def gen_HCN():
basis_sets, MO_matrix = read_qmcpack.parse_qmc_wf("hcn.wfnoj.xml")
pos_list, elements = read_qmcpack.read_structure_file("hcn.structure.xml")
gtos = gaussian_orbitals.GTO_centers(pos_list, elements, basis_sets)
pos = [0.0, 0.0, 0.0]
atomic_orbs = gtos.eval_v(*pos)
#print 'first MO',MO_matrix[0,:]
#print 'atomic_orbs',atomic_orbs
mol_orbs = np.dot(MO_matrix, atomic_orbs)
print ' // Generated from gen_mo.py for position %s' % str(pos)
for i in range(7):
print ' REQUIRE(values[%d] == Approx(%15.10g));' % (i, mol_orbs[i])
v, g, l = gtos.eval_vgl(*pos)
mo_v = np.dot(MO_matrix, v)
mo_g = np.dot(MO_matrix, g)
mo_l = np.dot(MO_matrix, l)
print ' // Generated from gen_mo.py for position %s' % str(pos)
for i in range(7):
print ' REQUIRE(values[%d] == Approx(%15.10g));' % (i, mo_v[i])
print ' REQUIRE(dpsi[%d][0] == Approx(%15.10g));' % (i, mo_g[i][0])
print ' REQUIRE(dpsi[%d][1] == Approx(%15.10g));' % (i, mo_g[i][1])
print ' REQUIRE(dpsi[%d][2] == Approx(%15.10g));' % (i, mo_g[i][2])
print ' REQUIRE(d2psi[%d] == Approx(%15.10g));' % (i, mo_l[i])
print ''
def gen_correction_for_hcn():
pos_list, elements = read_qmcpack.read_structure_file("hcn.structure.xml")
basis_sets, MO_matrix = read_qmcpack.parse_qmc_wf("hcn.wfnoj.xml", elements)
gtos = gaussian_orbitals.GTO_centers(pos_list, elements, basis_sets)
#print("MO matrix")
#for i in range(MO_matrix.shape[0]):
# print(i, MO_matrix[0:7, i])
phi_list, eta_list, C_no_S = split_by_angular_momentum(pos_list, elements, basis_sets, MO_matrix)
spo_name, cusp_data = read_qmcpack.read_cusp_correction_file("hcn_downdet.cuspInfo.xml")
cusp = CuspCorrection(cusp_data, pos_list, gtos, phi_list)
xgrid = get_grid()
for center_idx in range(3):
for mo_idx in range(7):
#val_data = vals[(center_idx, mo_idx)][0]
print(' // Center ',center_idx, ' MO',mo_idx, 'rc = ',cusp_data[center_idx][mo_idx].Rc)
for i,x in enumerate(xgrid):
epos = np.array([x, 0.0, 0.0]) + pos_list[center_idx]
v,g,l = cusp.compute_cusp_correction(center_idx, mo_idx, epos)
print(' REQUIRE(rad_orb[%d] == Approx(%.10f)); // x = %g'%(i,v,x))
print()
def gen_HCN():
basis_sets, MO_matrix = read_qmcpack.parse_qmc_wf("hcn.wfnoj.xml",
['N', 'C', 'H'])
pos_list, elements = read_qmcpack.read_structure_file("hcn.structure.xml")
gtos = gaussian_orbitals.GTO_centers(pos_list, elements, basis_sets)
pos = [0.0, 0.0, 0.0]
atomic_orbs = gtos.eval_v(*pos)
#print 'first MO',MO_matrix[0,:]
#print 'atomic_orbs',atomic_orbs
mol_orbs = np.dot(MO_matrix, atomic_orbs)
print ' // Generated from gen_mo.py for position %s' % str(pos)
for i in range(7):
print ' REQUIRE(values[%d] == Approx(%15.10g));' % (i, mol_orbs[i])
v, g, l = gtos.eval_vgl(*pos)
mo_v = np.dot(MO_matrix, v)
mo_g = np.dot(MO_matrix, g)
mo_l = np.dot(MO_matrix, l)
print ' // Generated from gen_mo.py for position %s' % str(pos)
for i in range(7):
print ' REQUIRE(values[%d] == Approx(%15.10g));' % (i, mo_v[i])
print ' REQUIRE(dpsi[%d][0] == Approx(%15.10g));' % (i, mo_g[i][0])
print ' REQUIRE(dpsi[%d][1] == Approx(%15.10g));' % (i, mo_g[i][1])
print ' REQUIRE(dpsi[%d][2] == Approx(%15.10g));' % (i, mo_g[i][2])
print ' REQUIRE(d2psi[%d] == Approx(%15.10g));' % (i, mo_l[i])
