def test_mdlc(self):
s = self.system
rho = 0.3
# This is only for box size calculation. The actual particle number is
# lower, because particles are removed from the mdlc gap region
n_particle = 100
particle_radius = 0.5
box_l = np.cbrt(4 * n_particle * np.pi / (3 * rho)) * particle_radius
s.box_l = 3 * [box_l]
ref_E_path = abspath("data/mdlc_reference_data_energy.dat")
ref_E = float(np.genfromtxt(ref_E_path)) * DIPOLAR_PREFACTOR
gap_size = 2.0
# Particles
data = np.genfromtxt(
abspath("data/mdlc_reference_data_forces_torques.dat"))
s.part.add(pos=data[:, 1:4], dip=data[:, 4:7])
s.part[:].rotation = (1, 1, 1)
p3m = magnetostatics.DipolarP3M(prefactor=DIPOLAR_PREFACTOR,
mesh=32,
accuracy=1E-4)
dlc = magnetostatic_extensions.DLC(maxPWerror=1E-5, gap_size=gap_size)
s.actors.add(p3m)
s.actors.add(dlc)
s.integrator.run(0)
err_f = self.vector_error(s.part[:].f,
data[:, 7:10] * DIPOLAR_PREFACTOR)
err_t = self.vector_error(s.part[:].torque_lab,
data[:, 10:13] * DIPOLAR_PREFACTOR)
err_e = s.analysis.energy()["dipolar"] - ref_E
tol_f = 2E-3
tol_t = 2E-3
tol_e = 1E-3
self.assertLessEqual(abs(err_e), tol_e, "Energy difference too large")
self.assertLessEqual(abs(err_t), tol_t, "Torque difference too large")
self.assertLessEqual(abs(err_f), tol_f, "Force difference too large")
# Check if error is thrown when particles enter the MDLC gap
# positive direction
s.part[0].pos = [
s.box_l[0] / 2, s.box_l[1] / 2, s.box_l[2] - gap_size / 2
]
with self.assertRaises(Exception):
self.system.analysis.energy()
with self.assertRaises(Exception):
self.integrator.run(2)
# negative direction
s.part[0].pos = [s.box_l[0] / 2, s.box_l[1] / 2, -gap_size / 2]
with self.assertRaises(Exception):
self.system.analysis.energy()
with self.assertRaises(Exception):
self.integrator.run(2)
def test_mdlc(self):
s = self.s
s.part.clear()
rho = 0.3
# This is only for box size calculation. The actual particle numbwe is
# lower, because particles are removed from the mdlc gap region
n_particle = 100
particle_radius = 0.5
box_l = pow(((4 * n_particle * 3.141592654) /
(3 * rho)), 1.0 / 3.0) * particle_radius
s.box_l = box_l, box_l, box_l
f = open(abspath("data/mdlc_reference_data_energy.dat"))
ref_E = float(f.readline())
f.close()
# Particles
data = np.genfromtxt(
abspath("data/mdlc_reference_data_forces_torques.dat"))
for p in data[:, :]:
s.part.add(id=int(p[0]), pos=p[1:4], dip=p[4:7])
s.part[:].rotation = (1, 1, 1)
p3m = magnetostatics.DipolarP3M(prefactor=1, mesh=32, accuracy=1E-4)
dlc = magnetostatic_extensions.DLC(maxPWerror=1E-5, gap_size=2.)
