def do_check(self, pot, **kwargs):
lbfgs = LBFGS_CPP(_xrand, pot, **kwargs)
res = lbfgs.run()
self.assertAlmostEqual(res.energy, _emin, 4)
self.assertTrue(res.success)
self.assertLess(np.max(np.abs(res.coords - _xmin)), 1e-2)
self.assertGreater(res.nfev, 0)
def optimize(self, nr_samples = 1):
self.optimizer = ModifiedFireCPP(self.x_initial, self.potential, tol = self.tol, maxstep = self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial, self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial, self.potential_cells, tol = self.tol, maxstep = self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial, self.potential_cells)
t0 = time.time()
self.optimizer.run(self.nstepsmax)
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
t2 = time.time()
self.optimizer_.run(self.nstepsmax)
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
t4 = time.time()
res_x_final = self.optimizer.get_result()
res_x_final_cells = self.optimizer_cells.get_result()
self.x_final = res_x_final.coords
self.x_final_cells = res_x_final_cells.coords
print "number of particles:", self.N
print "time no cell lists:", t1 - t0, "sec"
print "time cell lists:", t2 - t1, "sec"
print "ratio:", (t1 - t0) / (t2 - t1)
assert(res_x_final.success)
assert(res_x_final_cells.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10 * self.N)
if (passed is False):
print "xci", xci
print "xi", xi
assert(passed)
print "energy no cell lists:", res_x_final.energy
print "energy cell lists:", res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def test_run_niter3(self):
lbfgs1 = LBFGS_CPP(_xrand, _EG())
res1 = lbfgs1.run(10)
lbfgs2 = LBFGS_CPP(_xrand, _EG())
res2 = lbfgs2.run(5)
res2 = lbfgs2.run(5)
self.assert_same(res1, res2)
def lbfgs_cpp(coords, pot, **kwargs):
if not hasattr(pot, "getEnergyGradient"):
# for compatibility with old quenchers.
# assume pot is a getEnergyGradient function
pot = _getEnergyGradientWrapper(pot)
lbfgs = LBFGS_CPP(coords, pot, **kwargs)
return lbfgs.run()
def test_run_niter2(self):
lbfgs1 = LBFGS_CPP(_xrand, _EG())
res1 = lbfgs1.run()
lbfgs2 = LBFGS_CPP(_xrand, _EG())
res2 = lbfgs2.run(res1.nsteps / 2)
res2 = lbfgs2.run()
self.assert_same(res1, res2)
def __init__(self,
nr_particles=42,
hard_volume_fraction=0.5,
epsilon=1,
alpha=0.2):
np.random.seed(42)
self.nr_particles = nr_particles
self.hard_volume_fraction = hard_volume_fraction
self.epsilon = epsilon
self.alpha = alpha
self.hard_radii = np.random.normal(loc=1,
scale=0.1,
size=self.nr_particles)
self.box_length = np.power(
np.sum(np.asarray([4 * np.pi * r**3 / 3
for r in self.hard_radii])) /
self.hard_volume_fraction, 1 / 3)
self.nr_dof = 3 * self.nr_particles
self.x = np.random.uniform(-0.5 * self.box_length,
0.5 * self.box_length, self.nr_dof)
self.box_vector = np.ones(3) * self.box_length
self.rcut = 2 * (1 + alpha) * np.amax(self.hard_radii)
self.potential = HS_WCA(use_periodic=True,
use_cell_lists=False,
eps=self.epsilon,
sca=self.alpha,
radii=self.hard_radii,
boxvec=self.box_vector,
rcut=self.rcut)
self.optimizer = LBFGS_CPP(self.x, self.potential)
print "energy before:", self.potential.getEnergy(self.x)
self.optimizer.run()
print "minimization converged", self.optimizer.get_result().success
print "energy after:", self.potential.getEnergy(
self.optimizer.get_result().coords)
def do_check(self, pot, **kwargs):
lbfgs = LBFGS_CPP(_xrand, pot, **kwargs)
res = lbfgs.run()
self.assertAlmostEqual(res.energy, _emin, 4)
self.assertTrue(res.success)
self.assertLess(np.max(np.abs(res.coords - _xmin)), 1e-2)
self.assertGreater(res.nfev, 0)
class Config2D(object):
def __init__(self, nparticles_x, amplitude):
self.LX = nparticles_x
self.LY = self.LX
self.nparticles_x = nparticles_x
self.N = self.nparticles_x ** 2
self.amplitude = amplitude
self.x = np.zeros(2 * self.N)
for particle in xrange(self.N):
pid = 2 * particle
self.x[pid] = particle % self.LX
self.x[pid + 1] = int(particle / self.LX)
self.x_initial = [xi + np.random.uniform(- self.amplitude, self.amplitude) for xi in self.x]
self.radius = 0.25
self.sca = 1.1
self.radii = np.ones(self.N) * self.radius
self.eps = 1
self.boxvec = np.array([self.LX, self.LY])
self.potential = HS_WCA(self.eps, self.sca, self.radii, ndim=2, boxvec=self.boxvec)
self.rcut = 2 * (1 + self.sca) * self.radius
self.ncellx_scale = 1
self.potential_cells = HS_WCAPeriodicCellLists(self.eps, self.sca, self.radii, self.boxvec, self.x_initial, self.rcut, ndim = 2, ncellx_scale = self.ncellx_scale)
self.tol = 1e-7
self.maxstep = 1
self.nstepsmax = 1e5
def optimize(self, nr_samples = 1):
self.optimizer = ModifiedFireCPP(self.x_initial, self.potential, tol = self.tol, maxstep = self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial, self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial, self.potential_cells, tol = self.tol, maxstep = self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial, self.potential_cells)
t0 = time.time()
