def test_fene(self):
# system parameters
box_l = 10.0
system.box_l = [box_l, box_l, box_l]
skin = 0.4
time_step = 0.01
system.time_step = time_step
# thermostat and cell system
system.cell_system.skin = skin
system.periodicity = [1, 1, 1]
# particles and bond
system.part.add(
id=0, pos=[9.9, 9.75, 9.9], type=0, mol_id=0, fix=[1, 1, 1])
system.part.add(
id=1, pos=[9.9, 10.25, 9.9], type=0, mol_id=0, fix=[1, 1, 1])
k = 1e4
d_r_max = 1.5
r_0 = 0.1
fene = FeneBond(k=k, d_r_max=d_r_max, r_0=r_0)
system.bonded_inter.add(fene)
system.part[0].add_bond((fene, 1))
system.integrator.run(steps=0)
sim_stress_bonded = system.analysis.stress_tensor()['bonded']
sim_stress_fene = system.analysis.stress_tensor()[
'bonded', len(system.bonded_inter) - 1]
total_bonded_stresses = np.zeros([3, 3])
for i in range(len(system.bonded_inter)):
total_bonded_stresses = np.add(
total_bonded_stresses, system.analysis.stress_tensor()['bonded', i])
anal_stress_fene = self.get_anal_stress_fene(
system.part[0].pos, system.part[1].pos, k, d_r_max, r_0)
self.assertTrue(np.max(np.abs(sim_stress_bonded - anal_stress_fene))
< tol, 'bonded stress does not match analytical result')
self.assertTrue(np.max(np.abs(sim_stress_fene - anal_stress_fene))
< tol, 'bonded stress for fene does not match analytical result')
self.assertTrue(np.max(np.abs(sim_stress_bonded - total_bonded_stresses))
< tol, 'bonded stresses do not sum up to the total value')
sim_pressure_fene = system.analysis.pressure()[
'bonded', len(system.bonded_inter) - 1]
anal_pressure_fene = np.einsum("ii", anal_stress_fene) / 3.0
self.assertTrue(np.max(np.abs(sim_pressure_fene - anal_pressure_fene))
< tol, 'bonded pressure for fene does not match analytical result')
# Compare stress tensor observable to stress tensor from analysis
np.testing.assert_allclose(
StressTensor().calculate(),
system.analysis.stress_tensor()["total"].reshape(9),
atol=1E-10)
system.part.clear()
def test(self):
# system parameters
system.box_l = 3 * [10.0]
skin = 0.4
time_step = 0.01
system.time_step = time_step
# thermostat and cell system
system.thermostat.set_langevin(kT=0.0, gamma=1.0, seed=41)
system.cell_system.skin = skin
system.periodicity = [1, 1, 1]
# particles and bond
system.part.add(id=0, pos=[9.9, 9.75, 9.9], type=0, mol_id=0)
system.part.add(id=1, pos=[9.9, 10.25, 9.9], type=0, mol_id=0)
system.part.add(id=2, pos=[0.1, 9.7, 0.1], type=1, mol_id=1)
system.part.add(id=3, pos=[0.1, 10.3, 0.1], type=2, mol_id=2)
harmonic = HarmonicBond(k=1e4, r_0=0)
system.bonded_inter.add(harmonic)
system.part[0].add_bond((harmonic, 1))
system.part[2].add_bond((harmonic, 3))
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=2.0,
shift=0)
system.non_bonded_inter[1, 2].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=2.0,
shift=0)
system.integrator.run(steps=0)
system.part[0].v = [10.0, 20.0, 30.0]
system.part[1].v = [-15, -25, -35]
system.part[2].v = [27.0, 23.0, 17.0]
system.part[3].v = [13.0, 11.0, 19.0]
pos = system.part[:].pos
vel = system.part[:].v
sim_stress_kinetic = system.analysis.stress_tensor()['kinetic']
sim_stress_bonded = system.analysis.stress_tensor()['bonded']
sim_stress_bonded_harmonic = system.analysis.stress_tensor()[
'bonded', len(system.bonded_inter) - 1]
sim_stress_nonbonded = system.analysis.stress_tensor()['non_bonded']
sim_stress_nonbonded_inter = system.analysis.stress_tensor(
)['non_bonded_inter']
sim_stress_nonbonded_inter12 = system.analysis.stress_tensor()[
'non_bonded_inter', 1, 2]
