Automatize Tutorials html, py files creation (#496)
* workflow to export tutorials ---------
This commit is contained in:
Dario Coscia
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Nicola Demo
Nicola Demo
parent
aea24d0bee
commit
0146155c9b
29
tutorials/tutorial7/tutorial.ipynb
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29
tutorials/tutorial7/tutorial.ipynb
vendored
@@ -75,17 +75,18 @@
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"source": [
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"## routine needed to run the notebook on Google Colab\n",
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"try:\n",
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" import google.colab\n",
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" IN_COLAB = True\n",
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" import google.colab\n",
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"\n",
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" IN_COLAB = True\n",
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"except:\n",
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" IN_COLAB = False\n",
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" IN_COLAB = False\n",
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"if IN_COLAB:\n",
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" !pip install \"pina-mathlab\"\n",
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" # get the data\n",
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" !mkdir \"data\"\n",
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" !wget \"https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pinn_solution_0.5_0.5\" -O \"data/pinn_solution_0.5_0.5\"\n",
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" !wget \"https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pts_0.5_0.5\" -O \"data/pts_0.5_0.5\"\n",
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" \n",
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" !pip install \"pina-mathlab\"\n",
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" # get the data\n",
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" !mkdir \"data\"\n",
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" !wget \"https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pinn_solution_0.5_0.5\" -O \"data/pinn_solution_0.5_0.5\"\n",
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" !wget \"https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pts_0.5_0.5\" -O \"data/pts_0.5_0.5\"\n",
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"\n",
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"import matplotlib.pyplot as plt\n",
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"import torch\n",
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"import warnings\n",
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@@ -101,7 +102,7 @@
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"from lightning.pytorch import seed_everything\n",
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"from lightning.pytorch.callbacks import Callback\n",
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"\n",
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"warnings.filterwarnings('ignore')\n",
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"warnings.filterwarnings(\"ignore\")\n",
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"seed_everything(883)"
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]
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},
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@@ -152,11 +153,11 @@
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}
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],
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"source": [
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"points = data_input.extract(['x', 'y']).detach().numpy()\n",
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"points = data_input.extract([\"x\", \"y\"]).detach().numpy()\n",
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"truth = data_output.detach().numpy()\n",
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"\n",
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"plt.scatter(points[:, 0], points[:, 1], c=truth, s=8)\n",
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"plt.axis('equal')\n",
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"plt.axis(\"equal\")\n",
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"plt.colorbar()\n",
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"plt.show()"
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]
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@@ -255,8 +256,8 @@
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" layers=[20, 20, 20],\n",
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" func=torch.nn.Softplus,\n",
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" output_dimensions=len(problem.output_variables),\n",
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" input_dimensions=len(problem.input_variables)\n",
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" )"
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" input_dimensions=len(problem.input_variables),\n",
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")"
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]
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},
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{
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259
tutorials/tutorial7/tutorial.py
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259
tutorials/tutorial7/tutorial.py
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#!/usr/bin/env python
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# coding: utf-8
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# # Tutorial: Resolution of an inverse problem
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#
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# [](https://colab.research.google.com/github/mathLab/PINA/blob/master/tutorials/tutorial7/tutorial.ipynb)
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# ### Introduction to the inverse problem
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# This tutorial shows how to solve an inverse Poisson problem with Physics-Informed Neural Networks. The problem definition is that of a Poisson problem with homogeneous boundary conditions and it reads:
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# \begin{equation}
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# \begin{cases}
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# \Delta u = e^{-2(x-\mu_1)^2-2(y-\mu_2)^2} \text{ in } \Omega\, ,\\
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# u = 0 \text{ on }\partial \Omega,\\
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# u(\mu_1, \mu_2) = \text{ data}
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# \end{cases}
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# \end{equation}
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# where $\Omega$ is a square domain $[-2, 2] \times [-2, 2]$, and $\partial \Omega=\Gamma_1 \cup \Gamma_2 \cup \Gamma_3 \cup \Gamma_4$ is the union of the boundaries of the domain.
