def test_efg_kernel(self):
cell = gto.Cell()
cell.atom = 'H 1 0.8 0; H 0. 1.3 0'
cell.a = np.eye(3) * 3
cell.basis = [[0, (2.0, 1.)], [0, (0.5, 1.)]]
cell.mesh = [20] * 3
cell.build()
np.random.seed(12)
kpts = cell.make_kpts([2] * 3)
nao = cell.nao
dm = np.random.random((len(kpts), nao, nao))
mf = scf.RHF(cell)
mf.make_rdm1 = lambda *args, **kwargs: dm
vref = EFG(mf)
self.assertAlmostEqual(lib.finger(vref), 0.67090557110411564, 9)
mf.with_df = df.AFTDF(cell)
mf.with_df.eta = 0
v = EFG(mf)
self.assertAlmostEqual(abs(v - vref).max(), 0, 2)
mf.with_df = df.AFTDF(cell)
mf.with_df.mesh = [8] * 3
v = EFG(mf)
self.assertAlmostEqual(abs(v - vref).max(), 0, 2)
def test_pnucp(self):
cell1 = gto.Cell()
cell1.atom = '''
He 1.3 .2 .3
He .1 .1 1.1 '''
cell1.basis = {'He': [[0, [0.8, 1]], [1, [0.6, 1]]]}
cell1.mesh = [15] * 3
cell1.a = numpy.array(([2.0, .9, 0.], [0.1, 1.9, 0.4], [0.8, 0, 2.1]))
cell1.build()
charge = -cell1.atom_charges()
Gv = cell1.get_Gv(cell1.mesh)
SI = cell1.get_SI(Gv)
rhoG = numpy.dot(charge, SI)
coulG = tools.get_coulG(cell1, mesh=cell1.mesh, Gv=Gv)
vneG = rhoG * coulG
vneR = tools.ifft(vneG, cell1.mesh).real
coords = cell1.gen_uniform_grids(cell1.mesh)
aoR = dft.numint.eval_ao(cell1, coords, deriv=1)
ngrids, nao = aoR.shape[1:]
vne_ref = numpy.einsum('p,xpi,xpj->ij', vneR, aoR[1:4], aoR[1:4])
mydf = df.AFTDF(cell1)
dat = sfx2c1e.get_pnucp(mydf)
self.assertAlmostEqual(abs(dat - vne_ref).max(), 0, 7)
mydf.eta = 0
dat = sfx2c1e.get_pnucp(mydf)
self.assertAlmostEqual(abs(dat - vne_ref).max(), 0, 7)
def test_mdf_jk_0d(self):
L = 4.
cell = pgto.Cell()
cell.verbose = 0
cell.a = numpy.eye(3)*L
cell.atom =[['He' , ( L/2+0., L/2+0. , L/2+1.)],]
cell.basis = {'He': [[0, (4.0, 1.0)], [0, (1.0, 1.0)]]}
cell.dimension = 0
cell.mesh = [60]*3
cell.build()
nao = cell.nao
numpy.random.seed(1)
dm = numpy.random.random((nao,nao))
dm = dm.dot(dm.conj().T).reshape(1,nao,nao)
vj0, vk0 = scf.hf.get_jk(cell, dm, hermi=0, omega=0.5)
self.assertAlmostEqual(lib.fp(vj0), 0.08265798268352553, 9)
self.assertAlmostEqual(lib.fp(vk0), 0.2375705823780625 , 9)
vj1, vk1 = pbcdf.GDF(cell).get_jk(dm, hermi=0, omega=0.5, exxdiv=None)
vj2, vk2 = pbcdf.MDF(cell).get_jk(dm, hermi=0, omega=0.5, exxdiv=None)
vj3, vk3 = pbcdf.AFTDF(cell).get_jk(dm, hermi=0, omega=0.5, exxdiv=None)
self.assertAlmostEqual(abs(vj0-vj1).max(), 0, 3)
self.assertAlmostEqual(abs(vj0-vj2).max(), 0, 3)
self.assertAlmostEqual(abs(vj0-vj3).max(), 0, 3)
self.assertAlmostEqual(abs(vk0-vk1).max(), 0, 3)
self.assertAlmostEqual(abs(vk0-vk2).max(), 0, 3)
self.assertAlmostEqual(abs(vk0-vk3).max(), 0, 3)
def test_aft_bands(self):
mf = scf.KRHF(cell)
mf.with_df = df.AFTDF(cell)
mf.kpts = cell.make_kpts([2,1,1])
mf.kernel()
self.assertAlmostEqual(finger(mf.get_bands(kband[0])[0]), 1.968506055533682, 8)
self.assertAlmostEqual(finger(mf.get_bands(kband)[0]), 1.0538585525613609, 7)
def test_aft_bands(self):
mf = scf.KRHF(cell)
mf.with_df = df.AFTDF(cell)
mf.kpts = cell.make_kpts([2]*3)
mf.kernel()
