def test_rsh_df(self):
mf = pbcdft.KRKS(cell)
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.3032261128220544, 7)
mf = pbcdft.KRKS(cell).density_fit()
mf.xc = 'camb3lyp'
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.3987656490734555, 7)
def test_kpt_vs_supercell(self):
ngs = 5
nk = (3, 1, 1)
# Comparison is only perfect for odd-numbered supercells and kpt sampling
assert all(np.array(nk) % 2 == np.array([1, 1, 1]))
cell = make_primitive_cell(ngs)
scaled_kpts = ase.dft.kpoints.monkhorst_pack(nk)
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
#kmf.analytic_int = False
#kmf.verbose = 7
ekpt = kmf.scf()
supcell = pyscf.pbc.tools.super_cell(cell, nk)
supcell.gs = np.array([
nk[0] * ngs + (nk[0] - 1) // 2, nk[1] * ngs + (nk[1] - 1) // 2,
nk[2] * ngs + (nk[2] - 1) // 2
])
#supcell.verbose = 7
supcell.build()
mf = pbcdft.RKS(supcell)
mf.xc = 'lda,vwn'
#mf.verbose = 7
esup = mf.scf() / np.prod(nk)
#print("kpt sampling energy =", ekpt)
#print("supercell energy =", esup)
self.assertAlmostEqual(ekpt, esup, 5)
def test_gwcd_high_cost(self):
kpts = cell.make_kpts([3,1,1],scaled_center=[0,0,0])
gdf = df.GDF(cell, kpts)
gdf._cderi = gdf_fname = os.path.realpath(os.path.join(__file__, '..', 'gdf_ints_311.h5'))
if 1:
gdf._cderi_to_save = gdf_fname
gdf.build()
kmf = dft.KRKS(cell, kpts).density_fit(with_df=gdf)
kmf.xc = 'pbe'
kmf.kernel()
gw = krgw_cd.KRGWCD(kmf)
gw.linearized = False
# without finite size corrections
gw.fc = False
nocc = gw.nocc
gw.kernel(kptlist=[0,1,2],orbs=range(0,nocc+3))
self.assertAlmostEqual(gw.mo_energy[0][nocc-1], 0.62045796, 4)
self.assertAlmostEqual(gw.mo_energy[0][nocc], 0.96574426, 4)
self.assertAlmostEqual(gw.mo_energy[1][nocc-1], 0.52639129, 4)
self.assertAlmostEqual(gw.mo_energy[1][nocc], 1.07442235, 4)
# with finite size corrections
gw.fc = True
gw.kernel(kptlist=[0,1,2],orbs=range(0,nocc+3))
self.assertAlmostEqual(gw.mo_energy[0][nocc-1], 0.5427707 , 4)
self.assertAlmostEqual(gw.mo_energy[0][nocc], 0.80148557, 4)
self.assertAlmostEqual(gw.mo_energy[1][nocc-1], 0.45073751, 4)
self.assertAlmostEqual(gw.mo_energy[1][nocc], 0.92910117, 4)
def test_nr_krks_lda(self):
mf = dft.KRKS(cell, cell.make_kpts([2, 1, 1]))
mf.xc = 'lda,'
mf = scf.newton(mf)
mf.conv_tol_grad = 1e-4
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -10.307756038726733, 8)
def setUp(self):
cell = gto.Cell()
alat0 = 3.6
cell.a = (numpy.ones((3, 3)) - numpy.eye(3)) * alat0 / 2.0
cell.atom = (('C', 0, 0, 0), ('C',
numpy.array([0.25, 0.25, 0.25]) * alat0))
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.mesh = [
25
] * 3 # 10 grids on postive x direction, => 21^3 grids in total
cell.verbose = 0
cell.build()
self.cell = cell
nk = [2, 2, 2]
kpts = cell.make_kpts(nk)
mf = dft.KRKS(cell, kpts=kpts)
mf.chkfile = 'scf.dump'
ehf = mf.kernel()
self.mf = mf
self.nmo_pk = numpy.array([C.shape[-1] for C in mf.mo_coeff])
self.nkpts = len(kpts)
self.kpts = kpts
self.nmo_max = numpy.max(self.nmo_pk)
def test_nr_krks_gga(self):
mf = dft.KRKS(cell, cell.make_kpts([2, 1, 1]))
mf.xc = 'b88,'
mf = scf.newton(mf)
mf.conv_tol_grad = 1e-4
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -10.446717855794008, 8)
def test_multigrid_krks(self):
mf = dft.KRKS(cell_he)
mf.xc = 'lda,'
