0 0\",\n",
+ ")\n",
+ "model.processes.set_constitutive_relation(\n",
+ " type=\"LinearElasticIsotropic\", youngs_modulus=\"E\", poissons_ratio=\"nu\"\n",
+ ")\n",
+ "model.processes.add_process_variable(\n",
+ " process_variable=\"process_variable\", process_variable_name=\"displacement\"\n",
+ ")\n",
+ "model.processes.add_process_variable(secondary_variable=\"sigma\", output_name=\"sigma\")\n",
+ "model.timeloop.add_process(\n",
+ " process=\"SD\",\n",
+ " nonlinear_solver_name=\"basic_newton\",\n",
+ " convergence_type=\"DeltaX\",\n",
+ " norm_type=\"NORM2\",\n",
+ " abstol=\"1e-15\",\n",
+ " time_discretization=\"BackwardEuler\",\n",
+ ")\n",
+ "model.timeloop.set_stepping(\n",
+ " process=\"SD\",\n",
+ " type=\"FixedTimeStepping\",\n",
+ " t_initial=\"0\",\n",
+ " t_end=\"1\",\n",
+ " repeat=\"4\",\n",
+ " delta_t=\"0.25\",\n",
+ ")\n",
+ "model.timeloop.add_output(\n",
+ " type=\"VTK\",\n",
+ " prefix=prj_name,\n",
+ " repeat=\"1\",\n",
+ " each_steps=\"4\",\n",
+ " variables=[\"displacement\", \"sigma\"],\n",
+ ")\n",
+ "model.media.add_property(\n",
+ " medium_id=\"0\", phase_type=\"Solid\", name=\"density\", type=\"Constant\", value=\"1\"\n",
+ ")\n",
"model.parameters.add_parameter(name=\"E\", type=\"Constant\", value=\"1\")\n",
"model.parameters.add_parameter(name=\"nu\", type=\"Constant\", value=\"0.3\")\n",
- "model.parameters.add_parameter(name=\"displacement0\",\n",
- " type=\"Constant\",\n",
- " values=\"0 0\")\n",
+ "model.parameters.add_parameter(name=\"displacement0\", type=\"Constant\", values=\"0 0\")\n",
"model.parameters.add_parameter(name=\"dirichlet0\", type=\"Constant\", value=\"0\")\n",
"model.parameters.add_parameter(name=\"dirichlet1\", type=\"Constant\", value=\"0.05\")\n",
- "model.processvars.set_ic(process_variable_name=\"displacement\",\n",
- " components=\"2\",\n",
- " order=\"1\",\n",
- " initial_condition=\"displacement0\")\n",
- "model.processvars.add_bc(process_variable_name=\"displacement\",\n",
- " geometrical_set=\"square_1x1_geometry\",\n",
- " geometry=\"left\",\n",
- " type=\"Dirichlet\",\n",
- " component=\"0\",\n",
- " parameter=\"dirichlet0\")\n",
- "model.processvars.add_bc(process_variable_name=\"displacement\",\n",
- " geometrical_set=\"square_1x1_geometry\",\n",
- " geometry=\"bottom\",\n",
- " type=\"Dirichlet\",\n",
- " component=\"1\",\n",
- " parameter=\"dirichlet0\")\n",
- "model.processvars.add_bc(process_variable_name=\"displacement\",\n",
- " geometrical_set=\"square_1x1_geometry\",\n",
- " geometry=\"top\",\n",
- " type=\"Dirichlet\",\n",
- " component=\"1\",\n",
- " parameter=\"dirichlet1\")\n",
- "model.nonlinsolvers.add_non_lin_solver(name=\"basic_newton\",\n",
- " type=\"Newton\",\n",
- " max_iter=\"4\",\n",
- " linear_solver=\"general_linear_solver\")\n",
- "model.linsolvers.add_lin_solver(name=\"general_linear_solver\",\n",
- " kind=\"lis\",\n",
- " solver_type=\"cg\",\n",
