skphy / fastoverlap

Algorithms for fast alignment of structures in finite and periodic systems.

FASTOVERLAP

Algorithms for fast alignment of structures in finite and periodic systems. These methods are also implemented in the Cambridge Energy Landscape Software 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

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 or 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