def test_h4_fcc_k2(self):
'''Metallic hydrogen fcc lattice. Checks versus a corresponding
supercell calculation.
NOTE: different versions of the davidson may converge to a different
solution for the k-point IP/EA eom. If you're getting the wrong
root, check to see if it's contained in the supercell set of
eigenvalues.'''
cell = pbcgto.Cell()
cell.atom = [['H', (0.000000000, 0.000000000, 0.000000000)],
['H', (0.000000000, 0.500000000, 0.250000000)],
['H', (0.500000000, 0.500000000, 0.500000000)],
['H', (0.500000000, 0.000000000, 0.750000000)]]
cell.unit = 'Bohr'
cell.a = [[1., 0., 0.], [0., 1., 0], [0, 0, 2.2]]
cell.verbose = 7
cell.spin = 0
cell.charge = 0
cell.basis = [
[0, [1.0, 1]],
]
cell.pseudo = 'gth-pade'
cell.output = '/dev/null'
#cell.max_memory = 1000
for i in range(len(cell.atom)):
cell.atom[i][1] = tuple(
np.dot(np.array(cell.atom[i][1]), np.array(cell.a)))
cell.build()
nmp = [2, 1, 1]
kmf = pbcscf.KRHF(cell)
kmf.kpts = cell.make_kpts(nmp, scaled_center=[0.0, 0.0, 0.0])
e = kmf.kernel()
mycc = pbcc.KCCSD(kmf)
ekccsd, _, _ = mycc.kernel()
self.assertAlmostEqual(ekccsd, -0.06146759560406628, 6)
# Getting more roots than 1 is difficult
e = mycc.eaccsd(nroots=1, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], 5.079427283440857, 6)
e = mycc.eaccsd(nroots=1, koopmans=False, kptlist=(1, ))[0]
self.assertAlmostEqual(e[0][0], 4.183328878177331, 6)
e = mycc.ipccsd(nroots=1, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], -3.471710821544506, 6)
e = mycc.ipccsd(nroots=1, koopmans=False, kptlist=(1, ))[0]
self.assertAlmostEqual(e[0][0], -4.272015727359054, 6)
# Start of supercell calculations
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nmp)
supcell.build()
mf = pbcscf.KRHF(supcell)
e = mf.kernel()
myscc = pbcc.KCCSD(mf)
eccsd, _, _ = myscc.kernel()
eccsd /= np.prod(nmp)
self.assertAlmostEqual(eccsd, -0.06146759560406628, 6)
e = myscc.eaccsd(nroots=4, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], 4.183328873793568, 6)
self.assertAlmostEqual(e[0][1], 4.225034294249784, 6)
self.assertAlmostEqual(e[0][2], 5.068962665511664, 6)
self.assertAlmostEqual(e[0][3], 5.07942727935064, 6)
e = myscc.ipccsd(nroots=4, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], -4.272015724869052, 6)
self.assertAlmostEqual(e[0][1], -4.254298274388934, 6)
self.assertAlmostEqual(e[0][2], -3.471710821688812, 6)
self.assertAlmostEqual(e[0][3], -3.462817764320668, 6)
def test_h4_fcc_k2_frozen(self):
'''Metallic hydrogen fcc lattice with frozen lowest lying occupied
and highest lying virtual orbitals. Checks versus a corresponding
supercell calculation.
NOTE: different versions of the davidson may converge to a different
solution for the k-point IP/EA eom. If you're getting the wrong
root, check to see if it's contained in the supercell set of
eigenvalues.'''
cell = pbcgto.Cell()
cell.atom = [['H', (0.000000000, 0.000000000, 0.000000000)],
['H', (0.000000000, 0.500000000, 0.250000000)],
['H', (0.500000000, 0.500000000, 0.500000000)],
['H', (0.500000000, 0.000000000, 0.750000000)]]
cell.unit = 'Bohr'
cell.a = [[1., 0., 0.], [0., 1., 0], [0, 0, 2.2]]
cell.verbose = 7
cell.spin = 0
cell.charge = 0
cell.basis = [
[0, [1.0, 1]],
]
cell.pseudo = 'gth-pade'
cell.output = '/dev/null'
#cell.max_memory = 1000
for i in range(len(cell.atom)):
cell.atom[i][1] = tuple(
np.dot(np.array(cell.atom[i][1]), np.array(cell.a)))
cell.build()
nmp = [2, 1, 1]
kmf = pbcscf.KRHF(cell)
kmf.kpts = cell.make_kpts(nmp, scaled_center=[0.0, 0.0, 0.0])
e = kmf.kernel()
frozen = [[0, 3], []]
mycc = pbcc.KCCSD(kmf, frozen=frozen)
ekccsd, _, _ = mycc.kernel()
self.assertAlmostEqual(ekccsd, -0.04683399814247455, 6)
# Getting more roots than 1 is difficult
e = mycc.eaccsd(nroots=1, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], 5.060562738181741, 6)
e = mycc.eaccsd(nroots=1, koopmans=False, kptlist=(1, ))[0]
self.assertAlmostEqual(e[0][0], 4.188511644938458, 6)
