def getInitialCoords(natoms, pot):
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(0.3)
X = np.random.uniform(-1,1,natoms*3)*(1.*natoms)**(1./3)*.1
bh = BasinHopping(X, pot, takestep)
bh.run(30)
X = bh.coords
return X
def test_basin_hopping(pot, angles):
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(400)
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 getSetOfMinLJ(natoms = 11): #for testing purposes
from pele.potentials.lj import LJ
pot = LJ()
coords = np.random.uniform(-1,1,natoms*3)
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage.savenlowest import SaveN
saveit = SaveN(10)
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit, outstream=None)
bh.run(100)
return pot, saveit
def guesstsLJ():
from pele.potentials.lj import LJ
pot = LJ()
natoms = 9
coords = np.random.uniform(-1,1,natoms*3)
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage.savenlowest import SaveN
saveit = SaveN(10)
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit, outstream=None)
bh.run(100)
coords1 = saveit.data[0].coords
coords2 = saveit.data[1].coords
return guessts(coords1, coords2, pot)
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
m = getm(ret[0])
print "magnetization after quench", m
# do basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=10)
storage = savenlowest.SaveN(20)
bh = BasinHopping(coords, pot, takestepa, temperature=1.01, storage=storage)
bh.run(200)
print "lowest structures fount:"
with open("out.spins", "w") as fout:
for min in storage.data:
m = getm(min.coords)
print "energy", min.energy, "magnetization", m
fout.write("energy %g magnetization %g\n" % (min.energy, m))
printspins(fout, pot, min.coords)
fout.write("\n\n")
"""
view the spins with gnuplot using the command
h = 2.
s = 0.7
splot 'out.spins' u 1:2:(0) w p pt 5, '' index 1 u 1:2:(0):($6/h):($7/h):($8/h) w vectors t "fields", '' index 1 u 1:2:(0):($3*s):($4*s):($5*s) w vectors t "spins"
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)
# 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 = 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
"""
with open("out.energies", "w") as fout:
# 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
"""
with open("out.energies", "w") as fout:
m = getm(ret[0])
print "magnetization after quench", m
# do basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=10)
storage = savenlowest.SaveN(20)
bh = BasinHopping(coords, pot, takestepa, temperature=1.01, storage=storage)
bh.run(200)
print "lowest structures fount:"
with open("out.spins", "w") as fout:
for min in storage.data:
m = getm(min.coords)
print "energy", min.energy, "magnetization", m
fout.write("energy %g magnetization %g\n" % (min.energy, m))
printspins(fout, pot, min.coords)
fout.write("\n\n")
"""
view the spins with gnuplot using the command
h = 2.
s = 0.7
splot 'out.spins' u 1:2:(0) w p pt 5, '' index 1 u 1:2:(0):($6/h):($7/h):($8/h) w vectors t "fields", '' index 1 u 1:2:(0):($3*s):($4*s):($5*s) w vectors t "spins"
"""
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)
# 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)
coords[k : k + 3] = rot.random_aa()
#set up the takestep routine
from pele.potentials.rigid_bodies.take_step import RBTakeStep
takestep = RBTakeStep()
#set up the class to save lowest energy structures
from pele.storage.savenlowest import SaveN
saveit = SaveN(100)
#set up basinhopping
from pele.basinhopping import BasinHopping
bh = BasinHopping(coords, mysys, takestep, storage=saveit.insert )
#run basin hopping
bh.run(40)
#print the saved coords
fname = "otp.xyz"
print "saving xyz coords to", fname
from pele.utils.xyz import write_xyz
with open(fname, "w") as fout:
for minimum in saveit.data:
xyz = mysys.getxyz(minimum.coords)
write_xyz( fout, xyz, atomtypes=["N", "O", "O"])