def align(system, coords1, coords2):
c1 = system.coords_adapter(coords1)
c2 = system.coords_adapter(coords2)
R = findrotation_kabsch(c2.posRigid, c1.posRigid).transpose()
#R = rotations.aa2mx(p)
for x, p in zip(c2.posRigid, c2.rotRigid):
x[:] = np.dot(R, x)
p[:] = rotations.rotate_aa(p, rotations.mx2aa(R))
# now account for symmetry in water
for p1, p2 in zip(c1.rotRigid, c2.rotRigid):
theta1 = np.linalg.norm(rotations.rotate_aa(p2, -p1))
p2n = rotations.rotate_aa(np.array([0., 0., pi]), p2)
theta2 = np.linalg.norm(rotations.rotate_aa(p2n, -p1))
theta1 -= int(theta1 / 2. / pi) * 2. * pi
theta2 -= int(theta2 / 2. / pi) * 2. * pi
if (theta2 < theta1):
p2[:] = p2n
def align(system, coords1, coords2):
c1 = system.coords_adapter(coords1)
c2 = system.coords_adapter(coords2)
R = findrotation_kabsch(c2.posRigid, c1.posRigid).transpose()
#R = rotations.aa2mx(p)
for x, p in zip(c2.posRigid, c2.rotRigid):
x[:] = np.dot(R, x)
p[:] = rotations.rotate_aa(p, rotations.mx2aa(R))
# now account for symmetry in water
for p1, p2 in zip(c1.rotRigid,c2.rotRigid):
theta1 = np.linalg.norm(rotations.rotate_aa(p2,-p1))
p2n = rotations.rotate_aa(np.array([0., 0., pi]), p2)
theta2 = np.linalg.norm(rotations.rotate_aa(p2n,-p1))
theta1 -= int(theta1/2./pi)*2.*pi
theta2 -= int(theta2/2./pi)*2.*pi
if(theta2 < theta1):
p2[:]=p2n
e1 = []
e2 = []
e1.append(pot.getEnergy(path[0]))
e2.append(pot.getEnergy(path[0]))
#for i in xrange(1):
for i in xrange(len(path) - 1):
e1.append(pot.getEnergy(path[i + 1]))
c1 = CoordsAdapter(nrigid=13, coords=path[i])
c2 = CoordsAdapter(nrigid=13, coords=path[i + 1])
com1 = np.sum(c1.posRigid, axis=0) / float(13)
com2 = np.sum(c1.posRigid, axis=0) / float(13)
c1.posRigid -= com1
c2.posRigid -= com2
mx = findrotation_kabsch(c2.posRigid, c1.posRigid).transpose()
# print mx
c2.posRigid[:] = np.dot(mx, c2.posRigid.transpose()).transpose()
for p in c2.rotRigid:
p[:] = rotations.rotate_aa(p, rotations.mx2aa(mx))
e2.append(pot.getEnergy(path[i + 1]))
for p1, p2 in zip(c1.rotRigid, c2.rotRigid):
n2 = p2 / np.linalg.norm(p2) * 2. * pi
while True:
p2n = p2 + n2
if (np.linalg.norm(p2n - p1) > np.linalg.norm(p2 - p1)):
break
p2[:] = p2n
e1 = []
e2 = []
e1.append(pot.getEnergy(path[0]))
e2.append(pot.getEnergy(path[0]))
#for i in xrange(1):
for i in range(len(path) - 1):
e1.append(pot.getEnergy(path[i + 1]))
c1 = CoordsAdapter(nrigid=13, coords=path[i])
c2 = CoordsAdapter(nrigid=13, coords=path[i + 1])
com1 = np.sum(c1.posRigid, axis=0) / float(13)
com2 = np.sum(c1.posRigid, axis=0) / float(13)
c1.posRigid -= com1
c2.posRigid -= com2
mx = findrotation_kabsch(c2.posRigid, c1.posRigid).transpose()
# print mx
c2.posRigid[:] = np.dot(mx, c2.posRigid.transpose()).transpose()
for p in c2.rotRigid:
p[:] = rotations.rotate_aa(p, rotations.mx2aa(mx))
e2.append(pot.getEnergy(path[i + 1]))
for p1, p2 in zip(c1.rotRigid, c2.rotRigid):
n2 = old_div(p2, np.linalg.norm(p2) * 2. * pi)
while True:
p2n = p2 + n2
if (np.linalg.norm(p2n - p1) > np.linalg.norm(p2 - p1)):
break
p2[:] = p2n
