def test_finite_diff_uks_eph(self):
mf = dft.UKS(mol)
mf.grids.level = 6
mf.grids.build()
mf.xc = 'b3lyp'
mf.conv_tol = 1e-16
mf.conv_tol_grad = 1e-10
mf.kernel()
grad = mf.nuc_grad_method().kernel()
self.assertTrue(abs(grad).max() < 1e-5)
mat, omega = eph_fd.kernel(mf)
matmo, _ = eph_fd.kernel(mf, mo_rep=True)
myeph = uks.EPH(mf)
eph, _ = myeph.kernel()
ephmo, _ = myeph.kernel(mo_rep=True)
for i in range(len(omega)):
self.assertTrue(
min(np.linalg.norm(eph[:, i] - mat[:, i]),
np.linalg.norm(eph[:, i] + mat[:, i])) < 1e-5)
self.assertTrue(
min(
abs(eph[:, i] - mat[:, i]).max(),
abs(eph[:, i] + mat[:, i]).max()) < 1e-5)
self.assertTrue(
min(np.linalg.norm(ephmo[:, i] - matmo[:, i]),
np.linalg.norm(ephmo[:, i] + matmo[:, i])) < 1e-5)
self.assertTrue(
min(
abs(ephmo[:, i] - matmo[:, i]).max(),
abs(ephmo[:, i] + matmo[:, i]).max()) < 1e-5)
def test_finite_diff_rks_eph(self):
mf = dft.RKS(mol)
mf.chkfile = tempfile.NamedTemporaryFile().name
mf.grids.level = 3
mf.xc = 'b3lyp'
mf.conv_tol = 1e-14
mf.conv_tol_grad = 1e-9
mf.kernel()
grad = mf.nuc_grad_method().kernel()
self.assertTrue(abs(grad).max() < 1e-5)
mat, omega = eph_fd.kernel(mf)
matmo, _ = eph_fd.kernel(mf, mo_rep=True)
myeph = rks.EPH(mf)
eph, _ = myeph.kernel()
ephmo, _ = myeph.kernel(mo_rep=True)
for i in range(len(omega)):
self.assertTrue(
min(np.linalg.norm(eph[i] -
mat[i]), np.linalg.norm(eph[i] +
mat[i])) < 1e-5)
self.assertTrue(
min(abs(eph[i] - mat[i]).max(),
abs(eph[i] + mat[i]).max()) < 1e-5)
self.assertTrue(
min(np.linalg.norm(ephmo[i] - matmo[i]),
np.linalg.norm(ephmo[i] + matmo[i])) < 1e-5)
self.assertTrue(
min(
abs(ephmo[i] - matmo[i]).max(),
abs(ephmo[i] + matmo[i]).max()) < 1e-5)
def test_finite_diff_rhf_eph(self):
mf = scf.RHF(mol)
mf.conv_tol = 1e-16
mf.conv_tol_grad = 1e-10
mf.kernel()
grad = mf.nuc_grad_method().kernel()
self.assertTrue(abs(grad).max() < 1e-5)
mat, omega = eph_fd.kernel(mf)
matmo, _ = eph_fd.kernel(mf, mo_rep=True)
myeph = rhf.EPH(mf)
eph, _ = myeph.kernel()
ephmo, _ = myeph.kernel(mo_rep=True)
for i in range(len(omega)):
self.assertTrue(
min(np.linalg.norm(eph[i] -
mat[i]), np.linalg.norm(eph[i] +
mat[i])) < 1e-5)
self.assertTrue(
min(abs(eph[i] - mat[i]).max(),
abs(eph[i] + mat[i]).max()) < 1e-5)
self.assertTrue(
min(np.linalg.norm(ephmo[i] - matmo[i]),
np.linalg.norm(ephmo[i] + matmo[i])) < 1e-5)
self.assertTrue(
min(
abs(ephmo[i] - matmo[i]).max(),
abs(ephmo[i] + matmo[i]).max()) < 1e-5)
def test_finite_diff_uhf_eph(self):
mf = scf.UHF(mol)
mf.chkfile = tempfile.NamedTemporaryFile().name
mf.conv_tol = 1e-14
mf.conv_tol_grad = 1e-9
mf.kernel()
grad = mf.nuc_grad_method().kernel()
self.assertTrue(abs(grad).max() < 1e-5)
mat, omega = eph_fd.kernel(mf)
matmo, _ = eph_fd.kernel(mf, mo_rep=True)
myeph = uhf.EPH(mf)
eph, _ = myeph.kernel()
ephmo, _ = myeph.kernel(mo_rep=True)
for i in range(len(omega)):
self.assertTrue(
min(np.linalg.norm(eph[:, i] - mat[:, i]),
np.linalg.norm(eph[:, i] + mat[:, i])) < 1e-5)
self.assertTrue(
min(
abs(eph[:, i] - mat[:, i]).max(),
abs(eph[:, i] + mat[:, i]).max()) < 1e-5)
self.assertTrue(
min(np.linalg.norm(ephmo[:, i] - matmo[:, i]),
np.linalg.norm(ephmo[:, i] + matmo[:, i])) < 1e-5)
self.assertTrue(
min(
abs(ephmo[:, i] - matmo[:, i]).max(),
abs(ephmo[:, i] + matmo[:, i]).max()) < 1e-5)
#!/usr/bin/env python
'''
A simple example to run EPH calculation using finite difference.
'''
from pyscf import gto, dft
from pyscf.eph.eph_fd import kernel
mol = gto.M(atom='N 0 0 0; N 0 0 2.100825',
basis='def2-svp',
verbose=4,
unit="bohr")
# this is a pre-computed relaxed molecule
# for geometry relaxation, refer to pyscf/example/geomopt
mf = dft.RKS(mol, xc='pbe,pbe')
mf.run()
grad = mf.nuc_grad_method().kernel()
assert (abs(grad).sum() < 1e-5) # making sure the geometry is relaxed
mat, omega = kernel(mf, disp=1e-4, mo_rep=True)
print(mat.shape, omega)