e = mycc.ipccsd(nroots=1, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], -3.477663551987023, 6)
e = mycc.ipccsd(nroots=1, koopmans=False, kptlist=(1, ))[0]
self.assertAlmostEqual(e[0][0], -4.23523412155825, 6)
# Start of supercell calculations
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nmp)
supcell.build()
mf = pbcscf.KRHF(supcell)
e = mf.kernel()
myscc = pbcc.KCCSD(mf, frozen=[0, 7])
eccsd, _, _ = myscc.kernel()
eccsd /= np.prod(nmp)
self.assertAlmostEqual(eccsd, -0.04683401678904569, 6)
e = myscc.eaccsd(nroots=4, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], 4.188511680212755, 6)
self.assertAlmostEqual(e[0][1], 4.205924087610756, 6)
self.assertAlmostEqual(e[0][2], 5.060562771978923, 6)
self.assertAlmostEqual(e[0][3], 5.077249823137741, 6)
e = myscc.ipccsd(nroots=4, koopmans=False, kptlist=(0, ))[0]
self.assertAlmostEqual(e[0][0], -4.261818242746091, 6)
self.assertAlmostEqual(e[0][1], -4.235233956876479, 6)
self.assertAlmostEqual(e[0][2], -3.477663568390151, 6)
self.assertAlmostEqual(e[0][3], -3.459133332687474, 6)
from pyscf.pbc import gto, scf, cc
from pyscf.pbc.tools import pyscf_ase
from ase.lattice import bulk
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = gto.M(
a=ase_atom.cell,
atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom),
basis='gth-szv',
pseudo='gth-pade',
gs=[10] * 3,
verbose=4,
)
nk = [2, 2, 2]
kpts = cell.make_kpts(nk)
#
# Running HF
#
kmf = scf.KRHF(cell, kpts, exxdiv=None)
ehf = kmf.kernel()
#
# Running CCSD
#
kcc = cc.KCCSD(kmf)
ecc, t1, t2 = kcc.kernel()
print("cc energy (per unit cell) = %.17g" % ecc)
cell.spin = 0
cell.charge = 0
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
for i in range(len(cell.atom)):
cell.atom[i][1] = tuple(np.dot(np.array(cell.atom[i][1]),
np.array(cell.a)))
cell.build()
nmp = [2, 1, 1]
kmf = pbcscf.KRHF(cell)
kmf.kpts = cell.make_kpts(nmp, scaled_center=[0.0, 0.0, 0.0])
e = kmf.kernel() # 2.30510338236481
mycc = pbcc.KCCSD(kmf)
eris = mycc.ao2mo(kmf.mo_coeff)
eris.mo_energy = [eris.fock[k].diagonal() for k in range(mycc.nkpts)]
print('\nCCSD energy w/o level shift and MP2 initial guess:'
) # 0.02417522810234485
ekccsd, t1, t2 = mycc.kernel(eris=eris)
# Use a level shift with a level shift equal to the Madelung
# constant for this system. Using the previous t1/t2 as an initial
# guess, we see that these amplitudes still solve the CCSD amplitude
# equations.
def _adjust_occ(mo_energy, nocc, shift):
'''Modify occupied orbital energy'''
mo_energy = mo_energy.copy()
def run_kccsd(mf):
cc = pbccc.KCCSD(mf)
cc.verbose = 7
cc.ccsd()
return cc
flat_lattice_vectors[6:9]
]
num_frozen_cores = int(
results.frozen_cores) if results.frozen_cores is not None else 0
sys.argv = [sys.argv[0]]
# -----------------------
# PYSCF
# -----------------------
cell = gto.M(atom=atomic_coords,
basis=basis_set,
spin=spin,
charge=charge,
a=lattice_vectors,
pseudo=pseudo_potential,
precision=1e-6,
verbose=5)
kpts = cell.make_kpts(k_points)
mf = scf.KRHF(cell)
mf.with_df = getattr(df, density_fit)(cell)
if density_fit == "gdf" or density_fit == "mdf":
mf.with_df.auxbasis = aux_basis_set
mf.kpts = kpts
mf.kernel()
my_cc = cc.KCCSD(mf)
my_cc.kernel()
# scaled_center = np.random.rand(3)
log = logger.Logger(cell.stdout, 6)
for kmesh in ([
1,
1,
1,
], [2, 1, 1]):
kpts = cell.make_kpts(kmesh, scaled_center=scaled_center)
log.info("kmesh= %s", kmesh)
log.info("kpts = %s", kpts)
from pyscf.pbc import scf, mp, cc
mf = scf.KRHF(cell, kpts=kpts).rs_density_fit()
mf.kernel()
mf2 = scf.KRHF(cell, kpts=kpts).density_fit()
mf2.kernel()
log.info("HF/GDF energy : % .10f", mf2.e_tot)
log.info("HF/RSGDF energy : % .10f", mf.e_tot)
log.info("difference : % .3g", (mf.e_tot - mf2.e_tot))
mc = cc.KCCSD(mf)
mc.kernel()
mc2 = cc.KCCSD(mf2)
mc2.kernel()
log.info("CCSD/GDF energy : % .10f", mc2.e_corr)
log.info("CCSD/RSGDF energy : % .10f", mc.e_corr)
log.info("difference : % .3g\n", (mc.e_corr - mc2.e_corr))
