#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/minimal-diamond.py", sim_steps=10)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
ut.main()
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import importlib_wrapper
import numpy as np
try:
import pint # pylint: disable=unused-import
except ImportError:
tutorial = importlib_wrapper.MagicMock()
skipIfMissingFeatures = ut.skip(
"Python module pint not available, skipping test!")
else:
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/constant_pH/constant_pH.py",
script_suffix="ideal",
USE_WCA=False,
USE_ELECTROSTATICS=False,
NUM_PHS=10)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test(self):
ref_values = 1. / (1 + 10**(tutorial.pKa - tutorial.pHs))
sim_values = tutorial.av_alpha
sim_values_error = tutorial.err_alpha
# test alpha +/- 0.02 and standard error of alpha less than 0.02
np.testing.assert_allclose(sim_values, ref_values, rtol=0., atol=0.02)
np.testing.assert_array_less(sim_values_error, 0.02)
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
import pathlib
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/ekboundaries.py", gpu=True, n_int_cycles=50)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
def test_file_generation(self):
# test .vtk files exist
path_vtk_root = pathlib.Path("ek")
for basename in [
"pos_dens_0.vtk", "pos_flux_0.vtk", "ekv_0.vtk",
"neg_dens_0.vtk", "neg_flux_0.vtk", "ekb_0.vtk"
]:
filepath = path_vtk_root / basename
self.assertTrue(filepath.is_file(), f"File {filepath} not created")
# 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/>.
import unittest as ut
import importlib_wrapper
import os
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/09-swimmer_reactions/SOLUTIONS/reaction.py",
cmd_arguments=[1],
equi_steps=250,
equi_length=10,
prod_steps=200,
prod_length=10)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_file_generation(self):
for name in ["msd_0.dat", "avacf_0.dat"]:
filepath = os.path.join(tutorial.outdir, name)
self.assertTrue(os.path.isfile(filepath),
filepath + " not created")
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import importlib_wrapper
def disable_GUI(code):
# integrate without visualizer
breakpoint = "visualizer.update()"
assert breakpoint in code
code = code.replace(breakpoint, "")
breakpoint = "t = threading.Thread(target=main_thread)"
assert breakpoint in code
code = code.split(breakpoint, 1)[0] + "main_thread()"
return code
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/visualization_ljliquid.py",
substitutions=disable_GUI,
int_n_times=5)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/ferrofluid/ferrofluid_part1.py",
EQUIL_STEPS=200, EQUIL_ROUNDS=10,
CI_DP3M_PARAMS={'cao': 3, 'r_cut': 8.34, 'mesh': [8, 8, 8], 'alpha': 0.2115, 'tune': False})
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test(self):
self.assertEqual(
int(np.sum(tutorial.n_clusters)), len(tutorial.cluster_sizes))
for i in range(8):
self.assertLess(
tutorial.size_dist[0][i + 1],
tutorial.size_dist[0][i])
#
# 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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
np.random.seed(41)
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/raspberry_electrophoresis/raspberry_electrophoresis.py",
gpu=True, box_l=20., num_iterations=20, num_steps_per_iteration=20)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
'''Check the raspberry travels a longer distance on the x-axis'''
system = tutorial.system
def test_steepest_descent_convergence(self):
self.assertLess(tutorial.force_max, 10.)
def test_trajectory_sample(self):
trajectory = np.loadtxt('posVsTime_sample.dat')[:, 1:4]
x, y, z = np.abs(trajectory[-1, :] - trajectory[0, :])
self.assertGreater(x, y)
# (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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/lattice_boltzmann/lattice_boltzmann_poiseuille_flow.py",
gpu=True)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_flow_profile(self):
analytical = tutorial.y_values
simulation = tutorial.fluid_velocities
rmsd = np.sqrt(np.mean(np.square(analytical - simulation)))
self.assertLess(rmsd, 2e-5 * tutorial.AGRID / tutorial.lbf.tau)
if __name__ == "__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/>.
import unittest as ut
import importlib_wrapper
def shorten_loop(code):
breakpoint = "while True:"
assert breakpoint in code
code = code.replace(breakpoint, "for _ in range(6):", 1)
return code
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/load_checkpoint.py", substitutions=shorten_loop)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
# make simulation deterministic
np.random.seed(42)
benchmark, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@BENCHMARKS_DIR@/ferrofluid.py", measurement_steps=100, n_iterations=2,
cmd_arguments=["--particles_per_core", "400"], min_skin=0.225, max_skin=0.225,
dp3m_params={'prefactor': 1, 'accuracy': 1e-4, 'cao': 7, 'r_cut': 5.193,
'mesh': [20, 20, 20], 'alpha': 0.64788, 'tune': False})
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = benchmark.system
if __name__ == "__main__":
ut.main()
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/p3m.py", int_steps=100, int_n_times=5)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
ut.main()
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
benchmark, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@BENCHMARKS_DIR@/p3m.py",
cmd_arguments=["--particles_per_core", "800"],
n_iterations=2)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = benchmark.system
if __name__ == "__main__":
ut.main()
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
import os
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/active_matter/solutions/rectification_geometry.py")
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_file_generation(self):
filepath = os.path.join(tutorial.outdir, "boundary.vtk")
self.assertTrue(os.path.isfile(filepath), filepath + " not created")
if __name__ == "__main__":
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/>.
