def check_global(self, N, kT, steps, v_minmax, n_bins, error_tol,
recalc_forces):
"""
Test Langevin/Brownian dynamics velocity distribution with global kT
and gamma.
Parameters
----------
N : :obj:`int`
Number of particles.
kT : :obj:`float`
Global temperature.
steps : :obj:`int`
Number of sampling steps.
v_minmax : :obj:`float`
Velocity range.
n_bins : :obj:`int`
Number of bins.
error_tol : :obj:`float`
Error tolerance.
recalc_forces : :obj:`bool`
True if the forces should be recalculated after every step.
"""
system = self.system
# Place particles
system.part.add(pos=np.random.random((N, 3)))
# Enable rotation if compiled in
if espressomd.has_features("ROTATION"):
system.part[:].rotation = [1, 1, 1]
# Warmup
system.integrator.run(20)
vel_obs = ParticleVelocities(ids=system.part[:].id)
vel_acc = TimeSeries(obs=vel_obs)
system.auto_update_accumulators.add(vel_acc)
if espressomd.has_features("ROTATION"):
omega_obs = ParticleBodyAngularVelocities(ids=system.part[:].id)
omega_acc = TimeSeries(obs=omega_obs)
system.auto_update_accumulators.add(omega_acc)
# Sampling
v_stored = np.zeros((steps, N, 3))
omega_stored = np.zeros((steps, N, 3))
for i in range(steps):
system.integrator.run(1, recalc_forces=recalc_forces)
v_stored[i] = system.part[:].v
if espressomd.has_features("ROTATION"):
omega_stored[i] = system.part[:].omega_body
vel = vel_acc.time_series().reshape((-1, 3))
self.check_velocity_distribution(vel, v_minmax, n_bins, error_tol, kT)
if espressomd.has_features("ROTATION"):
omega = omega_acc.time_series().reshape((-1, 3))
self.check_velocity_distribution(omega, v_minmax, n_bins,
error_tol, kT)
def check_noise_correlation(self, kT, steps, delta):
"""Test the Langevin/Brownian noise is uncorrelated.
Parameters
----------
kT : :obj:`float`
Global temperature.
steps : :obj:`int`
Number of sampling steps.
delta : :obj:`float`
Error tolerance.
"""
system = self.system
vel_obs = ParticleVelocities(ids=system.part[:].id)
vel_series = TimeSeries(obs=vel_obs)
system.auto_update_accumulators.add(vel_series)
if espressomd.has_features("ROTATION"):
system.part[:].rotation = (1, 1, 1)
omega_obs = ParticleBodyAngularVelocities(ids=system.part[:].id)
omega_series = TimeSeries(obs=omega_obs)
system.auto_update_accumulators.add(omega_series)
system.integrator.run(steps)
# test translational noise correlation
vel = np.array(vel_series.time_series())
for ind in range(2):
for i in range(3):
for j in range(i, 3):
corrcoef = np.dot(vel[:, ind, i], vel[:, ind,
j]) / steps / kT
if i == j:
self.assertAlmostEqual(corrcoef, 1.0, delta=delta)
else:
self.assertAlmostEqual(corrcoef, 0.0, delta=delta)
# test rotational noise correlation
if espressomd.has_features("ROTATION"):
omega = np.array(omega_series.time_series())
for ind in range(2):
for i in range(3):
for j in range(3):
corrcoef = np.dot(omega[:, ind, i],
omega[:, ind, j]) / steps / kT
if i == j:
self.assertAlmostEqual(corrcoef, 1.0, delta=delta)
else:
self.assertAlmostEqual(corrcoef, 0.0, delta=delta)
# translational and angular velocities should be
# independent
corrcoef = np.dot(vel[:, ind, i],
omega[:, ind, j]) / steps / kT
self.assertAlmostEqual(corrcoef, 0.0, delta=delta)
def check_per_particle(self, N, kT, gamma_local, steps, v_minmax, n_bins,
error_tol):
"""
Test Langevin/Brownian dynamics velocity distribution with global and
particle-specific kT/gamma. Covers all combinations of particle
specific-gamma and temp set or not set.
Parameters
----------
N : :obj:`int`
Number of particles.
kT : :obj:`float`
Global temperature.
gamma_local : :obj:`float`
Per-particle gamma.
steps : :obj:`int`
Number of sampling steps.
v_minmax : :obj:`float`
Velocity range.
n_bins : :obj:`int`
Number of bins.
error_tol : :obj:`float`
Error tolerance.
