def test_init(self):
self.assertTrue(isinstance(cc.CCSD(mf), ccsd.CCSD))
self.assertTrue(isinstance(cc.CCSD(mf.density_fit()), dfccsd.RCCSD))
self.assertTrue(isinstance(cc.CCSD(mf.newton()), ccsd.CCSD))
self.assertTrue(isinstance(cc.CCSD(mf.density_fit().newton()), dfccsd.RCCSD))
self.assertTrue(isinstance(cc.CCSD(mf.newton().density_fit()), ccsd.CCSD))
self.assertTrue(not isinstance(cc.CCSD(mf.newton().density_fit()), dfccsd.RCCSD))
self.assertTrue(isinstance(cc.CCSD(mf.density_fit().newton().density_fit()), dfccsd.RCCSD))
self.assertTrue(isinstance(cc.UCCSD(mf), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.UCCSD(mf.newton()), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit().newton()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.UCCSD(mf.newton().density_fit()), uccsd.UCCSD))
# self.assertTrue(not isinstance(cc.UCCSD(mf.newton().density_fit()), dfccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit().newton().density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.CCSD(scf.GHF(mol)), gccsd.GCCSD))
umf = scf.convert_to_uhf(mf, scf.UHF(mol))
self.assertTrue(isinstance(cc.CCSD(umf), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.CCSD(umf.density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.CCSD(umf.newton()), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.CCSD(umf.density_fit().newton()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.CCSD(umf.newton().density_fit()), uccsd.UCCSD))
# self.assertTrue(not isinstance(cc.CCSD(umf.newton().density_fit()), dfccsd.UCCSD))
# self.assertTrue(isinstance(cc.CCSD(umf.density_fit().newton().density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.CCSD(mf, mo_coeff=mf.mo_coeff*1j), rccsd.RCCSD))
def test_init(self):
from pyscf.cc import ccsd
from pyscf.cc import uccsd
from pyscf.cc import dfccsd
self.assertTrue(isinstance(cc.CCSD(mf), ccsd.CCSD))
self.assertTrue(isinstance(cc.CCSD(mf.density_fit()), dfccsd.RCCSD))
self.assertTrue(isinstance(cc.CCSD(mf.newton()), ccsd.CCSD))
self.assertTrue(
isinstance(cc.CCSD(mf.density_fit().newton()), dfccsd.RCCSD))
self.assertTrue(
isinstance(cc.CCSD(mf.newton().density_fit()), ccsd.CCSD))
self.assertTrue(
not isinstance(cc.CCSD(mf.newton().density_fit()), dfccsd.RCCSD))
self.assertTrue(
isinstance(cc.CCSD(mf.density_fit().newton().density_fit()),
dfccsd.RCCSD))
self.assertTrue(isinstance(cc.UCCSD(mf), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.UCCSD(mf.newton()), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit().newton()), dfccsd.UCCSD))
self.assertTrue(
isinstance(cc.UCCSD(mf.newton().density_fit()), uccsd.UCCSD))
# self.assertTrue(not isinstance(cc.UCCSD(mf.newton().density_fit()), dfccsd.UCCSD))
# self.assertTrue(isinstance(cc.UCCSD(mf.density_fit().newton().density_fit()), dfccsd.UCCSD))
umf = scf.convert_to_uhf(mf, scf.UHF(mol))
self.assertTrue(isinstance(cc.CCSD(umf), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.CCSD(umf.density_fit()), dfccsd.UCCSD))
self.assertTrue(isinstance(cc.CCSD(umf.newton()), uccsd.UCCSD))
# self.assertTrue(isinstance(cc.CCSD(umf.density_fit().newton()), dfccsd.UCCSD))
self.assertTrue(
isinstance(cc.CCSD(umf.newton().density_fit()), uccsd.UCCSD))
def setUpModule():
global mol, mf, mol1, mf0, mf1, gmf, ucc, ucc0, ucc1, eris1
global ecc, orbspin, nocca, noccb, nvira, nvirb, r1, r2
mol = gto.Mole()
mol.verbose = 0
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = '631g'
mol.spin = 0
mol.build()
mf = scf.UHF(mol).run(conv_tol=1e-12)
mol1 = mol.copy()
mol1.spin = 2
mol1.build()
mf0 = scf.UHF(mol1).run(conv_tol=1e-12)
mf1 = copy.copy(mf0)
nocca, noccb = mol1.nelec
nmo = mol1.nao_nr()
nvira, nvirb = nmo - nocca, nmo - noccb
numpy.random.seed(12)
mf1.mo_coeff = numpy.random.random((2, nmo, nmo)) - .5
gmf = scf.addons.convert_to_ghf(mf1)
orbspin = gmf.mo_coeff.orbspin
ucc1 = cc.UCCSD(mf1)
eris1 = ucc1.ao2mo()
numpy.random.seed(11)
no = nocca + noccb
nv = nvira + nvirb
r1 = numpy.random.random((no, nv)) - .9
r2 = numpy.random.random((no, no, nv, nv)) - .9
r2 = r2 - r2.transpose(1, 0, 2, 3)
r2 = r2 - r2.transpose(0, 1, 3, 2)
r1 = cc.addons.spin2spatial(r1, orbspin)
r2 = cc.addons.spin2spatial(r2, orbspin)
r1, r2 = eom_uccsd.vector_to_amplitudes_ee(
eom_uccsd.amplitudes_to_vector_ee(r1, r2), ucc1.nmo, ucc1.nocc)
ucc1.t1 = r1
ucc1.t2 = r2
ucc = cc.UCCSD(mf)
ucc.max_space = 0
ucc.conv_tol = 1e-8
ecc = ucc.kernel()[0]
ucc0 = cc.UCCSD(mf0)
ucc0.conv_tol = 1e-8
ucc0.direct = True
ucc0.kernel()
def setUpModule():
global mol, rhf, mf, myucc, mol_s2, mf_s2, eris
mol = gto.Mole()
mol.verbose = 7
mol.output = '/dev/null'
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = '631g'
mol.build()
rhf = scf.RHF(mol)
rhf.conv_tol_grad = 1e-8
rhf.kernel()
mf = scf.addons.convert_to_uhf(rhf)
myucc = cc.UCCSD(mf).run(conv_tol=1e-10)
mol_s2 = gto.Mole()
mol_s2.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol_s2.basis = '631g'
mol_s2.spin = 2
mol_s2.verbose = 5
mol_s2.output = '/dev/null'
mol_s2.build()
mf_s2 = scf.UHF(mol_s2).run()
