def test_init_mp2(self):
mf0 = mf
mf1 = scf.RHF(gto.M(atom='H', spin=1))
self.assertTrue(isinstance(mp.MP2(mf0), mp.mp2.RMP2))
self.assertTrue(isinstance(mp.MP2(mf1), mp.ump2.UMP2))
self.assertTrue(isinstance(mp.MP2(mf0.density_fit()), mp.dfmp2.DFMP2))
#self.assertTrue(isinstance(mp.MP2(mf1.density_fit()), mp.dfmp2.DFUMP2))
self.assertTrue(isinstance(mp.MP2(mf0.newton()), mp.mp2.RMP2))
self.assertTrue(isinstance(mp.MP2(mf1.newton()), mp.ump2.UMP2))
def test_mbpt2(self):
myucc = uccsd.UCCSD(mf)
e = myucc.kernel(mbpt2=True)[0]
self.assertAlmostEqual(e, -0.12886859466216125, 10)
emp2 = mp.MP2(mf).kernel()[0]
self.assertAlmostEqual(e, emp2, 10)
myucc = uccsd.UCCSD(mf_s2)
e = myucc.kernel(mbpt2=True)[0]
self.assertAlmostEqual(e, -0.096257842171487293, 10)
emp2 = mp.MP2(mf_s2).kernel()[0]
self.assertAlmostEqual(e, emp2, 10)
def test_ump2_outcore_frozen(self):
pt = mp.MP2(mf)
pt.max_memory = 0
pt.nmo = (12, 11)
pt.frozen = [[4, 5], [2, 3]]
e = pt.kernel(with_t2=False)[0]
self.assertAlmostEqual(e, -0.033400699456971966, 9)
pt = mp.MP2(mf)
pt.nmo = (12, 11)
pt.nocc = (4, 2)
e = pt.kernel(with_t2=False)[0]
self.assertAlmostEqual(e, -0.033400699456971966, 9)
def _run_mp2(self, hf=None, **kwargs):
from pyscf import mp
if hf is None:
hf = self._get_hf(**kwargs)
mp2 = mp.MP2(hf)
mp2.kernel()
return mp2
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 _pyscf_qm(qm_atnm,
qm_crds,
qm_basis,
qm_chg_tot,
l_mp2=False,
l_esp=False,
esp_opts={}):
atm_list = []
for ia, xyz in enumerate(qm_crds):
sym = qm_atnm[ia]
atm_list.append([sym, (xyz[0], xyz[1], xyz[2])])
qm_mol = _pyscf_mol_build(atm_list, qm_basis, qm_chg_tot)
mf = scf.RHF(qm_mol)
mf.run()
esp_chg = None
if l_mp2:
postmf = mp.MP2(mf).run()
ener_QM = postmf.e_tot
grds_QM = postmf.Gradients().kernel()
if l_esp:
dm = make_rdm1_with_orbital_response(postmf)
esp_chg = esp_atomic_charges(qm_mol, dm, esp_opts)
else:
ener_QM = mf.e_tot
grds_QM = mf.Gradients().kernel()
if l_esp:
dm = mf.make_rdm1()
esp_chg = esp_atomic_charges(qm_mol, dm, esp_opts)
return ener_QM, grds_QM, esp_chg
def test_frozen(self):
pt = mp.MP2(mf)
pt.frozen = [0,1,10,11,12]
pt.max_memory = 1
pt.kernel()
g1 = ump2_grad.Gradients(pt).kernel(pt.t2)
self.assertAlmostEqual(lib.finger(g1), -0.22437278030057645, 6)
def test_make_natural_orbitals_from_restricted(self):
from pyscf import mp, ci, cc
npt = numpy.testing
mol = gto.M(atom='C 0 0 0; O 0 0 1.2', basis='3-21g', spin=0)
myhf = scf.RHF(mol).run()
ncas, nelecas = (8, 10)
mymc = mcscf.CASCI(myhf, ncas, nelecas)
# Test MP2
# Trusted results from ORCA v4.2.1
rmp2_noons = [
1.99992732, 1.99989230, 1.99204357, 1.98051334, 1.96825487,
1.94377615, 1.94376239, 0.05792320, 0.05791037, 0.02833335,
0.00847013, 0.00531989, 0.00420320, 0.00420280, 0.00257965,
0.00101638, 0.00101606, 0.00085503
]
mymp = mp.MP2(myhf).run()
noons, natorbs = mcscf.addons.make_natural_orbitals(mymp)
npt.assert_array_almost_equal(rmp2_noons, noons, decimal=5)
mymc.kernel(natorbs)
