MEP-Finder finds minimum (free) energy paths connecting minima on multidimensional (free) energy surfaces

The example data can be found in the data/ dir.

Import GridFunc and Flooder

from mepfinder.gridFunc import GridFunc
from mepfinder.flooder import Flooder

Use the vreco tool to generate V.final.out which contains the grid and the potential Initialize a GridFunc from V.final.out.

gf = GridFunc.from_file('data/V.final.out')

In this example the grid is 2D and contains 241 grid points in the first dimension and 101 in the second.

gf.shape
# (241, 101)

Next, you need to specify the two points between you like to find a path.

p1 = gf.g_minimize(None,
                   (None, 0.5))
print p1
# (58, 25)

p2 = gf.g_minimize(None,
                   (0.5, None))
print p2
# (87, 68)

Initialize a Flooder based on the GridFunc

flooder = Flooder(gf)

Find the minimum energy path connecting p1 and p2

path = flooder.flood(p1, p2)