self.optimizer.run(self.nstepsmax)
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
t2 = time.time()
self.optimizer_.run(self.nstepsmax)
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
t4 = time.time()
res_x_final = self.optimizer.get_result()
res_x_final_cells = self.optimizer_cells.get_result()
self.x_final = res_x_final.coords
self.x_final_cells = res_x_final_cells.coords
print "number of particles:", self.N
print "time no cell lists:", t1 - t0, "sec"
print "time cell lists:", t2 - t1, "sec"
print "ratio:", (t1 - t0) / (t2 - t1)
assert(res_x_final.success)
assert(res_x_final_cells.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10 * self.N)
if (passed is False):
print "xci", xci
print "xi", xi
assert(passed)
print "energy no cell lists:", res_x_final.energy
print "energy cell lists:", res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def test_event_raise(self):
class EventException(BaseException): pass
def myevent(*args, **kwargs): raise EventException
with self.assertRaises(EventException):
lbfgs = LBFGS_CPP(_xrand, _EG(), events=[myevent])
lbfgs.run()
def do_check(self, pot):
e, grad = pot.getEnergyGradient(_xrand)
lbfgs = LBFGS_CPP(_xrand, pot, energy=e, gradient=grad)
res = lbfgs.run()
self.assertAlmostEqual(res.energy, _emin, 4)
self.assertTrue(res.success)
self.assertLess(np.max(np.abs(res.coords - _xmin)), 1e-2)
self.assertGreater(res.nfev, 0)
def do_check(self, pot):
e, grad = pot.getEnergyGradient(_xrand)
lbfgs = LBFGS_CPP(_xrand, pot, energy=e, gradient=grad)
res = lbfgs.run()
self.assertAlmostEqual(res.energy, _emin, 4)
self.assertTrue(res.success)
self.assertLess(np.max(np.abs(res.coords - _xmin)), 1e-2)
self.assertGreater(res.nfev, 0)
def quench_LBFGS(x0, pot, steps=2000, **kwargs):
""" \"Subroutine\" for quenching LBFGS, add subtract yada yada
to control how information gets returned, basically simply passing
pot, x0 with these default parameters should give identical results
between different pieces.
"""
lbfgs = LBFGS_CPP(x0, pot, steps=2000, **kwargs)
lbfgs.run(nsteps)
res = LBFGS_CPP.get_result()
return res
def test_event_raise(self):
class EventException(BaseException):
pass
def myevent(*args, **kwargs):
raise EventException
with self.assertRaises(EventException):
lbfgs = LBFGS_CPP(_xrand, _EG(), events=[myevent])
lbfgs.run()
def test_result(self):
lbfgs = LBFGS_CPP(_xrand, _EG())
res = lbfgs.one_iteration()
self.assertIn("H0", res)
self.assertIn("energy", res)
self.assertIn("grad", res)
self.assertIn("success", res)
self.assertIn("coords", res)
self.assertIn("rms", res)
self.assertIn("nsteps", res)
self.assertIn("nfev", res)
def test_result(self):
lbfgs = LBFGS_CPP(_xrand, _EG())
res = lbfgs.one_iteration()
self.assertIn("H0", res)
self.assertIn("energy", res)
self.assertIn("grad", res)
self.assertIn("success", res)
self.assertIn("coords", res)
self.assertIn("rms", res)
self.assertIn("nsteps", res)
self.assertIn("nfev", res)
def mytest():
system = test_functions.BealeSystem()
print "do pot"
pot = system.get_potential()
print "done pot"
x = pot.target_coords.copy()
x += np.random.uniform(-0.2, 0.2, x.shape)
from pele.optimize import LBFGS_CPP
lbfgs = LBFGS_CPP(x, pot, verbosity=100)
print "done setting up"
res = lbfgs.run()
res = _quench.lbfgs_cpp(x, pot, verbosity=100)
# print res
print res
def mytest():
system = test_functions.BealeSystem()
print("do pot")
pot = system.get_potential()
print("done pot")
x = pot.target_coords.copy()
x += np.random.uniform(-0.2, 0.2, x.shape)
from pele.optimize import LBFGS_CPP
lbfgs = LBFGS_CPP(x, pot, verbosity=100)
print("done setting up")
lbfgs.run()
res = _quench.lbfgs_cpp(x, pot, verbosity=100)
# print res
print(res)
def __init__(self, boxdim=2, nr_particles=100, hard_phi=0.4,
nr_steps=1e6, epsilon=1, alpha=0.1, verbose=False):
# Settings.
np.random.seed(42)
# Input parameters.
self.boxdim = boxdim
self.nr_particles = nr_particles
self.hard_phi = hard_phi
self.nr_steps = nr_steps
self.epsilon = epsilon
self.alpha = alpha
self.verbose = verbose
# Derived quantities.
self.hard_radii = np.ones(self.nr_particles)
def volume_nball(radius, n):
return np.power(np.pi, n / 2) * np.power(radius, n) / gamma(n / 2 + 1)
self.box_length = np.power(np.sum(np.asarray([volume_nball(r, self.boxdim) for r in self.hard_radii])) / self.hard_phi, 1 / self.boxdim)
self.box_vector = np.ones(self.boxdim) * self.box_length
# HS-WCA potential.
self.potential = HS_WCA(use_periodic=True, use_cell_lists=True,
ndim=self.boxdim, eps=self.epsilon,
sca=self.alpha, radii=self.hard_radii,
boxvec=self.box_vector)
# Initial configuration by minimization.
self.nr_dof = self.boxdim * self.nr_particles
self.x = np.random.uniform(-0.5 * self.box_length, 0.5 * self.box_length, self.nr_dof)
optimizer = LBFGS_CPP(self.x, self.potential)
optimizer.run()
if not optimizer.get_result().success:
print ("warning: minimization has not converged")
self.x = optimizer.get_result().coords.copy()
