class MagnetostaticsInteractionsTests(ut.TestCase):
# Handle to espresso system
system = espressomd.System()
def setUp(self):
self.system.box_l = 10, 10, 10
if not self.system.part.exists(0):
self.system.part.add(id=0, pos=(0.1, 0.1, 0.1), dip=(1.3, 2.1, -6))
if not self.system.part.exists(1):
self.system.part.add(id=1, pos=(0, 0, 0), dip=(7.3, 6.1, -4))
if "DP3M" in espressomd.features():
test_DP3M = generate_test_for_class(
DipolarP3M,
dict(prefactor=1.0,
epsilon=0.0,
inter=1000,
mesh_off=[0.5, 0.5, 0.5],
r_cut=2.4,
mesh=[8, 8, 8],
cao=1,
alpha=12,
accuracy=0.01))
if "DIPOLAR_DIRECT_SUM" in espressomd.features():
test_DdsCpu = generate_test_for_class(DipolarDirectSumCpu,
dict(prefactor=3.4))
test_DdsRCpu = generate_test_for_class(
DipolarDirectSumWithReplicaCpu, dict(prefactor=3.4, n_replica=2))
class ewald_GPU_test(ut.TestCase):
if "ELECTROSTATICS" in espressomd.features(
) and "CUDA" in espressomd.features(
) and "EWALD_GPU" in espressomd.features():
from espressomd.electrostatics import EwaldGpu
def runTest(self):
es = espressomd.System()
test_params = {}
test_params["bjerrum_length"] = 2
test_params["num_kx"] = 2
test_params["num_ky"] = 2
test_params["num_kz"] = 2
test_params["K_max"] = 10
test_params["time_calc_steps"] = 100
test_params["rcut"] = 0.9
test_params["accuracy"] = 1e-1
test_params["precision"] = 1e-2
test_params["alpha"] = 3.5
ewald = EwaldGpu(**test_params)
es.actors.add(ewald)
self.assertTrue(
params_match(test_params, ewald._get_params_from_es_core()))
if __name__ == "__main__":
print("Features: ", espressomd.features())
ut.main()
class ElectrostaticInteractionsTests(ut.TestCase):
if "ELECTROSTATICS" in espressomd.features():
# Handle to espresso system
system = espressomd.System()
def setUp(self):
self.system.box_l = 10, 10, 10
if not self.system.part.exists(0):
self.system.part.add(id=0, pos=(2.0, 2.0, 2.0), q=1)
if not self.system.part.exists(1):
self.system.part.add(id=1, pos=(8.0, 8.0, 8.0), q=-1)
print("ut.TestCase setUp")
test_P3M = generate_test_for_class(system, P3M, dict(bjerrum_length=1.0,
epsilon=0.0,
inter=1000,
mesh_off=[0.5, 0.5, 0.5],
r_cut=2.4,
mesh=[2, 2, 2],
cao=1,
alpha=12,
accuracy=0.01,
tune=False))
if "COULOMB_DEBYE_HUECKEL" in espressomd.features():
test_CDH = generate_test_for_class(system, CDH, dict(bjerrum_length=1.0,
kappa=2.3,
r_cut=2,
r0=1,
r1=1.9,
eps_int=0.8,
eps_ext=1,
alpha=2))
class ElectrostaticInteractionsTests(ut.TestCase):
def setup(self):
self.system.box_l = 10, 10, 10
if not self.system.part.exists(0):
self.system.part.add(id=0, pos=(0.0, 0.0, 0.0), q=1)
if not self.system.part.exists(1):
self.system.part.add(id=1, pos=(0.1, 0.1, 0.1), q=-1)
test_P3M = generate_test_for_class(
P3M,
dict(bjerrum_length=1.0,
epsilon=0.0,
inter=1000,
mesh_off=[0.5, 0.5, 0.5],
r_cut=2.4,
mesh=[2, 2, 2],
cao=1,
alpha=12,
accuracy=0.01))
test_DH = generate_test_for_class(
DH, dict(bjerrum_length=1.0, kappa=2.3, r_cut=2))
if "CDG" in espressomd.features():
test_CDH = generate_test_for_class(
CDH,
dict(bjerrum_length=1.0,
kappa=2.3,
r_cut=2,
r0=1,
r1=2,
eps_int=0.8,
eps_ext=1,
alpha=2))
def check_dissipation(self, n):
"""
Check the dissipation relations: the simple viscous decelleration test.
Parameters
----------
n : :obj:`int`
Number of particles of the each type. There are 2 types.
"""
tol = 1.2E-3
for step in range(100):
self.system.integrator.run(2)
for i in range(n):
for k in range(2):
ind = i + k * n
for j in range(3):
# Note: velocity is defined in the lab frame of reference
# while gamma_tr is defined in the body one.
# Hence, only isotropic gamma_tran_p_validate could be
# tested here.
self.assertLess(
abs(self.system.part[ind].v[j] -
math.exp(-self.gamma_tran_p_validate[k, j] *
self.system.time / self.mass)), tol)
if "ROTATION" in espressomd.features():
self.assertLess(
abs(self.system.part[ind].omega_body[j] -
math.exp(-self.gamma_rot_p_validate[k, j] *
self.system.time / self.J[j])),
tol)
def test(self):
if "ROTATION" in espressomd.features():
n_test_cases = 5
else:
n_test_cases = 4
for i in range(n_test_cases):
self.run_test_case(i)
def setUp(self):
self.system.time = 0.0
self.system.part.clear()
if "BROWNIAN_DYNAMICS" in espressomd.features():
self.system.thermostat.turn_off()
# the default integrator is supposed implicitly
self.system.integrator.set_nvt()
def test(self):
if "CUDA" in espressomd.features():
system = espressomd.System(box_l=[1, 1, 1])
self.assertEqual(system.cuda_init_handle.device_list != {},
espressomd.gpu_available())
else:
self.assertFalse(espressomd.gpu_available())
def fluctuation_dissipation_param_setup(self,n):
"""
Setup the parameters for the following fluctuation-dissipation
test.
Parameters
----------
n : :obj:`int`
Number of particles of the each type. There are 2 types.
"""
## Time
self.es.time_step = 0.03
## Space
box = 10.0
self.es.box_l = box,box,box
if espressomd.has_features(("PARTIAL_PERIODIC",)):
self.es.periodicity = 0,0,0
## NVT thermostat
# Just some temperature range to cover by the test:
self.kT = self.generate_scalar_ranged_rnd(0.3,5)
# See the above comment regarding the gamma assignments.
# Note: here & hereinafter specific variations in these ranges are related to
# the test execution duration to achieve the required statistical averages faster.
self.gamma_global = self.generate_vec_ranged_rnd(0.5,2.0/3.0)
self.gamma_global_rot = self.generate_vec_ranged_rnd(0.2,20)
# Per-particle parameters
self.kT_p = 2.5,2.0
for k in range(2):
self.gamma_tran_p[k, :] = self.generate_vec_ranged_rnd(0.4,10.0)
self.gamma_rot_p[k, :] = self.generate_vec_ranged_rnd(0.2,20.0)
## Particles
# As far as the problem characteristic time is t0 ~ mass / gamma
# and the Langevin equation finite-difference approximation is stable
# only for time_step << t0, it is needed to set the mass higher than
# some minimal value according to the value min_mass_param.
# Also, it is expected to test the large enough mass (max_mass_param).
# It should be not very large, otherwise the thermalization will require
# too much of the CPU time.
min_mass_param = 0.2
max_mass_param = 7.0
self.mass = self.generate_scalar_ranged_rnd(min_mass_param,max_mass_param)
self.J = self.generate_vec_ranged_rnd(min_mass_param,max_mass_param)
for i in range(n):
for k in range(2):
ind = i + k * n
part_pos = np.random.random(3) * box
part_v = 0.0,0.0,0.0
part_omega_body = 0.0,0.0,0.0
self.es.part.add(rotation=(1,1,1), id=ind, mass=self.mass, rinertia=self.J,
pos=part_pos, v=part_v)
if "ROTATION" in espressomd.features():
self.es.part[ind].omega_body = part_omega_body
def rot_diffusion_param_setup(self, n):
"""
Setup the parameters for the rotational diffusion
test check_rot_diffusion().
Parameters
----------
n : :obj:`int`
Number of particles.
"""
# Time
# The time step should be less than t0 ~ mass / gamma
self.system.time_step = 3E-3
# Space
box = 10.0
self.system.box_l = box, box, box
if espressomd.has_features(("PARTIAL_PERIODIC", )):
self.system.periodicity = 0, 0, 0
# NVT thermostat
# Just some temperature range to cover by the test:
self.kT = uniform(1.5, 6.5)
# Note: here & hereinafter specific variations in the random parameter ranges are related to
# the test execution duration to achieve the required statistical averages faster.
# The friction gamma_global should be large enough in order to have the small enough D ~ kT / gamma and
# to observe the details of the original rotational diffusion: the Perrin1936 (see the reference below) tests are visible
# only when the diffusive rotation is ~pi due to the exponential temporal dependencies (see the equations referred in the check_rot_diffusion()).