ref = mf.get_veff(cell_he, dm_he, kpts=kpts)
out = multigrid.multigrid(mf).get_veff(cell_he, dm_he, kpts=kpts)
self.assertAlmostEqual(float(abs(ref - out).max()), 0, 9)
self.assertAlmostEqual(abs(ref.exc - out.exc).max(), 0, 9)
self.assertAlmostEqual(abs(ref.ecoul - out.ecoul).max(), 0, 9)
def test_klda8_primitive_kpt_222(self):
cell = make_primitive_cell([17]*3)
abs_kpts = cell.make_kpts([2]*3, with_gamma_point=False)
mf = pbcdft.KRKS(cell, abs_kpts)
#mf.analytic_int = False
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
self.assertAlmostEqual(e1, -11.353643583707452, 8)
def xtest_kpt_222(self):
cell = make_primitive_cell(8)
abs_kpts = cell.make_kpts([2, 2, 2], wrap_around=True)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
#kmf.analytic_int = False
#kmf.verbose = 7
e1 = kmf.scf()
self.assertAlmostEqual(e1, -11.3536435234900, 8)
def test_klda8_cubic_kpt_222(self):
cell = build_cell([17]*3)
abs_kpts = cell.make_kpts([2]*3, with_gamma_point=False)
mf = pbcdft.KRKS(cell, abs_kpts)
#mf.analytic_int = False
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
self.assertAlmostEqual(e1, -45.425834895129569, 8)
def test_gamma_vs_ks(self):
mf = pdft.KRKS(cell)
mf.kpts = cell.make_kpts([1, 1, 3])
ek = mf.kernel()
scell = ptools.super_cell(cell, [1, 1, 3])
scell.gs = [12, 12, 36]
mf = pdft.RKS(scell)
eg = mf.kernel()
self.assertAlmostEqual(ek, eg / 3, 5)
def test_band_kscf(self):
kpts = cell.make_kpts([2, 1, 1])
kmf = dft.KRKS(cell, kpts=kpts).run()
bands = []
h1 = kmf.get_hcore()
s1 = kmf.get_ovlp()
for i, kpt in enumerate(kpts):
fock = h1[i] + kmf.get_veff(kpt_band=kpt)
bands.append(scipy.linalg.eigh(fock, s1[i])[0])
self.assertAlmostEqual(finger(bands), -0.76745129086774599, 8)
def test_gamma_vs_ks_high_cost(self):
mf = pdft.KRKS(cell)
mf.kpts = cell.make_kpts([1, 1, 3])
ek = mf.kernel()
scell = ptools.super_cell(cell, [1, 1, 3])
scell.mesh = [25, 25, 73]
mf = pdft.RKS(scell)
eg = mf.kernel()
self.assertAlmostEqual(ek, eg / 3, 5)
def xtest_kpt_222(self):
cell = make_primitive_cell(8)
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
#kmf.analytic_int = False
#kmf.verbose = 7
e1 = kmf.scf()
self.assertAlmostEqual(e1, -11.3536435234900, 8)
def test_bands(self):
model = pbcdft.KRKS(self.cell, self.cell.make_kpts([3,3,1]))
model.xc = 'lda'
model.kernel()
e,w = model.get_bands(self.k_points_cartesian_bohr)
avg = numpy.mean(e-self.bands_hartree)
delta = e-self.bands_hartree-avg
dev_max = numpy.abs(delta).max()
print "Maximum deviation:", dev_max, " Hartree"
assert dev_max < 1e-4
def test_klda8_primitive_kpt_222(self):
ase_atom = bulk('C', 'diamond', a=LATTICE_CONST)
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
cell = build_cell(ase_atom, 8)
abs_kpts = cell.get_abs_kpts(scaled_kpts)
mf = pbcdft.KRKS(cell, abs_kpts)
#mf.analytic_int = False
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -11.353643738291005, 8)
def test_klda8_cubic_kpt_222(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
cell = build_cell(ase_atom, 8)
abs_kpts = cell.get_abs_kpts(scaled_kpts)
mf = pbcdft.KRKS(cell, abs_kpts)
#mf.analytic_int = False
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -45.425834895129569, 8)
def run_kdft(cell, nmp=[1, 1, 1], gamma=False):
"""Run a k-point-sampling DFT (LDA) calculation."""
