Update references to DeepXDE in about code and README

README.md

@@ -12,7 +12,7 @@
 [![License](https://img.shields.io/github/license/chaobrain/pinnx)](https://github.com/chaobrain/pinnx/blob/master/LICENSE)
 
 ``PINNx`` is a library for scientific machine learning and physics-informed learning in JAX. 
-It is inspired from [DeepXDE](https://github.com/lululxvi/deepxde) but is enhanced by our 
+It is a rewrite of [DeepXDE](https://github.com/lululxvi/deepxde) but is enhanced by our 
 [Brain Dynamics Programming (BDP) ecosystem](https://ecosystem-for-brain-dynamics.readthedocs.io/). 
 For example, it leverages 
 

docs/index.rst

@@ -2,7 +2,10 @@
 ========================
 
 `PINNx <https://github.com/chaobrain/pinnx>`_ is a library for scientific machine learning and physics-informed learning
-in JAX. It enables to define PINN problem with explicit variables (e.g. ``x``, ``y``, ``z``) and physical units
+in JAX. It is rewritten according to `DeepXDE <https://github.com/lululxvi/deepxde>`_ but is enhanced by our
+`Brain Dynamics Programming (BDP) ecosystem <https://ecosystem-for-brain-dynamics.readthedocs.io/>`_.
+
+`PINNx` enables to define PINN problem with explicit variables (e.g. ``x``, ``y``, ``z``) and physical units
 (e.g. ``meter``, ``second``, ``kelvin``) and to solve the problem with neural networks.
 
 `PINNx <https://github.com/chaobrain/pinnx>`_ is built on top of our `Brain Dynamics Programming (BDP) ecosystem <https://ecosystem-for-brain-dynamics.readthedocs.io/>`_.

pinnx/_trainer.py

@@ -1,17 +1,21 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 import time
 from typing import Union, Sequence, Callable, Optional
 
 import brainstate as bst
 import brainunit as u
-import jax.tree
 import jax.numpy as jnp
+import jax.tree
 import numpy as np
 
-from pinnx.utils._display import training_display
 from . import metrics as metrics_module
 from . import utils
 from .callbacks import CallbackList, Callback
 from .problem.base import Problem
+from .utils._display import training_display
 
 __all__ = [
     "Trainer",

pinnx/callbacks.py

@@ -1,3 +1,6 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
 import sys
 import time
 from typing import Dict, Callable
@@ -9,7 +12,6 @@
 
 from . import utils
 
-
 __all__ = [
     'Callback',
     'CallbackList',

pinnx/fnspace.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 __all__ = [
     "FunctionSpace",
     "PowerSeries",

pinnx/geometry/base.py

@@ -1,16 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
 

pinnx/geometry/geometry_1d.py

@@ -1,16 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
 from typing import Literal, Union

pinnx/geometry/geometry_2d.py

@@ -1,17 +1,6 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
+
 __all__ = ["Disk", "Ellipse", "Polygon", "Rectangle", "StarShaped", "Triangle"]
 
 from typing import Union, Literal

pinnx/geometry/geometry_3d.py

@@ -1,22 +1,11 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
+
 import itertools
 from typing import Union, Literal
 
-import jax.numpy as jnp
 import brainstate as bst
+import jax.numpy as jnp
 
 from .geometry_2d import Rectangle
 from .geometry_nd import Hypercube, Hypersphere

pinnx/geometry/geometry_nd.py

@@ -1,18 +1,7 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
+
 import itertools
 from typing import Literal
 

pinnx/geometry/pointcloud.py

@@ -1,17 +1,6 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
+
 import brainstate as bst
 import numpy as np
 

pinnx/geometry/timedomain.py

@@ -1,18 +1,7 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
+
 import itertools
 
 import brainstate as bst

pinnx/icbc/base.py

@@ -1,18 +1,7 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
+
 import abc
 from typing import Optional, Dict
 

pinnx/icbc/boundary_conditions.py

@@ -1,4 +1,6 @@
-"""Boundary conditions."""
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
 
 from __future__ import annotations
 

pinnx/icbc/initial_conditions.py

@@ -1,4 +1,5 @@
-"""Initial conditions."""
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
 
 from __future__ import annotations
 

pinnx/metrics.py

@@ -1,7 +1,10 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 import brainunit as u
 import jax
 
-
 __all__ = [
     'accuracy',
     'l2_relative_error',

pinnx/nn/__init__.py

@@ -27,8 +27,8 @@
 ]
 
 from .base import NN
+from .convert import DictToArray, ArrayToDict
 from .deeponet import DeepONet, DeepONetCartesianProd, PODDeepONet
 from .fnn import FNN, PFNN
-from .convert import DictToArray, ArrayToDict
 from .mionet import MIONetCartesianProd, PODMIONet
 from .model import Model

pinnx/nn/base.py

@@ -1,16 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
 

pinnx/nn/deeponet.py

@@ -1,3 +1,6 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
 from typing import Union, Callable, Sequence, Dict, Optional
 
 import brainstate as bst

pinnx/nn/deeponet_strategy.py

@@ -1,3 +1,6 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
 from abc import ABC, abstractmethod
 
 

pinnx/nn/mionet.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from typing import Optional, Callable
 
 import brainstate as bst

pinnx/nn/model.py

@@ -1,18 +1,7 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
 # ==============================================================================
 
+
 from __future__ import annotations
 
 from typing import Dict, Sequence

pinnx/problem/base.py

@@ -1,3 +1,6 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
 from __future__ import annotations
 
 import abc

pinnx/problem/dataset_function.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from typing import Callable, Sequence
 
 import brainstate as bst

pinnx/problem/dataset_general.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from typing import Sequence, Dict
 
 import brainstate as bst

pinnx/problem/dataset_mf.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 import numpy as np
 
 from pinnx.utils import run_if_any_none, standardize

pinnx/problem/dataset_quadruple.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from typing import Sequence
 
 import brainstate as bst

pinnx/problem/dataset_triple.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from typing import Sequence
 
 import brainstate as bst

pinnx/problem/fpde.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from __future__ import annotations
 
 import math

pinnx/problem/ide.py

@@ -1,3 +1,7 @@
+# Rewrite of the original file in DeepXDE: https://github.com/lululxvi/deepxde
+# ==============================================================================
+
+
 from __future__ import annotations
 
 from typing import Callable, Sequence, Union, Optional, Dict, Any