def test(self):
import object_in_fluid as oif
system = espressomd.System(box_l=(10, 10, 10))
self.assertEqual(system.max_oif_objects, 0)
system.time_step = 0.4
system.cell_system.skin = 0.5
system.thermostat.set_langevin(kT=0, gamma=0.7, seed=42)
# creating the template for OIF object
cell_type = oif.OifCellType(
nodes_file=abspath("data/sphere393nodes.dat"),
triangles_file=abspath("data/sphere393triangles.dat"),
system=system,
ks=1.0,
kb=1.0,
kal=1.0,
kag=0.1,
kv=0.1,
check_orientation=False,
resize=(3.0, 3.0, 3.0))
# creating the OIF object
cell0 = oif.OifCell(cell_type=cell_type,
particle_type=0,
origin=[5.0, 5.0, 5.0])
self.assertEqual(system.max_oif_objects, 1)
# cell0.output_vtk_pos_folded(file_name="cell0_0.vtk")
# fluid
diameter_init = cell0.diameter()
print("initial diameter = " + str(diameter_init))
# OIF object is being stretched by factor 1.5
maxCycle = 500
system.part[:].pos = (system.part[:].pos - 5) * 1.5 + 5
diameter_stretched = cell0.diameter()
print("stretched diameter = " + str(diameter_stretched))
# main integration loop
# OIF object is let to relax into relaxed shape of the sphere
for i in range(3):
system.integrator.run(steps=90)
diameter_final = cell0.diameter()
print("final diameter = " + str(diameter_final))
self.assertAlmostEqual(diameter_final / diameter_init - 1,
0,
delta=0.005)
# sim_info = open(directory + "/sim_info.dat", "a")
# sim_info.write("\n")
# sim_info.write("\n")
# sim_info.write("all cells were created: " + str(datetime.datetime.now()) + "\n")
# sim_info.close()
# # Pre seeding z nodes.dat
for id, pos in enumerate(cell_positions):
if id < diffCells:
# if (id < diffCells/2) or ((num_cells/2)-1 < id < (num_cells/2)+(diffCells/2)): # pre dlzku kanala 120mu - rovnaky seeding 2x za sebou
print("id = " + str(id) + " type_1")
sim_info = open(directory + "/sim_info.dat", "a")
sim_info.write("cell " + str(id) + " -> type_1 | ")
sim_info.close()
cell_rbc = oif.OifCell(cell_type=rbc_type_1,
particle_type=id,
origin=pos,
particle_mass=mass_rbc / nnode_rbc)
cell_rbc.set_mesh_points("seeding/seeding_hct15_4_cy1190000/nodes" +
str(id) + ".dat")
rbcs.append(cell_rbc)
else:
print("id = " + str(id) + " type_2")
sim_info = open(directory + "/sim_info.dat", "a")
sim_info.write("cell " + str(id) + " -> type_2 | ")
sim_info.close()
cell_rbc = oif.OifCell(cell_type=rbc_type_2,
particle_type=id,
origin=pos,
particle_mass=mass_rbc / nnode_rbc)
cell_rbc.set_mesh_points("seeding/seeding_hct15_4_cy1190000/nodes" +
str(id) + ".dat")
# creating the template for cells
cellType = oif.OifCellType(nodes_file=fileNodes,
triangles_file=fileTriangles,
system=system,
ks=ks,
kb=kb,
kal=kal,
kag=kag,
kv=kv,
kvisc=kvisc,
resize=[stretch, stretch, stretch])
# creating the RBC
cell = oif.OifCell(cell_type=cellType,
particle_type=0,
origin=[originX, originY, originZ],
rotate=[np.pi / 2.0, 0.0, 0.0],
particle_mass=partMass)
# fluid
lbf = lb.LBFluid(agrid=grid, dens=dens, visc=visc, tau=timeStep)
system.actors.add(lbf)
system.thermostat.set_lb(LB_fluid=lbf, gamma=friction)
# consider taking all nodes that have x coordinate approximately <5% or >95% total
rightStretchedParticles = list()
leftStretchedParticles = list()
for i in cell.mesh.points:
posI = (i.get_pos()[0] - cell.get_origin()[0]) / stretch
if (posI >= xBoundMinR and posI <= xBoundMaxR):
boxX = 22.0
boxY = 14.0
boxZ = 15.0
time_step = 0.1
system = espressomd.System(box_l=(boxX, boxY, boxZ))