# Also, t0 ~ J / gamma should be small enough
# in order to remove the small-time-scale diffusion effects which do not fit the Perrin1936's
# tests which are based on the partial differential equation (eq. (68), Perrin1934) leading only to the simple
# classical Einstein-Smoluchowski equations of the diffusion
# in a contrast of the eq. (10.2.26) [N. Pottier,
# https://doi.org/10.1007/s10955-010-0114-6 (2010)].
self.gamma_global = 1E2 * uniform(0.35, 1.05, (3))
# Particles
# As far as the problem characteristic time is t0 ~ J / gamma
# and the Langevin equation finite-difference approximation is stable
# only for time_step << t0, it is needed to set the moment of inertia higher than
# some minimal value.
# Also, it is expected to test the large enough J.
# It should be not very large, otherwise the thermalization will require
# too much of the CPU time: the in silico time should clock over the
# t0.
self.J = uniform(1.5, 16.5, (3))
for ind in range(n):
part_pos = np.random.random(3) * box
self.system.part.add(rotation=(1, 1, 1),
id=ind,
rinertia=self.J,
pos=part_pos)
if "ROTATION" in espressomd.features():
self.system.part[ind].omega_body = 0.0, 0.0, 0.0
def check_dissipation(self):
"""
Check the dissipation relations: the simple viscous decelleration test.
"""
tol = 1.25E-4
for i in range(100):
for k in range(2):
for j in range(3):
# Note: velocity is defined in the lab frame of reference
# while gamma_tr is defined in the body one.
# Hence, only isotropic gamma_tran_p_validate could be tested here.
self.assertLess(
abs(self.es.part[k].v[j] - math.exp(- self.gamma_tran_p_validate[k, j] * self.es.time / self.mass)), tol)
if "ROTATION" in espressomd.features():
self.assertLess(abs(
self.es.part[k].omega_body[j] - math.exp(- self.gamma_rot_p_validate[k, j] * self.es.time / self.J[j])), tol)
def set_particle_specific_gamma(self,n):
"""
Set the particle-specific gamma.
Parameters
----------
n : :obj:`int`
Number of particles of the each type. There are 2 types.
"""
for k in range(2):
self.gamma_tran_p_validate[k, :] = self.gamma_tran_p[k, :]
self.gamma_rot_p_validate[k, :] = self.gamma_rot_p[k, :]
for i in range(n):
ind = i + k * n
self.es.part[ind].gamma = self.gamma_tran_p[k, :]
if "ROTATION" in espressomd.features():
self.es.part[ind].gamma_rot = self.gamma_rot_p[k, :]
def test_configure_and_import(self):
with tempfile.TemporaryDirectory() as temp_dir:
path_in = pathlib.Path(temp_dir) / "sample.py"
path_out = pathlib.Path(temp_dir) / "sample_test_processed.py"
path_features = pathlib.Path(temp_dir) / "sample_impossible.py"
# test importing a simple sample
sys.argv.append("42")
sys_argv_ref = list(sys.argv)
path_in.write_text("""
import sys
from argparse import ArgumentParser
value = 42
argv = list(sys.argv)
import espressomd.visualization
""")
sample, _ = iw.configure_and_import(
path_in, move_to_script_dir=False, cmd_arguments=["TestCase"],
gpu=False, script_suffix="test", value=43)
self.assertEqual(sys.argv, sys_argv_ref)
self.assertEqual(sample.argv, [path_in.name, "TestCase"])
self.assertTrue(path_out.exists(), f"File {path_out} not found")
self.assertEqual(sample.value, 43)
self.assertIn(
"espressomd.visualization = unittest.mock.MagicMock()",
path_out.read_text())
# test importing a sample that relies on features not compiled in
inactive_features = espressomd.all_features() - set(espressomd.features())
if inactive_features:
path_features.write_text(f"""
import espressomd
espressomd.assert_features({list(inactive_features)})
""")
module, _ = iw.configure_and_import(path_features)
self.assertIsInstance(module, ut.mock.MagicMock)
# importing a valid sample is impossible after a failed import
sample, _ = iw.configure_and_import(
path_in, move_to_script_dir=True, script_suffix="test",
cmd_arguments=["TestCase"], gpu=False, value=43)
self.assertIsInstance(sample, ut.mock.MagicMock)
def run_test_case(self, test_case):
seed(1)
# Decelleration
self.es.time_step = 0.007
self.es.part.clear()
# gamma_tran/gamma_rot matrix: [2 types of particless] x [3 dimensions
# X Y Z]
gamma_tran = np.zeros((2, 3))
gamma_tr = np.zeros((2, 3))
gamma_rot = np.zeros((2, 3))
gamma_rot_validate = np.zeros((2, 3))
# The translational gamma isotropy is required here. See comments below.
# Global gamma for tests without particle-specific gammas:
# gamma_global = np.ones((3))
gamma_global = np.zeros((3))
gamma_global[0] = np.array((0.5 + np.random.random()) * 2.0 / 3.0)
gamma_global[1] = gamma_global[0]
gamma_global[2] = gamma_global[0]
# Additional test case (5th) for the specific global rotational gamma set.
gamma_global_rot = np.array((0.5 + np.random.random(3)) * 2.0 / 3.0)
# Per-paricle values for the remaining decelleration tests:
# Either translational friction isotropy is required
# or both translational and rotational ones.
# Otherwise these types of motion will interfere.
# ..Let's test both cases depending on the particle index.
gamma_tran[0, 0] = np.array(0.5 + np.random.random())
gamma_tran[0, 1] = gamma_tran[0, 0]
gamma_tran[0, 2] = gamma_tran[0, 0]
gamma_rot[0, :] = np.array((0.5 + random(3)) * 2.0 / 3.0)
gamma_tran[1, 0] = np.array(0.5 + np.random.random())
gamma_tran[1, 1] = gamma_tran[1, 0]
gamma_tran[1, 2] = gamma_tran[1, 0]
gamma_rot[1, 0] = np.array((0.5 + np.random.random()) * 2.0 / 3.0)
gamma_rot[1, 1] = gamma_rot[1, 0]
gamma_rot[1, 2] = gamma_rot[1, 0]
if test_case != 4:
self.es.thermostat.set_langevin(
kT=0.0,
gamma=[
gamma_global[0],
gamma_global[1],
gamma_global[2]])
else:
self.es.thermostat.set_langevin(
kT=0.0,
gamma=[
gamma_global[0],
gamma_global[1],
gamma_global[2]],
gamma_rotation=[
gamma_global_rot[0],
gamma_global_rot[1],
gamma_global_rot[2]])
self.es.cell_system.skin = 5.0
mass = 12.74
J = [10.0, 10.0, 10.0]
for i in range(len(self.es.part)):
self.es.part[i].remove()
for i in range(2):
self.es.part.add(rotation=(1,1,1), pos=np.array([0.0, 0.0, 0.0]), id=i)
self.es.part[i].v = np.array([1.0, 1.0, 1.0])
if "ROTATION" in espressomd.features():
self.es.part[i].omega_body = np.array([1.0, 1.0, 1.0])
self.es.part[i].mass = mass
self.es.part[i].rinertia = np.array(J)
print("\n")
for k in range(2):
if test_case == 0:
if (k == 0):
print("------------------------------------------------")
print("Test " + str(test_case) + ": no particle specific values")
print("------------------------------------------------")
# No assignments are needed.
if test_case == 1:
if (k == 0):
print("------------------------------------------------")
print("Test " + str(test_case) +
": particle specific gamma but not temperature")
print("------------------------------------------------")
self.es.part[k].gamma = gamma_tran[k, :]
if "ROTATION" in espressomd.features():
self.es.part[k].gamma_rot = gamma_rot[k, :]
if test_case == 2:
if (k == 0):
print("------------------------------------------------")
print("Test " + str(test_case) +
": particle specific temperature but not gamma")
print("------------------------------------------------")
self.es.part[k].temp = 0.0
if test_case == 3:
if (k == 0):
print("------------------------------------------------")
print("Test " + str(test_case) +
": both particle specific gamma and temperature")
print("------------------------------------------------")
self.es.part[k].temp = 0.0
self.es.part[k].gamma = gamma_tran[k, :]
if "ROTATION" in espressomd.features():
self.es.part[k].gamma_rot = gamma_rot[k, :]
if test_case == 4:
if (k == 0):
print("------------------------------------------------")
print("Test " + str(test_case) + ": no particle specific values.")