# Potential and MC rules.
self.temperature = 1
self.mc = MC(self.potential, self.x, self.temperature, self.nr_steps)
self.step = RandomCoordsDisplacement(42, 1, single=True, nparticles=self.nr_particles, bdim=self.boxdim)
if self.verbose:
print ("initial MC stepsize")
print self.step.get_stepsize()
self.mc.set_takestep(self.step)
self.eq_steps = self.nr_steps / 2
self.mc.set_report_steps(self.eq_steps)
self.gr_quench = RecordPairDistHistogram(self.box_vector, 50, self.eq_steps, self.nr_particles, optimizer=optimizer)
self.gr = RecordPairDistHistogram(self.box_vector, 50, self.eq_steps, self.nr_particles)
self.mc.add_action(self.gr_quench)
self.mc.add_action(self.gr)
self.test = MetropolisTest(44)
self.mc.add_accept_test(self.test)
def test_run_niter2(self):
lbfgs1 = LBFGS_CPP(_xrand, _EG())
res1 = lbfgs1.run()
lbfgs2 = LBFGS_CPP(_xrand, _EG())
res2 = lbfgs2.run(res1.nsteps // 2)
res2 = lbfgs2.run()
self.assert_same(res1, res2)
class MinimizeUniformHardsSpheres(object):
def __init__(self, nr_particles=42, hard_volume_fraction=0.5, epsilon=1, alpha=0.2):
np.random.seed(42)
self.nr_particles = nr_particles
self.hard_volume_fraction = hard_volume_fraction
self.epsilon = epsilon
self.alpha = alpha
self.hard_radii = np.random.normal(loc=1, scale=0.1, size=self.nr_particles)
self.box_length = np.power(np.sum(np.asarray([4 * np.pi * r**3 / 3 for r in self.hard_radii])) / self.hard_volume_fraction, 1/3)
self.nr_dof = 3 * self.nr_particles
self.x = np.random.uniform(-0.5 * self.box_length, 0.5 * self.box_length, self.nr_dof)
self.box_vector = np.ones(3) * self.box_length
self.rcut = 2 * (1 + alpha) * np.amax(self.hard_radii)
self.potential = HS_WCA(use_periodic=True, use_cell_lists=False, eps=self.epsilon, sca=self.alpha, radii=self.hard_radii, boxvec=self.box_vector, rcut=self.rcut)
self.optimizer = LBFGS_CPP(self.x, self.potential)
print "energy before:", self.potential.getEnergy(self.x)
self.optimizer.run()
print "minimization converged", self.optimizer.get_result().success
print "energy after:", self.potential.getEnergy(self.optimizer.get_result().coords)
def test_run_niter3(self):
lbfgs1 = LBFGS_CPP(_xrand, _EG())
res1 = lbfgs1.run(10)
lbfgs2 = LBFGS_CPP(_xrand, _EG())
res2 = lbfgs2.run(5)
res2 = lbfgs2.run(5)
self.assert_same(res1, res2)
def test_normal_estimates_OK(self):
observed = np.sqrt(self.ss) * randn(self.nr_points) + self.mu
pot = MLCost(observed, probf=gauss)
potl = MLCost(observed, log_probf=log_gauss)
parameters = [self.mu + 1, self.ss - 2]
optimizer = LBFGS_CPP(parameters, pot)
optimizerl = LBFGS_CPP(parameters, potl)
result = optimizer.run()
resultl = optimizerl.run()
opt_parameters = result.coords
opt_parametersl = resultl.coords
opt_mu = opt_parameters[0]
opt_mul = opt_parametersl[0]
opt_ss = opt_parameters[1]
opt_ssl = opt_parametersl[1]
self.assertAlmostEqual(opt_mu,
self.mu,
delta=2 * self.mu / np.sqrt(self.nr_points))
self.assertAlmostEqual(opt_ss,
self.ss,
delta=2 * self.ss / np.sqrt(self.nr_points))
self.assertAlmostEqual(opt_mu, opt_mul, delta=1e-4)
self.assertAlmostEqual(opt_ss, opt_ssl, delta=1e-4)
confidence_intervalsl = potl.get_error_estimate(opt_parametersl)
for i, par in enumerate(opt_parameters):
self.assertLessEqual(confidence_intervalsl[i][0], par)
self.assertLessEqual(par, confidence_intervalsl[i][1])
def test_normal_estimates_OK(self):
observed = np.sqrt(self.ss) * randn(self.nr_points) + self.mu
pot = MLCost(observed, probf=gauss)
potl = MLCost(observed, log_probf=log_gauss)
parameters = [self.mu + 1, self.ss - 2]
optimizer = LBFGS_CPP(parameters, pot)
optimizerl = LBFGS_CPP(parameters, potl)
result = optimizer.run()
resultl = optimizerl.run()
opt_parameters = result.coords
opt_parametersl = resultl.coords
opt_mu = opt_parameters[0]
opt_mul = opt_parametersl[0]
opt_ss = opt_parameters[1]
opt_ssl = opt_parametersl[1]
self.assertAlmostEqual(opt_mu, self.mu, delta=2*self.mu/np.sqrt(self.nr_points))
self.assertAlmostEqual(opt_ss, self.ss, delta=2*self.ss/np.sqrt(self.nr_points))
self.assertAlmostEqual(opt_mu, opt_mul, delta = 1e-4)
self.assertAlmostEqual(opt_ss, opt_ssl, delta = 1e-4)
confidence_intervalsl = potl.get_error_estimate(opt_parametersl)
for i, par in enumerate(opt_parameters):
self.assertLessEqual(confidence_intervalsl[i][0], par)
self.assertLessEqual(par, confidence_intervalsl[i][1])
def lbfgs_cpp(coords, pot, **kwargs):
lbfgs = LBFGS_CPP(coords, pot, **kwargs)
return lbfgs.run()
def test_raises(self):
with self.assertRaises(NotImplementedError):
lbfgs = LBFGS_CPP(_xrand, _Raise())
lbfgs.run()
def test_reset(self):
lbfgs1 = LBFGS_CPP(self.x0, self.pot)
lbfgs1.run()
res1 = lbfgs1.get_result()
x2 = self.x0.copy()
x2[1] = 2.
