def test_orca_water():
coord, atom = read_xyz.easy_read("test_coord.xyz", None, False, False)
coord = coord[0, :, :]
coord = read_xyz.xyz_to_bohr(coord)
zoa = read_xyz.atom_to_zoa(atom)
noa = atom.shape[0]
noo, orb_coord, orb_type, coef_mat, exp_mat = create_basis.basisset(
noa, zoa, coord)
read_xyz.plot_initial_orbs(noo, orb_coord, orb_type, coef_mat, exp_mat)
over_mat = eval_over.get_overlap_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
np.set_printoptions(precision=4, suppress=True)
kin_mat = eval_kin.get_kin_mat(noo, orb_coord, orb_type, coef_mat, exp_mat)
nuc_mat = eval_nuc.get_nuc_mat(noo, orb_coord, orb_type, coef_mat, exp_mat,
coord, zoa)
dip_matx = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 0)
dip_maty = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 1)
dip_matz = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 2)
dip_mat = np.array([dip_matx, dip_maty, dip_matz])
four_mat = eval_four.get_four_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
h = kin_mat + nuc_mat
##diagonalisation of S
#eig, u = np.linalg.eig(over_mat)
##creation of matrix x via canonical orthogonalisation
#x = u / (eig) ** 0.5
## xt is transposed of x
#xt = x.T
x = scf.ortho_basis(over_mat)
noe = zoa.sum()
#print("number of electron:", noe)
#en, p, c = scf.scf(four_mat, noe, noo, x, xt, h)
en, p, c, coeff = scf.scf(four_mat, noe, noo, x, h)
etot = scf.calc_tot_en(noa, en, coord, zoa)
#print(etot)
#dipole = dip_mat * p
#dipole = dipole.sum(axis=1)
#dipole = dipole.sum(axis=1)
dipole = eval_dipole.get_el_dipole(p, dip_mat)
nuc_pole = eval_dipole.get_nuc_pole(coord, zoa)
tot_dip = nuc_pole - dipole
orca_en = -74.962919685003
orca_dip = np.array([0.000000, 0.678999, -0.000000])
assert etot == pytest.approx(orca_en, rel=1e-5, abs=1e-4)
assert tot_dip == pytest.approx(orca_dip, rel=1e-5, abs=1e-3)
def test_nuc():
coord, atom = read_xyz.easy_read("test_coord.xyz", None, False, False)
coord = coord[0,:,:]
coord = read_xyz.xyz_to_bohr(coord)
zoa = read_xyz.atom_to_zoa(atom)
noa = atom.shape[0]
noo, orb_coord, orb_type, coef_mat, exp_mat = create_basis.basisset(noa, zoa, coord)
#NUCLEAR-ATTRACTION MATRIX
nuc_mat = eval_nuc.get_nuc_mat(noo, orb_coord, orb_type, coef_mat, exp_mat, coord, zoa)
#print("nuclear attraction matrix: ")
nuc_ref = np.array([[-61.72413, -7.44477, 0.00000, -0.01900, 0.00000, -1.74672, -1.74672],
[-7.44477, -10.14287, 0.00000, -0.22350, 0.00000, -3.86944, -3.86944],
[ 0.00000, 0.00000, -10.14262, 0.00000, 0.00000, -2.25477, 2.25477],
[-0.01900, -0.22350, 0.00000, -10.07996, 0.00000, -1.81819, -1.81819],
[ 0.00000, 0.00000, 0.00000, 0.00000, -9.98632, 0.00000, 0.00000],
[-1.74672, -3.86944, -2.25477, -1.81819, 0.00000, -5.83642, -1.61650],
[-1.74672, -3.86944, 2.25477, -1.81819, 0.00000, -1.61650, -5.83642]])
np.set_printoptions(precision=4, suppress=True)
print(nuc_ref - nuc_mat)
print(nuc_mat)
assert nuc_mat == pytest.approx(nuc_ref.astype('float64'), rel = 0.001)
def test_form_g_mat():
#dens_xxx_01 fock_xxx_01 coord_xxx_01.xyz
orca_dens = np.loadtxt("../data/dens_xxx_01")
orca_fock = np.loadtxt("../data/fock_xxx_01")
orca_h = np.loadtxt("../data/h_xxx_01")
orca_fock2 = np.zeros(orca_fock.shape)
orca_dens2 = np.zeros(orca_dens.shape)
orca_h2 = np.zeros(orca_h.shape)
dict1 = {}
dict1[0] = 0
dict1[1] = 1
dict1[2] = 4
dict1[3] = 2
dict1[4] = 3
dict1[5] = 5
dict1[6] = 6
for i in range(orca_fock2.shape[0]):
for j in range(orca_fock2.shape[1]):
#k = i
#l = j
#if i =
orca_fock2[dict1[i], dict1[j]] = orca_fock[i, j]
orca_dens2[dict1[i], dict1[j]] = orca_dens[i, j]
orca_h2[dict1[i], dict1[j]] = orca_h[i, j]
p = orca_dens2
#p =np.array([[2.10625, -0.44603, 0.00000, 0.10859, 0.00000, -0.02843, -0.02843],
# [-0.44603, 1.96730, 0.00000,-0.61771, 0.00000, -0.03406, -0.03406],
# [0.00000, 0.00000, 0.73554, 0.00000, 0.00000, 0.53974, -0.53974],
# [0.10859, -0.61771, 0.00000, 1.24023, 0.00000, 0.47272, 0.47272],
# [0.00000, 0.00000, 0.00000, 0.00000, 2.00000, 0.00000, 0.00000],
# [-0.02843,-0.03406, 0.53974, 0.47272, 0.00000, 0.60093, -0.19120],
# [-0.02843,-0.03406,-0.53974, 0.47272, 0.00000, -0.19120, 0.60093]])
coord, atom = read_xyz.easy_read("../data/coord_xxx_01.xyz", None, False,