self.assertAlmostEqual(finger(mf.get_bands(kband[0])[0]), -0.32214958122356513, 9)
self.assertAlmostEqual(finger(mf.get_bands(kband)[0]), -0.64207984898611348, 9)
def test_krhf_2d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=np.eye(3) * 4,
mesh=[10, 10, 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 = khf.KRHF(cell)
mf.with_df = df.AFTDF(cell)
mf.with_df.eta = 0.2
mf.with_df.mesh = cell.mesh
mf.kpts = cell.make_kpts([2, 1, 1])
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.5376801775171911, 5)
def test_kghf_1d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=np.eye(3) * 4,
mesh=[8, 20, 20],
atom='''He 2 0 0; He 3 0 0''',
dimension=1,
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 = pscf.KGHF(cell)
mf.with_df = df.AFTDF(cell)
mf.with_df.eta = 0.2
mf.init_guess = 'hcore'
mf.kpts = cell.make_kpts([2, 1, 1])
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.5112358424228809, 4)
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_mdf_jk_rsh(self):
L = 4.
cell = pgto.Cell()
cell.verbose = 0
cell.a = numpy.eye(3)*L
cell.atom =[['He' , ( L/2+0., L/2+0. , L/2+1.)],]
cell.basis = {'He': [[0, (4.0, 1.0)], [0, (1.0, 1.0)]]}
cell.build()
nao = cell.nao
kpts = [[0.2, 0.2, 0.4]]
numpy.random.seed(1)
dm = numpy.random.random((nao,nao)) + .2j*numpy.random.random((nao,nao))
dm = dm.dot(dm.conj().T).reshape(1,nao,nao)
vj0, vk0 = pbcdf.FFTDF(cell, kpts).get_jk(dm, hermi=0, kpts=kpts, omega=0.3, exxdiv='ewald')
vj1, vk1 = pbcdf.GDF(cell, kpts).get_jk(dm, hermi=0, kpts=kpts, omega=0.3, exxdiv='ewald')
vj2, vk2 = pbcdf.MDF(cell, kpts).get_jk(dm, hermi=0, kpts=kpts, omega=0.3, exxdiv='ewald')
vj3, vk3 = pbcdf.AFTDF(cell, kpts).get_jk(dm, hermi=0, kpts=kpts, omega=0.3, exxdiv='ewald')
self.assertAlmostEqual(lib.fp(vj0), 0.007500219791944259, 9)
self.assertAlmostEqual(lib.fp(vk0), 0.0007724337759304424+0.00018842136513478529j, 9)
self.assertAlmostEqual(abs(vj0-vj1).max(), 0, 8)
self.assertAlmostEqual(abs(vj0-vj2).max(), 0, 8)
self.assertAlmostEqual(abs(vj0-vj3).max(), 0, 8)
self.assertAlmostEqual(abs(vk0-vk1).max(), 0, 8)
self.assertAlmostEqual(abs(vk0-vk2).max(), 0, 8)
self.assertAlmostEqual(abs(vk0-vk3).max(), 0, 8)
def test_ghf_1d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=numpy.eye(3) * 4,
mesh=[10, 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 = pscf.GHF(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_khf(self):
with lib.light_speed(2) as c:
mf = scf.KRHF(cell).sfx2c1e()
mf.with_df = df.AFTDF(cell)
mf.kpts = cell.make_kpts([3,1,1])
dm = mf.get_init_guess()
h1 = mf.get_hcore()
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[0], h1[0]),-0.47578184212352159+0j, 8)
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[1], h1[1]),-0.09637799091491725+0j, 8)
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[2], h1[2]),-0.09637799091491725+0j, 8)
def test_hf(self):
with lib.light_speed(2) as c:
mf = scf.RHF(cell).sfx2c1e()
mf.with_df = df.AFTDF(cell)
dm = mf.get_init_guess()
