def face_center(self, i):
"""Return the coordinates (x, y, z) of the center of the face number i"""
if i == 0:
kx1, ky1, kz1 = 0, 0, 0
kx2, ky2, kz2 = 0, 0, -1
kx3, ky3, kz3 = -1, 0, 0
kx4, ky4, kz4 = -1, 0, -1
elif i == 1:
kx1, ky1, kz1 = -1, 0, 0
kx2, ky2, kz2 = -1, 0, -1
kx3, ky3, kz3 = -1, -1, 0
kx4, ky4, kz4 = -1, -1, -1
elif i == 2:
kx1, ky1, kz1 = 0, -1, 0
kx2, ky2, kz2 = 0, -1, -1
kx3, ky3, kz3 = -1, -1, 0
kx4, ky4, kz4 = -1, -1, -1
elif i == 3:
kx1, ky1, kz1 = 0, 0, 0
kx2, ky2, kz2 = 0, 0, -1
kx3, ky3, kz3 = 0, -1, 0
kx4, ky4, kz4 = 0, -1, -1
elif i == 4:
kx1, ky1, kz1 = 0, 0, 0
kx2, ky2, kz2 = 0, -1, 0
kx3, ky3, kz3 = -1, 0, 0
kx4, ky4, kz4 = -1, -1, 0
elif i == 5:
kx1, ky1, kz1 = 0, 0, -1
kx2, ky2, kz2 = 0, -1, -1
kx3, ky3, kz3 = -1, 0, -1
kx4, ky4, kz4 = -1, -1, -1
else:
logger.error(f"Invalid face number {i} (must be between 0 and 5)")
(x1, y1, z1) = self.pos[:, kz1, ky1, kx1]
(x2, y2, z2) = self.pos[:, kz2, ky2, kx2]
(x3, y3, z3) = self.pos[:, kz3, ky3, kx3]
(x4, y4, z4) = self.pos[:, kz4, ky4, kx4]
return (
0.25 * (x1 + x2 + x3 + x4),
0.25 * (y1 + y2 + y3 + y4),
0.25 * (z1 + z2 + z3 + z4),
)
def check_connectivity(self):
"""Check element connectivity, specifically for matching boundary
conditions and geometry. Errors are reported as logging messages.
"""
dim = self.ndim
err = False
for (iel, el), ibc, iface in product(enumerate(self.elem),
range(self.nbc), range(2 * dim)):
cbc = el.bcs[ibc, iface][0]
if cbc == "E" or cbc == "P":
connected_iel = int(el.bcs[ibc, iface][3]) - 1
connected_face = int(el.bcs[ibc, iface][4]) - 1
cbc1 = self.elem[connected_iel].bcs[ibc, connected_face][0]
iel1 = int(self.elem[connected_iel].bcs[ibc,
connected_face][3]) - 1
iface1 = int(
self.elem[connected_iel].bcs[ibc, connected_face][4]) - 1
if iel1 < 0 or iel1 >= self.nel:
err = True
logger.error(
f"face {iface} of element {iel} is connected to face "
f"{connected_face} of the nonexistent element {connected_iel}"
)
else:
if cbc1 != cbc:
err = True
logger.error(
"mismatched boundary conditions: "
f"face {iface + 1} of element {iel + 1} with "
f"condition {cbc} is connected to face {connected_face + 1} "
f"of element {connected_iel + 1} with condition {cbc1}"
)
if iel1 != iel:
err = True
logger.error(
"mismatched elements: "
f"face {iface + 1} of element {iel + 1} "
f"is connected to face {connected_face + 1} "
f"of element {connected_iel + 1} but that face is "
f"connected to face {iface + 1} of element {iel + 1}"
)
if iface1 != iface:
err = True
logger.error(
"mismatched faces: "
f"face {iface + 1} of element {iel + 1} "
f"is connected to face {connected_face + 1} "
f"of element {connected_iel + 1} but that face is "
f"connected to face {iface + 1} of element {iel + 1}"
)
return not err
def check_connectivity(self):
"""Check element connectivity, specifically for matching boundary
conditions and geometry. Errors are reported as logging messages.
