class SolutionFile(SolutionFile_Base):
# DOLFIN 2018.1.0.dev added (throughout the developement cycle) an optional append
# attribute to XDMFFile.write_checkpoint, which should be set to its non-default value,
# thus breaking backwards compatibility
append_attribute = XDMFFile.write_checkpoint.__doc__.find(
"append: bool") > -1
def __init__(self, directory, filename):
SolutionFile_Base.__init__(self, directory, filename)
self._visualization_file = XDMFFile(self._full_filename + ".xdmf")
self._visualization_file.parameters["flush_output"] = True
self._restart_file = XDMFFile(self._full_filename +
"_checkpoint.xdmf")
self._restart_file.parameters["flush_output"] = True
@staticmethod
def remove_files(directory, filename):
SolutionFile_Base.remove_files(directory, filename)
#
full_filename = os.path.join(str(directory), filename)
if is_io_process() and os.path.exists(full_filename + ".xdmf"):
os.remove(full_filename + ".xdmf")
os.remove(full_filename + ".h5")
os.remove(full_filename + "_checkpoint.xdmf")
os.remove(full_filename + "_checkpoint.h5")
def write(self, function, name, index):
assert index in (self._last_index, self._last_index + 1)
if index == self._last_index + 1: # writing out solutions after time stepping
self._update_function_container(function)
time = float(index)
self._visualization_file.write(self._function_container, time)
bak_log_level = get_log_level()
set_log_level(int(WARNING) + 1) # disable xdmf logs)
if self.append_attribute:
self._restart_file.write_checkpoint(
self._function_container, name, time, append=True)
else:
self._restart_file.write_checkpoint(
self._function_container, name, time)
set_log_level(bak_log_level)
# Once solutions have been written to file, update last written index
self._write_last_index(index)
elif index == self._last_index:
# corner case for problems with two (or more) unknowns which are written separately to file;
# one unknown was written to file, while the other was not: since the problem might be coupled,
# a recomputation of both is required, but there is no need to update storage
pass
else:
raise ValueError("Invalid index")
def read(self, function, name, index):
if index <= self._last_index:
time = float(index)
self._restart_file.read_checkpoint(function, name, index)
self._update_function_container(function)
self._visualization_file.write(self._function_container, time)
else:
raise OSError
class SolutionFileXDMF(SolutionFile_Base):
# DOLFIN 2018.1.0.dev added (throughout the developement cycle) an optional append
# attribute to XDMFFile.write_checkpoint, which should be set to its non-default value,
# thus breaking backwards compatibility
append_attribute = XDMFFile.write_checkpoint.__doc__.find("append: bool") > - 1
def __init__(self, directory, filename):
SolutionFile_Base.__init__(self, directory, filename)
self._visualization_file = XDMFFile(self._full_filename + ".xdmf")
self._visualization_file.parameters["flush_output"] = True
self._restart_file = XDMFFile(self._full_filename + "_checkpoint.xdmf")
self._restart_file.parameters["flush_output"] = True
@staticmethod
def remove_files(directory, filename):
SolutionFile_Base.remove_files(directory, filename)
#
full_filename = os.path.join(str(directory), filename)
def remove_files_task():
if os.path.exists(full_filename + ".xdmf"):
os.remove(full_filename + ".xdmf")
os.remove(full_filename + ".h5")
os.remove(full_filename + "_checkpoint.xdmf")
os.remove(full_filename + "_checkpoint.h5")
parallel_io(remove_files_task)
def write(self, function, name, index):
time = float(index)
# Write visualization file (no append available, will overwrite)
self._update_function_container(function)
self._visualization_file.write(self._function_container, time)
# Write restart file. It might be possible that the solution was written to file in a previous run
# and the execution was interrupted before last written index was updated. In this corner case
# there would be two functions corresponding to the same time, with two consecutive indices.
# For now the inelegant way is to try to read: if that works, assume that we are in the corner case;
# otherwise, we are in the standard case and we should write to file.
try:
self._restart_file.read_checkpoint(self._function_container, name, index)
except RuntimeError:
from dolfin.cpp.log import get_log_level, LogLevel, set_log_level
self._update_function_container(function)
bak_log_level = get_log_level()
set_log_level(int(LogLevel.WARNING) + 1) # disable xdmf logs
if self.append_attribute:
self._restart_file.write_checkpoint(self._function_container, name, time, append=True)
else:
self._restart_file.write_checkpoint(self._function_container, name, time)
set_log_level(bak_log_level)
# Once solutions have been written to file, update last written index
self._write_last_index(index)
def read(self, function, name, index):
if index <= self._last_index:
time = float(index)
self._restart_file.read_checkpoint(function, name, index)
self._update_function_container(function)
self._visualization_file.write(self._function_container, time) # because there is no append option available
else:
raise OSError
def calc_value_differences(file_path1, file_path2, output_path, func_space,
t_func_space, parameters):
f1 = XDMFFile(file_path1)
f2 = XDMFFile(file_path2)
f_out = XDMFFile(output_path)
value_func1 = Function(func_space)
value_func2 = Function(func_space)
result = Function(t_func_space)
f1.read_checkpoint(value_func1, 'value_func', 0)
f2.read_checkpoint(value_func2, 'value_func', 0)
result.vector()[:] \
= value_func1.vector()[:] - value_func2.vector()[:]
f_out.write_checkpoint(result, 'diff', parameters.T,
XDMFFile.Encoding.HDF5, True)
i = 1
dt = parameters.T / parameters.M
for k in range(parameters.M - 1, -1, -1):
if k % parameters.save_interval != 0:
continue
f1.read_checkpoint(value_func1, 'value_func', i)
f2.read_checkpoint(value_func2, 'value_func', i)
result.vector()[:] \
= value_func1.vector()[:] - value_func2.vector()[:]
f_out.write_checkpoint(result, 'diff', k * dt, XDMFFile.Encoding.HDF5,
True)
i += 1
def vedoPlotter(pygmsh_ms):