print("Rotational specific global thermostat")
print("------------------------------------------------")
# No assignments are needed.
if test_case == 1 or test_case == 3:
gamma_tr = gamma_tran
gamma_rot_validate = gamma_rot
else:
for k in range(2):
gamma_tr[k, :] = gamma_global[:]
if test_case != 4:
gamma_rot_validate[k, :] = gamma_global[:]
else:
gamma_rot_validate[k, :] = gamma_global_rot[:]
self.es.time = 0.0
tol = 1.25E-4
for i in range(100):
for k in range(2):
for j in range(3):
# Note: velocity is defined in the lab frame of reference
# while gamma_tr is defined in the body one.
# Hence, only isotropic gamma_tr could be tested here.
self.assertLess(
abs(self.es.part[k].v[j] - math.exp(- gamma_tr[k, j] * self.es.time / mass)), tol)
if "ROTATION" in espressomd.features():
self.assertLess(abs(
self.es.part[k].omega_body[j] - math.exp(- gamma_rot_validate[k, j] * self.es.time / J[j])), tol)
for i in range(len(self.es.part)):
self.es.part[i].remove()
# thermalization
# Checks if every degree of freedom has 1/2 kT of energy, even when
# mass and inertia tensor are active
# 2 different langevin parameters for particles
temp = np.array([2.5, 2.0])
D_tr = np.zeros((2, 3))
for k in range(2):
gamma_tran[k, :] = np.array((0.4 + np.random.random(3)) * 10)
gamma_rot[k, :] = np.array((0.2 + np.random.random(3)) * 20)
box = 10.0
self.es.box_l = [box, box, box]
if espressomd.has_features(("PARTIAL_PERIODIC",)):
self.es.periodicity = 0, 0, 0
# Random temperature
kT = (0.3 + np.random.random()) * 5
gamma_global = np.array((0.5 + np.random.random(3)) * 2.0 / 3.0)
gamma_global_rot = np.array((0.2 + np.random.random(3)) * 20)
if test_case == 2 or test_case == 3:
halfkT = temp / 2.0
else:
halfkT = np.array([kT, kT]) / 2.0
if test_case == 1 or test_case == 3:
gamma_tr = gamma_tran
else:
for k in range(2):
gamma_tr[k, :] = gamma_global[:]
# translational diffusion
for k in range(2):
D_tr[k, :] = 2.0 * halfkT[k] / gamma_tr[k, :]
if test_case != 4:
self.es.thermostat.set_langevin(
kT=kT,
gamma=[
gamma_global[0],
gamma_global[1],
gamma_global[2]])
else:
self.es.thermostat.set_langevin(
kT=kT,
gamma=[
gamma_global[0],
gamma_global[1],
gamma_global[2]],
gamma_rotation=[
gamma_global_rot[0],
gamma_global_rot[1],
gamma_global_rot[2]])
# no need to rebuild Verlet lists, avoid it
self.es.cell_system.skin = 5.0
self.es.time_step = 0.03
n = 200
mass = (0.2 + np.random.random()) * 7.0
J = np.array((0.2 + np.random.random(3)) * 7.0)
for i in range(n):
for k in range(2):
ind = i + k * n
part_pos = np.array(np.random.random(3) * box)
part_v = np.array([0.0, 0.0, 0.0])
part_omega_body = np.array([0.0, 0.0, 0.0])
self.es.part.add(rotation=(1,1,1), id=ind, mass=mass, rinertia=J,
pos=part_pos, v=part_v)
if "ROTATION" in espressomd.features():
self.es.part[ind].omega_body = part_omega_body
if test_case == 1:
self.es.part[ind].gamma = gamma_tran[k, :]
if "ROTATION" in espressomd.features():
self.es.part[ind].gamma_rot = gamma_rot[k, :]
if test_case == 2:
self.es.part[ind].temp = temp[k]
if test_case == 3:
self.es.part[ind].gamma = gamma_tran[k, :]
if "ROTATION" in espressomd.features():
self.es.part[ind].gamma_rot = gamma_rot[k, :]
self.es.part[ind].temp = temp[k]
# Get rid of short range calculations if exclusions are on
# if espressomd.has_features("EXCLUSIONS"):
# matrices: [2 types of particless] x [3 dimensions X Y Z]
# velocity^2, omega^2, position^2
v2 = np.zeros((2, 3))
o2 = np.zeros((2, 3))
dr2 = np.zeros((2, 3))
sigma2_tr = np.zeros((2))
dr_norm = np.zeros((2))
pos0 = np.zeros((2 * n, 3))
for p in range(n):
for k in range(2):
ind = p + k * n
pos0[ind, :] = self.es.part[ind].pos
dt0 = mass / gamma_tr
loops = 200
print("Thermalizing...")
therm_steps = 20
self.es.integrator.run(therm_steps)
print("Measuring...")
int_steps = 5
for i in range(loops):
self.es.integrator.run(int_steps)
# Get kinetic energy in each degree of freedom for all particles
for p in range(n):
for k in range(2):
ind = p + k * n
v = self.es.part[ind].v
if "ROTATION" in espressomd.features():
o = self.es.part[ind].omega_body
o2[k, :] = o2[k, :] + np.power(o[:], 2)
pos = self.es.part[ind].pos
v2[k, :] = v2[k, :] + np.power(v[:], 2)
dr2[k, :] = np.power((pos[:] - pos0[ind, :]), 2)
dt = (int_steps * (i + 1) + therm_steps) * \
self.es.time_step
# translational diffusion variance: after a closed-form
# integration of the Langevin EOM
sigma2_tr[k] = 0.0
for j in range(3):
sigma2_tr[k] = sigma2_tr[k] + D_tr[k,
j] * (2.0 * dt + dt0[k,
j] * (- 3.0 + 4.0 * math.exp(- dt / dt0[k,
j]) - math.exp(- 2.0 * dt / dt0[k,
j])))
dr_norm[k] = dr_norm[k] + \
(sum(dr2[k, :]) - sigma2_tr[k]) / sigma2_tr[k]
tolerance = 0.15
Ev = 0.5 * mass * v2 / (n * loops)
Eo = 0.5 * J * o2 / (n * loops)
dv = np.zeros((2))
do = np.zeros((2))
do_vec = np.zeros((2, 3))
for k in range(2):
dv[k] = sum(Ev[k, :]) / (3.0 * halfkT[k]) - 1.0
do[k] = sum(Eo[k, :]) / (3.0 * halfkT[k]) - 1.0
do_vec[k, :] = Eo[k, :] / halfkT[k] - 1.0
dr_norm = dr_norm / (n * loops)
for k in range(2):
print("\n")
print("k = " + str(k))
print("mass = " + str(mass))
print("gamma_tr = {0} {1} {2}".format(
gamma_tr[k, 0], gamma_tr[k, 1], gamma_tr[k, 2]))
if test_case == 1 or test_case == 3:
print("gamma_rot = {0} {1} {2}".format(
gamma_rot[k, 0], gamma_rot[k, 1], gamma_rot[k, 2]))
else:
print("gamma_global = {0} {1} {2}".format(
gamma_global[0], gamma_global[1], gamma_global[2]))
print("Moment of inertia principal components: = " + str(J))
print("1/2 kT = " + str(halfkT[k]))
print("Translational energy: {0} {1} {2}".format(
Ev[k, 0], Ev[k, 1], Ev[k, 2]))
print("Rotational energy: {0} {1} {2}".format(
Eo[k, 0], Eo[k, 1], Eo[k, 2]))
print("Deviation in translational energy: " + str(dv[k]))
if "ROTATION" in espressomd.features():
print("Deviation in rotational energy: " + str(do[k]))
print("Deviation in rotational energy per degrees of freedom: {0} {1} {2}".format(
do_vec[k, 0], do_vec[k, 1], do_vec[k, 2]))
print(
"Deviation in translational diffusion: {0} ".format(
dr_norm[k]))
self.assertLessEqual(
abs(
dv[k]),
tolerance,
msg='Relative deviation in translational energy too large: {0}'.format(
dv[k]))
if "ROTATION" in espressomd.features():
self.assertLessEqual(
abs(
do[k]),
tolerance,
msg='Relative deviation in rotational energy too large: {0}'.format(
do[k]))
self.assertLessEqual(abs(
do_vec[k, 0]), tolerance, msg='Relative deviation in rotational energy per the body axis X is too large: {0}'.format(do_vec[k, 0]))
self.assertLessEqual(abs(
do_vec[k, 1]), tolerance, msg='Relative deviation in rotational energy per the body axis Y is too large: {0}'.format(do_vec[k, 1]))
self.assertLessEqual(abs(
do_vec[k, 2]), tolerance, msg='Relative deviation in rotational energy per the body axis Z is too large: {0}'.format(do_vec[k, 2]))
self.assertLessEqual(
abs(
dr_norm[k]),
tolerance,
msg='Relative deviation in translational diffusion is too large: {0}'.format(
dr_norm[k]))
class RotDiffAniso(ut.TestCase):
longMessage = True
round_error_prec = 1E-14
# Handle for espresso system
system = espressomd.System(box_l=[1.0, 1.0, 1.0])
system.cell_system.skin = 5.0
# The NVT thermostat parameters
kT = 0.0
gamma_global = np.zeros((3))
# Particle properties
J = [0.0, 0.0, 0.0]
np.random.seed(4)
def setUp(self):
self.system.time = 0.0
self.system.part.clear()
if "BROWNIAN_DYNAMICS" in espressomd.features():
self.system.thermostat.turn_off()
# the default integrator is supposed implicitly
self.system.integrator.set_nvt()
def add_particles_setup(self, n):
"""
Adding particles according to the
previously set parameters.
Parameters
----------
n : :obj:`int`
Number of particles.
"""
for ind in range(n):
part_pos = np.random.random(3) * self.box
self.system.part.add(rotation=(1, 1, 1), id=ind, pos=part_pos)
self.system.part[ind].rinertia = self.J
if espressomd.has_features("ROTATION"):
self.system.part[ind].omega_body = [0.0, 0.0, 0.0]
def set_anisotropic_param(self):
"""
Select parameters for anisotropic particles.
