def compareTransformed(coords1, coords2, x1, x2, M):
# the lattice matrix
ml1 = lattice.lowerTriangular(coords1.lattice)
ml2 = lattice.lowerTriangular(coords2.lattice)
# the inerse lattice matrix
iml2 = vec3.invert3x3(ml2)
for i in xrange(coords1.nrigid):
ptest = coords1.rotRigid[i]
ptrans = rotations.mx2aa(rotations.np.dot(M, rotations.aa2mx(ptest)))
for d in [np.zeros(3),[0.,1.,0.],[0.,1.,0.],[0.,0.,1.]]:
xtest = coords1.posRigid[i] + np.array(d) - x1
xtrans = np.dot(iml2, np.dot(M, np.dot(ml1, xtest)))
match = False
for j in xrange(coords1.nrigid):
dx = coords2.posRigid[j] - xtrans - x2
dx = dx - np.floor(dx)
dx[dx>0.8]-=1.0
dp = rotations.mx2aa(np.dot(vec3.invert3x3(rotations.aa2mx(ptrans)),rotations.aa2mx(coords2.rotRigid[j])))
match = np.linalg.norm(np.dot(ml2, dx)) < tol_shift \
and np.linalg.norm(dp) < tol_rot
if(match):
break
if(not match):
return False
return True
def Align(self, coords1, coords2):
from pygmin.mindist import rmsfit,aamindist
potential = GMINPotential(GMIN)
ca1 = CoordsAdapter(nrigid=coords1.size/6, coords = coords1)
ca2 = CoordsAdapter(nrigid=coords2.size/6, coords = coords2)
rot = rmsfit.findrotation_kabsch(ca2.posRigid, ca1.posRigid)
ca2.posRigid[:] = np.dot(rot,ca2.posRigid.transpose()).transpose()
for p in ca2.rotRigid:
p[:] = rotations.mx2aa((np.dot(rot, rotations.aa2mx(p))))
print "before"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
for p1,p2 in zip(ca1.rotRigid, ca2.rotRigid):
p1[:],p2[:] = aamindist.aadistance(p1, p2)
print "after"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
path = InterpolatedPath(coords1, coords2, 40)
print potential.getEnergy(path[0])
print "Interpolated energies"
for x in InterpolatedPath(coords1, coords2, 40):
print potential.getEnergy(x)
print "done"
return coords1, coords2
def compareStructures(coords1, coords2):
for refmol1 in xrange(coords1.nrigid):
for refmol2 in xrange(refmol1, coords1.nrigid):
x1 = coords1.posRigid[refmol1]
x2 = coords2.posRigid[refmol2]
pref1 = coords1.rotRigid[refmol1]
pref2 = coords2.rotRigid[refmol2]
#print "pref",pref1,pref2
M = vec3.invert3x3(rotations.aa2mx(pref1))
M = np.dot(rotations.aa2mx(pref2), M)
# print x1,x2
ptest = pref1
ptrans = rotations.mx2aa(rotations.np.dot(M, rotations.aa2mx(ptest)))
#print "---------------- start try",refmol1,refmol2
match1 = compareTransformed(coords1, coords2, x1, x2, M)
match2 = compareTransformed(coords2, coords1, x2, x1, vec3.invert3x3(M))
if(match1 and match2):
#print "Structures match"
return True
#import dmagmin_ as GMIN
#GMIN.writeCIF("1.cif", coords1.coords)
#GMIN.writeCIF("2.cif", coords2.coords)
#import pickle
#pickle.dump(coords1, open("1.dat", "w"))
#pickle.dump(coords2, open("2.dat", "w"))
#exit()
return False
def align(self, coords1, coords2):
c1 = self.topology.coords_adapter(coords1)
c2 = self.topology.coords_adapter(coords2)
# now account for symmetry in water
for p1, p2, site in zip(c1.rotRigid,c2.rotRigid, self.topology.sites):
theta_min = 10.
