crisp-ase 1.1.2__py3-none-any.whl

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Files changed (42) hide show
  1. CRISP/__init__.py +99 -0
  2. CRISP/_version.py +1 -0
  3. CRISP/cli.py +41 -0
  4. CRISP/data_analysis/__init__.py +38 -0
  5. CRISP/data_analysis/clustering.py +838 -0
  6. CRISP/data_analysis/contact_coordination.py +915 -0
  7. CRISP/data_analysis/h_bond.py +772 -0
  8. CRISP/data_analysis/msd.py +1199 -0
  9. CRISP/data_analysis/prdf.py +404 -0
  10. CRISP/data_analysis/volumetric_atomic_density.py +527 -0
  11. CRISP/py.typed +1 -0
  12. CRISP/simulation_utility/__init__.py +31 -0
  13. CRISP/simulation_utility/atomic_indices.py +155 -0
  14. CRISP/simulation_utility/atomic_traj_linemap.py +278 -0
  15. CRISP/simulation_utility/error_analysis.py +254 -0
  16. CRISP/simulation_utility/interatomic_distances.py +200 -0
  17. CRISP/simulation_utility/subsampling.py +241 -0
  18. CRISP/tests/DataAnalysis/__init__.py +1 -0
  19. CRISP/tests/DataAnalysis/test_clustering_extended.py +212 -0
  20. CRISP/tests/DataAnalysis/test_contact_coordination.py +184 -0
  21. CRISP/tests/DataAnalysis/test_contact_coordination_extended.py +465 -0
  22. CRISP/tests/DataAnalysis/test_h_bond_complete.py +326 -0
  23. CRISP/tests/DataAnalysis/test_h_bond_extended.py +322 -0
  24. CRISP/tests/DataAnalysis/test_msd_complete.py +305 -0
  25. CRISP/tests/DataAnalysis/test_msd_extended.py +522 -0
  26. CRISP/tests/DataAnalysis/test_prdf.py +206 -0
  27. CRISP/tests/DataAnalysis/test_volumetric_atomic_density.py +463 -0
  28. CRISP/tests/SimulationUtility/__init__.py +1 -0
  29. CRISP/tests/SimulationUtility/test_atomic_traj_linemap.py +101 -0
  30. CRISP/tests/SimulationUtility/test_atomic_traj_linemap_extended.py +469 -0
  31. CRISP/tests/SimulationUtility/test_error_analysis_extended.py +151 -0
  32. CRISP/tests/SimulationUtility/test_interatomic_distances.py +223 -0
  33. CRISP/tests/SimulationUtility/test_subsampling.py +365 -0
  34. CRISP/tests/__init__.py +1 -0
  35. CRISP/tests/test_CRISP.py +28 -0
  36. CRISP/tests/test_cli.py +87 -0
  37. CRISP/tests/test_crisp_comprehensive.py +679 -0
  38. crisp_ase-1.1.2.dist-info/METADATA +141 -0
  39. crisp_ase-1.1.2.dist-info/RECORD +42 -0
  40. crisp_ase-1.1.2.dist-info/WHEEL +5 -0
  41. crisp_ase-1.1.2.dist-info/entry_points.txt +2 -0
  42. crisp_ase-1.1.2.dist-info/top_level.txt +1 -0
crisp_ase-1.1.2.dist-info/METADATA ADDED
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+ Metadata-Version: 2.4
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+ Name: crisp-ase
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+ Version: 1.1.2
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+ Author-email: IS <indranilsaha15@gmail.com>
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+ License: CC-BY-NC-SA-4.0 (see LICENSE)
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+ Requires-Python: >=3.8
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: numpy<2.3,>=1.24
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+ Requires-Dist: ase
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+ Requires-Dist: fpsample<1.0,>=0.3.3
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+ Requires-Dist: seaborn>=0.12.2
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+ Requires-Dist: dscribe>=2.0.0
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+ Requires-Dist: matplotlib>=3.3.4
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+ Requires-Dist: joblib>=1.0.0
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+ Requires-Dist: scikit-learn>=1.0.0
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+ Requires-Dist: plotly>=5.9.0
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+ Requires-Dist: pandas>=2.0.3
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+ Requires-Dist: networkx>=3.1
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+ Requires-Dist: statsmodels>=0.14.0
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+ Provides-Extra: test
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+ Requires-Dist: pytest>=6.1.2; extra == "test"
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+
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+ CRISP
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+ ==============================
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+ [//]: # (Badges)
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+ [![Documentation Status](https://readthedocs.org/projects/crisp-host/badge/?version=latest)](https://crisp-host.readthedocs.io/en/latest/?badge=latest)
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+ [![PyPI version](https://badge.fury.io/py/crisp-ase.svg)](https://badge.fury.io/py/crisp-ase)
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+ [![Python Version](https://img.shields.io/pypi/pyversions/crisp-ase.svg)](https://pypi.org/project/crisp-ase/)
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+ [![License](https://img.shields.io/github/license/Indranil17/CRISP_HOST.svg)](https://github.com/Indranil17/CRISP_HOST/blob/main/LICENSE)
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+ [![DOI](https://zenodo.org/badge/DOI/YOUR_DOI.svg)](https://doi.org/YOUR_DOI)
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+
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+
