simudo.io package

Submodules

simudo.io.csv module

class simudo.io.csv.LineCutCsvPlot(filename, function_subspace_registry=None, resolution=5001)

Bases: simudo.io.xdmf.PlotAddMixin

close()

new(timestamp)

timestamp = 0.0

simudo.io.h5yaml module

class simudo.io.h5yaml.BaseCustomTag

Bases: object

classmethod register_in_dumper(dumper)

classmethod register_in_loader(loader)

yaml_classes = ()

yaml_tag = None

class simudo.io.h5yaml.BaseDolfinMeshFunctionTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.DolfinObjectTag

property yaml_tag

classmethod(function) -> method

Convert a function to be a class method.

A class method receives the class as implicit first argument, just like an instance method receives the instance. To declare a class method, use this idiom:

class C:

@classmethod def f(cls, arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class. If a class method is called for a derived class, the derived class object is passed as the implied first argument.

Class methods are different than C++ or Java static methods. If you want those, see the staticmethod builtin.

class simudo.io.h5yaml.ClassProperty(fget=None, fset=None, fdel=None, doc=None)

Bases: property

class simudo.io.h5yaml.DolfinFunctionTag(scale=1.0, **kwargs)

Bases: simudo.io.h5yaml.ScaleDolfinObjectTag

yaml_classes = (<class 'dolfin.function.function.Function'>,)

yaml_tag = '!dolfin/function'

class simudo.io.h5yaml.DolfinH5Manager(basepath)

Bases: object

ensure_dir()

filename_from_key(key)

open(comm, key, mode)

returns (key, dolfin.HDF5File)

pass key=None to have a new one randomly generated

class simudo.io.h5yaml.DolfinMeshFunctionBoolTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.BaseDolfinMeshFunctionTag

meshfunction_type_name = 'bool'

yaml_classes = (<class 'dolfin.cpp.mesh.MeshFunctionBool'>,)

class simudo.io.h5yaml.DolfinMeshFunctionDoubleTag(scale=1.0, **kwargs)

Bases: simudo.io.h5yaml.ScaleMixin, simudo.io.h5yaml.BaseDolfinMeshFunctionTag

meshfunction_type_name = 'double'

yaml_classes = (<class 'dolfin.cpp.mesh.MeshFunctionDouble'>,)

class simudo.io.h5yaml.DolfinMeshFunctionIntTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.BaseDolfinMeshFunctionTag

meshfunction_type_name = 'int'

yaml_classes = (<class 'dolfin.cpp.mesh.MeshFunctionInt'>,)

class simudo.io.h5yaml.DolfinMeshFunctionSizetTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.BaseDolfinMeshFunctionTag

meshfunction_type_name = 'size_t'

yaml_classes = (<class 'dolfin.cpp.mesh.MeshFunctionSizet'>,)

class simudo.io.h5yaml.DolfinMeshTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.DolfinObjectTag

load_pass = -10

yaml_classes = (<class 'dolfin.cpp.mesh.Mesh'>,)

yaml_tag = '!dolfin/mesh'

class simudo.io.h5yaml.DolfinObjectTag(dolfin_h5_manager, key, **kwargs)

Bases: simudo.io.h5yaml.BaseCustomTag

classmethod from_yaml(loader, node)

classmethod get_object_mpi_comm(obj)

load_into(obj, comm=None)

load_pass = 0

needs_load_into = True

classmethod to_yaml(dumper, data)

class simudo.io.h5yaml.FrozenSetTag

Bases: simudo.io.h5yaml.BaseCustomTag

classmethod from_yaml(loader, node)

classmethod to_yaml(dumper, data)

yaml_classes = (<class 'frozenset'>,)

yaml_tag = '!frozenset'

class simudo.io.h5yaml.PintQTag

Bases: simudo.io.h5yaml.BaseCustomTag

classmethod from_yaml(loader, node)

classmethod to_yaml(dumper, data)

yaml_classes = (<class 'pint.quantity.Quantity'>,)

yaml_tag = '!pintq'

class simudo.io.h5yaml.ScaleDolfinObjectTag(scale=1.0, **kwargs)

