Automated Stepwise Addition Procedure for Extrafullerene.
Project description
AutoSteper
Automated Stepwise Addition Procedure for Extrafullerene.
A detailed description could be found in the article: Exploring exohedral functionalization of fullerene with Automation and Neural Network Potential.
Overview of the Stepwise model.Demonstration of core functions could be found in ./tests
. (Some test files are squeezed to minimize the project size. This issue will be addressed very soon)
Documentation could be found in ./doc
.
Install
1. Enumeration
AutoSteper relies on OpenSource projects FullereneDataParser and usenauty to properly enumerate non-isomorphic addition patterns.
FullereneDataParser is an excellent python package to handle fullerene-related research problems, this project utilizes it to convert 3D coordinates to graph6str format. For install:
git clone https://github.com/XJTU-ICP/FullereneDataParser
cd FullereneDataParser
pip install .
usenauty is a lightweight tool to enumerate non-isomorphic addition patterns with nauty algorithm. The original project is in usenauty, here we employ a branch version of it. For install:
git clone https://github.com/Franklalalala/usenauty
cd usenauty
mkdir build
cd build
cmake .. -G "Unix Makefiles"
make
Note: The CXX standard is set to be 17, which means the gcc version need to be 8 or higher, or a higher version of IDE, such as Visual Studio 2017. The cmake version need to be 3.1 or higher. There are two pre-compiled releases for Windows and Linux platform, respectively.
The absolute path of compiled cagesearch
file corresponds to the gen_core_path
button in generator
module.
2. Main project
To install the main project:
pip install AutoSteper
For other reliance:
pip install pytest-shutil, ase, numpy, pandas, networkx, tqdm, matplotlib, seaborn, dpdispatcher
To install from source code:
git clone https://github.com/Franklalalala/AutoSteper
cd AutoSteper
pip install .
pip install -r requirements.txt
Note
Issues are welcomed if you have any questions.
Contact me: 1660810667@qq.com
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