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
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 setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = old_div(coords.size, 6)
print("I have %d PAP molecules in the system" % nrigid)
print("The initial energy is", pot.getEnergy(coords))
water = create_pap()
system = RBTopology()
system.add_sites([deepcopy(water) for i in range(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in range(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def __init__(self):
GMIN.initialize()
self.natoms = GMIN.getNAtoms()
super(GUPTASystem, self).__init__(self.natoms)
qp = self.params.structural_quench_params
qp["tol"]=1e-5
qp["maxErise"]=1e-5
qp["maxstep"]=0.1
qp["iprint"]=-1
qp["debug"]=False
neb = self.params.double_ended_connect.local_connect_params.NEBparams
neb["image_density"]=5
neb["adjustk_freq"]=5
def setup_aatopology(self):
self.write_coords_data()
GMIN.initialize()
self.pot = GMINPotential(GMIN)
coords = self.pot.getCoords()
self.nrigid = coords.size / 6
assert (self.nrigid == self.nmol)
#self.nrigid = self.nmol
otp = self.make_otp()
topology = RBTopology()
topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)])
self.render_scale = 0.2
self.atom_types = topology.get_atomtypes()
self.draw_bonds = []
for i in xrange(self.nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10
return topology
def setup_aatopology(self):
self.write_coords_data()
GMIN.initialize()
self.pot = GMINPotential(GMIN)
coords = self.pot.getCoords()
self.nrigid = coords.size/6
assert(self.nrigid == self.nmol)
#self.nrigid = self.nmol
otp = self.make_otp()
topology = RBTopology()
topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)])
self.render_scale = 0.2
self.atom_types = topology.get_atomtypes()
self.draw_bonds = []
for i in xrange(self.nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10
return topology
import numpy as np from pygmin.potentials import GMINPotential import gmin_ as GMIN from pygmin.utils import rotations from pygmin.takestep import buildingblocks from pygmin.transition_states import NEB from pygmin import defaults 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
from past.utils import old_div
import numpy as np
from pele.potentials import GMINPotential
import gmin_ as GMIN
from pele.utils import rotations
from pele.takestep import buildingblocks
from pele.transition_states import NEB
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
