def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print "Creating boundary condition arrays"
# perhaps at some other time this class should be extended
# to allow obstacles within the lid-driven cavity
# obst_array = np.zeros(self.nnodes)
# obst_array[list(self.obst_list)] = 100.
#
# #print type(self.inlet_list)
# inlet_array = np.zeros(self.nnodes)
# inlet_array[list(self.inlet_list)] = 200.
#
# outlet_array = np.zeros(self.nnodes)
# outlet_array[list(self.outlet_list)] = 300.
print "length of lid_list = %d \n"%(len(list(self.lid_list)))
lid_array = np.zeros(int(self.nnodes))
lid_array[list(self.lid_list)] = 700.
solid_array = np.zeros(int(self.nnodes))
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print "Writing boundary conditions to VTK files"
#writeVTK(inlet_array,'inlet','inlet.vtk',dims,origin,spacing)
#writeVTK(outlet_array,'outlet','outlet.vtk',dims,origin,spacing)
#writeVTK(obst_array,'obst','obst.vtk',dims,origin,spacing)
writeVTK(lid_array,'lid','lid.vtk',dims,origin,spacing)
writeVTK(solid_array,'solid','solid.vtk',dims,origin,spacing)
def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print("Creating boundary condition arrays")
# perhaps at some other time this class should be extended
# to allow obstacles within the lid-driven cavity
# obst_array = np.zeros(self.nnodes)
# obst_array[list(self.obst_list)] = 100.
#
# #print type(self.inlet_list)
# inlet_array = np.zeros(self.nnodes)
# inlet_array[list(self.inlet_list)] = 200.
#
# outlet_array = np.zeros(self.nnodes)
# outlet_array[list(self.outlet_list)] = 300.
print("length of lid_list = %d \n" % (len(list(self.lid_list))))
lid_array = np.zeros(int(self.nnodes))
lid_array[list(self.lid_list)] = 700.
solid_array = np.zeros(int(self.nnodes))
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print("Writing boundary conditions to VTK files")
#writeVTK(inlet_array,'inlet','inlet.vtk',dims,origin,spacing)
#writeVTK(outlet_array,'outlet','outlet.vtk',dims,origin,spacing)
#writeVTK(obst_array,'obst','obst.vtk',dims,origin,spacing)
writeVTK(lid_array, 'lid', 'lid.vtk', dims, origin, spacing)
writeVTK(solid_array, 'solid', 'solid.vtk', dims, origin, spacing)
def write_vtk(self,file_name = 'partition_pa.vtk'):
"""
write out a vtk file to allow visualization of the partitioning
"""
dims = [self.Nx, self.Ny, self.Nz]
origin = [0., 0., 0.]
spacing = [0.1, 0.1, 0.1] #<-- no need for this to correspond to actual physical spacing
writeVTK(self.part_vert,'partitions',file_name,dims,origin,spacing)
def write_vtk(self, file_name='partition_pa.vtk'):
"""
write out a vtk file to allow visualization of the partitioning
"""
dims = [self.Nx, self.Ny, self.Nz]
origin = [0., 0., 0.]
spacing = [
0.1, 0.1, 0.1
] #<-- no need for this to correspond to actual physical spacing
writeVTK(self.part_vert, 'partitions', file_name, dims, origin,
spacing)
def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print "Creating boundary condition arrays"
obst_array = np.zeros(self.nnodes)
obst_array[list(self.obst_list)] = 100.
#print type(self.inlet_list)
inlet_array = np.zeros(self.nnodes)
inlet_array[list(self.inlet_list)] = 200.
outlet_array = np.zeros(self.nnodes)
outlet_array[list(self.outlet_list)] = 300.
solid_array = np.zeros(self.nnodes)
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print "Writing boundary conditions to VTK files"
writeVTK(inlet_array,'inlet','inlet.vtk',dims,origin,spacing)
writeVTK(outlet_array,'outlet','outlet.vtk',dims,origin,spacing)
writeVTK(obst_array,'obst','obst.vtk',dims,origin,spacing)
writeVTK(solid_array,'solid','solid.vtk',dims,origin,spacing)
def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print "Creating boundary condition arrays"
obst_array = np.zeros(self.nnodes)
obst_array[list(self.obst_list)] = 100.