sim_stress_nonbonded_intra = system.analysis.stress_tensor(
)['non_bonded_intra']
sim_stress_nonbonded_intra00 = system.analysis.stress_tensor()[
'non_bonded_intra', 0, 0]
sim_stress_total = system.analysis.stress_tensor()['total']
sim_pressure_kinetic = system.analysis.pressure()['kinetic']
sim_pressure_bonded = system.analysis.pressure()['bonded']
sim_pressure_bonded_harmonic = system.analysis.pressure()[
'bonded', len(system.bonded_inter) - 1]
sim_pressure_nonbonded = system.analysis.pressure()['non_bonded']
sim_pressure_nonbonded_inter = system.analysis.pressure(
)['non_bonded_inter']
sim_pressure_nonbonded_inter12 = system.analysis.pressure()[
'non_bonded_inter', 1, 2]
sim_pressure_nonbonded_intra = system.analysis.pressure(
)['non_bonded_intra']
sim_pressure_nonbonded_intra00 = system.analysis.pressure()[
'non_bonded_intra', 0, 0]
sim_pressure_total = system.analysis.pressure()['total']
anal_stress_kinetic = stress_kinetic(vel)
anal_stress_bonded = stress_bonded(pos)
anal_stress_nonbonded = stress_nonbonded(system.part.pairs())
anal_stress_nonbonded_inter = stress_nonbonded_inter(
system.part.pairs())
anal_stress_nonbonded_intra = stress_nonbonded_intra(
system.part.pairs())
anal_stress_total = anal_stress_kinetic + \
anal_stress_bonded + anal_stress_nonbonded
anal_pressure_kinetic = np.einsum('ii', anal_stress_kinetic) / 3.0
anal_pressure_bonded = np.einsum('ii', anal_stress_bonded) / 3.0
anal_pressure_nonbonded = np.einsum('ii', anal_stress_nonbonded) / 3.0
anal_pressure_nonbonded_inter = np.einsum(
'ii', anal_stress_nonbonded_inter) / 3.0
anal_pressure_nonbonded_intra = np.einsum(
'ii', anal_stress_nonbonded_intra) / 3.0
anal_pressure_total = anal_pressure_kinetic + \
anal_pressure_bonded + anal_pressure_nonbonded
system.part.clear()
self.assertTrue(
np.max(np.abs(sim_stress_kinetic - anal_stress_kinetic)) < tol,
'kinetic stress does not match analytical result')
self.assertTrue(
np.max(np.abs(sim_stress_bonded - anal_stress_bonded)) < tol,
'bonded stress does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_stress_bonded_harmonic - anal_stress_bonded)) < tol,
'bonded stress harmonic bond does not match analytical result')
self.assertTrue(
np.max(np.abs(sim_stress_nonbonded - anal_stress_nonbonded)) < tol,
'non-bonded stress does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_inter -
anal_stress_nonbonded_inter)) < tol,
'non-bonded intermolecular stress does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_inter12 -
anal_stress_nonbonded_inter)) < tol,
'non-bonded intermolecular stress molecules 1 and 2 does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_intra -
anal_stress_nonbonded_intra)) < tol,
'non-bonded intramolecular stress does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_intra00 -
anal_stress_nonbonded_intra)) < tol,
'non-bonded intramolecular stress molecule 0 does not match analytical result'
)
self.assertTrue(
np.max(np.abs(sim_stress_total - anal_stress_total)) < tol,
'total stress does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_stress_total - sim_stress_kinetic -
sim_stress_bonded - sim_stress_nonbonded)) < tol,
'total stress is not given as the sum of all major stress components'
)
self.assertTrue(
np.abs(sim_pressure_kinetic - anal_pressure_kinetic) < tol,
'kinetic pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_bonded - anal_pressure_bonded) < tol,
'bonded pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_bonded_harmonic - anal_pressure_bonded) < tol,
