def createFromMesh(density, vertices, triangles, inertia, niter):
import ymero as ymr
def recenter(coords, com):
coords = [[r[0] - com[0], r[1] - com[1], r[2] - com[2]]
for r in coords]
return coords
dt = 0.001
# bounding box
bb_hi = np.array(vertices).max(axis=0).tolist()
bb_lo = np.array(vertices).min(axis=0).tolist()
mesh_size = [hi - lo for lo, hi in zip(bb_lo, bb_hi)]
fact = 2.0
domain = (float(int(fact * mesh_size[0] + 1)),
float(int(fact * mesh_size[1] + 1)),
float(int(fact * mesh_size[2] + 1)))
ranks = (1, 1, 1)
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log')
dpd = ymr.Interactions.DPD('dpd',
1.0,
a=10.0,
gamma=10.0,
kbt=0.5,
power=0.5)
vv = ymr.Integrators.VelocityVerlet('vv')
coords = [bb_lo, bb_hi]
com_q = [[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 1., 0, 0, 0]]
mesh = ymr.ParticleVectors.Mesh(vertices, triangles)
fakeOV = ymr.ParticleVectors.RigidObjectVector('OV',
mass=1,
inertia=inertia,
object_size=len(coords),
mesh=mesh)
fakeIc = ymr.InitialConditions.Rigid(com_q=com_q, coords=coords)
belongingChecker = ymr.BelongingCheckers.Mesh("meshChecker")
pvMesh = u.makeFrozenRigidParticles(belongingChecker, fakeOV, fakeIc, dpd,
vv, density, niter)
if pvMesh:
frozenCoords = pvMesh.getCoordinates()
frozenCoords = recenter(frozenCoords, com_q[0])
else:
frozenCoords = [[]]
if u.isMasterTask():
return frozenCoords
else:
return None
def run(niter, statsFname, commAddress):
dt = 0.001
ranks = (2, 1, 1)
domain = (12, 8, 10)
u = ymr.ymero(commAddress,
ranks,
domain,
debug_level=8,
log_filename='log')
pv = ymr.ParticleVectors.ParticleVector('pv', mass=1)
ic = ymr.InitialConditions.Uniform(density=2)
u.registerParticleVector(pv=pv, ic=ic)
dpd = ymr.Interactions.DPD('dpd',
1.0,
a=10.0,
gamma=10.0,
kbt=1.0,
dt=dt,
power=0.5)
u.registerInteraction(dpd)
u.setInteraction(dpd, pv, pv)
vv = ymr.Integrators.VelocityVerlet('vv', dt=dt)
u.registerIntegrator(vv)
u.setIntegrator(vv, pv)
stats = ymr.Plugins.createStats('stats', statsFname, 1000)
u.registerPlugins(stats)
u.run(niter)
def createEllipsoid(density, axes, niter):
import ymero as ymr
def recenter(coords, com):
coords = [[r[0] - com[0], r[1] - com[1], r[2] - com[2]]
for r in coords]
return coords
dt = 0.001
axes = tuple(axes)
ranks = (1, 1, 1)
fact = 3
domain = (fact * axes[0], fact * axes[1], fact * axes[2])
u = ymr.ymero(ranks, domain, debug_level=3, log_filename='log')
dpd = ymr.Interactions.DPD('dpd',
1.0,
a=10.0,
gamma=10.0,
kbt=0.5,
dt=dt,
power=0.5)
vv = ymr.Integrators.VelocityVerlet('vv', dt=dt)
coords = [[-axes[0], -axes[1], -axes[2]], [axes[0], axes[1], axes[2]]]
com_q = [[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 1., 0, 0, 0]]
fakeOV = ymr.ParticleVectors.RigidEllipsoidVector('OV',
mass=1,
object_size=len(coords),
semi_axes=axes)
fakeIc = ymr.InitialConditions.Rigid(com_q=com_q, coords=coords)
belongingChecker = ymr.BelongingCheckers.Ellipsoid("ellipsoidChecker")
pvEllipsoid = u.makeFrozenRigidParticles(belongingChecker, fakeOV, fakeIc,
dpd, vv, density, niter)
if pvEllipsoid:
frozenCoords = pvEllipsoid.getCoordinates()
frozenCoords = recenter(frozenCoords, com_q[0])
else:
frozenCoords = [[]]
if u.isMasterTask():
return frozenCoords
else:
return None
def createEllipsoid(density, axes, niter):
import ymero as ymr
def recenter(coords, com):
coords = [[r[0]-com[0], r[1]-com[1], r[2]-com[2]] for r in coords]
return coords
dt = 0.001
axes = tuple(axes)
ranks = (1, 1, 1)
fact = 3
domain = (fact*axes[0], fact*axes[1], fact*axes[2])
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log')
dpd = ymr.Interactions.DPD('dpd', 1.0, a=10.0, gamma=10.0, kbt=0.5, power=0.5)
vv = ymr.Integrators.VelocityVerlet('vv')
coords = [[-axes[0], -axes[1], -axes[2]],
[ axes[0], axes[1], axes[2]]]
