def test_rhf_2d_fft(self):
L = 4
cell = pbcgto.Cell()
cell.build(unit = 'B',
a = [[L,0,0],[0,L,0],[0,0,L*5]],
mesh = [11,11,20],
atom = '''He 2 0 0; He 3 0 0''',
dimension = 2,
verbose = 0,
basis = { 'He': [[0, (0.8, 1.0)],
[0, (1.2, 1.0)]
]})
mf = pbchf.RHF(cell, exxdiv='ewald')
mf.with_df = pdf.FFTDF(cell)
mf.with_df.mesh = cell.mesh
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.5797041803667593, 5)
mf1 = pbchf.RHF(cell, exxdiv='ewald')
mf1.with_df = pdf.FFTDF(cell)
mf1.with_df.mesh = cell.mesh
mf1.direct_scf = True
e1 = mf1.kernel()
self.assertAlmostEqual(e1, -3.5797041803667593, 5)
mf2 = pbchf.RHF(cell, exxdiv=None)
mf2.with_df = pdf.FFTDF(cell)
mf2.with_df.mesh = cell.mesh
mf2.direct_scf = True
e2 = mf2.kernel()
self.assertAlmostEqual(e2, -1.629571720365774, 5)
def test_init_guess_by_chkfile(self):
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='vcut_sph')
e1 = mf.kernel()
dm1 = mf.make_rdm1()
mf1 = pbchf.RHF(cell, exxdiv='vcut_sph')
mf1.chkfile = mf.chkfile
mf1.init_guess = 'chkfile'
e1 = mf1.kernel()
self.assertAlmostEqual(e1, -4.29190260870812, 8)
self.assertTrue(mf1.mo_coeff.dtype == numpy.double)
def test_rhf_1d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=[[L, 0, 0], [0, L * 5, 0], [0, 0, L * 5]],
mesh=[11, 20, 20],
atom='''He 2 0 0; He 3 0 0''',
dimension=1,
low_dim_ft_type='inf_vacuum',
verbose=0,
basis={
'He': [
[0, (0.8, 1.0)],
#[0, (1.0, 1.0)],
[0, (1.2, 1.0)]
]
})
mf = pbchf.RHF(cell)
mf.with_df = pdf.AFTDF(cell)
mf.with_df.eta = 0.3
mf.with_df.mesh = cell.mesh
mf.init_guess = 'hcore'
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.24497234871167, 5)
def test_hf(pseudo=None):
# The molecular calculation
mol = gto.Mole()
mol.unit = 'B'
L = 60
mol.atom.extend([
['He', (L / 2., L / 2., L / 2.)],
])
# these are some exponents which are not hard to integrate
mol.basis = {'He': [[0, (0.8, 1.0)], [0, (1.0, 1.0)], [0, (1.2, 1.0)]]}
mol.build()
m = hf.RHF(mol)
print "Molecular HF energy"
print(m.scf()) # -2.63502450321874
# The periodic calculation
cell = pbcgto.Cell()
cell.unit = 'B'
cell.h = np.diag([L, L, L])
cell.gs = np.array([60, 60, 60])
cell.nimgs = [0, 0, 0]
cell.atom = mol.atom
cell.basis = mol.basis
cell.pseudo = pseudo
# cell.verbose = 4
cell.build(None, None)
mf = pbchf.RHF(cell)
print(mf.scf()) # -2.58766850182551: doesn't look good, but this is due
def test_band_kscf():
L = 1
cell = pbcgto.Cell()
cell.unit = 'B'
cell.h = np.diag([L, L, L])
cell.gs = np.array([10, 10, 10])
cell.atom.extend([['He', (L / 2., L / 2., L / 2.)]])