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#
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# This kind of problem, namely the "inverse problem", has two main goals:
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# - find the solution $u$ that satisfies the Poisson equation;
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# - find the unknown parameters ($\mu_1$, $\mu_2$) that better fit some given data (third equation in the system above).
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#
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# In order to achieve both goals we will need to define an `InverseProblem` in PINA.
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# Let's start with useful imports.
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# In[20]:
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## routine needed to run the notebook on Google Colab
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try:
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import google.colab
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IN_COLAB = True
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except:
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IN_COLAB = False
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if IN_COLAB:
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get_ipython().system('pip install "pina-mathlab"')
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# get the data
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get_ipython().system('mkdir "data"')
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get_ipython().system(
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'wget "https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pinn_solution_0.5_0.5" -O "data/pinn_solution_0.5_0.5"'
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)
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get_ipython().system(
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'wget "https://github.com/mathLab/PINA/raw/refs/heads/master/tutorials/tutorial7/data/pts_0.5_0.5" -O "data/pts_0.5_0.5"'
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)
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import matplotlib.pyplot as plt
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import torch
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import warnings
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from pina import Condition, Trainer
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from pina.problem import SpatialProblem, InverseProblem
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from pina.operator import laplacian
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from pina.model import FeedForward
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from pina.equation import Equation, FixedValue
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from pina.solver import PINN
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from pina.domain import CartesianDomain
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from pina.optim import TorchOptimizer
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from lightning.pytorch import seed_everything
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from lightning.pytorch.callbacks import Callback
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warnings.filterwarnings("ignore")
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seed_everything(883)
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# Then, we import the pre-saved data, for ($\mu_1$, $\mu_2$)=($0.5$, $0.5$). These two values are the optimal parameters that we want to find through the neural network training. In particular, we import the `input` points (the spatial coordinates), and the `target` points (the corresponding $u$ values evaluated at the `input`).
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# In[21]:
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data_output = torch.load(
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"data/pinn_solution_0.5_0.5", weights_only=False
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).detach()
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data_input = torch.load("data/pts_0.5_0.5", weights_only=False)
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# Moreover, let's plot also the data points and the reference solution: this is the expected output of the neural network.
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# In[22]:
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points = data_input.extract(["x", "y"]).detach().numpy()
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truth = data_output.detach().numpy()
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plt.scatter(points[:, 0], points[:, 1], c=truth, s=8)
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plt.axis("equal")
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plt.colorbar()
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plt.show()
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# ### Inverse problem definition in PINA
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# Then, we initialize the Poisson problem, that is inherited from the `SpatialProblem` and from the `InverseProblem` classes. We here have to define all the variables, and the domain where our unknown parameters ($\mu_1$, $\mu_2$) belong. Notice that the Laplace equation takes as inputs also the unknown variables, that will be treated as parameters that the neural network optimizes during the training process.
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# In[23]:
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def laplace_equation(input_, output_, params_):
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"""
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Implementation of the laplace equation.
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:param LabelTensor input_: Input data of the problem.
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:param LabelTensor output_: Output data of the problem.
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:param dict params_: Parameters of the problem.
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:return: The residual of the laplace equation.
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:rtype: LabelTensor
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"""
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force_term = torch.exp(
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-2 * (input_.extract(["x"]) - params_["mu1"]) ** 2
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- 2 * (input_.extract(["y"]) - params_["mu2"]) ** 2
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)
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delta_u = laplacian(output_, input_, components=["u"], d=["x", "y"])
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return delta_u - force_term
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class Poisson(SpatialProblem, InverseProblem):
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r"""
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Implementation of the inverse 2-dimensional Poisson problem in the square
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domain :math:`[0, 1] \times [0, 1]`,
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with unknown parameter domain :math:`[-1, 1] \times [-1, 1]`.
