From 8c7a9bc99506090210273c56021ccbd3da9fec6b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 16 Aug 2024 21:49:20 -0700
Subject: [PATCH 01/79] Bump boto3 from 1.34.160 to 1.34.162 (#323)

Bumps [boto3](https://github.com/boto/boto3) from 1.34.160 to 1.34.162.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.34.160...1.34.162)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index dc4dbb09..04030937 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.34.160
+boto3==1.34.162
 numpy==1.26.4
 sympy==1.13.2

From 38159eb0a0f79dd7e547701924463810a9a16bb4 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Sat, 17 Aug 2024 11:40:16 -0400
Subject: [PATCH 02/79] Create py.typed (#324)

* Create py.typed

As recommended in [pep 0561](https://peps.python.org/pep-0561/), a blank `py.typed` marker should be included when type hints are used so downstream codes can type check with `mypy` and similar tools.

Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>

* Update pyproject.toml

Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>

---------

Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>
---
 pyproject.toml     | 1 +
 src/matgl/py.typed | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 src/matgl/py.typed

diff --git a/pyproject.toml b/pyproject.toml
index 73c38354..6d40b501 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,6 +71,7 @@ mgl = "matgl.cli:main"
 where = ["src"]
 
 [tool.setuptools.package-data]
+matgl = ["py.typed"]
 "matgl.utils" = ["sb_roots.npy"]
 
 
diff --git a/src/matgl/py.typed b/src/matgl/py.typed
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/src/matgl/py.typed
@@ -0,0 +1 @@
+

From fd9dd065a94b5154f666654284b158419a323bfb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 19 Aug 2024 20:03:52 -0700
Subject: [PATCH 03/79] Bump boto3 from 1.34.162 to 1.35.0 (#325)

Bumps [boto3](https://github.com/boto/boto3) from 1.34.162 to 1.35.0.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.34.162...1.35.0)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 04030937..a4a138e1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.34.162
+boto3==1.35.0
 numpy==1.26.4
 sympy==1.13.2

From c2d69b00a00588a8cb3d5a72438470606e34ea0e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 20 Aug 2024 09:46:09 -0700
Subject: [PATCH 04/79] Bump boto3 from 1.35.0 to 1.35.1 (#327)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.0 to 1.35.1.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.0...1.35.1)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a4a138e1..afb0af7a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.0
+boto3==1.35.1
 numpy==1.26.4
 sympy==1.13.2

From c6088ce2c9065e4469b4f4d7bb706eb2048c3730 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 20 Aug 2024 13:17:49 -0700
Subject: [PATCH 05/79] Bump dgl from 2.1.0 to 2.2.1 (#302)

Bumps [dgl](https://github.com/dmlc/dgl) from 2.1.0 to 2.2.1.
- [Release notes](https://github.com/dmlc/dgl/releases)
- [Changelog](https://github.com/dmlc/dgl/blob/master/NEWS.md)
- [Commits](https://github.com/dmlc/dgl/compare/v2.1.0...v2.2.1)

---
updated-dependencies:
- dependency-name: dgl
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
---
 pyproject.toml   | 2 +-
 requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6d40b501..0bfde7e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ classifiers = [
 ]
 dependencies = [
     "ase",
-    "dgl<=2.1.0",
+    "dgl<=2.2.1",
     "pymatgen",
     "lightning<=2.4.0",
     "torch<=2.2.1",
diff --git a/requirements.txt b/requirements.txt
index afb0af7a..f772959f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-dgl==2.1.0
+dgl==2.2.1
 torch==2.4.0
 lightning==2.4.0
 pymatgen==2024.8.9

From 469648016558b2a1239564800d348d0197ba696b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 22 Aug 2024 11:33:19 -0700
Subject: [PATCH 06/79] Bump boto3 from 1.35.1 to 1.35.3 (#329)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.1 to 1.35.3.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.1...1.35.3)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index f772959f..8dd3c870 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.1
+boto3==1.35.3
 numpy==1.26.4
 sympy==1.13.2

From 634d4b8b21b3f5663d458d43ff259a278877c8f8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 22 Aug 2024 14:04:28 -0700
Subject: [PATCH 07/79] Bump rexml from 3.3.3 to 3.3.6 in /docs (#330)

Bumps [rexml](https://github.com/ruby/rexml) from 3.3.3 to 3.3.6.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](https://github.com/ruby/rexml/compare/v3.3.3...v3.3.6)

---
updated-dependencies:
- dependency-name: rexml
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 docs/Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
index b65d6021..436a4008 100644
--- a/docs/Gemfile.lock
+++ b/docs/Gemfile.lock
@@ -224,7 +224,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.3.3)
+    rexml (3.3.6)
       strscan
     rouge (3.26.0)
     ruby2_keywords (0.0.5)

From bf4e18850637dc00f0d4b031682dcb01c268ff1e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 25 Aug 2024 21:12:21 -0700
Subject: [PATCH 08/79] Bump boto3 from 1.35.3 to 1.35.4 (#331)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.3 to 1.35.4.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.3...1.35.4)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8dd3c870..9896f09d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.3
+boto3==1.35.4
 numpy==1.26.4
 sympy==1.13.2

From 37dcefce4c91f51be8c6f9b83812f963230d671a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 27 Aug 2024 13:15:58 -0700
Subject: [PATCH 09/79] Bump boto3 from 1.35.4 to 1.35.6 (#333)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.4 to 1.35.6.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.4...1.35.6)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 9896f09d..a3e707c9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.4
+boto3==1.35.6
 numpy==1.26.4
 sympy==1.13.2

From 15e8a9fe59a800525f7b991bbdf1d2c05f909185 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 30 Aug 2024 09:13:01 -0700
Subject: [PATCH 10/79] Bump boto3 from 1.35.6 to 1.35.9 (#337)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.6 to 1.35.9.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.6...1.35.9)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a3e707c9..f7880f7a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.6
+boto3==1.35.9
 numpy==1.26.4
 sympy==1.13.2

From 402fe1484f419370f1b815754582e96fa4b76474 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Sep 2024 10:20:23 -0700
Subject: [PATCH 11/79] Bump boto3 from 1.35.9 to 1.35.10 (#338)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.9 to 1.35.10.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.9...1.35.10)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index f7880f7a..4d7b143d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.9
+boto3==1.35.10
 numpy==1.26.4
 sympy==1.13.2

From 5c027946927f5111b03cf9451ad052c1ca1df4ba Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Wed, 4 Sep 2024 11:40:47 -0700
Subject: [PATCH 12/79] Update README.md for including CHGNet (#341)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 README.md     | 19 +++++++++++++++++++
 docs/index.md |  1 +
 2 files changed, 20 insertions(+)

diff --git a/README.md b/README.md
index 4a012972..dfc2a308 100644
--- a/README.md
+++ b/README.md
@@ -28,6 +28,7 @@ Nassar, Carmelo Gonzales).
 
 Major milestones are summarized below. Please refer to the [changelog] for details.
 
+- v1.1.0 (May 7 2024): Implementation of [CHGNet] + pre-trained models. 
 - v1.0.0 (Feb 14 2024): Implementation of [TensorNet] and [SO3Net].
 - v0.5.1 (Jun 9 2023): Model versioning implemented.
 - v0.5.0 (Jun 8 2023): Simplified saving and loading of models. Now models can be loaded with one line of code!
@@ -87,6 +88,8 @@ We have implemented other models in matgl as well. A non-exhaustive list is give
 - [TensorNet], an O(3)-equivariant message-passing neural network architecture that
   leverages Cartesian tensor representations.
 - [SO3Net],  a minimalist SO(3)-equivariant neural network.
+- [CHGNet],  an invariant message-passing neural network architecture that can predict
+  PES properties and magmoms. 
 
 ## Installation
 
@@ -226,6 +229,21 @@ information. If you are using any of the pretrained models, please cite the rele
 > Chen, C., Ong, S.P. *A universal graph deep learning interatomic potential for the periodic table.* Nature
 > Computational Science, 2023, 2, 718–728. DOI: [10.1038/s43588-022-00349-3][m3gnet].
 
+>**CHGNet**
+>
+> Deng, B., Zhong, P., Jun, K. et al. *CHGNet: as a pretrained universal neural network potential for charge-informed atomistic modelling.*
+> Nat Mach Intell 5, 1031–1041 (2023). DOI:[10.1038/s42256-023-00716-3][chgnet]
+
+>**TensorNet**
+>
+> Simeon, G.  De Fabritiis, G. *Tensornet: Cartesian tensor representations for efficient learning of molecular potentials.*
+> Adv. Neural Info. Process. Syst. 36, (2024). DOI: [10.48550/arXiv.2306.06482][tensornet]
+
+>**SO3Net**
+>
+> Schütt, K. T., Hessmann, S. S. P., Gebauer, N. W. A., Lederer, J., Gastegger, M. *SchNetPack 2.0: A neural network toolbox for atomistic machine learning.*
+> J. Chem. Phys. 158, 144801 (2023). DOI: [10.1063/5.0138367][so3net]
+
 ## FAQs
 
 1. **The `M3GNet-MP-2021.2.8-PES` differs from the original TensorFlow (TF) implementation!**
@@ -296,3 +314,4 @@ ACI-1548562.
 [tutorials]: https://matgl.ai/tutorials "Tutorials"
 [tensornet]: https://arxiv.org/abs/2306.06482 "TensorNet"
 [so3net]: https://pubs.aip.org/aip/jcp/article-abstract/158/14/144801/2877924/SchNetPack-2-0-A-neural-network-toolbox-for "SO3Net"
+[chgnet]: https://www.nature.com/articles/s42256-023-00716-3 "CHGNet"
diff --git a/docs/index.md b/docs/index.md
index 06a0d566..d72c5aeb 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -304,3 +304,4 @@ ACI-1548562.
 [tutorials]: https://matgl.ai/tutorials "Tutorials"
 [tensornet]: https://arxiv.org/abs/2306.06482 "TensorNet"
 [so3net]: https://pubs.aip.org/aip/jcp/article-abstract/158/14/144801/2877924/SchNetPack-2-0-A-neural-network-toolbox-for "SO3Net"
+[chgnet]: https://www.nature.com/articles/s42256-023-00716-3 "CHGNet"

