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 jk_method(self, J='FFTDF', K=None):
'''
Set up the schemes to evaluate Coulomb and exchange matrix
FFTDF: planewave density fitting using Fast Fourier Transform
AFTDF: planewave density fitting using analytic Fourier Transform
GDF: Gaussian density fitting
MDF: Gaussian and planewave mix density fitting
RS: range-separation JK builder
RSDF: range-separation density fitting
'''
if K is None:
K = J
if J != K:
raise NotImplementedError('J != K')
if 'DF' in J or 'DF' in K:
if 'DF' in J and 'DF' in K:
assert J == K
else:
df_method = J if 'DF' in J else K
self.with_df = getattr(df, df_method)(self.cell, self.kpts)
if 'RS' in J or 'RS' in K:
self.rsjk = RangeSeparationJKBuilder(self.cell, self.kpts)
self.rsjk.verbose = self.verbose
# For nuclear attraction
if J == 'RS' and K == 'RS' and not isinstance(self.with_df, df.GDF):
self.with_df = df.GDF(self.cell, self.kpts)
nuc = self.with_df.__class__.__name__
logger.debug1(self, 'Apply %s for J, %s for K, %s for nuc', J, K, nuc)
return self
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_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 make_cell(d, kmesh):
a = np.eye(3)
a[0,0] = 10
a[1,1] = 10
a[2,2] = 2*d
atoms = [['H',[5,5,0.25*a[2,2]+0.5]],['H',[5,5,0.75*a[2,2]-0.5]]]
cell = gto.Cell()
cell.atom = atoms
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.a = a
cell.verbose = 5
cell.build()
kpts = cell.make_kpts(kmesh,wrap_around=True)
krhf = scf.KRHF(cell, kpts).density_fit()
gdf = df.GDF(cell, kpts)
gdf._cderi_to_save = 'gdf.h5'
gdf.build()
krhf.with_df._cderi = 'gdf.h5'
krhf.exxdiv = None
krhf.run()
num_wann =2
keywords = \
'''
begin projections
H:s
end projections
num_iter = 100
'''
w90 = pywannier90.W90(krhf, cell, kmesh, num_wann, other_keywords = keywords)
w90.kernel()
w90.plot_wf(grid=[20,20,20], supercell=kmesh)
return cell, krhf, w90
def test_ao2mo(self):
kmf = make_rand_kmf()
rand_cc = pbcc.KRCCSD(kmf)
# incore
eris1 = pbcc.kccsd_rhf._ERIS(rand_cc, rand_kmf.mo_coeff)
self.assertAlmostEqual(finger(eris1.oooo),
0.13691900935600992 + 0.026617355192746089j, 12)
self.assertAlmostEqual(finger(eris1.ooov),
0.11364240700567171 - 0.041695025273248622j, 12)
self.assertAlmostEqual(finger(eris1.oovv),
-0.23285827477217841 + 0.019174699732188771j,
12)
self.assertAlmostEqual(finger(eris1.ovov),
-0.43577673177721338 - 0.25735127894943477j, 12)
self.assertAlmostEqual(finger(eris1.voov),
-0.38516873139657298 + 0.26042322219884251j, 12)
self.assertAlmostEqual(finger(eris1.vovv),
-0.12844875724711163 + 0.17587781601517866j, 12)
self.assertAlmostEqual(finger(eris1.vvvv),
-0.39587103797107615 - 0.001692506310261882j,
12)
# outcore
eris2 = pbcc.kccsd_rhf._ERIS(rand_cc,
rand_kmf.mo_coeff,
method='outcore')
self.assertAlmostEqual(abs(eris2.oooo - eris1.oooo).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.ooov - eris1.ooov).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.oovv - eris1.oovv).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.ovov - eris1.ovov).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.voov - eris1.voov).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.vovv - eris1.vovv).max(), 0, 12)
