nebscape 0.1.0__tar.gz

nebscape-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: nebscape
+Version: 0.1.0
+Summary: Automated workflow for surface reactions.
+Keywords: chemistry,materials,catalyst
+Author: Hyunwook Jung
+Author-email: Hyunwook Jung <hjung@fhi.mpg.de>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: pandas>=2.2.3,<3.0.0
+Requires-Dist: rdkit>=2024.9.6,<2025.0.0
+Requires-Dist: igraph>=0.11.8,<0.12.0
+Requires-Dist: networkx>=3.4.2,<4.0.0
+Requires-Dist: dscribe>=2.1.1,<3.0.0
+Requires-Dist: ase>=3.25.0,<4.0.0
+Requires-Dist: wfl>=0.3.5
+Requires-Dist: scikit-learn>=1.6.1,<2.0.0
+Requires-Dist: pymatgen==2025.10.7
+Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: ruff ; extra == 'dev'
+Requires-Dist: pre-commit ; extra == 'dev'
+Requires-Python: >=3.10
+Provides-Extra: dev
+Description-Content-Type: text/markdown
+
+# NEBscape
+[![ChemRxiv](https://img.shields.io/badge/ChemRxiv-Preprint-blue)](https://doi.org/10.26434/chemrxiv.15002133/v1)
+[![DOI](https://img.shields.io/badge/DOI-10.26434%2Fchemrxiv.15000180-blue)](https://doi.org/10.26434/chemrxiv.15002133/v1)
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+[![Tests Passing](https://img.shields.io/badge/tests-passing-brightgreen.svg)](https://gitlab.mpcdf.mpg.de/hjung/nebscape)
+![Ruff](https://img.shields.io/badge/lint-ruff-success?logo=ruff)
+
+Automated workflow for sampling minimum energy path for surface reactions with minimal human input.
+
+![image](./docs/workflow.png)
+
+## Installation from source
+```
+git clone https://gitlab.mpcdf.mpg.de/hjung/nebscape.git
+pip install .
+```
+
+## Required Inputs
+This workflow prepares initial and final geometry with global optimization (e.g. minima hopping) and provides automatic atom-mapping and generates possbile permutation of symmetric atoms. Only following three inputs are required.
+
+1. List of reaction SMILES string in `reaction_smiles.txt`
+(e.g. `O=[C][CH2][O]>>[C-]#[O+].[CH2]=O`)
+2. slab information in `slab.xyz`
+(Slab should use tag to indicate which atoms are fixed (tag=0) and which atoms are relaxsed(tag=1))
+3. Calculator (e.g. MLIP like MACE)
+
+## Setting
+This workflow uses [wfl](https://github.com/libAtoms/workflow) and [expyre](https://github.com/libAtoms/ExPyRe) for remote submission, so it is advised to configure related settings
+- `config.json` file has to be set for remote submission to HPC (Can be found in `/example`)
+- According to `config.json`, several `remote_info` should also be adapted on user's environment.
+
+## Documentation
+
+* **[Home](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/home)** - overview
+* **[Installation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-1)** - installation
+* **[Setting up local environment](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-2)** - setting for wfl and expyre
+* **[Input preparation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/Input-Preparation)** - input file preparation
+* **[Geometry generation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-4)** - running minima hopping
+* **[Interpolation generation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/Interpolation-generation)** - generating initial minimum energy paths
+
+(We are currently working on improving the documentation / tutorial. Let us know if you need help or suggestions.)
+
+
+## References
+If you use this code, please cite our paper:
+
+Hyunwook Jung, Emanuel Colombi Manzi, Tiago J. Goncalves, et al. From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers. ChemRxiv. 17 April 2026.
+
+https://doi.org/10.26434/chemrxiv.15002133/v1
+
+```
+@article{
+doi:10.26434/chemrxiv.15002133/v1,
+author = {Hyunwook Jung  and Emanuel Colombi Manzi  and Tiago J. Goncalves  and Vanessa J. Bukas  and Sandip De  and Johannes T. Margraf  and Karsten Reuter  and Hendrik H. Heenen },
+title = {From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers},
+journal = {ChemRxiv},
+volume = {2026},
+number = {0417},
+pages = {},
+year = {2026},
+doi = {10.26434/chemrxiv.15002133/v1},
+URL = {https://chemrxiv.org/doi/abs/10.26434/chemrxiv.15002133/v1},
+eprint = {https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15002133/v1}}
+```
+
+## Contact
+If you have any questions, please contact us at hjung@fhi.mpg.de
+Also for any bugs or issues, you can use [gitlab issues](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/issues).
+
+## License
+The NEBscape code is published and distributed under the [MIT License](LICENSE).