#print type(self.inlet_list)
inlet_array = np.zeros(self.nnodes)
inlet_array[list(self.inlet_list)] = 200.
outlet_array = np.zeros(self.nnodes)
outlet_array[list(self.outlet_list)] = 300.
solid_array = np.zeros(self.nnodes)
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print "Writing boundary conditions to VTK files"
writeVTK(inlet_array, 'inlet', 'inlet.vtk', dims, origin, spacing)
writeVTK(outlet_array, 'outlet', 'outlet.vtk', dims, origin, spacing)
writeVTK(obst_array, 'obst', 'obst.vtk', dims, origin, spacing)
writeVTK(solid_array, 'solid', 'solid.vtk', dims, origin, spacing)
def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print("Creating boundary condition arrays")
obst_array = np.zeros(int(self.nnodes))
obst_array[list(self.obst_list)] = 100.
#print type(self.inlet_list)
inlet_array = np.zeros(int(self.nnodes))
inlet_array[list(self.inlet_list)] = 200.
outlet_array = np.zeros(int(self.nnodes))
outlet_array[list(self.outlet_list)] = 300.
solid_array = np.zeros(int(self.nnodes))
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print("Writing boundary conditions to VTK files")
writeVTK(inlet_array, 'inlet', 'inlet.vtk', dims, origin, spacing)
writeVTK(outlet_array, 'outlet', 'outlet.vtk', dims, origin, spacing)
writeVTK(obst_array, 'obst', 'obst.vtk', dims, origin, spacing)
writeVTK(solid_array, 'solid', 'solid.vtk', dims, origin, spacing)
if len(self.subsetList) > 0:
print("Writing subset lists to VTK files")
ss_idx = 0
for ss in self.subsetList:
print('Writing subset %d to file' % ss_idx)
ssNodes = ss.get_members(self.x[:], self.y[:], self.z[:])
ss_array = np.zeros(int(self.nnodes))
ss_array[list(ssNodes)] = ss_idx * 1000. + 1000.
ssName = 'subSpace' + str(ss_idx)
ssFile = ssName + '.vtk'
writeVTK(ss_array, ssName, ssFile, dims, origin, spacing)
ss_idx += 1
def write_bc_vtk(self):
"""
write node lists to properly formatted VTK files
"""
print "Creating boundary condition arrays"
obst_array = np.zeros(int(self.nnodes))
obst_array[list(self.obst_list)] = 100.
#print type(self.inlet_list)
inlet_array = np.zeros(int(self.nnodes))
inlet_array[list(self.inlet_list)] = 200.
outlet_array = np.zeros(int(self.nnodes))
outlet_array[list(self.outlet_list)] = 300.
solid_array = np.zeros(int(self.nnodes))
solid_array[list(self.solid_list)] = 500.
dims = [int(self.Nx), int(self.Ny), int(self.Nz)]
origin = [0., 0., 0.]
dx = self.x[1] - self.x[0]
spacing = [dx, dx, dx] #uniform lattice
print "Writing boundary conditions to VTK files"
writeVTK(inlet_array,'inlet','inlet.vtk',dims,origin,spacing)
writeVTK(outlet_array,'outlet','outlet.vtk',dims,origin,spacing)
writeVTK(obst_array,'obst','obst.vtk',dims,origin,spacing)
writeVTK(solid_array,'solid','solid.vtk',dims,origin,spacing)
if len(self.subsetList) > 0:
print "Writing subset lists to VTK files"
ss_idx = 0;
for ss in self.subsetList:
print 'Writing subset %d to file'%ss_idx
ssNodes = ss.get_members(self.x[:],self.y[:],self.z[:])
ss_array = np.zeros(int(self.nnodes))
ss_array[list(ssNodes)] = ss_idx*1000. + 1000.
ssName = 'subSpace'+str(ss_idx)
ssFile = ssName+'.vtk'
writeVTK(ss_array,ssName,ssFile,dims,origin,spacing)
ss_idx+=1
# compute the number of data dumps I expect to process
nDumps = (Num_ts-Warmup_ts)/plot_freq +1 # Num_ts/plot_freq updates
for i in range(rank,nDumps,size):
# say something comforting
print 'processing data dump number %d of %d. '%(i+1,nDumps) # make this ones-based numbering
# filename format
rho_fn = 'density'+str(i)+'.b_dat'
ux_fn = 'ux'+str(i)+'.b_dat'
uy_fn = 'uy'+str(i)+'.b_dat'
uz_fn = 'uz'+str(i)+'.b_dat'
# at this point, ux, uy and uz are out of order
ux = np.fromfile(ux_fn,dtype=np.float32).astype(np.float64)
uy = np.fromfile(uy_fn,dtype=np.float32).astype(np.float64)
uz = np.fromfile(uz_fn,dtype=np.float32).astype(np.float64)
pressure = np.fromfile(rho_fn,dtype=np.float32).astype(np.float64)
# convert velocity to physical units
ux /= u_conv_fact
uy /= u_conv_fact
uz /= u_conv_fact
pressure /= p_conv_fact # please check this...
