class MPIIOTest(ut.TestCase):
"""
Test class for the MPI-IO core functionality.
Generates random particles, dumps them, reads them in,
again and then checks the input against the initially created random
particles.
"""
s = espressomd.system.System(box_l=[1, 1, 1])
# Just a bunch of random interactions such that add_bond does not throw
for i in range(nbonds):
s.bonded_inter[i] = AngleHarmonic(bend=i, phi0=i)
test_particles = random_particles()
def setUp(self):
"""Sets up a system from test_particles and prepares environment
for the tests."""
clean_files() # Prior call might not have completed successfully
for p in self.test_particles:
self.s.part.add(id=p.id, type=p.type, pos=p.pos, v=p.v)
for b in p.bonds:
self.s.part[p.id].add_bond(b)
def tearDown(self):
clean_files()
def check_files_exist(self):
"""Checks if all necessary files have been written."""
for fn in filenames:
self.assertTrue(os.path.isfile(fn))
def check_sample_system(self):
"""Checks the particles in the ESPResSo system "self.s" against the
true values in "self.test_particles"."""
for p, q in zip(self.s.part, self.test_particles):
self.assertEqual(p.id, q.id)
self.assertEqual(p.type, q.type)
numpy.testing.assert_array_equal(numpy.copy(p.pos), q.pos)
numpy.testing.assert_array_equal(numpy.copy(p.v), q.v)
self.assertEqual(len(p.bonds), len(q.bonds))
# Check all bonds
for bp, bq in zip(p.bonds, q.bonds):
# Bond type - "bend" stores the index of the bond
self.assertEqual(bp[0].params["bend"], bq[0])
# Bond partners
numpy.testing.assert_array_equal(bp[1:], bq[1:])
def test_mpiio(self):
espressomd.io.mpiio.mpiio.write(
filename, types=True, positions=True, velocities=True, bonds=True)
self.check_files_exist()
self.s.part.clear() # Clear to be on the safe side
espressomd.io.mpiio.mpiio.read(
filename, types=True, positions=True, velocities=True, bonds=True)
self.check_sample_system()
def test_bind_three_particles(self):
# Setup particles
self.s.part.clear()
dx = np.array((1, 0, 0))
dy = np.array((0, 1, 0))
dz = np.array((0, 0, 1))
a = np.array((0.499, 0.499, 0.499))
b = a + 0.1 * dx
c = a + 0.03 * dx + 0.03 * dy
d = a + 0.03 * dx - 0.03 * dy
e = a - 0.1 * dx
self.s.part.add(id=0, pos=a)
self.s.part.add(id=1, pos=b)
self.s.part.add(id=2, pos=c)
self.s.part.add(id=3, pos=d)
self.s.part.add(id=4, pos=e)
# Setup bonds
res = 181
for i in range(0, res, 1):
self.s.bonded_inter[i + 2] = AngleHarmonic(bend=1,
phi0=float(i) /
(res - 1) * np.pi)
cutoff = 0.11
self.s.collision_detection.set_params(
mode="bind_three_particles",
bond_centers=self.H,
bond_three_particles=2,
three_particle_binding_angle_resolution=res,
distance=cutoff)
self.get_state_set_state_consistency()
self.s.time_step = 1E-6
self.s.integrator.run(1, recalc_forces=True)
self.verify_triangle_binding(cutoff, self.s.bonded_inter[2], res)
# Make sure no extra bonds appear
self.s.integrator.run(1, recalc_forces=True)
self.verify_triangle_binding(cutoff, self.s.bonded_inter[2], res)
# Place the particles in two steps and make sure, the bonds are the
# same
self.s.part.clear()
self.s.part.add(id=0, pos=a)
self.s.part.add(id=2, pos=c)
self.s.part.add(id=3, pos=d)
self.s.integrator.run(1, recalc_forces=True)
self.s.part.add(id=4, pos=e)
self.s.part.add(id=1, pos=b)
self.s.cell_system.set_domain_decomposition()
self.s.integrator.run(1, recalc_forces=True)
self.verify_triangle_binding(cutoff, self.s.bonded_inter[2], res)
self.s.cell_system.set_n_square()
self.s.part[:].bonds = ()
self.s.integrator.run(1, recalc_forces=True)
self.verify_triangle_binding(cutoff, self.s.bonded_inter[2], res)
self.s.time_step = self.time_step
def set_bending_interaction(self):
angle_harmonic = AngleHarmonic(bend=3.2, phi0=np.pi)
sys.bonded_inter.add(angle_harmonic)
list_of_stuff = [
x.id for x in sys.part.select(
lambda p: p.id in self.attributes.realz_indices)
]
for x in list_of_stuff[1:-1]:
sys.part[x].add_bond((angle_harmonic, x - 1, x + 1))