def quenchCrystal(coords, pot, **kwargs):
''' Special quench routine for crystals which makes sure that the final structure is a reduced cell '''
coords, E, rms, calls = mylbfgs(coords, pot, **kwargs)
#while(GMIN.reduceCell(coords)):
if(GMIN.reduceCell(coords)):
#print "Reduced cell, redo minimization"
coords, E, rms, callsn = mylbfgs(coords, pot, **kwargs)
calls+=callsn
return coords, E, rms, calls
def takeStep(self, coords, **kwargs):
''' takeStep routine to generate random cell '''
ca = self.coordsadapter
ca.updateCoords(coords)
atomistic = np.zeros(3*GMIN.getNAtoms())
valid_configuration = False
for i in xrange(50):
volumeTarget = self.expand_current*lattice.volume(ca.lattice)
# random box
ca.lattice[[0,3,5]] = 1.0 + self.expand * np.random.random(3)
ca.lattice[[1,2,4]] = self.shear * np.random.random(3)
if(self.volume != None):
volumeTarget = self.volume[0] + (self.volume[1] - self.volume[0]) * np.random.random()
vol = lattice.volume(ca.lattice)
ca.lattice[:] = ca.lattice * (volumeTarget / vol)**(1.0/3.0)
GMIN.reduceCell(coords)
for i in xrange(50):# first choose random positions and rotations
for i in xrange(GMIN.getNRigidBody()):
ca.posRigid[i] = np.random.random()
ca.rotRigid[i] = rotations.random_aa()
if self.overlap is None:
return
GMIN.toAtomistic(atomistic, coords)
if not crystals.has_overlap(atomistic, self.overlap):
return
print "Could generate valid configuration for current box, choose new box"
raise Exception("GenRandomCrystal: failed to generate a non-overlapping configuration")