mx2 = rotations.aa2mx(p2)
mx1 = rotations.aa2mx(p1).transpose()
mx = np.dot(mx1, mx2)
for rot in site.symmetries:
mx_diff = np.dot(mx, rot)
theta = np.linalg.norm(rotations.mx2aa(mx_diff))
theta -= int(theta/2./pi)*2.*pi
if(theta < theta_min):
theta_min = theta
rot_best = rot
p2[:] = rotations.rotate_aa(rotations.mx2aa(rot_best), p2)
def rotate(self, X, mx):
ca = self.topology.coords_adapter(X)
if(ca.nrigid > 0):
ca.posRigid[:] = np.dot(mx, ca.posRigid.transpose()).transpose()
dp = rotations.mx2aa(mx)
for p in ca.rotRigid:
p[:] = rotations.rotate_aa(p, dp)
if(ca.natoms > 0):
ca.posAtom[:] = np.dot(mx, ca.posAtom.transpose()).transpose()
def align(system, coords1, coords2):
c1 = system.coords_adapter(coords1)
c2 = system.coords_adapter(coords2)
R = findrotation_kabsch(c2.posRigid, c1.posRigid)
#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)
#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 map_to_aa(xyz):
coords = np.zeros(6*13)
ca = CoordsAdapter(nrigid=13, coords=coords)
for i in xrange(13):
ca.posRigid[i] = 0.5*(xyz[2*i] + xyz[2*i+1])
a1 = -(xyz[2*i] - xyz[2*i+1])
if(i<12):
a3 = -(xyz[2*i+1] - xyz[2*i+3])
else:
a3 = -(xyz[2*i-1] - xyz[2*i+1])
a2 = -np.cross(a1, a3)
a3 = np.cross(a1, a2)
a1/=np.linalg.norm(a1)
a2/=np.linalg.norm(a2)
a3/=np.linalg.norm(a3)
# print np.dot(a1, a2), np.dot(a1, a3), np.dot(a2, a3)
mx = np.array([a1, a2, a3]).transpose()
p = rotations.mx2aa(mx)
#print mx - rotations.aa2mx(p)
# print a1-np.dot(rotations.aa2mx(p), np.array([1., 0., 0.]))
ca.rotRigid[i] = p
return coords
def map_to_aa(xyz):
coords = np.zeros(6 * 13)
ca = CoordsAdapter(nrigid=13, coords=coords)
for i in xrange(13):
ca.posRigid[i] = 0.5 * (xyz[2 * i] + xyz[2 * i + 1])
a1 = -(xyz[2 * i] - xyz[2 * i + 1])
if (i < 12):
a3 = -(xyz[2 * i + 1] - xyz[2 * i + 3])
else:
a3 = -(xyz[2 * i - 1] - xyz[2 * i + 1])
a2 = -np.cross(a1, a3)
a3 = np.cross(a1, a2)
a1 /= np.linalg.norm(a1)
a2 /= np.linalg.norm(a2)
a3 /= np.linalg.norm(a3)
# print np.dot(a1, a2), np.dot(a1, a3), np.dot(a2, a3)
mx = np.array([a1, a2, a3]).transpose()
p = rotations.mx2aa(mx)
#print mx - rotations.aa2mx(p)
# print a1-np.dot(rotations.aa2mx(p), np.array([1., 0., 0.]))
ca.rotRigid[i] = p
return coords
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)
#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
while True:
p2n = p2-n2
if(np.linalg.norm(p2n - p1) > np.linalg.norm(p2 - p1)):
break
def invert(self, X):
ca = self.topology.coords_adapter(X)
ca.posRigid[:] = - ca.posRigid
for p, site in zip(ca.rotRigid, self.topology.sites):
p[:] = rotations.rotate_aa(rotations.mx2aa(site.inversion), p)
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)
#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
while True:
p2n = p2 - n2
if (np.linalg.norm(p2n - p1) > np.linalg.norm(p2 - p1)):
break
