Name | virp JSON |
Version |
1.0.1
JSON |
| download |
home_page | None |
Summary | VIRtual cell generation by Permutation |
upload_time | 2025-02-18 08:56:49 |
maintainer | None |
docs_url | None |
author | None |
requires_python | None |
license | MIT License
Copyright (c) 2024 Kedar Hippalgaonkar's Materials by Design Lab
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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|
keywords |
disordered
virtual cell
cif
partial occupancy
|
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requirements |
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<img src="graphics/virpbanner.png" width="870">
# `virp`: VIRtual cell generation by Permutation
`virp` is a code for the fast generation of a virtual cell from a crystal structure (in CIF format) containing site disorder. It is named after Singapore's first superhero, VR Man, whose superpower is "Virping". The show was a flop, but we are still proud of him.
This project is inspired by the `Supercell` code of Okhotnikov, Charpentier and Cadars (<i>J. Cheminform. <b>8</b>, 17</i>), which formed the basis of our fast virtual cell generation algorithm, as well as the `aflow++` framework (<i>Comput. Mater. Sci. <b>217</b>, 111889</i>), for the statistical postprocessing of materials properties.
## Theory
(To be updated!)
## Requirements
`pymatgen`, `chgnet`, and `matgl` (`matgl==1.0.0`; `dgl==1.1.2`)<br>
__Optional__: You can also use git for the fancy installation. Otherwise, downloading the .py file will do.
## Installation
`pip install git+https://github.com/andypaulchen/virp.git`<br>
Update to latest release: uninstall and re-install
## Building a database
The root directory has a folder (`session`) which holds the python scripts which build a library of virtual cells (`generate.py`) and postprocessing scripts (`connectivity.py` and `properties.py`). After each script is run, the results are saved as `.csv` files.
1. To prepare for a session, copy the `session` folder in your workspace and place the `.cif` files you want to process (make virtual cells + postprocessing) in the subfolder `_disordered_cifs`. Feel free to rename `session` folder to something more identifiable
2. Run `generate.py` to create a supercell and (by default) 400 virtual cells.
- after this step, a structure subfolder (e.g. `structure`) is created in `session` for each `structure.cif` file in `_disordered_cifs`, with the same name. Inside this folder is a supercell CIF and folders for structure-optimized (`stropt`) and non-structure-optimized virtual cells (`no_stropt`). The details of this run is recorded in `virp_session_summary.csv`.
3. Run `connectivity.py` for atomic connectivity post-processing
- after this step, the results are written to `connectivity.csv` and `scatterplot.png` under `stropt` and `no_stropt`.
4. Run `properties.py` to predict materials properties. This is performed on `stropt` subfolders only.
- after this step, the results are written to `virtual_properties.csv` in the `structure` subfolder.
In summary, this is what a session looks like after all three routines have completed:
<img src="graphics/operation.png" width="870">
## Versions and changelog
`v0.1.1`: first workable code, with function to generate a virtual cell. <br>
`v0.2.1`: added enumeration function <br>
`v0.2.2`: enumeration can be imported now (fix) <br>
`v0.3.0`: you can now make a batch of virtual cells<br>
`v0.4.3`: added tools to build a database
## Debugging and support
The `virp` code has been tested on a limited number of platforms, so far Windows and Linux. If you are running into any problems during operation, please hound me (Andy Paul Chen) at la.vache.qui.vit(at)gmail.com, and I will try my best to help.
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"description": "<img src=\"graphics/virpbanner.png\" width=\"870\">\r\n\r\n# `virp`: VIRtual cell generation by Permutation\r\n `virp` is a code for the fast generation of a virtual cell from a crystal structure (in CIF format) containing site disorder. It is named after Singapore's first superhero, VR Man, whose superpower is \"Virping\". The show was a flop, but we are still proud of him. \r\n \r\n This project is inspired by the `Supercell` code of Okhotnikov, Charpentier and Cadars (<i>J. Cheminform. <b>8</b>, 17</i>), which formed the basis of our fast virtual cell generation algorithm, as well as the `aflow++` framework (<i>Comput. Mater. Sci. <b>217</b>, 111889</i>), for the statistical postprocessing of materials properties.\r\n\r\n ## Theory\r\n (To be updated!)\r\n\r\n ## Requirements\r\n`pymatgen`, `chgnet`, and `matgl` (`matgl==1.0.0`; `dgl==1.1.2`)<br>\r\n __Optional__: You can also use git for the fancy installation. Otherwise, downloading the .py file will do.\r\n\r\n ## Installation\r\n `pip install git+https://github.com/andypaulchen/virp.git`<br>\r\n Update to latest release: uninstall and re-install\r\n\r\n ## Building a database\r\n The root directory has a folder (`session`) which holds the python scripts which build a library of virtual cells (`generate.py`) and postprocessing scripts (`connectivity.py` and `properties.py`). After each script is run, the results are saved as `.csv` files.\r\n\r\n 1. To prepare for a session, copy the `session` folder in your workspace and place the `.cif` files you want to process (make virtual cells + postprocessing) in the subfolder `_disordered_cifs`. Feel free to rename `session` folder to something more identifiable\r\n\r\n 2. Run `generate.py` to create a supercell and (by default) 400 virtual cells.\r\n - after this step, a structure subfolder (e.g. `structure`) is created in `session` for each `structure.cif` file in `_disordered_cifs`, with the same name. Inside this folder is a supercell CIF and folders for structure-optimized (`stropt`) and non-structure-optimized virtual cells (`no_stropt`). The details of this run is recorded in `virp_session_summary.csv`.\r\n\r\n 3. Run `connectivity.py` for atomic connectivity post-processing\r\n - after this step, the results are written to `connectivity.csv` and `scatterplot.png` under `stropt` and `no_stropt`.\r\n\r\n 4. Run `properties.py` to predict materials properties. This is performed on `stropt` subfolders only.\r\n - after this step, the results are written to `virtual_properties.csv` in the `structure` subfolder.\r\n\r\n In summary, this is what a session looks like after all three routines have completed:\r\n\r\n <img src=\"graphics/operation.png\" width=\"870\">\r\n\r\n ## Versions and changelog\r\n `v0.1.1`: first workable code, with function to generate a virtual cell. <br>\r\n `v0.2.1`: added enumeration function <br>\r\n `v0.2.2`: enumeration can be imported now (fix) <br>\r\n `v0.3.0`: you can now make a batch of virtual cells<br>\r\n `v0.4.3`: added tools to build a database\r\n\r\n ## Debugging and support\r\n The `virp` code has been tested on a limited number of platforms, so far Windows and Linux. If you are running into any problems during operation, please hound me (Andy Paul Chen) at la.vache.qui.vit(at)gmail.com, and I will try my best to help.\r\n \r\n",
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