h1 = mf.get_hcore()
self.assertAlmostEqual(numpy.einsum('ij,ji', dm, h1),
-0.2458227312351979 + 0j, 8)
kpts = cell.make_kpts([3, 1, 1])
h1 = mf.get_hcore(kpt=kpts[1])
self.assertAlmostEqual(numpy.einsum('ij,ji', dm, h1),
-0.04113247191600125 + 0j, 8)
def test_khf(self):
with lib.light_speed(2) as c:
mf = scf.KRHF(cell).sfx2c1e()
mf.with_df = df.AFTDF(cell)
mf.kpts = cell.make_kpts([3, 1, 1])
dm = mf.get_init_guess()
h1 = mf.get_hcore()
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[0], h1[0]),
-0.31082970748083477 + 0j, 8)
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[1], h1[1]),
-0.05200981271862468 + 0j, 8)
self.assertAlmostEqual(numpy.einsum('ij,ji', dm[2], h1[2]),
-0.05200981271862468 + 0j, 8)
def test_hf(self):
with lib.light_speed(2) as c:
mf = scf.RHF(cell).sfx2c1e()
mf.with_df = df.AFTDF(cell)
dm = mf.get_init_guess()
h1 = mf.get_hcore()
self.assertAlmostEqual(
numpy.einsum('ij,ji', dm, h1),
2 / 3.7865300454631 * -0.47578184212352159 + 0j, 8)
kpts = cell.make_kpts([3, 1, 1])
h1 = mf.get_hcore(kpt=kpts[1])
self.assertAlmostEqual(
numpy.einsum('ij,ji', dm, h1),
2 / 3.7865300454631 * -0.09637799091491725 + 0j, 8)
def test_pp_int(self):
from pyscf import gto, scf
from pyscf.pbc import gto as pbcgto
from pyscf.pbc import scf as pbcscf
from pyscf.pbc import df
cell = pbcgto.Cell()
cell.atom = 'He 1. .5 .5; C .1 1.3 2.1'
cell.basis = {
'He': [(0, (2.5, 1)), (0, (1., 1))],
'C': 'gth-szv',
}
cell.pseudo = {
'C':
'gth-pade',
'He':
pbcgto.pseudo.parse('''He
2
0.40000000 3 -1.98934751 -0.75604821 0.95604821
2
0.29482550 3 1.23870466 .855 .3
.71 -1.1
.9
0.32235865 2 2.25670239 -0.39677748
0.93894690
''')
}
cell.a = numpy.eye(3)
cell.dimension = 0
cell.build()
mol = cell.to_mol()
hcore = scf.RHF(mol).get_hcore()
mydf = df.AFTDF(cell)
ref = mydf.get_pp() + mol.intor('int1e_kin')
self.assertAlmostEqual(abs(hcore - ref).max(), 0, 2)
mf = pbcscf.RHF(cell)
mf.with_df = mydf
mf.run()
e_ref = mf.e_tot
e_tot = scf.RHF(mol).run().e_tot
self.assertAlmostEqual(abs(e_ref - e_tot).max(), 0, 6)
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,
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
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.24497234871167, 5)
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.AFTDF(cell)
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.2684257145738229, 5)
def test_kuhf_1d(self):
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=np.eye(3) * 4,
mesh=[8, 20, 20],
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 = kuhf.KUHF(cell)
mf.with_df = df.AFTDF(cell)
mf.with_df.eta = 0.2
mf.init_guess = 'hcore'
mf.kpts = cell.make_kpts([2, 1, 1])
e1 = mf.kernel()
self.assertAlmostEqual(e1, -3.5112358424228809, 5)
import numpy as np
import time
from pyscf.pbc import gto, scf, df
import pyscf_cache
# Run without caching:
cell = gto.Cell()
cell.build(atom='He 0 0 1; He 1 0 1', basis='6-31g', a=np.eye(3)*3, mesh=[10,]*3, verbose=0)
rhf_old = scf.KRHF(cell)
rhf_old.with_df = df.AFTDF(cell)