From ffeba21f1c8a1812572b428de73c2e771ccc9dea Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Wed, 4 Sep 2024 16:25:39 -0700
Subject: [PATCH 13/79] Adding more descriptions for using CHGNet pretrained
 models in Relaxations and Simulations using the M3GNet Universal
 Potential.ipynb (#342)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 ...ations using the M3GNet Universal Potential.ipynb | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb b/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb
index fbb49856..4d67babb 100644
--- a/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb	
+++ b/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb	
@@ -7,7 +7,7 @@
    "source": [
     "# Introduction\n",
     "\n",
-    "This notebook demonstrates the use of the pre-trained M3GNet model to perform structural relaxations, molecular dynamics simulations and single-point calculations.\n",
+    "This notebook demonstrates the use of the pre-trained universal potentials to perform structural relaxations, molecular dynamics simulations and single-point calculations.\n",
     "\n",
     "Author: Tsz Wai Ko (Kenko)\n",
     "Email: t1ko@ucsd.edu"
@@ -42,7 +42,7 @@
    "source": [
     "# Loading the pre-trained M3GNet PES model\n",
     "\n",
-    "We will first load the M3GNet PES model, which is trained on the MP-2021.2.8 dataset. This can be done with a single line of code."
+    "We will first load the M3GNet PES model, which is trained on the MP-2021.2.8 dataset. This can be done with a single line of code. Here we only use M3GNet for demonstration and users can choose other available models."
    ]
   },
   {
@@ -52,7 +52,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pot = matgl.load_model(\"M3GNet-MP-2021.2.8-PES\")"
+    "# You can load any pretrained potentials such as CHGNet ('CHGNet-MPtrj-2023.12.1-PES-2.7M', 'CHGNet-MPtrj-2024.2.13-PES-11M')\n",
+    "# To see availabe models, use get_available_pretrained_models()\n",
+    "pot = matgl.load_model(\"M3GNet-MP-2021.2.8-PES\") "
    ]
   },
   {
@@ -120,7 +122,7 @@
    "source": [
     "# Single point energy calculation\n",
     "\n",
-    "Perform a single-point calculation for final structure using M3GNetCalculator."
+    "Perform a single-point calculation for final structure using PESCalculator."
    ]
   },
   {
@@ -154,7 +156,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,

From 86ba27521aced7f751543164962c02d7c7027e00 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 5 Sep 2024 13:36:15 -0700
Subject: [PATCH 14/79] Bump boto3 from 1.35.10 to 1.35.12 (#344)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.10 to 1.35.12.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.10...1.35.12)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 4d7b143d..5e8f8c64 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.8.2
 torchdata==0.8.0
-boto3==1.35.10
+boto3==1.35.12
 numpy==1.26.4
 sympy==1.13.2

From c00902bf6c709cd88f5d379d5c6c2e0a622bde1e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 6 Sep 2024 09:11:24 -0700
Subject: [PATCH 15/79] Bump pydantic from 2.8.2 to 2.9.0 (#346)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.8.2 to 2.9.0.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v2.8.2...v2.9.0)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 5e8f8c64..18cdf110 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ torch==2.4.0
 lightning==2.4.0
 pymatgen==2024.8.9
 ase==3.23.0
-pydantic==2.8.2
+pydantic==2.9.0
 torchdata==0.8.0
 boto3==1.35.12
 numpy==1.26.4

From 0e41820d65021efecf833501f4175207f6fc2d50 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 6 Sep 2024 11:55:07 -0700
Subject: [PATCH 16/79] Bump boto3 from 1.35.12 to 1.35.13 (#345)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.12 to 1.35.13.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.12...1.35.13)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 18cdf110..d0c8f3e0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.9.0
 torchdata==0.8.0
-boto3==1.35.12
+boto3==1.35.13
 numpy==1.26.4
 sympy==1.13.2

From 19fb21646155363064ae53adcf4b2ed3f67e1a27 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 9 Sep 2024 08:51:15 -0700
Subject: [PATCH 17/79] Bump pydantic from 2.9.0 to 2.9.1 (#348)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.9.0 to 2.9.1.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v2.9.0...v2.9.1)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index d0c8f3e0..62a99deb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ torch==2.4.0
 lightning==2.4.0
 pymatgen==2024.8.9
 ase==3.23.0
-pydantic==2.9.0
+pydantic==2.9.1
 torchdata==0.8.0
 boto3==1.35.13
 numpy==1.26.4

From 7d49ec0a703aabab8e9087087f708e9549cf73b2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 9 Sep 2024 08:51:34 -0700
Subject: [PATCH 18/79] Bump boto3 from 1.35.13 to 1.35.14 (#347)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.13 to 1.35.14.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.13...1.35.14)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 62a99deb..f28c6384 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0
-boto3==1.35.13
+boto3==1.35.14
 numpy==1.26.4
 sympy==1.13.2

From e6a89e56988f30b55f2d9ed95a606f3f2d3dfb59 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:34:40 -0700
Subject: [PATCH 19/79] Update DGL version for torch v2.4.1 (#351)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* Update the version of dgl in pyproject.toml for torch v2.4.1

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Update dgl version in requirements.txt for torch v2.4.1

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 pyproject.toml   | 2 +-
 requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0bfde7e0..1e184f39 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ classifiers = [
 ]
 dependencies = [
     "ase",
-    "dgl<=2.2.1",
+    "dgl<=2.4.0",
     "pymatgen",
     "lightning<=2.4.0",
     "torch<=2.2.1",
diff --git a/requirements.txt b/requirements.txt
index f28c6384..f82aad86 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-dgl==2.2.1
+dgl==2.4.0
 torch==2.4.0
 lightning==2.4.0
 pymatgen==2024.8.9

From 919cabd98b33fb9eeec1041ff951b994f5daaca8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 11 Sep 2024 11:35:20 -0700
Subject: [PATCH 20/79] Bump boto3 from 1.35.14 to 1.35.16 (#353)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.14 to 1.35.16.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.14...1.35.16)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index f82aad86..09e9b8c5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.8.9
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0
-boto3==1.35.14
+boto3==1.35.16
 numpy==1.26.4
 sympy==1.13.2

From 334f3aec55178a5a187dadc006511fd6721ed375 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 11 Sep 2024 12:20:50 -0700
Subject: [PATCH 21/79] Bump pymatgen from 2024.8.9 to 2024.9.10 (#352)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.8.9 to 2024.9.10.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.8.9...v2024.9.10)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 09e9b8c5..51abb6ad 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.4.0
 torch==2.4.0
 lightning==2.4.0
-pymatgen==2024.8.9
+pymatgen==2024.9.10
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0

From cae0ec13642bb3d3cc9162cdf58064c154f09524 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Sep 2024 20:50:26 -0700
Subject: [PATCH 22/79] Bump boto3 from 1.35.16 to 1.35.19 (#356)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.16 to 1.35.19.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.16...1.35.19)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 51abb6ad..f3fd441c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.10
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0
-boto3==1.35.16
+boto3==1.35.19
 numpy==1.26.4
 sympy==1.13.2

From e441e2b6fffe6cd7a0d193136de38ee370da2f77 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 17 Sep 2024 15:37:20 -0700
Subject: [PATCH 23/79] Bump boto3 from 1.35.19 to 1.35.20 (#357)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.19 to 1.35.20.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.19...1.35.20)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index f3fd441c..323c9873 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.10
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0
-boto3==1.35.19
+boto3==1.35.20
 numpy==1.26.4
 sympy==1.13.2

From 8489e11eede64ef1f543821e1aa02c284a994a3f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Sep 2024 09:11:41 -0700
Subject: [PATCH 24/79] Bump pymatgen from 2024.9.10 to 2024.9.17.1 (#359)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.9.10 to 2024.9.17.1.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.9.10...v2024.9.17.1)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 323c9873..a8a27811 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.4.0
 torch==2.4.0
 lightning==2.4.0
-pymatgen==2024.9.10
+pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0

From 03d2d32c88a9cb6445db8d1a41a62c0d49441eb4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Sep 2024 09:11:52 -0700
Subject: [PATCH 25/79] Bump boto3 from 1.35.20 to 1.35.21 (#360)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.20 to 1.35.21.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.20...1.35.21)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a8a27811..291af217 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.1
 torchdata==0.8.0
-boto3==1.35.20
+boto3==1.35.21
 numpy==1.26.4
 sympy==1.13.2

From 5186acec18b9b3ff1592b3f4069486033cf6ba35 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Sep 2024 09:12:02 -0700
Subject: [PATCH 26/79] Bump pydantic from 2.9.1 to 2.9.2 (#361)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.9.1 to 2.9.2.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v2.9.1...v2.9.2)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 291af217..064fd142 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ torch==2.4.0
 lightning==2.4.0
 pymatgen==2024.9.17.1
 ase==3.23.0
-pydantic==2.9.1
+pydantic==2.9.2
 torchdata==0.8.0
 boto3==1.35.21
 numpy==1.26.4

From 961195551373a14af7d264eb2cc11d0bd7504464 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Wed, 18 Sep 2024 10:12:16 -0700
Subject: [PATCH 27/79] A command-line interface for performing ASE MD
 simulations is added. (#362)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 README.md                                     |   4 +-
 ...using the M3GNet Universal Potential.ipynb |   2 +-
 src/matgl/cli.py                              | 202 +++++++++++++++++-
 src/matgl/py.typed                            |   1 -
 tests/test_cli.py                             |   5 +-
 5 files changed, 208 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index dfc2a308..25b7d6f5 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,7 @@ Nassar, Carmelo Gonzales).
 
 Major milestones are summarized below. Please refer to the [changelog] for details.
 