eris = uccsd.UCCSD(mf_s2).ao2mo()
def test_uccsd_t(self):
mf1 = copy.copy(mf)
nao, nmo = mf.mo_coeff[0].shape
numpy.random.seed(10)
mf1.mo_coeff = numpy.random.random((2, nao, nmo))
numpy.random.seed(12)
nocca, noccb = mol.nelec
nmo = mf1.mo_occ[0].size
nvira = nmo - nocca
nvirb = nmo - noccb
t1a = .1 * numpy.random.random((nocca, nvira))
t1b = .1 * numpy.random.random((noccb, nvirb))
t2aa = .1 * numpy.random.random((nocca, nocca, nvira, nvira))
t2aa = t2aa - t2aa.transpose(0, 1, 3, 2)
t2aa = t2aa - t2aa.transpose(1, 0, 2, 3)
t2bb = .1 * numpy.random.random((noccb, noccb, nvirb, nvirb))
t2bb = t2bb - t2bb.transpose(0, 1, 3, 2)
t2bb = t2bb - t2bb.transpose(1, 0, 2, 3)
t2ab = .1 * numpy.random.random((nocca, noccb, nvira, nvirb))
t1 = t1a, t1b
t2 = t2aa, t2ab, t2bb
mycc = cc.UCCSD(mf1)
eris = mycc.ao2mo(mf1.mo_coeff)
e3a = uccsd_t.kernel(mycc, eris, [t1a, t1b], [t2aa, t2ab, t2bb])
self.assertAlmostEqual(e3a, 8193.064821311109, 5)
e3a = mcc.ccsd_t()
self.assertAlmostEqual(e3a, -0.0009857042572475674, 11)
def test_uccsd_grad(self):
mol = gto.Mole()
mol.verbose = 0
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.spin = 2
mol.basis = '631g'
mol.build(0, 0)
mf = scf.UHF(mol)
mf.conv_tol_grad = 1e-8
mf.kernel()
mycc = cc.UCCSD(mf)
mycc.max_memory = 1
mycc.conv_tol = 1e-10
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
g_scan = mycc.nuc_grad_method().as_scanner()
g1 = g_scan(mol.atom)[1]
self.assertAlmostEqual(lib.finger(g1), -0.22892720804519961, 6)
cc_scanner = mycc.as_scanner()
mol.set_geom_(
[[8,
(0., 0., 0.001)], [1,
(0., -0.757, 0.587)], [1,
(0., 0.757, 0.587)]],
unit='Ang')
e1 = cc_scanner(mol)
mol.set_geom_([[8, (0., 0., -0.001)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
unit='Ang')
e2 = cc_scanner(mol)
self.assertAlmostEqual(g1[0, 2], (e1 - e2) / .002 * lib.param.BOHR, 5)
def get_ccsdt_energy(self):
#if self.spin == 0:
mf = scf.RHF(self.mol).run()
mycc = cc.UCCSD(mf)
t = mycc.kernel()
e = uccsd_t.kernel(mycc, mycc.ao2mo())
return e
def test_frozen(self):
mf1 = scf.UHF(mol1).run()
# Freeze 1s electrons
frozen = [[0, 1], [0, 1]]
ucc = cc.UCCSD(mf1, frozen=frozen)
ecc, t1, t2 = ucc.kernel()
self.assertAlmostEqual(ecc, -0.34869875247588372, 8)
def test_uccsd_t(self):
mf1 = copy.copy(mf)
nao, nmo = mf.mo_coeff[0].shape
numpy.random.seed(10)
mf1.mo_coeff = numpy.random.random((2,nao,nmo)) - .5
numpy.random.seed(12)
nocca, noccb = mol.nelec
nmo = mf1.mo_occ[0].size
nvira = nmo - nocca
nvirb = nmo - noccb
t1a = .1 * numpy.random.random((nocca,nvira))
t1b = .1 * numpy.random.random((noccb,nvirb))
t2aa = .1 * numpy.random.random((nocca,nocca,nvira,nvira))
t2aa = t2aa - t2aa.transpose(0,1,3,2)
t2aa = t2aa - t2aa.transpose(1,0,2,3)
t2bb = .1 * numpy.random.random((noccb,noccb,nvirb,nvirb))
t2bb = t2bb - t2bb.transpose(0,1,3,2)
t2bb = t2bb - t2bb.transpose(1,0,2,3)
t2ab = .1 * numpy.random.random((nocca,noccb,nvira,nvirb))
t1 = t1a, t1b
t2 = t2aa, t2ab, t2bb
mycc = cc.UCCSD(mf1)
eris = mycc.ao2mo(mf1.mo_coeff)
mycc.incore_complete = True
e3a = mycc.ccsd_t([t1a,t1b], [t2aa, t2ab, t2bb], eris)
self.assertAlmostEqual(e3a, 15.582860941071505, 8)
mycc.incore_complete = False
mycc.max_memory = 0
e3a = uccsd_t.kernel(mycc, eris, [t1a,t1b], [t2aa, t2ab, t2bb])
self.assertAlmostEqual(e3a, 15.582860941071505, 8)
e3a = mcc.ccsd_t()
self.assertAlmostEqual(e3a, -0.0009857042572475674, 11)
def test_uccsd_frozen(self):
# Freeze 1s electrons
frozen = [[0, 1], [0, 1]]
ucc = cc.UCCSD(mf_s2, frozen=frozen)
ucc.diis_start_cycle = 1
ecc, t1, t2 = ucc.kernel()
self.assertAlmostEqual(ecc, -0.07414978284611283, 8)
def test_eomee(self):
ucc = cc.UCCSD(mf)
ecc, t1, t2 = ucc.kernel()
self.assertAlmostEqual(ecc, -0.2133432430989155, 6)
e, v = ucc.eeccsd(nroots=4)
self.assertAlmostEqual(e[0], 0.2757159395886167, 6)
self.assertAlmostEqual(e[1], 0.2757159395886167, 6)
self.assertAlmostEqual(e[2], 0.2757159395886167, 6)
self.assertAlmostEqual(e[3], 0.3005716731825082, 6)
def test_uccsd_rdm2_mo2ao(self):
mol = gto.Mole()
mol.verbose = 0
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.spin = 2
mol.basis = '631g'
mol.build(0, 0)
mf = scf.UHF(mol)
mf.conv_tol_grad = 1e-8
mf.kernel()
mycc = cc.UCCSD(mf)
mycc.diis_start_cycle = 1
mycc.conv_tol = 1e-10
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
fdm2 = lib.H5TmpFile()
d2 = cc.uccsd_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, fdm2, True)
nao = mycc.mo_coeff[0].shape[0]
ref = cc.uccsd_rdm._make_rdm2(mycc, None, d2, with_dm1=False)
aa = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[0], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[0], mycc.mo_coeff[0])
ab = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[1], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[1], mycc.mo_coeff[1])
bb = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[2], mycc.mo_coeff[1],
mycc.mo_coeff[1], mycc.mo_coeff[1], mycc.mo_coeff[1])
aa = aa + aa.transpose(0, 1, 3, 2)
aa = aa + aa.transpose(1, 0, 2, 3)
aa = ao2mo.restore(4, aa, nao) * .5
bb = bb + bb.transpose(0, 1, 3, 2)