Bases: simudo.io.h5yaml.ScaleMixin, simudo.io.h5yaml.DolfinObjectTag

class simudo.io.h5yaml.ScaleMixin(scale=1.0, **kwargs)

Bases: object

class simudo.io.h5yaml.SolutionIOTest(methodName='runTest')

Bases: unittest.case.TestCase

helper_test_roundtrip(dedup)

test_roundtrip()

test_roundtrip_with_dedup()

class simudo.io.h5yaml.XDumper(*args, **kwargs)

Bases: yaml.dumper.Dumper

ignore_aliases(data)

yaml_multi_representers = {<class 'object'>: <function Representer.represent_object>, <class 'dolfin.cpp.mesh.Mesh'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinMeshTag'>>, <class 'dolfin.function.function.Function'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinFunctionTag'>>, <class 'dolfin.cpp.mesh.MeshFunctionSizet'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionSizetTag'>>, <class 'dolfin.cpp.mesh.MeshFunctionInt'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionIntTag'>>, <class 'dolfin.cpp.mesh.MeshFunctionDouble'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionDoubleTag'>>, <class 'dolfin.cpp.mesh.MeshFunctionBool'>: <bound method DolfinObjectTag.to_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionBoolTag'>>, <class 'frozenset'>: <bound method FrozenSetTag.to_yaml of <class 'simudo.io.h5yaml.FrozenSetTag'>>, <class 'pint.quantity.Quantity'>: <bound method PintQTag.to_yaml of <class 'simudo.io.h5yaml.PintQTag'>>}

class simudo.io.h5yaml.XLoader(*args, **kwargs)

Bases: yaml.loader.Loader

yaml_constructors = {'tag:yaml.org,2002:null': <function SafeConstructor.construct_yaml_null>, 'tag:yaml.org,2002:bool': <function SafeConstructor.construct_yaml_bool>, 'tag:yaml.org,2002:int': <function SafeConstructor.construct_yaml_int>, 'tag:yaml.org,2002:float': <function SafeConstructor.construct_yaml_float>, 'tag:yaml.org,2002:binary': <function SafeConstructor.construct_yaml_binary>, 'tag:yaml.org,2002:timestamp': <function SafeConstructor.construct_yaml_timestamp>, 'tag:yaml.org,2002:omap': <function SafeConstructor.construct_yaml_omap>, 'tag:yaml.org,2002:pairs': <function SafeConstructor.construct_yaml_pairs>, 'tag:yaml.org,2002:set': <function SafeConstructor.construct_yaml_set>, 'tag:yaml.org,2002:str': <function SafeConstructor.construct_yaml_str>, 'tag:yaml.org,2002:seq': <function SafeConstructor.construct_yaml_seq>, 'tag:yaml.org,2002:map': <function SafeConstructor.construct_yaml_map>, None: <function SafeConstructor.construct_undefined>, 'tag:yaml.org,2002:python/none': <function SafeConstructor.construct_yaml_null>, 'tag:yaml.org,2002:python/bool': <function SafeConstructor.construct_yaml_bool>, 'tag:yaml.org,2002:python/str': <function FullConstructor.construct_python_str>, 'tag:yaml.org,2002:python/unicode': <function FullConstructor.construct_python_unicode>, 'tag:yaml.org,2002:python/bytes': <function FullConstructor.construct_python_bytes>, 'tag:yaml.org,2002:python/int': <function SafeConstructor.construct_yaml_int>, 'tag:yaml.org,2002:python/long': <function FullConstructor.construct_python_long>, 'tag:yaml.org,2002:python/float': <function SafeConstructor.construct_yaml_float>, 'tag:yaml.org,2002:python/complex': <function FullConstructor.construct_python_complex>, 'tag:yaml.org,2002:python/list': <function SafeConstructor.construct_yaml_seq>, 'tag:yaml.org,2002:python/tuple': <function FullConstructor.construct_python_tuple>, 'tag:yaml.org,2002:python/dict': <function SafeConstructor.construct_yaml_map>, '!dolfin/mesh': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinMeshTag'>>, '!dolfin/function': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinFunctionTag'>>, '!dolfin/meshfunction/size_t': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionSizetTag'>>, '!dolfin/meshfunction/int': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionIntTag'>>, '!dolfin/meshfunction/double': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionDoubleTag'>>, '!dolfin/meshfunction/bool': <bound method DolfinObjectTag.from_yaml of <class 'simudo.io.h5yaml.DolfinMeshFunctionBoolTag'>>, '!frozenset': <bound method FrozenSetTag.from_yaml of <class 'simudo.io.h5yaml.FrozenSetTag'>>, '!pintq': <bound method PintQTag.from_yaml of <class 'simudo.io.h5yaml.PintQTag'>>}