import unittest as ut
import importlib_wrapper as iw
import numpy as np
import sys
# these tutorials need to be executed sequentially
tutorial_simulation, skipIfMissingFeatures_simulation = iw.configure_and_import(
"@TUTORIALS_DIR@/07-electrokinetics/07-electrokinetics.py",
gpu=True, integration_length=600, dt=0.5)
tutorial_analytical, skipIfMissingFeatures_plot = iw.configure_and_import(
"@TUTORIALS_DIR@/07-electrokinetics/scripts/eof_analytical.py")
tutorial_plot, skipIfMissingFeatures_plot = iw.configure_and_import(
"@TUTORIALS_DIR@/07-electrokinetics/scripts/plot.py")
@skipIfMissingFeatures_simulation
@skipIfMissingFeatures_plot
class Tutorial(ut.TestCase):
system = tutorial_simulation.system
def normalize_two_datasets(self, a, b):
offset = min(np.min(a), np.min(b))
a -= offset
# 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/>.
import unittest as ut
import importlib_wrapper
import os
import numpy as np
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/06-active_matter/SOLUTIONS/rectification_simulation.py",
cmd_arguments=[6.0],
prod_steps=80,
prod_length=100)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_rectification(self):
x = tutorial.system.part[:].pos[:, 0]
left_chamber = np.sum(x < tutorial.length / 2.0)
right_chamber = np.sum(x > tutorial.length / 2.0)
excess = (right_chamber - left_chamber) * 100. / tutorial.npart
# expecting at least 5% excess due to rectification
self.assertGreater(excess, 5.0)
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/10-reaction_ensemble/scripts/RE_vs_cpH.py")
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
if __name__ == "__main__":
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/>.
import unittest as ut
import importlib_wrapper
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/grand_canonical.py",
n_int_cycles=51,
n_int_steps=5,
warm_n_times=10,
warm_steps=50,
cmd_arguments=[0.01, 0.01])
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
def test_deviation_to_target_concentration(self):
# deviation < 10%
self.assertLess(abs(sample.deviation), 10.0)
if __name__ == "__main__":
# (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/>.
import unittest as ut
import importlib_wrapper
import os
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/active_matter/solutions/flow_field.py", gpu=True,
cmd_arguments=["pusher", 5.0], PROD_STEPS=100, PROD_LENGTH=50)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_file_generation(self):
for name in ["trajectory.dat", "position_0.vtk", "lb_velocity_0.vtk"]:
filepath = os.path.join(tutorial.outdir, name)
self.assertTrue(
os.path.isfile(filepath),
filepath + " not created")
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import importlib_wrapper
def disable_GUI(code):
# integrate without visualizer
breakpoint = "visualizer.run(1)"
assert breakpoint in code
code = code.replace(breakpoint, "steps=1\nsystem.integrator.run(steps)", 1)
return code
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/visualization_elc.py",
substitutions=disable_GUI, steps=5000)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
def test_dipole_moment(self):
import espressomd.observables
obs = espressomd.observables.DipoleMoment(
ids=self.system.part.all().id)
dipm = obs.calculate()
self.assertLess(dipm[2], 0, msg="charges moved in the wrong direction")
# the dipole moment should be the strongest along the z-axis
self.assertGreater(abs(dipm[2]), abs(dipm[0]))
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/minimal-charged-particles.py", box_l=6.0, int_steps=100)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
ut.main()
import unittest as ut
import importlib_wrapper
import numpy as np
# make simulation deterministic
np.random.seed(42)
benchmark, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@BENCHMARKS_DIR@/p3m.py",
cmd_arguments=["--particles_per_core", "400"],
measurement_steps=100,
n_iterations=2,
min_skin=0.262,
max_skin=0.262,
p3m_params={
'prefactor': 4,
'accuracy': 1e-4,
'cao': 7,
'r_cut': 3.182,
'mesh': [24, 24, 24],
'alpha': 1.02742,
'tune': False
})
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = benchmark.system
if __name__ == "__main__":
