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)
# for i in range(0,k,1):
# dist = DistanceBetween(ox, oy, oz, cell_positions[i][0], cell_positions[i][1], cell_positions[i][2])
# if dist < (1.0 - allowed_overlap)*2*radius_rbc + 1.0:
# origin_ok = 0
#
# # if everything was ok, remember origin
# if origin_ok == 1:
# print ("seeding of cell: "+str(k)+" with origin: "+str(ox)+", "+str(oy)+", "+str(oz))
# sim_info.write("seeding of cell: "+str(k)+" with origin: "+str(ox)+", "+str(oy)+", "+str(oz) + " time: " + str(datetime.datetime.now()) + " " + "\n")
# sim_info.write("\n")
# cell_positions.append([ox,oy,oz])
# sim_info.close()
########## END - RANDOM SEEDING OF CELLS
# CREATING TEMPLATES FOR CELLS
rbc_type_1 = oif.OifCellType(nodes_file=rbc_nodes, triangles_file=rbc_triangles, system = system, ks=ks_rbc_1, kb=kb_rbc_1, kal=kal_rbc_1, kag=kag_rbc_1, kv=kv_rbc_1, kvisc=kvisc_rbc\
, resize =[resize_rbc, resize_rbc, resize_rbc], check_orientation=False, normal= True)
rbc_type_2 = oif.OifCellType(nodes_file=rbc_nodes, triangles_file=rbc_triangles, system = system, ks=ks_rbc_2, kb=kb_rbc_2, kal=kal_rbc_2, kag=kag_rbc_2, kv=kv_rbc_2, kvisc=kvisc_rbc\
, resize =[resize_rbc, resize_rbc, resize_rbc], check_orientation=False, normal= True)
# CREATING CELLS
rbcs = list()
# #Pre nahodny seeding
# for id, pos in enumerate(cell_positions):
# if id < diffCells:
# print("id cell = " + 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, rotate=[random.random()*2*np.pi, random.random()*2*np.pi, random.random()*2*np.pi], particle_mass=mass_rbc/nnode_rbc)
foutParam.write("")
#####################################
#initialization
######################################
system = espressomd.System(box_l=[boxX, boxY, boxZ])
system.time_step = timeStep
system.cell_system.skin = 0.2
# 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)
else:
warnings.warn("Folder {} already exists, files will be overwritten"
.format(output_path))
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
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)
cell_positions.append([cluster_centerX,
cluster_centerY - (cell_radius + gap_size/2.0),
cluster_centerZ])
cell_positions.append([cluster_centerX + taznica_length,
cluster_centerY,
cluster_centerZ])
cell_positions.append([cluster_centerX + tazisko_distance_from_base,
cluster_centerY,
cluster_centerZ + taznica_length_from_center] )
typeCell_soft = oif.OifCellType(nodes_file="input/sphere642nodes.dat",
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