-- v1.1.0 (May 7 2024): Implementation of [CHGNet] + pre-trained models. 
+- v1.1.0 (May 7 2024): Implementation of [CHGNet] + pre-trained models.
 - v1.0.0 (Feb 14 2024): Implementation of [TensorNet] and [SO3Net].
 - v0.5.1 (Jun 9 2023): Model versioning implemented.
 - v0.5.0 (Jun 8 2023): Simplified saving and loading of models. Now models can be loaded with one line of code!
@@ -89,7 +89,7 @@ We have implemented other models in matgl as well. A non-exhaustive list is give
   leverages Cartesian tensor representations.
 - [SO3Net],  a minimalist SO(3)-equivariant neural network.
 - [CHGNet],  an invariant message-passing neural network architecture that can predict
-  PES properties and magmoms. 
+  PES properties and magmoms.
 
 ## Installation
 
diff --git a/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb b/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb
index 4d67babb..ff67b55a 100644
--- a/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb	
+++ b/examples/Relaxations and Simulations using the M3GNet Universal Potential.ipynb	
@@ -53,7 +53,7 @@
    "outputs": [],
    "source": [
     "# You can load any pretrained potentials such as CHGNet ('CHGNet-MPtrj-2023.12.1-PES-2.7M', 'CHGNet-MPtrj-2024.2.13-PES-11M')\n",
-    "# To see availabe models, use get_available_pretrained_models()\n",
+    "# To see available models, use get_available_pretrained_models()\n",
     "pot = matgl.load_model(\"M3GNet-MP-2021.2.8-PES\") "
    ]
   },
diff --git a/src/matgl/cli.py b/src/matgl/cli.py
index 3fb551ca..821fb513 100644
--- a/src/matgl/cli.py
+++ b/src/matgl/cli.py
@@ -9,11 +9,13 @@
 
 import numpy as np
 import torch
+from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
 from pymatgen.core.structure import Structure
 from pymatgen.ext.matproj import MPRester
+from pymatgen.io.ase import AseAtomsAdaptor
 
 import matgl
-from matgl.ext.ase import Relaxer
+from matgl.ext.ase import MolecularDynamics, Relaxer
 
 warnings.simplefilter("ignore")
 logger = logging.getLogger("MGL")
@@ -95,6 +97,49 @@ def predict_structure(args):
             print(f"{args.model} prediction for {mid} ({structure.composition.reduced_formula}): {val}.")
 
 
+def molecular_dynamics(args):
+    """
+    Use MaGL models to perform MD simulations on structures.
+
+    Args:
+        args: Args from CLI.
+    """
+    for file in args.infile:
+        name = file.split(".")[0]
+        structure = Structure.from_file(file)
+        adaptor = AseAtomsAdaptor()
+        atoms = adaptor.get_atoms(structure)
+
+        logger.info(f"Initial structure\n{structure}")
+        logger.info("Loading model...")
+        pot = matgl.load_model(args.model)
+        logger.info("Running MD...")
+        MaxwellBoltzmannDistribution(atoms, temperature_K=args.temp)
+        md = MolecularDynamics(
+            atoms,
+            potential=pot,
+            ensemble=args.ensemble,
+            pressure=args.pressure,
+            timestep=args.stepsize,
+            trajectory=name + ".traj",
+            logfile=name + ".log",
+            temperature=args.temp,
+            taut=args.taut,
+            taup=args.taup,
+            friction=args.friction,
+            andersen_prob=args.andersen_prob,
+            ttime=args.ttime,
+            pfactor=args.pfactor,
+            external_stress=args.external_stress,
+            compressibility_au=args.compressibility_au,
+            loginterval=args.loginterval,
+            append_trajectory=args.append_trajectory,
+            mask=args.mask,
+        )
+        md.run(args.nsteps)
+    return 0
+
+
 def clear_cache(args):
     """
     Clear cache command.
@@ -200,6 +245,161 @@ def main():
 
     p_predict.set_defaults(func=predict_structure)
 
+    # MD simulations
+    p_md = subparsers.add_parser("md", help="Perform MD simulations with pre-trained and customized models.")
+
+    p_md.add_argument(
+        "-i",
+        "--infile",
+        nargs="+",
+        dest="infile",
+        required=True,
+        help="Input files containing structure. Any format supported by pymatgen Structure.from_file method.",
+    )
+
+    p_md.add_argument(
+        "-m",
+        "--model",
+        dest="model",
+        #        choices=[m for m in matgl.get_available_pretrained_models() if m.endswith("PES")],
+        default="M3GNet-MP-2021.2.8-DIRECT-PES",
+        help="Path for loading MLIPs trained from MatGL. Default='M3GNet-MP-2021.2.8-DIRECT-PES'.",
+    )
+
+    p_md.add_argument(
+        "-e",
+        "--ensemble",
+        dest="ensemble",
+        choices=["nve", "nvt", "nvt_langevin", "nvt_andersen", "npt", "npt_berendsen", "npt_nose_hoover"],
+        default="nve",
+        help="Ensemble used for MD simulation. Default='nve'.",
+    )
+
+    p_md.add_argument(
+        "-n",
+        "--nsteps",
+        dest="nsteps",
+        type=int,
+        default=100,
+        help="Number of steps used for MD simulation. Default=100.",
+    )
+
+    p_md.add_argument(
+        "--stepsize",
+        dest="stepsize",
+        type=float,
+        default=1.0,
+        help="Step size used for MD simulation. Default=1.0 fs.",
+    )
+
+    p_md.add_argument(
+        "-t",
+        "--temp",
+        dest="temp",
+        type=float,
+        default=300.0,
+        help="Temperature used for MD simulation. Default=300.0 in K.",
+    )
+
+    p_md.add_argument(
+        "-p",
+        "--pressure",
+        dest="pressure",
+        type=float,
+        default=1.01325,
+        help="Pressure used for MD simulation. Default=1.01325 in Bar.",
+    )
+
+    p_md.add_argument(
+        "--taut",
+        dest="taut",
+        type=float,
+        default=None,
+        help="Time constant for Berendsen temperature coupling. Default is None.",
+    )
+
+    p_md.add_argument(
+        "--taup",
+        dest="taup",
+        type=float,
+        default=None,
+        help="Time constant for Berendsen pressure coupling. Default is None.",
+    )
+
+    p_md.add_argument(
+        "--andersen_prob",
+        dest="andersen_prob",
+        type=float,
+        default=0.01,
+        help="Random collision probability for nvt_andersen. Default is 0.01.",
+    )
+
+    p_md.add_argument(
+        "--friction",
+        dest="friction",
+        type=float,
+        default=0.001,
+        help="Friction coefficient for nvt_langevin. Default is 0.001.",
+    )
+
+    p_md.add_argument(
+        "--ttime",
+        dest="ttime",
+        type=float,
+        default=25.0,
+        help="Characteristic timescale of the thermostat in ASE internal units. Default is 25.0.",
+    )
+
+    p_md.add_argument(
+        "--pfactor",
+        dest="pfactor",
+        type=float,
+        default=75.0**2.0,
+        help="A constant in the barostat differential equation. Default is 25.0 in eV/A$^{3}$.",
+    )
+
+    p_md.add_argument(
+        "--external_stress",
+        dest="external_stress",
+        type=float,
+        default=None,
+        help="The external stress either 3x3 tensor, 6-vector or a scalar in eV/A$^{3}$. Default is None.",
+    )
+
+    p_md.add_argument(
+        "--compressibility_au",
+        dest="compressibility_au",
+        type=float,
+        default=None,
+        help="Compressibility of the material in eV/A^{3}. Default is None.",
+    )
+
+    p_md.add_argument(
+        "--loginterval",
+        dest="loginterval",
+        type=int,
+        default=1,
+        help="Write to log file every interval steps. Default is 1.",
+    )
+
+    p_md.add_argument(
+        "--append_trajectory",
+        dest="append_trajectory",
+        type=bool,
+        default=False,
+        help="Whether to append to prev trajectory. Default is False.",
+    )
+
+    p_md.add_argument(
+        "--mask",
+        dest="mask",
+        type=np.array,
+        default=None,
+        help="a symmetric 3x3 array indicating, which strain values may change for NPT simulations",
+    )
+
+    p_md.set_defaults(func=molecular_dynamics)
+
     p_clear = subparsers.add_parser("clear", help="Clear cache.")
 
     p_clear.add_argument(
diff --git a/src/matgl/py.typed b/src/matgl/py.typed
index 8b137891..e69de29b 100644
--- a/src/matgl/py.typed
+++ b/src/matgl/py.typed
@@ -1 +0,0 @@
-
diff --git a/tests/test_cli.py b/tests/test_cli.py
index f2efb2ae..b438fd10 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -20,7 +20,8 @@ def test_entrypoint(Mo):
     assert exit_status == 0
     exit_status = os.system("mgl predict -i Mo.cif -m MEGNet-MP-2018.6.1-Eform")
     assert exit_status == 0
-
+    exit_status = os.system("mgl md -i Mo.cif -e nve -t 300.0 -n 10 --stepsize=1.0")
+    assert exit_status == 0
     # if "PMG_MAPI_KEY" in SETTINGS:
     #     exit_status = os.system("mgl predict -p mp-19017 -m MEGNet-MP-2018.6.1-Eform")
     #     assert exit_status == 0
@@ -30,3 +31,5 @@ def test_entrypoint(Mo):
     os.remove("Mo.cif")
     os.remove("Mo_relaxed.cif")
     os.remove("Mo_hello.cif")
+    os.remove("Mo.traj")
+    os.remove("Mo.log")

From a6e0e1e18c2f615ad06d40f0896c1726bfd5229b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 19 Sep 2024 16:46:01 -0700
Subject: [PATCH 28/79] Bump boto3 from 1.35.21 to 1.35.22 (#364)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.21 to 1.35.22.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.21...1.35.22)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 064fd142..0752360e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.21
+boto3==1.35.22
 numpy==1.26.4
 sympy==1.13.2