# 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/>.
import unittest as ut
import importlib_wrapper
def disable_visualizer_GUI(code):
breakpoint = "while True:"
assert breakpoint in code
code = code.replace(breakpoint, "for _ in range(5):", 1)
breakpoint = "t = threading.Thread(target=main)"
assert breakpoint in code
code = code.split(breakpoint, 1)[0] + "main()"
return code
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/billiard.py", substitutions=disable_visualizer_GUI)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
ut.main()
# (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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/01-lennard_jones/01-lennard_jones.py",
substitutions=lambda code: code.replace('r_star = ', 'r_star = r #', 1))
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_global_variables(self):
self.assertLess(tutorial.standard_error_total_energy, 2.5)
def test_rdf_curve(self):
self.assertGreater(
np.corrcoef(tutorial.avg_rdf, tutorial.theo_rdf)[1, 0], 0.985)
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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/>.
import unittest as ut
import importlib_wrapper
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/minimal-polymer.py", t_steps=10)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
if __name__ == "__main__":
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/>.
import unittest as ut
import importlib_wrapper
import os
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/active_matter/solutions/enhanced_diffusion.py",
cmd_arguments=[5.0],
SAMP_STEPS=500,
SAMP_LENGTH=100)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_file_generation(self):
for name in ["msd_{}_0.dat", "vacf_{}_0.dat", "avacf_{}_0.dat"]:
filepath = os.path.join(tutorial.outdir, name.format(tutorial.vel))
self.assertTrue(os.path.isfile(filepath),
filepath + " not created")
#
# 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/>.
import unittest as ut
import importlib_wrapper
import numpy as np
implementation = "gpu" if "gpu" in "@TEST_LABELS@".split(";") else "cpu"
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/lbf.py", gpu=implementation == "gpu",
cmd_arguments=["--" + implementation], script_suffix=implementation)
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
def test_electrophoresis_gradient(self):
# the force is applied along the z-axis
gradient = np.mean(np.gradient(sample.f_list.T, axis=1), axis=1)
self.assertAlmostEqual(gradient[0], 0.0, places=11)
self.assertAlmostEqual(gradient[1], 0.0, places=11)
self.assertAlmostEqual(gradient[2], -7.66981e-7, places=11)
# (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/>.
import unittest as ut
import importlib_wrapper
import os
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/06-active_matter/SOLUTIONS/rectification_geometry.py",
gpu=True)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test_file_generation(self):
filepath = os.path.join(tutorial.outdir, "boundary.vtk")
self.assertTrue(os.path.isfile(filepath), filepath + " not created")
if __name__ == "__main__":
ut.main()
import importlib_wrapper
import numpy as np
sd_device = "--gpu" if "gpu" in "@TEST_SUFFIX@" else "--cpu"
sd_method = "--fts" if "fts" in "@TEST_SUFFIX@" else "--ft"
if sd_method == "--fts" and sd_device == "--cpu":
y_min = -555
intsteps = 5500
else:
y_min = -200
intsteps = 2100
sample, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@SAMPLES_DIR@/dancing.py",
script_suffix="@TEST_SUFFIX@",
gpu=(sd_device == "--gpu"),
cmd_arguments=[sd_device, sd_method],
intsteps=intsteps,
ref_data="@CMAKE_SOURCE_DIR@/testsuite/python/data/dancing.txt")
@skipIfMissingFeatures
class Sample(ut.TestCase):
system = sample.system
def test_trajectory(self):
# compare the simulated and published trajectories
simul = sample.positions[:, :, 0:2]
paper = sample.data.reshape([-1, 3, 2])
for pid in range(3):
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import importlib_wrapper
def disable_visualizer_GUI(code):
breakpoint = "t = Thread(target=main)"
assert breakpoint in code
code = code.split(breakpoint, 1)[0] + "main()"
return code
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/08-visualization/08-visualization.py",
substitutions=disable_visualizer_GUI,
int_n_times=5,
int_steps=100,
matplotlib_notebook=False)
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
if __name__ == "__main__":
ut.main()
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import importlib_wrapper
import numpy as np
try:
import pint # pylint: disable=unused-import
except ImportError:
tutorial = importlib_wrapper.MagicMock()
skipIfMissingFeatures = ut.skip(
"Python module pint not available, skipping test!")
else:
tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@TUTORIALS_DIR@/constant_pH/constant_pH.py", script_suffix="ideal")
@skipIfMissingFeatures
class Tutorial(ut.TestCase):
system = tutorial.system
def test(self):
expected_values = 1. / (1 + 10**(tutorial.pK - tutorial.pHs))
simulated_values = tutorial.av_alpha
simulated_values_error = tutorial.err_alpha
# test alpha +/- 0.05 and standard error of alpha less than 0.05
np.testing.assert_allclose(expected_values,
simulated_values,
rtol=0,
atol=0.05)