"""
# NVT thermostat
# Note: here & hereinafter specific variations in the random parameter
# ranges are related to the test execution duration to achieve the
# required statistical averages faster. The friction gamma_global should
# be large enough in order to have the small enough D ~ kT / gamma and
# to observe the details of the original rotational diffusion: the
# Perrin1936 (see the reference below) tests are visible only when the
# diffusive rotation is ~pi due to the exponential temporal dependencies
# (see the equations referred in the check_rot_diffusion()).
# Also, t0 ~ J / gamma should be small enough in order to remove the
# small-time-scale diffusion effects which do not fit the Perrin1936's
# tests which are based on the partial differential equation
# (eq. (68), Perrin1934) leading only to the simple classical
# Einstein-Smoluchowski equations of the diffusion in a contrast of the
# eq. (10.2.26) [N. Pottier, doi:10.1007/s10955-010-0114-6 (2010)].
self.gamma_global = 1E2 * np.random.uniform(0.35, 1.05, (3))
# Particles' properties
# As far as the problem characteristic time is t0 ~ J / gamma
# and the Langevin equation finite-difference approximation is stable
# only for time_step << t0, it is needed to set the moment of inertia
# higher than some minimal value.
# Also, it is expected to test the large enough J.
# It should be not very large, otherwise the thermalization will require
# too much of the CPU time: the in silico time should clock over the
# t0.
self.J = np.random.uniform(1.5, 16.5, (3))
def set_isotropic_param(self):
"""
Select parameters for isotropic particles.
Parameters
----------
"""
# NVT thermostat
# see the comments in set_anisotropic_param()
self.gamma_global[0] = 1E2 * np.random.uniform(0.35, 1.05)
self.gamma_global[1] = self.gamma_global[0]
self.gamma_global[2] = self.gamma_global[0]
# Particles' properties
# see the comments in set_anisotropic_param()
self.J[0] = np.random.uniform(1.5, 16.5)
self.J[1] = self.J[0]
self.J[2] = self.J[0]
def rot_diffusion_param_setup(self):
"""
Setup the parameters for the rotational diffusion
test check_rot_diffusion().
"""
# Time
# The time step should be less than t0 ~ mass / gamma
self.system.time_step = 3E-3
# Space
self.box = 10.0
self.system.box_l = 3 * [self.box]
self.system.periodicity = [0, 0, 0]
# NVT thermostat
# Just some temperature range to cover by the test:
self.kT = np.random.uniform(0.5, 1.5)
def check_rot_diffusion(self, n):
"""
The rotational diffusion tests based on the reference work
[Perrin, F. (1936) Journal de Physique et Le Radium, 7(1), 1-11.
https://doi.org/10.1051/jphysrad:01936007010100]
with a theoretical background of
[Perrin, F. (1934) Journal de Physique et Le Radium, 5(10), 497-511.
https://doi.org/10.1051/jphysrad:01934005010049700]
Parameters
----------
n : :obj:`int`
Number of particles.
"""
# Global diffusivity tensor in the body frame:
D = self.kT / self.gamma_global
# Thermalizing...
therm_steps = 100
self.system.integrator.run(therm_steps)
# Measuring...
# Set the initial conditions according to the [Perrin1936], p.3.
# The body angular velocity is rotated now, but there is only the
# thermal velocity, hence, this does not impact the test and its
# physical context.
for ind in range(n):
self.system.part[ind].quat = [1.0, 0.0, 0.0, 0.0]
# Average direction cosines
# Diagonal ones:
dcosjj_validate = np.zeros((3))
dcosjj_dev = np.zeros((3))
# same to the power of 2
dcosjj2_validate = np.zeros((3))
dcosjj2_dev = np.zeros((3))
# The non-diagonal elements for 2 different tests: negative ("nn") and
# positive ("pp") ones.
dcosijpp_validate = np.ones((3, 3))
dcosijpp_dev = np.zeros((3, 3))
dcosijnn_validate = np.ones((3, 3))
dcosijnn_dev = np.zeros((3, 3))
# The non-diagonal elements to the power of 2
dcosij2_validate = np.ones((3, 3))
dcosij2_dev = np.zeros((3, 3))
self.system.time = 0.0
int_steps = 20
loops = 100
for _ in range(loops):
self.system.integrator.run(steps=int_steps)
dcosjj = np.zeros((3))
dcosjj2 = np.zeros((3))
dcosijpp = np.zeros((3, 3))
dcosijnn = np.zeros((3, 3))
dcosij2 = np.zeros((3, 3))
for ind in range(n):
# Just a direction cosines functions averaging..
dir_cos = tests_common.rotation_matrix_quat(self.system, ind)
for j in range(3):
# the LHS of eq. (23) [Perrin1936].
dcosjj[j] += dir_cos[j, j]
# the LHS of eq. (32) [Perrin1936].
dcosjj2[j] += dir_cos[j, j]**2.0
for i in range(3):
if i != j:
# the LHS of eq. (24) [Perrin1936].
dcosijpp[i, j] += dir_cos[i, i] * dir_cos[j, j] + \
dir_cos[i, j] * dir_cos[j, i]
# the LHS of eq. (25) [Perrin1936].
dcosijnn[i, j] += dir_cos[i, i] * dir_cos[j, j] - \
dir_cos[i, j] * dir_cos[j, i]
# the LHS of eq. (33) [Perrin1936].
dcosij2[i, j] += dir_cos[i, j]**2.0
dcosjj /= n
dcosjj2 /= n
dcosijpp /= n
dcosijnn /= n
dcosij2 /= n
# Actual comparison.
tolerance = 0.2
# Too small values of the direction cosines are out of interest
# compare to 0..1 range.
min_value = 0.14
# Eq. (23) [Perrin1936].
dcosjj_validate[0] = np.exp(-(D[1] + D[2]) * self.system.time)
dcosjj_validate[1] = np.exp(-(D[0] + D[2]) * self.system.time)
dcosjj_validate[2] = np.exp(-(D[0] + D[1]) * self.system.time)
dcosjj_dev = np.absolute(dcosjj -
dcosjj_validate) / dcosjj_validate
for j in range(3):
if np.absolute(dcosjj_validate[j]) < min_value:
dcosjj_dev[j] = 0.0
# Eq. (24) [Perrin1936].
dcosijpp_validate[0, 1] = np.exp(-(4 * D[2] + D[1] + D[0]) *
self.system.time)
dcosijpp_validate[1, 0] = np.exp(-(4 * D[2] + D[1] + D[0]) *
self.system.time)
dcosijpp_validate[0, 2] = np.exp(-(4 * D[1] + D[2] + D[0]) *
self.system.time)
dcosijpp_validate[2, 0] = np.exp(-(4 * D[1] + D[2] + D[0]) *
self.system.time)
dcosijpp_validate[1, 2] = np.exp(-(4 * D[0] + D[2] + D[1]) *
self.system.time)
dcosijpp_validate[2, 1] = np.exp(-(4 * D[0] + D[2] + D[1]) *
self.system.time)
dcosijpp_dev = np.absolute(dcosijpp -
dcosijpp_validate) / dcosijpp_validate
for i in range(3):
for j in range(3):
if np.absolute(dcosijpp_validate[i, j]) < min_value:
dcosijpp_dev[i, j] = 0.0
# Eq. (25) [Perrin1936].
dcosijnn_validate[0, 1] = np.exp(-(D[1] + D[0]) * self.system.time)
dcosijnn_validate[1, 0] = np.exp(-(D[1] + D[0]) * self.system.time)
dcosijnn_validate[0, 2] = np.exp(-(D[2] + D[0]) * self.system.time)
dcosijnn_validate[2, 0] = np.exp(-(D[2] + D[0]) * self.system.time)
dcosijnn_validate[1, 2] = np.exp(-(D[2] + D[1]) * self.system.time)
dcosijnn_validate[2, 1] = np.exp(-(D[2] + D[1]) * self.system.time)
dcosijnn_dev = np.absolute(dcosijnn -
dcosijnn_validate) / dcosijnn_validate
for i in range(3):
for j in range(3):
if np.absolute(dcosijnn_validate[i, j]) < min_value:
dcosijnn_dev[i, j] = 0.0
# Eq. (30) [Perrin1936].
D0 = sum(D[:]) / 3.0
D1D1 = 0.0
for j in range(3):
for i in range(3):
if i != j:
D1D1 += D[i] * D[j]
D1D1 /= 6.0
# Technical workaround of a digital arithmetic issue for isotropic
# particle
if np.absolute(
(D0**2 - D1D1) / (D0**2 + D1D1)) < self.round_error_prec:
D1D1 *= (1.0 - 2.0 * self.round_error_prec)
# Eq. (32) [Perrin1936].
dcosjj2_validate = 1. / 3. + (1. / 3.) * (1. + (D - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 - np.sqrt(D0**2 - D1D1)) * self.system.time) \
+ (1. / 3.) * (1. - (D - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 + np.sqrt(D0**2 - D1D1)) * self.system.time)
dcosjj2_dev = np.absolute(dcosjj2 -
dcosjj2_validate) / dcosjj2_validate
for j in range(3):
if np.absolute(dcosjj2_validate[j]) < min_value:
