SHS4py is a Python-base script to calculate Scaled Hypersphere Searching method[1][2].
[1] Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384 (4–6), 277–282.
[2] Maeda, S.; Ohno, K. Chem. Phys. Lett. 2005, 404 (1–3), 95–99.
- Python 3
- fasteners
- numpy
- scipy
In addition, next packages are required to accelerate the calculations.
- Cython
In calculations of free energy surfaces of metadynamics, further accerelation can be applied. If your workstation use MPI multiprocessing, you can use multisred calculation by using next package.
- mpi4py
Furthermore, you can use GPGPU acceleration by using next package.
- cupy
I don't test environments under Windows. If you use this script, please refer the next article.
Mitsuta, Yuki, and Yasuteru Shigeta. "Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations." Journal of chemical theory and computation 16.6 (2020): 3869-3878. (https://pubs.acs.org/doi/10.1021/acs.jctc.0c00010)
- Yuki Mitsuta (満田祐樹）
- Department of Chemistory, Graduate School of Science, Osaka Prefecture University
- E-mail: mitsutay[at]c.s.osakafu-u.ac.jp
"SHS4py" is under MIT license.