From 3a2f91ac58a64850af5c197fd44942ec74dd63c3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 20 Sep 2024 11:04:48 -0700
Subject: [PATCH 29/79] Bump boto3 from 1.35.22 to 1.35.23 (#365)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.22 to 1.35.23.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.22...1.35.23)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 0752360e..8a32696d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.22
+boto3==1.35.23
 numpy==1.26.4
 sympy==1.13.2

From 8326e7ceae49cbbf6f6b1402f1d655a1d6d51ab7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 20 Sep 2024 12:16:50 -0700
Subject: [PATCH 30/79] Bump sympy from 1.13.2 to 1.13.3 (#363)

Bumps [sympy](https://github.com/sympy/sympy) from 1.13.2 to 1.13.3.
- [Release notes](https://github.com/sympy/sympy/releases)
- [Commits](https://github.com/sympy/sympy/compare/sympy-1.13.2...sympy-1.13.3)

---
updated-dependencies:
- dependency-name: sympy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8a32696d..05b6baad 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,4 +7,4 @@ pydantic==2.9.2
 torchdata==0.8.0
 boto3==1.35.23
 numpy==1.26.4
-sympy==1.13.2
+sympy==1.13.3

From 3a4f26d68cbd3379f0800152297ae0c9514d4b77 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Sun, 22 Sep 2024 14:37:32 -0700
Subject: [PATCH 31/79] clean up united tests in test_basis.py

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 tests/layers/test_basis.py | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/tests/layers/test_basis.py b/tests/layers/test_basis.py
index 81504564..cd0afbec 100644
--- a/tests/layers/test_basis.py
+++ b/tests/layers/test_basis.py
@@ -57,17 +57,6 @@ def test_spherical_bessel_function():
     assert [rbf.size(dim=0), rbf.size(dim=1)] == [11, 3]
 
 
-def test_spherical_bessel_function_smooth():
-    r = torch.linspace(1.0, 5.0, 11)
-    rbf_sb = SphericalBesselFunction(max_n=3, max_l=3, cutoff=5.0, smooth=False)
-    rbf = rbf_sb(r)
-    assert [rbf.size(dim=0), rbf.size(dim=1)] == [11, 9]
-
-    rbf_sb = SphericalBesselFunction(max_n=3, max_l=3, cutoff=5.0, smooth=True)
-    rbf = rbf_sb(r)
-    assert [rbf.size(dim=0), rbf.size(dim=1)] == [11, 3]
-
-
 def test_spherical_harmonic_function():
     theta = torch.linspace(-1, 1, 10)
     phi = torch.linspace(0, 2 * np.pi, 10)
@@ -80,15 +69,6 @@ def test_spherical_bessel_harmonics_function():
     r = torch.empty(10).normal_()
     sbf = SphericalBesselFunction(max_l=3, cutoff=5.0, max_n=3, smooth=False)
     res = sbf(r)
-    res2 = sbf.rbf_j0(r, cutoff=5.0, max_n=3)
-    assert np.allclose(res[:, :3].numpy().ravel(), res2.numpy().ravel(), atol=1e-07)
-
-    assert res.numpy().shape == (10, 9)
-
-    sbf2 = SphericalBesselFunction(max_l=3, cutoff=5.0, max_n=3, smooth=True)
-
-    res2 = sbf2(r)
-    assert tuple(res2.shape) == (10, 3)
 
     shf = SphericalHarmonicsFunction(max_l=3, use_phi=True)
     res_shf = shf(cos_theta=torch.linspace(-1, 1, 10), phi=torch.linspace(0, 2 * np.pi, 10))

From 3bc8467b5a280b3316a7a86a74bf062f34e39e42 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Sun, 22 Sep 2024 20:43:55 -0700
Subject: [PATCH 32/79] Added Exponent Normal Smearing for radial basis
 functions (#366)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 src/matgl/layers/_basis.py | 56 ++++++++++++++++++++++++++++++++++++++
 src/matgl/layers/_bond.py  |  8 ++++--
 tests/layers/test_basis.py | 12 ++++++++
 tests/layers/test_bond.py  |  7 +++++
 4 files changed, 80 insertions(+), 3 deletions(-)

diff --git a/src/matgl/layers/_basis.py b/src/matgl/layers/_basis.py
index 247275c2..f9018acc 100644
--- a/src/matgl/layers/_basis.py
+++ b/src/matgl/layers/_basis.py
@@ -9,6 +9,7 @@
 
 import matgl
 from matgl.layers._three_body import combine_sbf_shf
+from matgl.utils.cutoff import cosine_cutoff
 from matgl.utils.maths import SPHERICAL_BESSEL_ROOTS, _get_lambda_func
 
 
@@ -360,3 +361,58 @@ def forward(self, line_graph):
         sbf = self.sbf(line_graph.edata["triple_bond_lengths"])
         shf = self.shf(line_graph.edata["cos_theta"], line_graph.edata["phi"])
         return combine_sbf_shf(sbf, shf, max_n=self.max_n, max_l=self.max_l, use_phi=self.use_phi)
+
+
+class ExpNormalFunction(nn.Module):
+    """Implementation of radial basis function using exponential normal smearing."""
+
+    def __init__(self, cutoff: float = 5.0, num_rbf: int = 50, learnable: bool = True):
+        """
+        Initialize ExpNormalSmearing.
+
+        Args:
+            cutoff (float): The cutoff distance beyond which interactions are considered negligible. Default is 5.0.
+            num_rbf (int): The number of radial basis functions (RBF) to use. Default is 50.
+            learnable (bool): If True, the means and betas parameters are learnable.
+                              If False, they are fixed. Default is True.
+        """
+        super().__init__()
+        self.cutoff = cutoff
+        self.num_rbf = num_rbf
+        self.learnable = learnable
+
+        self.alpha = 5.0 / cutoff
+
+        means, betas = self._initial_params()
+        if learnable:
+            self.register_parameter("means", nn.Parameter(means))
+            self.register_parameter("betas", nn.Parameter(betas))
+        else:
+            self.register_buffer("means", means)
+            self.register_buffer("betas", betas)
+
+    def _initial_params(self):
+        """Initialize the means and betas parameters."""
+        start_value = torch.exp(torch.tensor(-self.cutoff, dtype=matgl.float_th))
+        means = torch.linspace(start_value, 1, self.num_rbf)
+        betas = torch.tensor([(2 / self.num_rbf * (1 - start_value)) ** -2] * self.num_rbf)
+        return means, betas
+
+    def reset_parameters(self):
+        """Reset the means and betas to their initial values."""
+        means, betas = self._initial_params()
+        self.means.data.copy_(means)
+        self.betas.data.copy_(betas)
+
+    def forward(self, r: torch.Tensor):
+        """
+        Compute the radial basis function for the input distances.
+
+        Args:
+            r (torch.Tensor): Input distances.
+
+        Returns:
+            torch.Tensor: Smearing function applied to the input distances.
+        """
+        r = r.unsqueeze(-1)
+        return cosine_cutoff(r, self.cutoff) * torch.exp(-self.betas * (torch.exp(self.alpha * (-r)) - self.means) ** 2)
diff --git a/src/matgl/layers/_bond.py b/src/matgl/layers/_bond.py
index 1a739af6..938d0083 100644
--- a/src/matgl/layers/_bond.py
+++ b/src/matgl/layers/_bond.py
@@ -7,7 +7,7 @@
 import torch
 from torch import nn
 
-from matgl.layers._basis import GaussianExpansion, SphericalBesselFunction
+from matgl.layers._basis import ExpNormalFunction, GaussianExpansion, SphericalBesselFunction
 
 
 class BondExpansion(nn.Module):
@@ -18,7 +18,7 @@ def __init__(
         max_l: int = 3,
         max_n: int = 3,
         cutoff: float = 5.0,
-        rbf_type: Literal["SphericalBessel", "Gaussian"] = "SphericalBessel",
+        rbf_type: Literal["SphericalBessel", "Gaussian", "ExpNorm"] = "SphericalBessel",
         smooth: bool = False,
         initial: float = 0.0,
         final: float = 5.0,
@@ -30,7 +30,7 @@ def __init__(
             max_l (int): order of angular part
             max_n (int): order of radial part
             cutoff (float): cutoff radius
-            rbf_type (str): type of radial basis function .i.e. either "SphericalBessel" or 'Gaussian'
+            rbf_type (str): type of radial basis function .i.e. either "SphericalBessel", "ExpNorm" or 'Gaussian'
             smooth (bool): whether apply the smooth version of spherical bessel functions or not
             initial (float): initial point for gaussian expansion
             final (float): final point for gaussian expansion
@@ -53,6 +53,8 @@ def __init__(
             self.rbf = SphericalBesselFunction(max_l, max_n, cutoff, smooth)  # type: ignore
         elif rbf_type.lower() == "gaussian":
             self.rbf = GaussianExpansion(initial, final, num_centers, width)  # type: ignore
+        elif rbf_type.lower() == "expnorm":
+            self.rbf = ExpNormalFunction(cutoff, num_centers, True)
         else:
             raise ValueError("Undefined rbf_type, please use SphericalBessel or Gaussian instead.")
 
diff --git a/tests/layers/test_basis.py b/tests/layers/test_basis.py
index cd0afbec..59115fc0 100644
--- a/tests/layers/test_basis.py
+++ b/tests/layers/test_basis.py
@@ -8,6 +8,7 @@
     create_line_graph,
 )
 from matgl.layers._basis import (
+    ExpNormalFunction,
     FourierExpansion,
     GaussianExpansion,
     RadialBesselFunction,
@@ -57,6 +58,17 @@ def test_spherical_bessel_function():
     assert [rbf.size(dim=0), rbf.size(dim=1)] == [11, 3]
 
