U12 = U21 = atom_obj[u-1]["u[0][1]"]
U13 = U31 = atom_obj[u-1]["u[0][2]"]
U23 = U32 = atom_obj[u-1]["u[1][2]"]
U = tlsvld.array([[U11,U12,U13],[U21,U22,U23],[U31,U32,U33]])
V11 = atom_obj[u]["u[0][0]"]
V22 = atom_obj[u]["u[1][1]"]
V33 = atom_obj[u]["u[2][2]"]
V12 = V21 = atom_obj[u]["u[0][1]"]
V13 = V31 = atom_obj[u]["u[0][2]"]
V23 = V32 = atom_obj[u]["u[1][2]"]
V = tlsvld.array([[V11,V12,V13],[V21,V22,V23],[V31,V32,V33]])
## Calculate all of the residuals
Suij = rosenfeld = diff_trace_UV = sum_square_diff = 0.0
cc_UV = tlsvld.calc_ccuij(U, V)
#cc_UV = AtomMath.calc_CCuij([[U11,U12,U13],
# [U21,U22,U23],
# [U31,U32,U33]],
# [[V11,V12,V13],
# [V21,V22,V23],
# [V31,V32,V33]])
rosenfeld = tlsvld.rosenfeld(Upos, Vpos, U, V)
sum_square_diff = tlsvld.sum_square_diff(U, V)
diff_trace_UV = tlsvld.diff_trace_uv(U, V)
## The actual output of this entire script.
print "%s\t%s:%s-%s:%s\t%s\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f" % (
bond_pos, cid1, res_name1, res_num1, bond, tls_group,
cc_UV, Suij, rosenfeld/10000,
diff_trace_UV/10000, sum_square_diff/10000**2)
#print "EIGENS = ", tlsvld.jacobi(U,3,3, EIGENS, EVECS ) print U print "EIGENS = ", tlsvld.eigenvalues(U) x1 = 1.00 y1 = 2.00 z1 = 3.00 x2 = 6.00 y2 = 5.00 z2 = 4.00 d = math.sqrt( (x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2 ) U = tlsvld.array([[0.37471362,-0.07411912,-0.0379023],[-0.07411912,0.39010298,-0.03240841],[-0.0379023,-0.03240841,0.33057791]]) V = tlsvld.array([[0.38484156,-0.06933809,-0.04994903],[-0.06933809,0.41376374,-0.03275701],[-0.04994903,-0.03275701,0.33967632]]) print d a = tlsvld.array([x1,y1,z1]) b = tlsvld.array([x2,y2,z2]) # n = numpy.array([(a[0] - b[0])/d, (a[1] - b[1])/d, (a[2] - b[2])/d]) # Un = numpy.dot(numpy.dot(n, U), numpy.transpose(n)) # Vn = numpy.dot(numpy.dot(n, V), numpy.transpose(n)) # return abs(Un - Vn) n = numpy.array([(a[0] - b[0])/d, (a[1] - b[1])/d, (a[2] - b[2])/d]) Un = numpy.dot(numpy.dot(n, U), numpy.transpose(n)) Vn = numpy.dot(numpy.dot(n, V), numpy.transpose(n)) print "[Python] DOT(n, U) = ", numpy.dot(n, U) print "[Python] d = ", d print "[Python] Rosenfeld = ", abs(Un - Vn) print "="*80 print "[Fortran] Rosenfeld = ", tlsvld.rosenfeld(a,b,U,V)
continue
#U = Ueq[u-1]
#V = Ueq[u]
U11 = atom_obj[u-1]["u[0][0]"]
U22 = atom_obj[u-1]["u[1][1]"]
U33 = atom_obj[u-1]["u[2][2]"]
U12 = U21 = atom_obj[u-1]["u[0][1]"]
U13 = U31 = atom_obj[u-1]["u[0][2]"]
U23 = U32 = atom_obj[u-1]["u[1][2]"]
U = tlsvld.array([[U11,U12,U13],[U21,U22,U23],[U31,U32,U33]])
V11 = atom_obj[u]["u[0][0]"]
V22 = atom_obj[u]["u[1][1]"]
V33 = atom_obj[u]["u[2][2]"]
V12 = V21 = atom_obj[u]["u[0][1]"]
V13 = V31 = atom_obj[u]["u[0][2]"]
V23 = V32 = atom_obj[u]["u[1][2]"]
V = tlsvld.array([[V11,V12,V13],[V21,V22,V23],[V31,V32,V33]])
Suij = rosenfeld = diff_trace_UV = sum_square_diff = 0.0
cc_UV = tlsvld.calc_ccuij(U, V)
#cc_UV = AtomMath.calc_CCuij([[U11,U12,U13],[U21,U22,U23],[U31,U32,U33]], [[V11,V12,V13],[V21,V22,V23],[V31,V32,V33]])
rosenfeld = tlsvld.rosenfeld(Upos, Vpos, U, V)
sum_square_diff = tlsvld.sum_square_diff(U, V)
diff_trace_UV = tlsvld.diff_trace_uv(U, V)
print "%s\t%s:%s-%s:%s\t%s\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f" % (
bond_pos, cid1, res_name1, res_num1, bond, tls_group,
cc_UV, Suij, rosenfeld/10000,
diff_trace_UV/10000, sum_square_diff/10000**2)