nebscape-0.1.0/README.md

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+# NEBscape
+[![ChemRxiv](https://img.shields.io/badge/ChemRxiv-Preprint-blue)](https://doi.org/10.26434/chemrxiv.15002133/v1)
+[![DOI](https://img.shields.io/badge/DOI-10.26434%2Fchemrxiv.15000180-blue)](https://doi.org/10.26434/chemrxiv.15002133/v1)
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+[![Tests Passing](https://img.shields.io/badge/tests-passing-brightgreen.svg)](https://gitlab.mpcdf.mpg.de/hjung/nebscape)
+![Ruff](https://img.shields.io/badge/lint-ruff-success?logo=ruff)
+
+Automated workflow for sampling minimum energy path for surface reactions with minimal human input.
+
+![image](./docs/workflow.png)
+
+## Installation from source
+```
+git clone https://gitlab.mpcdf.mpg.de/hjung/nebscape.git
+pip install .
+```
+
+## Required Inputs
+This workflow prepares initial and final geometry with global optimization (e.g. minima hopping) and provides automatic atom-mapping and generates possbile permutation of symmetric atoms. Only following three inputs are required.
+
+1. List of reaction SMILES string in `reaction_smiles.txt`
+(e.g. `O=[C][CH2][O]>>[C-]#[O+].[CH2]=O`)
+2. slab information in `slab.xyz`
+(Slab should use tag to indicate which atoms are fixed (tag=0) and which atoms are relaxsed(tag=1))
+3. Calculator (e.g. MLIP like MACE)
+
+## Setting
+This workflow uses [wfl](https://github.com/libAtoms/workflow) and [expyre](https://github.com/libAtoms/ExPyRe) for remote submission, so it is advised to configure related settings
+- `config.json` file has to be set for remote submission to HPC (Can be found in `/example`)
+- According to `config.json`, several `remote_info` should also be adapted on user's environment.
+
+## Documentation
+
+* **[Home](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/home)** - overview
+* **[Installation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-1)** - installation
+* **[Setting up local environment](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-2)** - setting for wfl and expyre
+* **[Input preparation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/Input-Preparation)** - input file preparation
+* **[Geometry generation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/page-4)** - running minima hopping
+* **[Interpolation generation](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/wikis/Interpolation-generation)** - generating initial minimum energy paths
+
+(We are currently working on improving the documentation / tutorial. Let us know if you need help or suggestions.)
+
+
+## References
+If you use this code, please cite our paper:
+
+Hyunwook Jung, Emanuel Colombi Manzi, Tiago J. Goncalves, et al. From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers. ChemRxiv. 17 April 2026.
+
+https://doi.org/10.26434/chemrxiv.15002133/v1
+
+```
+@article{
+doi:10.26434/chemrxiv.15002133/v1,
+author = {Hyunwook Jung  and Emanuel Colombi Manzi  and Tiago J. Goncalves  and Vanessa J. Bukas  and Sandip De  and Johannes T. Margraf  and Karsten Reuter  and Hendrik H. Heenen },
+title = {From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers},
+journal = {ChemRxiv},
+volume = {2026},
+number = {0417},
+pages = {},
+year = {2026},
+doi = {10.26434/chemrxiv.15002133/v1},
+URL = {https://chemrxiv.org/doi/abs/10.26434/chemrxiv.15002133/v1},
+eprint = {https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15002133/v1}}
+```
+
+## Contact
+If you have any questions, please contact us at hjung@fhi.mpg.de
+Also for any bugs or issues, you can use [gitlab issues](https://gitlab.mpcdf.mpg.de/hjung/nebscape/-/issues).
+
+## License
+The NEBscape code is published and distributed under the [MIT License](LICENSE).

nebscape-0.1.0/pyproject.toml

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+[project]
+name = "nebscape"
+version = "0.1.0"
+description = "Automated workflow for surface reactions."
+license = { text = "MIT" }  # or your actual license
+keywords = ["chemistry", "materials", "catalyst"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+]
+authors = [
+    {name = "Hyunwook Jung",email = "hjung@fhi.mpg.de"}
+]
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.10"
+dependencies = [
+    "pandas (>=2.2.3,<3.0.0)",
+    "rdkit (>=2024.9.6,<2025.0.0)",
+    "igraph (>=0.11.8,<0.12.0)",
+    "networkx (>=3.4.2,<4.0.0)",
+    "dscribe (>=2.1.1,<3.0.0)",
+    "ase (>=3.25.0,<4.0.0)",
+    "wfl (>=0.3.5)",
+    "scikit-learn (>=1.6.1,<2.0.0)",
+    "pymatgen==2025.10.7",
+]
+
+
+[build-system]
+requires = ["uv_build >= 0.10.10, <0.11.0"]
+build-backend = "uv_build"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+line-length = 100
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "ruff",
+    "pre-commit",
+]
+
+[tool.numpydoc_validation]
+checks = [
+    "all",   # report on all checks, except the below
+    "EX01",
+    "SA01",
+    "ES01",
+	"PR08",
+	"PR09"
+]
+exclude = [
+	"RT02",
+    "\\._.*"   # ignore private methods
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=9.0.2",
+]
+
+[tool.uv.extra-build-dependencies]
+torch-scatter = ["torch"]

nebscape-0.1.0/src/nebscape/__init__.py

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+from .nebscape import NEBscape, get_molecules_reactive_states
+
+__all__ = ["NEBscape", "get_molecules_reactive_states"]