def Align(self, coords1, coords2):
import pygmin.utils.rotations as rot
import pygmin.utils.crystals as cr
c1 = CoordsAdapter(nrigid=2, nlattice=6, coords=coords1)
c2 = CoordsAdapter(nrigid=2, nlattice=6, coords=coords2)
cr.compareStructures(c1, c2)
dcom=np.mean(c2.posRigid[0], axis=0) - np.mean(c1.posRigid, axis=0)
d1 = np.linalg.norm(c1.posRigid[0] - c2.posRigid[0] + dcom) + np.linalg.norm(c1.posRigid[1] - c2.posRigid[1] + dcom)
d2 = np.linalg.norm(c1.posRigid[0] - c2.posRigid[1] + dcom) + np.linalg.norm(c1.posRigid[1] - c2.posRigid[0] + dcom)
if(d1 > d2+1000000.):
print "permute"
tmp = c2.posRigid[0].copy()
c2.posRigid[0]=c2.posRigid[1]
c2.posRigid[1]=tmp
tmp = c2.rotRigid[0].copy()
c2.rotRigid[0]=c2.rotRigid[1]
c2.rotRigid[1]=tmp
for i in xrange(2):
q1 = rot.aa2q(c1.rotRigid[i])
q2 = rot.aa2q(c2.rotRigid[i])
if(np.dot(q1,q2)<0):
q2=-q2
c2.rotRigid[i] = rot.q2aa(q2)
return coords1, coords2
def createNEB(self, coords1, coords2):
from pygmin.utils import rotations as rot
pot = gminpot.GMINPotential(GMIN)
neb = NEB.NEB(coords1, coords2, pot, k = 100. ,nimages=20)
# replace rotational interpolation by slerp
c1 = CoordsAdapter(nrigid=2, nlattice=6, coords=neb.coords[0, :])
c2 = CoordsAdapter(nrigid=2, nlattice=6, coords=neb.coords[-1, :])
for i in xrange(1, neb.nimages):
ci = CoordsAdapter(nrigid=2, nlattice=6, coords=neb.coords[i, :])
t = float(i) / float(neb.nimages)
for j in xrange(2):
ci.rotRigid[j] = rot.q2aa(rot.q_slerp(
rot.aa2q(c1.rotRigid[j]),
rot.aa2q(c2.rotRigid[j]), t))
return neb
def interpolate_angleaxis(initial, final, t):
''' interpolate between 2 arrays of angle axis coordinates
Parameters
----------
initial: np.array
configuration 1
final: np.array
configuration 2
t: float
interpolation parameter with t in [0,1]
'''
conf = initial.copy()
for i in xrange(conf.shape[0]):
conf[i] = rotations.q2aa(rotations.q_slerp(rotations.aa2q(initial[i]),
rotations.aa2q(final[i]), t))
return conf
def interpolate_angleaxis(initial, final, t):
''' interpolate between 2 arrays of angle axis coordinates
Parameters
----------
initial: np.array
configuration 1
final: np.array
configuration 2
t: float
interpolation parameter with t in [0,1]
'''
conf = initial.copy()
for i in xrange(conf.shape[0]):
conf[i] = rotations.q2aa(rotations.q_slerp(rotations.aa2q(initial[i]),
rotations.aa2q(final[i]), t))
return conf