def test_MP2_hess(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import GradMP2
H2O2 = Mol_H2O2()
config = {
"scf_eng": H2O2.hf_eng,
"rotation": True,
}
grad_helper = GradMP2(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
}
helper = HessMP2(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(E_2, formchk.hessian(), atol=1e-6, rtol=1e-4))
def valid_assert(config, resource_path):
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
helper = DipoleSCF(config)
assert (np.allclose(helper.E_1, helper.scf_eng.dip_moment(unit="A.U."), atol=1e-6, rtol=1e-4))
formchk = FormchkInterface(resource_filename("pyxdh", resource_path))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6, rtol=1e-4))
def test_u_uhf_hess(self):
scf_eng = scf.UHF(self.mol); scf_eng.conv_tol = 1e-12; scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 256; scf_eng.run()
gradh = GradUSCF({"scf_eng": scf_eng})
hessh = HessUSCF({"deriv_A": gradh})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-HF-freq.fchk"))
assert np.allclose(hessh.E_2, formchk.hessian(), atol=1e-6, rtol=1e-4)
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_MP2_polar(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import DipoleMP2
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
dip_helper = DipoleMP2(config)
config = {
"deriv_A": dip_helper,
"deriv_B": dip_helper,
}
helper = PolarMP2(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(-E_2,
formchk.polarizability(),
atol=1e-6,
rtol=1e-4))
def test_B3LYP_hess(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import GradSCF
H2O2 = Mol_H2O2()
grids_cphf = H2O2.gen_grids(50, 194)
config = {
"scf_eng": H2O2.gga_eng
}
grad_helper = GradSCF(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
"cphf_grids": grids_cphf
}
helper = HessSCF(config)
E_2 = helper.E_2
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/H2O2-B3LYP-freq.fchk"))
assert(np.allclose(
E_2, formchk.hessian(),
atol=1e-5, rtol=1e-4
))
def test_B2PLYP_hess(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import GradMP2
import pickle
H2O2 = Mol_H2O2(xc="0.53*HF + 0.47*B88, 0.73*LYP")
config = {"scf_eng": H2O2.gga_eng, "cc": 0.27}
grad_helper = GradMP2(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
}
helper = HessMP2(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(E_2, formchk.hessian(), atol=1e-5, rtol=1e-4))
with open(
resource_filename(
"pyxdh",
"Validation/numerical_deriv/mp2_hessian_b2plyp.dat"),
"rb") as f:
ref_hess = pickle.load(f)["hess"]
assert (np.allclose(E_2, ref_hess, atol=1e-6, rtol=1e-4))
def test_B2PLYP_polar(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import DipoleMP2
H2O2 = Mol_H2O2(xc="0.53*HF + 0.47*B88, 0.73*LYP")
grids_cphf = H2O2.gen_grids(50, 194)
config = {
"scf_eng": H2O2.gga_eng,
"cc": 0.27,
"cphf_grids": grids_cphf
}
dip_helper = DipoleMP2(config)
config = {"deriv_A": dip_helper, "deriv_B": dip_helper}
helper = PolarMP2(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(-E_2,
formchk.polarizability(),
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_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 valid_assert(dip_helper, grad_helper, resource_path):
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
dipderiv_config = {"deriv_A": dip_helper, "deriv_B": grad_helper}
helper = DipDerivSCF(dipderiv_config)
E_2 = helper.E_2
formchk = FormchkInterface(resource_filename("pyxdh", resource_path))
assert (np.allclose(E_2.T, formchk.dipolederiv(), atol=1e-6,
rtol=1e-4))
def test_UMP2_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
CH3 = Mol_CH3()
helper = GradUMP2({"scf_eng": CH3.hf_eng.run(), "cphf_tol": 1e-10})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-MP2-freq.fchk"))
assert(np.allclose(helper.E_1, formchk.grad(), atol=1e-5, 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_u_uhf_dipole(self):
