def test_basin_hopping(pot, angles): # pragma: no cover
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=20)
bh = BasinHopping(angles, pot, takestepa, temperature=1.01)
bh.run(20)
def bh_no_system_class():
import numpy as np
from pele.potentials import LJ
natoms = 17
potential = LJ()
x0 = np.random.uniform(-1, 1, 3*natoms)
from pele.takestep import RandomDisplacement, AdaptiveStepsizeTemperature
displace = RandomDisplacement()
adaptive_displacement = AdaptiveStepsizeTemperature(displace)
from pele.storage import Database
database = Database("lj17.sqlite")
from pele.basinhopping import BasinHopping
bh = BasinHopping(x0, potential, adaptive_displacement, storage=database.minimum_adder)
bh.run(10)
for m in database.minima():
print m.energy
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)
# store all minima in a database
db = Database(db="storage.sqlite", accuracy=1e-2)
# create Basinhopping object
opt = BasinHopping(coords,
potential,
reseed,
db.minimum_adder(),
temperature=parameters.temperature)
# run for 100 steps
opt.run(parameters.nsteps)
# now dump all the minima
i = 0
for m in db.minima():
i += 1
GMIN.userpot_dump("lowest_%03d.dat" % (i), m.coords)
print(ret)
# set up and run basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
# should probably use a different take step routine which takes into account
# the cyclical periodicity of angles
takestep = RandomDisplacement(stepsize=old_div(np.pi, 4))
takestepa = AdaptiveStepsize(takestep, frequency=20)
storage = savenlowest.SaveN(500)
bh = BasinHopping(angles, pot, takestepa, temperature=1.01, storage=storage)
bh.run(400)
print("minima found")
with open("out.spin", "w") as fout:
for min in storage.data:
print("energy", min.energy)
fout.write("# %g\n" % (min.energy))
printspins(fout, pot, min.coords)
fout.write('\n\n')
"""
view this in gnuplot with the command
set size ratio -1
plot 'out.spin' index 0 u 1:2 w p pt 5, '' index 0 u 1:2:($3*0.5):($4*0.5) w vectors
"""
