def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system" % nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
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 setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system"%nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
return system
import pylab as pl
from copy import deepcopy, copy
from pygmin.optimize import mylbfgs, fire
from pygmin.angleaxis import RigidFragment, RBSystem
import tip4p
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)
import pylab as pl
from copy import deepcopy, copy
from pele.optimize import mylbfgs
from pele.angleaxis import RigidFragment, RBSystem
import tip4p
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)
