crisp-ase 1.0.0.post0.dev0__py3-none-any.whl

crisp_ase-1.0.0.post0.dev0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: crisp-ase
+Version: 1.0.0.post0.dev0
+Author-email: IS <indranilsaha15@gmail.com>
+License: CC-BY-NC-SA-4.0 (see LICENSE)
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: ase
+Provides-Extra: test
+Requires-Dist: pytest>=6.1.2; extra == "test"
+
+CRISP
+==============================
+[//]: # (Badges)
+[![Documentation Status](https://readthedocs.org/projects/crisp-host/badge/?version=latest)](https://crisp-host.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/CRISP.svg)](https://badge.fury.io/py/CRISP)
+[![Python Version](https://img.shields.io/pypi/pyversions/CRISP.svg)](https://pypi.org/project/CRISP/)
+[![License](https://img.shields.io/github/license/Indranil17/CRISP_HOST.svg)](https://github.com/Indranil17/CRISP_HOST/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/DOI/YOUR_DOI.svg)](https://doi.org/YOUR_DOI)
+
+
+<img src="https://github.com/Indranil17/CRISP_HOST/blob/main/crisp_logo2.png" width="300">
+
+# CRISP: Enhancing ASE Workflows with Advanced Molecular Simulation Post-Processing
+
+## What is CRISP?
+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.
+
+## Features
+- **User-friendly**: Optimised for ease of use with detailed examples and extensive outputs for nuanced data analysis.
+- **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.
+- **Interactive Visualisation**: HTML outputs to interact with, which can help to see structural changes.  
+- **Integration**: ASE, scikit-learn and other Python packages.  
+
+## Analysis Toolkit Highlights 
+
+### 1. Cluster Comprehension
+- Perform in-depth clustering analysis in molecular dynamics or Monte Carlo simulations using advanced algorithms like DBSCAN.
+- Works with both periodic and non-periodic systems.
+- Identify, visualise, and track distinct atom clusters to gain insights into unbiased clustering of selected atoms.
+
+### 2. Customizable Radial Distribution Functions
+- Compute and plot partial radial distribution functions (PRDF) for selected atoms or atom types.
+- Easily analyse radial relationships between atoms with periodic boundary conditions.
+
+### 3. Mean Square Displacement (MSD)
+- Quantify atomic motion over time using MSD calculations, providing key insights into diffusion and dynamics.
+- Customise analysis by selecting specific atom indices to focus on particular subsets of atoms.
+
+### 4. Hydrogen Bond Analysis
+- Identify and analyse hydrogen bonds with a single line of code.
+- Customise hydrogen bond parameters or atom indices for detailed and specific analysis.
+- Track structural parameters to understand the nature and stability of hydrogen bonds in your system.
+
+### 5. Coordination Analysis
+- Compute average coordination numbers for specific atom types with customizable cutoffs.
+- Analyse contact times of selected atom types to study dynamic behaviour efficiently.
+
+### 6. Error Analysis
+- Accurately estimate the error of any computed property using statistical techniques.
+- Choose between autocorrelation function or block averaging to calculate the error of the mean, improving result reliability.
+- Assess simulation convergence by analysing vector or scalar properties like atomic positions or energy.
+
+### 7. Efficient and Robust Sampling
+- Sample structures using Furthest Point Sampling (FPS) with SOAP descriptors.
+- Efficiently subsample large databases or simulations by selecting the most diverse structures while avoiding redundancy.
+
+### 7. Volumetric Density
+- Create 3D volumetric density maps to visualise the spatial distribution of atoms throughout a trajectory
+- Understanding diffusion pathways, adsorption sites etc.  
+
+
+
+# Requirements
+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).
+
+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).
+
+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).
+
+# Installation
+1. Now, for the testing period, just pull the folder to the local drive, and then go inside the "CRISP" folder locally inside the terminal. 
+
+2. In the same terminal type    
+```
+pip install .
+```
+, then you can run the package in your local system environment globally.
+
+3. In a virtual environment as a standalone installation, please install the dependencies via the command line, type 
+```
+pip install ase>=3.23.0 scikit-learn>=1.4.2 seaborn>=0.12.2 joblib>=1.2.0 fpsample>=0.3.3 statsmodels>=0.14.0 pandas>=2.0.3 plotly>=5.9.0 networkx>=3.1
+```
+
+# Current Modules
+
+To learn how to use each of the modules, please visit [examples](https://github.com/Indranil17/CRISP_HOST/tree/main/example).
+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.
+It has two sub-packages and ten modules.  
+Please see the package's UML map below. 
+ 
+<img src="https://github.com/Indranil17/CRISP_HOST/blob/main/crisp_map.png" width="800">
+
+
+
+# Acknowledgments
+The package is from the (Nano)Materials modelling group, at Charles University.  
+Email: lukas.grajciar@natur.cuni.cz  
+
+<img src="https://github.com/Indranil17/CRISP_HOST/blob/main/group_logo.png" width="100">
+
+### Contributors
+If there is something you would like to see added to this package or if you would like to contribute,  
+please email us at sahai@natur.cuni.cz or daniel.willimetz@natur.cuni.cz
+

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crisp_ase-1.0.0.post0.dev0.dist-info/WHEEL

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+Generator: setuptools (74.1.3)
+Root-Is-Purelib: true
+Tag: py3-none-any
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crisp_ase-1.0.0.post0.dev0.dist-info/entry_points.txt

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+[console_scripts]
+CRISP = CRISP.cli:main

crisp_ase-1.0.0.post0.dev0.dist-info/top_level.txt

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