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:
self._update_function_container(function)
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)
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")
from functools import reduce
import numpy as np
import petsc4py
from petsc4py import PETSc
from dolfin import MPI
import matplotlib.pyplot as plt
from dolfin.cpp.log import log, LogLevel, get_log_level
import mpi4py
import yaml
from dolfin import derivative, assemble
comm = mpi4py.MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
log_level = get_log_level()
class EigenSolver(object):
def __init__(
self,
a_k,
u,
a_m=None, # optional, for eigpb of the type (K-lambda M)x=0
bcs=None,
restricted_dofs_is=None,
slepc_options='',
option_prefix='eigen_',
comm=MPI.comm_world,
slepc_eigensolver=None,
initial_guess=None):
def _write_to_xdmf_file(fun, directory, filename, suffix, components=None):
if components is not None:
filename = filename + "_component_" + "".join(components)
function_name = "function_" + "".join(components)
else:
function_name = "function"
fun_rank = fun.value_rank()
fun_dim = product(fun.value_shape())
assert fun_rank <= 2
if ((fun_rank is 1 and fun_dim not in (2, 3))
or (fun_rank is 2 and fun_dim not in (4, 9))):
funs = fun.split(deepcopy=True)
for (i, fun_i) in enumerate(funs):
if components is not None:
filename_i = filename + "_subcomponent_" + str(i)
else:
filename_i = filename + "_component_" + str(i)
_write_to_xdmf_file(fun_i, directory, filename_i, suffix, None)
else:
full_filename_visualization = os.path.join(str(directory),
filename + ".xdmf")
full_filename_checkpoint = os.path.join(str(directory),
filename + "_checkpoint.xdmf")
if suffix is not None:
if full_filename_checkpoint in _all_xdmf_files:
assert _all_xdmf_latest_suffix[
full_filename_checkpoint] == suffix - 1
_all_xdmf_latest_suffix[full_filename_checkpoint] = suffix
else:
assert suffix == 0
# Remove existing files if any, as new functions should not be appended,
# but rather overwrite existing functions
if is_io_process() and os.path.exists(
full_filename_checkpoint):
os.remove(full_filename_checkpoint)
os.remove(full_filename_checkpoint.replace(".xdmf", ".h5"))
_all_xdmf_files[full_filename_visualization] = XDMFFile(
full_filename_visualization)
_all_xdmf_files[full_filename_checkpoint] = XDMFFile(
full_filename_checkpoint)
_all_xdmf_latest_suffix[
full_filename_checkpoint] = 0 # don't store these twice for both visualization
_all_xdmf_functions[full_filename_checkpoint] = fun.copy(
deepcopy=True) # and checkpoint, as they are the same!
# Make sure to always use the same function, otherwise dolfin
# changes the numbering and visualization is difficult in ParaView
assign(_all_xdmf_functions[full_filename_checkpoint], fun)
_all_xdmf_files[full_filename_visualization].write(
_all_xdmf_functions[full_filename_checkpoint], float(suffix))
bak_log_level = get_log_level()
set_log_level(int(WARNING) + 1) # disable xdmf logs
_all_xdmf_files[full_filename_checkpoint].write_checkpoint(
_all_xdmf_functions[full_filename_checkpoint], function_name,
float(suffix))
set_log_level(bak_log_level)
# Write out current suffix as well
SuffixIO.save_file(suffix, directory, filename + "_suffix")
else:
# Remove existing files if any, as new functions should not be appended,
# but rather overwrite existing functions
if is_io_process() and os.path.exists(full_filename_checkpoint):
os.remove(full_filename_checkpoint)
os.remove(full_filename_checkpoint.replace(".xdmf", ".h5"))
with XDMFFile(full_filename_visualization) as file_visualization:
file_visualization.write(fun, 0.)
with XDMFFile(full_filename_checkpoint) as file_checkpoint:
file_checkpoint.write_checkpoint(fun, function_name, 0.)