"""
system = self.system
system.part.add(pos=np.random.random((N, 3)))
if espressomd.has_features("ROTATION"):
system.part[:].rotation = [1, 1, 1]
if espressomd.has_features("PARTICLE_ANISOTROPY"):
gamma_local = 3 * [gamma_local]
# Set different gamma on 2nd half of particles
system.part[N // 2:].gamma = gamma_local
system.integrator.run(50)
vel_obs = ParticleVelocities(ids=system.part[:].id)
vel_acc = TimeSeries(obs=vel_obs)
system.auto_update_accumulators.add(vel_acc)
if espressomd.has_features("ROTATION"):
omega_obs = ParticleBodyAngularVelocities(ids=system.part[:].id)
omega_acc = TimeSeries(obs=omega_obs)
system.auto_update_accumulators.add(omega_acc)
system.integrator.run(steps)
vel = vel_acc.time_series().reshape((-1, 3))
self.check_velocity_distribution(vel, v_minmax, n_bins, error_tol, kT)
if espressomd.has_features("ROTATION"):
omega = omega_acc.time_series().reshape((-1, 3))
self.check_velocity_distribution(omega, v_minmax, n_bins,
error_tol, kT)
def test_08__noise_correlation(self):
"""Checks that the Brownian noise is uncorrelated"""
system = self.system
system.part.clear()
system.time_step = 0.01
system.cell_system.skin = 0.1
system.part.add(id=(0, 1), pos=np.zeros((2, 3)))
vel_obs = ParticleVelocities(ids=system.part[:].id)
vel_series = TimeSeries(obs=vel_obs)
system.auto_update_accumulators.add(vel_series)
if espressomd.has_features("ROTATION"):
system.part[:].rotation = (1, 1, 1)
omega_obs = ParticleBodyAngularVelocities(ids=system.part[:].id)
omega_series = TimeSeries(obs=omega_obs)
system.auto_update_accumulators.add(omega_series)
kT = 3.2
system.thermostat.set_brownian(kT=kT, gamma=2.1, seed=17)
steps = int(1e4)
system.integrator.run(steps)
system.auto_update_accumulators.clear()
# test translational noise correlation
vel = np.array(vel_series.time_series())
for ind in range(2):
for i in range(3):
for j in range(i, 3):
corrcoef = np.dot(vel[:, ind, i], vel[:, ind,
j]) / steps / kT
if i == j:
self.assertAlmostEqual(corrcoef, 1.0, delta=0.04)
else:
self.assertLessEqual(np.abs(corrcoef), 0.04)
# test rotational noise correlation
if espressomd.has_features("ROTATION"):
omega = np.array(omega_series.time_series())
for ind in range(2):
for i in range(3):
for j in range(3):
corrcoef = np.dot(omega[:, ind, i],
omega[:, ind, j]) / steps / kT
if i == j:
self.assertAlmostEqual(corrcoef, 1.0, delta=0.04)
else:
self.assertLessEqual(np.abs(corrcoef), 0.04)
# translational and angular velocities should be
# independent
corrcoef = np.dot(vel[:, ind, i],
omega[:, ind, j]) / steps / kT
self.assertLessEqual(np.abs(corrcoef), 0.04)
def test_06__diffusion(self):
"""This tests rotational and translational diffusion coeff via Green-Kubo"""
system = self.system
system.part.clear()
