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")
def takeStep(self, coords, **kwargs):
from pygmin.takestep import buildingblocks as bb
ca = CoordsAdapter(nrigid=GMIN.getNRigidBody(), nlattice=6, coords=coords)
#tmp = np.loadtxt("aligned.dat")
#coords[-6:]=tmp[-6:]
#coords[:]=tmp[:]
#return
conf_ok = False
if(not self.overlap_cutoff is None):
safe_coords = coords.copy()
while conf_ok is False:
indices=None
if(self.nmols):
indices=[]
indices = [np.random.randint(0,GMIN.getNRigidBody()) for i in xrange(self.nmols)]
if(self.rotate != 0.):
bb.rotate(self.rotate, ca.rotRigid, indices)
if(self.translate != 0.):
bb.uniform_displace(self.translate, ca.rotRigid, indices)
#from pygmin.utils import lattice
#bb.reduced_coordinates_displace(0.0, lattice.lowerTriangular(ca.lattice), ca.posRigid)
ca.lattice[:]*=self.expand
if(self.max_volume):
vol = lattice.volume(ca.lattice)
if(vol > self.max_volume):
ca.lattice[:]*=(self.max_volume / vol)**(1./3.)
conf_ok = True
if(self.overlap_cutoff):
atomistic = np.zeros(3*GMIN.getNAtoms())
GMIN.toAtomistic(atomistic, coords)
overlap = crystals.has_overlap(atomistic, self.overlap_cutoff)
if(overlap is True):
conf_ok = False
coords[:] = safe_coords