'bonded pressure harmonic bond does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_nonbonded - anal_pressure_nonbonded) < tol,
'non-bonded pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_nonbonded_inter -
anal_pressure_nonbonded_inter) < tol,
'non-bonded intermolecular pressure does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_inter12 -
anal_pressure_nonbonded_inter) < tol,
'non-bonded intermolecular pressure molecule 1 and 2 does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_intra -
anal_pressure_nonbonded_intra) < tol,
'non-bonded intramolecular pressure does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_intra00 -
anal_pressure_nonbonded_intra) < tol,
'non-bonded intramolecular pressure molecule 0 does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_total - anal_pressure_total) < tol,
'total pressure does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_pressure_total - sim_pressure_kinetic -
sim_pressure_bonded - sim_pressure_nonbonded)) < tol,
'total pressure is not given as the sum of all major pressure components'
)
# Compare stress tensor observable to stress tensor from analysis
np.testing.assert_allclose(
StressTensor().calculate(),
system.analysis.stress_tensor()["total"].reshape(9),
atol=1E-10)
def test(self):
# system parameters
box_l = 10.0
system.box_l = [box_l, box_l, box_l]
skin = 0.4
time_step = 0.01
system.time_step = time_step
# thermostat and cell system
system.thermostat.set_langevin(kT=0.0, gamma=1.0)
system.cell_system.skin = skin
system.periodicity = [1, 1, 1]
# particles and bond
system.part.add(id=0, pos=[9.9, 9.75, 9.9], type=0, mol_id=0)
system.part.add(id=1, pos=[9.9, 10.25, 9.9], type=0, mol_id=0)
system.part.add(id=2, pos=[0.1, 9.7, 0.1], type=1, mol_id=1)
system.part.add(id=3, pos=[0.1, 10.3, 0.1], type=2, mol_id=2)
harmonic = HarmonicBond(k=1e4, r_0=0)
system.bonded_inter.add(harmonic)
system.part[0].add_bond((harmonic, 1))
system.part[2].add_bond((harmonic, 3))
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=2.0,
shift=0)
system.non_bonded_inter[1, 2].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=2.0,
shift=0)
# calculate forces and stress with Lees-Edwards offset
le_offset = 0.3
system.lees_edwards_offset = le_offset
system.integrator.run(steps=0)
system.part[0].v = [10.0, 20.0, 30.0]
system.part[1].v = [-15, -25, -35]
system.part[2].v = [27.0, 23.0, 17.0]
system.part[3].v = [13.0, 11.0, 19.0]
pos = system.part[:].pos
vel = system.part[:].v
sim_stress_kinetic = system.analysis.stress_tensor()['kinetic']
sim_stress_bonded = system.analysis.stress_tensor()['bonded']
sim_stress_bonded_harmonic = system.analysis.stress_tensor()[
'bonded', len(system.bonded_inter) - 1]
sim_stress_nonbonded = system.analysis.stress_tensor()['non_bonded']
sim_stress_nonbonded_inter = system.analysis.stress_tensor(
)['non_bonded_inter']
sim_stress_nonbonded_inter12 = system.analysis.stress_tensor()[
'non_bonded_inter', 1, 2]
sim_stress_nonbonded_intra = system.analysis.stress_tensor(
)['non_bonded_intra']
sim_stress_nonbonded_intra00 = system.analysis.stress_tensor()[
'non_bonded_intra', 0, 0]
sim_stress_total = system.analysis.stress_tensor()['total']
sim_pressure_kinetic = system.analysis.pressure()['kinetic']
sim_pressure_bonded = system.analysis.pressure()['bonded']
sim_pressure_bonded_harmonic = system.analysis.pressure()[
'bonded', len(system.bonded_inter) - 1]
sim_pressure_nonbonded = system.analysis.pressure()['non_bonded']
sim_pressure_nonbonded_inter = system.analysis.pressure(
)['non_bonded_inter']