print ''
v, g, h = gtos.eval_vgh(*pos)
gh = gtos.eval_gradhess(*pos)
mo_v = np.dot(MO_matrix, v)
mo_g = np.dot(MO_matrix, g)
mo_h = np.dot(MO_matrix, h)
mo_gh = np.dot(MO_matrix, gh)
for i in range(7):
print ' // Generated from gen_mo.py for position %s' % str(pos)
print ' REQUIRE(values[%d] == Approx(%15.10g));' % (i, mo_v[i])
print ' REQUIRE(dpsi[%d][0] == Approx(%15.10g));' % (i, mo_g[i][0])
print ' REQUIRE(dpsi[%d][1] == Approx(%15.10g));' % (i, mo_g[i][1])
print ' REQUIRE(dpsi[%d][2] == Approx(%15.10g));' % (i, mo_g[i][2])
print ' //Hessian (xx,xy,xz,yy,yz,zz) '
print ' REQUIRE(dhpsi[%d][0] == Approx(%15.10g));' % (i, mo_h[i][0])
print ' REQUIRE(dhpsi[%d][1] == Approx(%15.10g));' % (i, mo_h[i][1])
print ' REQUIRE(dhpsi[%d][2] == Approx(%15.10g));' % (i, mo_h[i][2])
print ' REQUIRE(dhpsi[%d][3] == Approx(%15.10g));' % (i, mo_h[i][3])
print ' REQUIRE(dhpsi[%d][4] == Approx(%15.10g));' % (i, mo_h[i][4])
print ' REQUIRE(dhpsi[%d][5] == Approx(%15.10g));' % (i, mo_h[i][5])
print ' //GradHessian (xxx,xxy,xxz,xyy,xyz,xzz,yyy,yyz,yzz,zzz) '
print ' REQUIRE(dghpsi[%d][0] == Approx(%15.10g));' % (i, mo_gh[i][0])
print ' REQUIRE(dghpsi[%d][1] == Approx(%15.10g));' % (i, mo_gh[i][1])
print ' REQUIRE(dghpsi[%d][2] == Approx(%15.10g));' % (i, mo_gh[i][2])
print ' REQUIRE(dghpsi[%d][3] == Approx(%15.10g));' % (i, mo_gh[i][3])
print ' REQUIRE(dghpsi[%d][4] == Approx(%15.10g));' % (i, mo_gh[i][4])
print ' REQUIRE(dghpsi[%d][5] == Approx(%15.10g));' % (i, mo_gh[i][5])
print ' REQUIRE(dghpsi[%d][6] == Approx(%15.10g));' % (i, mo_gh[i][6])
print ' REQUIRE(dghpsi[%d][7] == Approx(%15.10g));' % (i, mo_gh[i][7])
print ' REQUIRE(dghpsi[%d][8] == Approx(%15.10g));' % (i, mo_gh[i][8])
print ' REQUIRE(dghpsi[%d][9] == Approx(%15.10g));' % (i, mo_gh[i][9])
print ''
def gen_wavefunction_plus_correction_for_ethanol():
pos_list, elements = read_qmcpack.read_structure_file("ethanol.structure.xml")
basis_sets, MO_matrix = read_qmcpack.parse_qmc_wf("ethanol.wfnoj.xml", elements)
gtos = gaussian_orbitals.GTO_centers(pos_list, elements, basis_sets)
phi_list, eta_list, C_no_S = split_by_angular_momentum(pos_list, elements, basis_sets, MO_matrix)
spo_name, cusp_data = read_qmcpack.read_cusp_correction_file("ethanol_downdet.cuspInfo.xml")
cusp = CuspCorrection(cusp_data, pos_list, gtos, phi_list)
# Bulk of the MO's - the non-cusp corrected parts
other_mo = gaussian_orbitals.MolecularOrbital(gtos, C_no_S)
# set electron position so it falls within rc near O atom
xyzgrid = [(-2.1, 0.5, 0.0)]
#xyzgrid = [(0.0, 0.0, 0.0)]
iat = 0
for i,epos in enumerate(xyzgrid):
mo_v, mo_g, mo_l = other_mo.eval_vgl(epos[0], epos[1], epos[2])
for mo_idx in range(13):
final_v = mo_v[mo_idx]
final_g = mo_g[mo_idx, :]
final_l = mo_l[mo_idx]
for center_idx in range(9):
cv,cg,cl = cusp.compute_cusp_correction(center_idx, mo_idx, epos)
final_v += cv
final_g += cg
final_l += cl
print(' # MO %d'%mo_idx)
print(' REQUIRE(values[%d] == Approx(%.10f));'%(mo_idx,final_v))
print(' REQUIRE(dpsi[%d][0] == Approx(%.10f));'%(mo_idx, final_g[0]))
print(' REQUIRE(dpsi[%d][1] == Approx(%.10f));'%(mo_idx, final_g[1]))
print(' REQUIRE(dpsi[%d][2] == Approx(%.10f));'%(mo_idx, final_g[2]))
