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 = create_base()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.15
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid-1):
self.draw_bonds.append((2*i, 2*i+1))
self.draw_bonds.append((2*i, 2*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 create_basinhopping(self):
potential = GMINPotential(GMIN)
coords = potential.getCoords()
# genearte a random configuration
OXDNAReseed().takeStep(coords)
opt = bh.BasinHopping(coords,potential,
temperature=0.1, takeStep=self.create_takestep(),
outstream = None)
return opt
class OTPSystem(RBSystem):
def __init__(self, nmol, boxl=None):
# super(OTPSystem, self)
self.nmol = nmol
if boxl is None:
self.periodic = False
self.boxl = 1e100
else:
self.periodic = True
self.boxl = boxl
super(OTPSystem, self).__init__()
self.setup_params(self.params)
def get_rigid_fragment(self):
return RigidFragment()
def make_otp(self):
otp = self.get_rigid_fragment()
otp.add_atom("O", np.array([0.0, -2. / 3 * np.sin(7. * pi / 24.),
0.0]), 1.)
otp.add_atom(
"O",
np.array([cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24.), 0.0]),
1.)
otp.add_atom(
"O",
np.array([-cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24), 0.0]),
1.)
otp.finalize_setup()
return otp
def setup_params(self, params):
params.gui["basinhopping_nsteps"] = 1000
nebparams = params.double_ended_connect.local_connect_params.NEBparams
nebparams.max_images = 50
nebparams.image_density = 5
nebparams.iter_density = 10.
nebparams.k = 5.
nebparams.reinterpolate = 50
nebparams.NEBquenchParams["iprint"] = 10
tssearch = params.double_ended_connect.local_connect_params.tsSearchParams
tssearch.nsteps_tangent1 = 10
tssearch.nsteps_tangent2 = 30
tssearch.lowestEigenvectorQuenchParams["nsteps"] = 50
tssearch.iprint = 1
tssearch.nfail_max = 100
def get_random_coordinates(self):
coords = np.zeros([self.nmol * 2, 3])
coords[:self.nmol, :] = np.random.uniform(
-1, 1, [self.nmol, 3]) * (self.nmol * 3)**(-1. / 3) * 1.5
from pygmin.utils.rotations import random_aa
for i in range(self.nmol, self.nmol * 2):
coords[i, :] = random_aa()
return coords.flatten()
def write_coords_data(self):
coords = self.get_random_coordinates()
coords = coords.reshape(-1, 3)
with open("coords", "w") as fout:
for xyz in coords:
fout.write("%f %f %f\n" % tuple(xyz))
data = "LWOTP 2.614\n"
if self.periodic:
data += "periodic %f %f %f\n" % (self.boxl, self.boxl, self.boxl)
with open("data", "w") as fout:
fout.write(data)
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 get_potential(self):
#return OTPPotential(self.aasystem)
return self.pot
def __call__(self):
return self
def load_coords_pymol(self, coordslist, oname, index=1):
import pymol
super(OTPSystem, self).load_coords_pymol(coordslist,
oname,
index=index)
pymol.cmd.set("sphere_scale", value=0.2, selection=oname)
class OTPSystem(RBSystem):
def __init__(self, nmol, boxl=None):
# super(OTPSystem, self)
self.nmol = nmol
if boxl is None:
self.periodic = False
self.boxl = 1e100
else:
self.periodic = True
self.boxl = boxl
super(OTPSystem, self).__init__()
self.setup_params(self.params)
def get_rigid_fragment(self):
return RigidFragment()
def make_otp(self):
otp = self.get_rigid_fragment()
otp.add_atom("O", np.array([0.0, -2./3 * np.sin( 7.*pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([cos( 7.*pi/24.), 1./3. * sin( 7.* pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([-cos( 7.* pi/24.), 1./3. * sin( 7.*pi/24), 0.0]), 1.)
otp.finalize_setup()
return otp
def setup_params(self, params):
params.gui["basinhopping_nsteps"] = 1000
nebparams = params.double_ended_connect.local_connect_params.NEBparams
nebparams.max_images = 50
nebparams.image_density = 5
nebparams.iter_density = 10.
nebparams.k = 5.
nebparams.reinterpolate = 50
nebparams.NEBquenchParams["iprint"] = 10
tssearch = params.double_ended_connect.local_connect_params.tsSearchParams
tssearch.nsteps_tangent1 = 10
tssearch.nsteps_tangent2 = 30
tssearch.lowestEigenvectorQuenchParams["nsteps"] = 50
tssearch.iprint=1
tssearch.nfail_max = 100
def get_random_coordinates(self):
coords = np.zeros([self.nmol*2, 3])
coords[:self.nmol,:] = np.random.uniform(-1,1,[self.nmol,3]) * (self.nmol*3)**(-1./3) * 1.5
from pygmin.utils.rotations import random_aa
for i in range(self.nmol, self.nmol*2):
coords[i,:] = random_aa()
return coords.flatten()
def write_coords_data(self):
coords = self.get_random_coordinates()
coords = coords.reshape(-1,3)
with open("coords", "w") as fout:
for xyz in coords:
fout.write( "%f %f %f\n" % tuple(xyz) )
data = "LWOTP 2.614\n"
if self.periodic:
data += "periodic %f %f %f\n" % (self.boxl, self.boxl, self.boxl)
with open("data", "w") as fout:
fout.write(data)
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 get_potential(self):
#return OTPPotential(self.aasystem)
return self.pot
def __call__(self):
return self
def load_coords_pymol(self, coordslist, oname, index=1):
import pymol
super(OTPSystem, self).load_coords_pymol(coordslist, oname, index=index)
pymol.cmd.set("sphere_scale", value=0.2, selection=oname)
fl = open("stat.dat", "a")
print "#found minimum"
t1= time.clock()
timespent= t1 - t0
fl.write("#quenches, functioncalls, time\n")
fl.write("%d %d %f\n"%(opt.stepnum , potential.ncalls , timespent))
fl.close()
exit()
# initialize GMIN
GMIN.initialize()
# create a potential which calls GMIN
potential = GMINPotential(GMIN)
# get the initial coorinates
coords=potential.getCoords()
coords=np.random.random(coords.shape)
# create takestep routine
# we combine a normal step taking
group = takestep.BlockMoves()
step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace, rotate=0.), frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0., rotate=parameters.rotate), frequency=50)
group.addBlock(100, step1)
group.addBlock(100, step2)
# with a generate random configuration
genrandom = OXDNAReseed()
# in a reseeding takestep procedure
reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed)
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 ca = system.coords_adapter(coords)
fl = open("stat.dat", "a")
print "#found minimum"
t1 = time.clock()
timespent = t1 - t0
fl.write("#quenches, functioncalls, time\n")
fl.write("%d %d %f\n" % (opt.stepnum, potential.ncalls, timespent))
fl.close()
exit()
# initialize GMIN
GMIN.initialize()
# create a potential which calls GMIN
potential = GMINPotential(GMIN)
# get the initial coorinates
coords = potential.getCoords()
coords = np.random.random(coords.shape)
# create takestep routine
# we combine a normal step taking
group = takestep.BlockMoves()
step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace,
rotate=0.),
frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0.,
rotate=parameters.rotate),
frequency=50)
group.addBlock(100, step1)
group.addBlock(100, step2)
# with a generate random configuration
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 import pylab as pl from copy import deepcopy, copy from pygmin.optimize import mylbfgs 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)