rhf_old.kpts = cell.make_kpts([2,2,1])
t0 = time.time()
rhf_old.run()
t1 = time.time()
# Assign desired cached functions and apply decorators:
pyscf_cache.to_cache = {
gto.Cell: ['energy_nuc', 'ewald'],
scf.KRHF: ['get_hcore'],
df.AFTDF: ['ft_loop'],
}
copy_policy = {}
def test_aft_band(self):
mf = scf.RHF(cell)
mf.with_df = df.AFTDF(cell)
mf.kernel()
self.assertAlmostEqual(lib.fp(mf.get_bands(kband[0])[0]),
1.9966027703000777, 7)
# 2D PBC with AFT
#
##################################################
cell = pbcgto.Cell()
cell.build(unit = 'B',
a = [[4.6298286730500005, 0.0, 0.0], [-2.3149143365249993, 4.009549246030899, 0.0], [0.0, 0.0, Lz]],
atom = 'C 0 0 0; C 0 2.67303283 0',
mesh = aft_mesh,
dimension=2,
pseudo = pseudo,
verbose = 7,
precision = 1e-6,
basis='gth-szv')
t0 = time.time()
mf = pbchf.KRHF(cell)
mf.with_df = pdf.AFTDF(cell)
mf.kpts = cell.make_kpts(kpts)
mf.conv_tol = 1e-6
e.append(mf.kernel())
t.append(time.time() - t0)
##################################################
#
# 2D PBC with FFT
#
##################################################
cell = pbcgto.Cell()
cell.build(unit = 'B',
a = [[4.6298286730500005, 0.0, 0.0], [-2.3149143365249993, 4.009549246030899, 0.0], [0.0, 0.0, Lz]],
atom = 'C 0 0 0; C 0 2.67303283 0',
ke_cutoff = fft_ke_cut,
def test_aft_band(self):
mf = scf.RHF(cell)
mf.with_df = df.AFTDF(cell)
mf.kernel()
self.assertAlmostEqual(finger(mf.get_bands(kband[0])[0]),
-0.093770552709347754, 9)
new = super_cell(cell, nmp)
cell = pbcgto.Cell()
#cell.unit = 'B'
cell.spin = 0
cell.symmetry = 0
cell.charge = 0
cell.verbose = 4
cell.atom = new.atom
cell.a = new.a
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.mesh = [10, 10, 10]
cell.build()
mf = pbchf.RHF(cell)
mf.with_df = pbcdf.AFTDF(cell)
mf.kernel()
nao = cell.nao_nr()
dm = mf.make_rdm1()
mo = mf.mo_coeff
c = numpy.eye(cell.nao_nr())
s = cell.pbc_intor('cint1e_ovlp_sph')
pop = einsum('ij,ji->', s, dm)
print('Population : %s' % pop)
pairs1 = einsum('ij,kl,ij,kl->', dm, dm, s, s) * 0.5 # J
pairs2 = einsum('ij,kl,li,kj->', dm, dm, s, s) * 0.25 # XC
pairs = (pairs1 - pairs2)
print('Coulomb Pairs : %12.6f' % (pairs1))
pqkR = pqkI = None
return eriR
def get_eri_2c2e(mydf):
from pyscf.gto.ft_ao import ft_ao
eriR = 0
kptijkl = numpy.zeros((4, 3))
q = numpy.zeros(3)
coulG = mydf.weighted_coulG(q, False, mydf.mesh)
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.mesh)
ao = ft_ao(cell, Gv)
return lib.dot(ao.T * coulG, ao.conj())
mydf = df.AFTDF(cell)
# Regular ERIs
eri0 = get_eri(mydf)
eri1 = cell.intor('int2e_sph', aosym='s4')
print('int2e', abs(eri0 - eri1).max(), abs(eri0).max())
eri0 = get_eri_ip1(mydf)
eri1 = cell.intor('int2e_ip1_sph', aosym='s1', comp=3)
eri1 = -eri1 - eri1.transpose(0, 2, 1, 3, 4)
print('int2e_ip1', abs(eri0 - eri1).max(), abs(eri0).max())
eri0 = get_eri_laplacian(mydf)
eri1_ipip1 = cell.intor('int2e_ipip1_sph', aosym='s1',
comp=9).reshape(3, 3, nao, nao, nao, nao)
eri1_ipvip1 = cell.intor('int2e_ipvip1_sph', aosym='s1',