def __init__(self,
fragments,
basis=None,
settings=None,
core=None,
fde=None,
pointcharges=None,
fitbas=None,
options=None):
"""
Initialize ADF fragments analysis / FDE job.
@param fragments:
the list of fragments to be used in this job.
@type fragments: list of L{fragment}s or L{fragmentlist}
@param fde:
a dictionary with options for FDE. They will be added in the FDE
block of the input.
The functional for the non-additive kinetic energy can be specified
under the key TNAD. If is is not specified, PW91k will be
chosen as default.
@type fde: dict
"""
if isinstance(fragments, list):
self._fragments = fragmentlist(fragments)
else:
self._fragments = fragments
if fde is None:
self._fde = {}
else:
self._fde = {}
for k, v in fde.iteritems():
self._fde[k.upper()] = v
adfsinglepointjob.__init__(self,
None,
basis,
core=core,
settings=settings,
pointcharges=pointcharges,
fitbas=fitbas,
options=options)
if self._fragments.has_fde_fragments():
if 'ALLOW PARTIALSUPERFRAGS' not in self._options:
self._options.append('ALLOW PARTIALSUPERFRAGS')
def __init__(self, mol, basis, settings=None, core=None, options=None):
"""
Constructor for ADF gradients jobs.
@param mol:
The molecular coordinates.
@type mol: L{molecule}
@param basis:
A string specifying the basis set to use (e.g. C{basis='TZ2P'}).
Alternatively, a dictionary can be given listing different basis sets
for different atom types. Such a dictionary must contain an entry "default"
giving the basis set to use for all other atom types
(e.g. C{basis={default:'DZP', 'C':'TZ2P'}}).
@type basis: str or dict
@param settings: The settings for this calculation, see L{adfsettings}
@type settings: L{adfsettings}
@param core:
A string specifying which frozen cores to use (C{None}, C{Small}, C{Medium}, or C{Large}).
Alternatively, a dictionary can be given to specify explicitly which core to
use for each atom type (e.g. C{core={O:'1s', H:'None'}}).
Such a dictionary can contain an entry 'default' giving the frozen core to
use with all other atoms (possible values are C{None}, C{Small}, C{Medium}, or C{Large}).
@type core: None or str or dict
@param options:
Additional options. These will each be included directly in the ADF input.
@type options: list of str
"""
import copy
if settings == None:
settings = adfsettings(accint=6.0)
if options is None:
opts = []
else:
opts = copy.copy(options)
opts.append('STOPAFTER GGRADS')
opts.append('GRAD_TRF_BTRF')
adfsinglepointjob.__init__(self,
mol,
basis,
core=core,
settings=settings,
options=opts)
def __init__(self, mol, basis, settings=None, geometrysettings=None, selected_atoms=None,
core=None, options=None):
"""
Create a new ADF geometry optimization job.
@param mol:
The molecular coordinates.
@type mol: L{molecule}
@param basis:
A string specifying the basis set to use (e.g. C{basis='TZ2P'}).
Alternatively, a dictionary can be given listing different basis sets
for different atom types. Such a dictionary must contain an entry "default"
giving the basis set to use for all other atom types
(e.g. C{basis={default:'DZP', 'C':'TZ2P'}}).
@type basis: str or dict
@param core:
A string specifying which frozen cores to use (C{None}, C{Small}, C{Medium}, or C{Large}).
Alternatively, a dictionary can be given to specify explicitly which core to
use for each atom type (e.g. C{core={O:'1s', H:'None'}}).
Such a dictionary can contain an entry 'default' giving the frozen core to
use with all other atoms (possible values are C{None}, C{Small}, C{Medium}, or C{Large}).
@type core: None or str or dict
@param options:
Additional options. These will each be included directly in the ADF input.
@type options: list of str
@param settings: The settings for this calculation, see L{adfsettings}
@type settings: L{adfsettings}
@param geometrysettings:
Settings for the geometry optimization
@type geometrysettings: L{adfgeometrysettings}
@param selected_atoms:
Optionally, a list of atoms for which the coordinates should be optimized.
(The atom numbering starts with 1). By default, all atoms are optimized.
@type selected_atoms:
list of int
"""
if settings is None:
settings = adfsettings(accint=6.0)
if geometrysettings is None:
self.geometrysettings = adfgeometrysettings()
else:
self.geometrysettings = geometrysettings
if selected_atoms:
self.geometrysettings.set_optim('Cartesian Selected')
if type(selected_atoms[0]) == int:
self._selected_atoms = selected_atoms
else:
symbs = mol.get_atom_symbols()
self._selected_atoms = []
for i, s in enumerate(symbs):
if s in selected_atoms:
self._selected_atoms.append(i + 1)
else:
self._selected_atoms = None
adfsinglepointjob.__init__(self, mol, basis, core=core, settings=settings, options=options)