def _load_eles(self, rallocs, mesh, initsoln):
basismap = {b.name: b for b in subclasses(BaseBasis, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = OrderedDict()
for f in mesh:
m = re.match('spt_(.+?)_p%d$' % rallocs.prank, f)
if m:
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self._cfg)
# Construct a proxylist to simplify collective operations
eles = proxylist(elemap.values())
# Set the initial conditions either from a pyfrs file or from
# explicit expressions in the config file
if initsoln:
# Load the config used to produce the solution
solncfg = Inifile(initsoln['config'].item())
# Process the solution
for k, ele in elemap.iteritems():
soln = initsoln['soln_%s_p%d' % (k, rallocs.prank)]
ele.set_ics_from_soln(soln, solncfg)
else:
eles.set_ics_from_cfg()
# Allocate these elements on the backend
eles.set_backend(self._backend, self._nreg)
return eles, elemap
def _load_eles(self, rallocs, mesh, initsoln):
basismap = {b.name: b for b in subclasses(BaseShape, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = OrderedDict()
for f in mesh:
m = re.match('spt_(.+?)_p%d$' % rallocs.prank, f)
if m:
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self._cfg)
# Construct a proxylist to simplify collective operations
eles = proxylist(elemap.values())
# Set the initial conditions either from a pyfrs file or from
# explicit expressions in the config file
if initsoln:
# Load the config used to produce the solution
solncfg = Inifile(initsoln['config'])
# Process the solution
for k, ele in elemap.iteritems():
soln = initsoln['soln_%s_p%d' % (k, rallocs.prank)]
ele.set_ics_from_soln(soln, solncfg)
else:
eles.set_ics_from_cfg()
# Allocate these elements on the backend
eles.set_backend(self._backend, self._nreg)
return eles, elemap
def array_info(self):
"""Indexes element types and data array shapes in an archive by file
Returns a dictionary of information about the numpy array
files containing pyfr {mesh, solution} data in a .pyfr{m, s}
archive.
The dictionary is indexed by array file name, and is ordered
such that element type counts faster than partition number.
Dictionary values contain the pyfr element type as a string,
and the shape of the array as a tuple.
:return: Element type and array shape of data arrays, indexed
by array file name.
:rtype: :class:`collections.OrderedDict`
:Example:
>>> from pyfr.readers import native
>>> example = read_pyfr_data('example.pyfrm')
>>> example.get_array_info
OrderedDict([('spt_hex_p0', ('hex', (27, 4, 3))),
('spt_tet_p0', ('tet', (27, 20, 3))),
('spt_hex_p1', ('hex', (27, 8, 3)))])
"""
info = OrderedDict()
# Retrieve list of {mesh, solution} array names, and set name prefix.
if self.spt_files:
ls_files = self.spt_files
prfx = 'spt'
elif self.soln_files:
ls_files = self.soln_files
prfx = 'soln'
else:
raise RuntimeError('"%s" does not contain solution or shape point '
'files' % (self.fname))
# Element types known to PyFR
eletypes = [
b.name for b in subclasses(BaseShape) if hasattr(b, 'name')
]
# Assembles possible array file names, then checks if present
# in .pyfr{m, s} archive. If so, the element type and array
# shape are assigned to the array file name in info.
prt = 0
while len(info) < len(ls_files):
for et in eletypes:
name = '%s_%s_p%d' % (prfx, et, prt)
if name in ls_files:
info[name] = (et, self[name].shape)
prt += 1
return info
def array_info(self):
"""Indexes element types and data array shapes in an archive by file
Returns a dictionary of information about the numpy array
files containing pyfr {mesh, solution} data in a .pyfr{m, s}
archive.
The dictionary is indexed by array file name, and is ordered
such that element type counts faster than partition number.
Dictionary values contain the pyfr element type as a string,
and the shape of the array as a tuple.
:return: Element type and array shape of data arrays, indexed
by array file name.
:rtype: :class:`collections.OrderedDict`
:Example:
>>> from pyfr.readers import native
>>> example = read_pyfr_data('example.pyfrm')
>>> example.get_array_info
OrderedDict([('spt_hex_p0', ('hex', (27, 4, 3))),
('spt_tet_p0', ('tet', (27, 20, 3))),
('spt_hex_p1', ('hex', (27, 8, 3)))])
"""
info = OrderedDict()
# Retrieve list of {mesh, solution} array names, and set name prefix.
if self.spt_files:
ls_files = self.spt_files
prfx = 'spt'
elif self.soln_files:
ls_files = self.soln_files
prfx = 'soln'
else:
raise RuntimeError('"%s" does not contain solution or shape point '
'files' % (self.fname))
# Element types known to PyFR
eletypes = [b.name for b in subclasses(BaseShape)
if hasattr(b, 'name')]