lbfgs2 = LBFGS_CPP(x2, self.pot)
H0 = lbfgs2.get_result()["H0"]
lbfgs2.run()
lbfgs2.reset(self.x0)
lbfgs2.set_H0(H0)
lbfgs2.run()
res2 = lbfgs2.get_result()
self.assertEqual(res1.rms, res2.rms)
self.assertEqual(res1.H0, res2.H0)
self.assertEqual(res1.nfev, res2.nfev)
self.assertEqual(res1.nsteps, res2.nsteps)
self.assertTrue(np.all(res1.coords == res2.coords))
def test_raises(self):
pot = _lj_cpp._ErrorPotential()
with self.assertRaises(RuntimeError):
lbfgs = LBFGS_CPP(_xrand, pot)
lbfgs.run()
def optimize(self, nr_samples = 1):
self.optimizer = ModifiedFireCPP(self.x_initial.copy(), self.potential,
dtmax=1, maxstep=self.maxstep,
tol=self.tol, nsteps=1e8, verbosity=-1, iprint=-1)
self.optimizer_ = LBFGS_CPP(self.x_initial.copy(), self.potential_)
self.optimizer_cells = ModifiedFireCPP(self.x_initial.copy(), self.potential_cells,
dtmax=1, maxstep=self.maxstep,
tol=self.tol, nsteps=1e8, verbosity=-1, iprint=-1)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial.copy(), self.potential_cells_)
print("initial E, x:", self.potential.getEnergy(self.x_initial.copy()))
print("initial E, x_:", self.potential_cells.getEnergy(self.x_initial.copy()))
t0 = time.time()
print("self.optimizer.run(self.nstepsmax)", self.nstepsmax)
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print("fire final E, x:", self.optimizer.get_result().energy)
print("fire final E, x_cells:", self.optimizer_cells.get_result().energy)
print("fire final E, plain: ", self.potential.getEnergy(self.x_final))
print("fire final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells))
print("fire number of particles:", self.N)
print("fire time no cell lists:", t1 - t0, "sec")
print("fire time cell lists:", t2 - t1, "sec")
print("fire ratio:", (t1 - t0) / (t2 - t1))
if not self.res_x_final.success or not self.res_x_final_cells.success:
print("-------------")
print("res_x_final.rms:", self.res_x_final.rms)
print("res_x_final.nfev:", self.res_x_final.nfev)
print("res_x_final_cells.rms:", self.res_x_final_cells.rms)
print("res_x_final_cells.nfev:", self.res_x_final_cells.nfev)
print("self.res_x_final.success", self.res_x_final.success)
print("self.res_x_final_cells.success", self.res_x_final_cells.success)
print("-------------")
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells, self.radii, self.boxvec, sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print("lbfgs final E, x:", self.optimizer_.get_result().energy)
print("lbfgs final E, x_cells:", self.optimizer_cells_.get_result().energy)
print("lbfgs final E, plain: ", self.potential_.getEnergy(self.x_final_))
print("lbfgs final E, cell: ", self.potential_cells_.getEnergy(self.x_final_cells_))
print("lbfgs number of particles:", self.N)
print("lbfgs time no cell lists:", t3 - t2, "sec")
print("lbfgs time cell lists:", t4 - t3, "sec")
print("lbfgs ratio:", (t3 - t2) / (t4 - t3))
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print("-------------")
print("res_x_final_.rms:", self.res_x_final_.rms)
print("res_x_final_.nfev:", self.res_x_final_.nfev)
print("res_x_final_cells_.rms:", self.res_x_final_cells_.rms)
print("res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev)
print("self.res_x_final_.success", self.res_x_final.success)
print("self.res_x_final_cells_.success", self.res_x_final_cells.success)
print("-------------")
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_, self.radii, self.boxvec, sca=self.sca)
assert(self.res_x_final.success)
assert(self.res_x_final_cells.success)
assert(self.res_x_final_.success)
assert(self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print("xci", xci)
print("xi", xi)
assert(passed)
print("energy no cell lists:", self.res_x_final.energy)
print("energy cell lists:", self.res_x_final_cells.energy)
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
class Config2DFrozenBoundary(object):
def __init__(self, nparticles_x, amplitude):
self.ndim = 2
self.LX = nparticles_x
self.LY = self.LX
self.nparticles_x = nparticles_x
self.N = self.nparticles_x**self.ndim
self.amplitude = amplitude
self.dof = self.ndim * self.N
self.x = np.zeros(self.dof)
self.frozen_atoms = []
for particle in xrange(self.N):
pid = self.ndim * particle
xcoor = particle % self.LX
ycoor = int(particle / self.LX)
self.x[pid] = xcoor
self.x[pid + 1] = ycoor
if xcoor == 0 or xcoor == self.LX - 1 or ycoor == 0 or ycoor == self.LY - 1:
self.frozen_atoms.append(particle)
self.x_initial = copy.copy(self.x)
for particle in xrange(self.N):
if particle not in self.frozen_atoms:
pid = self.ndim * particle
self.x_initial[pid] += np.random.uniform(
-self.amplitude, self.amplitude)
self.x_initial[pid + 1] += np.random.uniform(
-self.amplitude, self.amplitude)
self.x_initial = np.reshape(self.x_initial, (self.N, 2))
self.x_initial[:, 0] -= np.mean(self.x_initial[:, 0])
self.x_initial[:, 1] -= np.mean(self.x_initial[:, 1])
self.x_initial = self.x_initial.flatten()
min_x = np.amin(self.x_initial)
if min_x < 0:
self.x_initial -= min_x
#self.radius = 0.3
#self.sca = 1.5
self.radius = 0.25
self.sca = 1.8
self.radii = np.ones(self.N) * self.radius
self.eps = 1.0
max_edge = np.amax([
np.amax(self.x_initial),
np.abs(np.amin(self.x_initial))
]) + 2 * self.amplitude + (1 + self.sca) * self.radius
self.boxvec = np.array([max_edge, max_edge])
self.frozen_atoms1 = np.array(self.frozen_atoms)
self.frozen_atoms2 = np.array(self.frozen_atoms)
print "self.frozen_atoms1", self.frozen_atoms1
