def test_scafacos_dipoles(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],
rotation=(1, 1, 1))
scafacos = magnetostatics.Scafacos(prefactor=1,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 0,
"pnfft_N": "32,32,32",
"pnfft_n": "32,32,32",
"pnfft_window_name": "bspline",
"pnfft_m": "4",
"p2nfft_ignore_tolerance": "1",
"pnfft_diff_ik": "0",
"p2nfft_r_cut": "11",
"p2nfft_alpha": "0.31"
})
s.actors.add(scafacos)
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_scafacos_dipoles(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)
scafacos = magnetostatics.Scafacos(prefactor=DIPOLAR_PREFACTOR,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 0,
"pnfft_N": "32,32,32",
"pnfft_n": "32,32,32",
"pnfft_window_name": "bspline",
"pnfft_m": "4",
"p2nfft_ignore_tolerance": "1",
"pnfft_diff_ik": "0",
"p2nfft_r_cut": "11",
"p2nfft_alpha": "0.31"
})
s.actors.add(scafacos)
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")
def test_scafacos(self):
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 = pow(((4 * n_particle * np.pi) /
(3 * rho)), 1.0 / 3.0) * particle_radius
skin = 0.5
s = espressomd.System(box_l=[1.0, 1.0, 1.0])
# give Espresso some parameters
s.time_step = 0.01
s.cell_system.skin = skin
s.box_l = 3 * [box_l]
for dim in 2, 1:
print("Dimension", dim)
# Read reference data
if dim == 2:
file_prefix = "data/mdlc"
s.periodicity = [1, 1, 0]
else:
s.periodicity = [1, 0, 0]
file_prefix = "data/scafacos_dipoles_1d"
with open(abspath(file_prefix +
"_reference_data_energy.dat")) as f:
ref_E = float(f.readline())
# Particles
data = np.genfromtxt(
abspath(file_prefix + "_reference_data_forces_torques.dat"))
for p in data[:, :]:
s.part.add(id=int(p[0]),
pos=p[1:4],
dip=p[4:7],
rotation=(1, 1, 1))
if dim == 2:
scafacos = magnetostatics.Scafacos(
prefactor=1,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 0,
"pnfft_N": "80,80,160",
"pnfft_window_name": "bspline",
"pnfft_m": "4",
"p2nfft_ignore_tolerance": "1",
"pnfft_diff_ik": "0",
"p2nfft_r_cut": "6",
"p2nfft_alpha": "0.8",
"p2nfft_epsB": "0.05"
})
s.actors.add(scafacos)
# change box geometry in x,y direction to ensure that
# scafacos survives it
s.box_l = np.array((1, 1, 1.3)) * box_l
else:
if dim == 1:
# 1d periodic in x
scafacos = magnetostatics.Scafacos(
prefactor=1,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 1,
"pnfft_N": "32,128,128",
"pnfft_direct": 0,
"p2nfft_r_cut": 2.855,
"p2nfft_alpha": "1.5",
"p2nfft_intpol_order": "-1",
"p2nfft_reg_kernel_name": "ewald",
"p2nfft_p": "16",
"p2nfft_ignore_tolerance": "1",
"pnfft_window_name": "bspline",
"pnfft_m": "8",
"pnfft_diff_ik": "1",
"p2nfft_epsB": "0.125"
})
s.box_l = np.array((1, 1, 1)) * box_l
s.actors.add(scafacos)
else:
raise Exception("This shouldn't happen.")
s.thermostat.turn_off()
s.integrator.run(0)
# Calculate errors
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]
def test_scafacos(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]
for dim in (2, 1):
print("Dimension", dim)
# Read reference data
if dim == 2:
file_prefix = "data/mdlc"
s.periodicity = [1, 1, 0]
else:
s.periodicity = [1, 0, 0]
file_prefix = "data/scafacos_dipoles_1d"
ref_E_path = abspath(file_prefix + "_reference_data_energy.dat")
ref_E = float(np.genfromtxt(ref_E_path))
# Particles
data = np.genfromtxt(
abspath(file_prefix + "_reference_data_forces_torques.dat"))
s.part.add(pos=data[:, 1:4], dip=data[:, 4:7])
s.part[:].rotation = (1, 1, 1)
if dim == 2:
scafacos = magnetostatics.Scafacos(
prefactor=1,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 0,
"pnfft_N": "80,80,160",
"pnfft_window_name": "bspline",
"pnfft_m": "4",
"p2nfft_ignore_tolerance": "1",
"pnfft_diff_ik": "0",
"p2nfft_r_cut": "6",
"p2nfft_alpha": "0.8",
"p2nfft_epsB": "0.05"
})
s.actors.add(scafacos)
# change box geometry in x,y direction to ensure that
# scafacos survives it
s.box_l = np.array((1, 1, 1.3)) * box_l
else:
# 1d periodic in x
scafacos = magnetostatics.Scafacos(
prefactor=1,
method_name="p2nfft",
method_params={
"p2nfft_verbose_tuning": 1,
"pnfft_N": "32,128,128",
"pnfft_direct": 0,
"p2nfft_r_cut": 2.855,
"p2nfft_alpha": "1.5",
"p2nfft_intpol_order": "-1",
"p2nfft_reg_kernel_name": "ewald",
"p2nfft_p": "16",
"p2nfft_ignore_tolerance": "1",
"pnfft_window_name": "bspline",
"pnfft_m": "8",
"pnfft_diff_ik": "1",
"p2nfft_epsB": "0.125"
})
s.box_l = np.array((1, 1, 1)) * box_l
s.actors.add(scafacos)
s.integrator.run(0)
# Calculate errors
err_f = self.vector_error(s.part[:].f, data[:, 7:10])
err_t = self.vector_error(s.part[:].torque_lab, data[:, 10:13])
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")
s.part.clear()
s.actors.clear()