| maintainers: | andrewtarzia; matteobecchi; simonemartino |
|---|---|
| documentation: | https://dynsight.readthedocs.io |
dynsight is structured to support a wide range of tasks commonly
encountered in the analysis of many-body dynamical systems. These tasks
include handling trajectory data, computing single-particle descriptors,
performing time-series clustering and conducting various auxiliary analyses.
To achieve this, dynsight is organized into specialized modules, each
addressing a specific aspect of this workflow.
Previously in cpctools.
To get dynsight, you can install it with pip:
$ pip install dynsight
Old versions dynsight used cpctools for SOAP calculations, if
you are using Python 3.10 and below, you can use cpctools to access
SOAPify and hd5er using
$ pip install cpctools
If you want to use the dynsight.tica module you will need to install the
deeptime package. This can be done with with pip:
$ pip install deeptime
or with conda:
$ conda install -c conda-forge deeptime
If you want to use the dynsight.vision and dynsight.track modules
you will need to install a series of packages. This can be done with with pip:
$ pip install ultralytics PyYAML
If you make changes or improvements to the codebase, please open a pull request on our GitHub repository. This allows us to review, discuss, and integrate contributions in a transparent and collaborative manner. Make sure to include a clear description of the changes and link any related issues if applicable.
Install just.
In a new virtual environment run:
$ just dev
Run code checks:
$ just check
There are examples throughout the documentation and available in
the examples/ directory of this repository.
There are also examples available in the cpctools repository
here <https://github.com/GMPavanLab/cpctools/tree/main/Examples>
If you use dynsight please cite
https://github.com/GMPavanLab/dynsight
and
TBD
- Most modules also use MDAnalysis, https://www.mdanalysis.org/pages/citations/
- If you use SOAP, please cite https://doi.org/10.1103/PhysRevB.87.184115 and DScribe https://singroup.github.io/dscribe/latest/citing.html
- If you use timeSOAP, please cite https://doi.org/10.1063/5.0147025
- If you use LENS, please cite: https://doi.org/10.1073/pnas.2300565120
- If you use onion-clustering, please cite: https://doi.org/10.1073/pnas.2403771121
- If you use tICA, please cite
deeptimehttps://deeptime-ml.github.io/latest/index.html - If you use
dynsight.vision, please cite Ultralytics YOLO https://docs.ultralytics.com/it/models/yolo11/#usage-examples - If you use
dynsight.track, please cite Trackpy https://soft-matter.github.io/trackpy/dev/introduction.html
We developed this code when working in the Pavan group, https://www.gmpavanlab.polito.it/, whose members often provide very valuable feedback, which we gratefully acknowledge.
Much of the original code in cpctools was written by Daniele Rapetti (Iximiel).
The work was funded by the European Union and ERC under projects DYNAPOL and the NextGenerationEU project, CAGEX.