com_q = [[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 1., 0, 0, 0]]
fakeOV = ymr.ParticleVectors.RigidEllipsoidVector('OV', mass=1, object_size=len(coords), semi_axes=axes)
fakeIc = ymr.InitialConditions.Rigid(com_q=com_q, coords=coords)
belongingChecker = ymr.BelongingCheckers.Ellipsoid("ellipsoidChecker")
pvEllipsoid = u.makeFrozenRigidParticles(belongingChecker, fakeOV, fakeIc, [dpd], vv, density, niter)
if pvEllipsoid:
frozenCoords = pvEllipsoid.getCoordinates()
frozenCoords = recenter(frozenCoords, com_q[0])
else:
frozenCoords = [[]]
if u.isMasterTask():
return frozenCoords
else:
return None
def run(niter, statsFname, comm_address):
dt = 0.001
ranks = (2, 1, 1)
domain = (12, 8, 10)
u = ymr.ymero(ranks, domain, dt, debug_level=8, log_filename='log', comm_ptr=comm_address)
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.Uniform(density=2)
u.registerParticleVector(pv=pv, ic=ic)
dpd = ymr.Interactions.DPD('dpd', 1.0, a=10.0, gamma=10.0, kbt=1.0, power=0.5)
u.registerInteraction(dpd)
u.setInteraction(dpd, pv, pv)
vv = ymr.Integrators.VelocityVerlet('vv')
u.registerIntegrator(vv)
u.setIntegrator(vv, pv)
stats = ymr.Plugins.createStats('stats', statsFname, 1000)
u.registerPlugins(stats)
u.run(niter)
parser = argparse.ArgumentParser()
parser.add_argument('--kbounds', type=float, default=0.0)
parser.add_argument('--ktwist', type=float, default=0.0)
parser.add_argument('--kbending', type=float, nargs=3, default=(0.0, 0.0, 0.0))
parser.add_argument('--l0_factor', type=float, default=1.0)
parser.add_argument('--tau0', type=float, default=0.0)
parser.add_argument('--tau0_eq', type=float, default=0.0)
parser.add_argument('--center_line', type=str, choices=["helix", "line"])
args = parser.parse_args()
ranks = (1, 1, 1)
domain = [16, 16, 16]
dt = 1e-3
u = ymr.ymero(ranks, tuple(domain), dt, debug_level=8, log_filename='log', no_splash=True)
com_q = [[ 8., 8., 8., 1.0, 0.0, 0.0, 0.0]]
L = 5.0
P = 1.0
R = 1.0
if args.center_line == "helix":
def center_line(s):
t = s * L * np.pi / P
return (R * np.cos(t),
R * np.sin(t),
(s-0.5) * L)
def torsion(s):
parser = argparse.ArgumentParser()
parser.add_argument("--type", choices=["squarePipe", 'cylinderPipe'])
args = parser.parse_args()
dt = 0.001
ranks = (1, 1, 1)
domain = (16, 8, 8)
force = (1.0, 0, 0)
density = 4
rc = 1.0
u = ymr.ymero(ranks, domain, debug_level=3, log_filename='stdout')
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.Uniform(density=density)
u.registerParticleVector(pv=pv, ic=ic)
dpd = ymr.Interactions.DPD('dpd', rc=rc, a=10.0, gamma=50.0, kbt=0.01, dt=dt, power=0.5)
u.registerInteraction(dpd)
if args.type == "cylinderPipe":
center=(domain[1]*0.5, domain[2]*0.5)
wall = ymr.Walls.Cylinder("cylinder", center=center, radius=0.5*domain[1]-rc, axis="x", inside=True)
elif args.type == "squarePipe":
lo = ( -domain[0], rc, rc)
hi = (2*domain[0], domain[1]-rc, domain[2]-rc)
def report():
print('Started with the following parameters: ' + str(args))
if unknown is not None and len(unknown) > 0:
print('Some arguments are not recognized and will be ignored: ' + str(unknown))
print('')
sys.stdout.flush()
if args.dry_run:
report()
quit()
domain = args.domain
rc = args.rc
u = ymr.ymero(tuple(args.nranks), tuple(domain), debug_level=args.debug_lvl, log_filename='log')
if u.isMasterTask():
report()
#====================================================================================
#====================================================================================
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.Uniform(density=args.rho)
u.registerParticleVector(pv=pv, ic=ic)
dpd = ymr.Interactions.DPD('dpd', rc, args.a, args.gamma, args.kbt, args.dt, args.power)
u.registerInteraction(dpd)
vveq = ymr.Integrators.VelocityVerlet('vveq', args.dt)