cell.basis = {'He': [[0, (1.0, 1.0)]]}
cell.build()
mf = pbchf.RHF(cell)
mf.scf()
auxcell = cell.copy()
auxcell.gs = np.array([1, 1, 1])
auxcell.build()
invhT = scipy.linalg.inv(np.asarray(cell._h).T)
ncells = 2
kGvs = []
for i in range(ncells):
kGvs.append(i * 1. / ncells * 2 * pi * np.dot(invhT, (1, 0, 0)))
kpts = np.vstack(kGvs)
kmf = pbckscf.KRKS(cell, cell.gs, cell.ew_eta, cell.ew_cut, kpts)
kmf.init_guess = "atom"
print kmf.scf()
for i in range(1, 10):
band_kpt = 1. / i * auxcell.Gv[-1, :]
print pbchf.get_eig_kpt(kmf, band_kpt)[0]
def test_rhf_2d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=[[L, 0, 0], [0, L, 0], [0, 0, L * 5]],
mesh=[11, 11, 20],
atom='''He 2 0 0; He 3 0 0''',
dimension=2,
low_dim_ft_type='inf_vacuum',
verbose=0,
rcut=7.427535697575829,
basis={
'He': [
[0, (0.8, 1.0)],
#[0, (1.0, 1.0)],
[0, (1.2, 1.0)]
]
})
mf = pbchf.RHF(cell)
mf.with_df = pdf.AFTDF(cell)
mf.with_df.eta = 0.3
mf.with_df.mesh = cell.mesh
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.2681555164454039, 5)
def test_moints():
# not yet working
# The molecular calculation
mol = gto.Mole()
mol.unit = 'B'
L = 60
mol.atom.extend([
['He', (L / 2., L / 2., L / 2.)],
])
mol.basis = 'cc-pvdz'
mol.build()
# The periodic calculation
cell = pbcgto.Cell()
cell.unit = 'B'
cell.h = np.diag([L, L, L])
cell.gs = np.array([40, 40, 40])
cell.nimgs = [1, 1, 1]
cell.atom = mol.atom
cell.basis = mol.basis
cell.build()
#mf = hf.RHF(mol)
mf = pbchf.RHF(cell)
print(mf.scf())
print "mo coeff shape", mf.mo_coeff.shape
nmo = mf.mo_coeff.shape[1]
print mf.mo_coeff
eri_mo = pbcao2mo.get_mo_eri(cell, [mf.mo_coeff, mf.mo_coeff],
[mf.mo_coeff, mf.mo_coeff])
eri_ao = pbcao2mo.get_ao_eri(cell)
eri_mo2 = ao2mo.incore.general(
np.real(eri_ao), (mf.mo_coeff, mf.mo_coeff, mf.mo_coeff, mf.mo_coeff),
compact=False)
print eri_mo.shape
print eri_mo2.shape
for i in range(nmo * nmo):
for j in range(nmo * nmo):
print i, j, np.real(eri_mo[i, j]), eri_mo2[i, j]
print("ERI dimension")
print(eri_mo.shape), nmo
Ecoul = 0.
Ecoul2 = 0.
