simudo.io package

Submodules

simudo.io.csv module

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

Bases: 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: DolfinObjectTag

property yaml_tag

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: 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: BaseDolfinMeshFunctionTag

meshfunction_type_name = 'bool'

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

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

Bases: ScaleMixin, BaseDolfinMeshFunctionTag

meshfunction_type_name = 'double'

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

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

Bases: BaseDolfinMeshFunctionTag

meshfunction_type_name = 'int'

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

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

Bases: BaseDolfinMeshFunctionTag

meshfunction_type_name = 'size_t'

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

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

Bases: 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: 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: BaseCustomTag

classmethod from_yaml(loader, node)

classmethod to_yaml(dumper, data)

yaml_classes = (<class 'frozenset'>,)

yaml_tag = '!frozenset'

class simudo.io.h5yaml.PintQTag

Bases: 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: ScaleMixin, DolfinObjectTag

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

Bases: object

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

Bases: TestCase

helper_test_roundtrip(dedup)

test_roundtrip()

test_roundtrip_with_dedup()

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

Bases: Dumper

ignore_aliases(data)

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

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

Bases: Loader

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

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 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: SetattrInitMixin

add_row(meta)

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

Bases: SetattrInitMixin

call()

prefix = 'band_info:'

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

Bases: SetattrInitMixin

Variables:

• prefix (str) – String to add to quantites.

• facets (dict) – Facet regions where to extract quantities.

• cells (dict) – Cell regions where to extract quantities.

• 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: 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).

plot_du – Plot du (only if stepper is also given, default: False)

clip_finite_extent = True

format_parameter(solution, parameter_value)

get_iv_prefix(solution, parameter_value)

get_meta_csv_file(filename, meta)

get_plot_prefix(solution, parameter_value)

hj_condition_filename = None

hj_interface_condition = False

hj_position = None

hj_test_eps = 1e-10

hj_test_y = 0.5

line_cut_resolution = 5001

meta_extractors

parameter_name = 'parameter'

plot_1d = False

plot_du = False

plot_iv = True

plot_mesh = False

plot_mesh_full = False

stepper = None

vs_filename = 'vs_quantities'

vs_output_x = None

vs_output_y = None

vs_write_quantities = False

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, plot_du=True, clip_finite_extent=True)

simudo.io.output_writer.vs_plot(plotter, s, timestep, stepper)

simudo.io.output_writer.write_heterojunction_boundary_condition(solution, hj_position, filename_prefix, parameter_name, parameter, y_position, eps)

Write boundary condition for heterojunction interfaces, defined by hj_position

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: PlotAddMixin

close()

new(timestamp)

timestamp = 0.0

simudo.io.xdmf.magnitude(x)

Module contents