def takeStep(self, coords, **kwargs):
from pygmin.takestep import buildingblocks as bb
ca = CoordsAdapter(nrigid=GMIN.getNRigidBody(), nlattice=6, coords=coords)
bb.rotate(1.6, ca.rotRigid)
#from pygmin.utils import lattice
#bb.reduced_coordinates_displace(0.0, lattice.lowerTriangular(ca.lattice), ca.posRigid)
ca.lattice*=1.2
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
def takeStep(self, coords, **kwargs):
from pygmin.takestep import buildingblocks as bb
print coords.size
ca = CoordsAdapter(nrigid=2, nlattice=6, coords=coords)
bb.rotate(1.6, ca.rotRigid)
ca.lattice*=1.2