#!/usr/bin/env python
import ymero as ymr
import numpy as np
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
args = parser.parse_args()
ranks = (1, 1, 1)
domain = (4, 6, 8)
u = ymr.ymero(ranks, domain, dt=0, debug_level=3, log_filename='log', checkpoint_every = (5 if not args.restart else 0), no_splash=True)
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
u.registerParticleVector(pv=pv, ic=ymr.InitialConditions.Uniform(density=8))
coords = [[-1, -1, -1], [1, 1, 1]]
com_q = [[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 1., 0, 0, 0]]
ov = ymr.ParticleVectors.RigidEllipsoidVector('ov', mass=1, object_size=len(coords), semi_axes=(1,1,1))
u.registerParticleVector(pv=ov, ic=ymr.InitialConditions.Rigid(com_q=com_q, coords=coords))
checker = ymr.BelongingCheckers.Ellipsoid('checker')
u.registerObjectBelongingChecker(checker, ov)
inner = u.applyObjectBelongingChecker(checker, pv, inside='inner')
if args.restart:
u.restart("restart/")
u.run(7)
import trimesh
from mpi4py import MPI
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
parser.add_argument("--ranks", type=int, nargs=3)
args = parser.parse_args()
comm = MPI.COMM_WORLD
ranks = args.ranks
domain = (16, 16, 16)
dt = 0
if args.restart:
u = ymr.ymero(ranks, domain, dt, comm_ptr=MPI._addressof(comm), debug_level=8, log_filename='log', checkpoint_every=0)
else:
u = ymr.ymero(ranks, domain, dt, comm_ptr=MPI._addressof(comm), debug_level=8, log_filename='log', checkpoint_every=5)
mesh = trimesh.creation.icosphere(subdivisions=1, radius = 0.1)
udx_mesh = ymr.ParticleVectors.MembraneMesh(mesh.vertices.tolist(), mesh.faces.tolist())
pv = ymr.ParticleVectors.MembraneVector("pv", mass=1.0, mesh=udx_mesh)
if args.restart:
ic = ymr.InitialConditions.Restart("restart/")
else:
nobjs = 10
pos = [ np.array(domain) * t for t in np.linspace(0, 1.0, nobjs) ]
Q = [ np.array([1.0, 0., 0., 0.]) for i in range(nobjs) ]
#!/usr/bin/env python
import ymero as ymr
dt = 0.001
ranks = (1, 1, 1)
domain = (12, 8, 10)
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log')
pv = ymr.ParticleVectors.ParticleVector('pv', mass=1)
ic = ymr.InitialConditions.Uniform(density=2)
u.registerParticleVector(pv=pv, ic=ic)
dpd = ymr.Interactions.DPD('dpd', 1.0, a=10.0, gamma=10.0, kbt=1.0, power=0.5)
u.registerInteraction(dpd)
u.setInteraction(dpd, pv, pv)
vv = ymr.Integrators.VelocityVerlet('vv')
u.registerIntegrator(vv)
u.setIntegrator(vv, pv)
stats = ymr.Plugins.createStats('stats', "stats.txt", 1000)
u.registerPlugins(stats)
u.run(5001)
# nTEST: flow.rest
# cd flow
# rm -rf stats.txt
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
parser.add_argument("--ranks", type=int, nargs=3)
args = parser.parse_args()
ranks = args.ranks
domain = (4, 6, 8)
dt = 0
if args.restart:
restart_folder="restart2/"
else:
restart_folder="restart/"
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log', checkpoint_every=5, checkpoint_folder=restart_folder)
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.Uniform(density=2)
u.registerParticleVector(pv, ic)
dpd = ymr.Interactions.DPD('dpd', 1.0, a=10.0, gamma=10.0, kbt=1.0, power=0.5)
u.registerInteraction(dpd)
u.setInteraction(dpd, pv, pv)
if args.restart:
u.restart("restart/")
u.run(7)
# TEST: restart.interactions
#!/usr/bin/env python
import ymero as ymr
import numpy as np
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--ranks', type=int, nargs=3, required=True)
args = parser.parse_args()
domain = (8, 16, 4)
u = ymr.ymero(args.ranks, domain, dt=0, debug_level=8, log_filename='log')
pv = ymr.ParticleVectors.ParticleVector('pv', mass=1)
ic = ymr.InitialConditions.Uniform(density=3)
u.registerParticleVector(pv=pv, ic=ic)
sampleEvery = 1
dumpEvery = 1
binSize = (1., 1., 1.)