# Reading mesh data stored in .xdmf files.
mesh = Mesh()
with XDMFFile(pygmsh_ms) as infile:
infile.read(mesh)
# Define variational problem
V = FunctionSpace(mesh, 'P', 1)
u = Function(V)
R_path = "Output_data"
fU_in = XDMFFile(os.path.join(R_path, 'FuelRod_m.xdmf'))
fU_in.read_checkpoint(u, "T", 0)
axes_opts = dict(
xyGrid=True,
axesLineWidth=1,
xTickColor='black',
yTickColor='black',
xMinorTicks=1, # number of minor ticks btw two major ticks
yMinorTicks=1, # number of minor ticks btw two major ticks
xLabelSize=0.02, # size of the numeric labels along axis
yLabelSize=0.02, # offset of numeric labels
)
# nipy_spectral, gnuplot
plot(u,
interactive=True,
cmap='hot',
axes=0,
lw=2,
scalarbar='vertical',
wireframe=True,
alpha=10.,
warpZfactor=0.) # warpZfactor=0.01
plot()
def heston_transform(parameters,
get_error=False,
file_path=None,
plot_deltas=False):
experiment = parameters.experiment
domain_name = parameters.domain
mesh_name = parameters.mesh
mesh = Mesh()
mesh_path = parameters.get_mesh_path()
with XDMFFile(mesh_path) as f:
f.read(mesh)
# Create functions in function spaces defined by both original and
# transformed meshes and copy value function data from one to another
t_mesh_path = f'meshes/{domain_name}/t_{domain_name}_{mesh_name}.xdmf'
if not os.path.exists(t_mesh_path):
mesh2 = get_original_mesh(t_mesh_path, mesh, parameters)
else:
mesh2 = Mesh()
with XDMFFile(t_mesh_path) as f:
f.read(mesh2)
V = FunctionSpace(mesh, 'CG', 1)
t_V = FunctionSpace(mesh2, 'CG', 1)
value = Function(V)
control = Function(V)
t_value = Function(t_V)
t_control = Function(t_V)
if not file_path:
f = XDMFFile(f'out/{experiment}/{domain_name}/{mesh_name}/v.xdmf')
t_f = XDMFFile(f'out/{experiment}/{domain_name}/{mesh_name}/t_v.xdmf')
else:
f = XDMFFile(file_path)
path, file_name = os.path.split(file_path)
t_f = XDMFFile(os.path.join(path, f't_{file_name}'))
# Save Final Time Condition
f.read_checkpoint(value, 'value_func', 0)
t_value.vector()[:] = value.vector()[:]
t_f.write_checkpoint(t_value, 'value_func', parameters.T)
# Iterate through remaining timesteps (only some of them are
# saved to the file)
i = 1
parameters.calculate_save_interval()
dt = parameters.T / parameters.M
for k in range(parameters.M - 1, -1, -1):
if k % parameters.save_interval != 0:
continue
f.read_checkpoint(value, 'value_func', i)
f.read_checkpoint(control, 'control', i - 1)
t_value.vector()[:] = value.vector()[:]
t_control.vector()[:] = control.vector()[:]
t_f.write_checkpoint(t_value, 'value_func', k * dt,
XDMFFile.Encoding.HDF5, True)
t_f.write_checkpoint(t_control, 'control', k * dt,
XDMFFile.Encoding.HDF5, True)
if plot_deltas:
delta_S = project(t_value.dx(0), t_V)
t_f.write_checkpoint(delta_S, 'delta_S', k * dt,
XDMFFile.Encoding.HDF5, True)
delta_v = project(t_value.dx(1), t_V)
t_f.write_checkpoint(delta_v, 'delta_v', k * dt,
XDMFFile.Encoding.HDF5, True)
i += 1
if k == 0 and get_error:
error_calc(t_value, parameters.t_v_e, mesh2, f't_{mesh_name}',
f'out/{experiment}/{domain_name}/errors.json')
def initial_condition_from_file(self, path_u, path_p):
f_in = XDMFFile(path_u)
f_in.read_checkpoint(self.u_, "f", 0)
f_in = XDMFFile(path_p)
f_in.read_checkpoint(self.p_, "f", 0)
return