False)
coord = coord[0, :, :]
coord = read_xyz.xyz_to_bohr(coord)
zoa = read_xyz.atom_to_zoa(atom)
noa = atom.shape[0]
#basisset(noa, zoa, coord)
noo, orb_coord, orb_type, coef_mat, exp_mat = create_basis.basisset(
noa, zoa, coord)
#print(noo)
#print(orb_coord)
#print(orb_type)
#print(coef_mat)
#print(exp_mat)
read_xyz.plot_initial_orbs(noo, orb_coord, orb_type, coef_mat, exp_mat)
# print(coef_mat.dtype)
over_mat = eval_over.get_overlap_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
np.set_printoptions(precision=5, suppress=True)
kin_mat = eval_kin.get_kin_mat(noo, orb_coord, orb_type, coef_mat, exp_mat)
nuc_mat = eval_nuc.get_nuc_mat(noo, orb_coord, orb_type, coef_mat, exp_mat,
coord, zoa)
print("pre_noo:", noo)
four_mat = eval_four.get_four_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
h = kin_mat + nuc_mat
g = scf.formg(noo, four_mat, p)
f = h + g
#fock_ref = np.loadtxt("../data/fock.data")
#print()
#print(f - fock_ref)
#print()
#print((f - fock_ref)/fock_ref)
#print()
#print(f )
#print()
#print(fock_ref)
#../data/orca_dens_eq ../data/orca_fock_eq
#assert f == pytest.approx(fock_ref, rel=1e-3, abs=1e-5)
print(f - orca_fock2)
print()
#print((f - orca_fock2)/f)
print()
print(f)
print()
print(orca_fock2)
assert h == pytest.approx(orca_h2, rel=1e-3, abs=1e-4)
assert f == pytest.approx(orca_fock2, rel=1e-3, abs=1e-4)
assert p == pytest.approx(orca_dens2, rel=1e-3, abs=1e-4)
def main():
print("sonntag")
print(
"Performing a self-consistent HF calculation of the molecule given by the file coord.xyz in this directory ... "
)
print("Reading coordinates ... ")
coord, atom = read_xyz.easy_read("coord.xyz", None, False, False)
coord = coord[0, :, :]
coord = read_xyz.xyz_to_bohr(coord)
zoa = read_xyz.atom_to_zoa(atom)
noa = atom.shape[0]
noo, orb_coord, orb_type, coef_mat, exp_mat = create_basis.basisset(
noa, zoa, coord)
read_xyz.plot_initial_orbs(noo, orb_coord, orb_type, coef_mat, exp_mat)
over_mat = eval_over.get_overlap_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
print("overlap matrix: ")
np.set_printoptions(precision=4, suppress=True)
print(over_mat.astype('float64'))
kin_mat = eval_kin.get_kin_mat(noo, orb_coord, orb_type, coef_mat, exp_mat)
print("kinetic energy matrix: ")
print(kin_mat.astype('float64'))
nuc_mat = eval_nuc.get_nuc_mat(noo, orb_coord, orb_type, coef_mat, exp_mat,
coord, zoa)
print("nuclear attraction matrix: ")
print(nuc_mat.astype('float64'))
dip_matx = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 0)
dip_maty = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 1)
dip_matz = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 2)
dip_mat = np.array([dip_matx, dip_maty, dip_matz])
print("dipole moment matrix: ")
print(dip_mat.astype('float64'))
print("calculate four center integrals.... ")
four_mat = eval_four.get_four_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
#print(four_mat[0,0,0,0])
#print(four_mat[5,5,5,3])
#create core hamiltonian
h = kin_mat + nuc_mat
x = scf.ortho_basis(over_mat)
noe = zoa.sum()
print("number of electron:", noe)
en, p, coeff, energy_orb = scf.scf(four_mat, noe, noo, x, h)
print()
print("#######################################################")
print("final orbital energies:", energy_orb)
print("#######################################################")
#print()
print()
print("#######################################################")
print("final electronic energy:", en)
print("#######################################################")
print()
etot = scf.calc_tot_en(noa, en, coord, zoa)
print("#######################################################")
print("final total energy:", etot)
print("#######################################################")
#print(etot)
dipole = eval_dipole.get_el_dipole(p, dip_mat)
print()
print()
print()
print("#######################################################")
