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from pele.potentials import BasePotential
import numpy as np
__all__ = ["GMINPotential"]
class GMINPotential(BasePotential): # pragma: no cover
Interface to fortran GMIN potential
Potentials implemented in GMIN can be called from python if GMIN is compiled with the flag WITH_PYTHON enabled. This creates
python modules (dynamic libraries). However, the interface is still very rough and GMINPotential provides a wrapper for
easy access to GMIN.
The imported GMIN module requires a data file to be present in the current directory. All parameters except for the ones
responsible to setup the potential will be ignored and can be skipped. The first call after importing the module should be
reference to the gmin module
The following example imports the GMIN python interface and evaluates the energy
>>> import gmin_
>>> gmin_.initialize() # finish gmin initialization
>>> pot = GMINPotential(gmin_)
>>> coords = pot.getCoords()
>>> pot.getEnergy(coords)
def __init__(self, GMIN):
self.GMIN = GMIN
self.ncalls = 0
def getEnergy(self, coords):
self.ncalls += 1
return self.GMIN.getEnergy(coords)
def getEnergyGradient(self, coords):
self.ncalls += 1
grad = np.zeros(3 * self.GMIN.getNAtoms())
E = self.GMIN.getEnergyGradient(coords, grad)
return E, grad[0:coords.size]
def getCoords(self):
coords = np.zeros(self.GMIN.getDOF())
return coords