def test1(self):
system = LJCluster(6)
ss0 = 1.
displace = RandomDisplacement(stepsize=ss0)
ts = AdaptiveStepsize(displace, interval=10)
bh = system.get_basinhopping(takestep=ts)
bh.run(9)
self.assertAlmostEqual(displace.stepsize, ss0, 10)
bh.run(2)
self.assertNotAlmostEqual(displace.stepsize, ss0, 1)
def initialize_system():
system = LJCluster(natoms)
x0 = np.random.random(natoms * 3) #.reshape(natoms,3)
db = system.create_database()
step = RandomDisplacement(stepsize=1.0)
bh = system.get_basinhopping(database=db,
takestep=step,
coords=x0,
temperature=10.0)
return system, db, bh
def get_takestep(self, **kwargs):
"""return the takestep object for use in basinhopping, etc.
"""
d = dict(self.params.takestep)
d.update(kwargs)
kwargs = d
try:
stepsize = kwargs.pop("stepsize")
except KeyError:
stepsize = 0.6
takeStep = RandomDisplacement(stepsize=stepsize)
return takeStep
def build_lj_nested_sampling(system, db):
from pele.takestep import RandomDisplacement
nreplicas = 20
mciter = 10000
nminima = 10000
minima = db.minima()
if len(minima) > nminima:
minima = minima[:nminima]
takestep = RandomDisplacement(stepsize=0.5)
accept_tests = system.get_config_tests()
ns = NestedSamplingBS(system,
nreplicas,
takestep,
minima,
mciter=mciter,
accept_tests=accept_tests)
return ns
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
def get_takestep(self, **kwargs):
"""return the takestep object for use in basinhopping, etc.
Notes
-----
default is random displacement with adaptive step size and
adaptive temperature
See Also
--------
pele.takestep
"""
kwargs = dict_copy_update(self.params["takestep"], kwargs)
try:
stepsize = kwargs.pop("stepsize")
except KeyError:
stepsize = 0.6
takeStep = RandomDisplacement(stepsize=stepsize)
tsAdaptive = AdaptiveStepsizeTemperature(takeStep, **kwargs)
return tsAdaptive
def get_takestep(self, **kwargs):
"""return the takestep object for use in basinhopping, etc.
default is random displacement with adaptive step size
adaptive temperature
See Also
--------
pele.takestep
"""
if self.phi_disorder > 0.01:
return super(XYModlelSystem, self).get_takestep(**kwargs)
# if no disorder, turn off adaptive step and temperature.
from pele.takestep import RandomDisplacement
kwargs = dict(self.params["takestep"].items() + kwargs.items())
try:
stepsize = kwargs.pop("stepsize")
except KeyError:
stepsize = 2. * np.pi
takeStep = RandomDisplacement(stepsize=stepsize)
return takeStep
def run_basinhopping(ts, system, db, x):
if x == None: x = 0.1 * np.random.random() + 0.003
E0 = -44.5
step = RandomDisplacement(stepsize=x)
bh = system.get_basinhopping(database=db,
takestep=step,
coords=x0,
temperature=1.0)
t = time.time()
while True:
bh.run(1)
eps = np.abs(bh.trial_energy / E0 - 1.)
print "\n\n", bh.trial_energy, bh.takeStep.stepsize, "\n\n"
if eps < 0.02:
print "Finished\n\n", bh.trial_energy, bh.takeStep.stepsize
print bh.trial_energy
break
dt = time.time() - t
#ts.points = (ssize,dt)
ts.points = np.concatenate((ts.points, [[x, dt]]))
def test_BH(self, db, nsteps):
self.potential = self.get_potential()
from pele.takestep import RandomDisplacement, AdaptiveStepsizeTemperature
takeStepRnd = RandomDisplacement(stepsize=2)
tsAdaptive = AdaptiveStepsizeTemperature(takeStepRnd,
interval=10,
verbose=True)
self.params.basinhopping["temperature"] = 10.0
# todo - how do you save N lowest?
bh = self.get_basinhopping(database=db, takestep=takeStepRnd)
bh = self.get_basinhopping(database=db, takestep=tsAdaptive)
print 'Running BH .. '
bh.run(nsteps)
print "Number of minima found = ", len(db.minima())
min0 = db.minima()[0]
print "lowest minimum found has energy = ", min0.energy
def __init__(self, pot, T=10., nsteps=100, stepsize=0.1):
self.potential = pot
self.T = T
self.nsteps = nsteps
self.mcstep = RandomDisplacement(stepsize=stepsize)
"""
Example 4: modify the parameters of the adaptive stepsize
note that the system class uses adaptive stepsize by default,
so the previous examples also use adaptive stepsize
"""
from __future__ import print_function
from pele.systems import LJCluster
from pele.takestep import RandomDisplacement, AdaptiveStepsizeTemperature
natoms = 12
niter = 100
system = LJCluster(natoms)
db = system.create_database()
# create takestep routine manually
step = RandomDisplacement(stepsize=0.3)
# wrap it in the class which will adaptively improve the stepsize
wrapped_step = AdaptiveStepsizeTemperature(step, interval=30)
bh = system.get_basinhopping(database=db, takestep=wrapped_step)
bh.run(niter)
print("the lowest energy found after", niter, " basinhopping steps is", db.minima()[0].energy)
print("")
def runptmc(nsteps_tot=100000):
natoms = 31
nreplicas = 4
Tmin = 0.2
Tmax = 0.4
nsteps_equil = 10000
nsteps_tot = 100000
histiprint = nsteps_tot / 10
exchange_frq = 100 * nreplicas
coords = np.random.random(3 * natoms)
#quench the coords so we start from a reasonable location
mypot = lj.LJ()
ret = quench(coords, mypot)
coords = ret.coords
Tlist = getTemps(Tmin, Tmax, nreplicas)
replicas = []
ostreams = []
histograms = []
takesteplist = []
radius = 2.5
# create all the replicas which will be passed to PTMC
for i in range(nreplicas):
T = Tlist[i]
potential = lj.LJ()
takestep = RandomDisplacement(stepsize=0.01)
adaptive = AdaptiveStepsize(takestep, last_step=nsteps_equil)
takesteplist.append(adaptive)
file = "mcout." + str(i + 1)
ostream = open(file, "w")
hist = EnergyHistogram(-134., 10., 1000)
histograms.append(hist)
event_after_step = [hist]
radiustest = SphericalContainer(radius)
accept_tests = [radiustest]
mc = MonteCarlo(coords, potential, takeStep=takestep, temperature=T, \
outstream=ostream, event_after_step = event_after_step, \
confCheck = accept_tests)
mc.histogram = hist #for convienence
mc.printfrq = 1
replicas.append(mc)
#is it possible to pickle a mc object?