"""
dim = self.ndim
err = False
for (iel, el) in enumerate(self.elem):
for ibc in range(self.nbc):
for iface in range(2 * dim):
cbc = el.bcs[ibc, iface][0]
if cbc == 'E' or cbc == 'P':
connected_iel = int(el.bcs[ibc, iface][3]) - 1
connected_face = int(el.bcs[ibc, iface][4]) - 1
cbc1 = self.elem[connected_iel].bcs[ibc,
connected_face][0]
iel1 = int(self.elem[connected_iel].bcs[
ibc, connected_face][3]) - 1
iface1 = int(self.elem[connected_iel].bcs[
ibc, connected_face][4]) - 1
if iel1 < 0 or iel1 >= self.nel:
err = True
logger.error(
"face {:} of element {:} is connected to face {:} of the nonexistent element {:}"
.format(iface, iel, connected_face,
connected_iel))
else:
if cbc1 != cbc:
err = True
logger.error(
"mismatched boundary conditions: face {:} of element {:} with condition {:} is connected to face {:} of element {:} with condition {:}"
.format(iface + 1, iel + 1, cbc,
connected_face + 1,
connected_iel + 1, cbc1))
if iel1 != iel:
err = True
logger.error(
"mismatched elements: face {:} of element {:} is connected to face {:} of element {:} but that face is connected to face {:} of element {:}"
.format(iface + 1, iel + 1,
connected_face + 1,
connected_iel + 1, iface1 + 1,
iel1 + 1))
if iface1 != iface:
err = True
logger.error(
"mismatched faces: face {:} of element {:} is connected to face {:} of element {:} but that face is connected to face {:} of element {:}"
.format(iface + 1, iel + 1,
connected_face + 1,
connected_iel + 1, iface1 + 1,
iel1 + 1))
return not err
def readre2(fname):
"""A function for reading .re2 files for nek5000
Parameters
----------
fname : str
file name
"""
#
try:
infile = open(fname, 'rb')
except OSError as e:
logger.critical(f'I/O error ({e.errno}): {e.strerror}')
return -1
# the header for re2 files is 80 ASCII bytes, something like
# #v002 18669 2 18669 this is the hdr %
header = infile.read(80).split()
nel = int(header[1])
ndim = int(header[2])
# always double precision
wdsz = 8
realtype = 'd'
# detect endianness
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 = '<'
endian = 'little'
elif (etagB == 6.54321):
logger.debug('Reading big-endian file\n')
emode = '>'
endian = 'big'
else:
logger.error('Could not interpret endianness')
return -3
#
# there are no GLL points here, only quad/hex vertices
lr1 = [2, 2, ndim - 1]
npel = 2**ndim
# the file only contains geometry
var = [ndim, 0, 0, 0, 0]
# allocate structure
data = exdat.exadata(ndim, nel, lr1, var, 1)
