fucrimodo 1.0.0__tar.gz

fucrimodo-1.0.0/LICENSE

@@ -0,0 +1,202 @@
+
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fucrimodo-1.0.0/PKG-INFO

@@ -0,0 +1,216 @@
+Metadata-Version: 2.4
+Name: fucrimodo
+Version: 1.0.0
+Summary: Find Unknown Crystals by Inversion of ML Optimized Descriptors
+Author-email: Louis Böhm <louis.boehm@gmx.de>, Martin Kuban <kuban@physik.hu-berlin.de>
+Maintainer-email: Louis Böhm <louis.boehm@gmx.de>
+Project-URL: Repository, https://github.com/OHANAN1/fucrimodo
+Project-URL: Documentation, https://fucrimodo.readthedocs.io
+Keywords: tools,fucrimodo,Material Science,Descriptor,SOAP
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: ase>=3.25.0
+Requires-Dist: ase-ga>=1.0.3
+Requires-Dist: matid>=2.1.5
+Requires-Dist: matplotlib>=3.9.2
+Requires-Dist: deap>=1.4.1
+Requires-Dist: pyxtal>=1.0.6
+Requires-Dist: dscribe>=2.1.1
+Requires-Dist: click>=8.4.2
+Provides-Extra: docs
+Requires-Dist: sphinx==9.1.0; extra == "docs"
+Requires-Dist: sphinx_rtd_theme==3.1.0; extra == "docs"
+Requires-Dist: nbsphinx==0.9.8; extra == "docs"
+Requires-Dist: ipykernel>=7.3.0; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest==9.1.1; extra == "test"
+Provides-Extra: dev
+Requires-Dist: isort>=8.0.1; extra == "dev"
+Requires-Dist: black>=26.5.1; extra == "dev"
+Requires-Dist: pyright>=1.1.411; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+
+# FUCrIMODo
+
+<img src="./res/Fujimoto_legal.png" width="200" height="200" alt="Fujimoto from the movie Ponyo">
+
+**F**ind **U**nknown **C**rystals by **I**nversion of **M**L **O**ptimized **D**escriptors
+
+---
+
+</div>
+
+**FUCrIMODo** is a scientific framework for recovering atomic structures from
+machine-learning descriptors. It is built around a novel multi-stage Genetic
+Algorithm (GA). The method and program are introduced in [this
+publication](https://arxiv.org/abs/2608.23381).  FUCrIMODo comes with an
+inversion algorithm for the global SOAP descriptor out of the box, and more
+descriptors are on the way or can be added by you!
+
+## Table of Contents
+
+- [Requirements](#requirements)
+- [Install](#install)
+- [Tutorials](#tutorials)
+  - [Use fucrimodo CLI](#use-fucrimodo-cli)
+  - [Use fucrimodo as a library](#use-fucrimodo-as-a-library)
+- [Documentation](#documentation)
+- [Roadmap](#roadmap)
+- [Contact](#contact)
+- [Authors and acknowledgment](#authors-and-acknowledgment)
+- [License](#license)
+- [Citation](#citation)
+
+## Requirements
+
+- Python 3.12 or later
+- [Numpy](https://numpy.org/doc/stable/) (Handle arrays and calculations.)
+- [Pandas](https://pandas.pydata.org/docs/index.html) (Handle data.)
+- [DEAP](https://deap.readthedocs.io/en/master/) (GA framework.)
+- [ASE-GA](https://dtu-energy.github.io/ase-ga/) (Atomic structure GA Framework.)
+- [Atomic Simulation Environment (ASE)](https://docs.ase-lib.org/index.html)(Atomic structure framework.)
+- [PyXtal](https://pyxtal.readthedocs.io/en/latest/index.html) (Atomic structure sampling.)
+- [MatID](https://singroup.github.io/matid/index.html#) (Perform Atomic symmetry operations.)
+- [DScribe](https://singroup.github.io/dscribe/2.1.x/#) (Descriptor calculator.)
+- [Click](https://click.palletsprojects.com/en/stable/) (CLI backend.)
+- [Matplotlib](https://matplotlib.org/) (2D Plotting.)
+
+## Install
+
+To install the latest release:
+
+``` bash
+pip install fucrimodo
+```
+
+Or to install the development version:
+
+``` bash
+pip install git+git@github.com:OHANAN1/fucrimodo.git
+```
+
+For more detailed instructions, including setup with `uv` and `conda`, please refer to the [documentation](https://fucrimodo.readthedocs.io/en/latest/index.html).
