def __init__(self,
potential,
coords,
temperature,
stepsize,
niter,
hEmin=0,
hEmax=100,
hbinsize=0.01,
radius=2.5,
acceptance=0.5,
adjustf=0.9,
adjustf_niter=1e4,
adjustf_navg=100,
bdim=3,
single=False,
seeds=None):
#construct base class
super(Metropolis_MCrunner, self).__init__(potential, coords,
temperature, niter)
#get/set seeds
if not seeds:
i32max = np.iinfo(np.int32).max
seeds = dict(takestep=np.random.randint(i32max),
metropolis=np.random.randint(i32max))
self.seeds = seeds
#construct takestep: random step
self.step = RandomCoordsDisplacement(self.seeds['takestep'],
stepsize,
report_interval=adjustf_navg,
factor=adjustf,
min_acc_ratio=acceptance,
max_acc_ratio=acceptance,
single=single,
nparticles=int(
len(coords) / bdim),
bdim=bdim)
#construct early configuration test: check within spherical container
self.conftest = CheckSphericalContainer(radius, bdim)
#construct accept test: Metropolis
self.metropolis = MetropolisTest(self.seeds['metropolis'])
#construct action: energy histogram
self.binsize = hbinsize
self.histogram = RecordEnergyHistogram(hEmin, hEmax, self.binsize,
adjustf_niter)
#set up pele:MC
self.set_takestep(self.step)
self.set_report_steps(
adjustf_niter
) #set number of iterations for which steps are adapted
self.add_accept_test(self.metropolis)
self.add_conf_test(self.conftest)
self.add_action(self.histogram)
def __init__(self, potential, coords, temperature, stepsize, niter,
hEmin=0, hEmax=100, hbinsize=0.01, radius=2.5,
acceptance=0.5, adjustf=0.9, adjustf_niter = 1e4, adjustf_navg = 100, bdim=3):
#construct base class
super(Metropolis_MCrunner,self).__init__(potential, coords, temperature,
stepsize, niter)
#construct test/action classes
i32max = np.iinfo(np.int32).max
self.binsize = hbinsize
self.histogram = RecordEnergyHistogram(hEmin,hEmax,self.binsize, adjustf_niter)
self.adjust_step = AdjustStep(acceptance, adjustf, adjustf_niter, adjustf_navg)
self.step = RandomCoordsDisplacement(42)
#self.step = RandomCoordsDisplacement(np.random.randint(i32max))
self.metropolis = MetropolisTest(44)
#self.metropolis = MetropolisTest(np.random.randint(i32max))
self.conftest = CheckSphericalContainer(radius, bdim)
#set up pele:MC
self.set_takestep(self.step)
self.add_accept_test(self.metropolis)
self.add_conf_test(self.conftest)
self.add_action(self.histogram)
self.add_action(self.adjust_step)
def setUp(self):
self.box_dimension = 3
self.nr_particles = 10
self.k = 42
self.nr_dof = self.box_dimension * self.nr_particles
self.origin = np.zeros(self.nr_dof)
self.potential = Harmonic(self.origin, self.k, bdim=self.box_dimension, com=True)
self.temp = 1
self.nr_steps = 6e4
self.mc = MC(self.potential, self.origin, self.temp, self.nr_steps)
self.take_step_A = RandomCoordsDisplacement(42, 4, single=True, nparticles=self.nr_particles, bdim=self.box_dimension, min_acc_ratio=0.2, max_acc_ratio=0.2)
self.take_step_B = RandomCoordsDisplacement(44, 0.1, single=True, nparticles=self.nr_particles, bdim=self.box_dimension, min_acc_ratio=0.2, max_acc_ratio=0.2)
self.step = TakeStepProbabilities(46)
self.weight_A = 22
self.weight_B = 78
self.step.add_step(self.take_step_A, self.weight_A)
self.step.add_step(self.take_step_B, self.weight_B)
self.mc.set_takestep(self.step)
self.frequency_step_A = self.weight_A / (self.weight_A + self.weight_B)
self.frequency_step_B = self.weight_B / (self.weight_A + self.weight_B)
self.metropolis = MetropolisTest(50)
self.mc.add_accept_test(self.metropolis)
self.hist_min = 0
self.hist_max = 1e4
self.eq_steps = self.nr_steps / 2
self.mc.set_report_steps(self.eq_steps)
self.measure_energy = RecordEnergyHistogram(self.hist_min, self.hist_max, (self.hist_max - self.hist_min)/14, self.eq_steps)
self.mc.add_action(self.measure_energy)
self.true_energy = self.box_dimension * (self.nr_particles - 1) / 2
def __init__(
self,
potential,
coords,
temperature,
