def test_grad(self):
coords = [(0.0, 0.1, 0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges).run()
hfg = itrf.mm_charge_grad(grad.RHF(mf), coords, charges).run()
self.assertAlmostEqual(numpy.linalg.norm(hfg.de), 26.978089280783195,
9)
mfs = mf.as_scanner()
e1 = mfs('''
H -0.00000000 -0.000 0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
e2 = mfs('''
H -0.00000000 -0.000 -0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
self.assertAlmostEqual((e1 - e2) / 0.002 * lib.param.BOHR,
hfg.de[0, 2], 5)
bak = pyscf.DEBUG
pyscf.DEBUG = 1
ref = hfg.get_hcore()
pyscf.DEBUG = 0
v = hfg.get_hcore()
self.assertAlmostEqual(abs(ref - v).max(), 0, 12)
pyscf.DEBUG = bak
def test_grad(self):
coords = [(0.0,0.1,0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges).run()
hfg = itrf.mm_charge_grad(grad.RHF(mf), coords, charges).run()
self.assertAlmostEqual(numpy.linalg.norm(hfg.de), 26.978089280783195, 9)
mfs = mf.as_scanner()
e1 = mfs('''
H -0.00000000 -0.000 0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
e2 = mfs('''
H -0.00000000 -0.000 -0.001
H -0.00000000 -0.000 1.
H -0.00000000 -0.82 0.
H -0.91000000 -0.020 0.
''')
self.assertAlmostEqual((e1 - e2)/0.002*lib.param.BOHR, hfg.de[0,2], 5)
bak = pyscf.DEBUG
pyscf.DEBUG = 1
ref = hfg.get_hcore()
pyscf.DEBUG = 0
v = hfg.get_hcore()
self.assertAlmostEqual(abs(ref-v).max(), 0, 12)
pyscf.DEBUG = bak
def test_hcore_cart(self):
coords = [(0.0, 0.1, 0.0)]
charges = [1.00]
mol = gto.M(verbose=0,
atom='''C 0.000 -0.300 0.2
Ne 0.310 0.820 0.1''',
basis='cc-pvdz',
cart=True)
mf = itrf.mm_charge(scf.RHF(mol), coords, charges)
h = mf.get_hcore()
self.assertAlmostEqual(lib.finger(h), -147.92831183612765, 9)
h = mf.nuc_grad_method().get_hcore()
self.assertEqual(h.shape, (3, 30, 30))
self.assertAlmostEqual(lib.finger(h), -178.29768724184771, 9)
def test_hcore_cart(self):
coords = [(0.0,0.1,0.0)]
charges = [1.00]
mol = gto.M(
verbose = 0,
atom = '''C 0.000 -0.300 0.2
Ne 0.310 0.820 0.1''',
basis = 'cc-pvdz',
cart = True)
mf = itrf.mm_charge(scf.RHF(mol), coords, charges)
h = mf.get_hcore()
self.assertAlmostEqual(lib.finger(h), -147.92831183612765, 9)
h = mf.nuc_grad_method().get_hcore()
self.assertEqual(h.shape, (3,30,30))
self.assertAlmostEqual(lib.finger(h), -178.29768724184771, 9)
def test_energy(self):
coords = [(0.0,0.1,0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges)
self.assertAlmostEqual(mf.kernel(), 2.0042702433049024, 9)
def test_energy(self):
coords = [(0.0, 0.1, 0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges)
self.assertAlmostEqual(mf.kernel(), 2.0042702433049024, 9)
def test_grad(self):
coords = [(0.0,0.1,0.0)]
charges = [1.00]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges).run()
hfg = itrf.mm_charge_grad(grad.RHF(mf), coords, charges).run()
self.assertAlmostEqual(numpy.linalg.norm(hfg.de), 30.316453059873059, 9)
#!/usr/bin/python
from pyscf import gto, scf
from pyscf.qmmm import itrf
mol = gto.Mole()
mol.atom = ''' O 0.00000000 0.00000000 -0.11081188
H -0.00000000 -0.84695236 0.59109389
H -0.00000000 0.89830571 0.52404783 '''
mol.basis = 'cc-pvdz'
mol.verbose = 4
mol.build()
coords = [(0.5, 0.6, 0.8)]
charges = [-0.5]
mf = itrf.mm_charge(scf.RHF(mol), coords, charges)
mf = scf.RHF(mol)
ehf = mf.kernel()
