def test_zz_lj(self):
"""
Simulate an LJ liquid under linear shear and verify forces.
This is to make sure that no pairs get lost or are outdated
in the short range loop. To have deterministic forces, velocity
capping is used rather than a thermostat.
"""
system = self.system
self.setup_lj_liquid()
system.lees_edwards.protocol = espressomd.lees_edwards.LinearShear(
shear_velocity=0.3, initial_pos_offset=0.01)
system.lees_edwards.shear_direction = 2
system.lees_edwards.shear_plane_normal = 0
system.integrator.run(1, recalc_forces=True)
tests_common.check_non_bonded_loop_trace(system)
# Rewind the clock to get back the LE offset applied during force calc
system.time = system.time - system.time_step
tests_common.verify_lj_forces(system, 1E-7)
system.thermostat.set_langevin(kT=.1, gamma=5, seed=2)
system.integrator.run(50)
tests_common.check_non_bonded_loop_trace(system)
def run_test_lj(self):
"""This fills the system with vs-based dumbells, adds a lj potential,
integrates and verifies forces. This is to make sure that no pairs
get lost or are outdated in the short range loop"""
system = self.system
system.virtual_sites = VirtualSitesRelative()
# Parameters
n = 90
phi = 0.6
sigma = 1.
eps = .025
cut = sigma * 2**(1. / 6.)
kT = 2
gamma = .5
# box
l = (n / 6. * np.pi * sigma**3 / phi)**(1. / 3.)
# Setup
system.box_l = [l, l, l]
system.min_global_cut = 0.501
system.part.clear()
system.time_step = 0.01
system.thermostat.turn_off()
# Dumbells consist of 2 virtual lj spheres + central particle w/o interactions
# For n spheres, n/2 dumbells.
for i in range(int(n / 2)):
# Type=1, i.e., no lj ia for the center of mass particles
system.part.add(rotation=(1, 1, 1),
id=3 * i,
pos=random.random(3) * l,
type=1,
omega_lab=0.3 * random.random(3),
v=random.random(3))
# lj spheres
system.part.add(rotation=(1, 1, 1),
id=3 * i + 1,
pos=system.part[3 * i].pos +
system.part[3 * i].director / 2.,
type=0)
system.part.add(rotation=(1, 1, 1),
id=3 * i + 2,
pos=system.part[3 * i].pos -
system.part[3 * i].director / 2.,
type=0)
system.part[3 * i + 1].vs_auto_relate_to(3 * i)
self.verify_vs(system.part[3 * i + 1], verify_velocity=False)
system.part[3 * i + 2].vs_auto_relate_to(3 * i)
self.verify_vs(system.part[3 * i + 2], verify_velocity=False)
system.integrator.run(0, recalc_forces=True)
# interactions
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=eps,
sigma=sigma,
cutoff=cut,
shift="auto")
# Remove overlap
system.integrator.set_steepest_descent(f_max=0,
gamma=0.1,
max_displacement=0.1)
while system.analysis.energy()["total"] > 10 * n:
system.integrator.run(20)
# Integrate
system.integrator.set_vv()
for i in range(10):
# Langevin to maintain stability
system.thermostat.set_langevin(kT=kT, gamma=gamma, seed=42)
system.integrator.run(50)
system.thermostat.turn_off()
# Constant energy to get rid of thermostat forces in the
# verification
system.integrator.run(2)
# Check the virtual sites config,pos and vel of the lj spheres
for j in range(int(n / 2)):
self.verify_vs(system.part[3 * j + 1])
self.verify_vs(system.part[3 * j + 2])
# Verify lj forces on the particles. The non-virtual particles are
# skipped because the forces on them originate from the vss and not
# the lj interaction
verify_lj_forces(system, 1E-10,
3 * np.arange(int(n / 2), dtype=int))
# Test applying changes
enegry_pre_change = system.analysis.energy()['total']
pressure_pre_change = system.analysis.pressure()['total']
system.part[0].pos = system.part[0].pos + (2.2, -1.4, 4.2)
enegry_post_change = system.analysis.energy()['total']
pressure_post_change = system.analysis.pressure()['total']
self.assertNotAlmostEqual(enegry_pre_change, enegry_post_change)
self.assertNotAlmostEqual(pressure_pre_change, pressure_post_change)
# Turn off lj interaction
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=0,
sigma=0,
cutoff=0,
shift=0)