def test_basin_hopping(pot, angles):
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.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 pygmin.potentials.lj import LJ
pot = LJ()
coords = np.random.uniform(-1,1,natoms*3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.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 pygmin.potentials.lj import LJ
pot = LJ()
natoms = 9
coords = np.random.uniform(-1, 1, natoms * 3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.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 center(E, coords, accepted):
# c = np.reshape()
natoms = 40
coords = np.random.rand(natoms * 3)
lj = LJ()
ret = quench(coords, lj)
coords = ret.coords
takestep = TakeStep(stepsize=0.1)
#do equilibration steps, adjusting stepsize
tsadapt = AdaptiveStepsize(takestep)
mc = MonteCarlo(coords, lj, tsadapt, temperature=0.5)
equilout = open("equilibration", "w")
#mc.outstream = equilout
mc.setPrinting(equilout, 1)
mc.run(10000)
#fix stepsize and do production run
mc.takeStep = takestep
mcout = open("mc.out", "w")
mc.setPrinting(mcout, 10)
#print coords from time to time
xyzout = open("out.xyz", "w")
printevent = PrintEvent(xyzout, 300)
mc.addEventAfterStep(printevent.printwrapper)
print "quenched e = ", ret.energy, "funcalls", ret.nfev
print ret.coords
m = getm(ret[0])
print "magnetization after quench", m
#do basin hopping
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.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