bb = bb + bb.transpose(1, 0, 2, 3)
bb = ao2mo.restore(4, bb, nao) * .5
ab = ab + ab.transpose(0, 1, 3, 2)
ab = ab + ab.transpose(1, 0, 2, 3)
ab = ao2mo.restore(4, ab, nao) * .5
ref = (aa + ab, bb + ab.T)
rdm2 = uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff)
self.assertAlmostEqual(abs(ref[0] - rdm2[0]).max(), 0, 10)
self.assertAlmostEqual(abs(ref[1] - rdm2[1]).max(), 0, 10)
uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff, fdm2)
self.assertAlmostEqual(
abs(ref[0] - fdm2['dm2aa+ab'].value).max(), 0, 10)
self.assertAlmostEqual(
abs(ref[1] - fdm2['dm2bb+ab'].value).max(), 0, 10)
self.assertAlmostEqual(lib.finger(rdm2[0]), -1.6247203743431637, 7)
self.assertAlmostEqual(lib.finger(rdm2[1]), -0.44062825991527471, 7)
def setUpModule():
global mol, mol1, mf, myucc, mygcc
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [[8, (0., 0., 0.)], [1, (0., -.757, .587)],
[1, (0., .757, .587)]]
mol.spin = 2
mol.basis = '3-21g'
mol.symmetry = 'C2v'
mol.build()
mol1 = copy.copy(mol)
mol1.symmetry = False
mf = scf.UHF(mol1).run(conv_tol=1e-14)
myucc = cc.UCCSD(mf).run()
mygcc = cc.GCCSD(mf).run()
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [
[8 , (0. , 0. , 0.)],
[1 , (0. , -.757 , .587)],
[1 , (0. , .757 , .587)]]
mol.spin = 2
mol.basis = '3-21g'
mol.symmetry = 'C2v'
mol.build()
mol1 = copy.copy(mol)
mol1.symmetry = False
mf = scf.UHF(mol1).run(conv_tol=1e-14)
myucc = cc.UCCSD(mf).run()
mygcc = cc.GCCSD(mf).run()
def tearDownModule():
global mol, mol1, mf, myucc, mygcc
mol.stdout.close()
del mol, mol1, mf, myucc, mygcc
class KnownValues(unittest.TestCase):
def test_gccsd_t_compare_uccsd_t(self):
self.assertAlmostEqual(myucc.ccsd_t(), mygcc.ccsd_t(t1=None), 7)
def test_gccsd_t(self):
mf1 = copy.copy(mf)
nao, nmo = mf.mo_coeff[0].shape
numpy.random.seed(10)
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -.757, .587)],
[1, (0., .757, .587)]]
mol.basis = '631g'
mol.build()
rhf = scf.RHF(mol)
rhf.conv_tol = 1e-14
rhf.scf()
mcc = cc.CCSD(rhf)
mcc.conv_tol = 1e-12
mcc.ccsd()
t1a = t1b = mcc.t1
t2ab = mcc.t2
t2aa = t2bb = t2ab - t2ab.transpose(1, 0, 2, 3)
mycc = cc.UCCSD(scf.addons.convert_to_uhf(rhf))
eris = mycc.ao2mo()
e3a = kernel(mycc, eris, (t1a, t1b), (t2aa, t2ab, t2bb))
print(e3a - -0.00099642337843278096)
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -.757, .587)],
[1, (0., .757, .587)]]
mol.spin = 2
mol.basis = '3-21g'
mol.build()
mf = scf.UHF(mol).run(conv_tol=1e-14)
nao, nmo = mf.mo_coeff[0].shape
numpy.random.seed(10)
mf.mo_coeff = numpy.random.random((2, nao, nmo))
from pyscf.fci import direct_uhf
mol = gto.Mole()
mol.verbose = 7
mol.output = '/dev/null'
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = '631g'
mol.build()
rhf = scf.RHF(mol)
rhf.conv_tol_grad = 1e-8
rhf.kernel()
mf = scf.addons.convert_to_uhf(rhf)
myucc = cc.UCCSD(mf).run(conv_tol=1e-10)
mol_s2 = gto.Mole()
mol_s2.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol_s2.basis = '631g'
mol_s2.spin = 2
mol_s2.verbose = 5
mol_s2.output = '/dev/null'
mol_s2.build()
mf_s2 = scf.UHF(mol_s2).run()
eris = uccsd.UCCSD(mf_s2).ao2mo()
def tearDownModule():
global mol, rhf, mf, myucc, mol_s2, mf_s2, eris
mol.verbose = 4
mol.atom = '''
O 0.000000 0.000000 0.118351
H 0.000000 0.761187 -0.469725
H 0.000000 -0.761187 -0.469725
'''
mol.basis = 'sto-3g'
mol.symmetry = 0
mol.build()
a = scf.UHF(mol)
ehf = a.scf()
####### This can be removed ######
frozen = [[0], [0]] # 1sa and 1sb
mcc = cc.UCCSD(a)
mcc.frozen = frozen
mcc.diis_space = 10
mcc.conv_tol = 1e-6
mcc.conv_tol_normt = 1e-6
mcc.max_cycle = 150
ecc = mcc.kernel()[0]
eris = mcc.ao2mo()
e3 = uccsd_t.kernel(mcc, eris, mcc.t1, mcc.t2)
lib.logger.info(mcc, "* CCSD(T) energy : %12.6f" % (ehf + ecc + e3))
l1, l2 = uccsd_t_lambda.kernel(mcc, eris, mcc.t1, mcc.t2)[1:]
rdm1a, rdm1b = uccsd_t_rdm.make_rdm1(mcc, mcc.t1, mcc.t2, l1, l2, eris=eris)
rdm2aa, rdm2ab, rdm2bb = uccsd_t_rdm.make_rdm2(mcc,
mcc.t1,
mcc.t2,
def test_with_df_s2(self):
mf = scf.UHF(mol_s2).density_fit(auxbasis='weigend').run()
mycc = cc.UCCSD(mf).run()
self.assertAlmostEqual(mycc.e_tot, -75.83360033370676, 7)
numpy.random.seed(12)
mf1.mo_coeff = numpy.random.random((2, n, n))
dm = mf1.make_rdm1(mf1.mo_coeff, mf1.mo_occ)
fockao = mf1.get_hcore() + mf1.get_veff(mol1, dm)
mo_energya = numpy.einsum('pi,pq,qi->i', mf1.mo_coeff[0], fockao[0],
mf1.mo_coeff[0])
mo_energyb = numpy.einsum('pi,pq,qi->i', mf1.mo_coeff[1], fockao[1],
mf1.mo_coeff[1])
idxa = numpy.hstack(
[mo_energya[:no // 2].argsort(), no // 2 + mo_energya[no // 2:].argsort()])
idxb = numpy.hstack(
[mo_energyb[:no // 2].argsort(), no // 2 + mo_energyb[no // 2:].argsort()])
mf1.mo_coeff[0] = mf1.mo_coeff[0][:, idxa]
mf1.mo_coeff[1] = mf1.mo_coeff[1][:, idxb]
ucc1 = cc.UCCSD(mf1)
ucc1.eris = eris = ucc1.ao2mo()
numpy.random.seed(12)
r1 = numpy.random.random((no, nv)) - .9
r2 = numpy.random.random((no, no, nv, nv)) - .9
r1, r2 = ucc1.vector_to_amplitudes_ee(ucc1.amplitudes_to_vector_ee(r1, r2))
r1 = ucc1.spin2spatial(r1, eris.orbspin)