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+ <img src="https://github.com/Indranil17/CRISP_HOST/blob/main/crisp_logo2.png" width="300">
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+
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+ # CRISP: Enhancing ASE Workflows with Advanced Molecular Simulation Post-Processing
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+
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+ ## What is CRISP?
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+ CRISP is a post-simulation analysis package built on the Atomic Simulation Environment (ASE). It is designed for efficient and insightful analysis of molecular dynamics (MD) and other simulations, enabling in-depth exploration with just a few lines of code, including powerful visualisation options.
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+
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+ ## Features
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+ - **User-friendly**: Optimised for ease of use with detailed examples and extensive outputs for nuanced data analysis.
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+ - **Highly parallelised**: Utilises parallelisation techniques that scale linearly with the number of CPU cores, allowing for fast analysis of large systems and long simulations on high-performance computing clusters.
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+ - **Interactive Visualisation**: HTML outputs to interact with, which can help to see structural changes.
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+ - **Integration**: ASE, scikit-learn and other Python packages.
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+
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+ ## Analysis Toolkit Highlights
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+
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+ ### 1. Cluster Comprehension
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+ - Perform in-depth clustering analysis in molecular dynamics or Monte Carlo simulations using advanced algorithms like DBSCAN.
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+ - Works with both periodic and non-periodic systems.
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+ - Identify, visualise, and track distinct atom clusters to gain insights into unbiased clustering of selected atoms.
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+
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+ ### 2. Customizable Radial Distribution Functions
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+ - Compute and plot partial radial distribution functions (PRDF) for selected atoms or atom types.
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+ - Easily analyse radial relationships between atoms with periodic boundary conditions.
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+
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+ ### 3. Mean Square Displacement (MSD)
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+ - Quantify atomic motion over time using MSD calculations, providing key insights into diffusion and dynamics.
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+ - Customise analysis by selecting specific atom indices to focus on particular subsets of atoms.
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+
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+ ### 4. Hydrogen Bond Analysis
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+ - Identify and analyse hydrogen bonds with a single line of code.
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+ - Customise hydrogen bond parameters or atom indices for detailed and specific analysis.
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+ - Track structural parameters to understand the nature and stability of hydrogen bonds in your system.
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+
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+ ### 5. Coordination Analysis
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+ - Compute average coordination numbers for specific atom types with customizable cutoffs.
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+ - Analyse contact times of selected atom types to study dynamic behaviour efficiently.
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+
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+ ### 6. Error Analysis
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+ - Accurately estimate the error of any computed property using statistical techniques.
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+ - Choose between autocorrelation function or block averaging to calculate the error of the mean, improving result reliability.
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+ - Assess simulation convergence by analysing vector or scalar properties like atomic positions or energy.
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+
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+ ### 7. Efficient and Robust Sampling
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+ - Sample structures using Furthest Point Sampling (FPS) with SOAP descriptors.
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+ - Efficiently subsample large databases or simulations by selecting the most diverse structures while avoiding redundancy.
