Update tutorials 1 through 7

Author: MatteB03

tutorials/tutorial1/tutorial.ipynb

@@ -87,7 +87,7 @@ class TimeSpaceODE(SpatialProblem, TimeDependentProblem):
 
 # ### Write the problem class
 # 
-# Once the `Problem` class is initialized, we need to represent the differential equation in **PINA**. In order to do this, we need to load the **PINA** operators from `pina.operators` module. Again, we'll consider Equation (1) and represent it in **PINA**:
+# Once the `Problem` class is initialized, we need to represent the differential equation in **PINA**. In order to do this, we need to load the **PINA** operators from `pina.operator` module. Again, we'll consider Equation (1) and represent it in **PINA**:
 
 # In[2]:
 
@@ -99,7 +99,7 @@ class TimeSpaceODE(SpatialProblem, TimeDependentProblem):
 from pina.equation import Equation, FixedValue
 
 import torch
-
+import matplotlib.pyplot as plt
 
 class SimpleODE(SpatialProblem):
 
@@ -185,7 +185,6 @@ def truth_solution(self, pts):
 # In[6]:
 
 
-import matplotlib.pyplot as plt
 variables=problem.spatial_variables
 fig = plt.figure()
 proj = "3d" if len(variables) == 3 else None
@@ -197,15 +196,15 @@ def truth_solution(self, pts):
 
 # ## Perform a small training
 
-# Once we have defined the problem and generated the data we can start the modelling. Here we will choose a `FeedForward` neural network available in `pina.model`, and we will train using the `PINN` solver from `pina.solver`. We highlight that this training is fairly simple, for more advanced stuff consider the tutorials in the ***Physics Informed Neural Networks*** section of ***Tutorials***. For training we use the `Trainer` class from `pina.trainer`. Here we show a very short training and some method for plotting the results. Notice that by default all relevant metrics (e.g. MSE error during training) are going to be tracked using a `lightning` logger, by default `CSVLogger`. If you want to track the metric by yourself without a logger, use `pina.callbacks.MetricTracker`.
+# Once we have defined the problem and generated the data we can start the modelling. Here we will choose a `FeedForward` neural network available in `pina.model`, and we will train using the `PINN` solver from `pina.solver`. We highlight that this training is fairly simple, for more advanced stuff consider the tutorials in the ***Physics Informed Neural Networks*** section of ***Tutorials***. For training we use the `Trainer` class from `pina.trainer`. Here we show a very short training and some method for plotting the results. Notice that by default all relevant metrics (e.g. MSE error during training) are going to be tracked using a `lightning` logger, by default `CSVLogger`. If you want to track the metric by yourself without a logger, use `pina.callback.MetricTracker`.
 
 # In[7]:
 
 
 from pina import Trainer
 from pina.solver import PINN
 from pina.model import FeedForward
-from pina.callback import MetricTracker
+from lightning.pytorch.loggers import TensorBoardLogger
 
 
 # build the model
@@ -220,13 +219,13 @@ def truth_solution(self, pts):
 pinn = PINN(problem, model)
 
 # create the trainer
-trainer = Trainer(solver=pinn, max_epochs=1500, callbacks=[MetricTracker()], accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
+trainer = Trainer(solver=pinn, max_epochs=1500, logger=TensorBoardLogger('tutorial_logs'), accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
 
 # train
 trainer.train()
 
 
-# After the training we can inspect trainer logged metrics (by default **PINA** logs mean square error residual loss). The logged metrics can be accessed online using one of the `Lightinig` loggers. The final loss can be accessed by `trainer.logged_metrics`
+# After the training we can inspect trainer logged metrics (by default **PINA** logs mean square error residual loss). The logged metrics can be accessed online using one of the `Lightning` loggers. The final loss can be accessed by `trainer.logged_metrics`
 
 # In[8]:
 
@@ -250,24 +249,19 @@ def truth_solution(self, pts):
 plt.legend()
 
 
-# The solution is overlapped with the actual one, and they are barely indistinguishable. We can also plot easily the loss:
+# The solution is overlapped with the actual one, and they are barely indistinguishable. We can also take a look at the loss using `TensorBoard`:
 
 # In[10]:
 
 
-list_ = [
-            idx for idx, s in enumerate(trainer.callbacks)
-            if isinstance(s, MetricTracker)
-        ]
-trainer_metrics = trainer.callbacks[list_[0]].metrics
+# Load the TensorBoard extension
+get_ipython().run_line_magic('load_ext', 'tensorboard')
+
+# In[12]:
+
 
-loss = trainer_metrics['val_loss']
-epochs = range(len(loss))
-plt.plot(epochs, loss.cpu())
-# plotting
-plt.xlabel('epoch')
-plt.ylabel('loss')
-plt.yscale('log')
+# Show saved losses
+get_ipython().run_line_magic('tensorboard', "--logdir 'tutorial_logs'")
 
