def test_run_niter2(self):
modified_fire1 = ModifiedFireCPP(_xrand, _EG())
res1 = modified_fire1.run()
modified_fire2 = ModifiedFireCPP(_xrand, _EG())
res2 = modified_fire2.run(res1.nsteps // 2)
res2 = modified_fire2.run()
self.assert_same(res1, res2)
def test_run_niter3(self):
modified_fire1 = ModifiedFireCPP(_xrand, _EG())
res1 = modified_fire1.run(10)
modified_fire2 = ModifiedFireCPP(_xrand, _EG())
res2 = modified_fire2.run(5)
res2 = modified_fire2.run(5)
self.assert_same(res1, res2)
def setUp(self):
np.random.seed(42)
self.L_mobile = 4
self.L_total = self.L_mobile + 2
self.nr_particles_mobile = self.L_mobile * self.L_mobile
self.nr_particles_total = self.L_total * self.L_total
self.nr_particles_frozen = self.nr_particles_total - self.nr_particles_mobile
self.box_dimension = 2
self.ndof = self.nr_particles_total * self.box_dimension
self.n_frozen_dof = self.nr_particles_frozen * self.box_dimension
self.frozen_dof = []
self.frozen_atoms = []
for particle_index in range(self.nr_particles_total):
xmean = int(particle_index % self.L_total)
ymean = int(particle_index / self.L_total)
if ymean == 0 or ymean == self.L_total - 1 or xmean == 0 or xmean == self.L_total - 1:
self.frozen_dof.append(particle_index * self.box_dimension)
self.frozen_dof.append(particle_index * self.box_dimension + 1)
self.frozen_atoms.append(particle_index)
self.eps = 1
self.x = np.zeros(self.ndof)
for p in range(self.nr_particles_total):
xmean = int(p % self.L_total)
ymean = int(p / self.L_total)
self.x[p * self.box_dimension] = xmean + 0.1 * np.random.rand()
self.x[p * self.box_dimension + 1] = ymean + 0.1 * np.random.rand()
self.radii = np.asarray([0.3 + 0.01 * np.random.rand() for _ in range(self.nr_particles_total)])
self.sca = 1
self.rcut = 2 * (1 + self.sca) * np.amax(self.radii)
self.boxvec = (self.L_total + self.rcut) * np.ones(self.box_dimension)
self.pot_cells_N_frozen_N = HS_WCA(eps=self.eps, sca=self.sca,
radii=self.radii, ndim=self.box_dimension,
boxvec=self.boxvec, use_periodic=True,
use_frozen=False, use_cell_lists=False)
self.pot_cells_Y_frozen_N = HS_WCA(eps=self.eps, sca=self.sca,
radii=self.radii, ndim=self.box_dimension,
boxvec=self.boxvec, use_periodic=True,
use_frozen=False, use_cell_lists=True,
reference_coords=self.x, rcut=self.rcut)
self.pot_cells_N_frozen_Y = HS_WCA(eps=self.eps, sca=self.sca,
radii=self.radii, ndim=self.box_dimension,
boxvec=self.boxvec, use_periodic=True,
use_frozen=True, use_cell_lists=False,
frozen_atoms=self.frozen_atoms,
reference_coords=self.x)
self.pot_cells_Y_frozen_Y = HS_WCA(eps=self.eps, sca=self.sca,
radii=self.radii, ndim=self.box_dimension,
boxvec=self.boxvec, use_periodic=True,
use_frozen=True, use_cell_lists=True,
reference_coords=self.x,
frozen_atoms=self.frozen_atoms, rcut=self.rcut)
self.x_red = []
for atom in range(self.nr_particles_total):
if atom not in self.frozen_atoms:
self.x_red.extend(self.x[atom * self.box_dimension : (atom + 1) * self.box_dimension])
self.opt_NN = ModifiedFireCPP(self.x, self.pot_cells_N_frozen_N)
self.opt_YN = ModifiedFireCPP(self.x, self.pot_cells_Y_frozen_N)
self.opt_NY = ModifiedFireCPP(self.x_red, self.pot_cells_N_frozen_Y)
self.opt_YY = ModifiedFireCPP(self.x_red, self.pot_cells_Y_frozen_Y)
def do_check(self, pot, **kwargs):
modified_fire = ModifiedFireCPP(np.zeros(4), pot, stepback=True, **kwargs)
modified_fire.run()
modified_fire.reset(_xrand)
res = modified_fire.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 test_event_raise(self):
class EventException(BaseException):
pass
def myevent(*args, **kwargs):
raise EventException
with self.assertRaises(EventException):
modified_fire = ModifiedFireCPP(_xrand, _EG(), events=[myevent])
modified_fire.run()
def test_raises(self):
pot = _lj_cpp._ErrorPotential()
with self.assertRaises(RuntimeError):
modified_fire = ModifiedFireCPP(_xrand, pot)
modified_fire.run()
def test_raises(self):
with self.assertRaises(NotImplementedError):
modified_fire = ModifiedFireCPP(_xrand, _Raise())
modified_fire.run()
def modifiedfire_cpp(coords, pot, **kwargs):
modifiedfire = ModifiedFireCPP(coords, pot, **kwargs)
return modifiedfire.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 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)