sim_pressure_nonbonded_inter12 = system.analysis.pressure()[
'non_bonded_inter', 1, 2]
sim_pressure_nonbonded_intra = system.analysis.pressure(
)['non_bonded_intra']
sim_pressure_nonbonded_intra00 = system.analysis.pressure()[
'non_bonded_intra', 0, 0]
sim_pressure_total = system.analysis.pressure()['total']
anal_stress_kinetic = stress_kinetic(vel, box_l)
anal_stress_bonded = stress_bonded(pos, box_l)
anal_stress_nonbonded = stress_nonbonded(system.part.pairs(), box_l)
anal_stress_nonbonded_inter = stress_nonbonded_inter(
system.part.pairs(), box_l)
anal_stress_nonbonded_intra = stress_nonbonded_intra(
system.part.pairs(), box_l)
anal_stress_total = anal_stress_kinetic + anal_stress_bonded + anal_stress_nonbonded
anal_pressure_kinetic = np.einsum('ii', anal_stress_kinetic) / 3.0
anal_pressure_bonded = np.einsum('ii', anal_stress_bonded) / 3.0
anal_pressure_nonbonded = np.einsum('ii', anal_stress_nonbonded) / 3.0
anal_pressure_nonbonded_inter = np.einsum(
'ii', anal_stress_nonbonded_inter) / 3.0
anal_pressure_nonbonded_intra = np.einsum(
'ii', anal_stress_nonbonded_intra) / 3.0
anal_pressure_total = anal_pressure_kinetic + anal_pressure_bonded + anal_pressure_nonbonded
print('le_offset = {}'.format(system.lees_edwards_offset))
print('particle positions')
print(pos)
print('particle velocities')
print(vel)
print('\nsimulated kinetic pressure=')
print(sim_pressure_kinetic)
print('analytical kinetic pressure=')
print(anal_pressure_kinetic)
print('\nsimulated bonded pressure=')
print(sim_pressure_bonded)
print('analytical bonded pressure=')
print(anal_pressure_bonded)
print('\nsimulated bonded pressure harmonic bond=')
print(sim_pressure_bonded_harmonic)
print('analytical bonded pressure harmonic bond=')
print(anal_pressure_bonded)
print('\nsimulated non-bonded pressure=')
print(sim_pressure_nonbonded)
print('analytic non-bonded pressure=')
print(anal_pressure_nonbonded)
print('\nsimulated non-bonded intermolecular pressure=')
print(sim_pressure_nonbonded_inter)
print('analytic non-bonded intermolecular pressure=')
print(anal_pressure_nonbonded_inter)
print(
'\nsimulated non-bonded intermolecular pressure molecule 1 and 2=')
print(sim_pressure_nonbonded_inter12)
print('analytic non-bonded intermolecular pressure molecule 1 and 2=')
print(anal_pressure_nonbonded_inter)
print('\nsimulated non-bonded intramolecular pressure=')
print(sim_pressure_nonbonded_intra)
print('analytic non-bonded intramolecular pressure=')
print(anal_pressure_nonbonded_intra)
print('\nsimulated non-bonded intramolecular pressure molecule 0=')
print(sim_pressure_nonbonded_intra00)
print('analytic non-bonded intramolecular pressure molecule 0=')
print(anal_pressure_nonbonded_intra)
print('\nsimulated total pressure=')
print(sim_pressure_total)
print('analytic total pressure=')
print(anal_pressure_total)
print('\nsimulated kinetic stress=')
print(sim_stress_kinetic)
print('analytic kinetic stress=')
print(anal_stress_kinetic)
print('\nsimulated bonded stress=')
print(sim_stress_bonded)
print('analytic bonded stress=')
print(anal_stress_bonded)
print('\nsimulated bonded stress harmonic bond=')
print(sim_stress_bonded_harmonic)
print('analytic bonded stress harmonic bond=')
print(anal_stress_bonded)
print('\nsimulated non-bonded stress=')
print(sim_stress_nonbonded)
print('analytic non-bonded stress=')
print(anal_stress_nonbonded)
print('\nsimulated non-bonded intermolecular stress=')
print(sim_stress_nonbonded_inter)
print('analytic non-bonded intermolecular stress=')
