def dipole_generator(component, interval):
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1",
basis="6-31G",
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
scf_eng = scf.RHF(mol)
scf_eng.conv_tol_grad = 1e-8
nc_eng = dft.RKS(mol, xc="B3LYPg")
nc_eng.grids = grids
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
scf_eng.get_hcore = get_hcore
nc_eng.get_hcore = get_hcore
scf_eng.run()
diph = DipoleNCDFT({
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cphf_tol": 1e-10
})
return diph.E_1
def __init__(self, datafile):
self.verbose = logger.NOTE
self.stdout = sys.stdout
self.max_memory = lib.param.MAX_MEMORY
self.chkfile = datafile
self.scratch = lib.param.TMPDIR
self.nthreads = lib.num_threads()
self.non0tab = False
self.corr = False
self.occdrop = 1e-6
self.chf = 0.0
self.small_rho_cutoff = 1e-6
self.prune = False
##################################################
# don't modify the following attributes, they are not input options
self.mol = lib.chkfile.load_mol(self.chkfile)
self.grids = dft.Grids(self.mol)
self.frevol = None
self.rdm1 = None
self.nocc = None
self.mo_coeff = None
self.mo_occ = None
self.natm = None
self.coords = None
self.charges = None
self.nelectron = None
self.charge = None
self.spin = None
self.nprims = None
self.nmo = None
self._keys = set(self.__dict__.keys())
def gen_grids(self, rad_points=99, sph_points=590, atom_grid=None):
grids = dft.Grids(self.mol)
grids.atom_grid = atom_grid
if atom_grid is None:
grids.atom_grid = (rad_points, sph_points)
grids.radi_method = dft.gauss_chebyshev
grids.becke_scheme = dft.gen_grid.stratmann
grids.build()
return grids
def gen_grids(self, atom_grid=None):
grids = dft.Grids(self.mol)
grids.atom_grid = atom_grid
if atom_grid is None:
grids.atom_grid = (99, 590)
grids.radi_method = dft.gauss_chebyshev
grids.becke_scheme = dft.gen_grid.stratmann
grids.build()
return grids
def mol_to_eng(mol):
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
scf_eng = scf.RHF(mol)
scf_eng.conv_tol_grad = 1e-8
scf_eng.run()
nc_eng = dft.RKS(mol, xc="B3LYPg")
nc_eng.grids = grids
return nc_eng.energy_tot(dm=scf_eng.make_rdm1())
def mol_to_grad(mol):
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
scf_eng = scf.RHF(mol)
scf_eng.conv_tol = 1e-12
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 256
scf_eng.run()
nc_eng = dft.RKS(mol, xc="B3LYPg")
nc_eng.grids = grids
gradh = GradNCDFT({"scf_eng": scf_eng, "nc_eng": nc_eng})
return gradh.E_1
def gga_eng(self):
if self._gga_eng is not NotImplemented:
return self._gga_eng
grids = dft.Grids(self.mol)
grids.atom_grid = (99, 590)
grids.becke_scheme = dft.gen_grid.stratmann
grids.build()
gga_eng = scf.RKS(self.mol)
gga_eng.grids = grids
gga_eng.conv_tol = 1e-11
gga_eng.conv_tol_grad = 1e-9
gga_eng.max_cycle = 100
gga_eng.xc = self.xc
self._gga_eng = gga_eng
return self._gga_eng
def dipole_generator(component, interval):
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1",
basis="6-31G",
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
scf_eng = scf.RHF(mol)
nc_eng = dft.RKS(mol, xc="B3LYPg")
nc_eng.grids = grids
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
scf_eng.get_hcore = get_hcore
nc_eng.get_hcore = get_hcore
scf_eng.run()
return nc_eng.energy_tot(dm=scf_eng.make_rdm1())
#!/usr/bin/env python
'''
Show the functionality of the mode option.