 
+def test_exp_normal_function():
+    r = torch.linspace(1.0, 5.0, 11)
+    rbf = ExpNormalFunction(cutoff=5.0, num_rbf=3, learnable=False)
+    res = rbf(r)
+    assert [res.size(dim=0), res.size(dim=1)] == [11, 3]
+
+    rbf = ExpNormalFunction(cutoff=5.0, num_rbf=3, learnable=True)
+    res = rbf(r)
+    assert [res.size(dim=0), res.size(dim=1)] == [11, 3]
+
+
 def test_spherical_harmonic_function():
     theta = torch.linspace(-1, 1, 10)
     phi = torch.linspace(0, 2 * np.pi, 10)
diff --git a/tests/layers/test_bond.py b/tests/layers/test_bond.py
index 4d1e0bb4..6c7113c8 100644
--- a/tests/layers/test_bond.py
+++ b/tests/layers/test_bond.py
@@ -35,6 +35,13 @@ def test_spherical_bessel(self, graph_MoS, graph_CO):
         bond_basis = bond_expansion(g2.edata["bond_dist"])
         assert bond_basis.shape == (2, 9)
 
+    def test_exp_normal(self, graph_MoS, graph_CO):
+        _, g1, _ = graph_MoS
+        _, g2, _ = graph_CO
+        bond_expansion = BondExpansion(rbf_type="ExpNorm", cutoff=4.0, num_centers=9)
+        bond_basis = bond_expansion(g1.edata["bond_dist"])
+        assert bond_basis.shape == (28, 9)
+
     def test_exception(self):
         with pytest.raises(ValueError, match="Undefined rbf_type"):
             BondExpansion(rbf_type="nonsense")

From e5ebebc7312f352d63c4dd716455e589098f794f Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Sun, 22 Sep 2024 21:51:37 -0700
Subject: [PATCH 33/79] Remove unnecessary reset_parameters in ExpNormFunction
 class

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 src/matgl/layers/_basis.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/src/matgl/layers/_basis.py b/src/matgl/layers/_basis.py
index f9018acc..81fb7129 100644
--- a/src/matgl/layers/_basis.py
+++ b/src/matgl/layers/_basis.py
@@ -398,12 +398,6 @@ def _initial_params(self):
         betas = torch.tensor([(2 / self.num_rbf * (1 - start_value)) ** -2] * self.num_rbf)
         return means, betas
 
-    def reset_parameters(self):
-        """Reset the means and betas to their initial values."""
-        means, betas = self._initial_params()
-        self.means.data.copy_(means)
-        self.betas.data.copy_(betas)
-
     def forward(self, r: torch.Tensor):
         """
         Compute the radial basis function for the input distances.

From 00dd1e1ba14112bed210389e42a746bc10cbad5b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Sep 2024 17:58:44 -0700
Subject: [PATCH 34/79] Bump boto3 from 1.35.23 to 1.35.24 (#367)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.23 to 1.35.24.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.23...1.35.24)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 05b6baad..fc5c07e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.23
+boto3==1.35.24
 numpy==1.26.4
 sympy==1.13.3

From 4e48fa27dff5bdd370b36b36178963886d492c13 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 21:05:14 -0700
Subject: [PATCH 35/79] Bump boto3 from 1.35.24 to 1.35.25 (#368)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.24 to 1.35.25.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.24...1.35.25)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index fc5c07e9..e6d152b1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.24
+boto3==1.35.25
 numpy==1.26.4
 sympy==1.13.3

From f30b560cc398f2384f72798965088ca078bbe62f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 23:14:47 -0700
Subject: [PATCH 36/79] Bump webrick from 1.8.1 to 1.8.2 in /docs (#369)

Bumps [webrick](https://github.com/ruby/webrick) from 1.8.1 to 1.8.2.
- [Release notes](https://github.com/ruby/webrick/releases)
- [Commits](https://github.com/ruby/webrick/compare/v1.8.1...v1.8.2)

---
updated-dependencies:
- dependency-name: webrick
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 docs/Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
index 436a4008..26c8b11c 100644
--- a/docs/Gemfile.lock
+++ b/docs/Gemfile.lock
@@ -251,7 +251,7 @@ GEM
       unf_ext
     unf_ext (0.0.8.2)
     unicode-display_width (1.8.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
 
 PLATFORMS
   arm64-darwin-22

From 698d0fce4caae98d30d3da5f1c6bbb73920c7e10 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 25 Sep 2024 11:05:24 -0700
Subject: [PATCH 37/79] Bump boto3 from 1.35.25 to 1.35.26 (#370)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.25 to 1.35.26.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.25...1.35.26)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index e6d152b1..c2a2b21a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.25
+boto3==1.35.26
 numpy==1.26.4
 sympy==1.13.3

From 4c99cbfc839049dd609967fbb7a434e6ed0fded1 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Wed, 25 Sep 2024 23:45:13 -0700
Subject: [PATCH 38/79] change the intro in layer/__init__.py

MatGL supports more different GNN architectures and the intro needs to be changed.

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 src/matgl/layers/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/matgl/layers/__init__.py b/src/matgl/layers/__init__.py
index 466b5906..5bf11142 100644
--- a/src/matgl/layers/__init__.py
+++ b/src/matgl/layers/__init__.py
@@ -1,4 +1,4 @@
-"""This package implements the layers for M*GNet."""
+"""This package implements the layers for different Graph Neural Networks."""
 
 from __future__ import annotations
 

From 41879c125578b26be84866be08848568d0d53f3f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 26 Sep 2024 08:55:43 -0700
Subject: [PATCH 39/79] Bump boto3 from 1.35.26 to 1.35.27 (#373)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.26 to 1.35.27.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.26...1.35.27)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index c2a2b21a..7a2f9d07 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.26
+boto3==1.35.27
 numpy==1.26.4
 sympy==1.13.3

From 6232235dc7b542e98b42bdad666f919ffdc9e15c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Sep 2024 09:51:07 -0700
Subject: [PATCH 40/79] Bump boto3 from 1.35.27 to 1.35.28 (#375)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.27 to 1.35.28.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.27...1.35.28)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 7a2f9d07..57a05053 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.27
+boto3==1.35.28
 numpy==1.26.4
 sympy==1.13.3

From ad9bbe253279fd1d3f2936d2652201a18434682b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 10:12:17 -0700
Subject: [PATCH 41/79] Bump boto3 from 1.35.28 to 1.35.29 (#376)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.28 to 1.35.29.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.28...1.35.29)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 57a05053..66ead57e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.28
+boto3==1.35.29
 numpy==1.26.4
 sympy==1.13.3

From abbad80791e319220e8a4537748bdd9beed5d92f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 1 Oct 2024 11:09:11 -0700
Subject: [PATCH 42/79] Bump boto3 from 1.35.29 to 1.35.30 (#377)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.29 to 1.35.30.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.29...1.35.30)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 66ead57e..e55da725 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.29
+boto3==1.35.30
 numpy==1.26.4
 sympy==1.13.3

From 7d143fd3c165745491ef1a8089dc87cd9755a24f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 2 Oct 2024 10:38:51 -0700
Subject: [PATCH 43/79] Bump boto3 from 1.35.30 to 1.35.31 (#378)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.30 to 1.35.31.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.30...1.35.31)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index e55da725..e8bec381 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.30
+boto3==1.35.31
 numpy==1.26.4
 sympy==1.13.3

From cc13b15da8bf35790ec35b88ad6600af964003be Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Wed, 2 Oct 2024 22:17:16 -0700
Subject: [PATCH 44/79] adding back .cpu() before .numpy() in
 get_feature_matrix.py

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 src/matgl/layers/_atom_ref.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/matgl/layers/_atom_ref.py b/src/matgl/layers/_atom_ref.py
index cc77de79..eb717cd9 100644
--- a/src/matgl/layers/_atom_ref.py
+++ b/src/matgl/layers/_atom_ref.py
@@ -41,7 +41,7 @@ def get_feature_matrix(self, graphs: list[dgl.DGLGraph]) -> torch.Tensor:
         for i, graph in enumerate(graphs):
             atomic_numbers = graph.ndata["node_type"]
             features[i] = torch.bincount(atomic_numbers, minlength=self.max_z)
-        return features.numpy()
+        return features.cpu().numpy()
 
     def fit(self, graphs: list[dgl.DGLGraph], properties: torch.Tensor) -> None:
         """Fit the elemental reference values for the properties.

From f547253d28040be7cdd5f250ba9def388d353096 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 3 Oct 2024 17:33:19 -0700
Subject: [PATCH 45/79] Bump boto3 from 1.35.31 to 1.35.32 (#379)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.31 to 1.35.32.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.31...1.35.32)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index e8bec381..32717258 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.9.17.1
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.31
+boto3==1.35.32
 numpy==1.26.4
 sympy==1.13.3

From 362f93e78af977e603291395a391d36e88a98d9c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:28:27 -0700
Subject: [PATCH 46/79] Bump pymatgen from 2024.9.17.1 to 2024.10.3 (#381)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.9.17.1 to 2024.10.3.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.9.17.1...v2024.10.3)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 32717258..d2990054 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.4.0
 torch==2.4.0
 lightning==2.4.0
-pymatgen==2024.9.17.1
+pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0

From fede110edf9cc1d20bfe60675c97d0dc0c4b81c2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 4 Oct 2024 17:24:49 -0700
Subject: [PATCH 47/79] Bump boto3 from 1.35.32 to 1.35.33 (#380)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.32 to 1.35.33.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.32...1.35.33)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index d2990054..d29652a7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.32
+boto3==1.35.33
 numpy==1.26.4
 sympy==1.13.3

From f8fb2a54206b372e401b21e18ec98ff17cef843e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 23:16:27 -0700
Subject: [PATCH 48/79] Bump boto3 from 1.35.33 to 1.35.34 (#383)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.33 to 1.35.34.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.33...1.35.34)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index d29652a7..275c6833 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.33
+boto3==1.35.34
 numpy==1.26.4
 sympy==1.13.3

From 9ea6165c5e7496c726aea5e6dc12dfbce11befb0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 9 Oct 2024 14:16:14 -0700
Subject: [PATCH 49/79] Bump boto3 from 1.35.34 to 1.35.36 (#385)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.34 to 1.35.36.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.34...1.35.36)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 275c6833..fef698b2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.34
+boto3==1.35.36
 numpy==1.26.4
 sympy==1.13.3

From 9368a3095576a973e18490e113141358842f0f54 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Oct 2024 09:14:15 -0700
Subject: [PATCH 50/79] Bump boto3 from 1.35.36 to 1.35.37 (#387)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.36 to 1.35.37.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.36...1.35.37)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index fef698b2..bd7a3d4c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.36
+boto3==1.35.37
 numpy==1.26.4
 sympy==1.13.3

From 56f30b01203e114b26fba6da43942559f2119e27 Mon Sep 17 00:00:00 2001
From: Shyue Ping Ong <shyuep@gmail.com>
Date: Thu, 10 Oct 2024 11:15:32 -0500
Subject: [PATCH 51/79] Drop 3.9 supprot.