dcosjj2_dev[j] = 0.0
# Eq. (33) [Perrin1936].
dcosij2_validate[0, 1] = 1. / 3. - (1. / 6.) * (1. - (D[2] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 - np.sqrt(D0**2 - D1D1)) * self.system.time) \
- (1. / 6.) * (1. + (D[2] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 + np.sqrt(D0**2 - D1D1)) * self.system.time)
dcosij2_validate[1, 0] = dcosij2_validate[0, 1]
dcosij2_validate[0, 2] = 1. / 3. - (1. / 6.) * (1. - (D[1] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 - np.sqrt(D0**2 - D1D1)) * self.system.time) \
- (1. / 6.) * (1. + (D[1] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 + np.sqrt(D0**2 - D1D1)) * self.system.time)
dcosij2_validate[2, 0] = dcosij2_validate[0, 2]
dcosij2_validate[1, 2] = 1. / 3. - (1. / 6.) * (1. - (D[0] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 - np.sqrt(D0**2 - D1D1)) * self.system.time) \
- (1. / 6.) * (1. + (D[0] - D0) / (2. * np.sqrt(D0**2 - D1D1))) \
* np.exp(-6. * (D0 + np.sqrt(D0**2 - D1D1)) * self.system.time)
dcosij2_validate[2, 1] = dcosij2_validate[1, 2]
dcosij2_dev = np.absolute(dcosij2 -
dcosij2_validate) / dcosij2_validate
for i in range(3):
for j in range(3):
if np.absolute(dcosij2_validate[i, j]) < min_value:
dcosij2_dev[i, j] = 0.0
for j in range(3):
self.assertLessEqual(
abs(dcosjj_dev[j]),
tolerance,
msg='Relative deviation dcosjj_dev[{0}] in a rotational '
'diffusion is too large: {1}'.format(j, dcosjj_dev[j]))
self.assertLessEqual(
abs(dcosjj2_dev[j]),
tolerance,
msg='Relative deviation dcosjj2_dev[{0}] in a rotational '
'diffusion is too large: {1}'.format(j, dcosjj2_dev[j]))
for i in range(3):
if i != j:
self.assertLessEqual(
abs(dcosijpp_dev[i, j]),
tolerance,
msg='Relative deviation dcosijpp_dev[{0},{1}] in a '
'rotational diffusion is too large: {2}'.format(
i, j, dcosijpp_dev[i, j]))
self.assertLessEqual(
abs(dcosijnn_dev[i, j]),
tolerance,
msg='Relative deviation dcosijnn_dev[{0},{1}] in a '
'rotational diffusion is too large: {2}'.format(
i, j, dcosijnn_dev[i, j]))
self.assertLessEqual(
abs(dcosij2_dev[i, j]),
tolerance,
msg='Relative deviation dcosij2_dev[{0},{1}] in a '
'rotational diffusion is too large: {2}'.format(
i, j, dcosij2_dev[i, j]))
# Langevin Dynamics / Anisotropic
def test_case_00(self):
n = 800
self.rot_diffusion_param_setup()
self.set_anisotropic_param()
self.add_particles_setup(n)
self.system.thermostat.set_langevin(kT=self.kT,
gamma=self.gamma_global,
seed=42)
# Actual integration and validation run
self.check_rot_diffusion(n)
# Langevin Dynamics / Isotropic
def test_case_01(self):
n = 800
self.rot_diffusion_param_setup()
self.set_isotropic_param()
self.add_particles_setup(n)
self.system.thermostat.set_langevin(kT=self.kT,
gamma=self.gamma_global,
seed=42)
# Actual integration and validation run
self.check_rot_diffusion(n)
if "BROWNIAN_DYNAMICS" in espressomd.features():
# Brownian Dynamics / Isotropic
def test_case_10(self):
n = 800
self.system.thermostat.turn_off()
self.rot_diffusion_param_setup()
self.set_isotropic_param()
self.add_particles_setup(n)
self.system.thermostat.set_brownian(kT=self.kT,
gamma=self.gamma_global,
seed=42)
self.system.integrator.set_brownian_dynamics()
# Actual integration and validation run
self.check_rot_diffusion(n)
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Tests particle property setters/getters
from __future__ import print_function
import espressomd
import unittest as ut
import numpy as np
from tests_common import *
if "ELECTROSTATICS" in espressomd.features() and "CUDA" in espressomd.features():
from espressomd.electrostatics import P3M_GPU
class P3M_GPU_test(ut.TestCase):
def runTest(self):
es = espressomd.System()
test_params = {}
test_params["bjerrum_length"] = 2
test_params["cao"] = 2
test_params["inter"] = 3
test_params["r_cut"] = 0.9
test_params["accuracy"] = 1e-1
test_params["mesh"] = [10, 10, 10]
test_params["epsilon"] = 20.0
test_params["mesh_off"] = [0.8, 0.8, 0.8]
test_params["alpha"] = 1.1
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Tests particle property setters/getters
import espressomd
import unittest as ut
import numpy as np
if "P3M_GPU" in espressomd.features():
from espressomd.electrostatics import P3M_GPU
class P3M_GPU_test(ut.TestCase):
es = espressomd.System()
test_params = {}
test_params["bjerrum_length"] = 2
test_params["cao"] = 2
test_params["inter"] = 3
test_params["r_cut"] = 0.9
test_params["accuracy"] = 1e-1
test_params["mesh"] = [10, 10, 10]
test_params["epsilon"] = 20.0
test_params["mesh_off"] = [0.8, 0.8, 0.8]
test_params["alpha"] = 1.1
test_params["tune"] = False
class ParticleProperties(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# the system which will be tested
system = espressomd.System()
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
def bondsMatch(self, inType, outType, inParams, outParams):
"""Check, if the bond type set and gotten back as well as the bond
parameters set and gotten back match. Only check keys present in
inParams.
"""
if inType != outType:
return False
for k in list(inParams.keys()):
if k not in outParams:
return False
if outParams[k] != inParams[k]:
return False
return True
def setUp(self):
if not self.system.part.exists(self.pid):
self.system.part.add(id=self.pid, pos=(0, 0, 0, 0))
def generateTestForBondParams(_bondId, _bondClass, _params):
"""Generates test cases for checking bond parameters set and gotten back
from Es actually match. Only keys which are present in _params are checked
1st arg: Id of the bonded ia in Espresso to test on, i.e., 0,2,1...
2nd: Class of the bond potential to test, ie.e, FeneBond, HarmonicBond
3rd: Bond parameters as dictionary, i.e., {"k"=1.,"r_0"=0.
"""
bondId = _bondId
bondClass = _bondClass
params = _params
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
self.system.bonded_inter[bondId] = bondClass(**params)
outBond = self.system.bonded_inter[bondId]
tnIn = bondClass(**params).type_number()
tnOut = outBond.type_number()
outParams = outBond.params
self.assertTrue(
self.bondsMatch(tnIn, tnOut, params, outParams),
bondClass(**params).type_name() +
": value set and value gotten back differ for bond id " +
str(bondId) + ": " + params.__str__() + " vs. " +
outParams.__str__())
return func
test_fene = generateTestForBondParams(0, FeneBond, {
"r_0": 1.1,
"k": 5.2,
"d_r_max": 3.
})
test_fene2 = generateTestForBondParams(1, FeneBond, {
"r_0": 1.1,
"k": 5.2,
"d_r_max": 3.
})
test_harmonic = generateTestForBondParams(0, HarmonicBond, {
"r_0": 1.1,
"k": 5.2
})
test_harmonic2 = generateTestForBondParams(0, HarmonicBond, {
"r_0": 1.1,
"k": 5.2,
"r_cut": 1.3
})
if "ROTATION" in code_info.features():
test_harmonic_dumbbell = generateTestForBondParams(
0, HarmonicDumbbellBond, {
"k1": 1.1,
"k2": 2.2,
"r_0": 1.5
})
test_harmonic_dumbbell2 = generateTestForBondParams(
0, HarmonicDumbbellBond, {
"k1": 1.1,
"k2": 2.2,
"r_0": 1.5,
"r_cut": 1.9
})
test_dihedral = generateTestForBondParams(0, Dihedral, {
"mult": 3.0,
"bend": 5.2,
"phase": 3.
})
if "BOND_ANGLE" in espressomd.features():
test_angle_harm = generateTestForBondParams(0, Angle_Harmonic, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cos = generateTestForBondParams(0, Angle_Cosine, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cossquare = generateTestForBondParams(
0, Angle_Cossquare, {
"bend": 5.2,
"phi0": 0.
})
if "LENNARD_JONES" in espressomd.features():
test_subt_lj = generateTestForBondParams(0, Subt_Lj, {
"k": 5.2,
"r": 3.2
})
if "TABULATED" in espressomd.features():
test_tabulated = generateTestForBondParams(0, Tabulated, {
"type": "distance",
"filename": "lj1.tab"
})
e_kin = e - e_pot
print(" {} {} {} {}".format(time, e, e_pot, e_kin), file=f)
def calc_temperature(system):
E = system.analysis.energy()['total']
n_part = len(system.part)
return 2. / 3. * E / n_part
# check for necessary feature
required_features = ["MASS", "TABULATED"]
espressomd.assert_features(required_features)
print("Program Information:\n{}\n".format(espressomd.features()))
espresso_release = (espressomd.version.major(), espressomd.version.minor())
# set system properties:
skin = 0.5
time_step = 0.002
friction = 5.0
int_steps = 900
eq_steps = 100
steps_per_int = 100
atomnumber, box, atompos = readgrofile('spce.gro')
nm2Angstroem = 10
box_length = box * nm2Angstroem
positions = atompos * nm2Angstroem
mass = 18
class Non_bonded_interactionsTests(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# Handle to espresso system
es = espressomd.System()
def intersMatch(self, inType, outType, inParams, outParams):
"""Check, if the interaction type set and gotten back as well as the bond
parameters set and gotten back match. Only check keys present in
inParams.
"""
if inType != outType:
print("Type mismatch:", inType, outType)
return False
for k in inParams.keys():
if k not in outParams:
print(k, "missing from returned parameters")
return False
if outParams[k] != inParams[k]:
print("Mismatch in parameter ", k, inParams[k], outParams[k])
return False
return True
def generateTestForNon_bonded_interaction(_partType1, _partType2,
_interClass, _params,
_interName):
"""Generates test cases for checking interaction parameters set and gotten back
from Es actually match. Only keys which are present in _params are checked
1st and 2nd arg: Particle type ids to check on
3rd: Class of the interaction to test, ie.e, FeneBond, HarmonicBond
4th: Interaction parameters as dictionary, i.e., {"k"=1.,"r_0"=0.