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+
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+ ### 7. Volumetric Density
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+ - Create 3D volumetric density maps to visualise the spatial distribution of atoms throughout a trajectory
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+ - Understanding diffusion pathways, adsorption sites etc.
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+
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+
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+
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+ # Requirements
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+ This package is built around the ASE (Atomic Simulation Environment) and thus requires the installation of ASE, available at: [ASE Installation Guide](https://wiki.fysik.dtu.dk/ase/install.html).
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+
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+ The clustering uses DBSCAN (Density-Based Spatial Clustering of Applications with Noise) implemented by scikit-learn, available at: [scikit-learn Installation](https://scikit-learn.org/stable/install.html).
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+
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+ For interactive 3D plots of clustering, CRISP utilises the seaborn package. Ensure you have seaborn installed by following the instructions at: [Seaborn Installation](https://seaborn.pydata.org/installing.html).
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+
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+ # Installation
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+ - Recommended: install from PyPI (tested on Python 3.9–3.11 on Linux/macOS/Windows)
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+ ```
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+ pip install crisp-ase==1.1.2
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+ ```
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+
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+ - From a local checkout (same supported Python versions)
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+ ```
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+ git clone https://github.com/Indranil17/CRISP.git
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+ cd CRISP
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+ python -m pip install -U pip setuptools wheel
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+ python -m pip install .
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+ ```
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+
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+ - Dependencies (if installing manually)
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+ ```
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+ python -m pip install \
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+ ase>=3.23.0 \
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+ scikit-learn>=1.4.2 \
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+ seaborn>=0.12.2 \
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+ joblib>=1.2.0 \
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+ fpsample>=0.3.3,<1.0 \
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+ dscribe>=2.0.0 \
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+ statsmodels>=0.14.0 \
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+ pandas>=2.0.3 \
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+ plotly>=5.9.0 \
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+ networkx>=3.1
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+ ```
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+
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+ # Current Modules
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+
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+ To learn how to use each of the modules, please visit [examples](https://github.com/Indranil17/CRISP_HOST/tree/main/example).
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+ Inside the example folder, check the [Notebook](https://github.com/Indranil17/CRISP_HOST/blob/main/example/Introductory_Tutorial/CRISP_Introdcutory_Tutorial.ipynb) to see them in use and also check the other folders of the example folder to see the outputs.
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+ It has two sub-packages and ten modules.
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+ Please see the package's UML map below.
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+
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+ <img src="https://github.com/Indranil17/CRISP_HOST/blob/main/crisp_map.png" width="800">
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+
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+
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+
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+ # Acknowledgments
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+ The package is from the (Nano)Materials modelling group, at Charles University.
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+ Email: lukas.grajciar@natur.cuni.cz
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+