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 4f02f30e..4a96c0e4 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       max-parallel: 20
       matrix:
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.10", "3.12"]
         os: [ "ubuntu-latest", "macos-latest" ]
 
     runs-on: ${{ matrix.os }}

From 2f378bf385cae64a250646f72e14c4c779a6a80b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 11 Oct 2024 09:27:10 -0700
Subject: [PATCH 52/79] Bump boto3 from 1.35.37 to 1.35.38 (#389)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.37 to 1.35.38.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.37...1.35.38)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index bd7a3d4c..3c4d9ba3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.8.0
-boto3==1.35.37
+boto3==1.35.38
 numpy==1.26.4
 sympy==1.13.3

From 9dcf616b1968d34b17deff8d0e4f5af16d3eb08a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 15:34:21 -0700
Subject: [PATCH 53/79] Bump boto3 from 1.35.38 to 1.35.39 (#390)

* Bump boto3 from 1.35.38 to 1.35.39

Bumps [boto3](https://github.com/boto/boto3) from 1.35.38 to 1.35.39.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.38...1.35.39)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Downgrade Pytorch and DGL version  (#392)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* correct the downgrade for torch (#393)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

* correct the downgrade for torch

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* Correct the version of torch.data (#394)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

* correct the downgrade for torch

* fix the version of torchdata

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* Downgrade torch to 2.2.1 (#395)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

* correct the downgrade for torch

* fix the version of torchdata

* downgrade torch to 2.2.1

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
---
 pyproject.toml            |  2 +-
 requirements.txt          |  8 ++++----
 src/matgl/layers/_core.py | 14 ++++++++------
 tests/layers/test_bond.py |  3 +++
 4 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1e184f39..0bfde7e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ classifiers = [
 ]
 dependencies = [
     "ase",
-    "dgl<=2.4.0",
+    "dgl<=2.2.1",
     "pymatgen",
     "lightning<=2.4.0",
     "torch<=2.2.1",
diff --git a/requirements.txt b/requirements.txt
index 3c4d9ba3..4b1680f1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
-dgl==2.4.0
-torch==2.4.0
+dgl==2.2.1
+torch==2.2.1
 lightning==2.4.0
 pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
-torchdata==0.8.0
-boto3==1.35.38
+torchdata==0.7.1
+boto3==1.35.39
 numpy==1.26.4
 sympy==1.13.3
diff --git a/src/matgl/layers/_core.py b/src/matgl/layers/_core.py
index 201d8632..a2dc57ed 100644
--- a/src/matgl/layers/_core.py
+++ b/src/matgl/layers/_core.py
@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Callable, Literal
+from typing import TYPE_CHECKING, Any, Callable, Literal, cast
 
 import dgl
 import torch
@@ -130,21 +130,23 @@ def __init__(
         self.activate_last = activate_last
         self.normalize_hidden = normalize_hidden
         norm_kwargs = norm_kwargs or {}
+        norm_kwargs = cast(dict, norm_kwargs)
 
         for i, (in_dim, out_dim) in enumerate(zip(dims[:-1], dims[1:])):
             if i < self._depth - 1:
                 self.layers.append(Linear(in_dim, out_dim, bias=use_bias))
-                if normalize_hidden:
+                if normalize_hidden and self.norm_layers is not None:
                     if normalization == "graph":
                         self.norm_layers.append(GraphNorm(out_dim, **norm_kwargs))
                     elif normalization == "layer":
                         self.norm_layers.append(LayerNorm(out_dim, **norm_kwargs))
             else:
                 self.layers.append(Linear(in_dim, out_dim, bias=use_bias and bias_last))
-                if normalization == "graph":
-                    self.norm_layers.append(GraphNorm(out_dim, **norm_kwargs))
-                elif normalization == "layer":
-                    self.norm_layers.append(LayerNorm(out_dim, **norm_kwargs))
+                if self.norm_layers is not None:
+                    if normalization == "graph":
+                        self.norm_layers.append(GraphNorm(out_dim, **norm_kwargs))
+                    elif normalization == "layer":
+                        self.norm_layers.append(LayerNorm(out_dim, **norm_kwargs))
 
     def forward(self, inputs: torch.Tensor, g: dgl.Graph | None = None) -> torch.Tensor:
         """Applies all layers in turn.
diff --git a/tests/layers/test_bond.py b/tests/layers/test_bond.py
index 6c7113c8..a0ba0418 100644
--- a/tests/layers/test_bond.py
+++ b/tests/layers/test_bond.py
@@ -42,6 +42,9 @@ def test_exp_normal(self, graph_MoS, graph_CO):
         bond_basis = bond_expansion(g1.edata["bond_dist"])
         assert bond_basis.shape == (28, 9)
 
+        bond_basis = bond_expansion(g2.edata["bond_dist"])
+        assert bond_basis.shape == (2, 9)
+
     def test_exception(self):
         with pytest.raises(ValueError, match="Undefined rbf_type"):
             BondExpansion(rbf_type="nonsense")

From 3fbdc4613c466ebb7d817fb46885548f5195e741 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Mon, 14 Oct 2024 18:03:06 -0700
Subject: [PATCH 54/79] remove unused variable self.potential in Relaxer class

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 src/matgl/ext/ase.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/matgl/ext/ase.py b/src/matgl/ext/ase.py
index a4ac38b0..b5ae0631 100644
--- a/src/matgl/ext/ase.py
+++ b/src/matgl/ext/ase.py
@@ -243,7 +243,6 @@ def __init__(
             stress_weight=stress_weight,  # type: ignore
         )
         self.relax_cell = relax_cell
-        self.potential = potential
         self.ase_adaptor = AseAtomsAdaptor()
 
     def relax(

From 5228694d6c3deaa8d103b616334dacfd2d3f03e3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 15 Oct 2024 10:01:52 -0700
Subject: [PATCH 55/79] Bump boto3 from 1.35.39 to 1.35.40 (#396)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.39 to 1.35.40.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.39...1.35.40)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 4b1680f1..7a61d330 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.39
+boto3==1.35.40
 numpy==1.26.4
 sympy==1.13.3

From 1d2b18f0f2a73701cbc4d29a01739d8207b84dbb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 16 Oct 2024 08:51:49 -0700
Subject: [PATCH 56/79] Bump boto3 from 1.35.40 to 1.35.41 (#398)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.40 to 1.35.41.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.40...1.35.41)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 7a61d330..e63432f0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.40
+boto3==1.35.41
 numpy==1.26.4
 sympy==1.13.3

From 71536b455b0d2d536281fc359a450bf3474d4d98 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 18 Oct 2024 11:50:08 +0800
Subject: [PATCH 57/79] Bump boto3 from 1.35.41 to 1.35.42 (#399)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.41 to 1.35.42.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.41...1.35.42)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index e63432f0..df30b2bd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.41
+boto3==1.35.42
 numpy==1.26.4
 sympy==1.13.3

From 68a3870552aa634423eb8f4d57e9cfbec789cd1c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 19 Oct 2024 11:14:32 +0800
Subject: [PATCH 58/79] Bump boto3 from 1.35.42 to 1.35.43 (#400)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.42 to 1.35.43.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.42...1.35.43)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index df30b2bd..2eee71e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.42
+boto3==1.35.43
 numpy==1.26.4
 sympy==1.13.3

From 5a0ee2bdc78035aced2fc9e7a4b2edb917fc6f86 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Oct 2024 07:25:32 +0800
Subject: [PATCH 59/79] Bump boto3 from 1.35.43 to 1.35.44 (#401)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.43 to 1.35.44.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.43...1.35.44)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 2eee71e9..fef7b7c1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.3
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.43
+boto3==1.35.44
 numpy==1.26.4
 sympy==1.13.3

From 963225443440ba17af2988203c35d7958ea81f85 Mon Sep 17 00:00:00 2001
From: Bowen Deng <84425382+BowenD-UCB@users.noreply.github.com>
Date: Mon, 21 Oct 2024 17:36:48 -0700
Subject: [PATCH 60/79] Allow missing label in MGLDataset (#403)

* added function to allow missing lables for all tasks

* fixed bug

* minor fixes on testing
---
 src/matgl/utils/training.py  | 75 ++++++++++++++++++++----------------
 tests/utils/test_training.py | 64 ++++++++++++++++++++++++++++++
 2 files changed, 106 insertions(+), 33 deletions(-)

diff --git a/src/matgl/utils/training.py b/src/matgl/utils/training.py
index e8c03e22..394c3332 100644
--- a/src/matgl/utils/training.py
+++ b/src/matgl/utils/training.py
@@ -436,7 +436,7 @@ def loss_fn(
         loss: nn.Module,
         labels: tuple,
         preds: tuple,
-        num_atoms: int | None = None,
+        num_atoms: torch.Tensor | None = None,
     ):
         """Compute losses for EFS.
 