kT = 1.37
dt = 0.1
system.time_step = dt
# Translational gamma. We cannot test per-component, if rotation is on,
# because body and space frames become different.
gamma = 3.1
# Rotational gamma
gamma_rot_i = 4.7
gamma_rot_a = [4.2, 1, 1.2]
# If we have langevin per particle:
# per particle kT
per_part_kT = 1.6
# Translation
per_part_gamma = 1.63
# Rotational
per_part_gamma_rot_i = 2.6
per_part_gamma_rot_a = [2.4, 3.8, 1.1]
# Particle with global thermostat params
p_global = system.part.add(pos=(0, 0, 0))
# Make sure, mass doesn't change diff coeff
self.setup_diff_mass_rinertia(p_global)
# particle specific gamma, kT, and both
if espressomd.has_features("LANGEVIN_PER_PARTICLE"):
p_gamma = system.part.add(pos=(0, 0, 0))
self.setup_diff_mass_rinertia(p_gamma)
if espressomd.has_features("PARTICLE_ANISOTROPY"):
p_gamma.gamma = per_part_gamma, per_part_gamma, per_part_gamma
if espressomd.has_features("ROTATION"):
p_gamma.gamma_rot = per_part_gamma_rot_a
else:
p_gamma.gamma = per_part_gamma
if espressomd.has_features("ROTATION"):
p_gamma.gamma_rot = per_part_gamma_rot_i
p_kT = system.part.add(pos=(0, 0, 0))
self.setup_diff_mass_rinertia(p_kT)
p_kT.temp = per_part_kT
p_both = system.part.add(pos=(0, 0, 0))
self.setup_diff_mass_rinertia(p_both)
p_both.temp = per_part_kT
if espressomd.has_features("PARTICLE_ANISOTROPY"):
p_both.gamma = per_part_gamma, per_part_gamma, per_part_gamma
if espressomd.has_features("ROTATION"):
p_both.gamma_rot = per_part_gamma_rot_a
else:
p_both.gamma = per_part_gamma
if espressomd.has_features("ROTATION"):
p_both.gamma_rot = per_part_gamma_rot_i
# Thermostat setup
if espressomd.has_features("ROTATION"):
if espressomd.has_features("PARTICLE_ANISOTROPY"):
# particle anisotropy and rotation
system.thermostat.set_langevin(kT=kT,
gamma=gamma,
gamma_rotation=gamma_rot_a,
seed=41)
else:
# Rotation without particle anisotropy
system.thermostat.set_langevin(kT=kT,
gamma=gamma,
gamma_rotation=gamma_rot_i,
seed=41)
else:
# No rotation
system.thermostat.set_langevin(kT=kT, gamma=gamma, seed=41)
system.cell_system.skin = 0.4
system.integrator.run(100)
# Correlators
vel_obs = {}
omega_obs = {}
corr_vel = {}
corr_omega = {}
all_particles = [p_global]
if espressomd.has_features("LANGEVIN_PER_PARTICLE"):
all_particles.append(p_gamma)
all_particles.append(p_kT)
all_particles.append(p_both)
# linear vel
vel_obs = ParticleVelocities(ids=system.part[:].id)
corr_vel = Correlator(obs1=vel_obs,
tau_lin=10,
tau_max=1.4,
delta_N=2,
corr_operation="componentwise_product",
compress1="discard1")
system.auto_update_accumulators.add(corr_vel)
# angular vel
if espressomd.has_features("ROTATION"):
omega_obs = ParticleBodyAngularVelocities(ids=system.part[:].id)
corr_omega = Correlator(obs1=omega_obs,
tau_lin=10,
tau_max=1.5,
delta_N=2,
corr_operation="componentwise_product",
compress1="discard1")
system.auto_update_accumulators.add(corr_omega)
system.integrator.run(80000)
system.auto_update_accumulators.remove(corr_vel)
corr_vel.finalize()
if espressomd.has_features("ROTATION"):
system.auto_update_accumulators.remove(corr_omega)
corr_omega.finalize()
# Verify diffusion
# Translation
# Cast gammas to vector, to make checks independent of
# PARTICLE_ANISOTROPY
gamma = np.ones(3) * gamma
per_part_gamma = np.ones(3) * per_part_gamma
self.verify_diffusion(p_global, corr_vel, kT, gamma)
if espressomd.has_features("LANGEVIN_PER_PARTICLE"):
self.verify_diffusion(p_gamma, corr_vel, kT, per_part_gamma)
self.verify_diffusion(p_kT, corr_vel, per_part_kT, gamma)
self.verify_diffusion(p_both, corr_vel, per_part_kT,
per_part_gamma)
# Rotation
if espressomd.has_features("ROTATION"):
# Decide on effective gamma rotation, since for rotation it is
# direction dependent
eff_gamma_rot = None
per_part_eff_gamma_rot = None
if espressomd.has_features("PARTICLE_ANISOTROPY"):
eff_gamma_rot = gamma_rot_a
eff_per_part_gamma_rot = per_part_gamma_rot_a
else:
eff_gamma_rot = gamma_rot_i * np.ones(3)
eff_per_part_gamma_rot = per_part_gamma_rot_i * np.ones(3)
self.verify_diffusion(p_global, corr_omega, kT, eff_gamma_rot)
if espressomd.has_features("LANGEVIN_PER_PARTICLE"):
self.verify_diffusion(p_gamma, corr_omega, kT,
eff_per_part_gamma_rot)
self.verify_diffusion(p_kT, corr_omega, per_part_kT,
eff_gamma_rot)
self.verify_diffusion(p_both, corr_omega, per_part_kT,
eff_per_part_gamma_rot)
kT = 1.37
dt = 0.05
system = espressomd.System(box_l=[1.0, 1.0, 1.0])
system.set_random_state_PRNG()
#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
np.random.seed(seed=system.seed)
p = system.part.add(pos=(0, 0, 0), id=0)
system.time_step = dt
system.thermostat.set_langevin(kT=kT, gamma=gamma, seed=42)
system.cell_system.skin = 0.4
system.integrator.run(1000)
pos_obs = ParticlePositions(ids=(0, ))
vel_obs = ParticleVelocities(ids=(0, ))
c_pos = Correlator(obs1=pos_obs,
tau_lin=16,
tau_max=100.,
delta_N=10,
corr_operation="square_distance_componentwise",
compress1="discard1")
c_vel = Correlator(obs1=vel_obs,
tau_lin=16,
tau_max=20.,
delta_N=1,
corr_operation="scalar_product",
compress1="discard1")
system.auto_update_accumulators.add(c_pos)
system.auto_update_accumulators.add(c_vel)
rotation=3 * [True],
rinertia=3 * [1.])