scaled_kpts = ase.dft.kpoints.monkhorst_pack(nmp)
if gamma:
for i in range(3):
if nmp[i] % 2 == 0:
scaled_kpts[:, i] += 0.5 / nmp[i]
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
kmf.verbose = 7
print kmf.scf()
return kmf
def test_rks_gen_g_hop(self):
mf = dft.KRKS(cell, cell.make_kpts([2,1,1]))
mf.xc = 'b3lyp'
nao = cell.nao_nr()
numpy.random.seed(1)
mo = numpy.random.random((2,nao,nao)) + 0j
mo_occ = numpy.zeros((2,nao))
mo_occ[:,:5] = 2
nocc, nvir = 5, nao-5
dm1 = numpy.random.random(2*nvir*nocc) + .1j
mf = scf.newton(mf)
mf.grids.build()
g, hop, hdiag = mf.gen_g_hop(mo, mo_occ, mf.get_hcore())
self.assertAlmostEqual(numpy.linalg.norm(hop(dm1)), 37.967972033738519, 7)
def test_band_kscf(self):
kpts = cell.make_kpts([2,1,1])
kmf = dft.KRKS(cell, kpts=kpts).run()
np.random.seed(11)
kpts_band = np.random.random((4,3))
bands = kmf.get_bands(kpts_band)[0]
bands_ref = []
h1 = kmf.get_hcore(kpts=kpts_band)
s1 = kmf.get_ovlp(kpts=kpts_band)
vhf = kmf.get_veff(kpts_band=kpts_band)
for i, kpt in enumerate(kpts_band):
fock = h1[i] + vhf[i]
bands_ref.append(scipy.linalg.eigh(fock, s1[i])[0])
self.assertAlmostEqual(abs(np.array(bands_ref) - np.array(bands)).max(), 0, 9)
self.assertAlmostEqual(lib.fp(bands), -0.61562245312227049, 8)
def __prepare__(self, kpts=[1, 1, 1], xc="lda", **kwargs):
params = dict(
unit='Angstrom',
atom=list(
zip(['B', 'N'], self.atomic_coordinates_cartesian_angstrom)),
a=self.unit_cell_angstrom,
basis='gth-szv',
pseudo='gth-lda',
gs=[16, 16, 75],
verbose=0,
)
params.update(kwargs)
self.cell = pbcgto.M(**params)
self.model = pbcdft.KRKS(self.cell, self.cell.make_kpts(kpts))
self.model.xc = xc
def copy_mf(mf, cell):
if mf.__class__.__name__ == 'KRHF':
mf1 = scf.KRHF(cell)
elif mf.__class__.__name__ == 'KUHF':
mf1 = scf.KUHF(cell)
elif mf.__class__.__name__ == 'KRKS':
mf1 = dft.KRKS(cell)
mf1.xc = mf.xc
elif mf.__class__.__name__ == 'KUKS':
mf1 = dft.KUKS(cell)
mf1.xc = mf.xc
mf1.kpts = mf.kpts
mf1.exxdiv = getattr(mf, 'exxdiv', None)
mf1.conv_tol = mf.conv_tol
mf1.conv_tol_grad = mf.conv_tol_grad
return mf1
def test_ccsd_t_non_hf_frozen(self):
'''Tests ccsd and ccsd_t for non-Hartree-Fock references with frozen orbitals
using supercell vs k-point calculation.'''
