def Eigenvalue_Coulomb_Matrix(Z, R, N=0):
'''requires: : preordering of Z and R according to CM_full_sorted(Z, R, N)[1]
(otherwise two identical molecules with atoms 1 and 2 switched in the Z and R array
will be mapped onto different representations)
'''
#return(qml.representations.generate_eigenvalue_coulomb_matrix(Z, R, size = dim))
return (jrep.CM_ev_unsrt(Z, R, N))
def dd_CM_ev_unsrt(Z, R, N, dx_index=0, ddx_index=0):
Z = Z.astype(float)
R = R.astype(float)
N = float(N)
fM = jrep.CM_ev_unsrt(Z, R, N)
dim = len(Z)
Hraw = hessian(jrep.CM_ev_unsrt, dx_index, ddx_index)(Z, R, N)
#calculates dZdZ
if (dx_index == 0):
if (ddx_index == 0):
'''
sorting function, performs the following rearrangement:
[[[[HdZraw[k, m, n] for k in range(dim)] for m in order] for n in order])
'''
dZdZ_ordered = np.transpose(Hraw, (1, 2, 0))
return (dZdZ_ordered)
#calculates dRdR
if (dx_index == 1):
if (ddx_index == 1):
print("do dRdR sorting for unsorted ddCM_ev function")
'''
sorting function, performs the following rearrangement:
[[[[[[HdRraw[n, i, x, j, y] for n in range(dim)] for y in range(3)] for j in range(dim)] for x in range(3)] for i in range(dim)])
'''
dRdR_ordered = np.transpose(Hraw, (1, 2, 3, 4, 0))
return (dRdR_ordered)
if (dx_index == 0 and ddx_index == 1) or (dx_index == 1
and ddx_index == 0):
print("you want to calculate dZdR or dRdZ, line 443")
'''sorting function, performs the following reordering but in fast
[[[[[HdZdRraw[m, i, j, x] for m in range(dim)] for x in range(3)] for j in range(dim)] for i in range(dim)]
'''
dZdR_ordered = np.transpose(Hraw, (1, 2, 3, 0))
return (dZdR_ordered)
if (dx_index == 2 or ddx_index == 2):
return (Hraw)
def d_CM_ev_unsrt(Z, R, N, dx_index):
'''
Calculates first derivative of unsorted Coulomb Matrix eigenvalues w.r.t. dx_index
'''
dim = len(Z)
print("len of Z:", dim)
print("calculating Jacobian of Coulomb Matrix eigenvalues")
fM = jrep.CM_ev_unsrt(Z, R, N) #get order of sorted representation
#direct derivative as jacobian
dCM_ev = jacfwd(jrep.CM_ev_unsrt, dx_index)
ref_dCM_ev = dCM_ev(Z, R, N)
'''Not sure about reordering and values below. definitely need to recheck'''
if (dx_index == 0):
J_dZkl = jnp.asarray([[ref_dCM_ev[l][m] for l in range(dim)]
for m in range(dim)])
return (J_dZkl)
elif (dx_index == 1):
#unordered derivative taken from sorted matrix
J_dRkl = jnp.asarray([[[ref_dCM_ev[l][m][x] for l in range(dim)]
for x in range(3)] for m in range(dim)])
return (J_dRkl)
else:
return (ref_dCM_ev)
to then move both H simultaneously anti-clockwise by an angle phi:
H
/ phi
C===C.......
/
H
'''
#calculate reference values
compound = qml.Compound(reference)
Z = compound.nuclear_charges.astype(float)
R = compound.coordinates
ref_M_EVCM = jrep.CM_ev_unsrt(Z, R, size = 4)
dZ_eigenvalues = [] #list of eigenvalue vectors. length is same as len of name_vector
dimZ_list = [] #dimension of files may vary. store all dimensions here
dZ_slot1_list = [[],[],[],[]]
dZ_slot2_list = [[],[],[],[]]
dZ_slot3_list = [[],[],[],[]]
dZ_slot4_list = [[],[],[],[]]
EVCM_aberration = []
M_list = [[],[],[],[]]
compound1 = qml.Compound(names[0])
compound2 = qml.Compound(names[1])
if do_fingerprint_distance:
Z1 = compound1.nuclear_charges.astype(float)
R1 = compound1.coordinates
Z2 = compound2.nuclear_charges.astype(float)
R2 = compound2.coordinates
#calculate difference to reference constitution
M_CM1 = jrep.CM_full_unsorted_matrix(Z1, R1, size=4)
M_CM2 = jrep.CM_full_unsorted_matrix(Z2, R2, size=4)
M_EVCM1 = jrep.CM_ev_unsrt(Z1, R1, N=0, size=4)
M_EVCM2 = jrep.CM_ev_unsrt(Z2, R2, size=4)
M_BOB1 = np.asarray(ZRNrep.Bag_of_Bonds(Z1, R1))
M_BOB2 = np.asarray(ZRNrep.Bag_of_Bonds(Z2, R2))
M_OM1 = jrep.OM_full_unsorted_matrix(Z1, R1)
M_OM2 = jrep.OM_full_unsorted_matrix(Z2, R2)
M_EVOM1 = jrep.OM_ev(Z1, R1)[0]
M_EVOM2 = jrep.OM_ev(Z2, R2)[0]
diff1 = (M_EVCM1 - M_EVCM2)
diff2 = (M_BOB1 - M_BOB2)
diff3 = (M_CM1.flatten() - M_CM2.flatten())
diff4 = (M_OM1.flatten() - M_OM2.flatten())