# Initialize the mean squared displacement (MSD) correlator
tmax = system.time_step * SAMP_STEPS
pos_id = ParticlePositions(ids=[0])
msd = Correlator(obs1=pos_id,
corr_operation="square_distance_componentwise",
delta_N=1,
tau_max=tmax,
tau_lin=16)
system.auto_update_accumulators.add(msd)
# Initialize the velocity auto-correlation function (VACF) correlator
vel_id = ParticleVelocities(ids=[0])
vacf = Correlator(obs1=vel_id,
corr_operation="scalar_product",
delta_N=1,
tau_max=tmax,
tau_lin=16)
system.auto_update_accumulators.add(vacf)
# Initialize the angular velocity auto-correlation function (AVACF)
# correlator
ang_id = ParticleAngularVelocities(ids=[0])
avacf = Correlator(obs1=ang_id,
corr_operation="scalar_product",
delta_N=1,
tau_max=tmax,
tau_lin=16)
def test_particle_coupling(self):
part_vel = ParticleVelocities(ids=list(range(100)))
mean_velocity = np.mean(part_vel.calculate())
self.assertGreater(mean_velocity, 1e-5)
system.cell_system.skin = 0.4
# Set up the DPD friction interaction
system.non_bonded_inter[0, 0].dpd.set_params(
weight_function=1, gamma=gamma, r_cut=r_cut,
trans_weight_function=0, trans_gamma=0, trans_r_cut=0)
# Set up the repulsive interaction
system.non_bonded_inter[0,0].hat.set_params(F_max=F_max, cutoff=r_cut)
# Warm up and equilibration
system.integrator.run(10000)
# Set up of correlators for positions and velocity
pos_obs = ParticlePositions(ids=(np.arange(n_part)))
vel_obs = ParticleVelocities(ids=(np.arange(n_part)))
c_pos = Correlator(obs1=pos_obs, tau_lin=16, tau_max=10000., delta_N=10,
corr_operation="square_distance_componentwise",
compress1="discard1")
c_vel = Correlator(obs1=vel_obs, tau_lin=16, tau_max=10., delta_N=1,
corr_operation="scalar_product", compress1="discard1")
system.auto_update_accumulators.add(c_pos)
system.auto_update_accumulators.add(c_vel)
# Open h5md file
h5 = h5md.H5md(filename="./trajectory.h5", write_pos=True, write_lees_edwards_offset = True, write_vel = True, write_ordered=True)
for i in range(args.samples):
print(i, flush=True)
gamma = 2.4
kT = 1.37
dt = 0.05
system = espressomd.System(box_l=[1.0, 1.0, 1.0])
np.random.seed(seed=42)
p = system.part.add(pos=(0, 0, 0))
system.time_step = dt
system.thermostat.set_langevin(kT=kT, gamma=gamma, seed=42)
system.cell_system.skin = 0.4
system.integrator.run(1000)
pos_obs = ParticlePositions(ids=(p.id, ))
vel_obs = ParticleVelocities(ids=(p.id, ))
c_pos = Correlator(obs1=pos_obs,
tau_lin=16,
tau_max=100.,
delta_N=10,
corr_operation="square_distance_componentwise",
compress1="discard1")
c_vel = Correlator(obs1=vel_obs,
tau_lin=16,
tau_max=20.,
delta_N=1,
corr_operation="scalar_product",
compress1="discard1")
system.auto_update_accumulators.add(c_pos)
system.auto_update_accumulators.add(c_vel)