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_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_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_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_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_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_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_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_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_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_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_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))
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 valid_assert(config, resource_path):
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
helper = GradSCF(config)
formchk = FormchkInterface(resource_filename("pyxdh", resource_path))
assert (np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))
def valid_resource(helper, resource_path):
from pkg_resources import resource_filename
from pyxdh.Utilities import FormchkInterface
formchk = FormchkInterface(resource_filename("pyxdh", resource_path))
assert (np.allclose(helper.eng, formchk.total_energy()))
assert (np.allclose(helper.E_1, formchk.grad(), atol=1e-5, rtol=1e-4))