# The tests below are only to ensure that `make_natural_orbitals` can
# run at all since we've confirmed above that the NOONs are correct.
# Test CISD
mycisd = ci.CISD(myhf).run()
noons, natorbs = mcscf.addons.make_natural_orbitals(mycisd)
mymc.kernel(natorbs)
# Test CCSD
myccsd = cc.CCSD(myhf).run()
noons, natorbs = mcscf.addons.make_natural_orbitals(myccsd)
mymc.kernel(natorbs)
def run_pyscf_mp2(mol=None, hf=None, **kwargs):
from pyscf import mp
if hf is None:
hf = compute_pyscf_hf(mol=mol, **kwargs)
mp2 = mp.MP2(hf)
mp2.kernel()
return mp2
def get_h(self, iexe=True, href=None, frozen=0):
"""
get hamitonian of the sysem, which is to be described by
a hf/dft single slater determinant
:param href: reference hamiltonian, could be hf/uhf/rohf/rks/uks
:type href: str
"""
meth = self.meth
self.xc = None
if href is None:
if meth in [
'eht',
'hf',
'mp2',
'cisd',
'ccsd',
]:
fun = scf.RHF if self.restricted else scf.UHF
mf = fun(self.mol)
elif meth in ['pbe', 'b3lyp', 'w95xb']:
fun = dft.RKS if self.restricted else dft.UKS
mf = fun(self.mol)
mf.xc = meth
self.xc = meth
else:
raise Exception('Unknow method: %s' % meth)
else:
dct = {'rohf':scf.ROHF, 'rhf':scf.RHF, 'hf':scf.RHF,\
'rks': dft.RKS, 'uks':dft.UKS, 'ks':dft.RKS}
assert href in dct
fun = dct[href]
mf = fun(self.mol)
if 'ks' in href: mf.xc = meth
if iexe:
mf.kernel()
self.mf = mf
h2 = None
self.isd = T # single (slater) determinant
# final hamiltonian
if meth[:2] in ['mp', 'ci', 'cc']:
self.isd = F
if meth in ['mp2', 'mp3', 'mp4']:
h2 = mp.MP2(self.mf) #.set(frozen=frozen)
elif meth in [
'cisd',
]:
h2 = ci.CISD(self.mf) #.set(frozen=frozen)
elif meth in ['ccsd', 'ccsd(t)']:
h2 = cc.CCSD(self.mf) #.set(frozen=frozen)
h2.direct = True
else:
raise Exception('Todo')
if frozen:
h2.set(frozen=frozen)
if iexe:
h2.kernel()
self.h2 = h2
def test_as_scanner(self):
pt = mp.MP2(mf)
pt.frozen = [0,1,10,11,12]
gscan = pt.nuc_grad_method().as_scanner()
e, g1 = gscan(mol)
self.assertTrue(gscan.converged)
self.assertAlmostEqual(e, -75.759091758835353, 9)
self.assertAlmostEqual(lib.finger(g1), -0.22437278030057645, 6)
def test_energy_skip(self):
mol = gto.Mole(atom='Ne', basis='ccpvdz')
mf = scf.RHF(mol).run()
auxmol = gto.M(atom=mol.atom,
basis=('ccpvdz-fit', 'cc-pVDZ-F12-OptRI'),
verbose=0)
e = mp.MP2(mf).kernel()[0] + mp2f12.energy_f12(mf, auxmol, 1.)