5th: Name of the interaction property to set (i.e. "lennardJones")
"""
partType1 = _partType1
partType2 = _partType2
interClass = _interClass
params = _params
interName = _interName
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
# Set parameters
getattr(self.es.non_bonded_inter[partType1, partType2],
interName).set_params(**params)
# Read them out again
outInter = getattr(self.es.non_bonded_inter[partType1, partType2],
interName)
outParams = outInter.get_params()
self.assertTrue(
self.intersMatch(interClass, type(outInter), params,
outParams),
interClass(**params).type_name() +
": value set and value gotten back differ for particle types "
+ str(partType1) + " and " + str(partType2) + ": " +
params.__str__() + " vs. " + outParams.__str__())
return func
test_lj1 = generateTestForNon_bonded_interaction(
0, 0, LennardJonesInteraction, {
"epsilon": 1.,
"sigma": 2.,
"cutoff": 3.,
"shift": 4.,
"offset": 5.,
"min": 7.
}, "lennard_jones")
test_lj2 = generateTestForNon_bonded_interaction(
0, 0, LennardJonesInteraction, {
"epsilon": 1.3,
"sigma": 2.2,
"cutoff": 3.4,
"shift": 4.1,
"offset": 5.1,
"min": 7.1
}, "lennard_jones")
test_lj3 = generateTestForNon_bonded_interaction(
0, 0, LennardJonesInteraction, {
"epsilon": 1.3,
"sigma": 2.2,
"cutoff": 3.4,
"shift": 4.1,
"offset": 5.1,
"min": 7.1
}, "lennard_jones")
if "LENNARD_JONES_GENERIC" in espressomd.features():
test_ljgen1 = generateTestForNon_bonded_interaction(
0, 0, GenericLennardJonesInteraction, {
"epsilon": 1.,
"sigma": 2.,
"cutoff": 3.,
"shift": 4.,
"offset": 5.,
"e1": 7,
"e2": 8,
"b1": 9.,
"b2": 10.
}, "generic_lennard_jones")
test_ljgen2 = generateTestForNon_bonded_interaction(
0, 0, GenericLennardJonesInteraction, {
"epsilon": 1.1,
"sigma": 2.1,
"cutoff": 3.1,
"shift": 4.1,
"offset": 5.1,
"e1": 71,
"e2": 81,
"b1": 9.1,
"b2": 10.1
}, "generic_lennard_jones")
test_ljgen3 = generateTestForNon_bonded_interaction(
0, 0, GenericLennardJonesInteraction, {
"epsilon": 1.2,
"sigma": 2.2,
"cutoff": 3.2,
"shift": 4.2,
"offset": 5.2,
"e1": 72,
"e2": 82,
"b1": 9.2,
"b2": 10.2
}, "generic_lennard_jones")
def test_forcecap(self):
self.es.non_bonded_inter.set_force_cap(17.5)
self.assertEqual(self.es.non_bonded_inter.get_force_cap(), 17.5)
def dissipation_param_setup(self, n):
"""
Setup the parameters for the following dissipation
test.
Parameters
----------
n : :obj:`int`
Number of particles of the each type. There are 2 types.
"""
# Time
self.system.time_step = 0.007
# Space
box = 1.0
self.system.box_l = box, box, box
if espressomd.has_features(("PARTIAL_PERIODIC", )):
self.system.periodicity = 0, 0, 0
# NVT thermostat
self.kT = 0.0
# The translational gamma isotropy is required here.
# Global gamma for tests without particle-specific gammas.
#
# As far as the problem characteristic time is t0 ~ mass / gamma
# and the Langevin equation finite-difference approximation is stable
# only for time_step << t0, it is needed to set the gamma less than
# some maximal value according to the value gamma_max.
# Also, it cannot be very small (gamma_min), otherwise the thermalization will require
# too much of the CPU time. Same: for all such gamma assignments throughout the test.
#
gamma_min = self.gamma_min
gamma_max = self.gamma_max
gamma_rnd = uniform(gamma_min, gamma_max)
self.gamma_global = gamma_rnd, gamma_rnd, gamma_rnd
# Additional test case for the specific global rotational gamma set.
self.gamma_global_rot = uniform(gamma_min, gamma_max, 3)
# Per-paricle values:
self.kT_p = 0.0, 0.0
# Either translational friction isotropy is required
# or both translational and rotational ones.
# Otherwise these types of motion will interfere.
# ..Let's test both cases depending on the particle index.
self.gamma_tran_p[0, 0] = uniform(gamma_min, gamma_max)
self.gamma_tran_p[0, 1] = self.gamma_tran_p[0, 0]
self.gamma_tran_p[0, 2] = self.gamma_tran_p[0, 0]
self.gamma_rot_p[0, :] = uniform(gamma_min, gamma_max, 3)
self.gamma_tran_p[1, 0] = uniform(gamma_min, gamma_max)
self.gamma_tran_p[1, 1] = self.gamma_tran_p[1, 0]
self.gamma_tran_p[1, 2] = self.gamma_tran_p[1, 0]
self.gamma_rot_p[1, 0] = uniform(gamma_min, gamma_max)
self.gamma_rot_p[1, 1] = self.gamma_rot_p[1, 0]
self.gamma_rot_p[1, 2] = self.gamma_rot_p[1, 0]
# Particles
self.mass = 12.74
self.J = 10.0, 10.0, 10.0
for i in range(n):
for k in range(2):
ind = i + k * n
self.system.part.add(rotation=(1, 1, 1),
pos=(0.0, 0.0, 0.0),
id=ind)
self.system.part[ind].v = 1.0, 1.0, 1.0
if "ROTATION" in espressomd.features():
self.system.part[ind].omega_body = 1.0, 1.0, 1.0
self.system.part[ind].mass = self.mass
self.system.part[ind].rinertia = self.J
from __future__ import print_function
import unittest as ut
import numpy as np
import espressomd
if "ENGINE" in espressomd.features():
class SwimmerTest(ut.TestCase):
def test(self):
boxl = 12
sampsteps = 2000
tstep = 0.01
v_swim = 0.3
f_swim = 0.1
temp = 0.0
gamma = 1.0
pos_0 = np.array([boxl/2., boxl/2., 1.*boxl/3.])
pos_1 = np.array([boxl/2., boxl/2., 2.*boxl/3.])
def z_f(t,z0):
return f_swim/gamma*(-1./gamma + t + (1./gamma)*np.exp(-gamma*t))+z0
def z_v(t,z0):
return v_swim*(-1./gamma + t + (1./gamma)*np.exp(-gamma*t))+z0
S = espressomd.System()
S.box_l = [boxl, boxl, boxl]
S.cell_system.skin = 0.1
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Tests particle property setters/getters
import unittest as ut
import espressomd
import numpy as np
from espressomd.interactions import LennardJonesInteraction
if "LENNARD_JONES_GENERIC" in espressomd.features():
from espressomd.interactions import GenericLennardJonesInteraction
class Non_bonded_interactionsTests(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# Handle to espresso system
es = espressomd.System()
def intersMatch(self, inType, outType, inParams, outParams):
"""Check, if the interaction type set and gotten back as well as the bond
parameters set and gotten back match. Only check keys present in
inParams.
"""
"genericLennardJones",
)
test_ljgen3 = generateTestForNonBondedInteraction(
0,
0,
GenericLennardJonesInteraction,
{
"epsilon": 1.2,
"sigma": 2.2,
"cutoff": 3.2,
"shift": 4.2,
"offset": 5.2,
"e1": 72,
"e2": 82,
"b1": 9.2,
"b2": 10.2,
"lambda": 11.2,
"delta": 12.2,
},
"genericLennardJones",
)
def test_forcecap(self):
self.es.nonBondedInter.setForceCap(17.5)
self.assertEqual(self.es.nonBondedInter.getForceCap(), 17.5)
if __name__ == "__main__":
print("Features: ", espressomd.features())
ut.main()
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Tests particle property setters/getters
import unittest as ut
import espressomd
import numpy as np
from espressomd.interactions import LennardJonesInteraction
if "LENNARD_JONES_GENERIC" in espressomd.features():
from espressomd.interactions import GenericLennardJonesInteraction
class Non_bonded_interactionsTests(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# Handle to espresso system
es = espressomd.System()
def intersMatch(self, inType, outType, inParams, outParams):
"""Check, if the interaction type set and gotten back as well as the bond
parameters set and gotten back match. Only check keys present in
inParams.
"""
if inType != outType:
def dissipation_param_setup(self):
"""
Setup the parameters for the following dissipation
test.