- " precon_type=\"jacobi\",\n",
- " max_iteration_step=\"10000\",\n",
- " error_tolerance=\"1e-16\")\n",
- "model.linsolvers.add_lin_solver(name=\"general_linear_solver\",\n",
- " kind=\"eigen\",\n",
- " solver_type=\"CG\",\n",
- " precon_type=\"DIAGONAL\",\n",
- " max_iteration_step=\"10000\",\n",
- " error_tolerance=\"1e-16\")\n",
- "model.linsolvers.add_lin_solver(name=\"general_linear_solver\",\n",
- " kind=\"petsc\",\n",
- " prefix=\"sd\",\n",
- " solver_type=\"cg\",\n",
- " precon_type=\"bjacobi\",\n",
- " max_iteration_step=\"10000\",\n",
- " error_tolerance=\"1e-16\")\n",
+ "model.processvars.set_ic(\n",
+ " process_variable_name=\"displacement\",\n",
+ " components=\"2\",\n",
+ " order=\"1\",\n",
+ " initial_condition=\"displacement0\",\n",
+ ")\n",
+ "model.processvars.add_bc(\n",
+ " process_variable_name=\"displacement\",\n",
+ " geometrical_set=\"square_1x1_geometry\",\n",
+ " geometry=\"left\",\n",
+ " type=\"Dirichlet\",\n",
+ " component=\"0\",\n",
+ " parameter=\"dirichlet0\",\n",
+ ")\n",
+ "model.processvars.add_bc(\n",
+ " process_variable_name=\"displacement\",\n",
+ " geometrical_set=\"square_1x1_geometry\",\n",
+ " geometry=\"bottom\",\n",
+ " type=\"Dirichlet\",\n",
+ " component=\"1\",\n",
+ " parameter=\"dirichlet0\",\n",
+ ")\n",
+ "model.processvars.add_bc(\n",
+ " process_variable_name=\"displacement\",\n",
+ " geometrical_set=\"square_1x1_geometry\",\n",
+ " geometry=\"top\",\n",
+ " type=\"Dirichlet\",\n",
+ " component=\"1\",\n",
+ " parameter=\"dirichlet1\",\n",
+ ")\n",
+ "model.nonlinsolvers.add_non_lin_solver(\n",
+ " name=\"basic_newton\",\n",
+ " type=\"Newton\",\n",
+ " max_iter=\"4\",\n",
+ " linear_solver=\"general_linear_solver\",\n",
+ ")\n",
+ "model.linsolvers.add_lin_solver(\n",
+ " name=\"general_linear_solver\",\n",
+ " kind=\"lis\",\n",
+ " solver_type=\"cg\",\n",
+ " precon_type=\"jacobi\",\n",
+ " max_iteration_step=\"10000\",\n",
+ " error_tolerance=\"1e-16\",\n",
+ ")\n",
+ "model.linsolvers.add_lin_solver(\n",
+ " name=\"general_linear_solver\",\n",
+ " kind=\"eigen\",\n",
+ " solver_type=\"CG\",\n",
+ " precon_type=\"DIAGONAL\",\n",
+ " max_iteration_step=\"10000\",\n",
+ " error_tolerance=\"1e-16\",\n",
+ ")\n",
+ "model.linsolvers.add_lin_solver(\n",
+ " name=\"general_linear_solver\",\n",
+ " kind=\"petsc\",\n",
+ " prefix=\"sd\",\n",
+ " solver_type=\"cg\",\n",
+ " precon_type=\"bjacobi\",\n",
+ " max_iteration_step=\"10000\",\n",
+ " error_tolerance=\"1e-16\",\n",
+ ")\n",
"try:\n",
" model.write_input()\n",
- " model.run_model(logfile=os.path.join(out_dir, f\"{prj_name}.txt\"), args=f\"-o {out_dir}\")\n",
+ " model.run_model(\n",
+ " logfile=os.path.join(out_dir, f\"{prj_name}.txt\"), args=f\"-o {out_dir}\"\n",
+ " )\n",
"except Exception as inst:\n",
" print(f\"{type(inst)}: {inst.args[0]}\")\n",
"\n",
"from datetime import datetime\n",
+ "\n",
"print(datetime.now())"
]
},