self.assertAlmostEqual(e, -0.27522161783457028, 9)
def mol_electron(mol, frozen=0, chkfile=None, verbose=False):
if verbose:
start_t = time()
nao = mol.nao
natm = mol.natm
rhf = scf.RHF(mol)
if chkfile:
rhf.set(chkfile=chkfile)
erhf = rhf.kernel()
if verbose:
rhf_t = time()
print(f"time of rhf: {rhf_t - start_t}")
mo_energy = rhf.mo_energy
mo_occ = rhf.mo_occ
# mo_coeff = rhf.mo_coeff
mo_coeff_ = rhf.mo_coeff
mo_coeff = fix_gauge(mo_coeff_)
occ_a = (mo_occ > 0)
occ_a[:frozen] = False
# occ_b = (mo_occ[1]>0)
vir_a = (mo_occ == 0)
# vir_b = (mo_occ[1]==0)
nocc_a = sum(occ_a)
# nocc_b = sum(occ_b)
nocc = nocc_a
nvir_a = sum(vir_a)
# nvir_b = sum(vir_b)
nvir = nvir_a
assert (nocc + nvir + frozen == nao)
if verbose:
print('nao = %d, nocc = %d, nvir = %d' % \
(nao, nocc, nvir))
print('shape of a and b coeffs: ', mo_coeff[0].shape,
mo_coeff[1].shape)
c_occ = mo_coeff[:, occ_a]
c_vir = mo_coeff[:, vir_a]
e_occ = mo_energy[occ_a]
e_vir = mo_energy[vir_a]
c_occ = c_occ.T
c_vir = c_vir.T
meta = [natm, nao, nocc, nvir]
if verbose:
print('shape of coeff data ', c_occ.shape)
print('shape of ener data ', e_occ.shape)
print('shape of coeff data ', c_vir.shape)
print('shape of ener data ', e_vir.shape)
mid_t = time()
# print(f"time of collecting results: {mid_t - rhf_t}")
mp2 = mp.MP2(rhf, frozen=frozen)
# emp2 = mp2.kernel()
emp2, emp2_ij = my_kernel(mp2)
if verbose:
print('E(HF) = %.9g' % erhf)
print('E(RMP2) = %.9g' % emp2)
print(f"time of mp2: {time()-mid_t}")
return meta, erhf, emp2, emp2_ij, (e_occ, e_vir), (c_occ, c_vir)
def test_ump2(self):
pt = mp.MP2(mf)
emp2, t2 = pt.kernel(mf.mo_energy, mf.mo_coeff)
self.assertAlmostEqual(emp2, -0.16575150552336643, 9)
pt.max_memory = 1
pt.frozen = None
emp2, t2 = pt.kernel()
self.assertAlmostEqual(emp2, -0.16575150552336643, 9)
def get_mp2_energy(self):
if self.spin == 0:
mf = scf.RHF(self.mol)
else:
mf = scf.UHF(self.mol)
e0 = mf.kernel()
mp2 = mp.MP2(mf)
ecorr = mp2.kernel()[0]
return e0, ecorr, e0+ecorr
def test_check_mp2_energy(self):
mp2 = mp.MP2(mf)
e_mp2 = mp2.kernel()[0]
myadc.max_memory = 20
e_adc_mp2, t_amp1, t_amp2 = myadc.kernel_gs()
diff_mp2 = e_adc_mp2 - e_mp2
self.assertAlmostEqual(diff_mp2, 0.0000000000000, 6)
def __init__(self, mf):
self.mf = mf
self.mp_ee = mp.MP2(self.mf.mf_elec)
if(self.mf.unrestricted==True):
raise NotImplementedError('NEO-MP2 is for RHF wave functions only')
if(len(self.mf.mol.nuc)>1):
raise NotImplementedError('NEO-MP2 is for single quantum nuclei')