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+ <img src="https://github.com/Indranil17/CRISP_HOST/blob/main/group_logo.png" width="100">
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+
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+ ### Contributors
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+ If there is something you would like to see added to this package or if you would like to contribute,
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+ please email us at sahai@natur.cuni.cz or daniel.willimetz@natur.cuni.cz
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+
crisp_ase-1.1.2.dist-info/RECORD ADDED
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+ CRISP/__init__.py,sha256=DSjM6mmco8taQadq2Dlsa0suOTcZAUrTBuwHTbnhQEY,2012
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+ CRISP/_version.py,sha256=5SgGjThsHu_ITn8V83BvCziqCwxdXxTQqcC3KQMHPfM,22
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+ CRISP/cli.py,sha256=xpOaNpc-nBYk3tR8CsonV8XYMoj4Jo2WoNHKfRQ9_6M,1090
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+ CRISP/py.typed,sha256=o_skYYOgBqbwMt-5lUZDunyM7CcemHaJt2k9MsSACeY,61
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+ CRISP/data_analysis/__init__.py,sha256=qMsgiFJZPZ6DyokbZrkfMIKpzK6wV1fPX--_Te4kzZQ,871
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+ CRISP/data_analysis/clustering.py,sha256=NG31PGGlC6PvWIAI9wS2cXbVf5KDVO-EPYOI9fgFP4w,29774
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+ CRISP/data_analysis/contact_coordination.py,sha256=H5ofSGzm2lBRvsfqebacXnr_ch0O0755mT9pZCYO4Ok,33751
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+ CRISP/data_analysis/h_bond.py,sha256=-CJzvKUN9kA3yrxtRRimcS_-bcRZw7pcqSj7w1I-33M,29205
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+ CRISP/data_analysis/msd.py,sha256=wX94TcVi-limgwnnBOPo5a69O42UHo6QcS5Bn1FLXpU,46161
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+ CRISP/data_analysis/prdf.py,sha256=UzA5FSl2qkRXTKhClb_sb7sVHesdngDTwHcG-6OG7Ac,13803
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+ CRISP/data_analysis/volumetric_atomic_density.py,sha256=wiq-809FksAFcKS1ezpxIEOK8kayy8aKXH7Xr99LlwA,21061
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+ CRISP/simulation_utility/__init__.py,sha256=3kVq1Dhmz1dmiXlWxAl02EuoVsexB5WrM1_u5_wXsmU,727
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+ CRISP/simulation_utility/subsampling.py,sha256=SEOKvSYDIn5KLh0R3TYIOT0_onr44IsfJ9UqjGCc7L8,7472
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+ CRISP/tests/__init__.py,sha256=GTyjAbeobceTrJBpa4aIWczuSb9Kdr_QOR693Q6Yfh8,27
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+ CRISP/tests/test_CRISP.py,sha256=_OLG99OhGHritif2Gjx-tTycghvgW2uhbVScfPLhLOA,680
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+ CRISP/tests/test_cli.py,sha256=WmEkFHO8gR843J90dWbhYVMy-70hbC1SFyc3FuKh5lY,3109
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+ CRISP/tests/DataAnalysis/__init__.py,sha256=v9pypKiga8OePlL7MxbNTHf-WSZXTIFVaYmLIOczhrk,41
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+ CRISP/tests/DataAnalysis/test_clustering_extended.py,sha256=40zc91sCRMU5lm8kJs8BtLWbbPVPAhycwpNKOjGeie4,7226
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+ CRISP/tests/DataAnalysis/test_contact_coordination.py,sha256=Et4XV8syG14ajfBLHRtTb1Ra02QVD42r5QwDo397Z2c,5952
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+ CRISP/tests/DataAnalysis/test_h_bond_complete.py,sha256=6gvkgcVspKQiATUjnu6TWXQr-RiW5qodrisbIQZLbKE,10014
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+ CRISP/tests/DataAnalysis/test_msd_extended.py,sha256=-TQ0zEZyJhSBxn7IG0badjGFSytRx-N1mdXk8DK1M4I,19424
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+ CRISP/tests/DataAnalysis/test_prdf.py,sha256=BWdhla7_DSLkO1p_3G4uuGvqD6FSlNO6T-v2Mf9g7Lg,6094
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+ CRISP/tests/DataAnalysis/test_volumetric_atomic_density.py,sha256=L92uekvr04D1TDPMt6jAaAhffLoeZDU7xRIW37AWkU8,15516
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+ CRISP/tests/SimulationUtility/__init__.py,sha256=wcE35wJsyQ9WU3fbcgsarizdbzjUh58IEe7zqKkqdKs,46
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+ CRISP/tests/SimulationUtility/test_subsampling.py,sha256=89iDWrPHAZd7K0wStxvjckDud5pIm2gaaGBtcDlECbw,11877
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+ crisp_ase-1.1.2.dist-info/METADATA,sha256=qCw6xyHjKpZJOps2PQz8WvnnrY2Na-AYRUeabarS3rc,6658
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+ crisp_ase-1.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ crisp_ase-1.1.2.dist-info/RECORD,,
crisp_ase-1.1.2.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
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+ Wheel-Version: 1.0
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+ Generator: setuptools (80.9.0)
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
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+
crisp_ase-1.1.2.dist-info/entry_points.txt ADDED
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+ [console_scripts]
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+ CRISP = CRISP.cli:main
crisp_ase-1.1.2.dist-info/top_level.txt ADDED
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+ CRISP