def evaluatorTerms(self, universe, subset1, subset2, global_data):
self.collectAtomTypesAndIndices(universe, global_data)
self.collectCharges(universe, global_data)
lj = self._getLJForceField(universe)
es = self._getESForceField(universe)
compound = CompoundForceField(lj, es)
return compound.evaluatorTerms(universe, subset1, subset2, global_data)
def evaluatorTerms(self, universe, subset1, subset2, global_data):
self.collectAtomTypesAndIndices(universe, global_data)
self.collectCharges(universe, global_data)
lj = self._getLJForceField(universe)
es = self._getESForceField(universe)
compound = CompoundForceField(lj, es)
return compound.evaluatorTerms(universe, subset1, subset2, global_data)
def evaluatorParameters(self, universe, subset1, subset2, global_data):
self.collectAtomTypesAndIndices(universe, global_data)
return CompoundForceField.evaluatorParameters(self, universe, subset1,
subset2, global_data)
##################################################
############## HARMONIC WELL #####################
##################################################
#
# for i in range(nmolecules):
# ff.append(HarmonicWellForceField(universe.objectList()[i].atomList()[2], center[i][0], center[i][1], center[i][2], float(31.273e4)))
##################################################
############### EMPTY POTENTIAL ##################
##################################################
# for i in range(nmolecules):
# for j in range(i+1,nmolecules):
# ff.append(NoPotForceField(universe.objectList()[i].atomList()[ia],universe.objectList()[j].atomList()[ja],ia,ja))
universe.setForceField(CompoundForceField(*ff))
# Minimize
minimizer = ConjugateGradientMinimizer(universe,
actions=[StandardLogOutput(50)])
minimizer(convergence=1.e-3, steps=10000)
# gradientTest(universe)
# print universe.energy()
universe.writeToFile("u.pdb")
#universe.environmentObjectList(Environment.PathIntegrals)[0].include_spring_terms = False
#universe._changed(True)
universe.initializeVelocitiesToTemperature(temperature)
rhofile = open(rhoname, "r")
def evaluatorParameters(self, universe, subset1, subset2, global_data):
self.collectAtomTypesAndIndices(universe, global_data)
return CompoundForceField.evaluatorParameters(self, universe,
subset1, subset2,
global_data)