field = ymr.Plugins.createDumpAverage('field', [pv], sampleEvery, dumpEvery,
binSize,
[("velocity", "vector_from_float8")],
'h5/solvent-')
u.registerPlugins(field)
u.run(3)
# TEST: dump.h5
#!/usr/bin/env python
import numpy as np
import ymero as ymr
ranks = (1, 1, 1)
domain = [4., 4., 4.]
density = 8
u = ymr.ymero(ranks, tuple(domain), dt=0, debug_level=3, log_filename='log')
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.UniformSphere(density=density, center=(2., 2., 2.), radius=2.0, inside=True)
u.registerParticleVector(pv=pv, ic=ic)
u.run(2)
if pv:
icpos = pv.getCoordinates()
icvel = pv.getVelocities()
np.savetxt("pos.ic.txt", icpos)
np.savetxt("vel.ic.txt", icvel)
# TEST: ic.uniform.sphere
# cd ic
# rm -rf pos*.txt vel*.txt
# ymr.run --runargs "-n 2" ./sphere.py > /dev/null
# paste pos.ic.txt vel.ic.txt | LC_ALL=en_US.utf8 sort > ic.out.txt
import numpy as np
import argparse
import trimesh
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
parser.add_argument("--ranks", type=int, nargs=3)
args = parser.parse_args()
ranks = args.ranks
domain = (16, 16, 16)
if args.restart:
u = ymr.ymero(ranks,
domain,
debug_level=8,
log_filename='log',
checkpoint_every=0)
else:
u = ymr.ymero(ranks,
domain,
debug_level=8,
log_filename='log',
checkpoint_every=5)
mesh = trimesh.creation.icosphere(subdivisions=1, radius=0.1)
coords = [[-0.01, 0., 0.], [0.01, 0., 0.], [0., -0.01, 0.], [0., 0.01, 0.],
[0., 0., -0.01], [0., 0., 0.01]]
udx_mesh = ymr.ParticleVectors.Mesh(mesh.vertices.tolist(),
import argparse
from mpi4py import MPI
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
parser.add_argument("--ranks", type=int, nargs=3)
args = parser.parse_args()
ranks = args.ranks
domain = (4, 6, 8)
comm = MPI.COMM_WORLD
if args.restart:
u = ymr.ymero(MPI._addressof(comm), ranks, domain, debug_level=3, log_filename='log', checkpoint_every=0)
else:
u = ymr.ymero(MPI._addressof(comm), ranks, domain, debug_level=3, log_filename='log', checkpoint_every=5)
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
if args.restart:
ic = ymr.InitialConditions.Restart("restart/")
else:
ic = ymr.InitialConditions.Uniform(density=2)
u.registerParticleVector(pv=pv, ic=ic)
u.run(7)
rank = comm.Get_rank()
#!/usr/bin/env python
import ymero as ymr
import numpy as np
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--ranks', type=int, nargs=3, required=True)
args = parser.parse_args()
domain = (8, 16, 4)
u = ymr.ymero(args.ranks, domain, dt=0, debug_level=8, log_filename='log')
pv = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
ic = ymr.InitialConditions.Uniform(density=3)
u.registerParticleVector(pv=pv, ic=ic)
sampleEvery = 1
dumpEvery = 1
binSize = (1., 1., 1.)
field = ymr.Plugins.createDumpAverage('field', [pv], sampleEvery, dumpEvery, binSize, [("velocity", "vector_from_float8")], 'h5/solvent-')
u.registerPlugins(field)
u.run(3)
# TEST: dump.h5
# cd dump
# rm -rf h5
# ymr.run --runargs "-n 2" ./h5.py --ranks 1 1 1 > /dev/null
def report():
print('Started with the following parameters: ' + str(args))
if unknown is not None and len(unknown) > 0:
print('Some arguments are not recognized and will be ignored: ' + str(unknown))
print('Outer viscosity: %f, inner: %f' % (mu_outer, mu_inner))
print('Generated %d cells %s, real hematocrit is %f' % (len(rbcs_ic), str(ncells), real_ht))
print('Cell parameters: %s' % str(params2dict(params)))
print('')
sys.stdout.flush()
if args.dry_run:
report()
quit()
u = ymr.ymero(args.nranks, args.domain, debug_level=args.debug_lvl, log_filename='generate', restart_folder="generated/")
if u.isMasterTask():
report()
#====================================================================================
#====================================================================================
# Interactions:
# DPD
dpd = ymr.Interactions.DPD('dpd', rc=1.0, a=args.a, gamma=args.gamma, kbt=args.kbt, dt=args.dt, power=args.power)
u.registerInteraction(dpd)
# Contact (LJ)
contact = ymr.Interactions.LJ('contact', rc=1.0, epsilon=10, sigma=1.0, object_aware=True, max_force=2000)
u.registerInteraction(contact)
#!/usr/bin/env python
import numpy as np
import ymero as ymr
ranks = (1, 1, 1)
domain = [4., 6., 8.]