# Assembles possible array file names, then checks if present
# in .pyfr{m, s} archive. If so, the element type and array
# shape are assigned to the array file name in info.
prt = 0
while len(info) < len(ls_files):
for et in eletypes:
name = '%s_%s_p%d' % (prfx, et, prt)
if name in ls_files:
info[name] = (et, self.get_shape(name))
prt += 1
return info
def process_partition(args):
# Ensure outd is a directory
if not os.path.isdir(args.outd):
raise ValueError('Invalid output directory')
# Partition weights
if ':' in args.np:
pwts = [int(w) for w in args.np.split(':')]
else:
pwts = [1]*int(args.np)
# Element weights
if args.elewts:
ewts = {e: int(w) for e, w in (ew.split(':') for ew in args.elewts)}
else:
ewts = {'quad': 6, 'tri': 3, 'tet': 3, 'hex': 18, 'pri': 10, 'pyr': 6}
# Partitioner-specific options
opts = dict(s.split(':', 1) for s in args.popts)
# Create the partitioner
if args.partitioner:
part = get_partitioner(args.partitioner, pwts, ewts, opts=opts)
else:
for name in sorted(cls.name for cls in subclasses(BasePartitioner)):
try:
part = get_partitioner(name, pwts, ewts)
break
except OSError:
pass
else:
raise RuntimeError('No partitioners available')
# Partition the mesh
mesh, rnum, part_soln_fn = part.partition(NativeReader(args.mesh))
# Prepare the solutions
solnit = (part_soln_fn(NativeReader(s)) for s in args.solns)
# Output paths/files
paths = it.chain([args.mesh], args.solns)
files = it.chain([mesh], solnit)
# Iterate over the output mesh/solutions
for path, data in zip(paths, files):
# Compute the output path
path = os.path.join(args.outd, os.path.basename(path.rstrip('/')))
# Save to disk
write_pyfrms(path, data)
# Write out the renumbering table
if args.rnumf:
print('etype,pold,iold,pnew,inew', file=args.rnumf)
for etype, emap in sorted(rnum.items()):
for k, v in sorted(emap.items()):
print(etype, *k, *v, sep=',', file=args.rnumf)
def process_partition(args):
# Ensure outd is a directory
if not os.path.isdir(args.outd):
raise ValueError('Invalid output directory')
# Partition weights
if ':' in args.np:
pwts = [int(w) for w in args.np.split(':')]
else:
pwts = [1]*int(args.np)
# Partitioner-specific options
opts = dict(s.split(':', 1) for s in args.popts)
# Create the partitioner
if args.partitioner:
part = get_partitioner(args.partitioner, pwts, order=args.order,
opts=opts)
else:
for name in sorted(cls.name for cls in subclasses(BasePartitioner)):
try:
part = get_partitioner(name, pwts, order=args.order)
break
except OSError:
pass
else:
raise RuntimeError('No partitioners available')
# Partition the mesh
mesh, rnum, part_soln_fn = part.partition(NativeReader(args.mesh))
# Prepare the solutions
solnit = (part_soln_fn(NativeReader(s)) for s in args.solns)
# Output paths/files
paths = it.chain([args.mesh], args.solns)
files = it.chain([mesh], solnit)
# Iterate over the output mesh/solutions
for path, data in zip(paths, files):
# Compute the output path
path = os.path.join(args.outd, os.path.basename(path.rstrip('/')))
# Save to disk
with h5py.File(path, 'w') as f:
for k, v in data.items():
f[k] = v
# Write out the renumbering table
if args.rnumf:
print('etype,pold,iold,pnew,inew', file=args.rnumf)
for etype, emap in sorted(rnum.items()):
for k, v in sorted(emap.items()):
print(','.join(map(str, (etype, *k, *v))), file=args.rnumf)
def _load_eles(self, rallocs, mesh, initsoln, nregs, nonce):
basismap = {b.name: b for b in subclasses(BaseShape, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = {}
for f in mesh:
if (m := re.match(f'spt_(.+?)_p{rallocs.prank}$', f)):
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self.cfg)
def _load_eles(self, rallocs, mesh, initsoln, nregs, nonce):
basismap = {b.name: b for b in subclasses(BaseShape, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = {}
for f in mesh:
m = re.match(f'spt_(.+?)_p{rallocs.prank}$', f)
if m:
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self.cfg)
# Construct a proxylist to simplify collective operations
eles = proxylist(elemap.values())
# Set the initial conditions
if initsoln:
# Load the config and stats files from the solution
solncfg = Inifile(initsoln['config'])
solnsts = Inifile(initsoln['stats'])
# Get the names of the conserved variables (fields)
solnfields = solnsts.get('data', 'fields', '')
currfields = ','.join(eles[0].convarmap[eles[0].ndims])
# Ensure they match up
if solnfields and solnfields != currfields:
raise RuntimeError('Invalid solution for system')
# Process the solution
for etype, ele in elemap.items():
soln = initsoln[f'soln_{etype}_p{rallocs.prank}']
ele.set_ics_from_soln(soln, solncfg)
else:
eles.set_ics_from_cfg()
# Allocate these elements on the backend
for etype, ele in elemap.items():
k = f'spt_{etype}_p{rallocs.prank}'
try:
curved = ~mesh[k, 'linear']
linoff = np.max(*np.nonzero(curved), initial=-1) + 1
except KeyError:
linoff = ele.neles
ele.set_backend(self.backend, nregs, nonce, linoff)
return eles, elemap
def main():
ap = ArgumentParser(prog='pyfr-mesh', description='Generates and '
'manipulates PyFR mesh files')
sp = ap.add_subparsers(help='sub-command help')
# Mesh format conversion
ap_convert = sp.add_parser('convert', help='convert --help')
ap_convert.add_argument('inmesh', type=FileType('r'),
help='input mesh file')
ap_convert.add_argument('outmesh', type=FileType('wb'),