system.time_step = time_step
system.cell_system.skin = 0.2
# creating the template for RBCs
cell_type = oif.OifCellType(
nodes_file="input/rbc374nodes.dat", triangles_file="input/rbc374triangles.dat",
system=system, ks=0.04, kb=0.016, kal=0.02, kag=0.9, kv=1.0, check_orientation=False, resize=(2.0, 2.0, 2.0))
# creating the RBCs
cell0 = oif.OifCell(cell_type=cell_type,
particle_type=0, origin=[5.0, 5.0, 3.0])
cell1 = oif.OifCell(cell_type=cell_type,
particle_type=1, origin=[5.0, 5.0, 7.0])
# cell-wall interactions
system.non_bonded_inter[0, 10].soft_sphere.set_params(
a=0.0001, n=1.2, cutoff=0.1, offset=0.0)
system.non_bonded_inter[1, 10].soft_sphere.set_params(
a=0.0001, n=1.2, cutoff=0.1, offset=0.0)
# fluid
lbf = espressomd.lb.LBFluid(agrid=1, dens=1.0, visc=1.5, tau=0.1,
ext_force_density=[0.002, 0.0, 0.0])
system.actors.add(lbf)
system.thermostat.set_lb(LB_fluid=lbf, gamma=1.5)
def test(self):
import object_in_fluid as oif
system = espressomd.System(box_l=(10, 10, 10))
self.assertEqual(system.max_oif_objects, 0)
system.time_step = 0.4
system.cell_system.skin = 0.5
# creating the template for OIF object
cell_type = oif.OifCellType(
nodes_file=abspath("data/sphere393nodes.dat"),
triangles_file=abspath("data/sphere393triangles.dat"),
system=system,
ks=1.0,
kb=1.0,
kal=1.0,
kag=0.1,
kv=0.1,
check_orientation=False,
resize=(3.0, 3.0, 3.0))
# creating the OIF object
cell0 = oif.OifCell(cell_type=cell_type,
particle_type=0,
origin=[5.0, 5.0, 5.0])
self.assertEqual(system.max_oif_objects, 1)
# cell0.output_vtk_pos_folded(file_name="cell0_0.vtk")
# fluid
diameter_init = cell0.diameter()
print("initial diameter = " + str(diameter_init))
# OIF object is being stretched by factor 1.5
system.part[:].pos = (system.part[:].pos - 5) * 1.5 + 5
diameter_stretched = cell0.diameter()
print("stretched diameter = " + str(diameter_stretched))
# Apply non-isotropic deformation
system.part[:].pos = system.part[:].pos * np.array((0.96, 1.05, 1.02))
# Test that restoring forces net to zero and don't produce a torque
system.integrator.run(1)
np.testing.assert_allclose(np.sum(system.part[:].f, axis=0),
[0., 0., 0.],
atol=1E-12)
total_torque = np.zeros(3)
for p in system.part:
total_torque += np.cross(p.pos, p.f)
np.testing.assert_allclose(total_torque, [0., 0., 0.], atol=2E-12)
# main integration loop
system.thermostat.set_langevin(kT=0, gamma=0.7, seed=42)
# OIF object is let to relax into relaxed shape of the sphere
for _ in range(2):
system.integrator.run(steps=240)
diameter_final = cell0.diameter()
print("final diameter = " + str(diameter_final))
self.assertAlmostEqual(diameter_final / diameter_init - 1,
0,
delta=0.005)
triangles_file="input/sphere642triangles.dat",
check_orientation=False,
system=system,
ks=0.02,
kb=0.1,
kal=0.05,
kag=0.7,
kv=0.9,
normal=True,
resize=[cell_radius, cell_radius, cell_radius])
# create cells
cells = []
for i in range(4):
cells.append(oif.OifCell(cell_type=typeCell_soft,
particle_type=i,
origin=cell_positions[i],
particle_mass=0.5))
# cell-wall interactions
for i in range(len(cells)):
system.non_bonded_inter[i,boundary_particle_type].soft_sphere.set_params(a=0.002,
n=1.5,
cutoff=0.8,
offset=0.0)
# cell-cell interactions
# attractive Morse, repulsive soft_sphere (membrane collision can be used here instead of soft-sphere):
for i in range(len(cells)):
for j in range(i+1, len(cells)):
system.non_bonded_inter[i,j].morse.set_params(eps=0.4,
alpha=0.2,
