def __init__(self):
BaseSystem.__init__(self)
neb_params = BaseParameters()
self.params["neb"]=neb_params
neb_params["nimages"] = 15
neb_params["k"] = 10.
neb_params["aadist"] = True
defaults.NEBquenchParams["nsteps"] = 200
defaults.NEBquenchParams["iprint"] = 1
defaults.NEBquenchParams["maxstep"] = 0.1
#defaults.NEBquenchParams["maxErise"] = 0.1
defaults.NEBquenchParams["tol"] = 1e-6
defaults.NEBquenchRoutine = fire
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system"%nrigid
water = tip4p.water()
system = RBSystem()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.aasystem = system
self.potential = pot
self.nrigid = nrigid
def __init__(self):
BaseSystem.__init__(self)
self.aasystem = self.setup_aatopology()
self.params.basinhopping["temperature"]=8.
self.params.takestep["translate"]=0.0
self.params.takestep["rotate"]=1.6
self.params.double_ended_connect.local_connect_params.nrefine_max = 5
NEBparams = self.params.double_ended_connect.local_connect_params.NEBparams
self.params.double_ended_connect.local_connect_params.NEBparams.distance=self.aasystem.neb_distance
NEBparams.max_images=200
NEBparams.image_density=3.0
NEBparams.iter_density=10
NEBparams.k = 400.
NEBparams.adjustk_freq = 5
NEBparams.reinterpolate = 50
NEBparams.adaptive_nimages = True
NEBparams.adaptive_niter = True
NEBparams.interpolator=self.aasystem.interpolate
NEBparams.verbose = -1
quenchParams = NEBparams.NEBquenchParams
#quenchParams["nsteps"] = 1000
# quenchParams["iprint"] = -1
# quenchParams["maxstep"] = 0.1
# quenchParams["maxErise"] = 1000
# quenchParams["tol"] = 1e-6
#
tsSearchParams = self.params.double_ended_connect.local_connect_params.tsSearchParams
tsSearchParams["nfail_max"]=20