r2 = ucc1.spin2spatial(r2, eris.orbspin)
ucc1.eris = eris
ucc1.t1 = [x * 1e-5 for x in r1]
ucc1.t2 = [x * 1e-5 for x in r2]
class KnowValues(unittest.TestCase):
def test_frozen(self):
def test_ERIS(self):
ucc1 = cc.UCCSD(mf)
nao, nmo = mf.mo_coeff[0].shape
numpy.random.seed(1)
mo_coeff = numpy.random.random((2, nao, nmo))
eris = cc.uccsd._make_eris_incore(ucc1, mo_coeff)
self.assertAlmostEqual(lib.finger(eris.oooo), 4.9638849382825754, 11)
self.assertAlmostEqual(lib.finger(eris.ovoo), -1.3623681896983584, 11)
self.assertAlmostEqual(lib.finger(eris.ovov), 125.81550684442163, 11)
self.assertAlmostEqual(lib.finger(eris.oovv), 55.123681017639598, 11)
self.assertAlmostEqual(lib.finger(eris.ovvo), 133.48083527898248, 11)
self.assertAlmostEqual(lib.finger(eris.ovvv), 59.421927525288183, 11)
self.assertAlmostEqual(lib.finger(eris.vvvv), 43.556602622204778, 11)
self.assertAlmostEqual(lib.finger(eris.OOOO), -407.05319440524585, 11)
self.assertAlmostEqual(lib.finger(eris.OVOO), 56.284299937160796, 11)
self.assertAlmostEqual(lib.finger(eris.OVOV), -287.72899895597448, 11)
self.assertAlmostEqual(lib.finger(eris.OOVV), -85.484299959144522, 11)
self.assertAlmostEqual(lib.finger(eris.OVVO), -228.18996145476956, 11)
self.assertAlmostEqual(lib.finger(eris.OVVV), -10.715902258877399, 11)
self.assertAlmostEqual(lib.finger(eris.VVVV), -89.908425473958303, 11)
self.assertAlmostEqual(lib.finger(eris.ooOO), -336.65979260175226, 11)
self.assertAlmostEqual(lib.finger(eris.ovOO), -16.405125847288176, 11)
self.assertAlmostEqual(lib.finger(eris.ovOV), 231.59042209500075, 11)
self.assertAlmostEqual(lib.finger(eris.ooVV), 20.338077193028354, 11)
self.assertAlmostEqual(lib.finger(eris.ovVO), 206.48662856981386, 11)
self.assertAlmostEqual(lib.finger(eris.ovVV), -71.273249852220516, 11)
self.assertAlmostEqual(lib.finger(eris.vvVV), 172.47130671068496, 11)
self.assertAlmostEqual(lib.finger(eris.OVoo), -19.927660309103977, 11)
self.assertAlmostEqual(lib.finger(eris.OOvv), -27.761433381797019, 11)
self.assertAlmostEqual(lib.finger(eris.OVvo), -140.09648311337384, 11)
self.assertAlmostEqual(lib.finger(eris.OVvv), 40.700983950220547, 11)
uccsd.MEMORYMIN, bak = 0, uccsd.MEMORYMIN
ucc1.max_memory = 0
eris1 = ucc1.ao2mo(mo_coeff)
uccsd.MEMORYMIN = bak
self.assertAlmostEqual(
abs(numpy.array(eris1.oooo) - eris.oooo).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovoo) - eris.ovoo).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovov) - eris.ovov).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.oovv) - eris.oovv).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovvo) - eris.ovvo).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovvv) - eris.ovvv).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.vvvv) - eris.vvvv).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OOOO) - eris.OOOO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVOO) - eris.OVOO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVOV) - eris.OVOV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OOVV) - eris.OOVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVVO) - eris.OVVO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVVV) - eris.OVVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.VVVV) - eris.VVVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ooOO) - eris.ooOO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovOO) - eris.ovOO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovOV) - eris.ovOV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ooVV) - eris.ooVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovVO) - eris.ovVO).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.ovVV) - eris.ovVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.vvVV) - eris.vvVV).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVoo) - eris.OVoo).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OOvv) - eris.OOvv).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVvo) - eris.OVvo).max(), 0, 11)
self.assertAlmostEqual(
abs(numpy.array(eris1.OVvv) - eris.OVvv).max(), 0, 11)
# Testing the complex MO integrals
def ao2mofn(mos):
if isinstance(mos, numpy.ndarray) and mos.ndim == 2:
mos = [mos] * 4
nmos = [mo.shape[1] for mo in mos]
eri_mo = ao2mo.kernel(mf._eri, mos, compact=False).reshape(nmos)
return eri_mo * 1j
eris1 = cc.uccsd._make_eris_incore(ucc1, mo_coeff, ao2mofn=ao2mofn)
