class TestBasinhopping(unittest.TestCase):
def setUp(self):
natoms = 6
self.system = LJCluster(natoms)
self.e1 = -12.7120622568
self.e2 = -12.302927529580728
def assertEnergy(self, e):
self.assertTrue( abs(e-self.e1) < 1e-4 or abs(e-self.e2) < 1e-4)
def test_create_basinhopping(self):
bh = self.system.get_basinhopping(outstream=None)
bh.run(3)
self.assertEnergy(bh.result.energy)
self.assertEnergy(bh.markovE)
def test_takestep(self):
takestep = self.system.get_takestep(stepsize=1.)
bh = self.system.get_basinhopping(outstream=None, takestep=takestep)
bh.run(3)
self.assertEnergy(bh.result.energy)
self.assertEnergy(bh.markovE)
self.mcstep = RandomDisplacement(stepsize=stepsize)
def takeStep(self, coords, **kwargs):
#make a new monte carlo class
mc = MonteCarlo(coords, self.potential, self.mcstep,
temperature = self.T, outstream=None)
mc.run( self.nsteps )
coords[:] = mc.coords[:]
def updateStep(self, acc, **kwargs):
pass
natoms = 12
niter = 100
system = LJCluster(natoms)
# define a custom takestep routine
potential = system.get_potential()
reseed = TakeStepMonteCarlo(potential, T=100, nsteps=1000)
takestep = system.get_takestep()
stepGroup = Reseeding(takestep, reseed, maxnoimprove=20)
db = system.create_database()
bh = system.get_basinhopping(database=db, takestep=stepGroup)
bh.run(niter)
print "the lowest energy found after", niter, " basinhopping steps is", db.minima()[0].energy
print ""
def takeStep(self, coords, **kwargs):
#make a new monte carlo class
mc = MonteCarlo(coords,
self.potential,
self.mcstep,
temperature=self.T,
outstream=None)
mc.run(self.nsteps)
coords[:] = mc.coords[:]
def updateStep(self, acc, **kwargs):
pass
natoms = 12
niter = 100
system = LJCluster(natoms)
# define a custom takestep routine
potential = system.get_potential()
reseed = TakeStepMonteCarlo(potential, T=100, nsteps=1000)
takestep = system.get_takestep()
stepGroup = Reseeding(takestep, reseed, maxnoimprove=20)
db = system.create_database()
bh = system.get_basinhopping(database=db, takestep=stepGroup)
bh.run(niter)
print "the lowest energy found after", niter, " basinhopping steps is", db.minima(
)[0].energy
print ""