help='output PyFR mesh file')
types = sorted(cls.name for cls in subclasses(BaseReader))
ap_convert.add_argument('-t', dest='type', choices=types,
help='input file type; this is usually inferred '
'from the extension of inmesh')
ap_convert.set_defaults(process=process_convert)
# Mesh and solution partitioning
ap_partition = sp.add_parser('partition', help='partition --help')
ap_partition.add_argument('np', help='number of partitions or a colon '
'delimited list of weighs')
ap_partition.add_argument('mesh', help='input mesh file')
ap_partition.add_argument('solns', nargs='*',
help='input solution files')
ap_partition.add_argument(dest='outd', help='output directory')
partitioners = sorted(cls.name for cls in subclasses(BasePartitioner))
ap_partition.add_argument('-p', dest='partitioner', choices=partitioners,
help='partitioner to use')
ap_partition.add_argument('--popt', dest='popts', action='append',
default=[], metavar='key:value',
help='partitioner-specific option ')
ap_partition.set_defaults(process=process_partition)
args = ap.parse_args()
args.process(args)
def process_partition(args):
# Ensure outd is a directory
if not os.path.isdir(args.outd):
raise ValueError('Invalid output directory')
# Partition weights
if ':' in args.np:
pwts = [int(w) for w in args.np.split(':')]
else:
pwts = [1]*int(args.np)
# Partitioner-specific options
opts = dict(s.split(':', 1) for s in args.popts)
# Create the partitioner
if args.partitioner:
part = get_partitioner(args.partitioner, pwts, order=args.order,
opts=opts)
else:
for name in sorted(cls.name for cls in subclasses(BasePartitioner)):
try:
part = get_partitioner(name, pwts, order=args.order)
break
except OSError:
pass
else:
raise RuntimeError('No partitioners available')
# Partition the mesh
mesh, part_soln_fn = part.partition(NativeReader(args.mesh))
# Prepare the solutions
solnit = (part_soln_fn(NativeReader(s)) for s in args.solns)
# Output paths/files
paths = it.chain([args.mesh], args.solns)
files = it.chain([mesh], solnit)
# Iterate over the output mesh/solutions
for path, data in zip(paths, files):
# Compute the output path
path = os.path.join(args.outd, os.path.basename(path.rstrip('/')))
# Save to disk
with h5py.File(path, 'w') as f:
for k, v in data.items():
f[k] = v
def process_partition(args):
# Ensure outd is a directory
if not os.path.isdir(args.outd):
raise ValueError('Invalid output directory')
# Partition weights
if ':' in args.np:
pwts = [int(w) for w in args.np.split(':')]
else:
pwts = [1]*int(args.np)
# Partitioner-specific options
opts = dict(s.split(':', 1) for s in args.popts)
# Create the partitioner
if args.partitioner:
part = get_partitioner_by_name(args.partitioner, pwts, opts)
else:
for name in sorted(cls.name for cls in subclasses(BasePartitioner)):
try:
part = get_partitioner_by_name(name, pwts)
break
except RuntimeError:
pass
else:
raise RuntimeError('No partitioners available')
# Partition the mesh
mesh, part_soln_fn = part.partition(read_pyfr_data(args.mesh))
# Prepare the solutions
solnit = (part_soln_fn(read_pyfr_data(s)) for s in args.solns)
# Output paths/files
paths = it.chain([args.mesh], args.solns)
files = it.chain([mesh], solnit)
# Iterate over the output mesh/solutions
for path, data in it.izip(paths, files):
# Compute the output path
path = os.path.join(args.outd, os.path.basename(path.rstrip('/')))
# Open and save
with open(path, 'wb') as f:
np.savez(f, **data)
def _load_eles(self, rallocs, mesh, initsoln, nregs, nonce):
basismap = {b.name: b for b in subclasses(BaseShape, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = OrderedDict()
for f in mesh:
m = re.match('spt_(.+?)_p{0}$'.format(rallocs.prank), f)
if m:
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self.cfg)
# Construct a proxylist to simplify collective operations
eles = proxylist(elemap.values())
# Set the initial conditions
if initsoln:
# Load the config and stats files from the solution
solncfg = Inifile(initsoln['config'])
solnsts = Inifile(initsoln['stats'])
# Get the names of the conserved variables (fields)
solnfields = solnsts.get('data', 'fields', '')
currfields = ','.join(eles[0].convarmap[eles[0].ndims])
# Ensure they match up
if solnfields and solnfields != currfields:
raise RuntimeError('Invalid solution for system')
# Process the solution
for etype, ele in elemap.items():
soln = initsoln['soln_{0}_p{1}'.format(etype, rallocs.prank)]
ele.set_ics_from_soln(soln, solncfg)
else:
eles.set_ics_from_cfg()
# Compute the index of first strictly interior element
intoffs = self._compute_int_offsets(rallocs, mesh)
# Allocate these elements on the backend
for etype, ele in elemap.items():
ele.set_backend(self.backend, nregs, nonce, intoffs[etype])
return eles, elemap
def _load_eles(self, rallocs, mesh, initsoln, nreg):
basismap = {b.name: b for b in subclasses(BaseShape, just_leaf=True)}
# Look for and load each element type from the mesh
elemap = OrderedDict()
for f in mesh:
m = re.match('spt_(.+?)_p%d$' % rallocs.prank, f)
if m:
# Element type
t = m.group(1)
elemap[t] = self.elementscls(basismap[t], mesh[f], self.cfg)
# Construct a proxylist to simplify collective operations
eles = proxylist(elemap.values())
# Set the initial conditions either from a pyfrs file or from
# explicit expressions in the config file
if initsoln:
# Load the config and stats files from the solution
solncfg = Inifile(initsoln['config'])
solnsts = Inifile(initsoln['stats'])
# Get the names of the conserved variables (fields)
solnfields = solnsts.get('data', 'fields', '')
currfields = ','.join(eles[0].convarmap[eles[0].ndims])
# Ensure they match up
if solnfields and solnfields != currfields:
raise RuntimeError('Invalid solution for system')
# Process the solution
for k, ele in elemap.items():
soln = initsoln['soln_%s_p%d' % (k, rallocs.prank)]
ele.set_ics_from_soln(soln, solncfg)
else:
eles.set_ics_from_cfg()
# Allocate these elements on the backend
eles.set_backend(self.backend, nreg)
return eles, elemap
def main():
ap = ArgumentParser(prog='pyfr-mesh', description='Generates and '
'manipulates PyFR mesh files')
sp = ap.add_subparsers(help='sub-command help')
# Mesh format conversion
ap_convert = sp.add_parser('convert', help='convert --help')
ap_convert.add_argument('inmesh', type=FileType('r'),
help='Input mesh file')
ap_convert.add_argument('outmesh', type=FileType('wb'),
help='Output PyFR mesh file')
types = [cls.name for cls in subclasses(BaseReader)]
ap_convert.add_argument('-t', dest='type', choices=types, required=False,
help='Input file type; this is usually inferred '
'from the extension of inmesh')
ap_convert.set_defaults(process=process_convert)
args = ap.parse_args()
args.process(args)
def _load_bc_inters(self, rallocs, mesh, elemap):
bccls = self.bbcinterscls
bcmap = {b.type: b for b in subclasses(bccls, just_leaf=True)}
bc_inters = proxylist([])
for f in mesh:
m = re.match('bcon_(.+?)_p%d$' % rallocs.prank, f)
if m:
# Get the region name
rgn = m.group(1)
# Determine the config file section
cfgsect = 'soln-bcs-%s' % rgn
# Instantiate
bcclass = bcmap[self._cfg.get(cfgsect, 'type')]
bciface = bcclass(self._backend, mesh[f], elemap, cfgsect,
self._cfg)
bc_inters.append(bciface)
return bc_inters
def _load_bc_inters(self, rallocs, mesh, elemap):
bccls = self.bbcinterscls
bcmap = {b.type: b for b in subclasses(bccls, just_leaf=True)}
bc_inters = []
for f in mesh:
if (m := re.match(f'bcon_(.+?)_p{rallocs.prank}$', f)):
# Get the region name
rgn = m.group(1)
# Determine the config file section
cfgsect = f'soln-bcs-{rgn}'
# Get the interface
interarr = mesh[f].astype('U4,i4,i1,i2').tolist()
# Instantiate
bcclass = bcmap[self.cfg.get(cfgsect, 'type')]
bciface = bcclass(self.backend, interarr, elemap, cfgsect,
self.cfg)
bc_inters.append(bciface)
def _load_bc_inters(self, rallocs, mesh, elemap):
bccls = self.bbcinterscls
bcmap = {b.type: b for b in subclasses(bccls, just_leaf=True)}
bc_inters = proxylist([])
for f in mesh:
m = re.match('bcon_(.+?)_p%d$' % rallocs.prank, f)
if m:
# Get the region name
rgn = m.group(1)
# Determine the config file section
cfgsect = 'soln-bcs-%s' % rgn
# Instantiate
bcclass = bcmap[self._cfg.get(cfgsect, 'type')]
bciface = bcclass(self._backend, mesh[f].tolist(), elemap,
cfgsect, self._cfg)
bc_inters.append(bciface)
return bc_inters
def __init__(self):
self.mpi_init = False
self.ap = ArgumentParser(prog='pyfr')
self.sp = self.ap.add_subparsers(dest='cmd', help='sub-command help')
# Common options
self.ap.add_argument('--verbose', '-v', action='count')
# Run command
self.ap_run = self.sp.add_parser('run', help='run --help')
self.ap_run.add_argument('mesh', help='mesh file')
self.ap_run.add_argument('cfg', type=FileType('r'), help='config file')
self.ap_run.set_defaults(process=self.process_run)
# Restart command
self.ap_restart = self.sp.add_parser('restart', help='restart --help')
self.ap_restart.add_argument('mesh', help='mesh file')
self.ap_restart.add_argument('soln', help='solution file')
self.ap_restart.add_argument('cfg',
nargs='?',
type=FileType('r'),
help='new config file')
self.ap_restart.set_defaults(process=self.process_restart)
# Options common to run and restart
backends = sorted(cls.name for cls in subclasses(BaseBackend))
for p in [self.ap_run, self.ap_restart]:
p.add_argument('--backend',
'-b',
choices=backends,
required=True,
help='backend to use')
p.add_argument('--progress',
'-p',
action='store_true',
help='show a progress bar')
self.base_dir = os.path.dirname(__file__)
def get_reader_by_extn(extn, *args, **kwargs):
reader_map = {ex: cls
for cls in subclasses(BaseReader)
for ex in cls.extn}
return reader_map[extn](*args, **kwargs)
def main():
ap = ArgumentParser(prog='pyfr-postp', description='Post processes a '
'PyFR simulation')
sp = ap.add_subparsers(help='sub-command help')
ap_pack = sp.add_parser('pack', help='pack --help', description='Packs a '
'pyfr[ms]-directory into a pyfr[ms]-file. If no '
'output file is specified then that of the '
'input directory is taken. This command will '
'replace any existing file or directory.')
ap_pack.add_argument('indir', metavar='in',
help='Input PyFR mesh/solution directory')
ap_pack.add_argument('outf', metavar='out', nargs='?',
help='Out PyFR mesh/solution file')
ap_pack.set_defaults(process=process_pack)
ap_unpack = sp.add_parser('unpack', help='unpack --help', description=
'Unpacks a pyfr[ms]-file into a '
'pyfr[ms]-directory. If no output directory '
'name is specified then a directory named '
'after the input file is taken. This command '
'will remove any existing output file or '
'directory.')