self.assertAlmostEqual(abs(eris1.oooo.imag - eris.oooo).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovoo.imag - eris.ovoo).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovov.imag - eris.ovov).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.oovv.imag - eris.oovv).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovvo.imag - eris.ovvo).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.ovvv.imag-eris.ovvv).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.vvvv.imag-eris.vvvv).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OOOO.imag - eris.OOOO).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OVOO.imag - eris.OVOO).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OVOV.imag - eris.OVOV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OOVV.imag - eris.OOVV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OVVO.imag - eris.OVVO).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.OVVV.imag-eris.OVVV).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.VVVV.imag-eris.VVVV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ooOO.imag - eris.ooOO).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovOO.imag - eris.ovOO).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovOV.imag - eris.ovOV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ooVV.imag - eris.ooVV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.ovVO.imag - eris.ovVO).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.ovVV.imag-eris.ovVV).max(), 0, 11)
#self.assertAlmostEqual(abs(eris1.vvVV.imag-eris.vvVV).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OVoo.imag - eris.OVoo).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OOvv.imag - eris.OOvv).max(), 0, 11)
self.assertAlmostEqual(abs(eris1.OVvo.imag - eris.OVvo).max(), 0, 11)
print(abs(trdm2 - dm2ref).max())
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = '631g'
mol.spin = 2
mol.charge = 2
mol.build()
mf0 = mf = scf.UHF(mol).run(conv_tol=1)
mf = scf.addons.convert_to_ghf(mf)
from pyscf.cc import uccsd_t_slow
from pyscf.cc import uccsd_t_lambda
from pyscf.cc import uccsd_t_rdm
mycc0 = cc.UCCSD(mf0)
eris0 = mycc0.ao2mo()
mycc0.kernel(eris=eris0)
t1 = mycc0.t1
t2 = mycc0.t2
imds = uccsd_t_lambda.make_intermediates(mycc0, t1, t2, eris0)
l1, l2 = uccsd_t_lambda.update_lambda(mycc0, t1, t2, t1, t2, eris0, imds)
dm1ref = uccsd_t_rdm.make_rdm1(mycc0, t1, t2, l1, l2, eris0)
dm2ref = uccsd_t_rdm.make_rdm2(mycc0, t1, t2, l1, l2, eris0)
mycc = cc.GCCSD(mf)
eris = mycc.ao2mo()
t1 = mycc.spatial2spin(t1, mycc.mo_coeff.orbspin)
t2 = mycc.spatial2spin(t2, mycc.mo_coeff.orbspin)
l1 = mycc.spatial2spin(l1, mycc.mo_coeff.orbspin)
l2 = mycc.spatial2spin(l2, mycc.mo_coeff.orbspin)
mol1 = mol.copy()
mol1.spin = 2
mol1.build()
mf0 = scf.UHF(mol1).run(conv_tol=1e-12)
mf1 = copy.copy(mf0)
nocca, noccb = mol1.nelec
nmo = mol1.nao_nr()
nvira, nvirb = nmo-nocca, nmo-noccb
numpy.random.seed(12)
mf1.mo_coeff = numpy.random.random((2,nmo,nmo)) - .5
gmf = scf.addons.convert_to_ghf(mf1)
orbspin = gmf.mo_coeff.orbspin
ucc1 = cc.UCCSD(mf1)
eris1 = ucc1.ao2mo()
numpy.random.seed(11)
no = nocca + noccb
nv = nvira + nvirb
r1 = numpy.random.random((no,nv)) - .9
r2 = numpy.random.random((no,no,nv,nv)) - .9
r2 = r2 - r2.transpose(1,0,2,3)
r2 = r2 - r2.transpose(0,1,3,2)
r1 = cc.addons.spin2spatial(r1, orbspin)
r2 = cc.addons.spin2spatial(r2, orbspin)
r1,r2 = eom_uccsd.vector_to_amplitudes_ee(
eom_uccsd.amplitudes_to_vector_ee(r1,r2), ucc1.nmo, ucc1.nocc)
ucc1.t1 = r1
ucc1.t2 = r2
def ecw_energy(self, method, dim):
mf_energy, Vemb, Vxc = self.imp_mf_energy(dim)
Ne_frag = self.Ne_frag
ops = self.ops
subOEI = ops["subKin"] + ops["subVnuc1"] + Vemb
subTEI = ops["subTEI"]
mf = qcwrap.qc_scf(Ne_frag,
dim,
'hf',
mol=self.mol_frag,
oei=subOEI,
tei=subTEI,
dm0=self.P_imp)
mf.runscf()
e_hf = mf.elec_energy # - np.trace(np.dot(mf.rdm1,Vemb))
if (self.plot_mo):
self.ints.submo_molden(mf.mo_coeff, mf.mo_occ, self.loc2sub,
"mo_frag.molden", self.mol_frag)
exc = 0.0
if (Vxc is not None):
# exc = np.einsum('ij,ji', Vxc, mf.rdm1-self.P_imp)
exc = np.einsum('ij,ji', Vxc, self.P_imp)
print('exc = ', exc)
if (method == 'hf'):
energy = e_hf
elif (method == 'mp2'):
mp2 = mp.MP2(mf)
mp2.kernel()
energy = e_hf + mp2.e_corr
elif (method == 'ccsd' or method == 'ccsd(t)'):
mycc = cc.CCSD(mf)
mycc.max_cycle = 200
#mycc.conv_tol = 1e-6
#mycc.conv_tol_normt = 1e-4
mycc.kernel()
et = 0.0
if (method == 'ccsd(t)'):
print('CCSD(T) correction')
et = mycc.ccsd_t()
energy = e_hf + mycc.e_corr + et
elif (method == 'eomccsd'):
mf.verbose = 5
mycc = cc.RCCSD(mf)
mycc.kernel()
es, vs = mycc.eomee_ccsd_singlet(nroots=self.ex_nroots)
if (self.ex_nroots == 1):
r1, r2 = mycc.vector_to_amplitudes(vs)
print('debug: ', r1.shape)
else:
for vn in vs:
r1, r2 = mycc.vector_to_amplitudes(vn)
energy = e_hf + mycc.e_corr
elif (method == 'eomsfccsd'):
self.mol_frag.spin = 2
mf = qcwrap.pyscf_rks.rohf_pyscf(Ne_frag,
dim,
mol=self.mol_frag,
oei=subOEI,
tei=subTEI,
dm0=np.array((.5 * self.P_imp,
.5 * self.P_imp)))
mf.kernel(dm0=mf.dm_guess)
mf1 = qcwrap.pyscf_rks.uhf_pyscf(Ne_frag,
dim,
mol=self.mol_frag,
oei=subOEI,
tei=subTEI,
dm0=None)
mf1.convert_from_rhf(mf)
mycc = cc.UCCSD(mf1)
mycc.verbose = 5
mycc.kernel()
es, vs = mycc.eomsf_ccsd(nroots=self.ex_nroots)
if (self.ex_nroots == 1):
r1, r2 = cc.eom_uccsd.vector_to_amplitudes_eomsf(
vs, mycc.nmo, mycc.nocc)
tools.print_eomcc_t1(r1[0])
tools.print_eomcc_t1(r1[1])
else:
for vn in vs:
r1, r2 = cc.eom_uccsd.vector_to_amplitudes_eomsf(
vn, mycc.nmo, mycc.nocc)
tools.print_eomcc_t1(r1[0])
tools.print_eomcc_t1(r1[1])
energy = mf1.e_tot + mycc.e_corr
else:
raise Exception("ecw_method not supported!")