#
# some metadata
data.wdsz = wdsz
data.endian = endian
#
# read the whole geometry into a buffer
# for some reason each element is prefixed with 8 bytes of zeros, it's not clear to me why.
# This is the reason for the +1 here, then the first number is ignored.
buf = infile.read((ndim * npel + 1) * wdsz * nel)
elem_shape = [ndim, ndim - 1, 2, 2] # nvar, lz, ly, lx
for (iel, el) in enumerate(data.elem):
fi = np.frombuffer(buf,
dtype=emode + realtype,
count=ndim * npel + 1,
offset=(ndim * npel + 1) * wdsz * iel)
# 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
el.pos[idim, iz, 0, 0] = fi[npel * idim + 4 * iz + 1]
el.pos[idim, iz, 0, 1] = fi[npel * idim + 4 * iz + 2]
el.pos[idim, iz, 1, 1] = fi[npel * idim + 4 * iz + 3]
el.pos[idim, iz, 1, 0] = fi[npel * idim + 4 * iz + 4]
#
# read curved sides
# the number of curved sides is stored as a double,
# then each curved side is 64 bytes:
# iel iface p1 p2 p3 p4 p5 ctype
# where p1-5 are f64 parameters and ctype is the type of curvature in ASCII
ncparam = 8
buf = infile.read(wdsz)
ncurv = int(np.frombuffer(buf)[0])
logger.debug(f'Found {ncurv} curved sides')
data.ncurv = ncurv
buf = infile.read(wdsz * (ncparam * ncurv))
for icurv in range(ncurv):
# interpret the data
curv = np.frombuffer(buf,
dtype=emode + realtype,
count=ncparam,
offset=icurv * ncparam * wdsz)
iel = int(curv[0]) - 1
iedge = int(curv[1]) - 1
cparams = curv[2:7]
# select only the first byte, because it turns out the later bytes may contain garbage.
# typically, it's b'C\x00\x00\x00\x00\x00\x00\x00' or b'C\x00\x00\x00\x00\x00\xe0?'.
# AFAIK the curvature types are always one character long anyway.
ctype = curv[7].tobytes()[:1].decode('utf-8')
# fill in the data structure
data.elem[iel].curv[iedge, :] = cparams
data.elem[iel].ccurv[iedge] = ctype
#
# read boundary conditions
# there can be more than one field, and we won't know until we'vre reached the end
nbcparam = 8
buf = infile.read(wdsz)
ifield = 0
while buf != b'':
# the data is initialized with one BC field, we might need to allocate another
if ifield > 0:
data.nbc = data.nbc + 1
for el in data.elem:
empty_bcs = np.zeros(el.bcs[:1, :].shape, dtype=el.bcs.dtype)
el.bcs = np.concatenate((el.bcs, empty_bcs))
nbclines = int(np.frombuffer(buf)[0])
logger.debug(
f'Found {nbclines} external boundary conditions for field {ifield}'
)
buf = infile.read(wdsz * (nbcparam * nbclines))
for ibc in range(nbclines):
# interpret the data
bc = np.frombuffer(buf,
dtype=emode + realtype,
count=nbcparam,
offset=ibc * nbcparam * wdsz)
iel = int(bc[0]) - 1
iface = int(bc[1]) - 1
bcparams = bc[2:7]
bctype = bc[7].tobytes().decode(
'utf-8').rstrip() # remove trailing spaces
# fill in the data structure
data.elem[iel].bcs[ifield, iface][0] = bctype
data.elem[iel].bcs[ifield, iface][1] = iel + 1
data.elem[iel].bcs[ifield, iface][2] = iface + 1
for ipar in range(5):
data.elem[iel].bcs[ifield, iface][3 + ipar] = bcparams[ipar]
ifield = ifield + 1
# try reading the number of conditions in the next field
buf = infile.read(wdsz)
infile.close()
return data
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 readnek(fname):
"""A function for reading binary data from the nek5000 binary format
Parameters
----------
fname : str
file name
"""
#
try:
infile = open(fname, 'rb')
except OSError as e:
logger.critical(f'I/O error ({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(f"Variables: {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'):
# 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
data.elmap = np.array(elmap, dtype=np.int32)
if (emode == '<'):
data.endian = 'little'
elif (emode == '>'):
data.endian = 'big'
#
def read_file_into_data(data_var, index_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)
# 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.pos, idim)
#
# 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.vel, idim)
#
# 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.pres, ivar)
#
# 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.temp, ivar)
#
# 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.scal, ivar)
#
#
# close file
infile.close()
#
# output
return data
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 merge(self, other, tol=1e-9, ignore_empty=True):
"""
Merges another exadata into the current one and connects it
Parameters
----------
other: exadata
mesh to merge into self
tol: float
maximum distance at which points are considered identical
ignore_empty: bool
if True, the faces with an empty boundary condition ('') will be treated as internal faces and will not be merged.
This is useful if internal boundary conditions are not defined and will make the operation *much* faster,
but requires boundary conditions to be defined on the faces to be merged.
