def general(eri_or_mol, mo_coeffs, *args, **kwargs):
if isinstance(eri_or_mol, numpy.ndarray):
return incore.general(eri_or_mol, mo_coeffs, *args, **kwargs)
else:
if 'intor' in kwargs and ('_sph' not in kwargs['intor']):
mod = r_outcore
else:
mod = outcore
if len(args) > 0 and isinstance(args[0], str): # args[0] is erifile
fn = getattr(mod, 'general')
else:
fn = getattr(mod, 'general_iofree')
return fn(eri_or_mol, mo_coeffs, *args, **kwargs)
def general(eri_or_mol, mo_coeffs, *args, **kwargs):
r'''Given four sets of orbitals corresponding to the four MO indices,
transfer arbitrary spherical AO integrals to MO integrals.
Args:
eri_or_mol : ndarray or Mole object
If AO integrals are given as ndarray, it can be either 8-fold or
4-fold symmetry. The integral transformation are computed incore
(ie all intermediate are held in memory).
If Mole object is given, AO integrals are generated on the fly and
outcore algorithm is used (ie intermediate data are held on disk).
mo_coeffs : 4-item list of ndarray
Four sets of orbital coefficients, corresponding to the four
indices of (ij|kl)
erifile : str or h5py File or h5py Group object
*Note* this argument is effective when eri_or_mol is Mole object.
The file to store the transformed integrals. If not given, the
transformed integrals are held in memory.
Kwargs:
dataname : str
*Note* this argument is effective when eri_or_mol is Mole object.
The dataset name in the erifile (ref the hierarchy of HDF5 format
http://www.hdfgroup.org/HDF5/doc1.6/UG/09_Groups.html). By assigning
different dataname, the existed integral file can be reused. If
the erifile contains the dataname, the new integrals data will
overwrite the old one.
tmpdir : str
*Note* this argument is effective when eri_or_mol is Mole object.
The directory where to temporarily store the intermediate data
(the half-transformed integrals). By default, it's controlled by
shell environment variable ``TMPDIR``. The disk space requirement
is about comp*mo_coeffs[0].shape[1]*mo_coeffs[1].shape[1]*nao**2
intor : str
*Note* this argument is effective when eri_or_mol is Mole object.
Name of the 2-electron integral. Ref to :func:`getints_by_shell`
for the complete list of available 2-electron integral names
aosym : int or str
*Note* this argument is effective when eri_or_mol is Mole object.
Permutation symmetry for the AO integrals
| 4 or '4' or 's4': 4-fold symmetry (default)
| '2ij' or 's2ij' : symmetry between i, j in (ij|kl)
| '2kl' or 's2kl' : symmetry between k, l in (ij|kl)
| 1 or '1' or 's1': no symmetry
| 'a4ij' : 4-fold symmetry with anti-symmetry between i, j in (ij|kl) (TODO)
| 'a4kl' : 4-fold symmetry with anti-symmetry between k, l in (ij|kl) (TODO)
| 'a2ij' : anti-symmetry between i, j in (ij|kl) (TODO)
| 'a2kl' : anti-symmetry between k, l in (ij|kl) (TODO)
comp : int
*Note* this argument is effective when eri_or_mol is Mole object.
Components of the integrals, e.g. cint2e_ip_sph has 3 components.
max_memory : float or int
*Note* this argument is effective when eri_or_mol is Mole object.
The maximum size of cache to use (in MB), large cache may **not**
improve performance.
ioblk_size : float or int
*Note* this argument is effective when eri_or_mol is Mole object.
The block size for IO, large block size may **not** improve performance
verbose : int
Print level
compact : bool
When compact is True, depending on the four oribital sets, the
returned MO integrals has (up to 4-fold) permutation symmetry.
If it's False, the function will abandon any permutation symmetry,
and return the "plain" MO integrals
Returns:
If eri_or_mol is array or erifile is not give, the function returns 2D
array (or 3D array, if comp > 1) of transformed MO integrals. The MO
integrals may at most have 4-fold symmetry (if the four sets of orbitals
are identical) or may not have the permutation symmetry (controlled by
the kwargs compact).