energy -= mf_energy
energy -= exc
return energy
eris0 = mycc0.ao2mo()
mycc0.kernel(eris=eris0)
t1 = mycc0.t1
t2 = mycc0.t2
imds = ccsd_t_lambda.make_intermediates(mycc0, t1, t2, eris0)
l1, l2 = ccsd_t_lambda.update_lambda(mycc0, t1, t2, t1, t2, eris0, imds)
dm1ref = ccsd_t_rdm.make_rdm1(mycc0, t1, t2, l1, l2, eris0)
dm2ref = ccsd_t_rdm.make_rdm2(mycc0, t1, t2, l1, l2, eris0)
t1 = (t1, t1)
t2aa = t2 - t2.transpose(1, 0, 2, 3)
t2 = (t2aa, t2, t2aa)
l1 = (l1, l1)
l2aa = l2 - l2.transpose(1, 0, 2, 3)
l2 = (l2aa, l2, l2aa)
mycc = cc.UCCSD(mf)
eris = mycc.ao2mo()
dm1 = make_rdm1(mycc, t1, t2, l1, l2, eris)
dm2 = make_rdm2(mycc, t1, t2, l1, l2, eris)
trdm1 = dm1[0] + dm1[1]
trdm2 = dm2[0] + dm2[1] + dm2[1].transpose(2, 3, 0, 1) + dm2[2]
print(abs(trdm1 - dm1ref).max())
print(abs(trdm2 - dm2ref).max())
ecc = mycc.kernel(eris=eris)[0]
l1, l2 = mycc.solve_lambda(eris=eris)
e3ref = mycc.e_tot + mycc.ccsd_t()
nmoa, nmob = mycc.nmo
eri_aa = ao2mo.kernel(mf._eri, mf.mo_coeff[0],
compact=False).reshape([nmoa] * 4)
def test_with_df_s0(self):
mf = scf.UHF(mol).density_fit(auxbasis='weigend').run()
mycc = cc.UCCSD(mf).run()
self.assertAlmostEqual(mycc.e_tot, -76.118403942938741, 7)
def test_uccsd_t_complex(self):
mol = gto.M()
numpy.random.seed(12)
nocca, noccb, nvira, nvirb = 3, 2, 4, 5
nmo = nocca + nvira
eris = cc.uccsd._ChemistsERIs()
eris.nocca = nocca
eris.noccb = noccb
eris.nocc = (nocca, noccb)
eri1 = (numpy.random.random((3,nmo,nmo,nmo,nmo)) +
numpy.random.random((3,nmo,nmo,nmo,nmo)) * .8j - .5-.4j)
eri1 = eri1 + eri1.transpose(0,2,1,4,3).conj()
eri1[0] = eri1[0] + eri1[0].transpose(2,3,0,1)
eri1[2] = eri1[2] + eri1[2].transpose(2,3,0,1)
eri1 *= .1
eris.ovvv = eri1[0,:nocca,nocca:,nocca:,nocca:]
eris.ovov = eri1[0,:nocca,nocca:,:nocca,nocca:]
eris.ovoo = eri1[0,:nocca,nocca:,:nocca,:nocca]
eris.OVVV = eri1[2,:noccb,noccb:,noccb:,noccb:]
eris.OVOV = eri1[2,:noccb,noccb:,:noccb,noccb:]
eris.OVOO = eri1[2,:noccb,noccb:,:noccb,:noccb]
eris.voVP = eri1[1,nocca:,:nocca,noccb:,: ]
eris.ovVV = eri1[1,:nocca,nocca:,noccb:,noccb:]
eris.ovOV = eri1[1,:nocca,nocca:,:noccb,noccb:]
eris.ovOO = eri1[1,:nocca,nocca:,:noccb,:noccb]
eris.OVvv = eri1[1,nocca:,nocca:,:noccb,noccb:].transpose(2,3,0,1)
eris.OVoo = eri1[1,:nocca,:nocca,:noccb,noccb:].transpose(2,3,0,1)
t1a = .1 * numpy.random.random((nocca,nvira)) + numpy.random.random((nocca,nvira))*.1j
t1b = .1 * numpy.random.random((noccb,nvirb)) + numpy.random.random((noccb,nvirb))*.1j
t2aa = .1 * numpy.random.random((nocca,nocca,nvira,nvira)) + numpy.random.random((nocca,nocca,nvira,nvira))*.1j
t2aa = t2aa - t2aa.transpose(0,1,3,2)
t2aa = t2aa - t2aa.transpose(1,0,2,3)
t2bb = .1 * numpy.random.random((noccb,noccb,nvirb,nvirb)) + numpy.random.random((noccb,noccb,nvirb,nvirb))*.1j
t2bb = t2bb - t2bb.transpose(0,1,3,2)
t2bb = t2bb - t2bb.transpose(1,0,2,3)
t2ab = .1 * numpy.random.random((nocca,noccb,nvira,nvirb)) + numpy.random.random((nocca,noccb,nvira,nvirb))*.1j
f = (numpy.random.random((2,nmo,nmo)) * .4 +
numpy.random.random((2,nmo,nmo)) * .4j)
eris.focka = f[0]+f[0].T.conj() + numpy.diag(numpy.arange(nmo))
eris.fockb = f[1]+f[1].T.conj() + numpy.diag(numpy.arange(nmo))
eris.mo_energy = (eris.focka.diagonal().real,
eris.fockb.diagonal().real)
t1 = t1a, t1b
t2 = t2aa, t2ab, t2bb
mcc = cc.UCCSD(scf.UHF(mol))
mcc.nocc = eris.nocc
e0 = uccsd_t.kernel(mcc, eris, t1, t2)
eri2 = numpy.zeros((nmo*2,nmo*2,nmo*2,nmo*2), dtype=eri1.dtype)
orbspin = numpy.zeros(nmo*2,dtype=int)
orbspin[1::2] = 1
eri2[0::2,0::2,0::2,0::2] = eri1[0]
eri2[1::2,1::2,0::2,0::2] = eri1[1].transpose(2,3,0,1)
eri2[0::2,0::2,1::2,1::2] = eri1[1]
eri2[1::2,1::2,1::2,1::2] = eri1[2]
eri2 = eri2.transpose(0,2,1,3) - eri2.transpose(0,2,3,1)
fock = numpy.zeros((nmo*2,nmo*2), dtype=eris.focka.dtype)
fock[0::2,0::2] = eris.focka
fock[1::2,1::2] = eris.fockb
eris1 = gccsd._PhysicistsERIs()
nocc = nocca + noccb
eris1.ovvv = eri2[:nocc,nocc:,nocc:,nocc:]
eris1.oovv = eri2[:nocc,:nocc,nocc:,nocc:]
eris1.ooov = eri2[:nocc,:nocc,:nocc,nocc:]
eris1.fock = fock
eris1.mo_energy = fock.diagonal().real
t1 = gccsd.spatial2spin(t1, orbspin)
t2 = gccsd.spatial2spin(t2, orbspin)
gcc = gccsd.GCCSD(scf.GHF(gto.M()))
e1 = gccsd_t.kernel(gcc, eris1, t1, t2)
self.assertAlmostEqual(e0, e1.real, 9)
self.assertAlmostEqual(e1, -0.056092415718338388-0.011390417704868244j, 9)
def do_scf(inp):
'''Do the requested SCF.'''