self.potential = HS_WCA(use_frozen=True,
use_periodic=use_periodic_frozen,
reference_coords=self.x_initial,
frozen_atoms=self.frozen_atoms1,
eps=self.eps,
sca=self.sca,
radii=self.radii,
ndim=self.ndim,
boxvec=self.boxvec)
self.rcut = 2 * (1 + self.sca) * self.radius
self.ncellx_scale = 1.0
self.potential_cells = HS_WCA(use_frozen=True,
use_periodic=use_periodic_frozen,
use_cell_lists=True,
eps=self.eps,
sca=self.sca,
radii=self.radii,
boxvec=self.boxvec,
reference_coords=self.x_initial,
rcut=self.rcut,
ndim=self.ndim,
ncellx_scale=self.ncellx_scale,
frozen_atoms=self.frozen_atoms2)
self.tol = 1e-7
self.maxstep = np.amax(self.radii)
self.nstepsmax = int(1e6)
assert (self.boxvec[0] == self.boxvec[1])
self.x_initial_red = reduce_coordinates(self.x_initial,
self.frozen_atoms, self.ndim)
print "x_initial energy:", self.potential.getEnergy(self.x_initial_red)
print "x_initial cells energy:", self.potential_cells.getEnergy(
self.x_initial_red)
#assert abs(self.potential.getEnergy(self.x_initial_red) - self.potential_cells.getEnergy(self.x_initial_red)) < 1e-10
assert np.allclose(self.potential.getEnergy(self.x_initial_red),
self.potential_cells.getEnergy(self.x_initial_red),
rtol=1e-10)
print self.boxvec
def optimize(self, nr_samples=1):
self.x_initial_red = reduce_coordinates(self.x_initial,
self.frozen_atoms, self.ndim)
self.optimizer = ModifiedFireCPP(self.x_initial_red.copy(),
self.potential,
tol=self.tol,
maxstep=self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial_red.copy(),
self.potential_cells,
tol=self.tol,
maxstep=self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial_red.copy(),
self.potential_cells)
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result(
).energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(
self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells,
self.radii,
self.boxvec,
sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result(
).energy
print "lbfgs final E, plain: ", self.potential.getEnergy(self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells.getEnergy(
self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_,
self.radii,
self.boxvec,
sca=self.sca)
assert (self.res_x_final.success)
assert (self.res_x_final_cells.success)
assert (self.res_x_final_.success)
assert (self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert (passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
class Config2D(object):
def __init__(self, nparticles_x, amplitude):
self.ndim = 2
self.LX = nparticles_x
self.LY = self.LX
self.nparticles_x = nparticles_x
self.N = self.nparticles_x**self.ndim
self.dof = self.ndim * self.N
self.amplitude = amplitude
self.x = np.zeros(self.dof)
for particle in xrange(self.N):
pid = self.ndim * particle
self.x[pid] = particle % self.LX
self.x[pid + 1] = int(particle / self.LX)
self.x_initial = np.asarray([
xi + np.random.uniform(-self.amplitude, self.amplitude)
for xi in self.x
])
self.x_initial = np.reshape(self.x_initial, (self.N, 2))
self.x_initial[:, 0] -= np.mean(self.x_initial[:, 0])
self.x_initial[:, 1] -= np.mean(self.x_initial[:, 1])
self.x_initial = self.x_initial.flatten()
#self.radius = 0.3
#self.sca = 1.5
self.radius = 0.25
self.sca = 1.8
self.radii = np.ones(self.N) * self.radius
self.eps = 1.0
self.boxvec = np.array([self.LX, self.LY])
self.potential = HS_WCA(use_periodic=use_periodic,
eps=self.eps,
sca=self.sca,
radii=self.radii.copy(),
ndim=self.ndim,
boxvec=self.boxvec.copy())
self.potential_ = HS_WCA(use_periodic=use_periodic,
eps=self.eps,
sca=self.sca,
radii=self.radii.copy(),
ndim=self.ndim,
boxvec=self.boxvec.copy())
self.rcut = 2 * (1 + self.sca) * self.radius
self.ncellx_scale = 1
self.potential_cells = HS_WCA(use_periodic=use_periodic,
use_cell_lists=True,
eps=self.eps,
sca=self.sca,
radii=self.radii.copy(),
boxvec=self.boxvec.copy(),
rcut=self.rcut,
ndim=self.ndim,
ncellx_scale=self.ncellx_scale)
self.potential_cells_ = HS_WCA(use_periodic=use_periodic,
use_cell_lists=True,
eps=self.eps,
sca=self.sca,
radii=self.radii.copy(),
boxvec=self.boxvec.copy(),
rcut=self.rcut,
ndim=self.ndim,
ncellx_scale=self.ncellx_scale)
self.tol = 1e-7
self.maxstep = np.amax(self.radii)
self.nstepsmax = int(1e6)
assert (self.boxvec[0] == self.boxvec[1])
print "x_initial energy:", self.potential.getEnergy(self.x_initial)
print "x_initial cells energy:", self.potential_cells.getEnergy(
self.x_initial)
assert (self.potential.getEnergy(
self.x_initial) == self.potential_.getEnergy(self.x_initial))
assert (self.potential_cells.getEnergy(
self.x_initial) == self.potential_cells_.getEnergy(self.x_initial))
#assert abs(self.potential.getEnergy(self.x_initial) - self.potential_cells.getEnergy(self.x_initial)) < 1e-10
assert np.allclose(self.potential.getEnergy(self.x_initial),
self.potential_cells.getEnergy(self.x_initial),
rtol=1e-10)
print self.boxvec
#plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
def optimize(self, nr_samples=1):
self.optimizer = ModifiedFireCPP(self.x_initial.copy(),
self.potential,
dtmax=1,
maxstep=self.maxstep,
tol=self.tol,
nsteps=1e8,
verbosity=-1,
iprint=-1)
self.optimizer_ = LBFGS_CPP(self.x_initial.copy(), self.potential_)
self.optimizer_cells = ModifiedFireCPP(self.x_initial.copy(),
self.potential_cells,
dtmax=1,
maxstep=self.maxstep,
tol=self.tol,
nsteps=1e8,
verbosity=-1,
iprint=-1)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial.copy(),
self.potential_cells_)
print "initial E, x:", self.potential.getEnergy(self.x_initial.copy())
