def test_ecp_hess(self):
mol = gto.M(atom='Cu 0 0 0; H 0 0 1.5', basis='lanl2dz',
ecp={'Cu':'lanl2dz'}, verbose=0)
mf = scf.RHF(mol).run(conv_tol=1e-14)
hess = hessian.RHF(mf).kernel()
self.assertAlmostEqual(lib.finger(hess), -0.20927804440983355, 6)
mfs = mf.nuc_grad_method().as_scanner()
e1 = mfs(mol.set_geom_('Cu 0 0 0.001; H 0 0 1.5'))[1]
e2 = mfs(mol.set_geom_('Cu 0 0 -0.001; H 0 0 1.5'))[1]
self.assertAlmostEqual(abs(hess[0,:,2] - (e1-e2)/0.002*lib.param.BOHR).max(), 0, 5)
def initialization_pyscf(self):
self.scf_eng = scf.RHF(self.mol)
self.scf_eng.conv_tol = 1e-11
self.scf_eng.conv_tol_grad = 1e-9
self.scf_eng.max_cycle = 100
if self.init_scf:
self.eng = self.scf_eng.kernel()
if not self.scf_eng.converged:
warnings.warn("SCF not converged!")
self.scf_grad = grad.RHF(self.scf_eng)
self.scf_hess = hessian.RHF(self.scf_eng)
return
def test_finite_diff_rhf_hess(self):
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
e0 = mf.kernel()
hess = hessian.RHF(mf).kernel()
self.assertAlmostEqual(lib.finger(hess), -0.7816353049729151, 6)
g_scanner = mf.nuc_grad_method().as_scanner()
pmol = mol.copy()
e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
self.assertAlmostEqual(abs(hess[0,:,2] - (e1-e2)/2e-4*lib.param.BOHR).max(), 0, 4)
def initialization_pyscf(self):
if (self.scf_eng.mo_coeff is NotImplemented or self.scf_eng.mo_coeff is None) and self.init_scf:
self.scf_eng.kernel()
if not self.scf_eng.converged:
warnings.warn("SCF not converged!")
if isinstance(self.scf_eng, dft.rks.RKS):
self.xc = self.scf_eng.xc
self.grids = self.scf_eng.grids
self.xc_type = dft.libxc.xc_type(self.xc)
self.cx = dft.numint.NumInt().hybrid_coeff(self.xc)
self.scf_grad = grad.rks.Gradients(self.scf_eng)
self.scf_hess = hessian.rks.Hessian(self.scf_eng)
else:
self.scf_grad = grad.RHF(self.scf_eng)
self.scf_hess = hessian.RHF(self.scf_eng)
return
def test_finite_diff_x2c_rhf_hess(self):
mf = scf.RHF(mol).x2c()
mf.conv_tol = 1e-14
e0 = mf.kernel()
hess = hessian.RHF(mf).kernel()
self.assertAlmostEqual(lib.finger(hess), -0.7800532318291435, 6)
g_scanner = mf.nuc_grad_method().as_scanner()
pmol = mol.copy()
e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
self.assertAlmostEqual(abs(hess[0,:,2] - (e1-e2)/2e-4*lib.param.BOHR).max(), 0, 4)
# e1 = g_scanner(pmol.set_geom_('O 0. 0.0001 0.; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
# e2 = g_scanner(pmol.set_geom_('O 0. -.0001 0.; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
# self.assertAlmostEqual(abs(hess[0,:,1] - (e1-e2)/2e-4*lib.param.BOHR).max(), 0, 4)
#
# e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.; 1 0. -0.7571 0.587; 1 0. 0.757 0.587'))[1]
# e2 = g_scanner(pmol.set_geom_('O 0. 0. 0.; 1 0. -0.7569 0.587; 1 0. 0.757 0.587'))[1]
# self.assertAlmostEqual(abs(hess[1,:,1] - (e2-e1)/2e-4*lib.param.BOHR).max(), 0, 4)
e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.; 1 0. -0.757 0.5871; 1 0. 0.757 0.587'))[1]
e2 = g_scanner(pmol.set_geom_('O 0. 0. 0.; 1 0. -0.757 0.5869; 1 0. 0.757 0.587'))[1]
self.assertAlmostEqual(abs(hess[1,:,2] - (e1-e2)/2e-4*lib.param.BOHR).max(), 0, 4)
dump('Reduced mass [au] %s\n' % inline(r_mass, col0, col1))
dump('Force const [Dyne/A] %s\n' % inline(force, col0, col1))
dump('Char temp [K] %s\n' % inline(vib_t, col0, col1))
#dump('IR\n')
#dump('Raman\n')
dump('Normal mode %s\n' % (' x y z' *
(col1 - col0)))
for j, at in enumerate(symbols):
dump(' %4d%4s %s\n' %
(j, at, mode_inline(j, col0, col1)))
if __name__ == '__main__':
from pyscf import gto
from pyscf import hessian
mol = gto.M(atom='O 0 0 0; H 0 .757 .587; H 0 -.757 .587')
mass = mol.atom_mass_list(isotope_avg=True)
r = mol.atom_coords() - numpy.random.random((1, 3))
print(rotation_const(mass, r, 'GHz'))
print(rotation_const(mass[1:], r[1:], 'GHz'))
print(rotation_const(mass[2:], r[2:], 'GHz'))
mf = mol.apply('HF').run()
hess = hessian.RHF(mf).kernel()
results = harmonic_analysis(mol, hess)
dump_normal_mode(mol, results)
results = thermo(mf, results['freq_au'], 298.15, 101325)
dump_thermo(mol, results)
O 0.0 0.0 0.0
O 0.0 0.0 1.5
H 1.0 0.0 0.0
H 0.0 1.0 1.5
"""
mol.basis = "6-31G"
mol.build()
scf_eng = scf.RHF(mol)
scf_eng.kernel()
my_hess = my_hess_elec(scf_eng) + my_hess_nuc(scf_eng)
from pyscf import hessian
scf_hess = hessian.RHF(scf_eng)
pyscf_hess = scf_hess.kernel()
print("Hessian correct: ", np.allclose(my_hess, pyscf_hess))
import time
time0 = time.time()
[my_hess_elec(scf_eng) + my_hess_nuc(scf_eng) for i in range(5)]
time1 = time.time()
print("Average time for my_hess: ", (time1 - time0) / 5)
time0 = time.time()
[scf_hess.kernel() for i in range(5)]
time1 = time.time()
print("Average time for pyscf.hessian: ", (time1 - time0) / 5)