from pyscf import gto, scf, dft, cc, fci, ci, ao2mo, mcscf, mrpt, lib, mp, tdscf
from pyscf.cc import ccsd_t, uccsd_t
import numpy as np
from .fcidump import fcidump
# sort out the method
mol = inp.mol
method = inp.scf.method.lower()
# UHF
if method == 'uhf':
ehf, mSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
if inp.scf.exci is not None:
inp.timer.start('TDHF')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDHF')
# RHF
elif method in ('rhf', 'hf'):
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
if inp.scf.exci is not None:
inp.timer.start('TDHF')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDHF')
# CCSD and CCSD(T)
elif method in ('ccsd', 'ccsd(t)', 'uccsd', 'uccsd(t)', 'eomccsd'):
if 'u' in method:
ehf, tSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
else:
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('ccsd')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
if 'u' in method:
mSCF = cc.UCCSD(tSCF, frozen=frozen)
else:
mSCF = cc.CCSD(tSCF, frozen=frozen)
mSCF.max_cycle = inp.scf.maxiter
eccsd, t1, t2 = mSCF.kernel()
print_energy('CCSD', ehf + eccsd)
inp.timer.end('ccsd')
if method == 'eomccsd':
inp.timer.start('eomccsd')
ee = mSCF.eomee_ccsd_singlet(nroots=4)[0]
inp.timer.end('eomccsd')
for i in range(len(ee)):
print_energy('EOM-CCSD {0} (eV)'.format(i+1), ee[i] * 27.2114)
if method in ('ccsd(t)', 'uccsd(t)'):
inp.timer.start('ccsd(t)')
eris = mSCF.ao2mo()
if method == 'ccsd(t)':
e3 = ccsd_t.kernel(mSCF, eris)
else:
e3 = uccsd_t.kernel(mSCF, eris)
print_energy('CCSD(T)', ehf + eccsd + e3)
inp.timer.end('ccsd(t)')
# MP2
elif method == 'mp2':
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('mp2')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
mSCF = mp.MP2(tSCF, frozen=frozen)
emp2, t2 = mSCF.kernel()
print_energy('MP2', ehf+emp2)
inp.timer.end('mp2')
# CISD
elif method == 'cisd' or method == 'cisd(q)':
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('cisd')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
mSCF = ci.CISD(tSCF, frozen=frozen)
ecisd = mSCF.kernel()[0]
print_energy('CISD', ehf + ecisd)
inp.timer.end('cisd')
# perform Davison quadruples correction
c0 = np.max(np.abs(mSCF.ci))
c02 = c0**2
ne = mSCF.mol.nelectron
eq = ( 1.0 - c02 ) * ecisd
print_energy('CISD(Q) Davidson', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / c02 * ecisd
print_energy('CISD(Q) Renomalized-Davidson', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / ( 2.0 * c02 - 1.0 ) * ecisd
print_energy('CISD(Q) Davison-Silver', ehf + ecisd + eq)
eq = (( 2.0 * c02 ) / ((2.0*c02-1.0)*(1.0 + np.sqrt(1.0 + (8.0*c02*(1.0-c02))
/ ( ne * (2.0*c02-1.0)**2 )))) - 1.0 ) * ecisd
print_energy('CISD(Q) PC', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / c02 * ((ne-2)*(ne-3.0)) / (ne*(ne-1.0)) * ecisd
print_energy('CISD(Q) MC', ehf + ecisd + eq)
if ne > 2:
eq = ( 2.0 - c02 ) / (2.0 * (ne-1.0)/(ne-2.0) * c02 - 1.0)
else:
eq = 0.0
print_energy('CISD(Q) DD', ehf + ecisd + eq)
# UKS
elif method in ('uks' or 'udft'):
inp.timer.start('uks')
inp.timer.start('grids')
grids = dft.gen_grid.Grids(mol)
grids.level = inp.scf.grid
grids.build()
inp.timer.end('grids')
mSCF = dft.UKS(mol)
mSCF.grids = grids
mSCF.xc = inp.scf.xc
mSCF.conv_tol = inp.scf.conv
mSCF.conv_tol_grad = inp.scf.grad
mSCF.max_cycle = inp.scf.maxiter
mSCF.init_guess = inp.scf.guess
mSCF.small_rho_cutoff = 1e-20
eks = mSCF.kernel()
print_energy('UKS', eks)
inp.timer.end('uks')
if inp.scf.exci is not None:
inp.timer.start('TDDFT')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDDFT')
# RKS
elif method in ('rks', 'ks', 'rdft', 'dft'):
inp.timer.start('ks')
inp.timer.start('grids')
grids = dft.gen_grid.Grids(mol)
grids.level = inp.scf.grid
grids.build()
inp.timer.end('grids')
if mol.nelectron%2 == 0:
mSCF = dft.RKS(mol)
else:
mSCF = dft.ROKS(mol)
mSCF.grids = grids
mSCF.xc = inp.scf.xc
mSCF.conv_tol = inp.scf.conv
mSCF.conv_tol_grad = inp.scf.grad
mSCF.max_cycle = inp.scf.maxiter
mSCF.init_guess = inp.scf.guess
mSCF.small_rho_cutoff = 1e-20
mSCF.damp = inp.scf.damp
mSCF.level_shift = inp.scf.shift
eks = mSCF.kernel()
print_energy('RKS', eks)
inp.timer.end('ks')
if inp.scf.exci is not None:
inp.timer.start('TDDFT')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDDFT')
# Unrestricted FCI
elif method == 'ufci':
ehf, mSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
inp.timer.start('fci')
cis = fci.direct_uhf.FCISolver(mol)
norb = mSCF.mo_energy[0].size
nea = (mol.nelectron+mol.spin) // 2
neb = (mol.nelectron-mol.spin) // 2
nelec = (nea, neb)
mo_a = mSCF.mo_coeff[0]
mo_b = mSCF.mo_coeff[1]
h1e_a = reduce(np.dot, (mo_a.T, mSCF.get_hcore(), mo_a))
h1e_b = reduce(np.dot, (mo_b.T, mSCF.get_hcore(), mo_b))
g2e_aa = ao2mo.incore.general(mSCF._eri, (mo_a,)*4, compact=False)
g2e_aa = g2e_aa.reshape(norb,norb,norb,norb)
g2e_ab = ao2mo.incore.general(mSCF._eri, (mo_a,mo_a,mo_b,mo_b), compact=False)
g2e_ab = g2e_ab.reshape(norb,norb,norb,norb)
g2e_bb = ao2mo.incore.general(mSCF._eri, (mo_b,)*4, compact=False)
g2e_bb = g2e_bb.reshape(norb,norb,norb,norb)
h1e = (h1e_a, h1e_b)
eri = (g2e_aa, g2e_ab, g2e_bb)