print "initial E, x_:", self.potential_cells.getEnergy(
self.x_initial.copy())
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result(
).energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(
self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells,
self.radii,
self.boxvec,
sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result(
).energy
print "lbfgs final E, plain: ", self.potential_.getEnergy(
self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells_.getEnergy(
self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_,
self.radii,
self.boxvec,
sca=self.sca)
assert (self.res_x_final.success)
assert (self.res_x_final_cells.success)
assert (self.res_x_final_.success)
assert (self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert (passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def optimize(self, nr_samples=1):
self.x_initial_red = reduce_coordinates(self.x_initial,self.frozen_atoms,self.ndim)
self.optimizer = ModifiedFireCPP(self.x_initial_red.copy(), self.potential, tol = self.tol, maxstep = self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial_red.copy(), self.potential_cells, tol = self.tol, maxstep = self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential_cells)
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result().energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells, self.radii, self.boxvec, sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result().energy
print "lbfgs final E, plain: ", self.potential.getEnergy(self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_, self.radii, self.boxvec, sca=self.sca)
assert(self.res_x_final.success)
assert(self.res_x_final_cells.success)
assert(self.res_x_final_.success)
assert(self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert(passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def test_raises(self):
pot = _lj_cpp._ErrorPotential()
with self.assertRaises(RuntimeError):
lbfgs = LBFGS_CPP(_xrand, pot)
lbfgs.run()
def optimize(self, nr_samples=1):
self.x_initial_red = reduce_coordinates(self.x_initial,
self.frozen_atoms, self.ndim)
self.optimizer = ModifiedFireCPP(self.x_initial_red.copy(),
self.potential,
tol=self.tol,
maxstep=self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial_red.copy(),
self.potential_cells,
tol=self.tol,
maxstep=self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial_red.copy(),
self.potential_cells)
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result(
).energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(
self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells,
self.radii,
self.boxvec,
sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result(
).energy
print "lbfgs final E, plain: ", self.potential.getEnergy(self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells.getEnergy(
self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_,
self.radii,
self.boxvec,
sca=self.sca)
assert (self.res_x_final.success)
assert (self.res_x_final_cells.success)
assert (self.res_x_final_.success)
assert (self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert (passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def lbfgs_cpp(coords, pot, **kwargs):
lbfgs = LBFGS_CPP(coords, pot, **kwargs)
return lbfgs.run()
def test_reset(self):
lbfgs1 = LBFGS_CPP(self.x0, self.pot)
lbfgs1.run()
res1 = lbfgs1.get_result()
x2 = self.x0.copy()
x2[1] = 2.
lbfgs2 = LBFGS_CPP(x2, self.pot)
H0 = lbfgs2.get_result()["H0"]
lbfgs2.run()
lbfgs2.reset(self.x0)
lbfgs2.set_H0(H0)
lbfgs2.run()
res2 = lbfgs2.get_result()
self.assertEqual(res1.rms, res2.rms)
self.assertEqual(res1.H0, res2.H0)
self.assertEqual(res1.nfev, res2.nfev)
self.assertEqual(res1.nsteps, res2.nsteps)
self.assertTrue(np.all(res1.coords == res2.coords))
class Config2DFrozenBoundary(object):
def __init__(self, nparticles_x, amplitude):
self.ndim = 2
self.LX = nparticles_x
self.LY = self.LX
self.nparticles_x = nparticles_x
self.N = self.nparticles_x ** self.ndim
self.amplitude = amplitude
self.dof = self.ndim * self.N
self.x = np.zeros(self.dof)
self.frozen_atoms = []
for particle in xrange(self.N):
pid = self.ndim * particle
xcoor = particle % self.LX
ycoor = int(particle / self.LX)
self.x[pid] = xcoor
self.x[pid + 1] = ycoor
if xcoor == 0 or xcoor == self.LX - 1 or ycoor == 0 or ycoor == self.LY - 1:
self.frozen_atoms.append(particle)
self.x_initial = copy.copy(self.x)
for particle in xrange(self.N):
if particle not in self.frozen_atoms:
pid = self.ndim * particle
self.x_initial[pid] += np.random.uniform(- self.amplitude, self.amplitude)
self.x_initial[pid + 1] += np.random.uniform(- self.amplitude, self.amplitude)
self.x_initial = np.reshape(self.x_initial, (self.N,2))
self.x_initial[:,0] -= np.mean(self.x_initial[:,0])
self.x_initial[:,1] -= np.mean(self.x_initial[:,1])
self.x_initial = self.x_initial.flatten()
min_x = np.amin(self.x_initial)
if min_x < 0:
self.x_initial -= min_x
#self.radius = 0.3
#self.sca = 1.5
self.radius = 0.25
self.sca = 1.8
self.radii = np.ones(self.N) * self.radius
self.eps = 1.0
max_edge = np.amax([np.amax(self.x_initial), np.abs(np.amin(self.x_initial))]) + 2 * self.amplitude + (1 + self.sca) * self.radius
self.boxvec = np.array([max_edge, max_edge])
self.frozen_atoms1 = np.array(self.frozen_atoms)
self.frozen_atoms2 = np.array(self.frozen_atoms)
print "self.frozen_atoms1", self.frozen_atoms1
self.potential = HS_WCA(use_frozen=True, use_periodic=use_periodic_frozen,