'''
from pyscf import dft, gto
from var_mesh import var_mesh
mol = gto.M(atom='O 0 0 0; H 0 0 0.95691; H 0.95691 0 -0.23987')
mesh = dft.Grids(mol)
# Call var_mesh with the different mode options
print('mode=PySCF:')
var_mesh(mesh, mode='pyscf')
# If the code does not support different grids for different atom types, the
# precise option has no effect
print('\nmode=ERKALE:')
var_mesh(mesh, precise=True, mode='erkale')
print('\nmode=GAMESS:')
mesh = var_mesh(mesh, precise=False, mode='gamess')
# One can see, that the GAMESS grid differs from the PySCF grid
print('GAMESS grid: %s' % mesh.atom_grid)
class TestGradR:
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1", basis="6-31G", verbose=0).build()
grids = dft.Grids(mol); grids.atom_grid = (99, 590); grids.build()
grids_cphf = dft.Grids(mol); grids_cphf.atom_grid = (50, 194); grids_cphf.build()
def test_r_rhf_grad(self):
scf_eng = scf.RHF(self.mol).run()
scf_grad = scf_eng.Gradients().run()
gradh = GradSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-HF-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, scf_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=1e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, scf_grad.de, atol=1e-6, rtol=1e-4)
def test_r_b3lyp_grad(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg"); scf_eng.grids = self.grids; scf_eng.run()
scf_grad = scf_eng.Gradients().run()
gradh = GradSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-B3LYP-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, scf_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, scf_grad.de, atol=1e-6, rtol=1e-4)
def test_r_hfb3lyp_grad(self):
scf_eng = scf.RHF(self.mol).run()
nc_eng = dft.RKS(self.mol, xc="B3LYPg")
nc_eng.grids = self.grids
gradh = GradNCDFT({"scf_eng": scf_eng, "nc_eng": nc_eng})
with open(resource_filename("pyxdh", "Validation/numerical_deriv/NH3-HFB3LYP-grad.dat"), "rb") as f:
ref_grad = pickle.load(f).reshape(-1, 3)
# ASSERT: energy - theoretical
assert np.allclose(gradh.eng, nc_eng.energy_tot(dm=scf_eng.make_rdm1()))
# ASSERT: grad - numerical
assert np.allclose(gradh.E_1, ref_grad, atol=1e-6, rtol=1e-4)
def test_r_mp2_grad(self):
scf_eng = scf.RHF(self.mol).run()
mp2_eng = mp.MP2(scf_eng).run()
mp2_grad = mp2_eng.Gradients().run()
gradh = GradMP2({"scf_eng": scf_eng})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-MP2-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, mp2_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=1e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, mp2_grad.de, atol=1e-6, rtol=1e-4)
def test_r_b2plyp_grad(self):
scf_eng = dft.RKS(self.mol, xc="0.53*HF + 0.47*B88, 0.73*LYP"); scf_eng.grids = self.grids; scf_eng.run()
gradh = GradMP2({"scf_eng": scf_eng, "cc": 0.27, "cphf_grids": self.grids_cphf})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-B2PLYP-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=1e-6, rtol=1e-4)
def test_r_xyg3_grad(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg"); scf_eng.grids = self.grids; scf_eng.run()
nc_eng = dft.RKS(self.mol, xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP"); nc_eng.grids = self.grids
config = {"scf_eng": scf_eng, "nc_eng": nc_eng, "cc": 0.3211, "cphf_grids": self.grids_cphf}
gradh = GradXDH(config)
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-XYG3-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
def test_r_xygjos_grad(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg"); scf_eng.grids = self.grids; scf_eng.run()
nc_eng = dft.RKS(self.mol, xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP"); nc_eng.grids = self.grids
config = {"scf_eng": scf_eng, "nc_eng": nc_eng, "cc": 0.4364, "ss": 0., "cphf_grids": self.grids_cphf}
gradh = GradXDH(config)
