def update_ghost_particles(self, particles, mesh, domain):
# relabel all particles
self.flag_exterior_particles(particles, domain.xmin, domain.xmax)
boundary_indices = {
"left" : LongArray(),
"right" : LongArray(),
"bottom" : LongArray(),
"top" : LongArray(),
"left-top" : LongArray(),
"left-bottom" : LongArray(),
"right-top" : LongArray(),
"right-bottom" : LongArray()
}
# create new exterior boundary ghost particles
cumsum_neighbors = mesh["number of neighbors"].cumsum()
ghost_indices = np.where(particles["tag"] == ParticleTAGS.OldGhost)[0]
create_reflect_ghost(particles, boundary_indices, domain, ghost_indices,
ghost_indices, mesh['neighbors'], mesh['number of neighbors'],
cumsum_neighbors, -1)
# remove old ghost particles
particles.remove_tagged_particles(ParticleTAGS.OldGhost)
# place real particles in begginning of the array
particles.align_particles()
particles['type'][:] = ParticleTAGS.Undefined
def update_ghost_particles(self, particles, mesh, domain, load_balance, comm):
rank = comm.Get_rank()
size = comm.Get_size()
# allocate arrays for boundary indices
indices = LongArray()
corner_ghost = ParticleContainer()
send_particles = np.zeros(size, dtype=np.int32)
recv_particles = np.zeros(size, dtype=np.int32)
# we are puting new ghost at the end of the array
current_size = particles.get_number_of_particles()
boundary_indices = {
"left" : LongArray(),
"right" : LongArray(),
"bottom" : LongArray(),
"top" : LongArray(),
"left-top" : LongArray(),
"left-bottom" : LongArray(),
"right-top" : LongArray(),
"right-bottom" : LongArray()
}
# relabel all particles
particles["tag"][:] = ParticleTAGS.Undefined
particles["type"][:] = ParticleTAGS.Undefined
# flag particles that have left the domain and particles
# that remained
load_balance.flag_migrate_particles(particles, rank)
# find particles that have left the domain
export_indices = np.where(particles["type"] == ParticleTAGS.ExportInterior)[0]
if export_indices.size > 0:
# extract export particles
export_particles = particles.extract_items(export_indices)
# put particles in process order
ind = np.argsort(export_particles["process"])
for field in export_particles.properties.keys():
array = export_particles[field]
array[:] = array[ind]
export_particles["tag"][:] = ParticleTAGS.Real
export_particles["type"][:] = ParticleTAGS.Undefined
else:
export_particles = ParticleContainer()
# bin particle process
send_particles[:] = np.bincount(export_particles["process"], minlength=size)
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
# create container for incoming particles
import_particles = ParticleContainer(np.sum(recv_particles))
exchange_particles(import_particles, export_particles, send_particles, recv_particles,
0, comm)
# copy import particle data to ghost place holders and turn to real particles
migrate.transfer_migrate_particles(particles, import_particles)
# flag export particles back to interior ghost particles
particles["type"][export_indices] = ParticleTAGS.Interior
ghost_indices = np.where(particles["tag"] == ParticleTAGS.OldGhost)[0]
# find indices of interior/exterior ghost particles
cumsum_neighbors = mesh["number of neighbors"].cumsum()
exterior_ghost_indices = np.where(particles["type"] == ParticleTAGS.Exterior)[0]
interior_ghost_indices = np.where(particles["type"] == ParticleTAGS.Interior)[0]
#---------- create exterior ghost particles ----------#
num_exterior_ghost = 0
if exterior_ghost_indices.size > 0:
num_exterior_ghost = create_reflect_ghost(particles, boundary_indices,
domain, exterior_ghost_indices, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, -1)
#---------- create interior ghost particles ----------#
send_particles[:] = 0
recv_particles[:] = 0
interior_ghost_proc = particles["process"][interior_ghost_indices]
# arrange particles in process order
ind = interior_ghost_proc.argsort()
interior_ghost_proc = interior_ghost_proc[ind]
interior_ghost_indices = interior_ghost_indices[ind]
# bin processors
interior_ghost_proc_bin = np.bincount(interior_ghost_proc, minlength=size)
cumsum_neighbors = mesh["number of neighbors"].cumsum()
# collect the indices of particles to be export to each process
cumsum_proc = interior_ghost_proc_bin.cumsum()
for proc in range(size):
if interior_ghost_proc_bin[proc] != 0:
start = cumsum_proc[proc] - interior_ghost_proc_bin[proc]
end = cumsum_proc[proc]
send_particles[proc] = find_boundary_particles(indices, interior_ghost_indices[start:end], ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, False)
# extract data to send and remove the particles
send_data = {}
for prop in particles.properties.keys():
send_data[prop] = np.ascontiguousarray(particles[prop][indices.get_npy_array()])
send_data["tag"][:] = ParticleTAGS.Ghost
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
num_interior_ghost = np.sum(recv_particles)