Otherwise, return the file/fileobject where the MO integrals are saved.
Examples:
>>> from pyscf import gto, ao2mo
>>> import h5py
>>> def view(h5file, dataname='eri_mo'):
... with h5py.File(h5file) as f5:
... print('dataset %s, shape %s' % (str(f5.keys()), str(f5[dataname].shape)))
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> mo1 = numpy.random.random((mol.nao_nr(), 10))
>>> mo2 = numpy.random.random((mol.nao_nr(), 8))
>>> mo3 = numpy.random.random((mol.nao_nr(), 6))
>>> mo4 = numpy.random.random((mol.nao_nr(), 4))
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo4))
>>> print(eri1.shape)
(80, 24)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo3))
>>> print(eri1.shape)
(80, 21)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo3), compact=False)
>>> print(eri1.shape)
(80, 36)
>>> eri1 = ao2mo.general(eri, (mo1,mo1,mo2,mo2))
>>> print(eri1.shape)
(55, 36)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo1,mo2))
>>> print(eri1.shape)
(80, 80)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo4), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 24)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo3), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 21)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo3), 'oh2.h5', compact=False)
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 36)
>>> ao2mo.general(mol, (mo1,mo1,mo2,mo2), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (55, 36)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', dataname='new')
>>> view('oh2.h5', 'new')
dataset ['eri_mo', 'new'], shape (55, 55)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', intor='cint2e_ip1_sph', aosym='s1', comp=3)
>>> view('oh2.h5')
dataset ['eri_mo', 'new'], shape (3, 100, 100)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', intor='cint2e_ip1_sph', aosym='s2kl', comp=3)
>>> view('oh2.h5')
dataset ['eri_mo', 'new'], shape (3, 100, 55)
'''
if isinstance(eri_or_mol, numpy.ndarray):
return incore.general(eri_or_mol, mo_coeffs, *args, **kwargs)
else:
if 'intor' in kwargs and ('_sph' not in kwargs['intor']):
mod = r_outcore
else:
mod = outcore
if len(args) > 0 and isinstance(args[0], (str, h5py.Group)): # args[0] is erifile
fn = getattr(mod, 'general')
else:
fn = getattr(mod, 'general_iofree')
return fn(eri_or_mol, mo_coeffs, *args, **kwargs)
def general(eri_or_mol, mo_coeffs, *args, **kwargs):
r'''Given four sets of orbitals corresponding to the four MO indices,
transfer arbitrary spherical AO integrals to MO integrals.
Args:
eri_or_mol : ndarray or Mole object
If AO integrals are given as ndarray, it can be either 8-fold or
4-fold symmetry. The integral transformation are computed incore
(ie all intermediate are held in memory).
If Mole object is given, AO integrals are generated on the fly and
outcore algorithm is used (ie intermediate data are held on disk).
mo_coeffs : 4-item list of ndarray
Four sets of orbital coefficients, corresponding to the four
indices of (ij|kl)
erifile : str or h5py File or h5py Group object
*Note* this argument is effective when eri_or_mol is Mole object.
The file to store the transformed integrals. If not given, the
transformed integrals are held in memory.
Kwargs:
dataname : str
*Note* this argument is effective when eri_or_mol is Mole object.
The dataset name in the erifile (ref the hierarchy of HDF5 format
http://www.hdfgroup.org/HDF5/doc1.6/UG/09_Groups.html). By assigning
different dataname, the existed integral file can be reused. If
the erifile contains the dataname, the new integrals data will
overwrite the old one.
intor : str
*Note* this argument is effective when eri_or_mol is Mole object.
Name of the 2-electron integral. Ref to :func:`getints_by_shell`
for the complete list of available 2-electron integral names
aosym : int or str
*Note* this argument is effective when eri_or_mol is Mole object.
Permutation symmetry for the AO integrals
| 4 or '4' or 's4': 4-fold symmetry (default)
| '2ij' or 's2ij' : symmetry between i, j in (ij|kl)
| '2kl' or 's2kl' : symmetry between k, l in (ij|kl)
| 1 or '1' or 's1': no symmetry
| 'a4ij' : 4-fold symmetry with anti-symmetry between i, j in (ij|kl) (TODO)
| 'a4kl' : 4-fold symmetry with anti-symmetry between k, l in (ij|kl) (TODO)
| 'a2ij' : anti-symmetry between i, j in (ij|kl) (TODO)
| 'a2kl' : anti-symmetry between k, l in (ij|kl) (TODO)
comp : int
*Note* this argument is effective when eri_or_mol is Mole object.
