icSolvent = ymr.InitialConditions.FromArray(pos=pos.tolist(), vel=vel.tolist())
vv = ymr.Integrators.VelocityVerlet('vv')
u.registerParticleVector(pvSolvent, icSolvent)
u.registerIntegrator(vv)
u.setIntegrator(vv, pvSolvent)
meshRbc = ymr.ParticleVectors.MembraneMesh("rbc_mesh.off")
pvRbc = ymr.ParticleVectors.MembraneVector("rbc", mass=1.0, mesh=meshRbc)
icRbc = ymr.InitialConditions.Membrane(
[[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 0.7071, 0.0, 0.7071, 0.0]]
)
u.registerParticleVector(pvRbc, icRbc)
prm_rbc = lina_parameters(1.0)
int_rbc = ymr.Interactions.MembraneForces("int_rbc", "wlc", "Kantor", **prm_rbc, stress_free=True)
if args.subStep:
integrator = ymr.Integrators.SubStep('substep_membrane', substeps, int_rbc)
u.registerIntegrator(integrator)
u.setIntegrator(integrator, pvRbc)
else:
u.setIntegrator(vv, pvRbc)
u.registerInteraction(int_rbc)
u.setInteraction(int_rbc, pvRbc, pvRbc)
bb = ymr.Bouncers.Mesh("bounceRbc", kbt=0.0)
u.registerBouncer(bb)
u.setBouncer(bb, pvRbc, pvSolvent)
u = mir.Mirheo(ranks, domain, dt, debug_level=3, log_filename='log', no_splash=True)
pv_sol = mir.ParticleVectors.ParticleVector('solvent', mass = 1)
ic_sol = mir.InitialConditions.Uniform(number_density=8)
u.registerParticleVector(pv_sol, ic_sol)
mesh_rbc = mir.ParticleVectors.MembraneMesh("rbc_mesh.off")
pv_rbc = mir.ParticleVectors.MembraneVector("rbc", mass=1.0, mesh=mesh_rbc)
ic_rbc = mir.InitialConditions.Membrane([[8.0, 4.0, 5.0, 1.0, 0.0, 0.0, 0.0]])
u.registerParticleVector(pv_rbc, ic_rbc)
dpd = mir.Interactions.Pairwise('dpd', rc=1.0, kind="DPD", a=10.0, gamma=10.0, kBT=0.01, power=0.25)
prm_rbc = lina_parameters(1.0)
int_rbc = mir.Interactions.MembraneForces("int_rbc", "wlc", "Kantor", **prm_rbc, stress_free=True)
u.registerInteraction(dpd)
if args.substep:
integrator = mir.Integrators.SubStep('substep_membrane', substeps, [int_rbc])
u.registerIntegrator(integrator)
u.setIntegrator(integrator, pv_rbc)
else:
vv = mir.Integrators.VelocityVerlet('vv')
u.registerInteraction(int_rbc)
u.setInteraction(int_rbc, pv_rbc, pv_rbc)
u.registerIntegrator(vv)
u.setIntegrator(vv, pv_rbc)
log_filename='log',
no_splash=True)
mesh_rbc = mir.ParticleVectors.MembraneMesh("rbc_mesh.off")
inactive_id = 0
active_id = 1
pv_rbc = mir.ParticleVectors.MembraneVector("rbc", mass=1.0, mesh=mesh_rbc)
ic_rbc = mir.InitialConditions.MembraneWithTypeId(
[[8.0, 4.0, 5.0, 1.0, 0.0, 0.0, 0.0], [4.0, 4.0, 5.0, 1.0, 0.0, 0.0, 0.0]],
[active_id, inactive_id])
u.registerParticleVector(pv_rbc, ic_rbc)
# only the active membrane gets forces
prm_rbc = lina_parameters(1.0, args.fluctuations)
int_rbc = mir.Interactions.MembraneForces("int_rbc",
"wlc",
"Kantor",
**prm_rbc,
stress_free=args.stress_free,
filter_desc="by_type_id",
type_id=active_id)
vv = mir.Integrators.VelocityVerlet('vv')
u.registerIntegrator(vv)
u.setIntegrator(vv, pv_rbc)
u.registerInteraction(int_rbc)
u.setInteraction(int_rbc, pv_rbc, pv_rbc)
u.registerPlugins(
ranks = (1, 1, 1)
domain = (12, 8, 10)
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log')
if args.sphereStressFree:
mesh_rbc = ymr.ParticleVectors.MembraneMesh("rbc_mesh.off", "sphere_mesh.off")
else:
mesh_rbc = ymr.ParticleVectors.MembraneMesh("rbc_mesh.off")
pv_rbc = ymr.ParticleVectors.MembraneVector("rbc", mass=1.0, mesh=mesh_rbc)
ic_rbc = ymr.InitialConditions.Membrane([[8.0, 4.0, 5.0, 1.0, 0.0, 0.0, 0.0]])
u.registerParticleVector(pv_rbc, ic_rbc)
prm_rbc = lina_parameters(1.0, args.fluctuations)
int_rbc = ymr.Interactions.MembraneForces("int_rbc", "wlc", "Kantor", **prm_rbc, stress_free=args.stressFree)
vv = ymr.Integrators.VelocityVerlet('vv')
u.registerIntegrator(vv)
u.setIntegrator(vv, pv_rbc)
u.registerInteraction(int_rbc)
u.setInteraction(int_rbc, pv_rbc, pv_rbc)
u.registerPlugins(ymr.Plugins.createDumpMesh("mesh_dump", pv_rbc, 150, "ply/"))
u.run(5000)
if pv_rbc is not None:
rbc_pos = pv_rbc.getCoordinates()
np.savetxt("pos.rbc.txt", rbc_pos)