 
 # As we can see the loss has not reached a minimum, suggesting that we could train for longer

tutorials/tutorial1/tutorial.py

@@ -23,6 +23,8 @@
 
 import torch
 from torch.nn import Softplus
+import matplotlib.pyplot as plt
+import warnings
 
 from pina.problem import SpatialProblem
 from pina.operator import laplacian
@@ -31,9 +33,13 @@
 from pina.trainer import Trainer
 from pina.domain import CartesianDomain
 from pina.equation import Equation, FixedValue
-from pina import Condition, LabelTensor#,Plotter
+from pina import Condition, LabelTensor
 from pina.callback import MetricTracker
 
+from lightning.pytorch.loggers import TensorBoardLogger
+
+warnings.filterwarnings('ignore')
+
 
 # ## The problem definition
 
@@ -90,9 +96,9 @@ def poisson_sol(self, pts):
 
 # After the problem, the feed-forward neural network is defined, through the class `FeedForward`. This neural network takes as input the coordinates (in this case $x$ and $y$) and provides the unkwown field of the Poisson problem. The residual of the equations are evaluated at several sampling points (which the user can manipulate using the method `CartesianDomain_pts`) and the loss minimized by the neural network is the sum of the residuals.
 # 
-# In this tutorial, the neural network is composed by two hidden layers of 10 neurons each, and it is trained for 1000 epochs. We use the `MetricTracker` class to track the metrics during training.
+# In this tutorial, the neural network is composed by two hidden layers of 10 neurons each, and it is trained for 1000 epochs with a learning rate of 0.006 and $l_2$ weight regularization set to $10^{-8}$. These parameters can be modified as desired. 
 
-# In[4]:
+# In[ ]:
 
 
 # make model + solver + trainer
@@ -102,21 +108,58 @@ def poisson_sol(self, pts):
     output_dimensions=len(problem.output_variables),
     input_dimensions=len(problem.input_variables)
 )
+kwargs= {'lr':0.006, 'weight_decay':1e-8}
 pinn = PINN(problem, model)
-trainer = Trainer(pinn, max_epochs=1000, callbacks=[MetricTracker()], accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
+trainer = Trainer(pinn, max_epochs=1000, accelerator='cpu', enable_model_summary=False,
+   train_size=1.0,
+    val_size=0.0,
+    test_size=0.0,
+    logger=TensorBoardLogger("tutorial_logs"),
+    enable_progress_bar=False,
+    **kwargs
+) # we train on CPU and avoid model summary at beginning of training (optional)
 
 # train
 trainer.train()
 
 
-# Now the `Plotter` class is used to plot the results.
+# Now we plot the results using `matplotlib`.
 # The solution predicted by the neural network is plotted on the left, the exact one is represented at the center and on the right the error between the exact and the predicted solutions is showed. 
 
-# In[5]:
+# In[ ]:
+
+
+@torch.no_grad()
+def plot_solution(solver):
+    # get the problem
+    problem = solver.problem
+    # get spatial points
+    spatial_samples = problem.spatial_domain.sample(30, "grid")
+    # compute pinn solution, true solution and absolute difference
+    data = {
+        "PINN solution": solver(spatial_samples),
+        "True solution": problem.truth_solution(spatial_samples),
+        "Absolute Difference": torch.abs(
+            solver(spatial_samples) - problem.truth_solution(spatial_samples)
+        )
+    }
+    # plot the solution
+    for idx, (title, field) in enumerate(data.items()):
+        plt.subplot(1, 3, idx + 1)
+        plt.title(title)
+        plt.tricontourf(  # convert to torch tensor + flatten
+            spatial_samples.extract("x").tensor.flatten(),
+            spatial_samples.extract("y").tensor.flatten(),
+            field.tensor.flatten(),
+        )
+        plt.colorbar(), plt.tight_layout()
+
 
+# In[ ]:
 
-#plotter = Plotter()
-#plotter.plot(solver=pinn)
+
+plt.figure(figsize=(12, 6))
+plot_solution(solver=pinn)
 
 
 # ## Solving the problem with extra-features PINNs
@@ -135,7 +178,7 @@ def poisson_sol(self, pts):
 # 
 # Finally, we perform the same training as before: the problem is `Poisson`, the network is composed by the same number of neurons and optimizer parameters are equal to previous test, the only change is the new extra feature.
 
-# In[6]:
+# In[ ]:
 
 
 class SinSin(torch.nn.Module):
@@ -171,18 +214,25 @@ def forward(self, x):
     extra_features=[SinSin()])
 
 pinn_feat = PINN(problem, model_feat)
-trainer_feat = Trainer(pinn_feat, max_epochs=1000, callbacks=[MetricTracker()], accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
+trainer_feat = Trainer(pinn_feat, max_epochs=1000, accelerator='cpu', enable_model_summary=False,
+    lr=0.006, weight_decay=1e-8,
+    train_size=1.0,
+    val_size=0.0,
+    test_size=0.0,
+    logger=TensorBoardLogger("tutorial_logs"),
+    enable_progress_bar=False,) # we train on CPU and avoid model summary at beginning of training (optional)
 
 trainer_feat.train()
 
 
 # The predicted and exact solutions and the error between them are represented below.
 # We can easily note that now our network, having almost the same condition as before, is able to reach additional order of magnitudes in accuracy.
 