Components of the integrals, e.g. int2e_ip_sph has 3 components.
max_memory : float or int
*Note* this argument is effective when eri_or_mol is Mole object.
The maximum size of cache to use (in MB), large cache may **not**
improve performance.
ioblk_size : float or int
*Note* this argument is effective when eri_or_mol is Mole object.
The block size for IO, large block size may **not** improve performance
verbose : int
Print level
compact : bool
When compact is True, depending on the four oribital sets, the
returned MO integrals has (up to 4-fold) permutation symmetry.
If it's False, the function will abandon any permutation symmetry,
and return the "plain" MO integrals
Returns:
If eri_or_mol is array or erifile is not give, the function returns 2D
array (or 3D array, if comp > 1) of transformed MO integrals. The MO
integrals may at most have 4-fold symmetry (if the four sets of orbitals
are identical) or may not have the permutation symmetry (controlled by
the kwargs compact).
Otherwise, return the file/fileobject where the MO integrals are saved.
Examples:
>>> from pyscf import gto, ao2mo
>>> import h5py
>>> def view(h5file, dataname='eri_mo'):
... with h5py.File(h5file) as f5:
... print('dataset %s, shape %s' % (str(f5.keys()), str(f5[dataname].shape)))
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> mo1 = numpy.random.random((mol.nao_nr(), 10))
>>> mo2 = numpy.random.random((mol.nao_nr(), 8))
>>> mo3 = numpy.random.random((mol.nao_nr(), 6))
>>> mo4 = numpy.random.random((mol.nao_nr(), 4))
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo4))
>>> print(eri1.shape)
(80, 24)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo3))
>>> print(eri1.shape)
(80, 21)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo3,mo3), compact=False)
>>> print(eri1.shape)
(80, 36)
>>> eri1 = ao2mo.general(eri, (mo1,mo1,mo2,mo2))
>>> print(eri1.shape)
(55, 36)
>>> eri1 = ao2mo.general(eri, (mo1,mo2,mo1,mo2))
>>> print(eri1.shape)
(80, 80)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo4), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 24)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo3), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 21)
>>> ao2mo.general(mol, (mo1,mo2,mo3,mo3), 'oh2.h5', compact=False)
>>> view('oh2.h5')
dataset ['eri_mo'], shape (80, 36)
>>> ao2mo.general(mol, (mo1,mo1,mo2,mo2), 'oh2.h5')
>>> view('oh2.h5')
dataset ['eri_mo'], shape (55, 36)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', dataname='new')
>>> view('oh2.h5', 'new')
dataset ['eri_mo', 'new'], shape (55, 55)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', intor='int2e_ip1_sph', aosym='s1', comp=3)
>>> view('oh2.h5')
dataset ['eri_mo', 'new'], shape (3, 100, 100)
>>> ao2mo.general(mol, (mo1,mo1,mo1,mo1), 'oh2.h5', intor='int2e_ip1_sph', aosym='s2kl', comp=3)
>>> view('oh2.h5')
dataset ['eri_mo', 'new'], shape (3, 100, 55)
'''
if isinstance(eri_or_mol, numpy.ndarray):
return incore.general(eri_or_mol, mo_coeffs, *args, **kwargs)
else:
if 'intor' in kwargs and '_spinor' in kwargs['intor']:
mod = r_outcore
else:
mod = outcore
fn = getattr(mod, 'general_iofree')
if len(args) > 0:
if isinstance(args[0], (str, h5py.Group)): # args[0] is erifile
fn = getattr(mod, 'general')
elif isinstance(args[0], tempfile._TemporaryFileWrapper):
fn = getattr(mod, 'general')
args = (args[0].name,) + args[1:] # take the tmpfile name
return fn(eri_or_mol, mo_coeffs, *args, **kwargs)