@@ -183,19 +207,52 @@
"\n",
"pvdfile = vtuIO.PVDIO(f\"{out_dir}/{prj_name}.pvd\", interpolation_backend=\"scipy\", dim=2)\n",
"time = pvdfile.timesteps\n",
- "points={'pt0': (0.3,0.5,0.0), 'pt1': (0.24,0.21,0.0)}\n",
- "displacement_linear = pvdfile.read_time_series(\"displacement\", points, interpolation_method=\"linear\")\n",
- "displacement_nearest = pvdfile.read_time_series(\"displacement\", points, interpolation_method=\"nearest\")\n",
+ "points = {\"pt0\": (0.3, 0.5, 0.0), \"pt1\": (0.24, 0.21, 0.0)}\n",
+ "displacement_linear = pvdfile.read_time_series(\n",
+ " \"displacement\", points, interpolation_method=\"linear\"\n",
+ ")\n",
+ "displacement_nearest = pvdfile.read_time_series(\n",
+ " \"displacement\", points, interpolation_method=\"nearest\"\n",
+ ")\n",
"\n",
"import matplotlib.pyplot as plt\n",
- "plt.plot(time, displacement_linear[\"pt0\"][:,0], \"b-\", label=\"$u_x$ pt0 linear interpolated\")\n",
- "plt.plot(time, displacement_nearest[\"pt0\"][:,0], \"b--\", label=\"$u_x$ pt0 closest point value\")\n",
- "plt.plot(time, displacement_linear[\"pt0\"][:,1], \"g-\", label=\"$u_y$ pt0 linear interpolated\")\n",
- "plt.plot(time, displacement_nearest[\"pt0\"][:,1], \"g--\", label=\"$u_y$ pt0 closest point value\")\n",
- "plt.plot(time, displacement_linear[\"pt1\"][:,0], \"r-\", label=\"$u_x$ pt1 linear interpolated\")\n",
- "plt.plot(time, displacement_nearest[\"pt1\"][:,0], \"r--\", label=\"$u_x$ pt1 closest point value\")\n",
- "plt.plot(time, displacement_linear[\"pt1\"][:,1], \"m-\", label=\"$u_y$ pt1 linear interpolated\")\n",
- "plt.plot(time, displacement_nearest[\"pt1\"][:,1], \"m--\", label=\"$u_y$ pt1 closest point value\")\n",
+ "\n",
+ "plt.plot(\n",
+ " time, displacement_linear[\"pt0\"][:, 0], \"b-\", label=\"$u_x$ pt0 linear interpolated\"\n",
+ ")\n",
+ "plt.plot(\n",
+ " time,\n",
+ " displacement_nearest[\"pt0\"][:, 0],\n",
+ " \"b--\",\n",
+ " label=\"$u_x$ pt0 closest point value\",\n",
+ ")\n",
+ "plt.plot(\n",
+ " time, displacement_linear[\"pt0\"][:, 1], \"g-\", label=\"$u_y$ pt0 linear interpolated\"\n",
+ ")\n",
+ "plt.plot(\n",
+ " time,\n",
+ " displacement_nearest[\"pt0\"][:, 1],\n",
+ " \"g--\",\n",
+ " label=\"$u_y$ pt0 closest point value\",\n",
+ ")\n",
+ "plt.plot(\n",
+ " time, displacement_linear[\"pt1\"][:, 0], \"r-\", label=\"$u_x$ pt1 linear interpolated\"\n",
+ ")\n",
+ "plt.plot(\n",
+ " time,\n",
+ " displacement_nearest[\"pt1\"][:, 0],\n",
+ " \"r--\",\n",
+ " label=\"$u_x$ pt1 closest point value\",\n",
+ ")\n",
+ "plt.plot(\n",
+ " time, displacement_linear[\"pt1\"][:, 1], \"m-\", label=\"$u_y$ pt1 linear interpolated\"\n",
+ ")\n",
+ "plt.plot(\n",
+ " time,\n",
+ " displacement_nearest[\"pt1\"][:, 1],\n",
+ " \"m--\",\n",
+ " label=\"$u_y$ pt1 closest point value\",\n",
+ ")\n",
"plt.legend()\n",
"plt.xlabel(\"t\")\n",
"plt.ylabel(\"u\")"
--
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