def writenek(fname, data):
"""A function for writing binary data in the nek5000 binary format
Parameters
----------
fname : str
file name
data : exadata
data organised as readnek() output
"""
#
try:
outfile = open(fname, 'wb')
except OSError as e:
logger.critical(f'I/O error ({e.errno}): {e.strerror}')
return -1
#
#---------------------------------------------------------------------------
# WRITE HEADER
#---------------------------------------------------------------------------
#
# multiple files (not implemented)
fid = 0
nf = 1
nelf = data.nel
#
# get fields to be written
vars = ''
if (data.var[0] > 0): vars += 'X'
if (data.var[1] > 0): vars += 'U'
if (data.var[2] > 0): vars += 'P'
if (data.var[3] > 0): vars += 'T'
if (data.var[4] > 0):
# TODO: check if header for scalars are written with zeros filled as S01
vars += 'S{:02d}'.format(data.var[4])
#
# get word size
if (data.wdsz == 4):
logger.debug('Writing single-precision file')
elif (data.wdsz == 8):
logger.debug('Writing double-precision file')
else:
logger.error('Could not interpret real type (wdsz = %i)' % (data.wdsz))
return -2
#
# generate header
header = '#std %1i %2i %2i %2i %10i %10i %20.13E %9i %6i %6i %s' % (
data.wdsz, data.lr1[0], data.lr1[1], data.lr1[2], data.nel, nelf,
data.time, data.istep, fid, nf, vars)
#
# write header
header = header.ljust(132)
outfile.write(header.encode('utf-8'))
#
# decide endianness
if data.endian in ('big', 'little'):
byteswap = data.endian != sys.byteorder
logger.debug(f'Writing {data.endian}-endian file')
else:
byteswap = False
logger.warning(f'Unrecognized endianness {data.endian}, '
f'writing native {sys.byteorder}-endian file')
#
def correct_endianness(a):
''' Return the array with the requested endianness'''
if byteswap:
return a.byteswap()
else:
return a
#
# write tag (to specify endianness)
endianbytes = np.array([6.54321], dtype=np.float32)
correct_endianness(endianbytes).tofile(outfile)
#
# write element map for the file
correct_endianness(data.elmap).tofile(outfile)
#
#---------------------------------------------------------------------------
# WRITE DATA
#---------------------------------------------------------------------------
#
# compute total number of points per element
npel = data.lr1[0] * data.lr1[1] * data.lr1[2]
#
def write_ndarray_to_file(a):
'''Write a data array to the output file in the requested precision and endianness'''
if data.wdsz == 4:
correct_endianness(a.astype(np.float32)).tofile(outfile)
else:
correct_endianness(a).tofile(outfile)
#
# write geometry
for iel in data.elmap:
for idim in range(
data.var[0]): # if var[0] == 0, geometry is not written
write_ndarray_to_file(data.elem[iel - 1].pos[idim, :, :, :])
#
# write velocity
for iel in data.elmap:
for idim in range(
data.var[1]): # if var[1] == 0, velocity is not written
write_ndarray_to_file(data.elem[iel - 1].vel[idim, :, :, :])
#
# write pressure
for iel in data.elmap:
for ivar in range(
data.var[2]): # if var[2] == 0, pressure is not written
write_ndarray_to_file(data.elem[iel - 1].pres[ivar, :, :, :])
#
# write temperature
for iel in data.elmap:
for ivar in range(
data.var[3]): # if var[3] == 0, temperature is not written
write_ndarray_to_file(data.elem[iel - 1].temp[ivar, :, :, :])