outfilename = 'velocityAndPressure'+str(i)+'.vtk'
dims = (Nx,Ny,Nz)
writeVTK(pressure,ux,uy,uz,XX,YY,ZZ,outfilename,dims)
ZZ = np.reshape(Z,numEl)
# load the turbineChannel data from *.b_dat files
rho_fn = 'density'+str(dump_num)+'.b_dat'
ux_fn = 'ux'+str(dump_num)+'.b_dat'
uy_fn = 'uy'+str(dump_num)+'.b_dat'
uz_fn = 'uz'+str(dump_num)+'.b_dat'
ux = np.fromfile(ux_fn,dtype=np.float32)
uy = np.fromfile(uy_fn,dtype=np.float32)
uz = np.fromfile(uz_fn,dtype=np.float32)
pressure = np.fromfile(rho_fn,dtype=np.float32)
# convert velocity to physical units
ux *= u_conv_fact
uy *= u_conv_fact
uz *= u_conv_fact
pressure *= p_conv_fact
# compute differences
ux_d = ux - ux_m
uy_d = uy - uy_m
uz_d = uz - uz_m
pressure_d = pressure - pressure_m
# write the results to a vtk file
outfilename = 'velocityAndPressureDifferences.vtk'
dims = (Nx,Ny,Nz)
writeVTK(pressure_d,ux_d,uy_d,uz_d,XX,YY,ZZ,outfilename,dims)
# pray that things work better next time.
YY = np.reshape(Y, numEl) ZZ = np.reshape(Z, numEl) # load the turbineChannel data from *.b_dat files rho_fn = 'density' + str(dump_num) + '.b_dat' ux_fn = 'ux' + str(dump_num) + '.b_dat' uy_fn = 'uy' + str(dump_num) + '.b_dat' uz_fn = 'uz' + str(dump_num) + '.b_dat' ux = np.fromfile(ux_fn, dtype=np.float32) uy = np.fromfile(uy_fn, dtype=np.float32) uz = np.fromfile(uz_fn, dtype=np.float32) pressure = np.fromfile(rho_fn, dtype=np.float32) # convert velocity to physical units ux *= u_conv_fact uy *= u_conv_fact uz *= u_conv_fact pressure *= p_conv_fact # compute differences ux_d = ux - ux_m uy_d = uy - uy_m uz_d = uz - uz_m pressure_d = pressure - pressure_m # write the results to a vtk file outfilename = 'velocityAndPressureDifferences.vtk' dims = (Nx, Ny, Nz) writeVTK(pressure_d, ux_d, uy_d, uz_d, XX, YY, ZZ, outfilename, dims) # pray that things work better next time.
# compute the number of data dumps I expect to process
nDumps = (Num_ts - Warmup_ts
) / plot_freq + 1 # initial data plus Num_ts/plot_freq updates
# load obst_file.lbm to get the obstacle. Should also zero out the velocity of
# the walls.
for i in range(rank, nDumps, size):
# say something comforting
print 'processing data dump number %d of %d. ' % (
i + 1, nDumps) # make this ones-based numbering
# filename format
rho_fn = 'density' + str(i) + '.b_dat'
ux_fn = 'ux' + str(i) + '.b_dat'
uy_fn = 'uy' + str(i) + '.b_dat'
uz_fn = 'uz' + str(i) + '.b_dat'
ux = np.fromfile(ux_fn, dtype=np.float32).astype(np.float64)
uy = np.fromfile(uy_fn, dtype=np.float32).astype(np.float64)
uz = np.fromfile(uz_fn, dtype=np.float32).astype(np.float64)
pressure = np.fromfile(rho_fn, dtype=np.float32).astype(np.float64)
# convert velocity to physical units
ux /= u_conv_fact
uy /= u_conv_fact
uz /= u_conv_fact
pressure /= p_conv_fact # please check this...