stepsize,
niter,
hEmin=0,
hEmax=100,
hbinsize=0.01,
radius=2.5,
acceptance=0.5,
adjustf=0.9,
adjustf_niter=1e4,
adjustf_navg=100,
bdim=3,
single=False,
seeds=None,
):
# construct base class
super(Metropolis_MCrunner, self).__init__(potential, coords, temperature, niter)
# get/set seeds
if not seeds:
i32max = np.iinfo(np.int32).max
seeds = dict(takestep=np.random.randint(i32max), metropolis=np.random.randint(i32max))
self.seeds = seeds
# construct takestep: random step
self.step = RandomCoordsDisplacement(
self.seeds["takestep"],
stepsize,
report_interval=adjustf_navg,
factor=adjustf,
min_acc_ratio=acceptance,
max_acc_ratio=acceptance,
single=single,
nparticles=int(len(coords) / bdim),
bdim=bdim,
)
# construct early configuration test: check within spherical container
self.conftest = CheckSphericalContainer(radius, bdim)
# construct accept test: Metropolis
self.metropolis = MetropolisTest(self.seeds["metropolis"])
# construct action: energy histogram
self.binsize = hbinsize
self.histogram = RecordEnergyHistogram(hEmin, hEmax, self.binsize, adjustf_niter)
# set up pele:MC
self.set_takestep(self.step)
self.set_report_steps(adjustf_niter) # set number of iterations for which steps are adapted
self.add_accept_test(self.metropolis)
self.add_conf_test(self.conftest)
self.add_action(self.histogram)
class TestTakeStepProbabilityHarmoinc(unittest.TestCase):
def setUp(self):
self.box_dimension = 3
self.nr_particles = 10
self.k = 42
self.nr_dof = self.box_dimension * self.nr_particles
self.origin = np.zeros(self.nr_dof)
self.potential = Harmonic(self.origin, self.k, bdim=self.box_dimension, com=True)
self.temp = 1
self.nr_steps = 6e4
self.mc = MC(self.potential, self.origin, self.temp, self.nr_steps)
self.take_step_A = RandomCoordsDisplacement(42, 4, single=True, nparticles=self.nr_particles, bdim=self.box_dimension, min_acc_ratio=0.2, max_acc_ratio=0.2)
self.take_step_B = RandomCoordsDisplacement(44, 0.1, single=True, nparticles=self.nr_particles, bdim=self.box_dimension, min_acc_ratio=0.2, max_acc_ratio=0.2)
self.step = TakeStepProbabilities(46)
self.weight_A = 22
self.weight_B = 78
self.step.add_step(self.take_step_A, self.weight_A)
self.step.add_step(self.take_step_B, self.weight_B)
self.mc.set_takestep(self.step)
self.frequency_step_A = self.weight_A / (self.weight_A + self.weight_B)
self.frequency_step_B = self.weight_B / (self.weight_A + self.weight_B)
self.metropolis = MetropolisTest(50)
self.mc.add_accept_test(self.metropolis)
self.hist_min = 0
self.hist_max = 1e4
self.eq_steps = self.nr_steps / 2
self.mc.set_report_steps(self.eq_steps)
self.measure_energy = RecordEnergyHistogram(self.hist_min, self.hist_max, (self.hist_max - self.hist_min)/14, self.eq_steps)
self.mc.add_action(self.measure_energy)
self.true_energy = self.box_dimension * (self.nr_particles - 1) / 2
def test_basic_harmonic(self):
self.mc.run()
self.assertAlmostEqual(self.frequency_step_A, self.take_step_A.get_count() / self.nr_steps, delta=1e-2)
self.assertAlmostEqual(self.frequency_step_B, self.take_step_B.get_count() / self.nr_steps, delta=1e-2)
self.assertAlmostEqual(self.take_step_A.get_stepsize(), self.take_step_B.get_stepsize(), delta=1e-2)
mean_energy, var_energy = self.measure_energy.get_mean_variance()
self.assertAlmostEqual(mean_energy, self.true_energy, delta=3e-1)
class Metropolis_MCrunner(_BaseMCRunner):
"""This class is derived from the _base_MCrunner abstract
method and performs Metropolis Monte Carlo. This particular implementation of the algorithm:
* runs niter steps per run call
* takes steps by sampling a random vector in a n dimensional hypersphere (n is the number of coordinates);
* adjust the step size for the first adjustf_niter steps (averaging the acceptance for adjust_navg steps
and adjusting the stepsize by a factor of 'adjustf') to meet some target acceptance 'acceptance'.
