import numpy as np
import oxdnagmin_ as GMIN
from pygmin.potentials.gminpotential import GMINPotential
import pygmin.basinhopping as bh
from pygmin.takestep import displace
from pygmin.storage.database import Database
# 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
step = displace.RandomDisplacement(stepsize=1.)
# store all minima in a database
db = Database(db="storage.sqlite", accuracy=1e-2)
# create Basinhopping object
opt = bh.BasinHopping(coords, potential, step, db.minimum_adder())
# run for 100 steps
opt.run(1000)
# now dump all the minima
i = 0
for m in db.minima():
i += 1
GMIN.userpot_dump("lowest_%03d.dat" % (i), m.coords)
for i in xrange(index, ca.nrigid):
a = np.dot(rotations.aa2mx(ca.rotRigid[i]), np.array([1., 0., 0.]))
ca.rotRigid[i] = rotations.rotate_aa(p, ca.rotRigid[i])
x = ca.posRigid[i] - 0.4*a
ca.posRigid[i] = np.dot(mx, x - center) + center
a = np.dot(rotations.aa2mx(ca.rotRigid[i]), np.array([1., 0., 0.]))
ca.posRigid[i]+=0.4*a
# this is necessary for adaptive step taking
def scale(self, factor):
self.stepsize *= factor
# initialize GMIN
GMIN.initialize()
# create a potential which calls GMIN
potential = GMINPotential(GMIN)
# get the initial coorinates
coords=potential.getCoords()
# create takestep routine
step = OXDNAScrewTakestep()
#os.system(TO_PDB%"before.dat")
out = open("traj.xyz", "w")
export_xyz(out, coords)
for i in xrange(1,10):
step.takeStep(coords)
coords_opt, E, rms, fcalls = lbfgs_py(coords, potential.getEnergyGradient)
print E, fcalls
export_xyz(out, coords)
coords = coords_opt
export_xyz(out, coords)
parser.add_option("--maxstep",
dest="maxstep",
type=float,
default=0.1,
help="maximum stepsize for minimizer")
parser.add_option("-o",
dest="outfile",
default="results.txt",
help="outfile for results")
(options, args) = parser.parse_args()
configurations = pickle.load(open("quench_benchmark.dat"))
GMIN.initialize()
pot = GMINPotential(GMIN)
#fl = open("quenched.xyz", "w")
res = open("results.txt", "w")
t0 = time.time()
print "# energy nsteps rms"
res.write("# energy nsteps rms\n")
for coords in configurations[0:5]:
ret = mylbfgs(coords,
pot.getEnergyGradient,
tol=options.tol,
M=options.M,
maxstep=options.maxstep,
maxErise=options.maxErise)
energy = ret[1]
def getEnergyGradient(self, coords):
E, g = GMINPotential.getEnergyGradient(self, coords)
if self.freeze_lattice:
g[-6:]=0.
g*=self.energy_unit
return self.energy_unit * E, g
def getEnergy(self, coords):
return self.energy_unit * GMINPotential.getEnergy(self, coords)
def __init__(self):
GMINPotential.__init__(self, GMIN)
self.energy_unit = self.ENERGY_IN_KJMOL
self.freeze_lattice = False