n = 14
cell = make_test_cell.test_cell_n3([n] * 3)
#import sys
#cell.stdout = sys.stdout
#cell.verbose = 7
nk = [2, 1, 1]
kpts = cell.make_kpts(nk)
kpts -= kpts[0]
kks = pbcdft.KRKS(cell, kpts=kpts)
ekks = kks.kernel()
khf = pbcscf.KRHF(cell)
khf.__dict__.update(kks.__dict__)
mycc = pbcc.KRCCSD(khf, frozen=1)
eris = mycc.ao2mo()
ekcc, t1, t2 = mycc.kernel(eris=eris)
ekcc_t = mycc.ccsd_t(eris=eris)
# Run supercell
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nk)
rks = pbcdft.RKS(supcell)
erks = rks.kernel()
rhf = pbcscf.RHF(supcell)
rhf.__dict__.update(rks.__dict__)
mycc = pbcc.RCCSD(rhf, frozen=2)
eris = mycc.ao2mo()
ercc, t1, t2 = mycc.kernel(eris=eris)
self.assertAlmostEqual(ercc / np.prod(nk), -0.11467718013872311, 6)
self.assertAlmostEqual(ercc / np.prod(nk), ekcc, 6)
ercc_t = mycc.ccsd_t(eris=eris)
self.assertAlmostEqual(ercc_t / np.prod(nk), -0.00066503872045200996,
6)
self.assertAlmostEqual(ercc_t / np.prod(nk), ekcc_t, 6)
def test_gen_rhf_response(self):
numpy.random.seed(9)
dm1 = numpy.random.random(dm_he.shape)
dm1 = dm1 + dm1.transpose(0, 2, 1)
dm1[1] = dm1[0]
mydf = df.FFTDF(cell_he)
ni = dft.numint.KNumInt()
mf = dft.KRKS(cell_he)
mf.with_df = multigrid.MultiGridFFTDF(cell_he)
mf.kpts = kpts
mf.xc = 'lda,'
ref = dft.numint.nr_rks_fxc(ni,
cell_he,
mydf.grids,
mf.xc,
dm_he,
dm1,
hermi=1,
kpts=kpts)
vj = mydf.get_jk(dm1, with_k=False, kpts=kpts)[0]
ref += vj
v = multigrid._gen_rhf_response(mf, dm_he, hermi=1)(dm1)
self.assertEqual(ref.dtype, v.dtype)
self.assertEqual(ref.shape, v.shape)
self.assertAlmostEqual(abs(v - ref).max(), 0, 9)
mf.xc = 'b88,'
ref = dft.numint.nr_rks_fxc(ni,
cell_he,
mydf.grids,
mf.xc,
dm_he,
dm1,
hermi=1,
kpts=kpts)
ref += vj
v = multigrid._gen_rhf_response(mf, dm_he, hermi=1)(dm1)
self.assertEqual(ref.dtype, v.dtype)
self.assertEqual(ref.shape, v.shape)
self.assertAlmostEqual(abs(v - ref).max(), 0, 6)
def test_write_wfn_pbc(self):
cell = gto.Cell()
alat0 = 3.6
cell.a = (numpy.ones((3,3))-numpy.eye(3))*alat0/2.0
cell.atom = (('C',0,0,0),('C',numpy.array([0.25,0.25,0.25])*alat0))
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.mesh = [12]*3 # 10 grids on postive x direction, => 21^3 grids in total
cell.verbose = 0
cell.build()
nk = [2,2,1]
kpts = cell.make_kpts(nk)
mf = dft.KRKS(cell,kpts=kpts)
mf.chkfile = 'scf.dump'
emf = mf.kernel()
nmo_pk = numpy.array([C.shape[-1] for C in mf.mo_coeff])
nkpts = len(kpts)
kpts = kpts
nmo_max = numpy.max(nmo_pk)
hcore = mf.get_hcore()
fock = hcore + mf.get_veff()
scf_data = {'cell': cell,
'mo_coeff': mf.mo_coeff,
'Xocc': mf.mo_occ,
'X': mf.mo_coeff,
'fock': fock,
'isUHF': False,
'hcore': hcore,
'nmo_pk': nmo_pk,
'mo_energy': mf.mo_energy,
'kpts': kpts}
with h5py.File('wfn.h5', 'w') as fh5:
pass
pbc.write_wfn_pbc(scf_data, True, 'wfn.h5', rediag=True)
with h5py.File('wfn.h5', 'r') as fh5:
dims = fh5['Wavefunction/NOMSD/dims'][:]
print(dims)
self.assertTrue(numpy.allclose(dims, [32,16,16,1,1]))
def test_lda_grad(self):
mf = dft.KRKS(cell, kpts)
mf.xc = 'lda,vwn'
mf.conv_tol = 1e-10
mf.conv_tol_grad = 1e-6
g_scan = mf.nuc_grad_method().as_scanner()
g = g_scan(cell)[1]
self.assertAlmostEqual(lib.fp(g), -0.22166962318360375, 6)
mfs = g_scan.base.as_scanner()
e1 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 + disp / 2.0]
]])
e2 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 - disp / 2.0]
]])
self.assertAlmostEqual(g[1, 2], (e1 - e2) / disp, 6)
def test_ccsd_t_non_hf(self):
'''Tests ccsd and ccsd_t for non-Hartree-Fock references
using supercell vs k-point calculation.'''