+
+## Tutorials
+
+### Use fucrimodo CLI
+
+To use fucrimodo as a cli you need to set up a `fucrimodo_lab`.  The
+`fucrimodo_lab` is a human-readable database that allows you to manage 
+configurations, data, analysis and more. To set it up, go to a desired
+directory (ideally outside the library's git structure) and run:
+
+``` bash
+fucrimodo lab init
+```
+
+This creates a directory called fucrimodo_lab and sets up the required directory
+structure. Example raw data is provided so you can perform test runs. Please set
+it up and refer to the README.md file inside the lab for more info.
+
+### Use fucrimodo as a library
+
+To learn how to configure the CLI tool or use fucrimodo as a library, you can work through [this Jupyter notebook tutorial](tutorials/fucrimodo_as_library.ipynb). Also refer to the documentation for more details.
+
+## Documentation
+
+The documentation is hosted at [read the docs](https://fucrimodo.readthedocs.io/en/latest/index.html).
+It includes additional tutorials and documents the API of fucrimodo.
+
+To build it yourself, first install the dependencies:
+
+``` bash
+pip install ".[docs]"
+```
+
+Now an HTML version of the docs can be generated:
+
+``` bash
+cd docs/
+make html
+```
+
+The docs will be generated at _build/html/ and can then be opened with the
+browser of your choice. E.g.:
+
+``` bash
+qutebrowser _build/html/index.html
+```
+
+
+## Roadmap
+
+- [ ] Implement and test additional descriptors types
+- [ ] Implement new Stage types
+    - [ ] `ParallelGAStage` (Run multiple GA stages parallel.)
+    - [ ] `SwarmSearchStage` (Use a swarm search for the ideal descriptor.)
+    - [ ] `GradientDescentStage` (Follow the descriptor gradients.)
+- [ ] Improve current default run configuration for bigger structures
+- [ ] Add a proper way to update `fucrimodo_lab` defaults without overwriting
+      existing defaults.
+
+## Contact
+
+- GitHub issues: https://github.com/OHANAN1/fucrimodo/issues
+- Email: louis.boehm@gmx.de
+
+## Authors and acknowledgment
+
+- Main Author: Louis Böhm
+- Co-Author: Martin Kuban
+
+## License
+
+The program is licensed with the Apache 2.0 license.
+
+## Citation
+
+If you use this program in a scientific publication please add the following citation:
+(This is the preprint)
+
+``` bibtex
+@article{FUCrIMODo_Boehm_2026,
+  author = {Boehm, Louis and Kuban, Martin and Draxl, Claudia},
+  eprint = {2608.23381v1},
+  eprintclass = {cond-mat.mtrl-sci},
+  eprinttype = {arxiv},
+  title = {FUCrIMODo: structure recovery from atomistic descriptors via multi-stage genetic algorithms},
+  month = {8},
+  year = {2026},
+  url = {http://arxiv.org/abs/2608.23381v1},
+}
+```
+
+## Little Reward
+
+As a reward that you read the complete README.md file you can now look at this
+cute ASCII-Art. :D
+```txt
+  (\{\             .               ,@@@@                
+  { { \ ,~,  ^  .     ~        __ _ ),\\(\   _,::;
+   {   \|`) <*>   +  o------o  .)\)\\_(((\),:::::;
+  { {  /(\  /~      /|     /|   `\`._,)))))::::::`,
+   {/{/; ,\/       o------o |     `.__/(((:::::::' 
+      [[ '         | |    | |        \  (`:::::::.
+       \` \        | o----+-o         @**\ `:::::; 
+       (/ \\       |/mlp  |/         /    \ `::'    
+ejm    `)  `\      o------o         '*~*~*~`         
+                                      | //
+                                      \ \\
+                                       `.\\
+                                         \((
+                                          ` ` hjw
+```
+(`I will be a human, too!`~Ponyo)
+
+
+

