sovapy


Namesovapy JSON
Version 0.5.9 PyPI version JSON
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home_pagehttps://github.com/MotokiShiga/sova-cui
SummarySOVA (Structural Order Visualization and Analysis) with python
upload_time2024-11-23 12:01:15
maintainerMotoki Shiga
docs_urlNone
authorMotoki Shiga & Hidetoshi Morita
requires_python>=3.10
licenseMIT License Copyright (c) 2024 Motoki Shiga Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
keywords structure order analysis material science
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # SOVApy (Structural Order Viaualization and Analysis with Python)

SOVA can be installed in Windows, MacOS and Linux.    
(The package name to be imported is "sovapy".)

# Install from PyPI 

```sh
pip install sovapy
```

# Build and Install sovapy
1. Clone the SOVA repo

  ```sh
  git clone https://github.com/MotokiShiga/sova-cui.git
  ```
  And move to the downloaded directory
  ```sh
  cd sova-cui
  bash 
  ```

2. To compile and to generate so or dll files, run  
for macos and linux
  ```sh
  bash run_install_mac_linux.sh
  ```
For windows, use "x64 Native Tools Command Prompt for Visual Studio 2022" to run 
  ```sh
  install_win.bat
  ```
  
3. To install SOVA, run    
  ```sh
  pip install .  
  ```

For the usage, see example codes in the directory 'examples'.

## Environment

Major packages used for our development

<!-- framework & version -->
| Package  | Version |
| --------------------- | ---------- |
| Python                | 3.10.0     |
| ase                 | 3.22.1     |
| h5py              | 3.7.0    |
| igraph                 | 0.11.3     |
| matplotlib   | 3.6.3  |
| networkx                 | 3.1     |
| numpy                | 1.23.5      |
| PyCifRW             | 4.4.5      |
| scipy | 1.8.1    |
| spglib               | 2.0.2     |

  
The versions of other packages can be found in requirements.txt.

You can make the virtual environment for sova by
```
python -m venv sova-cui
source sova-cui/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
```

## Acknowledgements

SOVA reuses source codes of the following package:

- [pyMolDyn](https://github.com/sciapp/pyMolDyn)
- [cif2cell](https://pypi.org/project/cif2cell/#description)


## Examples
```sh
0_all_analysis  : All analysis and saving results in a hdf5
1_pdf_xyz       : PDF analysis from xyz file (amorphous SiO2)
2_pdf_cif       : PDF analysis from xyz file (beta-cristobalite)
3_pdf_cfg       : PDF analysis from cfg file generated by RMC++ (amorphous SiO2)
4_coordination  : Coordination number analysis (amorphous SiO2)
5_bond_angle    : Bond angle analysis (amorphous SiO2)
6_polyhedra     : Polyhedral symmetry analysis (q-value) (amorphous SiO2)
7_ring          : Ring analysis  (beta-cristobalite)
8_cavity        : Cavity analysis (amorphous SiO2)
9_save_result   : Save and load calculated results
``` 

            

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    "description": "# SOVApy (Structural Order Viaualization and Analysis with Python)\n\nSOVA can be installed in Windows, MacOS and Linux.    \n(The package name to be imported is \"sovapy\".)\n\n# Install from PyPI \n\n```sh\npip install sovapy\n```\n\n# Build and Install sovapy\n1. Clone the SOVA repo\n\n  ```sh\n  git clone https://github.com/MotokiShiga/sova-cui.git\n  ```\n  And move to the downloaded directory\n  ```sh\n  cd sova-cui\n  bash \n  ```\n\n2. To compile and to generate so or dll files, run  \nfor macos and linux\n  ```sh\n  bash run_install_mac_linux.sh\n  ```\nFor windows, use \"x64 Native Tools Command Prompt for Visual Studio 2022\" to run \n  ```sh\n  install_win.bat\n  ```\n  \n3. To install SOVA, run    \n  ```sh\n  pip install .  \n  ```\n\nFor the usage, see example codes in the directory 'examples'.\n\n## Environment\n\nMajor packages used for our development\n\n<!-- framework & version -->\n| Package  | Version |\n| --------------------- | ---------- |\n| Python                | 3.10.0     |\n| ase                 | 3.22.1     |\n| h5py              | 3.7.0    |\n| igraph                 | 0.11.3     |\n| matplotlib   | 3.6.3  |\n| networkx                 | 3.1     |\n| numpy                | 1.23.5      |\n| PyCifRW             | 4.4.5      |\n| scipy | 1.8.1    |\n| spglib               | 2.0.2     |\n\n  \nThe versions of other packages can be found in requirements.txt.\n\nYou can make the virtual environment for sova by\n```\npython -m venv sova-cui\nsource sova-cui/bin/activate\npip install --upgrade pip\npip install -r requirements.txt\n```\n\n## Acknowledgements\n\nSOVA reuses source codes of the following package:\n\n- [pyMolDyn](https://github.com/sciapp/pyMolDyn)\n- [cif2cell](https://pypi.org/project/cif2cell/#description)\n\n\n## Examples\n```sh\n0_all_analysis  : All analysis and saving results in a hdf5\n1_pdf_xyz       : PDF analysis from xyz file (amorphous SiO2)\n2_pdf_cif       : PDF analysis from xyz file (beta-cristobalite)\n3_pdf_cfg       : PDF analysis from cfg file generated by RMC++ (amorphous SiO2)\n4_coordination  : Coordination number analysis (amorphous SiO2)\n5_bond_angle    : Bond angle analysis (amorphous SiO2)\n6_polyhedra     : Polyhedral symmetry analysis (q-value) (amorphous SiO2)\n7_ring          : Ring analysis  (beta-cristobalite)\n8_cavity        : Cavity analysis (amorphous SiO2)\n9_save_result   : Save and load calculated results\n``` \n",
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