ap_unpack.add_argument('inf', metavar='in', type=FileType('rb'),
help='Input PyFR mesh/solution file')
ap_unpack.add_argument('outdir', metavar='out', nargs='?',
help='Out PyFR mesh/solution directory')
ap_unpack.set_defaults(process=process_unpack)
ap_conv = sp.add_parser('convert', help='convert --help', description=
'Converts .pyfr[ms] files for visualisation '
'in external software.')
ap_conv.add_argument('meshf', help='PyFR mesh file to be converted')
ap_conv.add_argument('solnf', help='PyFR solution file to be converted')
ap_conv.add_argument('outf', type=FileType('wb'), help='Output filename')
types = [cls.name for cls in subclasses(BaseWriter)]
ap_conv.add_argument('-t', dest='type', choices=types, required=False,
help='Output file type; this is usually inferred '
'from the extension of outf')
ap_pop = ap_conv.add_subparsers(help='Choose output mode for high-order '
'data.')
ap_pdiv = ap_pop.add_parser('divide', help='paraview *args divide --help',
description='Divides high-order elements '
'into multiple low-order elements. All '
'elements are split to the same level.')
ap_pdiv.add_argument('-d', '--divisor', type=int, choices=range(1, 17),
default=0, help='Sets the level to which high '
'order elements are divided along each edge. The '
'total node count produced by divisor is equivalent '
'to that of solution order, which is used as the '
'default. Note: the output is linear between '
'nodes, so increased resolution may be required.')
ap_pdiv.add_argument('-p', '--precision', choices=['single', 'double'],
default='single', help='Selects the precision of '
'floating point numbers written to the output file; '
'single is the default.')
ap_pdiv.set_defaults(process=process_convert)
ap_pap = ap_pop.add_parser('append', help='paraview *args append --help',
description='High-order solutions are written '
'as high-order data appended to low-order '
'elements. A Paraview plugin recursively '
'bisects each element to achieve a requirement '
'on the relative error of a solution variable. '
'Paraview requires the high-order plugin '
'written by Sébastien Blaise, available from: '
'http://perso.uclouvain.be/sebastien.blaise/'
'tools.html')
ap_pap.set_defaults(divisor=None, precision='double',
process=process_convert)
ap_tavg = sp.add_parser('time-avg', help='time-avg --help',
description='Computes the mean solution of a '
'time-wise series of pyfrs files.')
ap_tavg.add_argument('outf', type=str, help='Output PyFR solution file '
'name.')
ap_tavg.add_argument('infs', type=str, nargs='+', help='Input '
'PyFR solution files to be time-averaged.')
ap_tavg.add_argument('-l', '--limits', nargs=2, type=float,
help='Exclude solution files (passed in the infs '
'argument) that lie outside minimum and maximum '
'solution time limits.')
ap_tavg.set_defaults(process=process_tavg)
# Parse the arguments
args = ap.parse_args()
args.process(args)
def get_reader_by_extn(extn, *args, **kwargs):
reader_map = {ex: cls
for cls in subclasses(BaseReader)
for ex in cls.extn}
return reader_map[extn](*args, **kwargs)
def main():
ap = ArgumentParser(prog='pyfr')
sp = ap.add_subparsers(dest='cmd', help='sub-command help')
# Common options
ap.add_argument('--verbose', '-v', action='count')
# Import command
ap_import = sp.add_parser('import', help='import --help')
ap_import.add_argument('inmesh', type=FileType('r'),
help='input mesh file')
ap_import.add_argument('outmesh', help='output PyFR mesh file')
types = sorted(cls.name for cls in subclasses(BaseReader))
ap_import.add_argument('-t', dest='type', choices=types,
help='input file type; this is usually inferred '
'from the extension of inmesh')
ap_import.set_defaults(process=process_import)
# Partition command
ap_partition = sp.add_parser('partition', help='partition --help')
ap_partition.add_argument('np', help='number of partitions or a colon '
'delimited list of weighs')
ap_partition.add_argument('mesh', help='input mesh file')
ap_partition.add_argument('solns', nargs='*',
help='input solution files')
ap_partition.add_argument(dest='outd', help='output directory')
partitioners = sorted(cls.name for cls in subclasses(BasePartitioner))
ap_partition.add_argument('-p', dest='partitioner', choices=partitioners,
help='partitioner to use')
ap_partition.add_argument('--popt', dest='popts', action='append',
default=[], metavar='key:value',
help='partitioner-specific option')
ap_partition.set_defaults(process=process_partition)
# Export command
ap_export = sp.add_parser('export', help='export --help',
description='Converts .pyfr[ms] files for '
'visualisation in external software.')
ap_export.add_argument('meshf', help='PyFR mesh file to be converted')
ap_export.add_argument('solnf', help='PyFR solution file to be converted')
ap_export.add_argument('outf', type=str, help='Output filename')
types = [cls.name for cls in subclasses(BaseWriter)]
ap_export.add_argument('-t', dest='type', choices=types, required=False,
help='Output file type; this is usually inferred '
'from the extension of outf')
ap_export.add_argument('-d', '--divisor', type=int, default=0,
help='Sets the level to which high order elements '
'are divided along each edge. The total node count '
'produced by divisor is equivalent to that of '
'solution order, which is used as the default. '
'Note: the output is linear between nodes, so '
'increased resolution may be required.')
ap_export.add_argument('-p', '--precision', choices=['single', 'double'],
default='single', help='Selects the precision of '
'floating point numbers written to the output file; '
'single is the default.')