self.assertAlmostEqual(abs(eris2.vvvv - eris1.vvvv).max(), 0, 12)
# df
rand_cc.direct = True
rand_cc._scf.with_df = pbc_df.GDF(kmf.cell, kmf.kpts)
eris3 = pbcc.kccsd_rhf._ERIS(rand_cc,
rand_kmf.mo_coeff,
method='outcore')
self.assertAlmostEqual(finger(eris3.oooo),
0.13807643618081983 + 0.02706881005926997j, 12)
self.assertAlmostEqual(finger(eris3.ooov),
0.11503403213521873 - 0.04088028212967049j, 12)
self.assertAlmostEqual(finger(eris3.oovv),
-0.23166000424452704 + 0.01922808953198968j, 12)
self.assertAlmostEqual(finger(eris3.ovov),
-0.4333329222923895 - 0.2542273009739961j, 12)
self.assertAlmostEqual(finger(eris3.voov),
-0.3851423191571177 + 0.26086853075652333j, 12)
self.assertAlmostEqual(finger(eris3.vovv),
-0.12653400070346893 + 0.17634730801555784j, 12)
self.assertAlmostEqual(finger(np.array(eris3.Lpv.tolist())),
-2.2567245766867092 + 0.7648803028093745j, 12)
def scf_run(pmol, method='KROHF', df_method='gdf', use_saved_eri=False, \
eri_fname='./gdf_ints_atom_full_basis.h5'):
if method == 'KROHF':
pmf = scf.KROHF(pmol)
else:
raise NotImplementedError
pmf.max_cycle = 5000
pmf.conv_tol = 1e-10
if df_method == 'gdf':
gdf = df.GDF(pmol, kpts=pmol.make_kpts([1, 1, 1]))
else:
raise NotImplementedError
if not use_saved_eri:
gdf._cderi_to_save = eri_fname
gdf.build()
pmf.with_df = gdf
pmf.with_df._cderi = eri_fname
pmf.scf()
return pmf
def make_cell():
a = np.eye(3)
a[0,0] = 10
a[1,1] = 10
a[2,2] = 15
atoms = [['Li',[5,5,1.5]],['H',[5,5,3.5]],['H',[5,5,6.5]],['H',[5,5,8.5]],['H',[5,5,11.5]],['H',[5,5,13.5]]]
cell = gto.Cell()
cell.atom = atoms
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.a = a
cell.verbose = 5
cell.build()
kmesh = [1, 1, 1]
kpts = cell.make_kpts(kmesh)
krhf = scf.KRHF(cell, kpts).density_fit()
gdf = df.GDF(cell, kpts)
gdf._cderi_to_save = 'gdf_gamma.h5'
gdf.build()
krhf.with_df._cderi = 'gdf_gamma.h5'
krhf.exxdiv = None
krhf.run()
num_wann =7
keywords = \
'''
begin projections
Li:sp
H:s
end projections
num_iter = 100
'''
w90 = pywannier90.W90(krhf, cell, kmesh, num_wann, other_keywords = keywords)
w90.kernel()
w90.plot_wf(grid=[20,20,20], supercell=kmesh)
return cell, krhf, w90
cell = gto.Cell() cell.unit = 'A' cell.a = [[4, 0, 0], [0, 1, 0], [0, 0, 1]] cell.atom = ''' H 0.0000000 0.0000000 0.0000000 H 1.0000000 0.0000000 0.0000000 H 2.0000000 0.0000000 0.0000000 H 3.0000000 0.0000000 0.0000000 ''' cell.basis = 'sto-6g' cell.dimension = 1 cell.verbose = 4 cell.build() gdf = df.GDF(cell) mf = scf.RHF(cell) mf.with_df = gdf mf.with_df.auxbasis = 'cc-pvdz-jkfit' mf.max_cycle = 150 mf.chkfile = name + '.chk' #mf.with_df._cderi_to_save = name+'_eri.h5' #mf.with_df._cderi = name+'_eri.h5' #mf = mole_scf.addons.remove_linear_dep_(mf) #mf.__dict__.update(scf.chkfile.load(name+'.chk', 'scf')) #dm = mf.make_rdm1() ehf = mf.kernel() ncore = 0 nao, nmo = mf.mo_coeff.shape