reference_coords=self.x_initial,
frozen_atoms=self.frozen_atoms1,
eps=self.eps, sca=self.sca, radii=self.radii,
ndim=self.ndim, boxvec=self.boxvec)
self.rcut = 2 * (1 + self.sca) * self.radius
self.ncellx_scale = 1.0
self.potential_cells = HS_WCA(use_frozen=True,
use_periodic=use_periodic_frozen, use_cell_lists=True,
eps=self.eps, sca=self.sca,
radii=self.radii, boxvec=self.boxvec,
reference_coords=self.x_initial,
rcut=self.rcut, ndim=self.ndim,
ncellx_scale=self.ncellx_scale,
frozen_atoms=self.frozen_atoms2)
self.tol = 1e-7
self.maxstep = np.amax(self.radii)
self.nstepsmax = int(1e6)
assert(self.boxvec[0]==self.boxvec[1])
self.x_initial_red = reduce_coordinates(self.x_initial,self.frozen_atoms,self.ndim)
print "x_initial energy:", self.potential.getEnergy(self.x_initial_red)
print "x_initial cells energy:", self.potential_cells.getEnergy(self.x_initial_red)
#assert abs(self.potential.getEnergy(self.x_initial_red) - self.potential_cells.getEnergy(self.x_initial_red)) < 1e-10
assert np.allclose(self.potential.getEnergy(self.x_initial_red), self.potential_cells.getEnergy(self.x_initial_red), rtol=1e-10)
print self.boxvec
def optimize(self, nr_samples=1):
self.x_initial_red = reduce_coordinates(self.x_initial,self.frozen_atoms,self.ndim)
self.optimizer = ModifiedFireCPP(self.x_initial_red.copy(), self.potential, tol = self.tol, maxstep = self.maxstep)
self.optimizer_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential)
self.optimizer_cells = ModifiedFireCPP(self.x_initial_red.copy(), self.potential_cells, tol = self.tol, maxstep = self.maxstep)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial_red.copy(), self.potential_cells)
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result().energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells, self.radii, self.boxvec, sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result().energy
print "lbfgs final E, plain: ", self.potential.getEnergy(self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_, self.radii, self.boxvec, sca=self.sca)
assert(self.res_x_final.success)
assert(self.res_x_final_cells.success)
assert(self.res_x_final_.success)
assert(self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert(passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def test_raises(self):
with self.assertRaises(NotImplementedError):
lbfgs = LBFGS_CPP(_xrand, _Raise())
lbfgs.run()
class Config2D(object):
def __init__(self, nparticles_x, amplitude):
self.ndim = 2
self.LX = nparticles_x
self.LY = self.LX
self.nparticles_x = nparticles_x
self.N = self.nparticles_x ** self.ndim
self.dof = self.ndim * self.N
self.amplitude = amplitude
self.x = np.zeros(self.dof)
for particle in xrange(self.N):
pid = self.ndim * particle
self.x[pid] = particle % self.LX
self.x[pid + 1] = int(particle / self.LX)
self.x_initial = np.asarray([xi + np.random.uniform(- self.amplitude, self.amplitude) for xi in self.x])
self.x_initial = np.reshape(self.x_initial, (self.N,2))
self.x_initial[:,0] -= np.mean(self.x_initial[:,0])
self.x_initial[:,1] -= np.mean(self.x_initial[:,1])
self.x_initial = self.x_initial.flatten()
#self.radius = 0.3
#self.sca = 1.5
self.radius = 0.25
self.sca = 1.8
self.radii = np.ones(self.N) * self.radius
self.eps = 1.0
self.boxvec = np.array([self.LX, self.LY])
self.potential = HS_WCA(use_periodic=use_periodic, eps=self.eps,
sca=self.sca, radii=self.radii.copy(), ndim=self.ndim, boxvec=self.boxvec.copy())
self.potential_ = HS_WCA(use_periodic=use_periodic, eps=self.eps,
sca=self.sca, radii=self.radii.copy(), ndim=self.ndim, boxvec=self.boxvec.copy())
self.rcut = 2 * (1 + self.sca) * self.radius
self.ncellx_scale = 1
self.potential_cells = HS_WCA(use_periodic=use_periodic,
use_cell_lists=True, eps=self.eps,
sca=self.sca, radii=self.radii.copy(),
boxvec=self.boxvec.copy(),
rcut=self.rcut, ndim=self.ndim,
ncellx_scale=self.ncellx_scale)
self.potential_cells_ = HS_WCA(use_periodic=use_periodic,
use_cell_lists=True, eps=self.eps,
sca=self.sca, radii=self.radii.copy(),
boxvec=self.boxvec.copy(),
rcut=self.rcut, ndim=self.ndim,
ncellx_scale=self.ncellx_scale)
self.tol = 1e-7
self.maxstep = np.amax(self.radii)
self.nstepsmax = int(1e6)
assert(self.boxvec[0]==self.boxvec[1])
print "x_initial energy:", self.potential.getEnergy(self.x_initial)
print "x_initial cells energy:", self.potential_cells.getEnergy(self.x_initial)
assert(self.potential.getEnergy(self.x_initial) == self.potential_.getEnergy(self.x_initial))
assert(self.potential_cells.getEnergy(self.x_initial) == self.potential_cells_.getEnergy(self.x_initial))
#assert abs(self.potential.getEnergy(self.x_initial) - self.potential_cells.getEnergy(self.x_initial)) < 1e-10
assert np.allclose(self.potential.getEnergy(self.x_initial), self.potential_cells.getEnergy(self.x_initial), rtol=1e-10)
print self.boxvec
#plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
def optimize(self, nr_samples = 1):
self.optimizer = ModifiedFireCPP(self.x_initial.copy(), self.potential,
dtmax=1, maxstep=self.maxstep,
tol=self.tol, nsteps=1e8, verbosity=-1, iprint=-1)
self.optimizer_ = LBFGS_CPP(self.x_initial.copy(), self.potential_)
self.optimizer_cells = ModifiedFireCPP(self.x_initial.copy(), self.potential_cells,
dtmax=1, maxstep=self.maxstep,
tol=self.tol, nsteps=1e8, verbosity=-1, iprint=-1)
self.optimizer_cells_ = LBFGS_CPP(self.x_initial.copy(), self.potential_cells_)
print "initial E, x:", self.potential.getEnergy(self.x_initial.copy())