ap_export.set_defaults(process=process_export)
# Run command
ap_run = sp.add_parser('run', help='run --help')
ap_run.add_argument('mesh', help='mesh file')
ap_run.add_argument('cfg', type=FileType('r'), help='config file')
ap_run.set_defaults(process=process_run)
# Restart command
ap_restart = sp.add_parser('restart', help='restart --help')
ap_restart.add_argument('mesh', help='mesh file')
ap_restart.add_argument('soln', help='solution file')
ap_restart.add_argument('cfg', nargs='?', type=FileType('r'),
help='new config file')
ap_restart.set_defaults(process=process_restart)
# Options common to run and restart
for p in [ap_run, ap_restart]:
p.add_argument('--backend', '-b', default='cuda',
help='Backend to use')
p.add_argument('--progress', '-p', action='store_true',
help='show a progress bar')
# Parse the arguments
args = ap.parse_args()
# Invoke the process method
if hasattr(args, 'process'):
args.process(args)
else:
ap.print_help()
def main():
ap = ArgumentParser(prog='pyfr-postp',
description='Post processes a '
'PyFR simulation')
sp = ap.add_subparsers(help='sub-command help')
ap_pack = sp.add_parser('pack',
help='pack --help',
description='Packs a '
'pyfr[ms]-directory into a pyfr[ms]-file. If no '
'output file is specified then that of the '
'input directory is taken. This command will '
'replace any existing file or directory.')
ap_pack.add_argument('indir',
metavar='in',
help='Input PyFR mesh/solution directory')
ap_pack.add_argument('outf',
metavar='out',
nargs='?',
help='Out PyFR mesh/solution file')
ap_pack.set_defaults(process=process_pack)
ap_unpack = sp.add_parser('unpack',
help='unpack --help',
description='Unpacks a pyfr[ms]-file into a '
'pyfr[ms]-directory. If no output directory '
'name is specified then a directory named '
'after the input file is taken. This command '
'will remove any existing output file or '
'directory.')
ap_unpack.add_argument('inf',
metavar='in',
type=FileType('rb'),
help='Input PyFR mesh/solution file')
ap_unpack.add_argument('outdir',
metavar='out',
nargs='?',
help='Out PyFR mesh/solution directory')
ap_unpack.set_defaults(process=process_unpack)
ap_conv = sp.add_parser(
'convert',
help='convert --help',
description='Converts .pyfr[ms] files for visualisation '
'in external software.')
ap_conv.add_argument('meshf', help='PyFR mesh file to be converted')
ap_conv.add_argument('solnf', help='PyFR solution file to be converted')
ap_conv.add_argument('outf', type=FileType('wb'), help='Output filename')
types = [cls.name for cls in subclasses(BaseWriter)]
ap_conv.add_argument('-t',
dest='type',
choices=types,
required=False,
help='Output file type; this is usually inferred '
'from the extension of outf')
ap_pop = ap_conv.add_subparsers(help='Choose output mode for high-order '
'data.')
ap_pdiv = ap_pop.add_parser('divide',
help='paraview *args divide --help',
description='Divides high-order elements '
'into multiple low-order elements. All '
'elements are split to the same level.')
ap_pdiv.add_argument('-d',
'--divisor',
type=int,
choices=range(1, 17),
default=0,
help='Sets the level to which high '
'order elements are divided along each edge. The '
'total node count produced by divisor is equivalent '
'to that of solution order, which is used as the '
'default. Note: the output is linear between '
'nodes, so increased resolution may be required.')
ap_pdiv.add_argument('-p',
'--precision',
choices=['single', 'double'],
default='single',
help='Selects the precision of '
'floating point numbers written to the output file; '
'single is the default.')
ap_pdiv.set_defaults(process=process_convert)
ap_pap = ap_pop.add_parser('append',
help='paraview *args append --help',
description='High-order solutions are written '
'as high-order data appended to low-order '
'elements. A Paraview plugin recursively '
'bisects each element to achieve a requirement '
'on the relative error of a solution variable. '
'Paraview requires the high-order plugin '
'written by Sébastien Blaise, available from: '
'http://perso.uclouvain.be/sebastien.blaise/'
'tools.html')
ap_pap.set_defaults(divisor=None,
precision='double',
process=process_convert)
ap_tavg = sp.add_parser('time-avg',
help='time-avg --help',
description='Computes the mean solution of a '
'time-wise series of pyfrs files.')
ap_tavg.add_argument('outf',
type=str,
help='Output PyFR solution file '
'name.')
ap_tavg.add_argument('infs',
type=str,
nargs='+',
help='Input '
'PyFR solution files to be time-averaged.')
ap_tavg.add_argument('-l',
'--limits',
nargs=2,
type=float,
help='Exclude solution files (passed in the infs '
'argument) that lie outside minimum and maximum '
'solution time limits.')