eci = fci.direct_uhf.kernel(h1e, eri, norb, nelec)[0]
print_energy('FCI', eci)
inp.timer.end('fci')
# FCI
elif method in ('fci'):
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('fci')
if inp.scf.freeze is None:
mCI = fci.FCI(mSCF)
if inp.scf.roots is not None:
mCI.nroots = inp.scf.roots
mCI.kernel()[0]
eci = mCI.eci
else:
nel = mol.nelectron - inp.scf.freeze * 2
ncas = mol.nao_nr() - inp.scf.freeze
if mol.spin == 0:
nelecas = nel
mCI = mcscf.CASCI(mSCF, ncas, nelecas)
mCI.fcisolver = fci.solver(mol)
else:
if mol.spin%2 == 0:
nelecas = (nel//2+mol.spin//2, nel//2-mol.spin//2)
else:
nelecas = (nel//2+mol.spin//2+1, nel//2-mol.spin//2)
mCI = mcscf.CASCI(mSCF, ncas, nelecas)
mCI.fcisolver = fci.direct_spin1.FCISolver(mol)
eci = mCI.kernel()[0]
dm = mCI.make_rdm1()
dip = mSCF.dip_moment(dm=dm)
if inp.scf.roots is None:
print_energy('FCI', eci)
else:
for i in range(inp.scf.roots):
print_energy('FCI {0}'.format(i), eci[i])
inp.timer.end('fci')
# CASCI
elif method == 'casci':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
inp.timer.start('casci')
mCI = mcscf.CASCI(mSCF, ncasorb, nelecas)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASCI', eci)
inp.timer.end('casci')
# CASSCF
elif method == 'casscf' or method == 'ucasscf':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
lunrestricted = (method == 'ucasscf')
ehf, mSCF = do_hf(inp, unrestricted=lunrestricted)
print_energy('HF', ehf)
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
inp.timer.start('casscf')
mCI = mcscf.CASSCF(mSCF, ncasorb, nelecas)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASSCF', eci)
inp.timer.end('casscf')
# NEVPT2
elif method == 'nevpt2' or method == 'unevpt2':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('casscf')
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
mCI = mcscf.CASSCF(mSCF, ncasorb, nelecas, frozen=inp.scf.freeze)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASSCF', eci)
inp.timer.end('casscf')
inp.timer.start('nevpt2')
mpt2 = mrpt.NEVPT(mCI)
ept2 = mpt2.kernel() + eci
print_energy('NEVPT2', ept2)
inp.timer.end('nevpt2')
else:
print ('ERROR: Unrecognized SCF method!')
raise SystemExit
# dump fcidump file if needed
if inp.fcidump:
if inp.filename[-4:].lower() == '.inp':
fcifile = inp.filename[:-4] + '.fcidump'
else:
fcifile = inp.filename + '.fcidump'
fcidump(mSCF, filename=fcifile, tol=1e-6)
# plot MOs if needed
if inp.mo2cube:
from .mo_2_cube import save_MOs
save_MOs(inp, mSCF, mSCF.mo_coeff)
# save molden file if needed
if inp.molden:
from pyscf.tools import molden
molden_file = inp.filename[:-4] + '.molden'
molden.from_mo(inp.mol, molden_file, mSCF.mo_coeff, ene=mSCF.mo_energy)
# save and return
inp.mf = mSCF
return inp
eri1 *= .1
eris.ovov = eri1[0,nocca:,:nocca,nocca:,:nocca].transpose(1,0,3,2).conj()
eris.ovvv = eri1[0,nocca:,:nocca,nocca:,nocca:].transpose(1,0,3,2).conj()
eris.ovoo = eri1[0,nocca:,:nocca,:nocca,:nocca].transpose(1,0,3,2).conj()
eris.OVOV = eri1[2,noccb:,:noccb,noccb:,:noccb].transpose(1,0,3,2).conj()
eris.OVVV = eri1[2,noccb:,:noccb,noccb:,noccb:].transpose(1,0,3,2).conj()
eris.OVOO = eri1[2,noccb:,:noccb,:noccb,:noccb].transpose(1,0,3,2).conj()
eris.ovOV = eri1[1,nocca:,:nocca,noccb:,:noccb].transpose(1,0,3,2).conj()
eris.ovVV = eri1[1,nocca:,:nocca,noccb:,noccb:].transpose(1,0,3,2).conj()
eris.ovOO = eri1[1,nocca:,:nocca,:noccb,:noccb].transpose(1,0,3,2).conj()
eris.OVov = eri1[1,nocca:,:nocca,noccb:,:noccb].transpose(3,2,1,0).conj()
eris.OVvv = eri1[1,nocca:,nocca:,noccb:,:noccb].transpose(3,2,1,0).conj()
eris.OVoo = eri1[1,:nocca,:nocca,noccb:,:noccb].transpose(3,2,1,0).conj()
t1a = .1 * numpy.random.random((nocca,nvira)) + numpy.random.random((nocca,nvira))*.1j
t1b = .1 * numpy.random.random((noccb,nvirb)) + numpy.random.random((noccb,nvirb))*.1j
t2aa = .1 * numpy.random.random((nocca,nocca,nvira,nvira)) + numpy.random.random((nocca,nocca,nvira,nvira))*.1j
t2aa = t2aa - t2aa.transpose(0,1,3,2)
t2aa = t2aa - t2aa.transpose(1,0,2,3)
t2bb = .1 * numpy.random.random((noccb,noccb,nvirb,nvirb)) + numpy.random.random((noccb,noccb,nvirb,nvirb))*.1j
t2bb = t2bb - t2bb.transpose(0,1,3,2)
t2bb = t2bb - t2bb.transpose(1,0,2,3)
t2ab = .1 * numpy.random.random((nocca,noccb,nvira,nvirb)) + numpy.random.random((nocca,noccb,nvira,nvirb))*.1j
f = (numpy.random.random((2,nmo,nmo)) * .4 +
numpy.random.random((2,nmo,nmo)) * .4j)
eris.focka = f[0]+f[0].T.conj() + numpy.diag(numpy.arange(nmo))
eris.fockb = f[1]+f[1].T.conj() + numpy.diag(numpy.arange(nmo))
t1 = t1a, t1b
t2 = t2aa, t2ab, t2bb
mcc = cc.UCCSD(scf.UHF(mol))
print(kernel(mcc, eris, t1, t2) - (-0.056092415718338388-0.011390417704868244j))
#!/usr/bin/env python
#
# Author: Qiming Sun <*****@*****.**>
#
'''
A simple example to run CCSD(T) and UCCSD(T) calculation.
'''
from pyscf import gto, scf, cc
mol = gto.M(atom='H 0 0 0; F 0 0 1.1', basis='ccpvdz')
mf = scf.RHF(mol).run()
mycc = cc.CCSD(mf).run()
et = mycc.ccsd_t()
print('CCSD(T) correlation energy', mycc.e_corr + et)
mf = scf.UHF(mol).run()
mycc = cc.UCCSD(mf).run()
et = mycc.ccsd_t()
print('UCCSD(T) correlation energy', mycc.e_corr + et)