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_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_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_UHF_UB3LYP_grad(self):
from pyxdh.Utilities.test_molecules import Mol_CH3
from pkg_resources import resource_filename
import pickle
CH3 = Mol_CH3()
helper = GradUNCDFT({"scf_eng": CH3.hf_eng, "nc_eng": CH3.gga_eng, "cphf_tol": 1e-10})
with open(resource_filename("pyxdh", "Validation/numerical_deriv/ncdft_derivonce_uhf_ub3lyp.dat"), "rb") as f:
ref_grad = pickle.load(f)["grad"].reshape(-1, 3)
assert (np.allclose(helper.E_1, ref_grad, atol=1e-5, 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 dipole_generator(component, interval):
CH3 = Mol_CH3()
mol = CH3.mol
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
CH3.hf_eng.get_hcore = get_hcore
CH3.gga_eng.get_hcore = get_hcore
config = {"scf_eng": CH3.hf_eng, "nc_eng": CH3.gga_eng}
helper = GradUNCDFT(config)
return helper
def test_UHF_hess(self):
from pkg_resources import resource_filename
from pyxdh.Utilities.test_molecules import Mol_CH3
from pyxdh.Utilities import FormchkInterface
from pyxdh.DerivOnce import GradUSCF
CH3 = Mol_CH3()
config = {
"scf_eng": CH3.hf_eng,
"cphf_tol": 1e-10,
}
grad_helper = GradUSCF(config)
config = {
"deriv_A": grad_helper,
"deriv_B": grad_helper,
"cphf_tol": 1e-10,
}
helper = HessUSCF(config)
E_2 = helper.E_2
formchk = FormchkInterface(
resource_filename("pyxdh", "Validation/gaussian/CH3-HF-freq.fchk"))
assert (np.allclose(E_2, formchk.hessian(), atol=1e-5, rtol=1e-4))
def mol_to_grad_helper(mol):
CH3 = Mol_CH3(mol=mol)
CH3.hf_eng.kernel()
config = {"scf_eng": CH3.hf_eng, "nc_eng": CH3.gga_eng}
helper = GradUNCDFT(config)
return helper
mol = CH3.mol
def get_hcore(mol=mol):
return scf.rhf.get_hcore(
mol) - interval * mol.intor("int1e_r")[component]
CH3.hf_eng.get_hcore = get_hcore
CH3.gga_eng.get_hcore = get_hcore
config = {"scf_eng": CH3.hf_eng, "nc_eng": CH3.gga_eng}
helper = GradUNCDFT(config)
return helper
if __name__ == '__main__':
result_dict = {}
CH3 = Mol_CH3()
mol = CH3.mol
num_obj = NucCoordDerivGenerator(CH3.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_uhf_ub3lyp.dat", "wb") as f:
pickle.dump(result_dict, f, pickle.HIGHEST_PROTOCOL)