nocc = 1
print "diffs"
for i in range(nocc):
for j in range(nocc):
Ecoul += 2 * eri_mo[i * nmo + i, j * nmo + j] - eri_mo[i * nmo + j,
i * nmo + j]
Ecoul2 += 2 * eri_mo2[i * nmo + i, j * nmo +
j] - eri_mo2[i * nmo + j, i * nmo + j]
print Ecoul, Ecoul2
def test_rhf_0d(self):
from pyscf.df import mdf_jk
from pyscf.scf import hf
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=numpy.eye(3) * L * 5,
gs=[10] * 3,
atom='''He 2 2 2; He 2 2 3''',
dimension=0,
verbose=0,
basis={'He': [[0, (0.8, 1.0)], [0, (1.0, 1.0)], [0, (1.2, 1.0)]]})
mol = cell.to_mol()
mf = mdf_jk.density_fit(hf.RHF(mol))
mf.with_df.gs = [10] * 3
mf.with_df.auxbasis = {'He': [[0, (1e6, 1)]]}
mf.with_df.charge_constraint = False
mf.with_df.metric = 'S'
eref = mf.kernel()
mf = pbchf.RHF(cell)
mf.with_df = pdf.PWDF(cell)
mf.exxdiv = None
mf.get_hcore = lambda *args: hf.get_hcore(mol)
mf.energy_nuc = lambda *args: mol.energy_nuc()
e1 = mf.kernel()
self.assertAlmostEqual(e1, eref, 8)
def test_init_guess_by_chkfile(self):
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='vcut_sph')
mf.max_cycle = 1
mf.diis = None
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.132914531737784, 9)
mf1 = pbchf.RHF(cell, exxdiv='vcut_sph')
mf1.chkfile = mf.chkfile
mf1.init_guess = 'chkfile'
mf1.diis = None
mf1.max_cycle = 1
e1 = mf1.kernel()
self.assertAlmostEqual(e1, -4.291691793916943, 9)
self.assertTrue(mf1.mo_coeff.dtype == numpy.double)
def test_hcore(self):
h1ref = pbchf.get_hcore(cell)
h1 = pbchf.RHF(cell).get_hcore()
self.assertAlmostEqual(abs(h1-h1ref).max(), 0, 9)
self.assertAlmostEqual(lib.finger(h1), 0.14116483012673137, 9)
cell1 = cell.copy()
cell1.ecp = {'He': (2, ((-1, (((7.2, .3),),)),))}
cell1.build(0, 0)
kpt = numpy.ones(3) * .5
h1ref = pbchf.get_hcore(cell1, kpt)
h1 = pbchf.RHF(cell1).get_hcore(kpt=kpt)
self.assertAlmostEqual(abs(h1-h1ref).max(), 0, 9)
self.assertAlmostEqual(lib.finger(h1), -2.708431894877279-0.395390980665125j, 9)
h1 = pscf.KRHF(cell1).get_hcore(kpts=[kpt])
self.assertEqual(h1.ndim, 3)
self.assertAlmostEqual(abs(h1[0]-h1ref).max(), 0, 9)
def test_init_guess_by_chkfile(self):
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='vcut_sph')
mf.chkfile = tempfile.NamedTemporaryFile().name
mf.max_cycle = 1
mf.diis = None
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.132445328608581, 9)
mf1 = pbchf.RHF(cell, exxdiv='vcut_sph')
mf1.chkfile = mf.chkfile
mf1.init_guess = 'chkfile'
mf1.diis = None
mf1.max_cycle = 1
e1 = mf1.kernel()
self.assertAlmostEqual(e1, -4.291854736401251, 9)
self.assertTrue(mf1.mo_coeff.dtype == numpy.double)
def test_rhf_vcut_sph(self):
mf = pbchf.RHF(cell, exxdiv='vcut_sph')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.29190260870812, 8)
self.assertTrue(mf.mo_coeff.dtype == numpy.double)
mf = pscf.KRHF(cell, [[0,0,0]], exxdiv='vcut_sph')
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0,e1))
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='vcut_sph')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.1379172088570595, 8)
self.assertTrue(mf.mo_coeff.dtype == numpy.complex128)
mf = pscf.KRHF(cell, k, exxdiv='vcut_sph')
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0,e1))