print(' REQUIRE(d2psi[%d] == Approx(%.10f));'%(mo_idx,final_l))
print()
print(' REQUIRE(all_values[%d][%d] == Approx(%.10f));'%(iat, mo_idx, final_v))
print(' REQUIRE(all_grad[%d][%d][0] == Approx(%.10f));'%(iat, mo_idx, final_g[0]))
print(' REQUIRE(all_grad[%d][%d][1] == Approx(%.10f));'%(iat, mo_idx, final_g[1]))
print(' REQUIRE(all_grad[%d][%d][2] == Approx(%.10f));'%(iat, mo_idx, final_g[2]))
print(' REQUIRE(all_lap[%d][%d] == Approx(%.10f));'%(iat, mo_idx, final_l))
print()
def read_cusp_correction_file(fname):
tree = ET.parse(fname)
return parse_cusp_correction(tree)
if __name__ == '__main__':
# For He
basis_set, MO_matrix = parse_qmc_wf('he_sto3g.wfj.xml', ['He'])
# For HCN - need ion positions as well
pos_list, elements = read_structure_file("hcn.structure.xml")
basis_sets, MO_matrix = parse_qmc_wf('hcn.wfnoj.xml', elements)
gtos = gaussian_orbitals.GTO_centers(pos_list, elements, basis_sets)
atomic_orbs = gtos.eval_v(1.0, 0.0, 0.0)
print np.dot(MO_matrix, atomic_orbs)
#ccp = read_cusp_correction_file("hcn_downdet.cuspInfo.xml")
#print ccp
# Ethanol - example with repeated atoms
pos_list, elements = read_structure_file("ethanol.structure.xml")
print len(pos_list), pos_list
print 'elements', elements
basis_sets, MO_matrix = parse_qmc_wf("ethanol.wfnoj.xml", elements)
print MO_matrix.shape
def gen_HCN_force():
basis_sets, MO_matrix = read_qmcpack.parse_qmc_wf("hcn.wfnoj.xml",
['N', 'C', 'H'])
ionpos, elements = read_qmcpack.read_structure_file("hcn.structure.xml")
pos = [0.02, -0.1, 0.05]
delta = 1.0e-6
deltainv = 1.0 / delta
Natom = ionpos.shape[0]
norb = 7
print ' // Generated from gen_mo.py for position %s' % str(pos)
for iat in xrange(0, Natom):
for idim in xrange(0, 3):
ionpos_p = np.array(ionpos)
ionpos_m = np.array(ionpos)
ionpos_p[iat][idim] += delta
ionpos_m[iat][idim] -= delta
gtos_p = gaussian_orbitals.GTO_centers(ionpos_p, elements,
basis_sets)
gtos_m = gaussian_orbitals.GTO_centers(ionpos_m, elements,
basis_sets)
atomic_orbs_p = gtos_p.eval_v(*pos)
atomic_orbs_m = gtos_m.eval_v(*pos)
mol_orbs_p = np.dot(MO_matrix, atomic_orbs_p)
mol_orbs_m = np.dot(MO_matrix, atomic_orbs_m)
v_p, g_p, l_p = gtos_p.eval_vgl(*pos)
mo_v_p = np.dot(MO_matrix, v_p)
mo_g_p = np.dot(MO_matrix, g_p)
mo_l_p = np.dot(MO_matrix, l_p)
v_m, g_m, l_m = gtos_m.eval_vgl(*pos)
mo_v_m = np.dot(MO_matrix, v_m)
mo_g_m = np.dot(MO_matrix, g_m)
mo_l_m = np.dot(MO_matrix, l_m)
dmo_v = 0.5 * deltainv * (mo_v_p - mo_v_m)
dmo_g = 0.5 * deltainv * (mo_g_p - mo_g_m)
dmo_l = 0.5 * deltainv * (mo_l_p - mo_l_m)
print "//============== Ion ", iat, " Component ", idim, "==================="
for iorb in xrange(0, norb):
print ' REQUIRE( dionpsi[0][%d][%d] == Approx(%15.10g) ); ' % (
iorb, idim, dmo_v[iorb])
print ' REQUIRE( diongradpsi[0][%d](%d,0) == Approx(%15.10g) ); ' % (
iorb, idim, dmo_g[iorb][0])
print ' REQUIRE( diongradpsi[0][%d](%d,1) == Approx(%15.10g) ); ' % (
iorb, idim, dmo_g[iorb][1])
print ' REQUIRE( diongradpsi[0][%d](%d,2) == Approx(%15.10g) ); ' % (
iorb, idim, dmo_g[iorb][2])
print ' REQUIRE( dionlaplpsi[0][%d][%d] == Approx(%15.10g) ); ' % (
iorb, idim, dmo_l[iorb])
print ' // Generated from gen_mo.py for position %s' % str(pos)