print(anal_stress_nonbonded_inter)
print(
'\nsimulated non-bonded intermolecular stress between molecule 1 and 2='
)
print(sim_stress_nonbonded_inter12)
print(
'analytic non-bonded intermolecular stress between molecule 1 and 2='
)
print(anal_stress_nonbonded_inter)
print('\nsimulated total non-bonded intramolecular stress=')
print(sim_stress_nonbonded_intra)
print('analytic total non-bonded intramolecular stress=')
print(anal_stress_nonbonded_intra)
print('\nsimulated non-bonded intramolecular stress molecule 0=')
print(sim_stress_nonbonded_intra00)
print('analytic non-bonded intramolecular stress molecule 0=')
print(anal_stress_nonbonded_intra)
print('\nsimulated total stress=')
print(sim_stress_total)
print('analytic total stress=')
print(anal_stress_total)
system.part.clear()
self.assertTrue(
np.max(np.abs(sim_stress_kinetic - anal_stress_kinetic)) < tol,
'kinetic stress does not match analytical result')
self.assertTrue(
np.max(np.abs(sim_stress_bonded - anal_stress_bonded)) < tol,
'bonded stress does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_stress_bonded_harmonic - anal_stress_bonded)) < tol,
'bonded stress harmonic bond does not match analytical result')
self.assertTrue(
np.max(np.abs(sim_stress_nonbonded - anal_stress_nonbonded)) < tol,
'non-bonded stress does not match analytical result')
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_inter -
anal_stress_nonbonded_inter)) < tol,
'non-bonded intermolecular stress does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_inter12 -
anal_stress_nonbonded_inter)) < tol,
'non-bonded intermolecular stress molecules 1 and 2 does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_intra -
anal_stress_nonbonded_intra)) < tol,
'non-bonded intramolecular stress does not match analytical result'
)
self.assertTrue(
np.max(
np.abs(sim_stress_nonbonded_intra00 -
anal_stress_nonbonded_intra)) < tol,
'non-bonded intramolecular stress molecule 0 does not match analytical result'
)
self.assertTrue(
np.max(np.abs(sim_stress_total - anal_stress_total)) < tol,
'total stress does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_kinetic - anal_pressure_kinetic) < tol,
'kinetic pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_bonded - anal_pressure_bonded) < tol,
'bonded pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_bonded_harmonic - anal_pressure_bonded) < tol,
'bonded pressure harmonic bond does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_nonbonded - anal_pressure_nonbonded) < tol,
'non-bonded pressure does not match analytical result')
self.assertTrue(
np.abs(sim_pressure_nonbonded_inter -
anal_pressure_nonbonded_inter) < tol,
'non-bonded intermolecular pressure does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_inter12 -
anal_pressure_nonbonded_inter) < tol,
'non-bonded intermolecular pressure molecule 1 and 2 does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_intra -
anal_pressure_nonbonded_intra) < tol,
'non-bonded intramolecular pressure does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_nonbonded_intra00 -
anal_pressure_nonbonded_intra) < tol,
'non-bonded intramolecular pressure molecule 0 does not match analytical result'
)
self.assertTrue(
np.abs(sim_pressure_total - anal_pressure_total) < tol,
'total pressure does not match analytical result')
# Compare stress tensor observable to stress tensor from analysis
np.testing.assert_allclose(
StressTensor().calculate(),
system.analysis.stress_tensor()["total"].reshape(9),
atol=1E-10)