def test_rhf_exx_ewald(self):
mf = pbchf.RHF(cell, exxdiv='ewald')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.3511582284698633, 9)
self.assertTrue(mf.mo_coeff.dtype == numpy.double)
mf = pscf.KRHF(cell, [[0, 0, 0]], exxdiv='ewald')
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='ewald')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.2048655827967139, 9)
self.assertTrue(mf.mo_coeff.dtype == numpy.complex128)
mf = pscf.KRHF(cell, k, exxdiv='ewald')
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
def test_rhf_exx_None(self):
mf = pbchf.RHF(cell, exxdiv=None)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -2.9325094887283196, 9)
self.assertTrue(mf.mo_coeff.dtype == numpy.double)
mf = pscf.KRHF(cell, [[0, 0, 0]], exxdiv=None)
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv=None)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -2.7862168430230341, 9)
self.assertTrue(mf.mo_coeff.dtype == numpy.complex128)
mf = pscf.KRHF(cell, k, exxdiv=None)
e0 = mf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
def test_uhf_exx_ewald(self):
mf = pscf.UHF(cell, exxdiv=None)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -2.9325094887283196, 9)
self.assertTrue(mf.mo_coeff[0].dtype == numpy.double)
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv=None)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -2.7862168430230341, 9)
self.assertTrue(mf.mo_coeff[0].dtype == numpy.complex128)
def test_vkR(self):
cell = make_cell1(4, 20)
mf = phf.RHF(cell)
numpy.random.seed(1)
kpt1, kpt2 = numpy.random.random((2,3))
coords = pdft.gen_grid.gen_uniform_grids(cell)
aoR_k1 = pdft.numint.eval_ao(cell, coords, kpt1)
aoR_k2 = pdft.numint.eval_ao(cell, coords, kpt2)
gs = cell.gs
coords = pdft.gen_grid.gen_uniform_grids(cell, gs)
vkR = fft_jk.get_vkR(mf, cell, aoR_k1, aoR_k2, kpt1, kpt2, coords, gs, None)
self.assertAlmostEqual(finger(vkR), -0.24716036343105258+0.078117253956143579j, 9)
def test_rhf_exx_ewald(self):
mf = pbchf.RHF(cell, exxdiv='ewald')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.3511582284698633, 8)
self.assertTrue(mf.mo_coeff.dtype == numpy.double)
kmf = pscf.KRHF(cell, [[0, 0, 0]], exxdiv='ewald')
e0 = kmf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
# test bands
numpy.random.seed(1)
kpts_band = numpy.random.random((2, 3))
e1, c1 = mf.get_bands(kpts_band)
e0, c0 = kmf.get_bands(kpts_band)
self.assertAlmostEqual(abs(e0[0] - e1[0]).max(), 0, 7)
self.assertAlmostEqual(abs(e0[1] - e1[1]).max(), 0, 7)
self.assertAlmostEqual(lib.finger(e1[0]), -6.2986775452228283, 7)
self.assertAlmostEqual(lib.finger(e1[1]), -7.6616273746782362, 7)
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='ewald')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.2048655827967139, 8)
self.assertTrue(mf.mo_coeff.dtype == numpy.complex128)
kmf = pscf.KRHF(cell, k, exxdiv='ewald')
e0 = kmf.kernel()
self.assertTrue(numpy.allclose(e0, e1))
# test bands
numpy.random.seed(1)
kpts_band = numpy.random.random((2, 3))
e1, c1 = mf.get_bands(kpts_band)
e0, c0 = kmf.get_bands(kpts_band)
self.assertAlmostEqual(abs(e0[0] - e1[0]).max(), 0, 7)
self.assertAlmostEqual(abs(e0[1] - e1[1]).max(), 0, 7)
