def read(solution,
frame,
path='./',
file_prefix='claw',
read_aux=False,
options={}):
r"""
Read in pickles and PETSc data files representing the solution
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxiliary file will try to be read
in. ``default = False``
- *options* - (dict) Optional argument dictionary, see
`PETScIO Option Table`_
.. _`PETScIO Option Table`:
format : one of 'ascii' or 'binary'
"""
import os
# Option parsing
option_defaults = {'format': 'binary'}
for k in option_defaults.iterkeys():
if options.has_key(k):
pass
else:
options[k] = option_defaults[k]
pickle_filename = os.path.join(
path, '%s.pkl' % file_prefix) + str(frame).zfill(4)
viewer_filename = os.path.join(
path, '%s.ptc' % file_prefix) + str(frame).zfill(4)
aux_viewer_filename1 = os.path.join(
path, '%s_aux.ptc' % file_prefix) + str(frame).zfill(4)
aux_viewer_filename2 = os.path.join(
path, '%s_aux.ptc' % file_prefix) + str(0).zfill(4)
if os.path.exists(aux_viewer_filename1):
aux_viewer_filename = aux_viewer_filename1
else:
aux_viewer_filename = aux_viewer_filename2
if frame < 0:
# Don't construct file names with negative frameno values.
raise IOError("Frame " + str(frame) + " does not exist ***")
try:
pickle_file = open(pickle_filename, 'rb')
except IOError:
print "Error: file " + pickle_filename + " does not exist or is unreadable."
raise
# this dictionary is mostly holding debugging information, only nstates is needed
# most of this information is explicitly saved in the individual patches
value_dict = pickle.load(pickle_file)
nstates = value_dict['nstates']
num_dim = value_dict['num_dim']
num_aux = value_dict['num_aux']
num_eqn = value_dict['num_eqn']
# now set up the PETSc viewer
if options['format'] == 'ascii':
viewer = PETSc.Viewer().createASCII(viewer_filename,
PETSc.Viewer.Mode.READ)
if read_aux:
aux_viewer = PETSc.Viewer().createASCII(aux_viewer_filename,
PETSc.Viewer.Mode.READ)
elif options['format'] == 'binary':
if hasattr(PETSc.Viewer, 'createMPIIO'):
viewer = PETSc.Viewer().createMPIIO(viewer_filename,
PETSc.Viewer.Mode.READ)
else:
viewer = PETSc.Viewer().createBinary(viewer_filename,
PETSc.Viewer.Mode.READ)
if read_aux:
if os.path.exists(aux_viewer_filename):
if hasattr(PETSc.Viewer, 'createMPIIO'):
aux_viewer = PETSc.Viewer().createMPIIO(
aux_viewer_filename, PETSc.Viewer.Mode.READ)
else:
aux_viewer = PETSc.Viewer().createBinary(
aux_viewer_filename, PETSc.Viewer.Mode.READ)
else:
from warnings import warn
aux_file_path = os.path.join(path, aux_viewer_filename)
warn('read_aux=True but aux file %s does not exist' %
aux_file_path)
read_aux = False
else:
raise IOError('format type %s not supported' % options['format'])
patches = []
for m in xrange(nstates):
patch_dict = pickle.load(pickle_file)
level = patch_dict['level']
names = patch_dict['names']
lower = patch_dict['lower']
n = patch_dict['num_cells']
d = patch_dict['delta']
from clawpack import petclaw
dimensions = []
for i in xrange(num_dim):
dimensions.append(
#pyclaw.solution.Dimension(names[i],lower[i],lower[i] + n[i]*d[i],n[i]))
petclaw.Dimension(names[i], lower[i], lower[i] + n[i] * d[i],
n[i]))
#patch = pyclaw.solution.Patch(dimensions)
patch = petclaw.Patch(dimensions)
patch.level = level
#state = pyclaw.state.State(patch)
state = petclaw.State(patch, num_eqn, num_aux) ##
state.t = value_dict['t']
state.problem_data = value_dict['problem_data']
# DA View/Load is broken in Petsc-3.1.8, we can load/view the DA if needed in petsc-3.2
# state.q_da.load(viewer)
state.gqVec.load(viewer)
if read_aux:
state.gauxVec.load(aux_viewer)
solution.states.append(state)
patches.append(state.patch)
solution.domain = petclaw.geometry.Domain(patches)
pickle_file.close()
viewer.destroy()
if read_aux:
aux_viewer.destroy()
def read(solution,frame,path='./',file_prefix='claw',read_aux=True,
options={}):
r"""
Read in a HDF5 file into a Solution
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Pyclaw object to be
output
- *frame* - (int) Frame number
- *path* - (string) Root path
- *file_prefix* - (string) Prefix for the file name. ``default = 'claw'``
- *write_aux* - (bool) Boolean controlling whether the associated
auxiliary array should be written out. ``default = False``
- *options* - (dict) Optional argument dictionary, not used for reading.
