pele.potentials.potential

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this module holds the base classes for potentials

class pele.potentials.potential.BasePotential

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class BasePotential:

Base class for all potentials

Derived classes must overload getEnergy(). It is also highly recommended to overload getEnergyGradient(), otherwise gradients will be calculated numerically

getEnergyGradient()

BasePotential.getEnergy()

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def getEnergy(self, coords):

return the energy at the given coordinates

BasePotential.getEnergyGradient()

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def getEnergyGradient(self, coords):

return the energy and gradient at the given coordinates

BasePotential.NumericalDerivative()

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def NumericalDerivative(self, coords, eps=1e-6):

return the gradient calculated numerically

BasePotential.getGradient()

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def getGradient(self, coords):

return the gradient at the given coordinates

BasePotential.NumericalHessian()

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def NumericalHessian(self, coords, eps=1e-6):

return the Hessian matrix of second derivatives computed numerically

this takes 2*len(coords) calls to getGradient

BasePotential.getEnergyGradientHessian()

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def getEnergyGradientHessian(self, coords):

return the energy, gradient, and Hessian at the given coordinates

BasePotential.getHessian()

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def getHessian(self, coords):

return the hessian

BasePotential.test_potential()

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def test_potential(self, coords, eps=1e-6):

print some information testing whether the analytical gradients are correct

class pele.potentials.potential.potential

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class potential(BasePotential):

for backward compatibility

class pele.potentials.potential.BasePotentialAtomistic

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class BasePotentialAtomistic:

Base class for all potentials that can use interaction lists

See also

BasePotential

BasePotentialAtomistic.getEnergyList()

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def getEnergyList(self, coords, ilist):

the energy of select interactions defined in ilist

Parameters:

coordsarray

ilistarray, shape (*,2)

a numpy array containing pairs of atoms (ilist[i,:]).

BasePotentialAtomistic.getEnergyGradientList()

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def getEnergyGradientList(self, coords, ilist):

return the energy and gradient of select interactions defined in ilist

Parameters:

coordsarray

ilistarray, shape (*,2)

a numpy array containing pairs of atoms (ilist[i,:]).