def test_XYG3_hess(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.DerivOnce import GradXDH
from pyxdhalpha.DerivTwice import HessXDH
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")
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
}
grad_helper = GradXDH(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
}
helper = HessXDH(config)
E_2 = helper.E_2
with open(
resource_filename(
"pyxdhalpha",
"Validation/numerical_deriv/xdh_hessian_xyg3.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_XYG3_polar(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.DerivOnce import DipoleXDH
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")
config = {
"scf_eng": H2O2_sc.gga_eng,
"nc_eng": H2O2_nc.gga_eng,
"cc": 0.3211,
}
dip_helper = DipoleXDH(config)
config = {
"deriv_A": dip_helper,
"deriv_B": dip_helper,
}
helper = PolarXDH(config)
E_2 = helper.E_2
with open(resource_filename("pyxdhalpha", "Validation/numerical_deriv/xdh_polarizability_xyg3.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_XYG3_grad(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha", "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 mol_to_grad_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 = GradXDH(config)
return helper
def test_B2PLYP_polar(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
from pyxdhalpha.DerivOnce import DipoleMP2
H2O2 = Mol_H2O2(xc="0.53*HF + 0.47*B88, 0.73*LYP")
config = {
"scf_eng": H2O2.gga_eng,
"cc": 0.27
}
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("pyxdhalpha", "Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert(np.allclose(
- E_2, formchk.polarizability(),
atol=1e-6, rtol=1e-4
))
def test_DipoleDerivGenerator_by_SCF(self):
from pyxdhalpha.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_HF_B3LYP_polar(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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(
"pyxdhalpha",
"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_HF_polar(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
from pyxdhalpha.DerivOnce import DipoleSCF
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
dip_helper = DipoleSCF(config)
config = {
"deriv_A": dip_helper,
"deriv_B": dip_helper,
}
helper = PolarSCF(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdhalpha",
"Validation/gaussian/H2O2-HF-freq.fchk"))
assert (np.allclose(-E_2,
formchk.polarizability(),
atol=1e-6,
rtol=1e-4))
def test_MP2_grad(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha", "Validation/gaussian/H2O2-MP2-freq.fchk"))
assert(np.allclose(
gmh.E_1, formchk.grad(),
atol=1e-6, rtol=1e-4
))
def test_B2PLYP_hess(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
from pyxdhalpha.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("pyxdhalpha",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(E_2, formchk.hessian(), atol=1e-5, rtol=1e-4))
with open(
resource_filename(
"pyxdhalpha",
"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 pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
from pyxdhalpha.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("pyxdhalpha",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(E_2, formchk.hessian(), atol=1e-6, rtol=1e-4))
def test_HF_B3LYP_hess(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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(
"pyxdhalpha",
"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 mol_to_grad_helper(mol):
H2O2 = Mol_H2O2(mol=mol)
H2O2.hf_eng.kernel()
config = {
"scf_eng": H2O2.hf_eng,
"nc_eng": H2O2.gga_eng
}
helper = GradNCDFT(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 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_B2PLYP_dipole(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha",
"Validation/gaussian/H2O2-B2PLYP-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6,
rtol=1e-4))
def test_MP2_dipole(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng}
helper = DipoleMP2(config)
formchk = FormchkInterface(
resource_filename("pyxdhalpha",
"Validation/gaussian/H2O2-MP2-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6,
rtol=1e-4))
def test_HF_B3LYP_grad(self):
import pickle
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.hf_eng, "nc_eng": H2O2.gga_eng}
helper = GradNCDFT(config)
with open(
resource_filename(
"pyxdhalpha",
"Validation/numerical_deriv/ncdft_derivonce_hf_b3lyp.dat"),
"rb") as f:
ref_grad = pickle.load(f)["grad"].reshape(-1, 3)
assert (np.allclose(helper.E_1, ref_grad, atol=1e-6, rtol=1e-4))
def test_HF_grad(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha",
"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 pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha",
"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_B3LYP_dipole(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.Utilities import FormchkInterface
H2O2 = Mol_H2O2()
config = {"scf_eng": H2O2.gga_eng}
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("pyxdhalpha",
"Validation/gaussian/H2O2-B3LYP-freq.fchk"))
assert (np.allclose(helper.E_1, formchk.dipole(), atol=1e-6,
rtol=1e-4))
def test_NucCoordDerivGenerator_by_SCFgrad(self):
from pyxdhalpha.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_B2PLYP_grad(self):
from pkg_resources import resource_filename
from pyxdhalpha.Utilities.test_molecules import Mol_H2O2
from pyxdhalpha.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("pyxdhalpha", "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
))
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
if __name__ == '__main__':
result_dict = {}
H2O2 = Mol_H2O2()
mol = H2O2.mol
num_obj = NucCoordDerivGenerator(H2O2.mol, mol_to_grad_helper)
num_dif = NumericDiff(num_obj, lambda helper: helper.eng)
result_dict["grad"] = num_dif.derivative
num_obj = DipoleDerivGenerator(dipole_generator)
num_dif = NumericDiff(num_obj, lambda helper: helper.eng)
dip_nuc = np.einsum("A, At -> t", mol.atom_charges(), mol.atom_coords())
result_dict["dipole"] = num_dif.derivative + dip_nuc
with open("ncdft_derivonce_hf_b3lyp.dat", "wb") as f:
pickle.dump(result_dict, f, pickle.HIGHEST_PROTOCOL)