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-XYGJOS-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
class TestHessR:
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1",
basis="6-31G",
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
grids_cphf = dft.Grids(mol)
grids_cphf.atom_grid = (50, 194)
grids_cphf.build()
def test_r_rhf_hess(self):
scf_eng = scf.RHF(self.mol).run()
scf_hess = scf_eng.Hessian().run()
gradh = GradSCF({"scf_eng": scf_eng})
hessh = HessSCF({"deriv_A": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/NH3-HF-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(hessh.E_2, formchk.hessian(), atol=1e-6, rtol=1e-4)
# ASSERT: hessian - PySCF
assert np.allclose(hessh.E_2,
scf_hess.de.swapaxes(-2, -3).reshape(
(-1, self.mol.natm * 3)),
atol=1e-6,
rtol=1e-4)
def test_r_b3lyp_hess(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
scf_hess = scf_eng.Hessian().run()
gradh = GradSCF({"scf_eng": scf_eng, "cphf_grids": self.grids_cphf})
hessh = HessSCF({"deriv_A": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-B3LYP-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(hessh.E_2, formchk.hessian(), atol=1e-5, rtol=2e-4)
# ASSERT: hessian - PySCF
assert np.allclose(hessh.E_2,
scf_hess.de.swapaxes(-2, -3).reshape(
(-1, self.mol.natm * 3)),
atol=1e-6,
rtol=1e-4)
def test_r_hfb3lyp_hess(self):
scf_eng = scf.RHF(self.mol)
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 256
scf_eng.run()
nc_eng = dft.RKS(self.mol, xc="B3LYPg")
nc_eng.grids = self.grids
gradh = GradNCDFT({"scf_eng": scf_eng, "nc_eng": nc_eng})
hessh = HessNCDFT({"deriv_A": gradh})
with open(
resource_filename(
"pyxdh",
"Validation/numerical_deriv/NH3-HFB3LYP-hess.dat"),
"rb") as f:
ref_hess = pickle.load(f)
# ASSERT: hessian - numerical
assert np.allclose(hessh.E_2,
ref_hess.reshape((-1, self.mol.natm * 3)),
atol=5e-6,
rtol=1e-4)
def test_r_mp2_hess(self):
scf_eng = scf.RHF(self.mol).run()
gradh = GradMP2({"scf_eng": scf_eng})
hessh = HessMP2({"deriv_A": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-MP2-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(hessh.E_2, formchk.hessian(), atol=1e-6, rtol=1e-4)
def test_r_xyg3_hess(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.3211,
"cphf_grids": self.grids_cphf
}
gradh = GradXDH(config)
hessh = HessXDH({"deriv_A": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYG3-freq.fchk"))
# ASSERT: hessian - Gaussian
np.allclose(hessh.E_2, formchk.hessian(), atol=2e-5, rtol=2e-4)
def test_r_xygjos_hess(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.4364,
"ss": 0.,
"cphf_grids": self.grids_cphf
}
gradh = GradXDH(config)
hessh = HessXDH({"deriv_A": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYGJOS-freq.fchk"))
# ASSERT: hessian - Gaussian
np.allclose(hessh.E_2, formchk.hessian(), atol=2e-5, rtol=2e-4)
class TestGradU:
mol = gto.Mole(atom="C 0. 0. 0.; H 1. 0. 0.; H 0. 2. 0.; H 0. 0. 1.5",
basis="6-31G",
spin=1,
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
grids_cphf = dft.Grids(mol)
grids_cphf.atom_grid = (50, 194)
grids_cphf.build()
def test_u_uhf_grad(self):
scf_eng = scf.UHF(self.mol).run()
scf_grad = scf_eng.Gradients().run()
gradh = GradUSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/CH3-HF-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, scf_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, scf_grad.de, atol=1e-6, rtol=1e-4)
def test_u_b3lyp_grad(self):
scf_eng = dft.UKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
scf_grad = scf_eng.Gradients().run()
gradh = GradUSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/CH3-B3LYP-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, scf_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, scf_grad.de, atol=1e-6, rtol=1e-4)
def test_u_hfb3lyp_grad(self):