#
# write scalars
#
# NOTE: This is not a bug!
# Unlike other variables, scalars are in the outer loop and elements
# are in the inner loop
#
for ivar in range(data.var[4]): # if var[4] == 0, scalars are not written
for iel in data.elmap:
write_ndarray_to_file(data.elem[iel - 1].scal[ivar, :, :, :])
#
# write max and min of every field in every element (forced to single precision)
if (data.ndim == 3):
#
for iel in data.elmap:
for idim in range(data.var[0]):
correct_endianness(
np.min(data.elem[iel - 1].pos[idim, :, :, :]).astype(
np.float32)).tofile(outfile)
correct_endianness(
np.max(data.elem[iel - 1].pos[idim, :, :, :]).astype(
np.float32)).tofile(outfile)
for iel in data.elmap:
for idim in range(data.var[1]):
correct_endianness(
np.min(data.elem[iel - 1].vel[idim, :, :, :]).astype(
np.float32)).tofile(outfile)
correct_endianness(
np.max(data.elem[iel - 1].vel[idim, :, :, :]).astype(
np.float32)).tofile(outfile)
for iel in data.elmap:
for ivar in range(data.var[2]):
correct_endianness(
np.min(data.elem[iel - 1].pres[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
correct_endianness(
np.max(data.elem[iel - 1].pres[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
for iel in data.elmap:
for ivar in range(data.var[3]):
correct_endianness(
np.min(data.elem[iel - 1].temp[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
correct_endianness(
np.max(data.elem[iel - 1].temp[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
for iel in data.elmap:
for ivar in range(data.var[4]):
correct_endianness(
np.min(data.elem[iel - 1].scal[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
correct_endianness(
np.max(data.elem[iel - 1].scal[ivar, :, :, :]).astype(
np.float32)).tofile(outfile)
# close file
outfile.close()
#
# output
return 0
def writenek(fname, data):
"""A function for writing binary data in the nek5000 binary format
Parameters
----------
fname : str
file name
data : exadata
data organised as readnek() output
"""
#
try:
outfile = open(fname, 'wb')
except IOError as e:
logger.critical('I/O error ({0}): {1}'.format(e.errno, e.strerror))
return -1
#
#---------------------------------------------------------------------------
# WRITE HEADER
#---------------------------------------------------------------------------
#
# multiple files (not implemented)
fid = 0
nf = 1
nelf = data.nel
#
# get fields to be written
vars = ''
if (data.var[0] > 0): vars += 'X'
if (data.var[1] > 0): vars += 'U'
if (data.var[2] > 0): vars += 'P'
if (data.var[3] > 0): vars += 'T'
if (data.var[4] > 0):
logger.warning("Writing scalar variables is an experimental feature")
# TODO: check if header for scalars are written with zeros filled as S01
vars += 'S{:02d}'.format(data.var[4])
#
# get word size
if (data.wdsz == 4):
realtype = 'f'
elif (data.wdsz == 8):
realtype = 'd'
else:
logger.error('Could not interpret real type (wdsz = %i)' % (data.wdsz))
return -2
#
# generate header
header = '#std %1i %2i %2i %2i %10i %10i %20.13E %9i %6i %6i %s\n' %(
data.wdsz, data.lr1[0], data.lr1[1], data.lr1[2], data.nel, nelf,
data.time, data.istep, fid, nf, vars)
#
# write header
header = header.ljust(132)
outfile.write(header.encode('utf-8'))
#
# write tag (to specify endianness)
endianbytes = np.array([6.54321], dtype=np.float32)
endianbytes.tofile(outfile)
#
# generate and write element map for the file
elmap = np.linspace(1, data.nel, data.nel, dtype=np.int32)
elmap.tofile(outfile)
#
#---------------------------------------------------------------------------
# WRITE DATA
#---------------------------------------------------------------------------
#
# compute total number of points per element
npel = data.lr1[0] * data.lr1[1] * data.lr1[2]
#
def write_ndarray_to_file(a):
if data.wdsz == 4:
np.float32(a).tofile(outfile)
else:
a.tofile(outfile)
#
# write geometry
for iel in elmap:
for idim in range(data.var[0]): # if var[0] == 0, geometry is not written
write_ndarray_to_file(data.elem[iel-1].pos[idim, :, :, :])
#
# write velocity
for iel in elmap:
for idim in range(data.var[1]): # if var[1] == 0, velocity is not written
write_ndarray_to_file(data.elem[iel-1].vel[idim, :, :, :])
#
# write pressure
for iel in elmap:
for ivar in range(data.var[2]): # if var[2] == 0, pressure is not written
write_ndarray_to_file(data.elem[iel-1].pres[ivar, :, :, :])
#
# write temperature
for iel in elmap:
for ivar in range(data.var[3]): # if var[3] == 0, temperature is not written
write_ndarray_to_file(data.elem[iel-1].temp[ivar, :, :, :])
