def _setup_orbital(uni,
verbose,
vector,
fps,
icoefs,
log=None,
jcoefs=None,
irrep=None):
"""Boilerplate for starting the functions in this module."""
log = log or func_log(_setup_orbital)
t1 = datetime.now()
nbf = len(uni.basis_functions)
if irrep is not None:
nbf = len(uni.basis_set_order.groupby('irrep').get_group(irrep).index)
if verbose:
p1 = 'Evaluating {} basis functions once.'
log.debug(p1.format(nbf))
vector = _determine_vector(uni, vector, irrep)
fps = _determine_fps(uni, fps, len(vector))
x, y, z = numerical_grid_from_field_params(fps)
bvs = uni.basis_functions.evaluate(x, y, z, irrep=irrep, verbose=verbose)
icoefs = _check_column(uni, 'current_momatrix', icoefs)
icoefs = uni.current_momatrix.square(column=icoefs, irrep=irrep).values
if jcoefs is not None:
jcoefs = _check_column(uni, 'current_momatrix', jcoefs)
jcoefs = uni.current_momatrix.square(column=jcoefs).values
return t1, vector, fps, x, y, z, bvs, icoefs, jcoefs
return t1, vector, fps, x, y, z, bvs, icoefs
def add_molecular_orbitals(uni, field_params=None, mocoefs=None,
vector=None, frame=0, inplace=True,
replace=False, verbose=True, irrep=None):
"""A universe must contain basis_set, [basis_set_order], and
momatrix attributes to use this function. Evaluate molecular
orbitals on a numerical grid. Attempts to generate reasonable
defaults if none are provided. If vector is not provided,
attempts to calculate vector from the orbital table, or by the
sum of Z (Zeff) of the atoms in the atom table divided by two;
roughly (H**O-5, LUMO+7).
Args:
uni (:class:`~exatomic.core.universe.Universe`): a universe
field_params (dict): See :func:`~exatomic.algorithms.orbital_util.make_fps`
mocoefs (str): column in uni.current_momatrix (default 'coef')
vector (int, list, range, np.ndarray): the MO vectors to evaluate
inplace (bool): if False, return the field obj instead of modifying uni
replace (bool): if False, do not delete any previous fields
irrep (int): if symmetrized, the irrep to which the orbitals belong
Warning:
If replace is True, removes any fields previously attached to the universe
"""
log = func_log(add_molecular_orbitals)
if replace and hasattr(uni, '_field'): del uni.__dict__['_field']
t1, vector, fps, x, y, z, bvs, mocoefs = \
_setup_orbital(uni, verbose, vector, field_params, mocoefs, irrep=irrep, log=log)
ovs = _compute_orbital(verbose, len(x), bvs, vector, mocoefs, log=log)
field = _make_field(ovs, fps)
return _teardown_orbital(uni, verbose, field, t1, inplace, log=log)
def _compute_orbital(verbose, npts, bvs, vector, cmat, log=None):
log = log or func_log(_compute_orbital)
try: ovs = _compute_orbitals_numba(npts, bvs, vector, cmat)
except (ValueError, IndexError, AssertionError, TypingError):
if verbose: log.error('numba eval failed, falling back to numpy')
ovs = _compute_orbitals_numpy(npts, bvs, vector, cmat)
return ovs
def add_orb_ang_mom(uni,
field_params=None,
rcoefs=None,
icoefs=None,
frame=0,
orbocc=None,
maxes=None,
inplace=True,
norm='Nd',
verbose=True):
"""A universe must contain basis_set, [basis_set_order], and
momatrix attributes to use this function. Compute the orbital
angular momentum. Requires C matrices from SODIZLDENS.X.X.R,I
files from Molcas.
Args:
uni (:class:`~exatomic.container.Universe`): a universe
field_params (dict): See :func:`~exatomic.algorithms.orbital_util.make_fps`
rcoefs (str): column in uni.current_momatrix (default 'lreal')
icoefs (str): column in uni.current_momatrix (default 'limag')
maxes (np.ndarray): 3x3 array of magnetic axes (default np.eye(3))
orbocc (str): column in uni.orbital (default 'lreal')
inplace (bool): if False, return the field obj instead of modifying uni
"""
log = func_log(add_orb_ang_mom)
if rcoefs is None or icoefs is None:
raise Exception("Must specify rcoefs and icoefs")
rcol = rcoefs
t1, vector, fps, x, y, z, bvs, rcoefs, icoefs = \
_setup_orbital(uni, verbose, None, field_params, rcoefs, jcoefs=icoefs)
orbocc = rcol if orbocc is None else orbocc
if maxes is None:
maxes = np.eye(3)
if verbose:
log.debug(
"If magnetic axes are not an identity matrix, specify maxes.")
occvec = uni.orbital[orbocc].values
grx = uni.basis_functions.evaluate_diff(x, y, z, cart='x', verbose=verbose)
gry = uni.basis_functions.evaluate_diff(x, y, z, cart='y', verbose=verbose)
grz = uni.basis_functions.evaluate_diff(x, y, z, cart='z', verbose=verbose)
t2 = datetime.now()
if verbose:
p1 = 'Timing: grid evaluation - {:>8.2f}s.'
log.info(p1.format((t2 - t1).total_seconds()))
curx, cury, curz = _compute_current_density(bvs,
grx,
gry,
grz,
rcoefs,
icoefs,
occvec,
verbose=verbose)
t3 = datetime.now()
if verbose:
p2 = 'Timing: current density - {:>8.2f}s.'
log.info(p2.format((t3 - t2).total_seconds()))
field = _make_field(_compute_orb_ang_mom(x, y, z, curx, cury, curz, maxes),
fps)
return _teardown_orbital(uni, verbose, field, t1, inplace, name='angmom')
def _teardown_orbital(uni, verbose, field, t1, inplace, name='orbitals', log=None):
"""Boilerplate for finishing the functions in this module."""
log = log or func_log(_teardown_orbital)
if verbose:
t2 = datetime.now()
p2 = 'Timing: compute {:<8} - {:>8.2f}s.'
log.info(p2.format(name, (t2-t1).total_seconds()))
if not inplace: return field
uni.add_field(field)
def add_density(uni,
field_params=None,
mocoefs=None,
orbocc=None,
inplace=True,
frame=0,
norm='Nd',
verbose=True):
"""A universe must contain basis_set, [basis_set_order], and
momatrix attributes to use this function. Compute a density
with C matrix mocoefs and occupation vector orbocc.
Args:
uni (:class:`~exatomic.container.Universe`): a universe
field_params (dict): See :func:`~exatomic.algorithms.orbital_util.make_fps`
mocoefs (str): column in uni.current_momatrix (default 'coef')
orbocc (str): column in uni.orbital (default 'occupation')
inplace (bool): if False, return the field obj instead of modifying uni
"""
log = func_log(add_density)
mocol = mocoefs
t1, vector, fps, x, y, z, bvs, mocoefs = \
_setup_orbital(uni, verbose, None, field_params, mocoefs, log=log)
orbocc = mocol if orbocc is None and mocol != 'coef' else orbocc
orbocc = _check_column(uni, 'orbital', orbocc)
vector = uni.orbital[~np.isclose(uni.orbital[orbocc], 0)].index.values
orbocc = uni.orbital.loc[vector][orbocc].values
ovs = _compute_orbital(verbose, len(x), bvs, vector, mocoefs, log=log)
field = _make_field(_compute_density(ovs, orbocc), fps.loc[0])
return _teardown_orbital(uni,
verbose,
field,
t1,
inplace,
name='density',
log=log)