def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = old_div(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 range(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.15
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in range(nrigid-1):
self.draw_bonds.append((2*i, 2*i+1))
self.draw_bonds.append((2*i, 2*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 = 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 xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
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
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 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
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
genrandom = OXDNAReseed()
# in a reseeding takestep procedure
reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed)
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 pele.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)
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 = 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)