* configuration test: accept if within a spherical box of radius 'radius'
* acceptance test: metropolis for some particular temperature
* record energy histogram (the energy histogram is resizable, but the bounds are defined by hEmin and hEmax,
furthermore the bin size is set with hbinsize. Care must be taken because the array is resizable, if the step size
is small and extremely high or low energies are sampled the memory for the histogram will be reallocated and this
might cause a badalloc error, if trying to allocate a huge array. If you are sampling unwanted extremely high or low energies
then you might want to add a pele::EnergyWindow test that guarantees to keep you within a specific energy range and/or
make the stepsize larger or you might want to re-think about your simulation. Generally you shouldn't be
spanning energies that differ by several orders of magnitude, if that is the case, resizable or not resizable arrays are
not the problem, you'd be incurring in memory issues no matter what you do, unless you write to disk at every iteration)
* NOTE: some of the modules (e.g. take step and acceptance tests) require to be seeded. Users are free to do this as they think
* is best, here we generate a random integer in [0,i32max) where i32max is the largest signed integer, for each seed. Each module
* has a separate rng engine, therefore it's best if each receives a different randomly sampled seed
"""
def __init__(self,
potential,
coords,
temperature,
stepsize,
niter,
hEmin=0,
hEmax=100,
hbinsize=0.01,
radius=2.5,
acceptance=0.5,
adjustf=0.9,
adjustf_niter=1e4,
adjustf_navg=100,
bdim=3,
single=False,
seeds=None):
#construct base class
super(Metropolis_MCrunner, self).__init__(potential, coords,
temperature, niter)
#get/set seeds
if not seeds:
i32max = np.iinfo(np.int32).max
seeds = dict(takestep=np.random.randint(i32max),
metropolis=np.random.randint(i32max))
self.seeds = seeds
#construct takestep: random step
self.step = RandomCoordsDisplacement(self.seeds['takestep'],
stepsize,
report_interval=adjustf_navg,
factor=adjustf,
min_acc_ratio=acceptance,
max_acc_ratio=acceptance,
single=single,
nparticles=int(
len(coords) / bdim),
bdim=bdim)
#construct early configuration test: check within spherical container
self.conftest = CheckSphericalContainer(radius, bdim)
#construct accept test: Metropolis
self.metropolis = MetropolisTest(self.seeds['metropolis'])
#construct action: energy histogram
self.binsize = hbinsize
self.histogram = RecordEnergyHistogram(hEmin, hEmax, self.binsize,
adjustf_niter)
#set up pele:MC
self.set_takestep(self.step)
self.set_report_steps(
adjustf_niter
) #set number of iterations for which steps are adapted
self.add_accept_test(self.metropolis)
self.add_conf_test(self.conftest)
self.add_action(self.histogram)
def set_control(self, T):
"""set temperature, canonical control parameter"""
self.temperature = T
self.set_temperature(T)
def get_stepsize(self):
return self.step.get_stepsize()
def dump_histogram(self, fname):
"""write histogram to fname"""
Emin, Emax = self.histogram.get_bounds_val()
histl = self.histogram.get_histogram()
hist = np.array(histl)
Energies, step = np.linspace(Emin,
Emax,
num=len(hist),
endpoint=False,
retstep=True)
assert (abs(step - self.binsize) < self.binsize / 100)
np.savetxt(fname, np.column_stack((Energies, hist)), delimiter='\t')
mean, variance = self.histogram.get_mean_variance()
return mean, variance
def get_histogram(self):
"""returns a energy list and a histogram list"""
Emin, Emax = self.histogram.get_bounds_val()
histl = self.histogram.get_histogram()
hist = np.array(histl)
Energies, step = np.linspace(Emin,
Emax,
num=len(hist),
endpoint=False,
retstep=True)
mean, variance = self.histogram.get_mean_variance()
assert (abs(step - self.binsize) < self.binsize / 100)
return Energies, hist, mean, variance
def show_histogram(self):
"""shows the histogram"""
hist = self.histogram.get_histogram()
val = [i * self.binsize for i in xrange(len(hist))]
plt.hist(val, weights=hist, bins=len(hist))
plt.show()
class Metropolis_MCrunner(_BaseMCRunner):
"""This class is derived from the _base_MCrunner abstract
method and performs Metropolis Monte Carlo. This particular implementation of the algorithm:
* runs niter steps per run call
* takes steps by sampling a random vector in a n dimensional hypersphere (n is the number of coordinates);
* adjust the step size for the first adjustf_niter steps (averaging the acceptance for adjust_navg steps
and adjusting the stepsize by a factor of 'adjustf') to meet some target acceptance 'acceptance'.
