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