#
# write scalars
#
# NOTE: This is not a bug!
# Unlike other variables, scalars are in the outer loop and elements
# are in the inner loop
#
for ivar in range(data.var[4]): # if var[4] == 0, scalars are not written
for iel in elmap:
write_ndarray_to_file(data.elem[iel-1].scal[ivar, :, :, :])
#
# write max and min of every field in every element (forced to single precision)
if (data.ndim==3):
#
for iel in elmap:
for idim in range(data.var[0]):
np.min(data.elem[iel-1].pos[idim, :,:,:]).tofile(outfile)
np.max(data.elem[iel-1].pos[idim, :,:,:]).tofile(outfile)
for idim in range(data.var[1]):
np.min(data.elem[iel-1].vel[idim, :,:,:]).tofile(outfile)
np.max(data.elem[iel-1].vel[idim, :,:,:]).tofile(outfile)
for idim in range(data.var[2]):
np.min(data.elem[iel-1].pres[idim, :,:,:]).tofile(outfile)
np.max(data.elem[iel-1].pres[idim, :,:,:]).tofile(outfile)
for idim in range(data.var[3]):
np.min(data.elem[iel-1].temp[idim, :,:,:]).tofile(outfile)
np.max(data.elem[iel-1].temp[idim, :,:,:]).tofile(outfile)
# close file
outfile.close()
#
# output
return 0
def writere2(fname, data):
"""A function for writing binary .re2 files for nek5000
Parameters
----------
fname : str
file name
data : exadata
data organised as in exadata.py
"""
#
#---------------------------------------------------------------------------
# CHECK INPUT DATA
#---------------------------------------------------------------------------
#
# We could extract the corners, but for now just return an error if lr1 is too large
if data.lr1 != [2, 2, data.ndim - 1]:
logger.critical(
'wrong element dimensions for re2 file! {} != {}'.format(
data.lr1, [2, 2, data.ndim - 1]))
return -2
#
if data.var[0] != data.ndim:
logger.critical(
'wrong number of geometric variables for re2 file! expected {}, found {}'
.format(data.ndim, data.var[0]))
return -3
#
# Open file
try:
outfile = open(fname, 'wb')
except OSError as e:
logger.critical(f'I/O error ({e.errno}): {e.strerror}')
return -1
#
#---------------------------------------------------------------------------
# WRITE HEADER
#---------------------------------------------------------------------------
#
# always double precision
wdsz = 8
realtype = 'd'
nel = data.nel
ndim = data.ndim
header = f'#v002{nel:9d}{ndim:3d}{nel:9d} this is the hdr'
header = header.ljust(80)
outfile.write(header.encode('utf-8'))
#
# decide endianness
if data.endian in ('big', 'little'):
byteswap = data.endian != sys.byteorder
logger.debug(f'Writing {data.endian}-endian file')
else:
byteswap = False
logger.warning(f'Unrecognized endianness {data.endian}, '
f'writing native {sys.byteorder}-endian file')
#
def correct_endianness(a):
''' Return the array with the requested endianness'''
if byteswap:
return a.byteswap()
else:
return a
#
# write tag (to specify endianness)
endianbytes = np.array([6.54321], dtype=np.float32)
correct_endianness(endianbytes).tofile(outfile)
#
#---------------------------------------------------------------------------
# WRITE DATA
#---------------------------------------------------------------------------
#
# compute total number of points per element
npel = 2**ndim
#
def write_data_to_file(a):
'''Write the geometry of an element to the output file in double precision'''
correct_endianness(a).tofile(outfile)
#
# write geometry (adding eight bytes of zeros before each element)
xyz = np.zeros(