* configuration test: accept if within a spherical box of radius 'radius'
* acceptance test: metropolis for some particular temperature
* record energy histogram (the energy histogram is resizable, but the bounds are defined by hEmin and hEmax,
furthermore the bin size is set with hbinsize. Care must be taken because the array is resizable, if the step size
is small and extremely high or low energies are sampled the memory for the histogram will be reallocated and this
might cause a badalloc error, if trying to allocate a huge array. If you are sampling unwanted extremely high or low energies
then you might want to add a pele::EnergyWindow test that guarantees to keep you within a specific energy range and/or
make the stepsize larger or you might want to re-think about your simulation. Generally you shouldn't be
spanning energies that differ by several orders of magnitude, if that is the case, resizable or not resizable arrays are
not the problem, you'd be incurring in memory issues no matter what you do, unless you write to disk at every iteration)
* NOTE: some of the modules (e.g. take step and acceptance tests) require to be seeded. Users are free to do this as they think
* is best, here we generate a random integer in [0,i32max) where i32max is the largest signed integer, for each seed. Each module
* has a separate rng engine, therefore it's best if each receives a different randomly sampled seed
"""
def __init__(
self,
potential,
coords,
temperature,
stepsize,
niter,
hEmin=0,
hEmax=100,
hbinsize=0.01,
radius=2.5,
acceptance=0.5,
adjustf=0.9,
adjustf_niter=1e4,
adjustf_navg=100,
bdim=3,
single=False,
seeds=None,
):
# construct base class
super(Metropolis_MCrunner, self).__init__(potential, coords, temperature, niter)
# get/set seeds
if not seeds:
i32max = np.iinfo(np.int32).max
seeds = dict(takestep=np.random.randint(i32max), metropolis=np.random.randint(i32max))
self.seeds = seeds
# construct takestep: random step
self.step = RandomCoordsDisplacement(
self.seeds["takestep"],
stepsize,
report_interval=adjustf_navg,
factor=adjustf,
min_acc_ratio=acceptance,
max_acc_ratio=acceptance,
single=single,
nparticles=int(len(coords) / bdim),
bdim=bdim,
)
# construct early configuration test: check within spherical container
self.conftest = CheckSphericalContainer(radius, bdim)
# construct accept test: Metropolis
self.metropolis = MetropolisTest(self.seeds["metropolis"])
# construct action: energy histogram
self.binsize = hbinsize
self.histogram = RecordEnergyHistogram(hEmin, hEmax, self.binsize, adjustf_niter)
# set up pele:MC
self.set_takestep(self.step)
self.set_report_steps(adjustf_niter) # set number of iterations for which steps are adapted
self.add_accept_test(self.metropolis)
self.add_conf_test(self.conftest)
self.add_action(self.histogram)
def set_control(self, T):
"""set temperature, canonical control parameter"""
self.temperature = T
self.set_temperature(T)
def get_stepsize(self):
return self.step.get_stepsize()
def dump_histogram(self, fname):
"""write histogram to fname"""
Emin, Emax = self.histogram.get_bounds_val()
histl = self.histogram.get_histogram()
hist = np.array(histl)
Energies, step = np.linspace(Emin, Emax, num=len(hist), endpoint=False, retstep=True)
assert abs(step - self.binsize) < self.binsize / 100
np.savetxt(fname, np.column_stack((Energies, hist)), delimiter="\t")
mean, variance = self.histogram.get_mean_variance()
return mean, variance
def get_histogram(self):
"""returns a energy list and a histogram list"""
Emin, Emax = self.histogram.get_bounds_val()
histl = self.histogram.get_histogram()
hist = np.array(histl)
Energies, step = np.linspace(Emin, Emax, num=len(hist), endpoint=False, retstep=True)
mean, variance = self.histogram.get_mean_variance()
assert abs(step - self.binsize) < self.binsize / 100
return Energies, hist, mean, variance
def show_histogram(self):
"""shows the histogram"""
hist = self.histogram.get_histogram()
val = [i * self.binsize for i in xrange(len(hist))]
plt.hist(val, weights=hist, bins=len(hist))
plt.show()