print("electronic contribution dipole moment:", dipole)
nuc_pole = eval_dipole.get_nuc_pole(coord, zoa)
print("nucear contribution dipole moment:", nuc_pole)
print("total dipole moment:", nuc_pole - dipole,
np.linalg.norm(nuc_pole - dipole))
print("#######################################################")
np.savetxt("coefficients", coeff[:int(noe / 2), :])
np.savetxt("density_mat", p)
def main():
original_stdout = sys.stdout
print("Calculation of the first three moment expanded states")
print()
print("initalize system and calculating one and two electron matrices...")
with open('detailed_output_moment_expansion.txt', 'w') as f:
sys.stdout = f
print("Reading coordinates ... ")
coord, atom = read_xyz.easy_read("coord.xyz", None, False, False)
coord = coord[0, :, :]
coord = read_xyz.xyz_to_bohr(coord)
zoa = read_xyz.atom_to_zoa(atom)
noa = atom.shape[0]
noo, orb_coord, orb_type, coef_mat, exp_mat = create_basis.basisset(
noa, zoa, coord)
read_xyz.plot_initial_orbs(noo, orb_coord, orb_type, coef_mat, exp_mat)
over_mat = eval_over.get_overlap_mat(noo, orb_coord, orb_type,
coef_mat, exp_mat)
print("overlap matrix: ")
np.set_printoptions(precision=4, suppress=True)
print(over_mat.astype('float64'))
kin_mat = eval_kin.get_kin_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
print("kinetic energy matrix: ")
print(kin_mat.astype('float64'))
nuc_mat = eval_nuc.get_nuc_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, coord, zoa)
print("nuclear attraction matrix: ")
print(nuc_mat.astype('float64'))
dip_matx = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 0)
dip_maty = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 1)
dip_matz = eval_dipole.get_dip_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat, 2)
dip_mat = np.array([dip_matx, dip_maty, dip_matz])
print("dipole moment matrix: ")
print(dip_mat.astype('float64'))
print("calculate four center integrals.... ")
four_mat = eval_four.get_four_mat(noo, orb_coord, orb_type, coef_mat,
exp_mat)
#print(four_mat[0,0,0,0])
#print(four_mat[5,5,5,3])
#create core hamiltonian
h = kin_mat + nuc_mat
x = scf.ortho_basis(over_mat)
noe = zoa.sum()
print("number of electron:", noe)
diff_dens_list = []
#for i in range([0,1,2,3]):
sys.stdout = original_stdout
print(
"performing single point calculation with and without external potentials"
)
sys.stdout = f
for i in [0, 1, 2, 3]:
if i == 0:
ext = None
else:
ext = 0.0001 * dip_mat[i - 1, :, :]
print()
print()
print()
print()
print()
print("#######################################################",
file=f)
print("start of new single point calculation for the " + str(i) +
"-th moment expanded state",
file=f)
print("#######################################################")
print()
h = kin_mat + nuc_mat
en, p, coeff, energy_orb = scf.scf(four_mat, noe, noo, x, h, ext)
print()
print("#######################################################")
print("final orbital energies:", energy_orb)
print("#######################################################")
#print()
print()
print("#######################################################")
print("final electronic energy:", en)
print("#######################################################")
print()
etot = scf.calc_tot_en(noa, en, coord, zoa)
print("#######################################################")
print("final total energy:", etot)
print("#######################################################")
#print(etot)
dipole = eval_dipole.get_el_dipole(p, dip_mat)
print()
print()
print()
print("#######################################################")
print("electronic contribution dipole moment:", dipole)
nuc_pole = eval_dipole.get_nuc_pole(coord, zoa)
print("nucear contribution dipole moment:", nuc_pole)
print("total dipole moment:", nuc_pole - dipole)
print("#######################################################")
str1 = "coefficients" + str(i)
#np.savetxt("coefficients", coeff[:int(noe/2),:])
np.savetxt(str1, coeff[:int(noe / 2), :])
str4 = "density_mat" + str(i)
#np.savetxt("coefficients", coeff[:int(noe/2),:])
