def test_XYG3_dipderiv(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.DerivOnce import DipoleXDH, GradXDH
import pickle
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
grids_cphf = H2O2_sc.gen_grids(50, 194)
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
"cphf_grids": grids_cphf
}
dip_helper = DipoleXDH(config)
grad_helper = GradXDH(config)
config = {
"deriv_A": dip_helper,
"deriv_B": grad_helper,
}
helper = DipDerivXDH(config)
E_2 = helper.E_2
with open(resource_filename("pyxdh", "Validation/numerical_deriv/xdh_dipderiv_xyg3.dat"), "rb") as f:
ref_polar = pickle.load(f)["dipderiv"]
assert(np.allclose(E_2.T, ref_polar, atol=1e-6, rtol=1e-4))
def test_SCF_dipderiv(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.DerivOnce import DipoleSCF, GradSCF
# HF
H2O2 = Mol_H2O2()
dip_deriv = DipoleSCF({"scf_eng": H2O2.hf_eng, "cphf_tol": 1e-10})
grad_deriv = GradSCF({"scf_eng": H2O2.hf_eng, "cphf_tol": 1e-10})
self.valid_assert(dip_deriv, grad_deriv,
"Validation/gaussian/H2O2-HF-freq.fchk")
# B3LYP
H2O2 = Mol_H2O2()
grids_cphf = H2O2.gen_grids(50, 194)
dip_deriv = DipoleSCF({
"scf_eng": H2O2.gga_eng,
"cphf_grids": grids_cphf,
"cphf_tol": 1e-10
})
grad_deriv = GradSCF({
"scf_eng": H2O2.gga_eng,
"cphf_grids": grids_cphf,
"cphf_tol": 1e-10
})
self.valid_assert(dip_deriv, grad_deriv,
"Validation/gaussian/H2O2-B3LYP-freq.fchk")
def test_XYG3_polar(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.DerivOnce import DipoleXDH
import pickle
with open(
resource_filename(
"pyxdh",
"Validation/numerical_deriv/xdh_polarizability_xyg3.dat"),
"rb") as f:
ref_polar = pickle.load(f)["polarizability"]
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
grids_cphf = H2O2_sc.gen_grids(50, 194)
dip_config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
"cphf_grids": grids_cphf
}
# With rotation
dip_helper = DipoleXDH(dip_config)
polar_config = {"deriv_A": dip_helper, "deriv_B": dip_helper}
helper = PolarXDH(polar_config)
assert (np.allclose(-helper.E_2, ref_polar, atol=1e-6, rtol=1e-4))
# No rotation
dip_config["rotation"] = False
dip_helper = DipoleXDH(dip_config)
polar_config = {"deriv_A": dip_helper, "deriv_B": dip_helper}
helper = PolarXDH(polar_config)
assert (np.allclose(-helper.E_2, ref_polar, atol=1e-6, rtol=1e-4))
def mol_to_dip_helper(mol):
print("Processing...")