C 1.7834 0. 1.7834
C 2.6751 0.8917 2.6751
C 0. 1.7834 1.7834
C 0.8917 2.6751 2.6751'''
cell.a = np.eye(3) * 3.5668
cell.basis = 'sto-3g'
#cell.precision = 1e-10
cell.verbose = 4
cell.build()
kmesh = [2, 2, 2]
abs_kpts = cell.make_kpts(kmesh)
scaled_kpts = cell.get_scaled_kpts(abs_kpts)
kmf = pscf.KRHF(cell, abs_kpts).density_fit()
gdf = df.GDF(cell, abs_kpts)
kmf.with_df = gdf
#kmf.checkfile = './ch4.chk'
kmf.verbose = 5
#kmf = pscf.KRHF(cell, abs_kpts)
#kmf.__dict__.update(scf.chkfile.load('ch4.chk', 'scf')) # test
ekpt = kmf.run()
print np.asarray(kmf.mo_coeff)
kmf_sc = k2gamma(kmf,
abs_kpts,
kmesh,
realize=True,
tol_deg=5e-5,
real_split=False)
mf = pbchf.KRHF(cell, exxdiv='ewald') #mf = pbchf.KRHF(cell, exxdiv=None) mf.with_df = pdf.FFTDF(cell) mf.kpts = cell.make_kpts(kpts) mf.conv_tol = 1e-6 e.append(mf.kernel()) t.append(time.time() - t0) ################################################## # # 2D PBC with GDF # ################################################## t0 = time.time() mf = pbchf.KRHF(cell) mf.with_df = pdf.GDF(cell) mf.kpts = cell.make_kpts(kpts) mf.conv_tol = 1e-6 e.append(mf.kernel()) t.append(time.time() - t0) ################################################## # # 2D PBC with MDF # ################################################## t0 = time.time() mf = pbchf.KRHF(cell) mf.with_df = pdf.MDF(cell) mf.kpts = cell.make_kpts(kpts) mf.conv_tol = 1e-6
# '''
cell.basis = '321g'
cell.a = np.array([[6.00, 0.0, 0.0], [0.0, 20.0, 0.0],[0.0, 0.0, 20.0]])
#cell.mesh = [21, 21, 21 ]
cell.precision = 1e-10
cell.verbose = 6
cell.unit='B'
cell.build()
kmesh = [3, 1, 1]
abs_kpts = cell.make_kpts(kmesh)
scaled_kpts = cell.get_scaled_kpts(abs_kpts)
kmf = pscf.KRHF(cell, abs_kpts).density_fit()
gdf = df.GDF(cell, abs_kpts)
kmf.with_df = gdf
kmf.checkfile = './ch4.chk'
kmf.verbose = 5
#kmf = pscf.KRHF(cell, abs_kpts)
#kmf.__dict__.update(scf.chkfile.load('ch4.chk', 'scf')) # test
ekpt = kmf.run()
kmf_sc = k2gamma(kmf, abs_kpts, kmesh, realize = False, tol_deg = 5e-5, real_split = False)
c_g_ao = kmf_sc.mo_coeff[0]
print "Supercell gamma MO in AO basis from conversion:"
print c_g_ao
mo_coeff_occ = kmf_sc.mo_coeff[0][:,kmf_sc.mo_occ[0]>0]
lo_iao = lo.iao.iao(kmf_sc.cell, mo_coeff_occ)
import inp
# Initialize geometry
geoms = read(inp.filename, ":")
geom = geoms[iconf]
symb = geom.get_chemical_symbols()
coords = geom.get_positions()
cell = geom.get_cell()
natoms = len(coords)
atoms = []
for i in range(natoms):
coord = coords[i]
atoms.append([symb[i], (coord[0], coord[1], coord[2])])
# Get PySCF objects for wave-function and density-fitted basis
mol = gto.M(atom=atoms, basis=inp.qmbasis, a=cell)
gdf = df.GDF(mol)
#mol = gto.M(atom=atoms, basis='gth-dzvp', pseudo = 'gth-pade', a=cell)
mol.verbose = 4
# Run restricted hartree-fock calculation
m = dft.RKS(mol)
m.xc = inp.functional
m.with_df = gdf
# Save density matrix
m.kernel()
dm = m.make_rdm1()