#cp = copy.deepcopy(replicas[0])
#import pickle
#with open("mc.pickle", "w") as fout:
#pickle.dump(takesteplist[0], fout)
#attach an event to print xyz coords
from pele.printing.print_atoms_xyz import PrintEvent
printxyzlist = []
for n, rep in enumerate(replicas):
outf = "dumpstruct.%d.xyz" % (n + 1)
printxyz = PrintEvent(outf, frq=500)
printxyzlist.append(printxyz)
rep.addEventAfterStep(printxyz)
#attach an event to print histograms
for n, rep in enumerate(replicas):
outf = "hist.%d" % (n + 1)
histprint = PrintHistogram(outf, rep.histogram, histiprint)
rep.addEventAfterStep(histprint)
ptmc = PTMC(replicas)
ptmc.use_independent_exchange = True
ptmc.exchange_frq = exchange_frq
ptmc.run(nsteps_tot)
#do production run
#fix the step sizes
#for takestep in takesteplist:
# takestep.useFixedStep()
#ptmc.run(30000)
if False: #this doesn't work
print "final energies"
for rep in ptmc.replicas:
print rep.temperature, rep.markovE
for rep in ptmc.replicas_par:
print rep.mcsys.markovE
for k in range(nreplicas):
e, T = ptmc.getRepEnergyT(k)
print T, e
if False: #this doesn't work
print "histograms"
for i, hist in enumerate(histograms):
fname = "hist." + str(i)
print fname
with open(fname, "w") as fout:
for (e, visits) in hist:
fout.write("%g %d\n" % (e, visits))
ptmc.end() #close the open threads
def takeStep(self, coords, **kwargs):
self.count += 1
RandomDisplacement.takeStep(self, coords, **kwargs)
def run_nested_sampling_lj(system,
nreplicas=300,
mciter=1000,
target_ratio=0.7,
label="test",
minima=None,
use_compiled=True,
nproc=1,
triv_paral=True,
minprob=1,
maxiter=1e100,
**kwargs):
takestep = RandomDisplacement(stepsize=0.07)
accept_tests = system.get_config_tests()
if type(system) is LJClusterNew:
if use_compiled:
mc_runner = MonteCarloCompiled(system.radius)
# import pickle
# with open("testpickle", "w") as pout:
# pickle.dump(mc_runner, pout)
else:
mc_runner = MonteCarloChain(system.get_potential(),
takestep,
accept_tests=accept_tests)
print "using the compiled MC = ", use_compiled
elif type(system) is HarParticle:
mc_runner = HarRunner(system)
print "using HarRunner"
elif type(system) is IsingSystem:
mc_runner = IsingRunnerC(system)
print "using IsingRunner"
else:
raise TypeError('system type is not known')
print "using", nproc, "processors"
if minima is not None:
assert (len(minima) > 0)
print "using", len(minima), "minima"
ns = NestedSamplingBS(system,
nreplicas,
mc_runner,
minima,
mciter=mciter,
target_ratio=target_ratio,
stepsize=0.07,
nproc=nproc,
triv_paral=triv_paral,
minprob=minprob,
**kwargs)
else:
ns = NestedSampling(system,
nreplicas,
mc_runner,
mciter=mciter,
target_ratio=target_ratio,
stepsize=0.07,
nproc=nproc,
triv_paral=triv_paral,
**kwargs)
etol = 0.01
ns = run_nested_sampling(ns, label, etol, maxiter=maxiter)
return ns
import numpy as np
from src.runmc import mc_cython
from lj_run import LJClusterNew, MonteCarloCompiled
from nested_sampling import MonteCarloChain
from pele.takestep import RandomDisplacement
from pele.utils.xyz import write_xyz
system = LJClusterNew(31)
x = system.get_random_configuration()
with open("test.xyz", "w") as fout:
write_xyz(fout, x)
mciter = 100000
stepsize = .01
Emax = 1e20
radius = 2.5
mcc = MonteCarloCompiled(system, radius)
mcc(x.copy(), mciter, stepsize, Emax)
print mcc.naccept, mcc.nsteps, mcc.energy
takestep = RandomDisplacement(stepsize=stepsize)
mc = MonteCarloChain(system.get_potential(), x.copy(), takestep, Emax,
system.get_config_tests())
for i in xrange(mciter):
mc.step()
print mc.naccept, mc.nsteps, mc.energy
def takeStep(self, coords, **kwargs):
self.count += 1
RandomDisplacement.takeStep(self, coords, **kwargs)
def get_takestep(self, **kwargs):
"""return the takestep object for use in basinhopping, etc."""
return RandomDisplacement(stepsize=self.scale)