simudo.io.h5yaml.delete_attached(filename)

simudo.io.h5yaml.dump(data, stream=None, Dumper=None, x_attr_dict=None, pint_unit_registry=None, **kwargs)

simudo.io.h5yaml.kl

alias of simudo.io.h5yaml.PintQTag

simudo.io.h5yaml.load(stream, Loader=None, x_attr_dict=None, pint_unit_registry=None, **kwargs)

simudo.io.h5yaml.xattr(loader_or_dumper)

simudo.io.output_writer module

class simudo.io.output_writer.MetaCSVWriter(filename, meta)

Bases: simudo.util.setattr_init_mixin.SetattrInitMixin

add_row(meta)

class simudo.io.output_writer.MetaExtractorBandInfo(**kwargs)

Bases: simudo.util.setattr_init_mixin.SetattrInitMixin

call()

prefix = 'band_info:'

class simudo.io.output_writer.MetaExtractorIntegrals(**kwargs)

Bases: simudo.util.setattr_init_mixin.SetattrInitMixin

prefix

String to add to quantites.

Type

str

facets

Facet regions where to extract quantities.

Type

dict

cells

Cell regions where to extract quantities.

Type

dict

solution

Solution object.

parameter_value

Parameter value.

meta

Metadata dictionary to write to.

add_quantity(name, location_name, value, units)

add_surface_flux(k, expr, **kwargs)

add_surface_total(k, expr_ds, expr_dS, internal=True, external=True, average=False, units=None)

add_volume_total(k, expr, average=False, units=None)

call()

pdd

prefix = ''

class simudo.io.output_writer.OutputWriter(**kwargs)

Bases: simudo.util.setattr_init_mixin.SetattrInitMixin

Write output data extracted from a solution object.

The output can be any of a plot on a mesh, on a 1D linecut, or in a csv file containing data from multiple solutions during a parameter sweep.

parameter_name: label for the parameter being swept

filename_prefix: a prefix to any filenames that will be saved.

plot_mesh – Save data on the original mesh. (default: False)

plot_1d – Extract data along a 1D line cut and save to a csv file. (default: False)

plot_iv – Save a csv file with terminal voltages, currents and other extracted data. (default: True)

stepper – (optional) give access to the stepper. Allows plotting quantities related to solution such as error metric (du).

format_parameter(solution, parameter_value)

get_iv_prefix(solution, parameter_value)

get_meta_csv_file(filename, meta)

get_plot_prefix(solution, parameter_value)

line_cut_resolution = 5001

meta_extractors

parameter_name = 'parameter'

plot_1d = False

plot_iv = True

plot_mesh = False

stepper = None

write_output(solution, parameter_value)

exception simudo.io.output_writer.ZeroAreaWarning

Bases: RuntimeWarning

simudo.io.output_writer.solution_plot(plotter, s, timestep, solver=None, stepper=None)

simudo.io.xdmf module

class simudo.io.xdmf.PlotAddMixin

Bases: object

add(name, units, expr, space=None, subdomain=None)

class simudo.io.xdmf.XdmfPlot(filename, function_subspace_registry=None, checkpoint=False)

Bases: simudo.io.xdmf.PlotAddMixin

close()

new(timestamp)

timestamp = 0.0

simudo.io.xdmf.magnitude(x)

Module contents