scf_eng = scf.UHF(self.mol)
scf_eng.conv_tol_grad = 1e-10
scf_eng.run()
nc_eng = dft.UKS(self.mol, xc="B3LYPg")
nc_eng.grids = self.grids
gradh = GradUNCDFT({
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cphf_tol": 1e-15
})
with open(
resource_filename(
"pyxdh",
"Validation/numerical_deriv/CH3-HFB3LYP-grad.dat"),
"rb") as f:
ref_grad = pickle.load(f).reshape(-1, 3)
# ASSERT: energy - theoretical
assert np.allclose(gradh.eng,
nc_eng.energy_tot(dm=scf_eng.make_rdm1()))
# ASSERT: grad - numerical
assert np.allclose(gradh.E_1, ref_grad, atol=1e-6, rtol=1e-4)
def test_u_mp2_grad(self):
scf_eng = scf.UHF(self.mol)
scf_eng.conv_tol_grad = 1e-8
scf_eng.max_cycle = 128
scf_eng.run()
assert scf_eng.converged
mp2_eng = mp.MP2(scf_eng).run()
mp2_grad = mp2_eng.Gradients().run()
gradh = GradUMP2({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/CH3-MP2-freq.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: energy - PySCF
assert np.allclose(gradh.eng, mp2_eng.e_tot)
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=1e-6, rtol=1e-4)
# ASSERT: grad - PySCF
assert np.allclose(gradh.E_1, mp2_grad.de, atol=1e-6, rtol=1e-4)
def test_u_xyg3_grad(self):
scf_eng = dft.UKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 128
scf_eng.run()
nc_eng = dft.UKS(self.mol,
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.3211,
"cphf_grids": self.grids_cphf,
"cphf_tol": 1e-10
}
gradh = GradUXDH(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/CH3-XYG3-force.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
def test_u_xygjos_grad(self):
scf_eng = dft.UKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 128
scf_eng.run()
nc_eng = dft.UKS(self.mol,
xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.4364,
"ss": 0.,
"cphf_grids": self.grids_cphf
}
gradh = GradUXDH(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/CH3-XYGJOS-force.fchk"))
# ASSERT: energy - Gaussian
assert np.allclose(gradh.eng, formchk.total_energy())
# ASSERT: grad - Gaussian
assert np.allclose(gradh.E_1, formchk.grad(), atol=5e-6, rtol=1e-4)
mf._numint.libxc = dft.xcfun # PySCF-1.6.1 and newer supports the .TDDFT method to create a TDDFT # object after importing tdscf module. td = mf.TDDFT() print(td.kernel()[0] * 27.2114) # # Overwriting the relevant attributes of the ground state mf object, # the TDDFT calculations can be run with different XC, grids. # mf.xc = 'lda,vwn' mf.grids.set(level=2).kernel(with_non0tab=True) td = mf.TDDFT() print(td.kernel()[0] * 27.2114) # # Overwriting the ground state SCF object is unsafe. A better solution is to # create a new fake SCF object to hold different XC, grids parameters. # from pyscf.dft import numint mf = dft.RKS(mol).run(xc='pbe0') mf1 = copy.copy(mf) mf1.xc = 'lda,vwn' mf1.grids = dft.Grids(mol) mf1.grids.level = 2 mf1._numint = numint.NumInt() mf1._numint.libxc = dft.xcfun td = mf1.TDDFT() print(td.kernel()[0] * 27.2114)
class TestDipoleR:
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1",
basis="6-31G",
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
grids_cphf = dft.Grids(mol)
grids_cphf.atom_grid = (50, 194)
grids_cphf.build()
def test_r_rhf_dipole(self):
scf_eng = scf.RHF(self.mol).run()
diph = DipoleSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/NH3-HF-freq.fchk"))
# ASSERT: dipole - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
def test_r_b3lyp_dipole(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
diph = DipoleSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-B3LYP-freq.fchk"))
# ASSERT: dipole - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
def test_r_hfb3lyp_dipole(self):
scf_eng = scf.RHF(self.mol)
scf_eng.conv_tol_grad = 1e-8
scf_eng.run()
nc_eng = dft.RKS(self.mol, xc="B3LYPg")
nc_eng.grids = self.grids