# resize arrays to give room for incoming particles
sp = particles.get_number_of_particles()
particles.extend(num_interior_ghost)
exchange_particles(particles, send_data, send_particles, recv_particles,
sp, comm)
#---------- create exterior corner ghost particles ----------#
indices.reset()
send_particles[:] = 0
recv_particles[:] = 0
if boundary_indices['left'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["left"], indices, send_particles, 'x', domain.xmin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['right'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["right"], indices, send_particles, 'x', domain.xmax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['bottom'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["bottom"], indices, send_particles, 'y', domain.ymin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['top'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["top"], indices, send_particles, 'y', domain.ymax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
sp = particles.get_number_of_particles()
particles.extend(np.sum(recv_particles))
# to export corners have to be reorderd by process
if corner_ghost.get_number_of_particles() > 0:
ind = np.argsort(corner_ghost['process'])
for field in corner_ghost.properties.keys():
array = corner_ghost[field]
array[:] = array[ind]
corner_ghost["process"][:] = -1
# exchange patch corners
exchange_particles(particles, corner_ghost, send_particles, recv_particles,
sp, comm)
# finally remove old ghost particles from previous time step
# and also put real particles in front and ghost in the back
particles.remove_tagged_particles(ParticleTAGS.OldGhost)
particles.align_particles()
particles['type'][:] = ParticleTAGS.Undefined
def create_ghost_particles(self, particles, mesh, domain, load_balance, comm, iteration=6):
"""Create initial ghost particles that hug the boundary after
load balance
"""
rank = comm.Get_rank()
size = comm.Get_size()
# remove current (if any) ghost particles
particles.remove_tagged_particles(ParticleTAGS.Ghost)
current_size = particles.get_number_of_particles()
# create initial ghost particles, particles is now larger
# these particles are centered in neighboring boundary leaf
# cells of the octree
load_balance.create_boundary_particles(particles, rank)
# reorder ghost in processors order: exterior have a process id of -1 so
# their put before interior ghost particles
ghost_proc = np.array(particles["process"][current_size:])
ind = np.argsort(ghost_proc)
ghost_proc = ghost_proc[ind]
for field in particles.properties.keys():
array = particles[field][current_size:]
array[:] = array[ind]
# allocate arrays for boundary indices
indices = LongArray()
corner_ghost = ParticleContainer()
# sides
boundary_indices = {
"left" : LongArray(),
"right" : LongArray(),
"bottom" : LongArray(),
"top" : LongArray(),
"left-top" : LongArray(),
"left-bottom" : LongArray(),
"right-top" : LongArray(),
"right-bottom" : LongArray()
}
send_particles = np.zeros(size, dtype=np.int32)
recv_particles = np.zeros(size, dtype=np.int32)
# create ghost interior and exterior particles by iteration, using
# the mesh to extract the needed neighbors
for i in range(iteration):
# build the mesh
mesh.tessellate()
cumsum_neighbors = mesh["number of neighbors"].cumsum()
#---------- create exterior ghost particles ----------#
# create indices for ghost particles
ghost_indices = np.arange(current_size, particles.get_number_of_particles())
# label current ghost as old ghost
particles['tag'][ghost_indices] = ParticleTAGS.OldGhost
# select exterior ghost particles
exterior_ghost = ghost_proc == -1
exterior_ghost_indices = ghost_indices[exterior_ghost]
if np.sum(exterior_ghost_indices) > 0:
num_exterior_ghost = create_reflect_ghost(particles, boundary_indices,
domain, exterior_ghost_indices, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, -1)
#---------- create interior ghost particles ----------#
interior_ghost_indices = ghost_indices[~exterior_ghost]
interior_ghost_proc = ghost_proc[~exterior_ghost]
# bin processors - they are in order
interior_ghost_proc_bin = np.bincount(interior_ghost_proc, minlength=size)
send_particles[:] = 0
recv_particles[:] = 0
indices.reset()
# collect the indices of particles to be export to each process
cumsum_proc = interior_ghost_proc_bin.cumsum()
for proc in range(size):
if interior_ghost_proc_bin[proc] != 0:
start = cumsum_proc[proc] - interior_ghost_proc_bin[proc]
end = cumsum_proc[proc]
send_particles[proc] = find_boundary_particles(indices, interior_ghost_indices[start:end], ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, False)
# extract data to send and remove the particles
send_data = {}
for prop in particles.properties.keys():
send_data[prop] = np.ascontiguousarray(particles[prop][indices.get_npy_array()])