outfilename = 'velocityAndPressure' + str(i) + '.vtk'
dims = (Nx, Ny, Nz)
writeVTK(pressure, ux, uy, uz, XX, YY, ZZ, outfilename, dims)
print 'total nodes = %d ' % nnodes dims = [Nx,Ny,Nz] origin = [0,0,0] dx = x[1]-x[0]; dy = dx; dz = dx; spacing = [dx,dy,dz] print 'preparing output for vtk' obst_array = np.ones(len(x)); #for i in obst_list: # obst_array[i] = 100.0 #obst_array[obst_list]= 100.0 print 'writing to vtk file' writeVTK(obst_array,'obstacle','obst.vtk',dims,origin,spacing); inlet_list = np.where(z==0) inlet_array = np.ones(len(x)) #inlet_array[inlet_list] = 200.0 #writeVTK(inlet_array,'inlet','inlet.vtk',dims,origin,spacing) outlet_list = np.where(z==Lz_p) outlet_array = np.ones(len(x)) #outlet_array[outlet_list] = 300.0 #writeVTK(outlet_array,'outlet','outlet.vtk',dims,origin,spacing) # make the solid nodes on the x == 0, x == Lx_p, y == 0, and y == Ly_p boundaries # God help us; this appears to be the best way
##################################################################
#uncomment when ready for performance testing
#print (time.time() - start_time)
# write to disk a partition map giving the global point number in order for all partitions
filename = 'partMap.b_dat'
amode = MPI.MODE_WRONLY | MPI.MODE_CREATE #<- bit mask for file mode
fh = MPI.File.Open(comm,filename,amode)
offset = intOffset*np.dtype(np.int32).itemsize
fh.Write_at_all(offset,myPart)
fh.Close()
comm.Barrier() # make sure everyone is done
# rank 0 load this file and print to screen
if rank==0:
partMap = np.fromfile(filename,dtype='int32')
for i in range(gen):
vtkname = "state_" + str(i) + ".vtk"
dataName = "data_" + str(i) + ".b_dat"
data_i = np.fromfile(dataName,dtype='int32')
data = np.zeros_like(data_i)
data[partMap] = data_i
dims = [Nx, Nx,1]
origin = [0,0,0]
spacing = [1,1,1]
writeVTK(data,'state',vtkname,dims,origin,spacing)
#u_conv_fact = l_conv_fact/t_conv_fact;
u_conv_fact = t_conv_fact / l_conv_fact
if (rank == 0):
print("u_conv_fact = %15.15f \n" % u_conv_fact)
nnodes = Nx * Ny * Nz
# compute geometric data only once
x = np.linspace(0., Lx_p, Nx).astype(np.float64)
y = np.linspace(0., Ly_p, Ny).astype(np.float64)
z = np.linspace(0., Lz_p, Nz).astype(np.float64)
numEl = Nx * Ny * Nz
Y, Z, X = np.meshgrid(y, z, x)
XX = np.reshape(X, numEl)
YY = np.reshape(Y, numEl)
ZZ = np.reshape(Z, numEl)
if rank == 0:
dat_name = 'snl'
elif rank == 1:
dat_name = 'inl'
elif rank == 2:
dat_name = 'onl'
in_fn = dat_name + '.b_dat'
out_fn = dat_name + '.vtk'
my_dat = np.fromfile(in_fn, dtype=np.int32)
dims = (Nx, Ny, Nz)
writeVTK(my_dat, dat_name, XX, YY, ZZ, out_fn, dims)
if(rank == 0):
print("u_conv_fact = %15.15f \n"%u_conv_fact)
nnodes = Nx*Ny*Nz
# compute geometric data only once
x = np.linspace(0.,Lx_p,Nx).astype(np.float64);
y = np.linspace(0.,Ly_p,Ny).astype(np.float64);
z = np.linspace(0.,Lz_p,Nz).astype(np.float64);
numEl = Nx*Ny*Nz
Y,Z,X = np.meshgrid(y,z,x);
XX = np.reshape(X,numEl)
YY = np.reshape(Y,numEl)
ZZ = np.reshape(Z,numEl)
if rank==0:
dat_name = 'snl';
elif rank==1:
dat_name = 'inl';
elif rank==2:
dat_name = 'onl';
in_fn = dat_name + '.b_dat'
out_fn = dat_name + '.vtk'
my_dat = np.fromfile(in_fn,dtype=np.int32)
dims = (Nx,Ny,Nz)
writeVTK(my_dat,dat_name,XX,YY,ZZ,out_fn,dims)