(npel * ndim + 1, )
) # array storing reordered geometry data (with a zero in the first position)
for el in data.elem:
# the data is stored in the following order (2D|3D):
# x1, x2, x4, x3; | x5, x6, x8, x7;
# y1, y2, y4, y3; | y5, y6, y8, y7;
# ----------------
# z1, z2, z4, z3; z5, z6, z8, z7;
# where 1-8 is the ordering of the points in memory
for idim in range(ndim): # x, y, [z]
for iz in range(
ndim - 1
): # this does only one iteration in 2D, and in 3D does one iteration for 1-4 and one for 5-8
xyz[npel * idim + 4 * iz + 1] = el.pos[idim, iz, 0, 0]
xyz[npel * idim + 4 * iz + 2] = el.pos[idim, iz, 0, 1]
xyz[npel * idim + 4 * iz + 3] = el.pos[idim, iz, 1, 1]
xyz[npel * idim + 4 * iz + 4] = el.pos[idim, iz, 1, 0]
write_data_to_file(xyz)
#
# write curve sides data
# locate curved edges
curved_edges = []
for (iel, el) in enumerate(data.elem):
for iedge in range(12):
if el.ccurv[iedge] != '':
curved_edges.append((iel, iedge))
# write number of curved edges
ncurv = len(curved_edges)
if ncurv != data.ncurv:
logger.warning(
f'wrong number of curved edges: expected {data.ncurv}, found {ncurv}'
)
ncurvf = np.array([ncurv], dtype=np.float64)
write_data_to_file(ncurvf)
# format curve data
cdata = np.zeros((ncurv, ), dtype='f8, f8, f8, f8, f8, f8, f8, S8')
for (cdat, (iel, iedge)) in zip(cdata, curved_edges):
el = data.elem[iel]
cdat[0] = iel + 1
cdat[1] = iedge + 1
# curve parameters
for j in range(5):
cdat[2 + j] = el.curv[iedge, j]
# encode the string as a byte array padded with spaces
cdat[7] = el.ccurv[iedge].encode('utf-8')
# write to file
write_data_to_file(cdata)
#
# write boundary conditions for each field
for ifield in range(data.nbc):
# locate faces with boundary conditions
bc_faces = []
for (iel, el) in enumerate(data.elem):
for iface in range(2 * ndim):
bctype = el.bcs[ifield, iface][0]
# internal boundary conditions are not written to .re2 files by reatore2
# and are apparently ignored by Nek5000 even in .rea files
if bctype != '' and bctype != 'E':
bc_faces.append((iel, iface))
nbcs = len(bc_faces)
nbcsf = np.array([nbcs], dtype=np.float64)
write_data_to_file(nbcsf)
# initialize and format data
bcdata = np.zeros((nbcs, ), dtype='f8, f8, f8, f8, f8, f8, f8, S8')
for (bc, (iel, iface)) in zip(bcdata, bc_faces):
el = data.elem[iel]
bc[0] = iel + 1
bc[1] = iface + 1
for j in range(5):
bc[2 + j] = el.bcs[ifield, iface][3 + j]
# encode the string as a byte array padded with spaces
bc[7] = el.bcs[ifield, iface][0].encode('utf-8').ljust(8)
# write to file
write_data_to_file(bcdata)
#
# close file
outfile.close()
# rerurn
return 0
def readnek(fname):
"""A function for reading binary data from the nek5000 binary format
Parameters
----------
fname : str
file name
"""
#
try:
infile = open(fname, 'rb')
except IOError as e:
logger.critical('I/O error ({0}): {1}'.format(e.errno, e.strerror))
return -1
#
#---------------------------------------------------------------------------
# READ HEADER
#---------------------------------------------------------------------------
#
# read header
header = infile.read(132).split()
logger.debug('Header: {}'.format(b' '.join(header).decode('utf-8')))
# get word size: single or double precision
wdsz = int(header[1])
if (wdsz == 4):
realtype = 'f'
elif (wdsz == 8):
realtype = 'd'
else:
logger.error('Could not interpret real type (wdsz = %i)' % (wdsz))
return -2
