# cpctools: SOAPify and SOAPify.HDF5er
[](https://pypi.org/project/cpctools/)
[](https://github.com/psf/black)
[](https://github.com/pypa/hatch)
[](https://soapify.readthedocs.io/en/latest/?badge=latest)
[](https://coveralls.io/github/GMPavanLab/SOAPify?branch=main)
[](https://www.mdanalysis.org)
SOAPify is a python 3.8/3.9/3.10 library aimed at simplifying the analysis of Molecular Dynamics simulation using the Smooth Overlap of Atomic Position (SOAP) in the context that includes the time along the geometrical information of the frames of the simulation.
SOAPify uses `h5py` to store the trajectories, the SOAP fingerprints, and the analysis results in a binary format.
SOAPify also offers a suite for (simple) state analysis for your simulations.
## How To Install
To install the stable version of SOAPify just type:
```bash
pip install cpctools
```
_cpctools_ stands for **C**omputational **P**hysical **C**hemistry **TOOLS**, or, if you prefer, for **C**hemical **P**hysics **C**omputational **TOOLS**.
If you want to use _dscribe_ or _quippy_ for calculating the SOAP features you should install them separately, since they are quite heavy packages on their own, and usually you would use only one of these packages:
```bash
pip install "dscribe<=1.2.2,>1.2.0"
pip install "quippy-ase==0.9.10"
```
### Installing the latest version
We always recommend to install your code in a dedicated environment:
```bash
python3 -m venv /path/to/new/venv --prompt SOAPify
source /path/to/new/venv/bin/activate
pip install --upgrade pip
```
Then to install SOAPify you can simply go to the repository directory and run the following:
```bash
cd /path/to/SOAPify/directory
pip install .
```
or if you do not want to download the repo, you can have pip install from source:
```bash
pip install 'cpctools @ git+https://github.com/GMPavanLab/SOAPify.git'
```
Or if you desire an older version you can install it from a tag:
```bash
pip install 'cpctools @ git+https://github.com/GMPavanLab/SOAPify.git@0.0.6'
```
We have a (very basic) [documentation](https://gmpavanlab.github.io/SOAPify/SOAPify.html) of the latest version available on the GitHub pages.
A more complete history of the documentation is available on [read the docs](https://soapify.readthedocs.io/en/latest/). There you can consult the documentation for each available version of the package.
## SOAPify
This package contains:
- a toolbox to calculate the [SOAP fingerprints](https://doi.org/10.1103/PhysRevB.87.184115) of a system of atoms. The principal aim is to simplify the setup of the calculation. This toolbox depends on `dscribe` or `quippy` and 'unify' the output of the two codes.
- a toolbox to calculate the distances between SOAP fingerprints
- a simple analysis tool for trajectories of classified atoms
## SOAPify.HDF5er
This package is a toolbox to create [hdf5 files](https://www.hdfgroup.org/) with [h5py](https://www.h5py.org/) from the trajectory and topology files. The format we use **do not** align with [h5md](https://www.nongnu.org/h5md/h5md.html)
Our format is thought to speed up the calculations without occupying too much RAM, thanks to the hdf5 dataset chunking capabilities.
- The data within the files are organized into Group categories:
- "Trajectories" contains subgroups that represent the various stored trajectories, each trajectory subgroup contains three datasets:
- "Types" contains the types of atoms in the simulation
- "Box" contains the history of the box dimensions
- "Trajectory" contains the history of the particle positions
- "SOAP" group contains the Dastasets of the calculated SOAP fingerprints, each SOAP Dataset contains attributes with the settings to reproduce the results.
- "Classification" contain a group per trajectory, the format of the Dataset contained within is not fixed
- The user can choose to use a single file per project or to store separately the results of the various steps of the analysis project (this is more recommended).