print "initial E, x_:", self.potential_cells.getEnergy(self.x_initial.copy())
t0 = time.time()
print "self.optimizer.run(self.nstepsmax)", self.nstepsmax
self.optimizer.run(self.nstepsmax)
self.res_x_final = self.optimizer.get_result()
t1 = time.time()
self.optimizer_cells.run(self.nstepsmax)
self.res_x_final_cells = self.optimizer_cells.get_result()
t2 = time.time()
self.x_final = self.res_x_final.coords
self.x_final_cells = self.res_x_final_cells.coords
print "fire final E, x:", self.optimizer.get_result().energy
print "fire final E, x_cells:", self.optimizer_cells.get_result().energy
print "fire final E, plain: ", self.potential.getEnergy(self.x_final)
print "fire final E, cell: ", self.potential_cells.getEnergy(self.x_final_cells)
print "fire number of particles:", self.N
print "fire time no cell lists:", t1 - t0, "sec"
print "fire time cell lists:", t2 - t1, "sec"
print "fire ratio:", (t1 - t0) / (t2 - t1)
if not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final.rms:", self.res_x_final.rms
print "res_x_final.nfev:", self.res_x_final.nfev
print "res_x_final_cells.rms:", self.res_x_final_cells.rms
print "res_x_final_cells.nfev:", self.res_x_final_cells.nfev
print "self.res_x_final.success", self.res_x_final.success
print "self.res_x_final_cells.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells, self.radii, self.boxvec, sca=self.sca)
self.optimizer_.run(self.nstepsmax)
self.res_x_final_ = self.optimizer_.get_result()
t3 = time.time()
self.optimizer_cells_.run(self.nstepsmax)
self.res_x_final_cells_ = self.optimizer_cells_.get_result()
t4 = time.time()
self.x_final_ = self.res_x_final_.coords
self.x_final_cells_ = self.res_x_final_cells_.coords
print "lbfgs final E, x:", self.optimizer_.get_result().energy
print "lbfgs final E, x_cells:", self.optimizer_cells_.get_result().energy
print "lbfgs final E, plain: ", self.potential_.getEnergy(self.x_final_)
print "lbfgs final E, cell: ", self.potential_cells_.getEnergy(self.x_final_cells_)
print "lbfgs number of particles:", self.N
print "lbfgs time no cell lists:", t3 - t2, "sec"
print "lbfgs time cell lists:", t4 - t3, "sec"
print "lbfgs ratio:", (t3 - t2) / (t4 - t3)
if not self.res_x_final_.success or not self.res_x_final_cells_.success or not self.res_x_final.success or not self.res_x_final_cells.success:
print "-------------"
print "res_x_final_.rms:", self.res_x_final_.rms
print "res_x_final_.nfev:", self.res_x_final_.nfev
print "res_x_final_cells_.rms:", self.res_x_final_cells_.rms
print "res_x_final_cells_.nfev:", self.res_x_final_cells_.nfev
print "self.res_x_final_.success", self.res_x_final.success
print "self.res_x_final_cells_.success", self.res_x_final_cells.success
print "-------------"
plot_disks(self.x_initial, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_, self.radii, self.boxvec, sca=self.sca)
plot_disks(self.x_final_cells_, self.radii, self.boxvec, sca=self.sca)
assert(self.res_x_final.success)
assert(self.res_x_final_cells.success)
assert(self.res_x_final_.success)
assert(self.res_x_final_cells_.success)
for (xci, xi) in zip(self.x_final_cells, self.x_final):
passed = (np.abs(xci - xi) < 1e-10)
if (passed is False):
print "xci", xci
print "xi", xi
assert(passed)
print "energy no cell lists:", self.res_x_final.energy
print "energy cell lists:", self.res_x_final_cells.energy
self.t_ratio = (t1 - t0) / (t2 - t1)
self.t_ratio_lbfgs = (t3 - t2) / (t4 - t3)
def __init__(self,
boxdim=2,
nr_particles=100,
hard_phi=0.4,
nr_steps=1e6,
epsilon=1,
alpha=0.1,
verbose=False):
# Settings.
np.random.seed(42)
# Input parameters.
self.boxdim = boxdim
self.nr_particles = nr_particles
self.hard_phi = hard_phi
self.nr_steps = nr_steps
self.epsilon = epsilon
self.alpha = alpha
self.verbose = verbose
# Derived quantities.
self.hard_radii = np.ones(self.nr_particles)
def volume_nball(radius, n):
return np.power(np.pi, n / 2) * np.power(radius,
n) / gamma(n / 2 + 1)
self.box_length = np.power(
np.sum(
np.asarray(
[volume_nball(r, self.boxdim)
for r in self.hard_radii])) / self.hard_phi,
1 / self.boxdim)
self.box_vector = np.ones(self.boxdim) * self.box_length
# HS-WCA potential.
self.potential = HS_WCA(use_periodic=True,
use_cell_lists=True,
ndim=self.boxdim,
eps=self.epsilon,
sca=self.alpha,
radii=self.hard_radii,
boxvec=self.box_vector)
# Initial configuration by minimization.
self.nr_dof = self.boxdim * self.nr_particles
self.x = np.random.uniform(-0.5 * self.box_length,
0.5 * self.box_length, self.nr_dof)
optimizer = LBFGS_CPP(self.x, self.potential)
optimizer.run()
if not optimizer.get_result().success:
print("warning: minimization has not converged")
self.x = optimizer.get_result().coords.copy()
# Potential and MC rules.
self.temperature = 1
self.mc = MC(self.potential, self.x, self.temperature, self.nr_steps)
self.step = RandomCoordsDisplacement(42,
1,
single=True,
nparticles=self.nr_particles,
bdim=self.boxdim)
if self.verbose:
print("initial MC stepsize")
print self.step.get_stepsize()
self.mc.set_takestep(self.step)
self.eq_steps = self.nr_steps / 2
self.mc.set_report_steps(self.eq_steps)
self.gr_quench = RecordPairDistHistogram(self.box_vector,
50,
self.eq_steps,
self.nr_particles,
optimizer=optimizer)
self.gr = RecordPairDistHistogram(self.box_vector, 50, self.eq_steps,
self.nr_particles)
self.mc.add_action(self.gr_quench)
self.mc.add_action(self.gr)
self.test = MetropolisTest(44)
self.mc.add_accept_test(self.test)