u = ymr.ymero(ranks, tuple(domain), debug_level=3, log_filename='log')
a = (0.1, 0.2, 0.3)
coords = [[-a[0], -a[1], -a[2]], [-a[0], -a[1], a[2]], [-a[0], a[1], -a[2]],
[-a[0], a[1], a[2]], [a[0], a[1], -a[2]], [a[0], a[1], a[2]]]
com_q = [
[1., 0., 0., 1.0, 0.0, 0.0, 0.0],
[3., 0., 0., 1.0, 2.0, 0.0, 0.0],
[-1., 0., 0., 1.0, 0.0, 3.0, 0.0], # out of the domain
[2., 0., 0., 1.0, 0.0, 0.0, 1.0]
]
pv = ymr.ParticleVectors.RigidEllipsoidVector('ellipsoid',
mass=1,
object_size=len(coords),
semi_axes=a)
ic = ymr.InitialConditions.Rigid(com_q=com_q, coords=coords)
u.registerParticleVector(pv=pv, ic=ic)
# xyz = ymr.Plugins.createDumpXYZ('xyz', pv, 1, "xyz/")
# u.registerPlugins(xyz)
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
parser.add_argument("--ranks", type=int, nargs=3)
args = parser.parse_args()
comm = MPI.COMM_WORLD
ranks = args.ranks
domain = (16, 16, 16)
dt = 0
if args.restart:
u = ymr.ymero(ranks,
domain,
dt,
comm_ptr=MPI._addressof(comm),
debug_level=8,
log_filename='log',
checkpoint_every=0)
else:
u = ymr.ymero(ranks,
domain,
dt,
comm_ptr=MPI._addressof(comm),
debug_level=8,
log_filename='log',
checkpoint_every=5)
mesh = trimesh.creation.icosphere(subdivisions=1, radius=0.1)
udx_mesh = ymr.ParticleVectors.MembraneMesh(mesh.vertices.tolist(),
parser = argparse.ArgumentParser()
parser.add_argument('--subStep', action='store_true', default=False)
parser.add_argument('--vis', action='store_true', default=False)
args = parser.parse_args()
dt = 0.001
substeps = 10
if args.subStep:
dt = dt * substeps
ranks = (1, 1, 1)
domain = (8, 8, 8)
u = ymr.ymero(ranks, domain, dt, debug_level=3, log_filename='log')
nparts = 1000
pos = np.random.normal(loc = [0.5, 0.5 * domain[1] + 1.0, 0.5 * domain[2]],
scale = [0.1, 0.3, 0.3],
size = (nparts, 3))
vel = np.random.normal(loc = [1.0, 0., 0.],
scale = [0.1, 0.01, 0.01],
size = (nparts, 3))
pvSolvent = ymr.ParticleVectors.ParticleVector('pv', mass = 1)
icSolvent = ymr.InitialConditions.FromArray(pos=pos.tolist(), vel=vel.tolist())
vv = ymr.Integrators.VelocityVerlet('vv')
u.registerParticleVector(pvSolvent, icSolvent)
#!/usr/bin/env python
import ymero as ymr
import numpy as np
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--restart", action='store_true', default=False)
args = parser.parse_args()
ranks = (1, 1, 1)
domain = (4, 6, 8)
u = ymr.ymero(ranks,
domain,
dt=0,
debug_level=3,
log_filename='log',
checkpoint_every=(5 if not args.restart else 0))
if args.restart:
u.restart("restart/")
pv = ymr.ParticleVectors.ParticleVector('pv', mass=1)
u.registerParticleVector(pv=pv, ic=ymr.InitialConditions.Uniform(density=8))
coords = [[-1, -1, -1], [1, 1, 1]]
com_q = [[0.5 * domain[0], 0.5 * domain[1], 0.5 * domain[2], 1., 0, 0, 0]]
ov = ymr.ParticleVectors.RigidEllipsoidVector('ov',
mass=1,
object_size=len(coords),
semi_axes=(1, 1, 1))
u.registerParticleVector(pv=ov,