self.assertAlmostEqual(lib.finger(e1[0]), -6.8312867098806249, 7)
self.assertAlmostEqual(lib.finger(e1[1]), -6.1120214505413086, 7)
def setUpModule():
global cell, mf, kmf
L = 4
n = 21
cell = pbcgto.Cell()
cell.build(
unit='B',
verbose=7,
output='/dev/null',
a=((L, 0, 0), (0, L, 0), (0, 0, L)),
mesh=[n, n, n],
atom=[['He', (L / 2. - .5, L / 2., L / 2. - .5)],
['He', (L / 2., L / 2., L / 2. + .5)]],
basis={'He': [[0, (0.8, 1.0)], [0, (1.0, 1.0)], [0, (1.2, 1.0)]]})
mf = pbchf.RHF(cell, exxdiv='ewald').run()
kmf = pscf.KRHF(cell, [[0, 0, 0]], exxdiv='ewald').run()
def test_rhf_2d(self):
L = 4
cell = pbcgto.Cell()
cell.build(unit = 'B',
a = [[L,0,0],[0,L,0],[0,0,L*5]],
gs = [5,5,10],
atom = '''He 2 0 0; He 3 0 0''',
dimension = 2,
verbose = 0,
basis = { 'He': [[0, (0.8, 1.0)],
#[0, (1.0, 1.0)],
[0, (1.2, 1.0)]
]})
mf = pbchf.RHF(cell)
mf.with_df = pdf.PWDF(cell)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.2683014249123516, 5)
def test_rhf_exx_ewald_with_kpt(self):
numpy.random.seed(1)
k = numpy.random.random(3)
mf = pbchf.RHF(cell, k, exxdiv='ewald')
e1 = mf.kernel()
self.assertAlmostEqual(e1, -4.2048655827967139, 8)
self.assertTrue(mf.mo_coeff.dtype == numpy.complex128)
kmf = pscf.KRHF(cell, k, exxdiv='ewald')
e0 = kmf.kernel()
self.assertTrue(numpy.allclose(e0,e1))
# test bands
numpy.random.seed(1)
kpt_band = numpy.random.random(3)
e1, c1 = mf.get_bands(kpt_band)
e0, c0 = kmf.get_bands(kpt_band)
self.assertAlmostEqual(abs(e0-e1).max(), 0, 7)
self.assertAlmostEqual(lib.finger(e1), -6.8312867098806249, 7)
def test_rhf_1d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=[[L, 0, 0], [0, L * 5, 0], [0, 0, L * 5]],
gs=[5, 10, 10],
atom='''He 2 0 0; He 3 0 0''',
dimension=1,
verbose=0,
basis={
'He': [
[0, (0.8, 1.0)],
#[0, (1.0, 1.0)],
[0, (1.2, 1.0)]
]
})
mf = pbchf.RHF(cell)
mf.with_df = pdf.AFTDF(cell)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.2455039593257098, 5)
def test_band():
L = 1
cell = pbcgto.Cell()
cell.unit = 'B'
cell.h = np.diag([L, L, L])
cell.gs = np.array([10, 10, 10])
cell.atom.extend([['He', (L / 2., L / 2., L / 2.)]])
cell.basis = {'He': [[0, (1.0, 1.0)]]}
cell.build()
mf = pbchf.RHF(cell)
mf.scf()
auxcell = cell.copy()
auxcell.gs = np.array([1, 1, 1])
auxcell.build()
for i in range(1, 10):
kpt = 1. / i * auxcell.Gv[-1, :]
print pbchf.get_eig_kpt(mf, kpt)[0]
L = 4
n = 21
cell = pbcgto.Cell()
cell.build(unit = 'B',
verbose = 7,
output = '/dev/null',
a = ((L,0,0),(0,L,0),(0,0,L)),
mesh = [n,n,n],
atom = [['He', (L/2.-.5,L/2.,L/2.-.5)],
['He', (L/2. ,L/2.,L/2.+.5)]],
basis = { 'He': [[0, (0.8, 1.0)],
[0, (1.0, 1.0)],
[0, (1.2, 1.0)]]})
mf = pbchf.RHF(cell, exxdiv='ewald').run()
kmf = pscf.KRHF(cell, [[0,0,0]], exxdiv='ewald').run()
def tearDownModule():
global cell, mf, kmf
cell.stdout.close()
del cell, mf, kmf
class KnownValues(unittest.TestCase):
def test_hcore(self):
h1ref = pbchf.get_hcore(cell)
h1 = pbchf.RHF(cell).get_hcore()
self.assertAlmostEqual(abs(h1-h1ref).max(), 0, 9)
self.assertAlmostEqual(lib.finger(h1), 0.14116483012673137, 9)
cell1 = cell.copy()
def test_hcore(self):
h1ref = pbchf.get_hcore(cell)
h1 = pbchf.RHF(cell).get_hcore()
self.assertAlmostEqual(abs(h1 - h1ref).max(), 0, 9)