import warnings
from festim import Export
import fenics as f
import numpy as np
field_to_label = {
"solute": "mobile_concentration",
"T": "temperature",
"retention": "retention",
"trap": "trap_i_concentration",
}
[docs]
class XDMFExport(Export):
"""
Args:
field (str): the exported field ("solute", "1", "retention", "T"...)
label (str, optional): label of the field in the written file.
If None, an automatic label will be given. Defaults to None.
filename (str, optional): the file path, needs to end with '.xdmf'.
If None, the label will be used. Defaults to None.
mode (int, str, optional): if "last" only the last
timestep will be exported. Otherwise the number of
iterations between each export can be provided as an integer.
Defaults to 1.
checkpoint (bool, optional): If set to True,
fenics.XDMFFile.write_checkpoint will be use, else
fenics.XDMFFile.write. Defaults to True.
folder (str, optional): path of the export folder. Defaults to None.
"""
def __init__(
self, field, label=None, filename=None, mode=1, checkpoint=True, folder=None
) -> None:
super().__init__(field=field)
self.label = label
self.folder = folder
self.filename = filename
self.files = None
self.define_xdmf_file()
self.mode = mode
self.checkpoint = checkpoint
if type(self.checkpoint) != bool:
raise TypeError("checkpoint must be a bool")
self.append = False
@property
def label(self):
return self._label
@label.setter
def label(self, value):
if value is None:
if self.field in field_to_label.keys():
self._label = field_to_label[self.field]
elif self.field.isdigit():
self._label = field_to_label["trap"].replace("i", self.field, 1)
else:
self._label = value
@property
def mode(self):
return self._mode
@mode.setter
def mode(self, value):
accepted_values = "accepted values for mode are int and 'last'"
if not isinstance(value, (str, int)):
raise ValueError(accepted_values)
if isinstance(value, int) and value <= 0:
raise ValueError("mode must be positive")
if isinstance(value, str) and value != "last":
raise ValueError(accepted_values)
self._mode = value
@property
def folder(self):
return self._folder
@folder.setter
def folder(self, value):
if value is not None:
if not isinstance(value, str):
raise TypeError("folder must be a string")
self._folder = value
@property
def filename(self):
return self._filename
@filename.setter
def filename(self, value):
if value is not None:
if not isinstance(value, str):
raise TypeError("filename must be a string")
if not value.endswith(".xdmf"):
raise ValueError("filename must end with .xdmf")
self._filename = value
else:
self._filename = "{}.xdmf".format(self.label)
[docs]
def define_xdmf_file(self):
"""Creates the file"""
if self.folder is None:
filename = self.filename
else:
filename = "{}/{}".format(self.folder, self.filename)
self.file = f.XDMFFile(filename)
self.file.parameters["flush_output"] = True
self.file.parameters["rewrite_function_mesh"] = False
[docs]
def write(self, t):
"""Writes to file
Args:
t (float): current time
"""
self.function.rename(self.label, "label")
if self.checkpoint:
# warn users if checkpoint is True and 1D
dimension = self.function.function_space().mesh().topology().dim()
if dimension == 1:
msg = "in 1D, checkpoint needs to be set to False to "
msg += "visualise the XDMF file in Paraview (see issue "
msg += "https://github.com/festim-dev/festim/issues/134)"
warnings.warn(msg)
self.file.write_checkpoint(
self.function,
self.label,
t,
f.XDMFFile.Encoding.HDF5,
append=self.append,
)
else:
self.file.write(self.function, t)
[docs]
def is_export(self, t, final_time, nb_iterations):
"""Checks if export should be exported.
Args:
t (float): the current time
final_time (float): the final time of the simulation
nb_iterations (int): the current number of time steps
Returns:
bool: True if export should be exported, else False
"""
if self.mode == "last" and np.isclose(t, final_time, atol=0):
return True
elif isinstance(self.mode, int):
if nb_iterations % self.mode == 0:
return True
return False
