def main(args):
"""Convert FCIDUMP to QMCPACK readable Hamiltonian format.
Parameters
----------
args : list of strings
command-line arguments.
"""
options = parse_args(args)
(hcore, eri, ecore, nelec) = read_fcidump(options.input_file,
symmetry=options.symm,
verbose=options.verbose)
norb = hcore.shape[-1]
# If the ERIs are complex then we need to form M_{(ik),(lj}} which is
# Hermitian. For real integrals we will have 8-fold symmetry so trasposing
# will have no effect.
eri = numpy.transpose(eri, (0, 1, 3, 2))
chol = modified_cholesky(eri.reshape(norb**2, norb**2),
options.thresh,
options.verbose,
cmax=20).T.copy()
cplx_chol = options.write_complex or numpy.any(abs(eri.imag) > 1e-14)
write_qmcpack_dense(hcore,
chol,
nelec,
norb,
enuc=ecore,
real_chol=(not cplx_chol),
filename=options.output_file)
def dump_pauxy(chkfile=None,
mol=None,
mf=None,
hamil_file='afqmc.h5',
verbose=True,
wfn_file='afqmc.h5',
chol_cut=1e-5,
sparse_zero=1e-16,
cas=None,
ortho_ao=True,
sparse=False):
scf_data = load_from_pyscf_chkfile(chkfile)
mol = scf_data['mol']
hcore = scf_data['hcore']
if ortho_ao:
oao = scf_data['X']
else:
oao = scf_data['mo_coeff']
hcore, chol, nelec, enuc = generate_integrals(mol,
hcore,
oao,
chol_cut=chol_cut,
verbose=verbose,
cas=cas)
nbasis = hcore.shape[-1]
msq = nbasis * nbasis
# Why did I transpose everything?
# QMCPACK expects [M^2, N_chol]
# Internally store [N_chol, M^2]
chol = chol.T.copy()
if sparse:
print(" # Writing integrals in sparse format.")
write_qmcpack_sparse(hcore,
chol,
nelec,
nbasis,
enuc,
filename=hamil_file,
real_chol=True,
verbose=verbose,
ortho=oao)
else:
print(" # Writing integrals in dense format.")
write_qmcpack_dense(hcore,
chol,
nelec,
nbasis,
enuc,
filename=hamil_file,
ortho=oao,
real_chol=True)
write_wfn_mol(scf_data, ortho_ao, wfn_file, mode='a')
def write_integrals(self, filename='hamil.h5'):
if self.sparse:
write_qmcpack_sparse(self.H1[0],
self.chol_vecs.reshape(
(-1, self.nbasis * self.nbasis)).T.copy(),
self.nelec,
self.nbasis,
ecuc=self.ecore,
filename=filename)
else:
write_qmcpack_dense(self.H1[0],
self.chol_vecs.reshape(
(-1, self.nbasis * self.nbasis)).T.copy(),
self.nelec,
self.nbasis,
enuc=self.ecore,
filename=filename,
real_chol=not self.cplx_chol)
def test_read():
numpy.random.seed(7)
nmo = 13
nelec = (4, 3)
h1e, chol, enuc, eri = generate_hamiltonian(nmo, nelec, cplx=True, sym=4)
from pauxy.utils.io import write_qmcpack_dense
chol_ = chol.reshape((-1, nmo * nmo)).T.copy()
write_qmcpack_dense(h1e,
chol_,
nelec,
nmo,
enuc=enuc,
filename='hamil.h5',
real_chol=False)
options = {'nup': nelec[0], 'ndown': nelec[1], 'integrals': 'hamil.h5'}
sys = Generic(inputs=options)
schol = sys.chol_vecs
assert numpy.linalg.norm(chol - schol) == pytest.approx(0.0)
write_input
)
mol = gto.M(atom=[('N', 0, 0, 0), ('N', (0,0,3.0))], basis='sto-3g', verbose=3,
unit='Bohr')
mf = scf.RHF(mol)
mf.chkfile = 'scf.chk'
ehf = mf.kernel()
M = 6
N = 6
mc = mcscf.CASSCF(mf, M, N)
mc.chkfile = 'scf.chk'
mc.kernel()
e_tot, e_cas, fcivec, mo, mo_energy = mc.kernel()
print(ehf, e_tot)
# Rotate by casscf mo coeffs.
h1e, chol, nelec, enuc = generate_integrals(mol, mf.get_hcore(), mo,
chol_cut=1e-5, verbose=True)
write_qmcpack_dense(h1e, chol.T.copy(), nelec,
h1e.shape[-1], enuc=enuc, filename='afqmc.h5')
coeff, occa, occb = zip(*fci.addons.large_ci(fcivec, M, (3,3),
tol=0.1, return_strs=False))
core = [i for i in range(mc.ncore)]
occa = [numpy.array(core + [o + mc.ncore for o in oa]) for oa in occa]
occb = [numpy.array(core + [o + mc.ncore for o in ob]) for ob in occb]
coeff = numpy.array(coeff,dtype=numpy.complex128)
nmo = mf.mo_coeff.shape[-1]
write_qmcpack_wfn('afqmc.h5', (coeff,occa,occb), 'uhf', mol.nelec, nmo, mode='a')
write_input('input.json', 'afqmc.h5', 'afqmc.h5',
options={'system': {'sparse': False}})