"""
## Time
self.es.time_step = 0.007
## Space
box = 1.0
self.es.box_l = box,box,box
if espressomd.has_features(("PARTIAL_PERIODIC",)):
self.es.periodicity = 0,0,0
## NVT thermostat
self.kT = 0.0
# The translational gamma isotropy is required here.
# Global gamma for tests without particle-specific gammas.
#
# As far as the problem characteristic time is t0 ~ mass / gamma
# and the Langevin equation finite-difference approximation is stable
# only for time_step << t0, it is needed to set the gamma less than
# some maximal value according to the value max_gamma_param.
# Also, it cannot be very small (min_gamma_param), otherwise the thermalization will require
# too much of the CPU time. Same: for all such gamma assignments throughout the test.
#
min_gamma_param = 0.5
max_gamma_param = 2.0/3.0
gamma_rnd = self.generate_scalar_ranged_rnd(min_gamma_param, max_gamma_param)
self.gamma_global = gamma_rnd, gamma_rnd, gamma_rnd
# Additional test case for the specific global rotational gamma set.
self.gamma_global_rot = self.generate_vec_ranged_rnd(0.5,2.0/3.0)
# Per-paricle values:
self.kT_p = 0.0,0.0
# Either translational friction isotropy is required
# or both translational and rotational ones.
# Otherwise these types of motion will interfere.
# ..Let's test both cases depending on the particle index.
self.gamma_tran_p[0, 0] = self.generate_scalar_ranged_rnd(0.5,1.0)
self.gamma_tran_p[0, 1] = self.gamma_tran_p[0, 0]
self.gamma_tran_p[0, 2] = self.gamma_tran_p[0, 0]
self.gamma_rot_p[0, :] = self.generate_vec_ranged_rnd(0.5,2.0/3.0)
self.gamma_tran_p[1, 0] = self.generate_scalar_ranged_rnd(0.5,1.0)
self.gamma_tran_p[1, 1] = self.gamma_tran_p[1, 0]
self.gamma_tran_p[1, 2] = self.gamma_tran_p[1, 0]
self.gamma_rot_p[1, 0] = self.generate_scalar_ranged_rnd(0.5,2.0/3.0)
self.gamma_rot_p[1, 1] = self.gamma_rot_p[1, 0]
self.gamma_rot_p[1, 2] = self.gamma_rot_p[1, 0]
## Particles
self.mass = 12.74
self.J = 10.0,10.0,10.0
for i in range(2):
self.es.part.add(rotation=(1,1,1), pos=(0.0,0.0,0.0), id=i)
self.es.part[i].v = 1.0,1.0,1.0
if "ROTATION" in espressomd.features():
self.es.part[i].omega_body = 1.0,1.0,1.0
self.es.part[i].mass = self.mass
self.es.part[i].rinertia = self.J
class ParticleProperties(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
# Handle for espresso system
es = espressomd.System()
def arraysNearlyEqual(self, a, b):
"""Test, if the magnitude of the difference between two arrays is smaller than the tolerance"""
# Check length
if len(a) != len(b):
return False
# We have to use a loop, since we can't be sure, we're getting numpy arrays
sum = 0.
for i in range(len(a)):
sum += abs(a[i] - b[i])
if sum > self.tol:
return False
return True
def setUp(self):
self.es.part[self.pid].pos = 0, 0, 0
self.es.bondedInter[0] = FeneBond(k=1, d_r_max=5)
self.es.bondedInter[1] = FeneBond(k=1, d_r_max=5)
def generateTestForVectorProperty(_propName, _value):
"""Generates test cases for vectorial particle properties such as
position, velocity...
1st arg: name of the property (e.g., "pos"),
2nd array: value to be used for testing. Has to be numpy.array of floats
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.es.part[self.pid], propName, value)
print(propName, value, getattr(self.es.part[self.pid], propName))
self.assertTrue(
self.arraysNearlyEqual(
getattr(self.es.part[self.pid], propName), value),
propName + ": value set and value gotten back differ.")
return func
def generateTestForScalarProperty(_propName, _value):
"""Generates test cases for scalar particle properties such as
type, mass, charge...
1st arg: name of the property (e.g., "type"),
2nd array: value to be used for testing. int or float
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.es.part[self.pid], propName, value)
print(propName, value, getattr(self.es.part[self.pid], propName))
self.assertTrue(
getattr(self.es.part[self.pid], propName) == value,
propName + ": value set and value gotten back differ.")
return func
test_pos = generateTestForVectorProperty("pos", np.array([0.1, 0.2, 0.3]))
test_v = generateTestForVectorProperty("v", np.array([0.2, 0.3, 0.4]))
test_f = generateTestForVectorProperty("f", np.array([0.2, 0.3, 0.7]))
test_type = generateTestForScalarProperty("type", int(3))
test_bonds_property = generateTestForScalarProperty(
"bonds", ((0, 1), (1, 2)))
if "MASS" in espressomd.features():
test_mass = generateTestForScalarProperty("mass", 1.3)
if "ROTATION" in espressomd.features():
test_omega_lab = generateTestForVectorProperty("omega_lab",
np.array([4., 2., 1.]))
test_omega_body = generateTestForVectorProperty(
"omega_body", np.array([4., 72., 1.]))
test_torque_lab = generateTestForVectorProperty(
"torque_lab", np.array([4., 72., 3.7]))
# The tested value has to be nromalized!
test_quat = generateTestForVectorProperty(
"quat", np.array([0.5, 0.5, 0.5, 0.5]))
# test_director=generateTestForVectorProperty("director",np.array([0.5,0.4,0.3]))
if "ELECTROSTATICS" in espressomd.features():
test_charge = generateTestForScalarProperty("q", -19.7)
if "DIPOLES" in espressomd.features():
test_dip = generateTestForVectorProperty("dip",
np.array([0.5, -0.5, 3]))
test_dipm = generateTestForScalarProperty("dipm", -9.7)
if "VIRTUAL_SITES" in espressomd.features():
test_virtual = generateTestForScalarProperty("virtual", 1)
if "VIRTUAL_SITES_RELATIVE" in espressomd.features():
test_zz_vs_relative = generateTestForScalarProperty(
"vs_relative", ((0, 5.0)))
class CoulombCloudWall(ut.TestCase):
"""This compares p3m, p3m_gpu, scafacos_p3m and scafacos_p2nfft
electrostatic forces and energy against stored data."""
S = espressomd.System()
forces = {}
tolerance = 1E-3
# Reference energy from p3m in the tcl test case
reference_energy = 148.94229549
def setUp(self):
self.S.box_l = (10, 10, 10)
self.S.time_step = 0.01
self.S.skin = 0.4
# Clear actors that might be left from prev tests
if len(self.S.actors):
del self.S.actors[0]
self.S.part.clear()
data = np.genfromtxt("data/coulomb_cloud_wall_system.data")
# Add particles to system and store reference forces in hash
# Input format: id pos q f
for particle in data:
id = particle[0]
pos = particle[1:4]
q = particle[4]
f = particle[5:]
self.S.part.add(id=int(id), pos=pos, q=q)
self.forces[id] = f
def compare(self, method_name, energy=True):
# Compare forces and energy now in the system to stored ones
# Force
force_abs_diff = 0.
for p in self.S.part:
force_abs_diff += abs(np.sqrt(sum((p.f - self.forces[p.id])**2)))
force_abs_diff /= len(self.S.part)
print method_name, "force difference", force_abs_diff
# Energy
if energy:
energy_abs_diff = abs(self.S.analysis.energy(
self.S)["total"] - self.reference_energy)
print method_name, "energy difference", energy_abs_diff
self.assertTrue(energy_abs_diff <= self.tolerance, "Absolte energy difference " +
str(energy_abs_diff) + " too large for " + method_name)
self.assertTrue(force_abs_diff <= self.tolerance, "Asbolute force difference " +
str(force_abs_diff) + " too large for method " + method_name)
# Tests for individual methods
if "P3M" in espressomd.features():
def test_p3m(self):
self.S.actors.add(P3M(bjerrum_length=1, r_cut=1.001,
mesh=64, cao=7, alpha=2.70746, tune=False))
integrate(0)
self.compare("p3m", energy=True)
if "ELECTROSTATICS" in espressomd.features() and "CUDA" in espressomd.features():
def test_p3m_gpu(self):
self.S.actors.add(P3M_GPU(
bjerrum_length=1, r_cut=1.001, mesh=64, cao=7, alpha=2.70746, tune=False))
integrate(0)
self.compare("p3m_gpu", energy=False)
if "SCAFACOS" in espressomd.features():
if "p3m" in scafacos.available_methods():
def test_scafacos_p3m(self):
self.S.actors.add(Scafacos(bjerrum_length=1, method_name="p3m", method_params={
"p3m_r_cut": 1.001, "p3m_grid": 64, "p3m_cao": 7, "p3m_alpha": 2.70746}))
integrate(0)
self.compare("scafacos_p3m", energy=True)
if "p2nfft" in scafacos.available_methods():
def test_scafacos_p2nfft(self):
self.S.actors.add(Scafacos(bjerrum_length=1, method_name="p2nfft", method_params={
"p2nfft_r_cut": 1.001, "tolerance_field": 1E-4}))
integrate(0)
self.compare("scafacos_p2nfft", energy=True)
def test_zz_deactivation(self):
# Is the energy 0, if no methods active
self.assertTrue(self.S.analysis.energy(self.S)["total"] == 0.0)
import unittest as ut
import numpy as np
import espressomd
from espressomd import thermostat
from espressomd import integrate
if "ENGINE" in espressomd.features():
class SwimmerTest(ut.TestCase):
def test(self):
boxl = 12
sampsteps = 2000
tstep = 0.01
v_swim = 0.3
f_swim = 0.1
temp = 0.0
gamma = 1.0
pos_0 = np.array([boxl / 2., boxl / 2., 1. * boxl / 3.])
pos_1 = np.array([boxl / 2., boxl / 2., 2. * boxl / 3.])
def z_f(t, z0):
return f_swim / gamma * (
-1. / gamma + t + (1. / gamma) * np.exp(-gamma * t)) + z0
def z_v(t, z0):
return v_swim * (-1. / gamma + t +
(1. / gamma) * np.exp(-gamma * t)) + z0
S = espressomd.System()
self.s.part.add(id=0, pos=[0, 0, 0], type=0, q=+1.)
self.s.part.add(id=1, pos=[1, 0, 0], type=0, q=-1.)