def get_MP2_natural_orbitals(mf, n, nfreeze):
mp2 = mp.MP2(mf, nfreeze)
mp2.kernel()
C_mf = mf.mo_coeff
rho = mp2.make_rdm1()
n_mp, UU = np.linalg.eigh(rho)
idx = n_mp.argsort()[::-1]
n_mp = n_mp[idx]
UU = UU[:, idx]
C_mp = np.dot(mf.mo_coeff, UU)
return C_mp[:, :n]
def mp2_energy(self, dim):
print("ECW method is MP2")
energy = 0.0
Ne_frag = self.Ne_frag
ops = self.ops
umat = self.umat
Ne_env = self.Ne_env
P_bath_JK = libgen.coreJK_sub(
self.ints, self.loc2sub, dim,
tools.dm_sub2ao(self.P_bath, self.loc2sub[:, :dim]), Ne_env, 1.0)
subOEI = ops["subKin"] + ops["subVnuc1"] + ops[
"subVnuc2"] + P_bath_JK + 0.5 * 1e4 * self.P_bath
#subOEI = ops["subKin"]+ops["subVnuc1"]+ops["subVnuc_bound1"]+umat
subTEI = ops["subTEI"]
mf = qcwrap.qc_scf(Ne_frag,
dim,
'hf',
mol=self.mol,
oei=subOEI,
tei=subTEI,
dm0=self.P_imp)
mf.runscf()
#self.ints.submo_molden( mf.mo_coeff, mf.mo_occ, self.loc2sub, 'mo_imp.molden' )
print('|diffP| = ',
np.linalg.norm(mf.rdm1 + self.P_bath - self.P_ref_sub))
print("mo_energy")
print(mf.mo_energy)
e_emb = 0.0
#onedm = mf.make_rdm1()
#e_emb=np.trace(np.dot(umat,onedm))
#print "diffP = ",np.linalg.norm(self.P_imp - onedm)
mp2 = mp.MP2(mf)
mp2.kernel()
e_mp2 = mf.elec_energy + mp2.e_corr
e_mp2 -= e_emb
imp_mf_energy = self.imp_mf_energy(dim)
energy = e_mp2 - imp_mf_energy
print("dmfet correction energy = ", energy)
return energy
def test_r_mp2_grad(self):
scf_eng = scf.RHF(self.mol).run()
mp2_eng = mp.MP2(scf_eng).run()
mp2_grad = mp2_eng.Gradients().run()
gradh = GradMP2({"scf_eng": scf_eng})
formchk = FormchkInterface(resource_filename("pyxdh", "Validation/gaussian/NH3-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 FNOCCSD(mf, thresh=1e-6, pct_occ=None, nvir_act=None):
"""Frozen natural orbital CCSD
Attributes:
thresh : float
Threshold on NO occupation numbers. Default is 1e-6 (very conservative).
pct_occ : float
Percentage of total occupation number. Default is None. If present, overrides `thresh`.
nvir_act : int
Number of virtual NOs to keep. Default is None. If present, overrides `thresh` and `pct_occ`.
"""
from pyscf import mp
pt = mp.MP2(mf).set(verbose=0).run()
frozen, no_coeff = pt.make_fno(thresh=thresh,
pct_occ=pct_occ,
nvir_act=nvir_act)
pt_no = mp.MP2(mf, frozen=frozen, mo_coeff=no_coeff).set(verbose=0).run()
mycc = ccsd.CCSD(mf, frozen=frozen, mo_coeff=no_coeff)
mycc.delta_emp2 = pt.e_corr - pt_no.e_corr
from pyscf.lib import logger
def _finalize(self):
'''Hook for dumping results and clearing up the object.'''