#
# get polynomial order
lr1 = [
int(header[2]),
int(header[3]),
int(header[4])
]
#
# compute total number of points per element
npel = lr1[0] * lr1[1] * lr1[2]
#
# get number of physical dimensions
ndim = 2 + (lr1[2]>1)
#
# get number of elements
nel = int(header[5])
#
# get number of elements in the file
nelf = int(header[6])
#
# get current time
time = float(header[7])
#
# get current time step
istep = int(header[8])
#
# get file id
fid = int(header[9])
#
# get tot number of files
nf = int(header[10])
#
# get variables [XUPTS[01-99]]
variables = header[11].decode('utf-8')
logger.debug("Variables: {}".format(variables))
var = [0 for i in range(5)]
for v in variables:
if (v == 'X'):
var[0] = ndim
elif (v == 'U'):
var[1] = ndim
elif (v == 'P'):
var[2] = 1
elif (v == 'T'):
var[3] = 1
elif (v == 'S'):
logger.warning("Reading scalar variables is an experimental feature")
# For example: variables = 'XS44'
index_s = variables.index('S')
nb_scalars = int(variables[index_s+1:])
var[4] = nb_scalars
#
# identify endian encoding
etagb = infile.read(4)
etagL = struct.unpack('<f', etagb)[0]; etagL = int(etagL*1e5)/1e5
etagB = struct.unpack('>f', etagb)[0]; etagB = int(etagB*1e5)/1e5
if (etagL == 6.54321):
logger.debug('Reading little-endian file\n')
emode = '<'
elif (etagB == 6.54321):
logger.debug('Reading big-endian file\n')
emode = '>'
else:
logger.error('Could not interpret endianness')
return -3
#
# read element map for the file
elmap = infile.read(4*nelf)
elmap = list(struct.unpack(emode+nelf*'i', elmap))
#
#---------------------------------------------------------------------------
# READ DATA
#---------------------------------------------------------------------------
#
# initialize data structure
data = exdat.exadata(ndim, nel, lr1, var, 0)
data.time = time
data.istep = istep
data.wdsz = wdsz
if (emode == '<'):
data.endian = 'little'
elif (emode == '>'):
data.endian = 'big'
#
def read_file_into_data(elem, index_var, name_var):
"""Read binary file into an array attribute of ``data.elem``"""
fi = infile.read(npel*wdsz)
fi = np.frombuffer(fi, dtype=emode+realtype, count=npel)
# Fetch elem array, for example `data.elem.pos`
data_var = getattr(elem, name_var)
# Replace elem array in-place with
# array read from file after reshaping as
elem_shape = lr1[::-1] # lz, ly, lx
data_var[index_var, ...] = fi.reshape(elem_shape)
#
# read geometry
for iel in elmap:
el = data.elem[iel-1]
for idim in range(var[0]): # if var[0] == 0, geometry is not read
read_file_into_data(el, idim, 'pos')
#
# read velocity
for iel in elmap:
el = data.elem[iel-1]
for idim in range(var[1]): # if var[1] == 0, velocity is not read
read_file_into_data(el, idim, 'vel')
#
# read pressure
for iel in elmap:
el = data.elem[iel-1]
for ivar in range(var[2]): # if var[2] == 0, pressure is not read
read_file_into_data(el, ivar, 'pres')
#
# read temperature
for iel in elmap:
el = data.elem[iel-1]
for ivar in range(var[3]): # if var[3] == 0, temperature is not read
read_file_into_data(el, ivar, 'temp')
#
# read scalar fields
#
# NOTE: This is not a bug!
# Unlike other variables, scalars are in the outer loop and elements
# are in the inner loop
#
for ivar in range(var[4]): # if var[4] == 0, scalars are not read
for iel in elmap:
el = data.elem[iel-1]
read_file_into_data(el, ivar, 'scal')
#
#
# close file
infile.close()
#
# output
return data