# Small alpha means large short-range contribution
self.s.actors.add(P3M(prefactor=1, r_cut=3.0, accuracy=1e-3,
mesh=32, cao=7, alpha=0.1, tune=False))
# Only short-range part of the coulomb energy
pair_energy = self.s.analysis.energy()[('coulomb', 0)]
self.assertGreater(abs(pair_energy), 0.)
self.s.integrator.run(0)
pair_force = self.s.part[0].f[0]
self.assertGreater(abs(pair_force), 0.)
self.assertAlmostEqual(self.s.part[1].f[0], -pair_force, places=7)
pair_pressure = self.s.analysis.pressure()[('coulomb', 0)]
self.assertGreater(abs(pair_pressure), 0.)
self.s.part[0].exclusions = [1]
# Force and energy should not be changed by the exclusion
self.s.integrator.run(0)
self.assertAlmostEqual(self.s.part[0].f[0], pair_force, places=7)
self.assertAlmostEqual(self.s.part[1].f[0], -pair_force, places=7)
self.assertAlmostEqual(self.s.analysis.energy()[('coulomb', 0)], pair_energy, places=7)
self.assertAlmostEqual(self.s.analysis.pressure()[('coulomb', 0)], pair_pressure, places=7)
if __name__ == "__main__":
print("Features: ", espressomd.features())
ut.main()
class CoulombCloudWall(ut.TestCase):
if "ELECTROSTATICS" in espressomd.features():
"""This compares p3m, p3m_gpu, scafacos_p3m and scafacos_p2nfft
electrostatic forces and energy against stored data."""
S = espressomd.System(box_l=[1.0, 1.0, 1.0])
S.seed = S.cell_system.get_state()['n_nodes'] * [1234]
np.random.seed(S.seed)
forces = {}
tolerance = 1E-3
# Reference energy from p3m in the tcl test case
reference_energy = 2. * 148.94229549
def setUp(self):
self.S.box_l = (10, 10, 20)
self.S.time_step = 0.01
self.S.cell_system.skin = 0.4
# Clear actors that might be left from prev tests
if self.S.actors:
del self.S.actors[0]
self.S.part.clear()
data = np.genfromtxt(
abspath("data/coulomb_cloud_wall_duplicated_system.data"))
# Add particles to system and store reference forces in hash
# Input format: id pos q f
for particle in data:
id = particle[0]
pos = particle[1:4]
q = particle[4]
f = particle[5:]
self.S.part.add(id=int(id), pos=pos, q=q)
self.forces[id] = f
def compare(self, method_name, energy=True):
# Compare forces and energy now in the system to stored ones
# Force
force_abs_diff = 0.
for p in self.S.part:
force_abs_diff += abs(
np.sqrt(sum((p.f - self.forces[p.id])**2)))
force_abs_diff /= len(self.S.part)
# Energy
if energy:
energy_abs_diff = abs(self.S.analysis.energy()["total"] -
self.reference_energy)
self.assertTrue(
energy_abs_diff <= self.tolerance,
"Absolute energy difference " + str(energy_abs_diff) +
" too large for " + method_name)
self.assertTrue(
force_abs_diff <= self.tolerance,
"Absolute force difference " + str(force_abs_diff) +
" too large for method " + method_name)
# Tests for individual methods
if "P3M" in espressomd.features():
def test_p3m(self):
self.S.actors.add(
espressomd.electrostatics.P3M(prefactor=1,
r_cut=1.001,
accuracy=1e-3,
mesh=[64, 64, 128],
cao=7,
alpha=2.70746,
tune=False))
self.S.integrator.run(0)
self.compare("p3m", energy=True)
@ut.skipIf(not espressomd.gpu_available(), "No gpu")
def test_p3m_gpu(self):
if str(espressomd.cuda_init.CudaInitHandle().device_list[0]
) == "Device 687f":
print("Test skipped on AMD GPU")
return
self.S.actors.add(
espressomd.electrostatics.P3MGPU(prefactor=1,
r_cut=1.001,
accuracy=1e-3,
mesh=[64, 64, 128],
cao=7,
alpha=2.70746,
tune=False))
self.S.integrator.run(0)
self.compare("p3m_gpu", energy=False)
def test_zz_deactivation(self):
# Is the energy 0, if no methods active
self.assertTrue(self.S.analysis.energy()["total"] == 0.0)
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
This sample illustrates how particles of interest can be accessed via slicing.
"""
import espressomd
from espressomd import thermostat
import numpy as np
print("""
=======================================================
= slice_input.py =
=======================================================
Program Information:""")
print(espressomd.features())
# System parameters
#############################################################
box_l = 10.0
# Integration parameters
#############################################################
system = espressomd.System(box_l=[box_l] * 3)
system.set_random_state_PRNG()
#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
np.random.seed(seed=system.seed)
system.time_step = 0.01
def check_fluctuation_dissipation(self,n):
"""
Check the fluctuation-dissipation relations: thermalization
and diffusion properties.
Parameters
----------
n : :obj:`int`
Number of particles of the each type. There are 2 types.
"""
## The thermalization and diffusion test
# Checks if every degree of freedom has 1/2 kT of energy, even when
# mass and inertia tensor are active
# Check the factual translational diffusion.
#
# matrices: [2 types of particless] x [3 dimensions X Y Z]
# velocity^2, omega^2, position^2
v2 = np.zeros((2, 3))
o2 = np.zeros((2, 3))
dr2 = np.zeros((2, 3))
# Variance to compare with:
sigma2_tr = np.zeros((2))
# Comparable variance:
dr_norm = np.zeros((2))
pos0 = np.zeros((2 * n, 3))
for p in range(n):
for k in range(2):
ind = p + k * n
pos0[ind, :] = self.es.part[ind].pos
dt0 = self.mass / self.gamma_tran_p_validate
loops = 250
print("Thermalizing...")
therm_steps = 20
self.es.integrator.run(therm_steps)
print("Measuring...")
int_steps = 5
for i in range(loops):
self.es.integrator.run(int_steps)
# Get kinetic energy in each degree of freedom for all particles
for p in range(n):
for k in range(2):
ind = p + k * n
v = self.es.part[ind].v
if "ROTATION" in espressomd.features():
o = self.es.part[ind].omega_body
o2[k, :] = o2[k, :] + np.power(o[:], 2)
pos = self.es.part[ind].pos
v2[k, :] = v2[k, :] + np.power(v[:], 2)
dr2[k, :] = np.power((pos[:] - pos0[ind, :]), 2)
dt = (int_steps * (i + 1) + therm_steps) * \
self.es.time_step
# translational diffusion variance: after a closed-form
# integration of the Langevin EOM;
# ref. the eq. (10.2.26) N. Pottier, https://doi.org/10.1007/s10955-010-0114-6 (2010)
# after simple transformations and the dimensional model matching (cf. eq. (10.1.1) there):
sigma2_tr[k] = 0.0
for j in range(3):
sigma2_tr[k] += self.D_tran_p_validate[k,
j] * (2.0 * dt + dt0[k,
j] * (- 3.0 + 4.0 * math.exp(- dt / dt0[k,
j]) - math.exp(- 2.0 * dt / dt0[k,
j])))
dr_norm[k] += (sum(dr2[k, :]) - sigma2_tr[k]) / sigma2_tr[k]
tolerance = 0.15
Ev = 0.5 * self.mass * v2 / (n * loops)
Eo = 0.5 * self.J * o2 / (n * loops)
dv = np.zeros((2))
do = np.zeros((2))
do_vec = np.zeros((2, 3))
for k in range(2):
dv[k] = sum(Ev[k, :]) / (3.0 * self.halfkT_p_validate[k]) - 1.0
do[k] = sum(Eo[k, :]) / (3.0 * self.halfkT_p_validate[k]) - 1.0
do_vec[k, :] = Eo[k, :] / self.halfkT_p_validate[k] - 1.0
dr_norm /= (n * loops)
for k in range(2):
print("\n")
print("k = " + str(k))
self.assertLessEqual(
abs(
dv[k]),
tolerance,
msg='Relative deviation in translational energy too large: {0}'.format(
dv[k]))
if "ROTATION" in espressomd.features():
self.assertLessEqual(
abs(
do[k]),
tolerance,
msg='Relative deviation in rotational energy too large: {0}'.format(
do[k]))
self.assertLessEqual(abs(
do_vec[k, 0]), tolerance, msg='Relative deviation in rotational energy per the body axis X is too large: {0}'.format(do_vec[k, 0]))
self.assertLessEqual(abs(
do_vec[k, 1]), tolerance, msg='Relative deviation in rotational energy per the body axis Y is too large: {0}'.format(do_vec[k, 1]))
self.assertLessEqual(abs(
do_vec[k, 2]), tolerance, msg='Relative deviation in rotational energy per the body axis Z is too large: {0}'.format(do_vec[k, 2]))
self.assertLessEqual(
abs(
dr_norm[k]),
tolerance,
msg='Relative deviation in translational diffusion is too large: {0}'.format(
dr_norm[k]))