s.actors.add(p3m)
s.actors.add(dlc)
s.thermostat.turn_off()
s.integrator.run(0)
err_f = np.sum(np.sqrt(np.sum(
(s.part[:].f - data[:, 7:10])**2, 1)), 0) / np.sqrt(data.shape[0])
err_t = np.sum(
np.sqrt(np.sum((s.part[:].torque_lab - data[:, 10:13])**2, 1)),
0) / np.sqrt(data.shape[0])
err_e = s.analysis.energy()["dipolar"] - ref_E
print("Energy difference", err_e)
print("Force difference", err_f)
print("Torque difference", err_t)
tol_f = 2E-3
tol_t = 2E-3
tol_e = 1E-3
self.assertLessEqual(abs(err_e), tol_e, "Energy difference too large")
self.assertLessEqual(abs(err_t), tol_t, "Torque difference too large")
self.assertLessEqual(abs(err_f), tol_f, "Force difference too large")
s.part.clear()
del s.actors[0]
del s.actors[0]
def test_p3m(self):
s = self.s
s.part.clear()
rho = 0.09
# This is only for box size calculation. The actual particle numbwe is
# lower, because particles are removed from the mdlc gap region
n_particle = 1000
particle_radius = 1
box_l = pow(((4 * n_particle * 3.141592654) /
(3 * rho)), 1.0 / 3.0) * particle_radius
s.box_l = box_l, box_l, box_l
# Particles
data = np.genfromtxt(abspath("data/p3m_magnetostatics_system.data"))
for p in data[:, :]:
s.part.add(id=int(p[0]), pos=p[1:4], dip=p[4:7])
s.part[:].rotation = (1, 1, 1)
p3m = magnetostatics.DipolarP3M(prefactor=1,
mesh=32,
accuracy=1E-6,
epsilon="metallic")
s.actors.add(p3m)
s.integrator.run(0)
expected = np.genfromtxt(
abspath("data/p3m_magnetostatics_expected.data"))[:, 1:]
err_f = np.sum(np.sqrt(np.sum((s.part[:].f - expected[:, 0:3])**2, 1)),
0) / np.sqrt(data.shape[0])
err_t = np.sum(
np.sqrt(np.sum((s.part[:].torque_lab - expected[:, 3:6])**2, 1)),
0) / np.sqrt(data.shape[0])
ref_E = 5.570
err_e = s.analysis.energy()["dipolar"] - ref_E
print("Energy difference", err_e)
print("Force difference", err_f)
print("Torque difference", err_t)
tol_f = 2E-3
tol_t = 2E-3
tol_e = 1E-3
self.assertLessEqual(abs(err_e), tol_e, "Energy difference too large")
self.assertLessEqual(abs(err_t), tol_t, "Torque difference too large")
self.assertLessEqual(abs(err_f), tol_f, "Force difference too large")
s.part.clear()
del s.actors[0]
def test_p3m(self):
s = self.system
rho = 0.09
# This is only for box size calculation. The actual particle number is
# lower, because particles are removed from the mdlc gap region
n_particle = 1000
particle_radius = 1
box_l = np.cbrt(4 * n_particle * np.pi / (3 * rho)) * particle_radius
s.box_l = 3 * [box_l]
# Particles
data = np.genfromtxt(abspath("data/p3m_magnetostatics_system.data"))
s.part.add(pos=data[:, 1:4], dip=data[:, 4:7])
s.part[:].rotation = (1, 1, 1)
p3m = magnetostatics.DipolarP3M(prefactor=DIPOLAR_PREFACTOR,
mesh=32,
accuracy=1E-6,
epsilon="metallic")
s.actors.add(p3m)
s.integrator.run(0)
expected = np.genfromtxt(
abspath("data/p3m_magnetostatics_expected.data"))[:, 1:]
err_f = self.vector_error(s.part[:].f,
expected[:, 0:3] * DIPOLAR_PREFACTOR)
err_t = self.vector_error(s.part[:].torque_lab,
expected[:, 3:6] * DIPOLAR_PREFACTOR)
ref_E = 5.570 * DIPOLAR_PREFACTOR
err_e = s.analysis.energy()["dipolar"] - ref_E
tol_f = 2E-3
tol_t = 2E-3
tol_e = 1E-3
self.assertLessEqual(abs(err_e), tol_e, "Energy difference too large")
self.assertLessEqual(abs(err_t), tol_t, "Torque difference too large")
self.assertLessEqual(abs(err_f), tol_f, "Force difference too large")
gamma=0.001,
max_displacement=0.01)
# warmup
while system.analysis.energy()["total"] > 0.1 * n_part:
print("minimization: {:.1f}".format(system.analysis.energy()["total"]))
system.integrator.run(20)
print("minimization: {:.1f}".format(system.analysis.energy()["total"]))
print()
system.integrator.set_vv()
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)
system.integrator.run(min(5 * measurement_steps, 60000))
system.actors.add(magnetostatics.DipolarP3M(prefactor=1, accuracy=1E-4))
print("Tune skin: {}".format(
system.cell_system.tune_skin(min_skin=0.2,
max_skin=1,
tol=0.05,
int_steps=100)))
system.integrator.run(min(5 * measurement_steps, 2500))
print(system.non_bonded_inter[0, 0].lennard_jones)
if not args.visualizer:
# print initial energies
energies = system.analysis.energy()
print(energies)