n = 14
cell = make_test_cell.test_cell_n3([n] * 3)
nk = [2, 1, 1]
kpts = cell.make_kpts(nk)
kpts -= kpts[0]
kks = pbcdft.KRKS(cell, kpts=kpts)
ekks = kks.kernel()
khf = pbcscf.KRHF(cell)
khf.__dict__.update(kks.__dict__)
mycc = pbcc.KRCCSD(khf)
eris = mycc.ao2mo()
ekcc, t1, t2 = mycc.kernel(eris=eris)
ekcc_t = mycc.ccsd_t(eris=eris)
# Run supercell
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nk)
rks = pbcdft.RKS(supcell)
erks = rks.kernel()
rhf = pbcscf.RHF(supcell)
rhf.__dict__.update(rks.__dict__)
mycc = pbcc.RCCSD(rhf)
eris = mycc.ao2mo()
ercc, t1, t2 = mycc.kernel(eris=eris)
self.assertAlmostEqual(ercc / np.prod(nk), -0.15632445245405927, 6)
self.assertAlmostEqual(ercc / np.prod(nk), ekcc, 6)
ercc_t = mycc.ccsd_t(eris=eris)
self.assertAlmostEqual(ercc_t / np.prod(nk), -0.00114619248449, 6)
self.assertAlmostEqual(ercc_t / np.prod(nk), ekcc_t, 6)
def test_gga_grad(self):
mf = dft.KRKS(cell, kpts)
mf.xc = 'pbe,pbe'
mf.conv_tol = 1e-10
mf.conv_tol_grad = 1e-6
g_scan = mf.nuc_grad_method().as_scanner()
g = g_scan(cell)[1]
self.assertAlmostEqual(lib.fp(g), -0.21844074846755882, 6)
mfs = g_scan.base.as_scanner()
e1 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 + disp / 2.0]
]])
e2 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 - disp / 2.0]
]])
self.assertAlmostEqual(g[1, 2], (e1 - e2) / disp, 6)
def test_kpt_vs_supercell(self):
n = 11
nk = (3, 1, 1)
# Comparison is only perfect for odd-numbered supercells and kpt sampling
assert all(np.array(nk) % 2 == np.array([1, 1, 1]))
cell = make_primitive_cell([n] * 3)
abs_kpts = cell.make_kpts(nk, wrap_around=True)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
#kmf.analytic_int = False
#kmf.verbose = 7
ekpt = kmf.scf()
supcell = pyscf.pbc.tools.super_cell(cell, nk)
supcell.build()
mf = pbcdft.RKS(supcell)
mf.xc = 'lda,vwn'
#mf.verbose = 7
esup = mf.scf() / np.prod(nk)
#print("kpt sampling energy =", ekpt)
#print("supercell energy =", esup)
self.assertAlmostEqual(ekpt, esup, 5)
def test_hybrid_grad(self):
mf = dft.KRKS(cell, kpts)
mf.xc = 'b3lyp'
mf.exxdiv = None
mf.conv_tol = 1e-10
mf.conv_tol_grad = 1e-6
g_scan = mf.nuc_grad_method().as_scanner()
g = g_scan(cell)[1]
self.assertAlmostEqual(lib.fp(g), -0.19544969829285652, 6)
mfs = g_scan.base.as_scanner()
e1 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 + disp / 2.0]
]])
e2 = mfs(
[['C', [0.0, 0.0, 0.0]],
[
'C',
[1.685068664391, 1.685068664391, 1.685068664391 - disp / 2.0]
]])
self.assertAlmostEqual(g[1, 2], (e1 - e2) / disp, 6)