"""
# perform some consistency checks
if self.ndim != other.ndim:
logger.error(
f"Cannot merge meshes of dimensions {self.ndim} and {other.ndim}!"
)
return -1
if self.lr1[0] != other.lr1[0]:
logger.error(
"Cannot merge meshes of different polynomial orders ({} != {})"
.format(self.lr1[0], other.lr1[0]))
return -2
# add the new elements (in an inconsistent state if there are internal boundary conditions)
nel1 = self.nel
self.nel = self.nel + other.nel
self.ncurv = self.ncurv + other.ncurv
self.elmap = np.concatenate((self.elmap, other.elmap + nel1))
# the deep copy is required here to avoid leaving the 'other' mesh in an inconsistent state by modifying its elements
self.elem = self.elem + copy.deepcopy(other.elem)
# check how many boundary condition fields we have
nbc = min(self.nbc, other.nbc)
# correct the boundary condition numbers:
# the index of the elements and neighbours have changed
for iel, ibc, iface in product(range(nel1, self.nel), range(other.nbc),
range(6)):
self.elem[iel].bcs[ibc, iface][1] = iel + 1
bc = self.elem[iel].bcs[ibc, iface][0]
if bc == "E" or bc == "P":
neighbour = self.elem[iel].bcs[ibc, iface][3]
self.elem[iel].bcs[ibc, iface][3] = neighbour + nel1
# glue common faces together
# only look for the neighbour in the first BC field because it should be the same in all fields.
# FIXME: this will fail to correct periodic conditions if periodic domains are merged together.
nfaces = 2 * self.ndim
nchanges = 0 # counter for the boundary conditions connected
if nbc == 0:
# Quickly exit the function
logger.debug("no pairs of faces to merge")
return nchanges
for iel0, iface0 in product(range(nel1, self.nel), range(nfaces)):
elem0 = self.elem[iel0]
bc0 = elem0.bcs[0, iface0][0]
if bc0 != "E" and not (ignore_empty and bc0 == ""):
# boundary element, look if it can be connected to something
for iel1, iface1 in product(range(nel1), range(nfaces)):
elem1 = self.elem[iel1]
bc1 = elem1.bcs[0, iface1][0]
if bc1 != "E" and not (ignore_empty and bc1 == ""):
# if the centers of the faces are close, connect them together
x0, y0, z0 = elem0.face_center(iface0)
x1, y1, z1 = elem1.face_center(iface1)
dist2 = (x1 - x0)**2 + (y1 - y0)**2 + (z1 - z0)**2
if dist2 <= tol**2:
# reconnect the periodic faces together (assumes that all fields are periodic)
if bc0 == bc1 == "P":
iel_p0 = int(elem0.bcs[0, iface0][3]) - 1
iel_p1 = int(elem1.bcs[0, iface1][3]) - 1
iface_p0 = int(elem0.bcs[0, iface0][4]) - 1
iface_p1 = int(elem1.bcs[0, iface1][4]) - 1
for ibc in range(nbc):
elem_p0_bcs = self.elem[iel_p0].bcs[
ibc, iface_p0]
elem_p1_bcs = self.elem[iel_p1].bcs[
ibc, iface_p1]
elem_p0_bcs[0] = "P"
elem_p1_bcs[0] = "P"
elem_p0_bcs[3] = iel_p1 + 1
elem_p1_bcs[3] = iel_p0 + 1
elem_p0_bcs[4] = iface_p1 + 1
elem_p1_bcs[4] = iface_p0 + 1
for ibc in range(nbc):
elem0.bcs[ibc, iface0][0] = "E"
elem1.bcs[ibc, iface1][0] = "E"
elem0.bcs[ibc, iface0][3] = iel1 + 1
elem1.bcs[ibc, iface1][3] = iel0 + 1
elem0.bcs[ibc, iface0][4] = iface1 + 1
elem1.bcs[ibc, iface1][4] = iface0 + 1
nchanges = nchanges + 1
logger.debug(f"merged {nchanges} pairs of faces")
return nchanges