def test_kin(): 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) kin_mat = eval_kin.get_kin_mat(noo, orb_coord, orb_type, coef_mat, exp_mat) kin_ref = np.array([[29.00324, -0.16801, 0.00000, 0.00000, 0.00000, -0.00252, -0.00252], [-0.16801, 0.80813, 0.00000, 0.00000, 0.00000, 0.12857, 0.12857], [ 0.00000, 0.00000, 2.52873, 0.00000, 0.00000, 0.22476, -0.22476], [ 0.00000, 0.00000, 0.00000, 2.52873, 0.00000, 0.17396, 0.17396], [ 0.00000, 0.00000, 0.00000, 0.00000, 2.52873, 0.00000, 0.00000], [-0.00252, 0.12857, 0.22476, 0.17396, 0.00000, 0.76003, 0.00848], [ -0.00252, 0.12857, -0.22476, 0.17396, 0.00000, 0.00848, 0.76003]]) #assert kin_mat == pytest.approx(kin_ref.astype('float64'), rel = 0.01) #np.set_printoptions(precision=4, suppress=True) #print(kin_mat-kin_ref) #print() #print(kin_mat) #print() #print(kin_ref) #print() #print((kin_mat-kin_ref)/kin_mat) #print() assert kin_mat == pytest.approx(kin_ref.astype('float64') , rel=1e-3, abs=1e-4)
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_over(): 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) over_ref = np.array([[1.00000, 0.23670, 0.00000, 0.00000, 0.00000, 0.05397, 0.05397], [0.23670, 1.00000, 0.00000, 0.00000, 0.00000, 0.47475, 0.47475], [0.00000, 0.00000, 1.00000, 0.00000, 0.00000, 0.31112, -0.31112], [ 0.00000, 0.00000, 0.00000, 1.00000, 0.00000, 0.24081, 0.24081], [ 0.00000, 0.00000, 0.00000, 0.00000, 1.00000, 0.00000, 0.00000], [ 0.05397, 0.47475, 0.31112, 0.24081, 0.00000, 1.00000, 0.25167], [ 0.05397, 0.47475, -0.31112, 0.24081, 0.00000, 0.25167, 1.00000]]) assert over_mat == pytest.approx(over_ref.astype('float64'), rel = 0.001)
def test_easy_read(): ref_coord = np.array([[0.00000, 0.00000, 0.0000], [0.75690, 0.58585, 0.0000], [-0.75690, 0.58585, 0.0000]]) ref_atom = np.array(["O", "H", "H"]) ref_z = np.array([8, 1, 1]) coord, atom = read_xyz.easy_read("test_coord.xyz", None, False, False) coord = coord[0, :, :] zoa = read_xyz.atom_to_zoa(atom) assert coord == pytest.approx(ref_coord) #print(ref_atom == atom) #assert assert (atom == ref_atom).all() #assert len(actual) == len(expected) #assert all([a == b for a, b in zip(actual, expected)]) #assert atom.all() == ref_atom.all() assert (ref_z == zoa).all() #assert coord == pytest.approx(ref_coord) bohr_in_a = 0.529177210903 coord = read_xyz.xyz_to_bohr(coord) ref_coord /= bohr_in_a assert coord == pytest.approx(ref_coord)
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_four_ss(): 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) four_mat = eval_four.get_four_mat(noo, orb_coord, orb_type, coef_mat, exp_mat) assert four_mat[0,0,0,0] == pytest.approx(4.78508, rel = 0.001) #ssss assert four_mat[0,1,0,0] == pytest.approx(0.74138, rel = 0.001) #ssss assert four_mat[5,5,5,3] == pytest.approx(0.19847, rel = 0.001) #psss assert four_mat[6,6,6,3] == pytest.approx(0.19847, rel = 0.001) #psss assert four_mat[6,6,6,2] == pytest.approx(-0.25641, rel = 0.001)#psss #0.19847 #7 7 5 5 0.48275 assert four_mat[6,6,4,4] == pytest.approx(0.48275, rel = 0.001)#ppss assert four_mat[6,6,4,3] == pytest.approx(0.0, rel = 0.001)#ppss #7 5 7 5 0.02343 assert four_mat[6,4,6,4] == pytest.approx(0.02343, rel = 0.001)#psps #test_nuc() #7 4 3 3 0.15098 ##7 4 4 1 0.01162 ##7 4 4 2 0.07176 #7 4 4 3 -0.01229 assert four_mat[6,3,2,2] == pytest.approx(0.15098, rel = 0.001)#ppps assert four_mat[6,3,3,2] == pytest.approx(-0.01229, rel = 0.001)#ppps #4 4 4 4 0.88016 assert four_mat[3,3,3,3] == pytest.approx(0.88016, rel = 0.001)#ppps #def test_four_full(): four_pre = np.loadtxt("../data/FOUR_CENTRE_TEST_DATA.dat") for i in range(four_pre.shape[0]): # for i in range(3): # print("hallllllllllllllllllllloooooooooooooooooooo") print(i) #assert four_mat[int(four_pre[i,0])-1,int(four_pre[i,1])-1,int(four_pre[i,2])-1,int(four_pre[i,3])-1] == pytest.approx(four_pre[i,4], rel = 0.05) assert four_mat[int(four_pre[i,0])-1,int(four_pre[i,1])-1,int(four_pre[i,2])-1,int(four_pre[i,3])-1] == pytest.approx(four_pre[i,4], rel=1e-3, abs=1e-5)