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"""
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output_variables = ["u"]
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x_min, x_max = -2, 2
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y_min, y_max = -2, 2
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spatial_domain = CartesianDomain({"x": [x_min, x_max], "y": [y_min, y_max]})
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unknown_parameter_domain = CartesianDomain({"mu1": [-1, 1], "mu2": [-1, 1]})
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domains = {
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"g1": CartesianDomain({"x": [x_min, x_max], "y": y_max}),
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"g2": CartesianDomain({"x": [x_min, x_max], "y": y_min}),
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"g3": CartesianDomain({"x": x_max, "y": [y_min, y_max]}),
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"g4": CartesianDomain({"x": x_min, "y": [y_min, y_max]}),
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"D": CartesianDomain({"x": [x_min, x_max], "y": [y_min, y_max]}),
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}
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conditions = {
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"g1": Condition(domain="g1", equation=FixedValue(0.0)),
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"g2": Condition(domain="g2", equation=FixedValue(0.0)),
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"g3": Condition(domain="g3", equation=FixedValue(0.0)),
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"g4": Condition(domain="g4", equation=FixedValue(0.0)),
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"D": Condition(domain="D", equation=Equation(laplace_equation)),
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"data": Condition(input=data_input, target=data_output),
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}
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problem = Poisson()
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# Then, we define the neural network model we want to use. Here we used a model which imposes hard constrains on the boundary conditions, as also done in the Wave tutorial!
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# In[24]:
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model = FeedForward(
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layers=[20, 20, 20],
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func=torch.nn.Softplus,
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output_dimensions=len(problem.output_variables),
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input_dimensions=len(problem.input_variables),
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)
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# After that, we discretize the spatial domain.
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# In[25]:
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problem.discretise_domain(20, "grid", domains=["D"])
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problem.discretise_domain(
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1000,
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"random",
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domains=["g1", "g2", "g3", "g4"],
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)
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# Here, we define a simple callback for the trainer. We use this callback to save the parameters predicted by the neural network during the training. The parameters are saved every 100 epochs as `torch` tensors in a specified directory (`tmp_dir` in our case).
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# The goal is to read the saved parameters after training and plot their trend across the epochs.
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# In[26]:
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# temporary directory for saving logs of training
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tmp_dir = "tmp_poisson_inverse"
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class SaveParameters(Callback):
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"""
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Callback to save the parameters of the model every 100 epochs.
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"""
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def on_train_epoch_end(self, trainer, __):
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if trainer.current_epoch % 100 == 99:
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torch.save(
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trainer.solver.problem.unknown_parameters,
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"{}/parameters_epoch{}".format(tmp_dir, trainer.current_epoch),
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)
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# Then, we define the `PINN` object and train the solver using the `Trainer`.
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# In[27]:
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max_epochs = 1500
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pinn = PINN(
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problem, model, optimizer=TorchOptimizer(torch.optim.Adam, lr=0.005)
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)
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# define the trainer for the solver
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trainer = Trainer(
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solver=pinn,
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accelerator="cpu",
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max_epochs=max_epochs,
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default_root_dir=tmp_dir,
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enable_model_summary=False,
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callbacks=[SaveParameters()],
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train_size=1.0,
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val_size=0.0,
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test_size=0.0,
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)
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trainer.train()
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# One can now see how the parameters vary during the training by reading the saved solution and plotting them. The plot shows that the parameters stabilize to their true value before reaching the epoch $1000$!
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# In[28]:
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epochs_saved = range(99, max_epochs, 100)
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parameters = torch.empty((int(max_epochs / 100), 2))
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for i, epoch in enumerate(epochs_saved):
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params_torch = torch.load(
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"{}/parameters_epoch{}".format(tmp_dir, epoch), weights_only=False
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)
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for e, var in enumerate(pinn.problem.unknown_variables):
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parameters[i, e] = params_torch[var].data
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# Plot parameters
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plt.close()
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plt.plot(epochs_saved, parameters[:, 0], label="mu1", marker="o")
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plt.plot(epochs_saved, parameters[:, 1], label="mu2", marker="s")
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plt.ylim(-1, 1)
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plt.grid()
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plt.legend()
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plt.xlabel("Epoch")
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plt.ylabel("Parameter value")
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plt.show()
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# ## What's next?
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#
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# We have shown the basic usage PINNs in inverse problem modelling, further extensions include:
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#
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# 1. Train using different Physics Informed strategies
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#
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# 2. Try on more complex problems
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#
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# 3. Many more...
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