https://github.com/matthewghgriffiths/fastoverlap
Algorithms for fast alignment of structures in finite and periodic systems.
https://github.com/matthewghgriffiths/fastoverlap
alignment energy-landscapes numpy python special-orthogonal-group-transforms
Last synced: 3 months ago
JSON representation
Algorithms for fast alignment of structures in finite and periodic systems.
- Host: GitHub
- URL: https://github.com/matthewghgriffiths/fastoverlap
- Owner: matthewghgriffiths
- License: gpl-2.0
- Created: 2017-02-17T11:28:32.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2022-08-11T15:09:49.000Z (over 3 years ago)
- Last Synced: 2023-10-19T21:41:59.187Z (over 2 years ago)
- Topics: alignment, energy-landscapes, numpy, python, special-orthogonal-group-transforms
- Language: Fortran
- Size: 7.47 MB
- Stars: 10
- Watchers: 2
- Forks: 6
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# FASTOVERLAP
Algorithms for fast alignment of structures in finite and periodic systems. These methods are also implemented in the [Cambridge Energy Landscape Software](http://www-wales.ch.cam.ac.uk/software.html) in `GMIN` and `OPTIM`.
FASTOVERLAP can be run 'as is' with no compilation required using `PeriodicAlign` and `SphericalAlign`. The Fortran modules need to be compiled to peform branch and bound alignments with `BranchnBoundAlignment`.
These algorithms have been detailed in the paper,
**Optimal Alignment of Structures for Finite and Periodic Systems** Matthew Griffiths, Samuel P. Niblett, and David J. Wales _Journal of Chemical
Theory and Computation_ **2017** 13(10), 4914-4931, doi:[10.1021/acs.jctc.7b00543](http://dx.doi.org/10.1021/acs.jctc.7b00543)
If you use this module, please cite the above paper.
## INSTALLATION
## Required packages
### python packages:
1. `numpy`:
We use numpy everywhere for doing numerical work. It also installs `f2py` which is used to compile fortran code into modules callable by python.
2. `scipy`:
For some of the optimizers and various scientific tools
3. [`munkres`](https://pypi.org/project/munkres/) or [`pele`](http://pele-python.github.io/pele/):
To solve the linear assignment problem for permutational alignment.
### for compilation:
1. Fortran compiler
2. `fftw`
3. `lapack`
## Compilation
The modules can be compiled using `numpy.distutils` to build the Fortran Modules in place
```
$ python setup.py build_ext -i
```
alternative the `f2py` modules can be directly compiled by running
```
$ ./compile.sh
```