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 dens_to_cube(): print("command line:") print(sys.argv) fn_dens = str(sys.argv[1]) np.set_printoptions(precision=4, suppress=True) dens = np.loadtxt(fn_dens) 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) n_grid = 140 cube_length_au = 7 / bohr_in_a data = np.zeros((n_grid, n_grid, n_grid)) mesh = data.shape origin_au = np.array([ cube_length_au / 2, cube_length_au / 2, cube_length_au / 2 ]) #punkt in rechter!!!!! unterer ecke, nicht die box mitte!!! cell_au = np.eye(3) * cube_length_au / n_grid grid = CubeFileTools.CalcGridPositions(cell_au, mesh, origin_au) comment1 = " " comment2 = " " #numbers = zoa cell_data = dict() cell_data['numbers'] = zoa #cell_data['coords_au'] = coords_au cell_data['coords_au'] = coord cell_data['cell_au'] = cell_au #cell_data['symbols' ] = [constants.symbols[int(e)-1] for e in cell_data['numbers']] cell_data['symbols'] = atom cell_data['species'] = list(set(cell_data['symbols'])) cell_data['mesh'] = data.shape cell_data['d3r_au'] = cell_au[0, 0] * cell_au[1, 1] * cell_au[2, 2] cell_data['volume_au'] = cell_data['d3r_au'] * data.shape[0] * data.shape[ 1] * data.shape[2] cell_data['r_au'] = grid #cell_data['r_au' ] = CalcGridPositions(cell_au, data.shape, origin_au=origin_au) cell_data['data'] = data cell_data['comment1'] = comment1 cell_data['comment2'] = comment2 cell_data['origin_au'] = -origin_au #species symbols numbers comment1 comment2 #def WriteCubeFile(filename, comment1, comment2, numbers, coords, cell, data, origin=np.zeros(3)): #fn_out = "test.cube" fn_out = fn_dens + ".cube" print("start to calc density on grid") basis_at_grid = [] for i in range(noo): #print("input ",orb_type[i], exp_mat[i], coef_mat[i], orb_coord[i]) data = basis_func_to_grid(grid, orb_type[i], exp_mat[i], coef_mat[i], orb_coord[i]) #str1 = "basis_function"+str(i)+".cube" #cube.WriteCubeFile(str1, cell_data['comment1' ], cell_data['comment2' ], cell_data['numbers' ], cell_data['coords_au'], cell_data['cell_au' ], data, cell_data['origin_au']) basis_at_grid.append(data) basis_at_grid = np.array(basis_at_grid) basis_overlapp_states = [] for i in range(noo): basis_overlapp_states.append([]) for j in range(noo): basis_overlapp_states[i].append(basis_at_grid[i] * basis_at_grid[j]) basis_overlapp_states = np.array(basis_overlapp_states) #print(basis_overlapp_states.shape) #strange_dens_mat = basis_overlapp_states.sum(axis=(2,3,4)) #print(strange_dens_mat) #basis_overlapp_states = basis_overlapp_states*dens basis_overlapp_states1 = basis_overlapp_states * dens[:, :, np.newaxis, np.newaxis, np.newaxis] data = basis_overlapp_states1.sum(axis=(0, 1)) #fn_out = cube.WriteCubeFile(fn_out, cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], data, cell_data['origin_au'])