np.savetxt(str4, p)
print()
print("#######################################################")
#print("coefficients matrix of " + str(i)+"th single point")
#print(coeff[:int(noe/2),:])
print("density matrix obtained by " + str(i) +
"-th single point calculation")
print(p)
print("#######################################################")
print()
if i == 0:
equi_coeff = np.copy(coeff[:int(noe / 2), :])
equi_p = np.copy(p)
else:
str2 = "coefficients_mes" + str(i)
str3 = "denstiy_mes" + str(i)
diff = coeff[:int(noe / 2), :] - equi_coeff
diff_p = p - equi_p
np.savetxt(str2, diff)
np.savetxt(str3, diff_p)
diff_dens_list.append(diff_p)
print()
#print("#######################################################")
#print("coefficients matrix of equilibrium single point")
#print(equi_coeff)
#print("#######################################################")
#print("coefficients matrix of" + str(i)+"th moment expanded state")
#print(diff)
#print("#######################################################")
print(
"#######################################################")
print(
"density matrix from obtained from single point calculation without applied external potentials"
)
print(equi_p)
print(
"#######################################################")
#print("density matrix of" + str(i)+"-th moment expanded state")
print(
"density matrix of electron density difference obtained by single point calculations with the "
+ str(i) + "-th and without an external potential")
print(diff_p)
print(
"#######################################################")
print()
print("#######################################################")
print("end of single point calculation for the " + str(i) +
"-th moment expanded state")
print("#######################################################")
print()
print(
"#########################################################################################################################"
)
print()
sys.stdout = original_stdout
print(
"post processing of response densities obtained by the external potential"
)
diff_dens_list = np.array(diff_dens_list)
diff_dens_list2 = np.copy(diff_dens_list)
#print(diff_dens_list.shape, dip_mat.shape)
#print(
dip_mat2 = np.copy(dip_mat)
tilde_mom = diff_dens_list[np.newaxis, :, :, :] * dip_mat[:,
np.newaxis, :, :]
tilde_mom = tilde_mom.sum(axis=(2, 3))
print()
print("#######################################################")
print(
"moment matrix of response densities obtained by the electron density difference of single point calculation with and without an external potential "
)
print(tilde_mom * 10000)
print("#######################################################")
tilde_mom = diff_dens_list2[
np.newaxis, :, :, :] * dip_mat2[:, np.newaxis, :, :]
tilde_mom = tilde_mom.sum(axis=(2, 3))
tilde_mom = (tilde_mom + tilde_mom.T) / 2
chol_left = np.linalg.cholesky(tilde_mom * -1)
#chol_right = chol_left
chol_right = chol_left.T
inv_chol_right = np.linalg.inv(chol_right)
print("#######################################################")
print("MES moment matrix from choleky decompostion:")
print("#######################################################")
print(chol_right * 10000)
#print()
#print(inv_chol_right)
mom_states = np.zeros(diff_dens_list2.shape)
#for k in range(3)
for i in range(3):
for j in range(3):
#mom_states[i] = inv_chol_right[i,j] * diff_dens_list[j]
mom_states[i] += inv_chol_right[j, i] * diff_dens_list2[j]
print("MES moment matrix obtaned by integrating over MES")
#mom_mat = mom_states[np.newaxis,:,:,:] * dip_mat2[:, np.newaxis ,:,:]
mom_mat = dip_mat2[np.newaxis, :, :, :] * mom_states[:, np.newaxis, :, :]
mom_mat = mom_mat.sum(axis=(2, 3))
print(mom_mat * 10000)
#tilde_mom = diff_dens_list2[np.newaxis, :,:,:] * dip_mat2[:, np.newaxis ,:,:]
#tilde_mom = tilde_mom.sum(axis = (2,3))
#print("HIST")
#print(tilde_mom*10000)
print()
print("saving density matrix of moment expanded states ... ")
for j in range(mom_states.shape[0]):
fn_mes = "mes_" + str(j + 1)
np.savetxt(fn_mes, mom_states[j])
print(fn_mes)