fucrimodo-1.0.0/README.md

@@ -0,0 +1,177 @@
+<div align="center">
+
+# FUCrIMODo
+
+<img src="./res/Fujimoto_legal.png" width="200" height="200" alt="Fujimoto from the movie Ponyo">
+
+**F**ind **U**nknown **C**rystals by **I**nversion of **M**L **O**ptimized **D**escriptors
+
+---
+
+</div>
+
+**FUCrIMODo** is a scientific framework for recovering atomic structures from
+machine-learning descriptors. It is built around a novel multi-stage Genetic
+Algorithm (GA). The method and program are introduced in [this
+publication](https://arxiv.org/abs/2608.23381).  FUCrIMODo comes with an
+inversion algorithm for the global SOAP descriptor out of the box, and more
+descriptors are on the way or can be added by you!
+
+## Table of Contents
+
+- [Requirements](#requirements)
+- [Install](#install)
+- [Tutorials](#tutorials)
+  - [Use fucrimodo CLI](#use-fucrimodo-cli)
+  - [Use fucrimodo as a library](#use-fucrimodo-as-a-library)
+- [Documentation](#documentation)
+- [Roadmap](#roadmap)
+- [Contact](#contact)
+- [Authors and acknowledgment](#authors-and-acknowledgment)
+- [License](#license)
+- [Citation](#citation)
+
+## Requirements
+
+- Python 3.12 or later
+- [Numpy](https://numpy.org/doc/stable/) (Handle arrays and calculations.)
+- [Pandas](https://pandas.pydata.org/docs/index.html) (Handle data.)
+- [DEAP](https://deap.readthedocs.io/en/master/) (GA framework.)
+- [ASE-GA](https://dtu-energy.github.io/ase-ga/) (Atomic structure GA Framework.)
+- [Atomic Simulation Environment (ASE)](https://docs.ase-lib.org/index.html)(Atomic structure framework.)
+- [PyXtal](https://pyxtal.readthedocs.io/en/latest/index.html) (Atomic structure sampling.)
+- [MatID](https://singroup.github.io/matid/index.html#) (Perform Atomic symmetry operations.)
+- [DScribe](https://singroup.github.io/dscribe/2.1.x/#) (Descriptor calculator.)
+- [Click](https://click.palletsprojects.com/en/stable/) (CLI backend.)
+- [Matplotlib](https://matplotlib.org/) (2D Plotting.)
+
+## Install
+
+To install the latest release:
+
+``` bash
+pip install fucrimodo
+```
+
+Or to install the development version:
+
+``` bash
+pip install git+git@github.com:OHANAN1/fucrimodo.git
+```
+
+For more detailed instructions, including setup with `uv` and `conda`, please refer to the [documentation](https://fucrimodo.readthedocs.io/en/latest/index.html).
+
+## Tutorials
+
+### Use fucrimodo CLI
+
+To use fucrimodo as a cli you need to set up a `fucrimodo_lab`.  The
+`fucrimodo_lab` is a human-readable database that allows you to manage 
+configurations, data, analysis and more. To set it up, go to a desired
+directory (ideally outside the library's git structure) and run:
+
+``` bash
+fucrimodo lab init
+```
+
+This creates a directory called fucrimodo_lab and sets up the required directory
+structure. Example raw data is provided so you can perform test runs. Please set
+it up and refer to the README.md file inside the lab for more info.
+
+### Use fucrimodo as a library
+
+To learn how to configure the CLI tool or use fucrimodo as a library, you can work through [this Jupyter notebook tutorial](tutorials/fucrimodo_as_library.ipynb). Also refer to the documentation for more details.
+
+## Documentation
+
+The documentation is hosted at [read the docs](https://fucrimodo.readthedocs.io/en/latest/index.html).
+It includes additional tutorials and documents the API of fucrimodo.
+
+To build it yourself, first install the dependencies:
+
+``` bash
+pip install ".[docs]"
+```
+
+Now an HTML version of the docs can be generated:
+
+``` bash
+cd docs/
+make html
+```
+
+The docs will be generated at _build/html/ and can then be opened with the
+browser of your choice. E.g.:
+
+``` bash
+qutebrowser _build/html/index.html
+```
+
+
+## Roadmap
+
+- [ ] Implement and test additional descriptors types
+- [ ] Implement new Stage types
+    - [ ] `ParallelGAStage` (Run multiple GA stages parallel.)
+    - [ ] `SwarmSearchStage` (Use a swarm search for the ideal descriptor.)
+    - [ ] `GradientDescentStage` (Follow the descriptor gradients.)
+- [ ] Improve current default run configuration for bigger structures
+- [ ] Add a proper way to update `fucrimodo_lab` defaults without overwriting
+      existing defaults.
+
+## Contact
+
+- GitHub issues: https://github.com/OHANAN1/fucrimodo/issues
+- Email: louis.boehm@gmx.de
+
+## Authors and acknowledgment
+
+- Main Author: Louis Böhm
+- Co-Author: Martin Kuban
+
+## License
+
+The program is licensed with the Apache 2.0 license.
+
+## Citation
+
+If you use this program in a scientific publication please add the following citation:
+(This is the preprint)
+
+``` bibtex
+@article{FUCrIMODo_Boehm_2026,
+  author = {Boehm, Louis and Kuban, Martin and Draxl, Claudia},
+  eprint = {2608.23381v1},
+  eprintclass = {cond-mat.mtrl-sci},
+  eprinttype = {arxiv},
+  title = {FUCrIMODo: structure recovery from atomistic descriptors via multi-stage genetic algorithms},
+  month = {8},
+  year = {2026},
+  url = {http://arxiv.org/abs/2608.23381v1},
+}
+```
+
+## Little Reward
+
+As a reward that you read the complete README.md file you can now look at this
+cute ASCII-Art. :D
+```txt
+  (\{\             .               ,@@@@                
+  { { \ ,~,  ^  .     ~        __ _ ),\\(\   _,::;
+   {   \|`) <*>   +  o------o  .)\)\\_(((\),:::::;
+  { {  /(\  /~      /|     /|   `\`._,)))))::::::`,
+   {/{/; ,\/       o------o |     `.__/(((:::::::' 
+      [[ '         | |    | |        \  (`:::::::.
+       \` \        | o----+-o         @**\ `:::::; 
+       (/ \\       |/mlp  |/         /    \ `::'    
+ejm    `)  `\      o------o         '*~*~*~`         
+                                      | //
+                                      \ \\
+                                       `.\\
+                                         \((
+                                          ` ` hjw
+```
+(`I will be a human, too!`~Ponyo)
+
+
+