-# In[7]:
+# In[ ]:
 
 
-#plotter.plot(solver=pinn_feat)
+plt.figure(figsize=(12, 6))
+plot_solution(solver=pinn_feat)
 
 
 # ## Solving the problem with learnable extra-features PINNs
@@ -199,7 +249,7 @@ def forward(self, x):
 # where $\alpha$ and $\beta$ are the abovementioned parameters.
 # Their implementation is quite trivial: by using the class `torch.nn.Parameter` we cam define all the learnable parameters we need, and they are managed by `autograd` module!
 
-# In[8]:
+# In[ ]:
 
 
 class SinSinAB(torch.nn.Module):
@@ -219,34 +269,46 @@ def forward(self, x):
 
 
 # make model + solver + trainer
-model_lean = FeedForwardWithExtraFeatures(
+model_learn = FeedForwardWithExtraFeatures(
     input_dimensions=len(problem.input_variables) + 1, #we add one as also we consider the extra feature dimension
     output_dimensions=len(problem.output_variables),
     func=Softplus,
     layers=[10, 10],
     extra_features=[SinSinAB()])
 
-pinn_lean = PINN(problem, model_lean)
-trainer_learn = Trainer(pinn_lean, max_epochs=1000, accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
+pinn_learn = PINN(problem, model_learn)
+trainer_learn = Trainer(pinn_learn, max_epochs=1000, enable_model_summary=False,
+    lr=0.006, weight_decay=1e-8,
+    train_size=1.0,
+    val_size=0.0,
+    test_size=0.0,
+    logger=TensorBoardLogger("tutorial_logs"),
+    enable_progress_bar=False) # we train on CPU and avoid model summary at beginning of training (optional)
 
 # train
 trainer_learn.train()
 
 
 # Umh, the final loss is not appreciabily better than previous model (with static extra features), despite the usage of learnable parameters. This is mainly due to the over-parametrization of the network: there are many parameter to optimize during the training, and the model in unable to understand automatically that only the parameters of the extra feature (and not the weights/bias of the FFN) should be tuned in order to fit our problem. A longer training can be helpful, but in this case the faster way to reach machine precision for solving the Poisson problem is removing all the hidden layers in the `FeedForward`, keeping only the $\alpha$ and $\beta$ parameters of the extra feature.
 
-# In[9]:
+# In[ ]:
 
 
 # make model + solver + trainer
-model_lean= FeedForwardWithExtraFeatures(
+model_learn= FeedForwardWithExtraFeatures(
     layers=[],
     func=Softplus,
     output_dimensions=len(problem.output_variables),
     input_dimensions=len(problem.input_variables)+1,
     extra_features=[SinSinAB()])
-pinn_learn = PINN(problem, model_lean)
-trainer_learn = Trainer(pinn_learn, max_epochs=1000, callbacks=[MetricTracker()], accelerator='cpu', enable_model_summary=False) # we train on CPU and avoid model summary at beginning of training (optional)
+pinn_learn = PINN(problem, model_learn)
+trainer_learn = Trainer(pinn_learn, max_epochs=1000, accelerator='cpu', enable_model_summary=False,
+    lr=0.006, weight_decay=1e-8,
+    train_size=1.0,
+    val_size=0.0,
+    test_size=0.0,
+    logger=TensorBoardLogger("tutorial_logs"),
+    enable_progress_bar=False) # we train on CPU and avoid model summary at beginning of training (optional)
 
 # train
 trainer_learn.train()
@@ -257,20 +319,14 @@ def forward(self, x):
 # 
 # We conclude here by showing the graphical comparison of the unknown field and the loss trend for all the test cases presented here: the standard PINN, PINN with extra features, and PINN with learnable extra features.
 
-# In[10]:
-
-
-#plotter.plot(solver=pinn_learn)
-
-
 # Let us compare the training losses for the various types of training
 
-# In[11]:
+# In[ ]:
 
 
-#plotter.plot_loss(trainer, logy=True, label='Standard')
-#plotter.plot_loss(trainer_feat, logy=True,label='Static Features')
-#plotter.plot_loss(trainer_learn, logy=True, label='Learnable Features')
+# Load the TensorBoard extension
+get_ipython().run_line_magic('load_ext', 'tensorboard')
+get_ipython().run_line_magic('tensorboard', "--logdir 'tutorial_logs'")
 
 
 # ## What's next?

tutorials/tutorial2/tutorial.ipynb

@@ -44,14 +44,13 @@
     "\n",
     "import torch \n",
     "import matplotlib.pyplot as plt \n",
-    "plt.style.use('tableau-colorblind10')\n",
+    "import torchvision # for MNIST dataset\n",
     "\n",
     "from pina.problem import AbstractProblem\n",
     "from pina.solver import SupervisedSolver\n",
     "from pina.trainer import Trainer\n",
     "from pina import Condition, LabelTensor\n",
     "from pina.model.block import ContinuousConvBlock \n",
-    "import torchvision # for MNIST dataset\n",
     "from pina.model import FeedForward # for building AE and MNIST classification"
    ]
   },
@@ -928,7 +927,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,