"""
filename = os.path.join(path,'%s%s.hdf' %
(file_prefix,str(frame).zfill(4)))
patches = []
with h5py.File(filename,'r',driver='mpio',comm=MPI.COMM_WORLD) as f:
for patch in six.itervalues(f):
# Construct each dimension
dimensions = []
dim_names = [ name.decode('ascii')
for name in patch.attrs['dimensions'] ]
for dim_name in dim_names:
dim = geometry.Dimension(
patch.attrs["%s.lower" % dim_name],
patch.attrs["%s.upper" % dim_name],
patch.attrs["%s.num_cells" % dim_name],
name = dim_name)
# Optional attributes
for attr in ['units']:
attr_name = "%s.%s" % (dim_name,attr)
if patch.attrs.get(attr_name, None):
setattr(dim,attr,patch.attrs["%s.%s" % (dim_name,attr)])
dimensions.append(dim)
pyclaw_patch = petclaw.Patch(dimensions)
# Fetch general patch properties
for attr in ['t','num_eqn','patch_index','level']:
setattr(pyclaw_patch,attr,patch.attrs[attr])
state = petclaw.state.State(pyclaw_patch, \
patch.attrs['num_eqn'],patch.attrs['num_aux'])
state.t = patch.attrs['t']
globalSize = []
globalSize.append(state.q.shape[0])
globalSize.extend(pyclaw_patch.num_cells_global)
r = pyclaw_patch._da.getRanges()
dset = patch['q'][:].reshape(globalSize)
state.q = from_hdf5_dataset(dset, len(pyclaw_patch.dimensions), r, state.q.shape)
# Read in aux if applicable
if read_aux and patch.get('aux',None) is not None:
dset = patch['aux'][:]
state.aux = from_hdf5_dataset(dset, len(pyclaw_patch.dimensions), r, state.aux.shape)
solution.states.append(state)
patches.append(pyclaw_patch)
solution.domain = geometry.Domain(patches)
def read(solution,frame,path='./',file_prefix='claw',read_aux=False,options={}):
r"""
Read in pickles and PETSc data files representing the solution
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxiliary file will try to be read
in. ``default = False``
- *options* - (dict) Optional argument dictionary, see
`PETScIO Option Table`_
.. _`PETScIO Option Table`:
format : one of 'ascii' or 'binary'
"""
# Default format is binary
file_format = options.get('format', 'binary')
filenames = set_filenames(frame,path,file_format,file_prefix,read_aux)
if read_aux:
if not os.path.exists(filenames['aux']):
# If no aux file for this frame, assume it is time-independent
filenames['aux'] = os.path.join(path, '%s_aux.ptc' % file_prefix) + str(0).zfill(4)
try:
metadata_file = open(filenames['metadata'],'rb')
except IOError:
print "Error: file " + filenames['metadata'] + " does not exist or is unreadable."