H2O2_sc = Mol_H2O2(mol=mol, xc="B3LYPg")
H2O2_nc = Mol_H2O2(mol=mol, xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211
}
helper = DipoleXDH(config)
return helper
def test_dipole_xyg3(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
grids_cphf = H2O2_sc.gen_grids(50, 194)
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
"cphf_grids": grids_cphf
}
helper = DipoleXDH(config)
self.valid_assert(helper, "Validation/gaussian/H2O2-XYG3-force.fchk")
def test_dipole_xygjos(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(
xc="0.7731*HF + 0.2269*LDA, 0.2309*VWN3 + 0.2754*LYP")
grids_cphf = H2O2_sc.gen_grids(50, 194)
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.4364,
"ss": 0.,
"cphf_grids": grids_cphf
}
helper = DipoleXDH(config)
self.valid_assert(helper, "Validation/gaussian/H2O2-XYGJOS-force.fchk")
def test_HF_B3LYP_hess(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.DerivOnce import GradNCDFT
import pickle
H2O2 = Mol_H2O2()
config = {
"scf_eng": H2O2.hf_eng,
"nc_eng": H2O2.gga_eng,
"rotation": True,
}
grad_helper = GradNCDFT(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
}
helper = HessNCDFT(config)
E_2 = helper.E_2
with open(resource_filename("pyxdh", "Validation/numerical_deriv/ncdft_hessian_hf_b3lyp.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_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_DipoleDerivGenerator_by_SCF(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2 = Mol_H2O2()
mol = H2O2.mol
hf_eng = H2O2.hf_eng
hf_eng.kernel()
def mf_func(t, interval):
mf = scf.RHF(mol)
mf.get_hcore = lambda mol_: scf.rhf.get_hcore(mol_) - interval * mol_.intor("int1e_r")[t]
return mf.kernel()
generator = DipoleDerivGenerator(mf_func)
diff = NumericDiff(generator)
dip_nuc = np.einsum('i,ix->x', mol.atom_charges(), mol.atom_coords())
assert(np.allclose(
diff.derivative + dip_nuc,
hf_eng.dip_moment(unit="A.U."),
atol=1e-6, rtol=1e-4
))
generator = DipoleDerivGenerator(mf_func, stencil=5)
diff = NumericDiff(generator)
assert(np.allclose(
diff.derivative + dip_nuc,
hf_eng.dip_moment(unit="A.U."),
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_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_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 test_SCF_dipole(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2 = Mol_H2O2()
grids_cphf = H2O2.gen_grids(50, 194)
self.valid_assert({"scf_eng": H2O2.hf_eng}, "Validation/gaussian/H2O2-HF-freq.fchk")
self.valid_assert({"scf_eng": H2O2.gga_eng, "cphf_grids": grids_cphf}, "Validation/gaussian/H2O2-B3LYP-freq.fchk")
def mol_to_grad_helper(mol):
print("Processing...")
H2O2 = Mol_H2O2(mol=mol, xc="0.53*HF + 0.47*B88, 0.73*LYP")
config = {
"scf_eng": H2O2.gga_eng,
"cc": 0.27
}
helper = GradMP2(config)
return helper
def mol_to_dip_helper(mol):
H2O2 = Mol_H2O2(mol=mol)
H2O2.hf_eng.kernel()
config = {
"scf_eng": H2O2.hf_eng,
"nc_eng": H2O2.gga_eng
}
helper = DipoleNCDFT(config)
return helper
def dipole_generator(component, interval):
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
mol = H2O2_sc.mol
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
H2O2_sc.gga_eng.get_hcore = get_hcore
H2O2_nc.gga_eng.get_hcore = get_hcore
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
}
helper = DipoleXDH(config)
return helper
def test_dipole_b2plyp(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
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
}
helper = DipoleMP2(config)
self.valid_assert(helper, "Validation/gaussian/H2O2-B2PLYP-freq.fchk")
def test_XYG3_grad(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2_sc = Mol_H2O2(xc="B3LYPg")
H2O2_nc = Mol_H2O2(
xc="0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP")
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211
}
gmh = GradXDH(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-XYG3-force.fchk"))
assert (np.allclose(gmh.eng, formchk.total_energy()))
assert (np.allclose(gmh.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
def test_HF_B3LYP_dipole(self):
import pickle
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng, "nc_eng": H2O2.gga_eng}
helper = DipoleNCDFT(config)
with open(resource_filename("pyxdh", "Validation/numerical_deriv/ncdft_derivonce_hf_b3lyp.dat"), "rb") as f:
