def get_density(self, grid=None, spacing=0.5, fit=False):
if grid is None:
grid = cubegrid(self.job.get_molecule(), spacing)
dens = [f.results.get_nonfrozen_density(grid, fit=fit) for f in iter(self._frags)]
dens = reduce(lambda x, y: x + y, dens)
return dens
def __init__(self, adfres, prop, grid=None, spacing=0.5, frag=None):
"""
Constructor for densfjob.
@param adfres:
The results of the ADF job for which the density
(or related quantity) should be calculated.
@type adfres: L{adfsinglepointresults} or subclass.
@param prop:
The property to calculate.
@type prop: L{PlotProperty}
@param grid:
The grid to use. If None, a default L{cubegrid} is used.
@type grid: subclass of L{grid}
@param frag:
Which fragment to use. Default is 'Active'.
This can be used to get the densities of specific frozen
fragments.
@type frag: str
"""
# pylint: disable=W0621
adfjob.__init__(self)
self._adfresults = adfres
if grid is None:
self.grid = cubegrid(adfres.get_molecule(), spacing)
else:
self.grid = grid
if frag is None:
self._frag = 'Active'
else:
self._frag = frag
if not isinstance(prop, PlotProperty):
raise PyAdfError(
'densfjob needs to be initialized with PlotProperty')
else:
self.prop = prop
# consistency checks for properties that are not implemented
if 'orbs' in self.prop.opts:
if ('Loc' not in self.prop.opts['orbs']) and \
not (self.prop.opts['orbs'].keys() == ['A']):
raise PyAdfError(
'CJDENSF only working for NSYM=1 (irrep A) orbitals')
if self.prop.pclass == 'potential':
if 'func' in self.prop.opts:
if self.prop.ptype not in ['kinpot', 'nadkin']:
raise PyAdfError(
"Functional cannot be selected in CJDENSF "
"with this potential type")
self._olddensf = False
def get_potential(self, grid=None, pot='total'):
if grid == None:
grid = cubegrid(self.job.get_molecule(), spacing)
pospot = [
f.results.get_nonfrozen_potential(grid, pot=pot)
for f in self._frags.fragiter()
]
cappot = [
c.results.get_nonfrozen_potential(grid, pot=pot)
for c in self._frags.capiter()
]
posdens = reduce(lambda x, y: x + y, pospot)
capdens = reduce(lambda x, y: x + y, cappot)
return posdens - capdens
def get_density(self, grid=None, spacing=0.5, fit=False):
if grid == None:
grid = cubegrid(self.job.get_molecule(), spacing)
posdens = [
f.results.get_nonfrozen_density(grid, fit=fit)
for f in self._frags.fragiter()
]
capdens = [
c.results.get_nonfrozen_density(grid, fit=fit)
for c in self._frags.capiter()
]
posdens = reduce(lambda x, y: x + y, posdens)
capdens = reduce(lambda x, y: x + y, capdens)
return posdens - capdens