raise
# this dictionary is mostly holding debugging information, only nstates is needed
# most of this information is explicitly saved in the individual patches
value_dict = pickle.load(metadata_file)
nstates = value_dict['nstates']
num_dim = value_dict['num_dim']
num_aux = value_dict['num_aux']
num_eqn = value_dict['num_eqn']
if read_aux and not os.path.exists(filenames['aux']):
# Don't abort if aux file is missing
from warnings import warn
aux_file_path = os.path.join(path,filenames['aux'])
warn('read_aux=True but aux file %s does not exist' % aux_file_path)
read_aux = False
q_viewer = set_up_viewers(filenames['q'],file_format.lower(),PETSc.Viewer.Mode.READ)
if read_aux:
aux_viewer = set_up_viewers(filenames['aux'],file_format.lower(),PETSc.Viewer.Mode.READ)
patches = []
for m in xrange(nstates):
patch_dict = pickle.load(metadata_file)
level = patch_dict['level']
names = patch_dict['names']
lower = patch_dict['lower']
n = patch_dict['num_cells']
d = patch_dict['delta']
from clawpack import petclaw
dimensions = []
for i in xrange(num_dim):
dimensions.append(
petclaw.Dimension(lower[i],lower[i] + n[i]*d[i],n[i],name=names[i]))
patch = petclaw.Patch(dimensions)
patch.level = level
state = petclaw.State(patch,num_eqn,num_aux)
state.t = value_dict['t']
state.problem_data = value_dict.get('problem_data',{})
if value_dict.has_key('mapc2p'):
# If no mapc2p is provided, leave the default identity map in grid
state.grid.mapc2p = value_dict['mapc2p']
# DA View/Load is broken in Petsc-3.1.8, we can load/view the DA if needed in petsc-3.2
# state.q_da.load(q_viewer)
state.gqVec.load(q_viewer)
if read_aux:
state.gauxVec.load(aux_viewer)
solution.states.append(state)
patches.append(state.patch)
solution.domain = petclaw.geometry.Domain(patches)
metadata_file.close()
q_viewer.destroy() # Destroys aux_viewer also
def read_petsc(self):
if hasattr(self, 'frame'): frame = self.frame
if hasattr(self, 'file_prefix'): file_prefix = self.file_prefix
if hasattr(self, 'path'): path = self.path
if hasattr(self, 'write_aux'): write_aux = self.write_aux
if hasattr(self, 'write_aux'): read_aux = self.read_aux
if hasattr(self, 'write_p'): write_p = self.write_p
pickle_filename = os.path.join(
path, '%s.pkl' % file_prefix) + str(frame).zfill(4)
viewer_filename = os.path.join(
path, '%s.ptc' % file_prefix) + str(frame).zfill(4)
aux_viewer_filename1 = os.path.join(
path, '%s_aux.ptc' % file_prefix) + str(frame).zfill(4)
aux_viewer_filename2 = os.path.join(
path, '%s_aux.ptc' % file_prefix) + str(0).zfill(4)
if os.path.exists(aux_viewer_filename1):
aux_viewer_filename = aux_viewer_filename1
else:
aux_viewer_filename = aux_viewer_filename2
pickle_file = open(pickle_filename, 'rb')
# this dictionary is mostly holding debugging information, only nstates is needed
# most of this information is explicitly saved in the individual patches
value_dict = pickle.load(pickle_file)
nstates = value_dict['nstates']
num_dim = value_dict['num_dim']
num_aux = value_dict['num_aux']
num_eqn = value_dict['num_eqn']
self.__setattr__('num_dim', num_dim)
self.__setattr__('num_aux', num_aux)
self.__setattr__('num_eqn', num_eqn)
# now set up the PETSc viewer (assuming binary)
viewer = PETSc.Viewer().createBinary(viewer_filename,
PETSc.Viewer.Mode.READ)
if read_aux:
aux_viewer = PETSc.Viewer().createBinary(aux_viewer_filename,
PETSc.Viewer.Mode.READ)
patches = []
for m in xrange(nstates):
patch_dict = pickle.load(pickle_file)
level = patch_dict['level']
names = patch_dict['names']
lower = patch_dict['lower']
n = patch_dict['num_cells']
d = patch_dict['delta']
from clawpack import petclaw
dimensions = []
for i in xrange(num_dim):
dimensions.append(
petclaw.Dimension(names[i], lower[i],
lower[i] + n[i] * d[i], n[i]))
patch = petclaw.Patch(dimensions)
self.__setattr__('_patch', patch)
if num_dim == 1:
self.__setattr__('x', patch.x)
elif num_dim == 2:
self.__setattr__('x', patch.x)
self.__setattr__('y', patch.y)
elif num_dim == 3:
self.__setattr__('y', patch.y)
self.__setattr__('z', path.z)
self.__setattr__('num_cells', patch.num_cells_global)
claw = petclaw.State(patch, num_eqn, num_aux) ##
self.__setattr__('_claw', claw)
self.t = value_dict['t']
self.problem_data = value_dict['problem_data']
self.nstates = value_dict['nstates']
self._claw.gqVec.load(viewer)
if read_aux:
self._claw.gauxVec.load(aux_viewer)
self.__setattr__('aux', self._claw.aux)
self.__setattr__('q', self._claw.q)
self.__setattr__('frame', frame)
self.__setattr__('file_prefix', file_prefix)
self.__setattr__('read_aux', read_aux)
self.__setattr__('write_aux', write_aux)
self.__setattr__('write_p', write_p)
self.__setattr__('path', path)
return self