if self.converged:
logger.info(self, 'FNO-%s converged', self.__class__.__name__)
else:
logger.note(self, 'FNO-%s not converged', self.__class__.__name__)
logger.note(self, 'E(FNO-%s) = %.16g E_corr = %.16g',
self.__class__.__name__, self.e_tot, self.e_corr)
logger.note(self, 'E(FNO-%s+delta-MP2) = %.16g E_corr = %.16g',
self.__class__.__name__, self.e_tot + self.delta_emp2,
self.e_corr + self.delta_emp2)
return self
mycc._finalize = _finalize.__get__(mycc, mycc.__class__)
return mycc
def test_mp2(self):
nocc = mol.nelectron // 2
nmo = mf.mo_energy.size
nvir = nmo - nocc
co = mf.mo_coeff[:, :nocc]
cv = mf.mo_coeff[:, nocc:]
g = ao2mo.incore.general(mf._eri, (co, cv, co, cv)).ravel()
eia = mf.mo_energy[:nocc, None] - mf.mo_energy[nocc:]
t2ref0 = g / (eia.reshape(-1, 1) + eia.reshape(-1)).ravel()
t2ref0 = t2ref0.reshape(nocc, nvir, nocc, nvir).transpose(0, 2, 3, 1)
pt = mp.MP2(mf)
emp2, t2 = pt.kernel()
self.assertAlmostEqual(emp2, -0.204019967288338, 9)
def test_rdm_complex(self):
mol = gto.M()
mol.verbose = 0
nocc = 3
nvir = 4
mf = scf.RHF(mol)
nmo = nocc + nvir
numpy.random.seed(1)
eri = (numpy.random.random((nmo, nmo, nmo, nmo)) + numpy.random.random(
(nmo, nmo, nmo, nmo)) * 1j - (.5 + .5j))
eri = eri + eri.transpose(1, 0, 3, 2).conj()
eri = eri + eri.transpose(2, 3, 0, 1)
eri *= .1
eris = lambda: None
eris.ovov = eri[:nocc, nocc:, :nocc,
nocc:].reshape(nocc * nvir, nocc * nvir)
mo_energy = numpy.arange(nmo)
mo_occ = numpy.zeros(nmo)
mo_occ[:nocc] = 2
dm = numpy.diag(mo_occ)
vhf = numpy.einsum('ijkl,lk->ij', eri, dm)
vhf -= numpy.einsum('ijkl,jk->il', eri, dm) * .5
hcore = numpy.diag(mo_energy) - vhf
mf.get_hcore = lambda *args: hcore
mf.get_ovlp = lambda *args: numpy.eye(nmo)
eris.mo_energy = mf.mo_energy = mo_energy
mf.mo_coeff = numpy.eye(nmo)
mf.mo_occ = mo_occ
mf.e_tot = numpy.einsum('ij,ji', hcore,
dm) + numpy.einsum('ij,ji', vhf, dm) * .5
mf.converged = True
pt = mp.MP2(mf)
pt.ao2mo = lambda *args, **kwargs: eris
pt.kernel(eris=eris)
dm1 = pt.make_rdm1()
dm2 = pt.make_rdm2()
e1 = numpy.einsum('ij,ji', hcore, dm1)
e1 += numpy.einsum('ijkl,ijkl', eri, dm2) * .5
self.assertAlmostEqual(e1, pt.e_tot, 12)
#self.assertAlmostEqual(abs(numpy.einsum('ijkk->ji', dm2)/(nocc*2-1) - dm1).max(), 0, 9)
self.assertAlmostEqual(
abs(dm2 - dm2.transpose(1, 0, 3, 2).conj()).max(), 0, 9)
self.assertAlmostEqual(
abs(dm2 - dm2.transpose(2, 3, 0, 1)).max(), 0, 9)
def setUp(self):
geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))]
basis = '6-31g'
multiplicity = 1
charge = 0
self.molecule = PyscfMolecularData(geometry, basis, multiplicity,
charge)
mol = prepare_pyscf_molecule(self.molecule)
mol.verbose = 0
self.molecule._pyscf_data['mol'] = mol
self.molecule._pyscf_data['scf'] = mf = scf.RHF(mol).run()
self.molecule._pyscf_data['mp2'] = mp.MP2(mf).run()
self.molecule._pyscf_data['cisd'] = ci.CISD(mf).run()
self.molecule._pyscf_data['ccsd'] = cc.CCSD(mf).run()
self.molecule._pyscf_data['fci'] = fci.FCI(mf).run()
def test_ump2_dm(self):
pt = mp.MP2(mf)
emp2, t2 = pt.kernel()
dm1 = pt.make_rdm1()
dm2 = pt.make_rdm2()
gpt = mp.GMP2(mf).run()
dm1ref = gpt.make_rdm1()
dm2ref = gpt.make_rdm2()
ia = gpt._scf.mo_coeff.orbspin == 0
ib = gpt._scf.mo_coeff.orbspin == 1
mo_a, mo_b = mf.mo_coeff
nmoa = mo_a.shape[1]
nmob = mo_b.shape[1]
nocca, noccb = mol.nelec
self.assertTrue(numpy.allclose(dm1[0], dm1ref[ia][:, ia]))
self.assertTrue(numpy.allclose(dm1[1], dm1ref[ib][:, ib]))
self.assertTrue(
numpy.allclose(dm2[0], dm2ref[ia][:, ia][:, :, ia][:, :, :, ia]))
self.assertTrue(
numpy.allclose(dm2[2], dm2ref[ib][:, ib][:, :, ib][:, :, :, ib]))
self.assertTrue(
numpy.allclose(dm2[1], dm2ref[ia][:, ia][:, :, ib][:, :, :, ib]))
hcore = mf.get_hcore()
eriaa = ao2mo.kernel(mf._eri, mo_a, compact=False).reshape([nmoa] * 4)
eribb = ao2mo.kernel(mf._eri, mo_b, compact=False).reshape([nmob] * 4)
eriab = ao2mo.kernel(mf._eri, (mo_a, mo_a, mo_b, mo_b), compact=False)
eriab = eriab.reshape([nmoa, nmoa, nmob, nmob])
h1a = reduce(numpy.dot, (mo_a.T.conj(), hcore, mo_a))
h1b = reduce(numpy.dot, (mo_b.T.conj(), hcore, mo_b))
e1 = numpy.einsum('ij,ji', h1a, dm1[0])
e1 += numpy.einsum('ij,ji', h1b, dm1[1])
e1 += numpy.einsum('ijkl,ijkl', eriaa, dm2[0]) * .5
e1 += numpy.einsum('ijkl,ijkl', eriab, dm2[1])
e1 += numpy.einsum('ijkl,ijkl', eribb, dm2[2]) * .5
e1 += mol.energy_nuc()
self.assertAlmostEqual(e1, pt.e_tot, 9)
vhf = mf.get_veff(mol, mf.make_rdm1())
h1a = reduce(numpy.dot, (mo_a.T, hcore + vhf[0], mo_a))
h1b = reduce(numpy.dot, (mo_b.T, hcore + vhf[1], mo_b))
dm1[0][numpy.diag_indices(nocca)] -= 1
dm1[1][numpy.diag_indices(noccb)] -= 1
e = numpy.einsum('pq,qp', h1a, dm1[0])
e += numpy.einsum('pq,qp', h1b, dm1[1])
self.assertAlmostEqual(e, -emp2, 9)
def pyscf_mp2_amplitude_calculator(domain):
"""
Calculates MP2 amplitudes in the domain.
Args:
domain (Domain): a domain to calculate at;
Returns:
MP2 amplitudes.