diph = DipoleNCDFT({"scf_eng": scf_eng, "nc_eng": nc_eng})
with open(
resource_filename(
"pyxdh", "Validation/numerical_deriv/NH3-HFB3LYP-dip.dat"),
"rb") as f:
ref_dip = pickle.load(f)
# ASSERT: dipole - numerical
assert np.allclose(diph.E_1, ref_dip, atol=1e-6, rtol=1e-4)
def test_r_mp2_dipole(self):
scf_eng = scf.RHF(self.mol).run()
diph = DipoleMP2({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-MP2-freq.fchk"))
# ASSERT: dipole - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
def test_r_b2plyp_dipole(self):
scf_eng = dft.RKS(self.mol, xc="0.53*HF + 0.47*B88, 0.73*LYP")
scf_eng.grids = self.grids
scf_eng.run()
diph = DipoleMP2({
"scf_eng": scf_eng,
"cc": 0.27,
"cphf_grids": self.grids_cphf
})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-B2PLYP-freq.fchk"))
# ASSERT: dipole - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
def test_r_xyg3_dipole(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.3211,
"cphf_grids": self.grids_cphf
}
diph = DipoleXDH(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYG3-freq.fchk"))
# ASSERT: grad - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
def test_r_xygjos_dipole(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.4364,
"ss": 0.,
"cphf_grids": self.grids_cphf
}
diph = DipoleXDH(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYGJOS-freq.fchk"))
# ASSERT: grad - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4)
class TestDipDerivSCF:
mol = gto.Mole(atom="N 0. 0. 0.; H .9 0. 0.; H 0. 1. 0.; H 0. 0. 1.1",
basis="6-31G",
verbose=0).build()
grids = dft.Grids(mol)
grids.atom_grid = (99, 590)
grids.build()
grids_cphf = dft.Grids(mol)
grids_cphf.atom_grid = (50, 194)
grids_cphf.build()
def test_r_rhf_dipderiv(self):
scf_eng = scf.RHF(self.mol).run()
gradh = GradSCF({"scf_eng": scf_eng})
diph = DipoleSCF({"scf_eng": scf_eng})
ddh = DipDerivSCF({"deriv_A": diph, "deriv_B": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/NH3-HF-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(ddh.E_2.T,
formchk.dipolederiv(),
atol=5e-6,
rtol=2e-4)
def test_r_b3lyp_dipderiv(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
gradh = GradSCF({"scf_eng": scf_eng, "cphf_grids": self.grids_cphf})
diph = DipoleSCF({"scf_eng": scf_eng, "cphf_grids": self.grids_cphf})
ddh = DipDerivSCF({"deriv_A": diph, "deriv_B": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-B3LYP-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(ddh.E_2.T,
formchk.dipolederiv(),
atol=5e-6,
rtol=2e-4)
def test_r_mp2_dipderiv(self):
scf_eng = scf.RHF(self.mol).run()
gradh = GradMP2({"scf_eng": scf_eng})
diph = DipoleMP2({"scf_eng": scf_eng})
ddh = DipDerivMP2({"deriv_A": diph, "deriv_B": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-MP2-freq.fchk"))
# ASSERT: hessian - Gaussian
assert np.allclose(ddh.E_2.T,
formchk.dipolederiv(),
atol=5e-6,
rtol=2e-4)
def test_r_xyg3_dipderiv(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.3211,
"cphf_grids": self.grids_cphf
}
gradh = GradXDH(config)
diph = DipoleXDH(config)
ddh = DipDerivXDH({"deriv_A": diph, "deriv_B": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYG3-freq.fchk"))
# ASSERT: hessian - Gaussian
np.allclose(ddh.E_2.T, formchk.dipolederiv(), atol=5e-6, rtol=2e-4)
def test_r_xygjos_dipderiv(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
nc_eng = dft.RKS(self.mol,
xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
nc_eng.grids = self.grids
config = {
"scf_eng": scf_eng,
"nc_eng": nc_eng,
"cc": 0.4364,
"ss": 0.,
"cphf_grids": self.grids_cphf
}
gradh = GradXDH(config)
diph = DipoleXDH(config)
ddh = DipDerivXDH({"deriv_A": diph, "deriv_B": gradh})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-XYGJOS-freq.fchk"))
# ASSERT: hessian - Gaussian
np.allclose(ddh.E_2.T, formchk.dipolederiv(), atol=5e-6, rtol=2e-4)