dirpath = os.path.join(inp.path2indata, "density_matrices")
if not os.path.exists(dirpath):
os.mkdir(dirpath)
np.save(inp.path2indata + "density_matrices/dm_conf" + str(iconf + 1) + ".npy",
cell.atom = '''
C 0.00000000 0.00000000 0.00000000
C 1.686580575 1.686580575 1.686580575
'''
cell.basis = 'bfd-vtz'
cell.ecp = 'bfd'
cell.unit = 'B'
cell.drop_exponent = 0.1
cell.verbose = 5
cell.build()
kpts = cell.make_kpts(kmesh)
kpts -= kpts[0]
supcell = cell
mydf = df.GDF(supcell, kpts)
mydf.auxbasis = 'weigend'
mf = scf.KRHF(supcell, kpts).density_fit()
mf.exxdiv = 'ewald'
mf.with_df = mydf
e_scf = mf.kernel()
title = "C_Diamond-211"
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(supcell, mf, title=title, kpts=kpts, kmesh=kmesh)
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)
if __name__ == '__main__':
print("Full kpoint_rhf test")
#unittest.main()
if 1:
kmf = make_rand_kmf()
rand_cc = pbcc.KRCCSD(kmf)
rand_cc.direct = True
rand_cc._scf.with_df = pbc_df.GDF(kmf.cell, kmf.kpts)
eris3 = pbcc.kccsd_rhf._ERIS(rand_cc,
rand_kmf.mo_coeff,
method='outcore')
print(
lib.fp(eris3.oooo) - (0.13807643618081983 + 0.02706881005926997j))
print(
lib.fp(eris3.ooov) - (0.11503403213521873 - 0.04088028212967049j))
print(
lib.fp(eris3.oovv) - (-0.23166000424452704 + 0.01922808953198968j))
print(lib.fp(eris3.ovov) - (-0.4333329222923895 - 0.2542273009739961j))
print(
lib.fp(eris3.voov) - (-0.3851423191571177 + 0.26086853075652333j))
print(
lib.fp(eris3.vovv) - (-0.12653400070346893 + 0.17634730801555784j))
print(
cell = gto.Cell()
cell.build(unit='B',
a=[[0., 6.74027466, 6.74027466], [6.74027466, 0., 6.74027466],
[6.74027466, 6.74027466, 0.]],
atom='''H 0 0 0
H 1.68506866 1.68506866 1.68506866
H 3.37013733 3.37013733 3.37013733''',
basis='gth-dzvp',
pseudo='gth-pade',
verbose=5,
charge=0,
spin=1)
cell.spin = cell.spin * 3
kpts = cell.make_kpts([3, 1, 1], scaled_center=[0, 0, 0])
gdf = df.GDF(cell, kpts)
gdf_fname = 'h3_ints_311.h5'
gdf._cderi_to_save = gdf_fname
if not os.path.isfile(gdf_fname):
gdf.build()
chkfname = 'h_311.chk'
if os.path.isfile(chkfname):
kmf = scf.KUHF(cell, kpts, exxdiv=None)
kmf.with_df = gdf
kmf.with_df._cderi = gdf_fname
data = chkfile.load(chkfname, 'scf')
kmf.__dict__.update(data)
else:
kmf = scf.KUHF(cell, kpts, exxdiv=None)
kmf.with_df = gdf
cell.atom='''
H 0.000000000000 0.000000000000 0.000000000000
H 1.685068664391 1.685068664391 1.685068664391
'''
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.a = '''
0.000000000, 3.370137329, 3.370137329
3.370137329, 0.000000000, 3.370137329
3.370137329, 3.370137329, 0.000000000'''
cell.unit = 'B'
cell.verbose = 5
cell.build()
kpts = cell.make_kpts([1,1,3])
mydf = GDF(cell, kpts)
mydf.mesh = [5,5,5]
mydf.build()
mydf.dump_to_file('erimpi.int')
if rank==0:
mf = scf.KRHF(cell, kpts)
mf.with_df = mydf # USING ERI FILE from MPIGDF for SCF
mf.kernel()
mf= scf.KRHF(cell,kpts)
mf.with_df = df.GDF(cell,kpts) # USING SERIAL GDF ERI
mf.with_df.mesh = [5,5,5]
mf.kernel()