def calc_moments_numerically(): #fn1 = "../data/dens_h2o.cube" #fn1 = "/home/dressler/projects/HF/develop_bombanitio/minus9/data/dens_h2o.cube" #fn1 = "/home/dressler/projects/HF/develop_bombanitio/minus9/data/DENSITY.cube" #cube1 = CubeFileTools.LoadCellData(fn1) #for i in cube1.keys(): # print(i) #print(cube1["origin_au"]) ##print(cube1["cell_au"]) #print(cube1["data"].shape) #print(cube1["coords_au"]) np.set_printoptions(precision=4, suppress=True) print("Reading coordinates ... ") fn_dens = "density_mat0" #dens = np.loadtxt("density_mat0") dens = np.loadtxt(fn_dens) 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) #n_grid = 108 #n_grid = 216 n_grid = 140 cube_length_au = 7 / bohr_in_a #cube_length_au = 10 / bohr_in_a #data = np.zeros((108,108,108)) data = np.zeros((n_grid, n_grid, n_grid)) mesh = data.shape #origin_au = [-5,-5,-5]/bohr_in_a #punkt in linker unterer ecke, nicht die box mitte!!! origin_au = np.array([ cube_length_au / 2, cube_length_au / 2, cube_length_au / 2 ]) #punkt in rechter!!!!! unterer ecke, nicht die box mitte!!! #origin_au = np.array([cube_length_au ,cube_length_au,cube_length_au]) #punkt in rechter!!!!! unterer ecke, nicht die box mitte!!! cell_au = np.eye(3) * cube_length_au / n_grid #def CalcGridPositions(cell_au, mesh, origin_au=None): grid = CubeFileTools.CalcGridPositions(cell_au, mesh, origin_au) comment1 = "bla" comment2 = "blub" #numbers = zoa cell_data = dict() cell_data['numbers'] = zoa #cell_data['coords_au'] = coords_au cell_data['coords_au'] = coord cell_data['cell_au'] = cell_au #cell_data['symbols' ] = [constants.symbols[int(e)-1] for e in cell_data['numbers']] cell_data['symbols'] = atom cell_data['species'] = list(set(cell_data['symbols'])) cell_data['mesh'] = data.shape cell_data['d3r_au'] = cell_au[0, 0] * cell_au[1, 1] * cell_au[2, 2] cell_data['volume_au'] = cell_data['d3r_au'] * data.shape[0] * data.shape[ 1] * data.shape[2] cell_data['r_au'] = grid #cell_data['r_au' ] = CalcGridPositions(cell_au, data.shape, origin_au=origin_au) cell_data['data'] = data cell_data['comment1'] = comment1 cell_data['comment2'] = comment2 cell_data['origin_au'] = -origin_au #species symbols numbers comment1 comment2 #def WriteCubeFile(filename, comment1, comment2, numbers, coords, cell, data, origin=np.zeros(3)): fn_out = "test.cube" #cube.WriteCubeFile(fn_out, cell_data['comment1' ], cell_data['comment2' ], cell_data['numbers' ], cell_data['coords_au'], cell_data['cell_au' ], cell_data['data' ], cell_data['origin_au']) mompol = dict() moments = dict() exp_order = 1 n_states = 3 for i_order in range(1, exp_order + 1): #f cartesian: # mompol['%02d'%i_order] = CubeFileTools.CartesianMoments(r_au, order=i_order) #lse: #mompol['%02d'%i_order] = CubeFileTools.CartesianMoments(r_au, order=i_order) mompol['%02d' % i_order] = CubeFileTools.CartesianMoments( grid, order=i_order) #mompol['%02d'%i_order] = SphericalHarmonics.RealRegularSolidHarmonics(r_au, order=i_order) #moments['%02d'%i_order] = np.zeros((n_states, mompol['%02d'%i_order].shape[0])) #print(mompol) #print(moments) #mom_pol_ar = np.zeros((n_states, 108, 108 , 108)) #mom_pol_ar = np.zeros((n_states + 1 , 108, 108 , 108)) #mom_pol_ar = np.zeros((n_states , 108, 108 , 108)) mom_pol_ar = np.zeros((n_states, n_grid, n_grid, n_grid)) #for i in range(n_states): #mom_pol_ar[0] = np.ones((108, 108 , 108)) print(n_states) for j in range(n_states): #k = j +1 k = j if (j < 3) and (j > -1): mom_pol_ar[k] = mompol['01'][j] elif (j < 9) and (j > 2): # ipdb.set_trace() mom_pol_ar[k] = mompol['02'][j - 3] elif (j < 19) and (j > 8): mom_pol_ar[k] = mompol['03'][j - 9] elif (j < 34) and (j > 18): mom_pol_ar[k] = mompol['04'][j - 19] elif (j < 