scf_eng = scf.UHF(self.mol)
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 128
scf_eng.run()
diph = DipoleUSCF({"scf_eng": scf_eng})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/CH3-HF-freq.fchk"))
# ASSERT: dipole - Gaussian
assert np.allclose(diph.E_1, formchk.dipole(), atol=1e-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)
def test_UB3LYP_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
CH3 = Mol_CH3()
helper = GradUSCF({"scf_eng": CH3.gga_eng})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-B3LYP-freq.fchk"))
assert(np.allclose(helper.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_rhf_polar(self):
scf_eng = scf.RHF(self.mol).run()
diph = DipoleSCF({"scf_eng": scf_eng})
polh = PolarSCF({"deriv_A": diph})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/NH3-HF-freq.fchk"))
# ASSERT: polar - Gaussian
assert np.allclose(-polh.E_2,
formchk.polarizability(),
atol=1e-6,
rtol=1e-4)
def test_UB2PLYP_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
CH3 = Mol_CH3(xc="0.53*HF + 0.47*B88, 0.73*LYP")
grids_cphf = CH3.gen_grids(atom_grid=(50, 194))
helper = GradUMP2({"scf_eng": CH3.gga_eng.run(), "cphf_tol": 1e-10, "cc": 0.27, "cphf_grids": grids_cphf})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-B2PLYP-freq.fchk"))
assert(np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
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_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_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 valid_assert(dip_config, resource_path):
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import DipoleSCF
dip_helper = DipoleSCF(dip_config)
polar_config = {"deriv_A": dip_helper, "deriv_B": dip_helper}
helper = PolarSCF(polar_config)
E_2 = helper.E_2
formchk = FormchkInterface(resource_filename("pyxdh", resource_path))
assert (np.allclose(-E_2,
formchk.polarizability(),
atol=1e-6,
rtol=1e-4))
def test_u_uhf_polar(self):
scf_eng = scf.UHF(self.mol)
scf_eng.conv_tol = 1e-12
scf_eng.conv_tol_grad = 1e-10
scf_eng.max_cycle = 256
scf_eng.run()
diph = DipoleUSCF({"scf_eng": scf_eng})
polh = PolarUSCF({"deriv_A": diph})
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/CH3-HF-freq.fchk"))
assert np.allclose(-polh.E_2,
formchk.polarizability(),
atol=1e-6,
rtol=1e-4)
def test_r_b3lyp_polar(self):
scf_eng = dft.RKS(self.mol, xc="B3LYPg")
scf_eng.grids = self.grids
scf_eng.run()
diph = DipoleSCF({"scf_eng": scf_eng, "cphf_grids": self.grids_cphf})
polh = PolarSCF({"deriv_A": diph})
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/NH3-B3LYP-freq.fchk"))
# ASSERT: polar - Gaussian
assert np.allclose(-polh.E_2,
formchk.polarizability(),
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_UXYGJOS_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
CH3_sc = Mol_CH3(xc="B3LYPg")
CH3_nc = Mol_CH3(xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
grids_cphf = CH3_sc.gen_grids(atom_grid=(50, 194))
helper = GradUXDH({"scf_eng": CH3_sc.gga_eng, "nc_eng": CH3_nc.gga_eng,
"cc": 0.4364, "ss": 0.,
"cphf_tol": 1e-10, "cphf_grids": grids_cphf})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-XYGJOS-force.fchk"))
assert(np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
def test_UXYG3_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
CH3_sc = Mol_CH3(xc="B3LYPg")
CH3_nc = Mol_CH3(xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
grids_cphf = CH3_sc.gen_grids(atom_grid=(50, 194))
helper = GradUXDH({
"scf_eng": CH3_sc.gga_eng, "nc_eng": CH3_nc.gga_eng,
"cc": 0.3211,
"cphf_tol": 1e-10, "cphf_grids": grids_cphf})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/CH3-XYG3-force.fchk"))
assert(np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
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_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)