def __init__(self, system, ai, settings, ffrefs=[]):
'''
**Arguments**
system
a Yaff `System` instance defining the system
ai
a `Reference` instance corresponding to the ab initio input data
settings
a `Settings` instance defining all QuickFF settings
**Optional Arguments**
ffrefs
a list of `Reference` instances defining the a-priori force
field contributions.
'''
with log.section('INIT', 1, timer='Initializing'):
log.dump('Initializing program')
self.settings = settings
self.system = system
self.ai = ai
self.ffrefs = ffrefs
self.valence = ValenceFF(system, settings)
self.perturbation = RelaxedStrain(system, self.valence, settings)
self.trajectories = None
self.print_system()
def __init__(self, system, ai, **kwargs):
'''
**Arguments**
system
a Yaff `System` object defining the system
ai
a `Reference` instance corresponding to the ab initio input data
**Keyword Arguments**
ffrefs
a list of `Reference` objects corresponding to a priori determined
contributions to the force field (such as eg. electrostatics
or van der Waals contributions)
fn_yaff
the name of the file to write the final parameters to in Yaff
format. The default is `pars.txt`.
fn_sys
the name of the file to write the system to. The default is
`system.chk`.
fn_traj
a cPickle filename to read/write the perturbation trajectories
from/to. If the file exists, the trajectories are read from the
file. If the file does not exist, the trajectories are written
to the file.
only_traj
specifier to determine for which terms a perturbation trajectory
needs to be constructed. If ONLY_TRAJ is a single string, it is
interpreted as a task (only terms that have this task in their
tasks attribute will get a trajectory). If ONLY_TRAJ is a list
of strings, each string is interpreted as the basename of the
term for which a trajectory will be constructed.
plot_traj
if set to True, all energy contributions along each perturbation
trajectory will be plotted using the final force field.
xyz_traj
if set to True, each perturbation trajectory will be written to
an XYZ file.
'''
with log.section('PROG', 2, timer='Initializing'):
log.dump('Initializing program')
self.system = system
self.ai = ai
self.kwargs = kwargs
self.valence = ValenceFF(system)
self.perturbation = RelaxedStrain(system, self.valence)
self.trajectories = None