def __init__(self):
RBSystem.__init__(self)
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 = 10.
NEBparams.iter_density = 6
NEBparams.quenchRoutine = fire
del NEBparams.NEBquenchParams["maxErise"]
NEBparams.NEBquenchParams["maxstep"] = 0.01
fts = self.params.double_ended_connect.local_connect_params.tsSearchParams
fts["iprint"] = 1
fts["nsteps"] = 3000
fts["nsteps_tangent1"] = 3
fts["nsteps_tangent2"] = 30
fts["tol"] = 1e-3
fts["lowestEigenvectorQuenchParams"]["nsteps"] = 200
fts["lowestEigenvectorQuenchParams"]["tol"] = 0.002
fts["lowestEigenvectorQuenchParams"]["iprint"] = -1
self.params.structural_quench_params["tol"] = 1e-7
self.params.structural_quench_params["nsteps"] = 1e7
def __init__(self):
RBSystem.__init__(self)
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=10.
NEBparams.iter_density=6
NEBparams.quenchRoutine = fire
del NEBparams.NEBquenchParams["maxErise"]
NEBparams.NEBquenchParams["maxstep"]=0.01
fts = self.params.double_ended_connect.local_connect_params.tsSearchParams
fts["iprint"] = 1
fts["nsteps"] = 3000
fts["nsteps_tangent1"] = 3
fts["nsteps_tangent2"] = 30
fts["tol"]=1e-3
fts["lowestEigenvectorQuenchParams"]["nsteps"]=200
fts["lowestEigenvectorQuenchParams"]["tol"]=0.002
fts["lowestEigenvectorQuenchParams"]["iprint"]=-1
self.params.structural_quench_params["tol"] = 1e-7
self.params.structural_quench_params["nsteps"] = 1e7
def load_coords_pymol(self, *args, **kwargs):
import pymol
RBSystem.load_coords_pymol(self, *args, **kwargs)
# draw the spheres slightly smaller
pymol.cmd.set("sphere_scale", value=.25)
def __init__(self):
RBSystem.__init__(self)
def load_coords_pymol(self, *args, **kwargs):
import pymol
RBSystem.load_coords_pymol(self, *args, **kwargs)
# draw the spheres slightly smaller
pymol.cmd.set("sphere_scale", value=.25)
def __init__(self):
RBSystem.__init__(self)
def __init__(self, xyzfile):
self.xyzfile = xyzfile
RBSystem.__init__(self)
from tip4p import dump_path
# initialize GMIN and potential
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = old_div(coords.size, 6)
print("I have %d water molecules in the system" % nrigid)
water = tip4p.water()
#water.S = np.identity(3, dtype="float64")
#water.S*=10.
# define the whole water system
system = RBSystem()
system.add_sites([deepcopy(water) for i in range(nrigid)])
# this is an easy access wrapper for coordinates array
ca = system.coords_adapter(coords)
#buildingblocks.rotate(3.0, ca.rotRigid[-1:])
#ret = mylbfgs(coords, pot.getEnergyGradient, iprint=0)
#coords2 = ret[0]
#np.savetxt("coords1_2.txt", coords1)
#np.savetxt("coords2_2.txt", coords2)
coords1 = np.loadtxt("coords1.txt")
coords2 = np.loadtxt("coords2.txt")
print(pot.getEnergy(coords1), pot.getEnergy(coords2))
from tip4p import dump_path
# initialize GMIN and potential
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()
#water.S = np.identity(3, dtype="float64")
#water.S*=10.
# define the whole water system
system = RBSystem()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
# this is an easy access wrapper for coordinates array
ca = system.coords_adapter(coords)
#buildingblocks.rotate(3.0, ca.rotRigid[-1:])
#ret = mylbfgs(coords, pot.getEnergyGradient, iprint=0)
#coords2 = ret[0]
#np.savetxt("coords1_2.txt", coords1)
#np.savetxt("coords2_2.txt", coords2)
coords1 = np.loadtxt("coords1.txt")
coords2 = np.loadtxt("coords2.txt")
print pot.getEnergy(coords1), pot.getEnergy(coords2)