ref_dipole = pickle.load(f)["dipole"]
assert (np.allclose(helper.E_1, ref_dipole, atol=1e-6, rtol=1e-4))
def dipole_generator(component, interval):
H2O2 = Mol_H2O2()
mol = H2O2.mol
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
H2O2.hf_eng.get_hcore = get_hcore
H2O2.gga_eng.get_hcore = get_hcore
config = {"scf_eng": H2O2.hf_eng, "nc_eng": H2O2.gga_eng}
helper = GradNCDFT(config)
return helper
def test_MP2_dipole(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
helper = DipoleMP2(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6,
rtol=1e-4))
def test_B2PLYP_dipole(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2 = Mol_H2O2(xc="0.53*HF + 0.47*B88, 0.73*LYP")
config = {"scf_eng": H2O2.gga_eng, "cc": 0.27}
helper = DipoleMP2(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6,
rtol=1e-4))
def test_B2PLYP_grad(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2 = Mol_H2O2(xc="0.53*HF + 0.47*B88, 0.73*LYP")
config = {"scf_eng": H2O2.gga_eng, "cc": 0.27}
gmh = GradMP2(config)
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(gmh.eng, formchk.total_energy()))
assert (np.allclose(gmh.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
def test_MP2_dipderiv(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, GradMP2
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng, "cphf_tol": 1e-10}
dip_helper = DipoleMP2(config)
grad_helper = GradMP2(config)
config = {"deriv_A": dip_helper, "deriv_B": grad_helper}
helper = DipDerivMP2(config)
E_2 = helper.E_2
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/H2O2-MP2-freq.fchk"))
assert(np.allclose(E_2.T, formchk.dipolederiv(), atol=1e-6, rtol=1e-4))
def test_HF_grad(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
helper = GradSCF(config)
hf_grad = helper.scf_grad
assert (np.allclose(helper.E_1, hf_grad.grad(), atol=1e-6, rtol=1e-4))
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-HF-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.grad(), atol=1e-6, rtol=1e-4))
def test_B3LYP_grad(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.gga_eng}
helper = GradSCF(config)
gga_grad = helper.scf_grad
assert (np.allclose(helper.E_1, gga_grad.grad(), atol=1e-6, rtol=1e-4))
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-B3LYP-freq.fchk"))
# TODO: This is a weaker compare! Try to modulize that someday.
assert (np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
def test_NucCoordDerivGenerator_by_SCFgrad(self):
from pyxdh.Utilities.test_molecules import Mol_H2O2
H2O2 = Mol_H2O2()
mol = H2O2.mol
hf_grad = H2O2.hf_grad
generator = NucCoordDerivGenerator(mol, lambda mol_: scf.RHF(mol_).run())
diff = NumericDiff(generator, lambda mf: mf.kernel())
assert(np.allclose(
hf_grad.kernel(),
diff.derivative.reshape(mol.natm, 3),
atol=1e-6, rtol=1e-4
))
generator = NucCoordDerivGenerator(mol, lambda mol_: scf.RHF(mol_).run(), stencil=5)
diff = NumericDiff(generator, lambda mf: mf.kernel())
assert(np.allclose(
hf_grad.kernel(),
diff.derivative.reshape(mol.natm, 3),
atol=1e-6, rtol=1e-4
))
def test_HF_B3LYP_polar(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.DerivOnce import DipoleNCDFT
import pickle
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng, "nc_eng": H2O2.gga_eng}
dip_helper = DipoleNCDFT(config)
config = {"deriv_A": dip_helper, "deriv_B": dip_helper}
helper = PolarNCDFT(config)
E_2 = helper.E_2
with open(
resource_filename(
"pyxdh",
"Validation/numerical_deriv/ncdft_polarizability_hf_b3lyp.dat"
), "rb") as f:
ref_polar = pickle.load(f)["polarizability"]
assert (np.allclose(-E_2, ref_polar, atol=1e-6, rtol=1e-4))
def test_MP2_grad(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_H2O2
from pyxdh.Utilities import FormchkInterface
from pyscf import mp, grad
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
gmh = GradMP2(config)
mp2_eng = mp.MP2(gmh.scf_eng)
mp2_eng.kernel()
mp2_grad = grad.mp2.Gradients(mp2_eng)
mp2_grad.kernel()
assert (np.allclose(gmh.E_1, mp2_grad.de, atol=1e-6, rtol=1e-4))
formchk = FormchkInterface(
resource_filename("pyxdh",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(gmh.E_1, formchk.grad(), atol=1e-6, rtol=1e-4))