55) and (j > 33): mom_pol_ar[k] = mompol['05'][j - 34] else: print('index error') #mom_pol_ar.shape #if 5 > 10: #lime.print_states_dict(mom_pol_ar*0.001, cell_data5, n_states, '/shared/dressler/chi/cartesian-storage-fac-0.001/cartesian-functions-%05d', pure = True, pert = True) #lime.print_states_dict(mom_pol_ar*0.001, cell_data5, n_states + 1, '/shared/dressler/chi/paper_no4_theorem/data/v1/center-chi4-basis-polynoms-shift/cartesian-functions-%05d', pure = True, pert = True) #lime. print_states_dict(mom_pol_ar*0.001, cell_data, n_states + 1, 'cartesian-functions-%05d', pure = True, pert = True) #lime.print_states_dict(mom_pol_ar*0.001, cell_data, n_states, 'cartesian-functions-%05d', pure = True, pert = True) for i in range(n_states): fnx = "cartesian-functions" + str(i) + ".cube" cube.WriteCubeFile(fnx, cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], mom_pol_ar[i], cell_data['origin_au']) print("start to calc density on grid") #print(grid.shape) #dist1 = np.linalg.norm(grid, axis=0) #print(dist1.shape) ##data = np.exp(np. #exp1 = np.exp(dist1) #print(exp1.shape) basis_at_grid = [] for i in range(noo): #noo, orb_coord, orb_type, coef_mat, exp_mat #data = basis_func_to_grid(grid, orb_type ,exp, coeff, pos) #if orb_type[i] > 0: print("input ", orb_type[i], exp_mat[i], coef_mat[i], orb_coord[i]) data = basis_func_to_grid(grid, orb_type[i], exp_mat[i], coef_mat[i], orb_coord[i]) #print(data.shape, abs(data).sum()) print(data.shape, abs(data**2).sum()) print(data[52, 52, 52]) str1 = "basis_function" + str(i) + ".cube" cube.WriteCubeFile(str1, cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], data, cell_data['origin_au']) basis_at_grid.append(data) #fn_dens + #basis_func_to_grid(grid,orb_type ,exp, coeff, pos) basis_at_grid = np.array(basis_at_grid) basis_overlapp_states = [] for i in range(noo): basis_overlapp_states.append([]) for j in range(noo): basis_overlapp_states[i].append(basis_at_grid[i] * basis_at_grid[j]) basis_overlapp_states = np.array(basis_overlapp_states) print(basis_overlapp_states.shape) strange_dens_mat = basis_overlapp_states.sum(axis=(2, 3, 4)) print(strange_dens_mat) #basis_overlapp_states = basis_overlapp_states*dens diff_list = [] for fn_dens in [ "density_mat0", "density_mat1", "density_mat2", "density_mat3" ]: #fn_dens = "density_mat0" dens = np.loadtxt(fn_dens) basis_overlapp_states1 = basis_overlapp_states * dens[:, :, np.newaxis, np.newaxis, np.newaxis] data = basis_overlapp_states1.sum(axis=(0, 1)) str1 = fn_dens + ".cube" cube.WriteCubeFile(str1, cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], data, cell_data['origin_au']) print("summ of electrons: ", data.sum()) if fn_dens == "density_mat0": ref = np.copy(data) else: diff = data - ref str1 = "diff_" + fn_dens + ".cube" cube.WriteCubeFile(str1, cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], diff, cell_data['origin_au']) print("summ of diff electrons: ", diff.sum()) diff_list.append(diff) diff_list = np.array(diff_list) #mom_mat = lib_dme.create_overlap_mat(diff_list[1:], mom_pol_ar) mom_mat = lib_dme.create_overlap_mat(diff_list, mom_pol_ar) print("mom mat") print(mom_mat) print(abs(diff_list[0]).sum()) print((diff_list[0] * mom_pol_ar[1]).sum()) special = diff_list[0] * mom_pol_ar[1] cube.WriteCubeFile("special.cube", cell_data['comment1'], cell_data['comment2'], cell_data['numbers'], cell_data['coords_au'], cell_data['cell_au'], special, cell_data['origin_au'])
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)