"""
mf = scf.RHF(domain.mol)
mf.build(domain.mol)
mf.mo_coeff = domain.psi
mf.mo_energy = domain.e
mf.mo_occ = domain.occupations
domain_mp2 = mp.MP2(mf)
domain_mp2.kernel()
return None, domain_mp2.t2.swapaxes(1, 2)
def kernel(self, h1, h2, norb, nelec, ci0=None, ecore=0, **kwargs):
fakemol = gto.M(verbose=0)
fakemol.nelectron = sum(nelec)
# Build a mean-field object fake_hf without SCF iterations
fake_hf = scf.RHF(fakemol)
fake_hf._eri = h2
fake_hf.get_hcore = lambda *args: h1
fake_hf.get_ovlp = lambda *args: numpy.eye(norb)
fake_hf.mo_coeff = numpy.eye(norb)
fake_hf.mo_occ = numpy.zeros(norb)
fake_hf.mo_occ[:fakemol.nelectron // 2] = 2
self.mp2 = mp.MP2(fake_hf)
e_corr, t2 = self.mp2.kernel()
e_tot = self.mp2.e_tot + ecore
return e_tot, t2
def get_potential_energy(self, atoms=None, force_consistent=False):
if self.method == 'HF':
#energy = self.hf_scanner(gto.M(atom=ase_atoms_to_pyscf(atoms), basis=self.basis))
mf = scf.RHF(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0))
energy = mf.kernel()
energy *= convert_energy
self.results['energy'] = energy
return energy
elif self.method == "DFT":
mf = dft.RKS(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0))
mf.xc = self.xc
energy = mf.kernel()
energy *= convert_energy
self.results['energy'] = energy
return energy
elif self.method == "MP2":
#energy = self.mp2_scanner(gto.M(atom=ase_atoms_to_pyscf(atoms), basis=self.basis))
mf = scf.RHF(
gto.M(atom=ase_atoms_to_pyscf(atoms),
basis=self.basis,
charge=0,
verbose=0))
e_hf = mf.kernel()
mp2 = mp.MP2(mf)
e_mp = mp2.kernel()[0]
energy = e_hf + e_mp
energy *= convert_energy
self.results['energy'] = energy
return energy
def test_mp2_with_df(self):
pt = mp.MP2(mf.density_fit('weigend'))
pt.frozen = [1]
e = pt.kernel(with_t2=False)[0]
self.assertAlmostEqual(e, -0.14708846352674113, 9)
pt = mp.dfmp2.DFMP2(mf.density_fit('weigend'))
e = pt.kernel(mf.mo_energy, mf.mo_coeff)[0]
self.assertAlmostEqual(e, -0.20425449198334983, 9)
pt.frozen = [1]
e = pt.kernel()[0]
self.assertAlmostEqual(e, -0.14708846352674113, 9)
pt = mp.dfmp2.DFMP2(mf)
pt.frozen = [1]
pt.with_df = mf.density_fit('weigend').with_df
e = pt.kernel()[0]
self.assertAlmostEqual(e, -0.14708846352674113, 9)
def test_check_mp2_high_cost(self):
mol = gto.Mole()
mol.atom = [
['C', (0.0, 0.0, 0.0)],
['O', (0.0, r_CO, 0.0)],
['H', (0.0, -x, y)],
['H', (0.0, -x, -y)],
]
mol.basis = {
'H': 'aug-cc-pVQZ',
'C': 'aug-cc-pVQZ',
'O': 'aug-cc-pVQZ',
}
mol.verbose = 7
mol.output = '/dev/null'
mol.build()
mf = scf.RHF(mol)
mf.conv_tol = 1e-12
mf.kernel()
# Ensure phase
mf.mo_coeff[:, mf.mo_coeff.sum(axis=0) < 0] *= -1
mp2 = mp.MP2(mf)
e_mp2 = mp2.kernel()[0]
myadc = adc.ADC(mf)
myadc.max_memory = 20
e_adc_mp2, t_amp1, t_amp2 = myadc.kernel_gs()
diff_mp2 = e_adc_mp2 - e_mp2
self.assertAlmostEqual(diff_mp2, 0.0000000000000, 6)
t_amp1_n = numpy.linalg.norm(t_amp1[0])
t_amp2_n = numpy.linalg.norm(t_amp2[0])
self.assertAlmostEqual(t_amp1_n, 0.0456504320024, 6)
self.assertAlmostEqual(t_amp2_n, 0.2977897530749, 6)
self.assertAlmostEqual(lib.fp(t_amp1[0]), -0.008983054536, 6)
self.assertAlmostEqual(lib.fp(t_amp2[0]), -0.639727653133, 6)