@@ -462,14 +462,31 @@ def loss_fn(
 
         """
         # labels and preds are (energy, force, stress, (optional) site_wise)
-        e_loss = self.loss(labels[0] / num_atoms, preds[0] / num_atoms, **self.loss_params)
-        f_loss = self.loss(labels[1], preds[1], **self.loss_params)
+        if num_atoms is None:
+            num_atoms = torch.ones_like(preds[0])
+        if self.allow_missing_labels:
+            valid_labels, valid_preds = [], []
+            for index, label in enumerate(labels):
+                valid_value_indices = ~torch.isnan(label)
+                valid_labels.append(label[valid_value_indices])
+                if index == 0:
+                    valid_num_atoms = num_atoms[valid_value_indices]
+                    pred = preds[index].view(1) if preds[index].shape == torch.Size([]) else preds[index]
+                else:
+                    pred = preds[index]
+                valid_preds.append(pred[valid_value_indices])
+        else:
+            valid_labels, valid_preds = list(labels), list(preds)
+            valid_num_atoms = num_atoms
+
+        e_loss = self.loss(valid_labels[0] / valid_num_atoms, valid_preds[0] / valid_num_atoms, **self.loss_params)
+        f_loss = self.loss(valid_labels[1], valid_preds[1], **self.loss_params)
 
-        e_mae = self.mae(labels[0] / num_atoms, preds[0] / num_atoms)
-        f_mae = self.mae(labels[1], preds[1])
+        e_mae = self.mae(valid_labels[0] / valid_num_atoms, valid_preds[0] / valid_num_atoms)
+        f_mae = self.mae(valid_labels[1], valid_preds[1])
 
-        e_rmse = self.rmse(labels[0] / num_atoms, preds[0] / num_atoms)
-        f_rmse = self.rmse(labels[1], preds[1])
+        e_rmse = self.rmse(valid_labels[0] / valid_num_atoms, valid_preds[0] / valid_num_atoms)
+        f_rmse = self.rmse(valid_labels[1], valid_preds[1])
 
         s_mae = torch.zeros(1)
         s_rmse = torch.zeros(1)
@@ -480,36 +497,28 @@ def loss_fn(
         total_loss = self.energy_weight * e_loss + self.force_weight * f_loss
 
         if self.model.calc_stresses:
-            s_loss = loss(labels[2], preds[2], **self.loss_params)
-            s_mae = self.mae(labels[2], preds[2])
-            s_rmse = self.rmse(labels[2], preds[2])
+            s_loss = loss(valid_labels[2], valid_preds[2], **self.loss_params)
+            s_mae = self.mae(valid_labels[2], valid_preds[2])
+            s_rmse = self.rmse(valid_labels[2], valid_preds[2])
             total_loss = total_loss + self.stress_weight * s_loss
 
-        if self.model.calc_magmom:
-            if self.allow_missing_labels:
-                valid_values = ~torch.isnan(labels[3])
-                labels_3 = labels[3][valid_values]
-                preds_3 = preds[3][valid_values]
+        if self.model.calc_magmom and labels[3].numel() > 0:
+            if self.magmom_target == "symbreak":
+                m_loss = torch.min(
+                    loss(valid_labels[3], valid_preds[3], **self.loss_params),
+                    loss(valid_labels[3], -valid_preds[3], **self.loss_params),
+                )
+                m_mae = torch.min(self.mae(valid_labels[3], valid_preds[3]), self.mae(valid_labels[3], -valid_preds[3]))
+                m_rmse = torch.min(
+                    self.rmse(valid_labels[3], valid_preds[3]), self.rmse(valid_labels[3], -valid_preds[3])
+                )
             else:
-                labels_3 = labels[3]
-                preds_3 = preds[3]
-
-            if len(labels_3) > 0:
-                if self.magmom_target == "symbreak":
-                    m_loss = torch.min(
-                        loss(labels_3, preds_3, **self.loss_params), loss(labels_3, -preds_3, **self.loss_params)
-                    )
-                    m_mae = torch.min(self.mae(labels_3, preds_3), self.mae(labels_3, -preds_3))
-                    m_rmse = torch.min(self.rmse(labels_3, preds_3), self.rmse(labels_3, -preds_3))
-                else:
-                    if self.magmom_target == "absolute":
-                        labels_3 = torch.abs(labels_3)
-
-                    m_loss = loss(labels_3, preds_3, **self.loss_params)
-                    m_mae = self.mae(labels_3, preds_3)
-                    m_rmse = self.rmse(labels_3, preds_3)
+                labels_3 = torch.abs(valid_labels[3]) if self.magmom_target == "absolute" else valid_labels[3]
+                m_loss = loss(labels_3, valid_preds[3], **self.loss_params)
+                m_mae = self.mae(labels_3, valid_preds[3])
+                m_rmse = self.rmse(labels_3, valid_preds[3])
 
-                total_loss = total_loss + self.magmom_weight * m_loss
+            total_loss = total_loss + self.magmom_weight * m_loss
 
         return {
             "Total_Loss": total_loss,
diff --git a/tests/utils/test_training.py b/tests/utils/test_training.py
index 83c165ff..90c25cf4 100644
--- a/tests/utils/test_training.py
+++ b/tests/utils/test_training.py
@@ -773,6 +773,70 @@ def test_chgnet_training_without_m(self, LiFePO4, BaNiO3):
 
         self.teardown_class()
 
+    def test_chgnet_training_with_missing_label(self, LiFePO4, BaNiO3):
+        structures = [LiFePO4, BaNiO3] * 5
+        energies = [-2.0, -3.0] * 5
+        forces = [np.ones((len(s), 3)).tolist() for s in structures]
+        stresses = [np.zeros((3, 3)).tolist()] * len(structures)
+        magmoms = [np.ones((len(s), 1)).tolist() for s in structures]
+        # Create some missing labels
+        energies[2] = np.nan
+        forces[4] = (np.nan * np.ones((len(structures[4]), 3))).tolist()
+        stresses[6] = (np.nan * np.ones((3, 3))).tolist()
+        magmoms[8] = (np.nan * np.ones((len(structures[8]), 1))).tolist()
+        element_types = get_element_list([LiFePO4, BaNiO3])
+        converter = Structure2Graph(element_types=element_types, cutoff=6.0)
+        dataset = MGLDataset(
+            threebody_cutoff=3.0,
+            structures=structures,
+            converter=converter,
+            include_line_graph=True,
+            directed_line_graph=True,
+            labels={
+                "energies": energies,
+                "forces": forces,
+                "stresses": stresses,
+                "magmoms": magmoms,
+            },
+            save_cache=False,
+        )
+        train_data, val_data, test_data = split_dataset(
+            dataset,
+            frac_list=[0.8, 0.1, 0.1],
+            shuffle=True,
+            random_state=42,
+        )
+        train_loader, val_loader, test_loader = MGLDataLoader(
+            train_data=train_data,
+            val_data=val_data,
+            test_data=test_data,
+            collate_fn=partial(collate_fn_pes, include_magmom=True, include_line_graph=True),
+            batch_size=4,
+            num_workers=0,
+            generator=torch.Generator(device=device),
+        )
+        model = CHGNet(element_types=element_types, is_intensive=False)
+        lit_model = PotentialLightningModule(
+            model=model,
+            stress_weight=0.1,
+            magmom_weight=0.1,
+            include_line_graph=True,
+            allow_missing_labels=True,
+        )
+        # We will use CPU if MPS is available since there is a serious bug.
+        trainer = pl.Trainer(max_epochs=2, accelerator=device, inference_mode=False)
+
+        trainer.fit(model=lit_model, train_dataloaders=train_loader, val_dataloaders=val_loader)
+        trainer.test(lit_model, dataloaders=test_loader)
+
+        pred_LFP_energy = model.predict_structure(LiFePO4)
+        pred_BNO_energy = model.predict_structure(BaNiO3)
+
+        assert torch.any(pred_LFP_energy < 0)
+        assert torch.any(pred_BNO_energy < 0)
+
+        self.teardown_class()
+
     @classmethod
     def teardown_class(cls):
         try:

From a7729ede067986664ff9b8c624a6b50c04689a87 Mon Sep 17 00:00:00 2001
From: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Date: Tue, 22 Oct 2024 10:26:19 +0800
Subject: [PATCH 61/79] improve code coverage by including "symbreak" for
 chgnet training (#404)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* Bump boto3 from 1.35.38 to 1.35.39

Bumps [boto3](https://github.com/boto/boto3) from 1.35.38 to 1.35.39.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.38...1.35.39)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

* Downgrade Pytorch and DGL version  (#392)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* correct the downgrade for torch

* fix the version of torchdata

* downgrade torch to 2.2.1

---------

Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 tests/utils/test_training.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/utils/test_training.py b/tests/utils/test_training.py
index 90c25cf4..0b3f2da2 100644
--- a/tests/utils/test_training.py
+++ b/tests/utils/test_training.py
@@ -680,7 +680,9 @@ def test_chgnet_training(self, LiFePO4, BaNiO3):
             generator=torch.Generator(device=device),
         )
         model = CHGNet(element_types=element_types, is_intensive=False)
-        lit_model = PotentialLightningModule(model=model, stress_weight=0.1, magmom_weight=0.1, include_line_graph=True)
+        lit_model = PotentialLightningModule(
+            model=model, stress_weight=0.1, magmom_weight=0.1, include_line_graph=True, magmom_target="symbreak"
+        )
         # We will use CPU if MPS is available since there is a serious bug.
         trainer = pl.Trainer(max_epochs=2, accelerator=device, inference_mode=False)
 

From 428a0057bc24d27bb8133235ef335dae32c06613 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Oct 2024 22:07:52 +0800
Subject: [PATCH 62/79] Bump pymatgen from 2024.10.3 to 2024.10.22 (#406)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.10.3 to 2024.10.22.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.10.3...v2024.10.22)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index fef7b7c1..0b5d4324 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.2.1
 torch==2.2.1
 lightning==2.4.0
-pymatgen==2024.10.3
+pymatgen==2024.10.22
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1