ap_tavg.set_defaults(process=process_tavg)
# Parse the arguments
args = ap.parse_args()
args.process(args)
def get_writer_by_extn(extn, *args, **kwargs):
writer_map = {ex: cls for cls in subclasses(BaseWriter) for ex in cls.extn}
return writer_map[extn](*args, **kwargs)
def get_writer_by_extn(extn, *args, **kwargs):
writer_map = {ex: cls
for cls in subclasses(BaseWriter)
for ex in cls.extn}
return writer_map[extn](*args, **kwargs)
def main():
ap = ArgumentParser(prog='pyfr')
sp = ap.add_subparsers(dest='cmd', help='sub-command help')
# Common options
ap.add_argument('--verbose', '-v', action='count')
# Import command
ap_import = sp.add_parser('import', help='import --help')
ap_import.add_argument('inmesh', type=FileType('r'),
help='input mesh file')
ap_import.add_argument('outmesh', help='output PyFR mesh file')
types = sorted(cls.name for cls in subclasses(BaseReader))
ap_import.add_argument('-t', dest='type', choices=types,
help='input file type; this is usually inferred '
'from the extension of inmesh')
ap_import.set_defaults(process=process_import)
# Partition command
ap_partition = sp.add_parser('partition', help='partition --help')
ap_partition.add_argument('np', help='number of partitions or a colon '
'delimited list of weighs')
ap_partition.add_argument('mesh', help='input mesh file')
ap_partition.add_argument('solns', nargs='*',
help='input solution files')
ap_partition.add_argument(dest='outd', help='output directory')
partitioners = sorted(cls.name for cls in subclasses(BasePartitioner))
ap_partition.add_argument('-p', dest='partitioner', choices=partitioners,
help='partitioner to use')
ap_partition.add_argument('--popt', dest='popts', action='append',
default=[], metavar='key:value',
help='partitioner-specific option')
ap_partition.set_defaults(process=process_partition)
# Export command
ap_export = sp.add_parser('export', help='export --help',
description='Converts .pyfr[ms] files for '
'visualisation in external software.')
ap_export.add_argument('meshf', help='PyFR mesh file to be converted')
ap_export.add_argument('solnf', help='PyFR solution file to be converted')
ap_export.add_argument('outf', type=str, help='Output filename')
types = [cls.name for cls in subclasses(BaseWriter)]
ap_export.add_argument('-t', dest='type', choices=types, required=False,
help='Output file type; this is usually inferred '
'from the extension of outf')
ap_export.add_argument('-d', '--divisor', type=int, default=0,
help='Sets the level to which high order elements '
'are divided; output is linear between nodes, so '
'increased resolution may be required')
ap_export.add_argument('-g', '--gradients', action='store_true',
help='Compute gradients')
ap_export.add_argument('-p', '--precision', choices=['single', 'double'],
default='single', help='Output number precision, '
'defaults to single')
ap_export.set_defaults(process=process_export)
# Run command
ap_run = sp.add_parser('run', help='run --help')
ap_run.add_argument('mesh', help='mesh file')
ap_run.add_argument('cfg', type=FileType('r'), help='config file')
ap_run.set_defaults(process=process_run)
# Restart command
ap_restart = sp.add_parser('restart', help='restart --help')
ap_restart.add_argument('mesh', help='mesh file')
ap_restart.add_argument('soln', help='solution file')
ap_restart.add_argument('cfg', nargs='?', type=FileType('r'),
help='new config file')
ap_restart.set_defaults(process=process_restart)
# Options common to run and restart
backends = sorted(cls.name for cls in subclasses(BaseBackend))
for p in [ap_run, ap_restart]:
p.add_argument('--backend', '-b', choices=backends, required=True,
help='Backend to use')
p.add_argument('--progress', '-p', action='store_true',
help='show a progress bar')
# Parse the arguments
args = ap.parse_args()
# Invoke the process method
if hasattr(args, 'process'):
args.process(args)
else:
ap.print_help()
def main():
ap = ArgumentParser(prog='pyfr')
sp = ap.add_subparsers(dest='cmd', help='sub-command help')
# Common options
ap.add_argument('--verbose', '-v', action='count')
# Import command
ap_import = sp.add_parser('import', help='import --help')
ap_import.add_argument('inmesh', type=FileType('r'),
help='input mesh file')
ap_import.add_argument('outmesh', help='output PyFR mesh file')
types = sorted(cls.name for cls in subclasses(BaseReader))
ap_import.add_argument('-t', dest='type', choices=types,
help='input file type; this is usually inferred '
'from the extension of inmesh')
ap_import.add_argument('-l', dest='lintol', type=float, default=1e-5,
help='linearisation tolerance')
ap_import.set_defaults(process=process_import)
# Partition command
ap_partition = sp.add_parser('partition', help='partition --help')
ap_partition.add_argument('np', help='number of partitions or a colon '
'delimited list of weights')
ap_partition.add_argument('mesh', help='input mesh file')
ap_partition.add_argument('solns', metavar='soln', nargs='*',
help='input solution files')
ap_partition.add_argument('outd', help='output directory')
partitioners = sorted(cls.name for cls in subclasses(BasePartitioner))
ap_partition.add_argument('-p', dest='partitioner', choices=partitioners,
help='partitioner to use')
ap_partition.add_argument('-r', dest='rnumf', type=FileType('w'),
help='output renumbering file')
ap_partition.add_argument('-e', dest='elewts', action='append',
default=[], metavar='shape:weight',
help='element weighting factor')
ap_partition.add_argument('--popt', dest='popts', action='append',
default=[], metavar='key:value',
help='partitioner-specific option')
ap_partition.set_defaults(process=process_partition)
# Export command
ap_export = sp.add_parser('export', help='export --help')
ap_export.add_argument('meshf', help='PyFR mesh file to be converted')
ap_export.add_argument('solnf', help='PyFR solution file to be converted')
ap_export.add_argument('outf', type=str, help='output file')
types = [cls.name for cls in subclasses(BaseWriter)]