send_data["tag"][:] = ParticleTAGS.Ghost
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
num_interior_ghost = np.sum(recv_particles)
# resize arrays to give room for incoming particles
sp = particles.get_number_of_particles()
#particles.resize(current_size + num_exterior_ghost + num_interior_ghost)
particles.extend(num_interior_ghost)
exchange_particles(particles, send_data, send_particles, recv_particles,
sp, comm)
#---------- create exterior corner ghost particles ----------#
indices.reset()
send_particles[:] = 0
recv_particles[:] = 0
# clear out corner ghost
corner_ghost.resize(0)
if boundary_indices['left'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["left"], indices, send_particles, 'x', domain.xmin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['right'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["right"], indices, send_particles, 'x', domain.xmax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['bottom'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["bottom"], indices, send_particles, 'y', domain.ymin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['top'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["top"], indices, send_particles, 'y', domain.ymax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
#print rank, current_size, particles.get_number_of_particles(), current_size + num_exterior_ghost + num_interior_ghost
sp = particles.get_number_of_particles()
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
particles.extend(np.sum(recv_particles))
# to export corners have to be reorderd by process
if corner_ghost.get_number_of_particles() > 0:
ind = np.argsort(corner_ghost['process'])
for field in corner_ghost.properties.keys():
array = corner_ghost[field]
array[:] = array[ind]
corner_ghost["process"][:] = -1
# exchange patch corners
exchange_particles(particles, corner_ghost, send_particles, recv_particles,
sp, comm)
for bd in boundary_indices:
boundary_indices[bd].reset()
particles.remove_tagged_particles(ParticleTAGS.OldGhost)
# put particles in process order for next loop
ind = np.argsort(particles["process"][current_size:])
for field in particles.properties.keys():
array = particles[field][current_size:]
array[:] = array[ind]
ghost_proc = np.array(particles["process"][current_size:])
print 'rank:', rank, 'fraction of real to ghost:', (particles.get_number_of_particles()-current_size)*1.0/particles.get_number_of_particles()
def create_reflect_ghost(parray, boundary_indices, domain, exterior_ghost_indices,
ghost_indices, neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank):
indices = LongArray()
# sides
left = boundary_indices["left"]
right = boundary_indices["right"]
bottom = boundary_indices["bottom"]
top = boundary_indices["top"]
# corners
lt = boundary_indices["left-top"]
lb = boundary_indices["left-bottom"]
rt = boundary_indices["right-top"]
rb = boundary_indices["right-bottom"]
xmin = domain.xmin
xmax = domain.xmax
ymin = domain.ymin
ymax = domain.ymax
x = parray['position-x']
y = parray['position-y']
for i in exterior_ghost_indices:
xi = x[i]; yi = y[i]
# left boundary condition
if xi < xmin:
# left top corner
if yi > ymax:
lt.append(i)
# left bottom corner
elif yi < ymin:
lb.append(i)
# left
else:
left.append(i)
# right boundary condition
elif xi > xmax:
# left top corner
if yi > ymax:
rt.append(i)
# left bottom corner
elif yi < ymin:
rb.append(i)
# right
else:
right.append(i)
# bottom boundary condition
elif yi < ymin:
bottom.append(i)
# top boundary condition
elif yi > ymax:
top.append(i)
num_new_ghost = 0
# left
if left.length > 0:
num_new_ghost += reflect_axis(parray, indices, left, 'x', xmin, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# right
if right.length > 0:
num_new_ghost += reflect_axis(parray, indices, right, 'x', xmax, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# bottom
if bottom.length > 0:
num_new_ghost += reflect_axis(parray, indices, bottom, 'y', ymin, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# top
if top.length > 0:
num_new_ghost += reflect_axis(parray, indices, top, 'y', ymax, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# left top
if lt.length > 0:
num_new_ghost += reflect_corner(parray, indices, lt, xmin, ymax, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# left bottom
if lb.length > 0:
num_new_ghost += reflect_corner(parray, indices, lb, xmin, ymin, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# right top
if rt.length > 0:
num_new_ghost += reflect_corner(parray, indices, rt, xmax, ymax, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
# right bottom
if rb.length > 0:
num_new_ghost += reflect_corner(parray, indices, rb, xmax, ymin, ghost_indices,
neighbors_graph, neighbors_graph_size, cumsum_neighbors, rank)
return num_new_ghost