SOAPify.HDF5er contains a tool for exporting the trajectories from the hdf5 file to [extended xyz](https://www.ovito.org/docs/current/reference/file_formats/input/xyz.html#extended-xyz-format) format, compatible with [ovito](https://www.ovito.org/)
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"description": "# cpctools: SOAPify and SOAPify.HDF5er\n\n\n[](https://pypi.org/project/cpctools/)\n\n[](https://github.com/psf/black)\n[](https://github.com/pypa/hatch)\n[](https://soapify.readthedocs.io/en/latest/?badge=latest)\n[](https://coveralls.io/github/GMPavanLab/SOAPify?branch=main)\n[](https://www.mdanalysis.org)\n\nSOAPify is a python 3.8/3.9/3.10 library aimed at simplifying the analysis of Molecular Dynamics simulation using the Smooth Overlap of Atomic Position (SOAP) in the context that includes the time along the geometrical information of the frames of the simulation.\n\nSOAPify uses `h5py` to store the trajectories, the SOAP fingerprints, and the analysis results in a binary format.\n\nSOAPify also offers a suite for (simple) state analysis for your simulations.\n\n## How To Install\n\nTo install the stable version of SOAPify just type:\n```bash\npip install cpctools\n```\n_cpctools_ stands for **C**omputational **P**hysical **C**hemistry **TOOLS**, or, if you prefer, for **C**hemical **P**hysics **C**omputational **TOOLS**.\n\nIf you want to use _dscribe_ or _quippy_ for calculating the SOAP features you should install them separately, since they are quite heavy packages on their own, and usually you would use only one of these packages:\n\n```bash\npip install \"dscribe<=1.2.2,>1.2.0\"\npip install \"quippy-ase==0.9.10\"\n```\n\n### Installing the latest version\n\nWe always recommend to install your code in a dedicated environment:\n\n```bash\npython3 -m venv /path/to/new/venv --prompt SOAPify\nsource /path/to/new/venv/bin/activate\npip install --upgrade pip\n```\n\nThen to install SOAPify you can simply go to the repository directory and run the following:\n```bash\ncd /path/to/SOAPify/directory\npip install .\n```\nor if you do not want to download the repo, you can have pip install from source:\n```bash\npip install 'cpctools @ git+https://github.com/GMPavanLab/SOAPify.git'\n```\nOr if you desire an older version you can install it from a tag:\n```bash\npip install 'cpctools @ git+https://github.com/GMPavanLab/SOAPify.git@0.0.6'\n```\n\nWe have a (very basic) [documentation](https://gmpavanlab.github.io/SOAPify/SOAPify.html) of the latest version available on the GitHub pages.\n\nA more complete history of the documentation is available on [read the docs](https://soapify.readthedocs.io/en/latest/). There you can consult the documentation for each available version of the package.\n\n\n## SOAPify\n\nThis package contains:\n - a toolbox to calculate the [SOAP fingerprints](https://doi.org/10.1103/PhysRevB.87.184115) of a system of atoms. The principal aim is to simplify the setup of the calculation. This toolbox depends on `dscribe` or `quippy` and 'unify' the output of the two codes.\n - a toolbox to calculate the distances between SOAP fingerprints\n - a simple analysis tool for trajectories of classified atoms\n\n\n## SOAPify.HDF5er\n\nThis package is a toolbox to create [hdf5 files](https://www.hdfgroup.org/) with [h5py](https://www.h5py.org/) from the trajectory and topology files. The format we use **do not** align with [h5md](https://www.nongnu.org/h5md/h5md.html)\n\nOur format is thought to speed up the calculations without occupying too much RAM, thanks to the hdf5 dataset chunking capabilities.\n- The data within the files are organized into Group categories:\n - \"Trajectories\" contains subgroups that represent the various stored trajectories, each trajectory subgroup contains three datasets:\n - \"Types\" contains the types of atoms in the simulation\n - \"Box\" contains the history of the box dimensions\n - \"Trajectory\" contains the history of the particle positions\n - \"SOAP\" group contains the Dastasets of the calculated SOAP fingerprints, each SOAP Dataset contains attributes with the settings to reproduce the results.\n - \"Classification\" contain a group per trajectory, the format of the Dataset contained within is not fixed\n- The user can choose to use a single file per project or to store separately the results of the various steps of the analysis project (this is more recommended).\nSOAPify.HDF5er contains a tool for exporting the trajectories from the hdf5 file to [extended xyz](https://www.ovito.org/docs/current/reference/file_formats/input/xyz.html#extended-xyz-format) format, compatible with [ovito](https://www.ovito.org/)\n",
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