ap_export.add_argument('-t', dest='type', choices=types, required=False,
help='output file type; this is usually inferred '
'from the extension of outf')
output_options = ap_export.add_mutually_exclusive_group(required=False)
output_options.add_argument('-d', '--divisor', type=int,
help='sets the level to which high order '
'elements are divided; output is linear '
'between nodes, so increased resolution '
'may be required')
output_options.add_argument('-k', '--order', type=int, dest="order",
help='sets the order of high order elements')
ap_export.add_argument('-g', '--gradients', action='store_true',
help='compute gradients')
ap_export.add_argument('-p', '--precision', choices=['single', 'double'],
default='single', help='output number precision; '
'defaults to single')
ap_export.set_defaults(process=process_export)
# Run command
ap_run = sp.add_parser('run', help='run --help')
ap_run.add_argument('mesh', help='mesh file')
ap_run.add_argument('cfg', type=FileType('r'), help='config file')
ap_run.set_defaults(process=process_run)
# Restart command
ap_restart = sp.add_parser('restart', help='restart --help')
ap_restart.add_argument('mesh', help='mesh file')
ap_restart.add_argument('soln', help='solution file')
ap_restart.add_argument('cfg', nargs='?', type=FileType('r'),
help='new config file')
ap_restart.set_defaults(process=process_restart)
# Options common to run and restart
backends = sorted(cls.name for cls in subclasses(BaseBackend))
for p in [ap_run, ap_restart]:
p.add_argument('--backend', '-b', choices=backends, required=True,
help='backend to use')
p.add_argument('--progress', '-p', action='store_true',
help='show a progress bar')
# Parse the arguments
args = ap.parse_args()
# Invoke the process method
if hasattr(args, 'process'):
args.process(args)
else:
ap.print_help()
def main():
ap = ArgumentParser(prog="pyfr")
sp = ap.add_subparsers(dest="cmd", help="sub-command help")
# Common options
ap.add_argument("--verbose", "-v", action="count")
# Import command
ap_import = sp.add_parser("import", help="import --help")
ap_import.add_argument("inmesh", type=FileType("r"), help="input mesh file")
ap_import.add_argument("outmesh", help="output PyFR mesh file")
types = sorted(cls.name for cls in subclasses(BaseReader))
ap_import.add_argument(
"-t",
dest="type",
choices=types,
help="input file type; this is usually inferred " "from the extension of inmesh",
)
ap_import.set_defaults(process=process_import)
# Partition command
ap_partition = sp.add_parser("partition", help="partition --help")
ap_partition.add_argument("np", help="number of partitions or a colon " "delimited list of weighs")
ap_partition.add_argument("mesh", help="input mesh file")
ap_partition.add_argument("solns", nargs="*", help="input solution files")
ap_partition.add_argument(dest="outd", help="output directory")
partitioners = sorted(cls.name for cls in subclasses(BasePartitioner))
ap_partition.add_argument("-p", dest="partitioner", choices=partitioners, help="partitioner to use")
ap_partition.add_argument(
"--popt", dest="popts", action="append", default=[], metavar="key:value", help="partitioner-specific option"
)
ap_partition.set_defaults(process=process_partition)
# Export command
ap_export = sp.add_parser(
"export",
help="export --help",
description="Converts .pyfr[ms] files for " "visualisation in external software.",
)
ap_export.add_argument("meshf", help="PyFR mesh file to be converted")
ap_export.add_argument("solnf", help="PyFR solution file to be converted")
ap_export.add_argument("outf", type=str, help="Output filename")
types = [cls.name for cls in subclasses(BaseWriter)]
ap_export.add_argument(
"-t",
dest="type",
choices=types,
required=False,
help="Output file type; this is usually inferred " "from the extension of outf",
)
ap_export.add_argument(
"-d",
"--divisor",
type=int,
default=0,
help="Sets the level to which high order elements "
"are divided along each edge. The total node count "
"produced by divisor is equivalent to that of "
"solution order, which is used as the default. "
"Note: the output is linear between nodes, so "
"increased resolution may be required.",
)
ap_export.add_argument(
"-p",
"--precision",
choices=["single", "double"],
default="single",
help="Selects the precision of " "floating point numbers written to the output file; " "single is the default.",
)
ap_export.set_defaults(process=process_export)
# Run command
ap_run = sp.add_parser("run", help="run --help")
ap_run.add_argument("mesh", help="mesh file")
ap_run.add_argument("cfg", type=FileType("r"), help="config file")
ap_run.set_defaults(process=process_run)
# Restart command
ap_restart = sp.add_parser("restart", help="restart --help")
ap_restart.add_argument("mesh", help="mesh file")
ap_restart.add_argument("soln", help="solution file")
ap_restart.add_argument("cfg", nargs="?", type=FileType("r"), help="new config file")
ap_restart.set_defaults(process=process_restart)
# Options common to run and restart
for p in [ap_run, ap_restart]:
p.add_argument("--backend", "-b", default="cuda", help="Backend to use")
p.add_argument("--progress", "-p", action="store_true", help="show a progress bar")
# Time average command
ap_tavg = sp.add_parser(
"time-avg",
help="time-avg --help",
description="Computes the mean solution of a " "time-wise series of pyfrs files.",
)
ap_tavg.add_argument("outf", type=str, help="Output PyFR solution file " "name.")
ap_tavg.add_argument("infs", type=str, nargs="+", help="Input " "PyFR solution files to be time-averaged.")
ap_tavg.add_argument(
"-l",
"--limits",
nargs=2,
type=float,
help="Exclude solution files (passed in the infs "
"argument) that lie outside minimum and maximum "
"solution time limits.",
)
ap_tavg.set_defaults(process=process_tavg)
# Parse the arguments
args = ap.parse_args()
# Invoke the process method
if hasattr(args, "process"):
args.process(args)
else:
ap.print_help()