From 2abba2988b90fbc60988b5725ea5a62789f2561c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Oct 2024 22:08:12 +0800
Subject: [PATCH 63/79] Bump boto3 from 1.35.44 to 1.35.45 (#405)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.44 to 1.35.45.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.44...1.35.45)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 0b5d4324..669a9cd0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.22
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.44
+boto3==1.35.45
 numpy==1.26.4
 sympy==1.13.3

From 4601abb040f5c4ed15b5f6d19a92cd148e734687 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 24 Oct 2024 09:07:37 +0800
Subject: [PATCH 64/79] Bump boto3 from 1.35.45 to 1.35.46 (#407)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.45 to 1.35.46.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.45...1.35.46)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 669a9cd0..4a4901dc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.22
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.45
+boto3==1.35.46
 numpy==1.26.4
 sympy==1.13.3

From 28b87c84fea3b82108f6f9409ccbda7bdbd432ab Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 25 Oct 2024 10:19:46 +0800
Subject: [PATCH 65/79] Bump boto3 from 1.35.46 to 1.35.47 (#409)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.46 to 1.35.47.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.46...1.35.47)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 4a4901dc..59a46be0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.22
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.46
+boto3==1.35.47
 numpy==1.26.4
 sympy==1.13.3

From 126ea69b17cc1b991b280ddbfb6358d9b8c1dd8a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 25 Oct 2024 22:12:37 +0800
Subject: [PATCH 66/79] Bump boto3 from 1.35.47 to 1.35.48 (#410)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.47 to 1.35.48.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.47...1.35.48)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 59a46be0..69d79bf5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.22
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.47
+boto3==1.35.48
 numpy==1.26.4
 sympy==1.13.3

From 644d9439c83183dde3450f30931f94bec9c2bd77 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 12:26:14 +0800
Subject: [PATCH 67/79] Bump rexml from 3.3.6 to 3.3.9 in /docs (#413)

Bumps [rexml](https://github.com/ruby/rexml) from 3.3.6 to 3.3.9.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](https://github.com/ruby/rexml/compare/v3.3.6...v3.3.9)

---
updated-dependencies:
- dependency-name: rexml
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 docs/Gemfile.lock | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
index 26c8b11c..90c26507 100644
--- a/docs/Gemfile.lock
+++ b/docs/Gemfile.lock
@@ -224,8 +224,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.3.6)
-      strscan
+    rexml (3.3.9)
     rouge (3.26.0)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
@@ -240,7 +239,6 @@ GEM
       faraday (>= 0.17.3, < 3)
     simpleidn (0.2.1)
       unf (~> 0.1.4)
-    strscan (3.1.0)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     typhoeus (1.4.0)

From 770c842b8c96febfa3c87589f35bd68538990a50 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 12:55:36 +0800
Subject: [PATCH 68/79] Bump pymatgen from 2024.10.22 to 2024.10.27 (#412)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.10.22 to 2024.10.27.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.10.22...v2024.10.27)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 69d79bf5..c43199c6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.2.1
 torch==2.2.1
 lightning==2.4.0
-pymatgen==2024.10.22
+pymatgen==2024.10.27
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1

From 053c4322488cf548c4380bbafc0668bf1eceabaa Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:35:56 +0800
Subject: [PATCH 69/79] Bump boto3 from 1.35.48 to 1.35.49 (#411)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.48 to 1.35.49.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.48...1.35.49)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index c43199c6..b55b6133 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.27
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.48
+boto3==1.35.49
 numpy==1.26.4
 sympy==1.13.3

From 2743e72d15da75490a1b3a4645571592bb97a4fc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 30 Oct 2024 21:26:41 +0800
Subject: [PATCH 70/79] Bump boto3 from 1.35.49 to 1.35.50 (#415)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.49 to 1.35.50.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.49...1.35.50)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index b55b6133..c4ce53a1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.27
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.49
+boto3==1.35.50
 numpy==1.26.4
 sympy==1.13.3

From 65d22abd30161dcff2b90923600cbfa2ef3a9dfc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 30 Oct 2024 23:20:25 +0800
Subject: [PATCH 71/79] Bump boto3 from 1.35.50 to 1.35.51 (#417)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.50 to 1.35.51.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.50...1.35.51)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index c4ce53a1..9c27709d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,6 +5,6 @@ pymatgen==2024.10.27
 ase==3.23.0
 pydantic==2.9.2
 torchdata==0.7.1
-boto3==1.35.50
+boto3==1.35.51
 numpy==1.26.4
 sympy==1.13.3

From bb78cabc1fb0073f26098463950ae65b44dc04d9 Mon Sep 17 00:00:00 2001
From: Bowen Deng <84425382+BowenD-UCB@users.noreply.github.com>
Date: Wed, 30 Oct 2024 23:45:21 -0700
Subject: [PATCH 72/79] Added missing dtype in pymatgen graph converter (#418)

* added function to allow missing lables for all tasks

* fixed bug

* minor fixes on testing

* adding dtype in converter
---
 src/matgl/graph/converters.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/matgl/graph/converters.py b/src/matgl/graph/converters.py
index cf880239..cb8c9056 100644
--- a/src/matgl/graph/converters.py
+++ b/src/matgl/graph/converters.py
@@ -50,7 +50,7 @@ def get_graph_from_processed_structure(
             DGLGraph object, state_attr
 
         """
-        u, v = torch.tensor(src_id), torch.tensor(dst_id)
+        u, v = torch.tensor(src_id, dtype=matgl.int_th), torch.tensor(dst_id, dtype=matgl.int_th)
         g = dgl.graph((u, v), num_nodes=len(structure))
         # TODO: Need to check if the variable needs to be double or float, now use float
         pbc_offset = torch.tensor(images, dtype=matgl.float_th)

From f043888bea7953338ea1e4226ee49d9f6ab7967f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:52:10 +0800
Subject: [PATCH 73/79] Bump numpy from 1.26.4 to 2.0.1 (#307)

Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.0.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Co-authored-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
---
 pyproject.toml   | 2 +-
 requirements.txt | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0bfde7e0..ba02846b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,7 @@ dependencies = [
     "pydantic",
     "torchdata<=0.7.1",
     "boto3",
-    "numpy<2.0.0"
+    "numpy<3.0.0"
 ]
 version = "1.1.3"
 
diff --git a/requirements.txt b/requirements.txt
index 9c27709d..67801353 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,8 @@ lightning==2.4.0
 pymatgen==2024.10.27
 ase==3.23.0
 pydantic==2.9.2
+numpy==2.0.1
 torchdata==0.7.1
 boto3==1.35.51
-numpy==1.26.4
 sympy==1.13.3
+

From ab080b9a09fa135635dcbd3f2a736658cb1ad5f3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:19:19 +0800
Subject: [PATCH 74/79] Bump pymatgen from 2024.10.27 to 2024.10.29 (#416)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.10.27 to 2024.10.29.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.10.27...v2024.10.29)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 67801353..56106dab 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dgl==2.2.1
 torch==2.2.1
 lightning==2.4.0
-pymatgen==2024.10.27
+pymatgen==2024.10.29
 ase==3.23.0
 pydantic==2.9.2
 numpy==2.0.1

From ebbfca6124c918768a6e2c20ceb30ea6253eb182 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Oct 2024 22:04:45 +0800
Subject: [PATCH 75/79] Bump numpy from 2.0.1 to 2.1.2 (#420)

Bumps [numpy](https://github.com/numpy/numpy) from 2.0.1 to 2.1.2.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 56106dab..4863fb0a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,7 @@ lightning==2.4.0
 pymatgen==2024.10.29
 ase==3.23.0
 pydantic==2.9.2
-numpy==2.0.1
+numpy==2.1.2
 torchdata==0.7.1
 boto3==1.35.51
 sympy==1.13.3

From 98cf12651e8baea03439ef2219837da2598b1737 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Oct 2024 23:03:19 +0800
Subject: [PATCH 76/79] Bump boto3 from 1.35.51 to 1.35.52 (#419)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.51 to 1.35.52.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.51...1.35.52)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 4863fb0a..41597121 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,6 +6,6 @@ ase==3.23.0
 pydantic==2.9.2
 numpy==2.1.2
 torchdata==0.7.1
-boto3==1.35.51
+boto3==1.35.52
 sympy==1.13.3
 

From 824c1c4cefa9129c0af7066523d1665515f42899 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Nov 2024 21:47:31 +0800
Subject: [PATCH 77/79] Bump boto3 from 1.35.52 to 1.35.53 (#421)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.52 to 1.35.53.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.52...1.35.53)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 41597121..b56f9e56 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,6 +6,6 @@ ase==3.23.0
 pydantic==2.9.2
 numpy==2.1.2
 torchdata==0.7.1
-boto3==1.35.52
+boto3==1.35.53
 sympy==1.13.3
 

From 0808d56139dc2a6908eaaf95f356b2ccdb02767e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 5 Nov 2024 08:09:38 +0800
Subject: [PATCH 78/79] Bump boto3 from 1.35.53 to 1.35.54 (#422)

Bumps [boto3](https://github.com/boto/boto3) from 1.35.53 to 1.35.54.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](https://github.com/boto/boto3/compare/1.35.53...1.35.54)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index b56f9e56..2e247c7f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,6 +6,6 @@ ase==3.23.0
 pydantic==2.9.2
 numpy==2.1.2
 torchdata==0.7.1
-boto3==1.35.53
+boto3==1.35.54
 sympy==1.13.3
 

From 16e9447b0c3f871b05d21dc4a99e9a22eb55e00c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 5 Nov 2024 08:52:35 +0800
Subject: [PATCH 79/79] Bump numpy from 2.1.2 to 2.1.3 (#423)

Bumps [numpy](https://github.com/numpy/numpy) from 2.1.2 to 2.1.3.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.2...v2.1.3)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 2e247c7f..61660d6d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,7 @@ lightning==2.4.0
 pymatgen==2024.10.29
 ase==3.23.0
 pydantic==2.9.2
-numpy==2.1.2
+numpy==2.1.3
 torchdata==0.7.1
 boto3==1.35.54
 sympy==1.13.3