Initial commit for the codes

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
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+# C extensions
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+# Distribution / packaging
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+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Results directory
+results/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+    - id: ruff
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix ]
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

LICENSE

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+MIT License
+
+Copyright (c) 2024 Juno Nam and Rafael Gomez-Bombarelli
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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 # Alchemical MLIP
+[![arXiv](https://img.shields.io/badge/arXiv-2404.10746-84cc16)](https://arxiv.org/abs/2404.10746)
+[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.11081395-14b8a6.svg)](https://zenodo.org/doi/10.5281/zenodo.11081395)
+[![MIT](https://img.shields.io/badge/License-MIT-3b82f6.svg)](https://opensource.org/license/mit)
+
 This repository contains the code to modify machine learning interatomic potentials (MLIPs) to enable continuous and differentiable alchemical transformations.
+Currently, we provide the alchemical modification for the [MACE](https://github.com/ACEsuit/mace) model.
 The details of the method are described in the paper: [Interpolation and differentiation of alchemical degrees of freedom in machine learning interatomic potentials](https://arxiv.org/abs/2404.10746).
 
-> **Note:** The code is currently under final preparation and will be uploaded here shortly.
-> We anticipate having the code ready by the end of this week.
-> Please stay tuned for updates!
+## Installation
+We tested the code with Python 3.10 and the packages in `requirements.txt`.
+For example, you can create a conda environment and install the required packages as follows (assuming CUDA 11.8):
+```bash
+conda create -n alchemical-mlip python=3.10
+conda activate alchemical-mlip
+pip install torch==2.0.1 --index-url https://download.pytorch.org/whl/cu118
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Static calculations
+We provide the jupyter notebooks for the lattice parameter calculations (Fig. 2 in the paper) and the compositional optimization (Fig. 3) in the `notebook` directory.
+```
+notebook/
+├── 1_solid_solution.ipynb
+└── 2_compositional_optimization.ipynb
+```
+
+## Free energy calculations
+We provide the scripts for the free energy calculations for the vacancy (Fig. 4) and perovskites (Fig. 5) in the `scripts` directory.
+```
+scripts/
+├── vacancy_frenkel_ladd.py
+├── perovskite_frenkel_ladd.py
+└── perovskite_alchemy.py
+```
+
+The arguments for the scripts are as follows:
+```bash
+# Vacancy Frenkel-Ladd calculation
+python vacancy_frenkel_ladd.py \
+    --structure-file data/structures/Fe.cif \
+    --supercell 5 5 5 \
+    --temperature 100 \
+    --output-dir data/results/vacancy/Fe_5x5x5_100K/0
+
+# Perovskite Frenkel-Ladd calculation (alpha phase)
+python perovskite_frenkel_ladd.py \
+    --structure-file data/structures/CsPbI3_alpha.cif \
+    --supercell 6 6 6 \
+    --temperature 400 \
+    --output-dir data/results/perovskite/frenkel_ladd/CsPbI3_alpha_6x6x6_400K/0
+
+# Perovskite Frenkel-Ladd calculation (delta phase)
+python perovskite_frenkel_ladd.py \
+    --structure-file data/structures/CsPbI3_delta.cif \
+    --supercell 6 3 3 \
+    --temperature 400 \
+    --output-dir data/results/perovskite/frenkel_ladd/CsPbI3_delta_6x3x3_400K/0
+
+# Perovskite alchemy calculation (alpha phase)
+python -u perovskite_alchemy.py \
+    --structure-file data/structures/CsPbI3_alpha.cif \
+    --supercell 6 6 6 \
+    --switch-pair Pb Sn \
+    --temperature 400 \
+    --output-dir data/results/perovskite/alchemy/CsPbI3_CsSnI3_alpha_400K/0
+
+# Perovskite alchemy calculation (delta phase)
+python -u perovskite_alchemy.py \
+    --structure-file data/structures/CsPbI3_delta.cif \
+    --supercell 6 3 3 \
+    --switch-pair Pb Sn \
+    --temperature 400 \
+    --output-dir data/results/perovskite/alchemy/CsPbI3_CsSnI3_delta_400K/0
+```
+
+The result files are large and not included in the repository.
+If you want to reproduce the results without running the calculations, the result files are uploaded in the [Zenodo repository](https://zenodo.org/doi/10.5281/zenodo.11081395).
+Please download the files and place them in the `data/results` directory.
+
+The post-processing scripts for the free energy calculations are provided in the `notebook` directory.
+```
+notebook/
+├── 3_vacancy_analysis.ipynb
+└── 4_perovskite_analysis.ipynb
+```
 
 ## Citation
 ```

THIRD-PARTY-LICENSES

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+Code in alchemical_mace/{calculator,model}.py is adapted from
+https://github.com/ACEsuit/mace
+
+MIT License
+
+Copyright (c) 2022 ACEsuit/mace
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+-------------------------------------------------------------------------------
+
+Code in alchemical_mace/utils.py is adapted from
+https://github.com/CederGroupHub/chgnet
+
+Crystal Hamiltonian Graph neural Network (CHGNet) Copyright (c) 2023, The Regents
+of the University of California, through Lawrence Berkeley National
+Laboratory (subject to receipt of any required approvals from the U.S.
+Dept. of Energy) and the University of California, Berkeley. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy, University of California,
+Berkeley nor the names of its contributors may be used to endorse or
+promote products derived from this software without specific prior written
+permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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+You are under no obligation whatsoever to provide any bug fixes, patches,
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