def test_remove_lindep(self):
mol = gto.M(verbose = 0,
atom = [('H', 0, 0, i*.5) for i in range(4)],
basis = ('sto-3g',[[0, [.002,1]]]))
mf = addons.remove_linear_dep_(scf.RHF(mol), threshold=1e-8,
lindep=1e-9).run()
self.assertAlmostEqual(mf.e_tot, -1.6291001503057689, 7)
def run_kcell(cell, nk):
abs_kpts = cell.make_kpts(nk, wrap_around=True)
kmf = pbcscf.KRHF(cell, abs_kpts)
kmf = remove_linear_dep_(kmf, threshold=1e-5, lindep=1e-6)
kmf.conv_tol = 1e-12
ekpt = kmf.scf()
mp = pyscf.pbc.mp.kmp2.KMP2(kmf).run()
return ekpt, mp.e_corr
def test_from_pyscf_lindep(self):
atom = gto.M(atom='Ne 0 0 0', basis='aug-ccpvtz', verbose=0)
from pyscf.scf.addons import remove_linear_dep_
mf = scf.RHF(atom)
remove_linear_dep_(mf, 0.1, 0.1)
mf.chkfile = 'scf.chk'
energy = mf.kernel()
X = get_ortho_ao_mol(atom.intor('int1e_ovlp_sph'), 0.1)
with h5py.File('scf.chk', 'r+') as fh5:
fh5['scf/orthoAORot'] = X
self.assertAlmostEqual(energy, -128.11089429105502)
write_qmcpack('scf.chk',
'afqmc.h5',
1e-8,
wfn_file='afqmc.h5',
dense=True,
real_chol=True,
ortho_ao=True)
etot, e1b, e2b = calculate_hf_energy('afqmc.h5', 'afqmc.h5')
self.assertAlmostEqual(etot, -128.11089429105502)
def run_scf(chkfile):
from pyscf import gto, scf
from pyscf.scf.addons import remove_linear_dep_
mol = gto.M(atom="H 0 0 0; H 0 0 1.4",
basis="ccecpccpvdz",
ecp="ccecp",
unit="bohr")
mf = scf.RHF(mol)
mf.chkfile = chkfile
mf = remove_linear_dep_(mf)
energy = mf.kernel()
def test_221(self):
cell1 = cell.copy()
cell1.basis = 'gth-dzv'
cell1.build()
nk = [2, 2, 1]
abs_kpts = cell1.make_kpts(nk, wrap_around=True)
kmf = pbcscf.KRHF(cell1, abs_kpts)
kmf = remove_linear_dep_(kmf, threshold=1e-4, lindep=1e-6)
ekpt = kmf.scf()
mp = pyscf.pbc.mp.kmp2.KMP2(kmf).run()
self.assertAlmostEqual(ekpt, -10.835614361742607, 8)
self.assertAlmostEqual(mp.e_corr, -0.1522294774708119, 8)
def multislater(kind=0, nk=(1, 1, 1)):
L = 3
mol = gto.Cell(
atom="""H {0} {0} {0}
H {1} {1} {1}""".format(0.0, L / 2),
basis="cc-pvtz",
spin=0,
unit="bohr",
)
mol.exp_to_discard = 0.1
mol.build(a=np.eye(3) * L)
kpts = mol.make_kpts(nk)
mf = scf.UKS(mol, (0, 0, 0))
mf.xc = "pbe"
mf = multigrid(mf)
mf = remove_linear_dep_(mf)
mf.chkfile = "h_bcc.chkfile"
mf = mf.run()
runtest(mol, mf, kind=kind, do_mc=True)
for s in [0,1]:
dm[s,p,p]=1
#Control the 3d occupancy for CrO...
if (el=='Cr'):
for i,d in enumerate(TM_3d_orbitals):
#These are the 3d orbitals we want to fill to get the correct symmetry
if ( ('xy' in aos[d]) or ('yz' in aos[d]) or ('z^2' in aos[d]) or ('x2-y2' in aos[d]) ):
print('We are singly filling this d-orbital: '+np.str(aos[d]) )
dm[0,d,d]=1
m.chkfile=el+basis+"_r"+str(r)+"_s"+str(S[run])+"_"+method+"_"+str(run)+".chk"
m.irrep_nelec = symm_dict[run]
m.max_cycle=100
m = addons.remove_linear_dep_(m)
m.conv_tol=1e-6
#Only need an initial guess for CrO and CuO...
if (el=='Cr' or el=='Cu'):
total_energy=m.kernel(dm)
else:
total_energy=m.kernel()
#Compute the Mulliken orbital occupancies...
m.analyze()
assert(np.sum(m.mo_occ)==25)
#Once we get past the vdz basis, just read-in the existing chk file...
else:
##############################################################################################
deltax = eigvec[1:, idx] / eigvec[0, idx]
return deltax
if __name__ == '__main__':
from pyscf import gto, scf, mcscf, fci, lo, ci, cc, lib
from pyscf.scf import ROHF, ROKS, UHF, UKS, addons
chkfile = '../ub3lyp_full/Cuvtz_r1.725_s1_UB3LYP_0.chk'
mol = lib.chkfile.load_mol(chkfile)
mol.verbose = 4
mf = UKS(mol)
mf.__dict__.update(lib.chkfile.load(chkfile, 'scf'))
mf.xc = 'B3LYP'
mf.max_cycle = 100
mf = addons.remove_linear_dep_(mf)
mf.conv_tol = 1e-5
mf.diis = scf.ADIIS()
#3dpi - 2ppi constraint
'''
id0 = list(mol.search_ao_label('Cu 3dyz')) + list(mol.search_ao_label('Cu 3dxz'))
id1 = mol.search_ao_label('Cu 4s')
orbital_indices = [[id0[0],id0[0]],[id1[0],id1[0]]]
spin_labels = [[0,1],[0,1]]
nelec_required = [1.,0.3]
mf.chkfile = 'Cuvtz_r1.725_s1_UB3LYP_0c.chk'
mf.irrep_nelec = {'A1':(5,5),'E1x':(3,3),'E1y':(3,2),'E2x':(1,1),'E2y':(1,1)}
'''
#3dz2 - 2ppi