fucrimodo-1.0.0/pyproject.toml

@@ -0,0 +1,71 @@
+[build-system]
+requires = ["setuptools >= 61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "fucrimodo"
+version = "1.0.0"
+description = "Find Unknown Crystals by Inversion of ML Optimized Descriptors"
+authors = [
+  {name = "Louis Böhm", email =  "louis.boehm@gmx.de"},
+  {name = "Martin Kuban", email = "kuban@physik.hu-berlin.de"},
+]
+maintainers = [
+  {name = "Louis Böhm", email = "louis.boehm@gmx.de"}
+]
+readme = "README.md"
+keywords = ["tools", "fucrimodo", "Material Science", "Descriptor", "SOAP"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+	"Operating System :: POSIX :: Linux",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Physics"
+]
+dependencies = [
+    "numpy>=1.26.4",
+    "pandas>=2.2.3",
+    "ase>=3.25.0",
+    "ase-ga>=1.0.3",
+    "matid>=2.1.5",
+    "matplotlib>=3.9.2",
+    "deap>=1.4.1",
+    "pyxtal>=1.0.6",
+    "dscribe>=2.1.1",
+    "click>=8.4.2",
+]
+requires-python = ">=3.12"
+
+[project.optional-dependencies]
+docs = ['sphinx == 9.1.0', 'sphinx_rtd_theme == 3.1.0', 'nbsphinx == 0.9.8', 'ipykernel>=7.3.0']
+test = ['pytest == 9.1.1']
+dev = ['isort >= 8.0.1', 'black >= 26.5.1', 'pyright >= 1.1.411']
+
+[project.urls]
+Repository = "https://github.com/OHANAN1/fucrimodo"
+Documentation = "https://fucrimodo.readthedocs.io"
+
+# Adds fucrimodo.__main__() in the executables path
+[project.scripts]
+fucrimodo = "fucrimodo.__main__:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+fucrimodo = [
+  "lab_template/*.md",
+  "lab_template/configs/*/*.py",
+  "lab_template/configs/*/*/*.py",
+  "lab_template/data/raw/*.xyz",
+  "lab_template/scripts/*.sh"
+]
+
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = [
+    "slow: tests that take a long time (> 10s).",
+]
+
+# High verbosity and short tracebacks
+addopts = "-v --tb=short"

fucrimodo-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

fucrimodo-1.0.0/src/fucrimodo/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

fucrimodo-1.0.0/src/fucrimodo/__main__.py

@@ -0,0 +1 @@
+from fucrimodo.cli.main import main

fucrimodo-1.0.0/src/fucrimodo/analysis/__init__.py

@@ -0,0 +1,2 @@
+from .run_analysis import RunData
+from .stage_analysis import StageData