Errors running examples #1006

agoncalvescoel · 2024-02-09T15:29:13Z

agoncalvescoel
Feb 9, 2024

Hey guys,

I'm learning how to use this amazing tool, and while I was going through the manual, I had some errors running some scripts from the examples folder: coupled.py, and circle.py.

It gives me extensive lists of errors and the program crashes. Here's a print of the first ones:

When writing coupled one myself I did notice that I only had errors when trying the vector form.
Anyone can help me with what I am doing wrong here?

wd15 · 2024-02-09T16:15:16Z

wd15
Feb 9, 2024
Collaborator

Hi Ana,

On the face of it these don't look like fipy errors necessarily. What happens if you run a problem just using numpy or scipy for example without importing fipy. Something like

import numpy

print(numpy.array([1, 2, 3]) * 2)

0 replies

agoncalvescoel · 2024-02-12T08:31:31Z

agoncalvescoel
Feb 12, 2024
Author

Hello, sorry it took me a while to answer back.
It works normally:

1 reply

guyer Feb 12, 2024
Maintainer

You'll need to tell us more about your environment. None of the errors you've posted are in FiPy code. fipy isn't mentioned at all in the tracebacks. pyface and envisage are both Enthought libraries and suggest that maybe something is wrong when FiPy tries to create a Viewer.

When testing FiPy, it should output something that looks like the text below; please post what it says for you.

python      3.11.4 | packaged by conda-forge | (main, Jun 10 2023, 18:08:41) [Clang 15.0.7 ]
fipy        3.4.4
numpy       1.24.3
pysparse    not installed
scipy       1.10.1
matplotlib  3.7.1
mpi4py      3.1.4
petsc4py    3.18.4
pyamgx      not installed
PyTrilinos  not installed
mayavi      4.8.1
gmsh        4.11.1
solver      petsc

It looks like you've only shown us the beginning of the error messages. I realize that it looks like the same thing over and over, but It's possible that something more informative about FiPy is reported later on. Please post the entirety of the output, or at least what it says at the end (I realize that Windows is fundamentally broken and that it's hard to post anything other than a screenshot, but actual text would be much easier to diagnose).

agoncalvescoel · 2024-02-14T14:16:18Z

agoncalvescoel
Feb 14, 2024
Author

Also built the environment in Linux, but keeps giving me:

(MYFIPYENV) anacoelho@HYHNB053:~/fipy$ python examples/diffusion/circle.py
ERROR|2024-02-14 15:15:08,183|error creating view control [envisage.plugins.python_shell_view]
Traceback (most recent call last):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 106, in add_view
    self._qt4_add_view(view, position, relative_to, size)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 469, in _qt4_add_view
    dw = self._qt4_create_view_dock_widget(view, size)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 541, in _qt4_create_view_dock_widget
    view.control = view.create_control(dw.widget())
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugins/python_shell/view/python_shell_view.py", line 123, in create_control
    self.bind(name, value)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugins/python_shell/view/python_shell_view.py", line 178, in bind
    self.shell.bind(name, value)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/i_python_shell.py", line 124, in bind
    self.interpreter().locals[name] = value
    ^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/python_shell.py", line 88, in interpreter
    return self.control.interpreter
           ^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'interpreter'
ERROR|2024-02-14 15:15:08,291|Exception occurred in traits notification handler for object: <envisage.ui.workbench.workbench_window.WorkbenchWindow object at 0x7fb558510130>, trait: active_perspective, old value: None, new value: Perspective(Mayavi)
Traceback (most recent call last):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 106, in add_view
    self._qt4_add_view(view, position, relative_to, size)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 469, in _qt4_add_view
    dw = self._qt4_create_view_dock_widget(view, size)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 541, in _qt4_create_view_dock_widget
    view.control = view.create_control(dw.widget())
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugins/python_shell/view/python_shell_view.py", line 123, in create_control
    self.bind(name, value)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugins/python_shell/view/python_shell_view.py", line 178, in bind
    self.shell.bind(name, value)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/i_python_shell.py", line 124, in bind
    self.interpreter().locals[name] = value
    ^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/python_shell.py", line 88, in interpreter
    return self.control.interpreter
           ^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'interpreter'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_notifiers.py", line 342, in __call__
    self.handler(*args)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/workbench_window.py", line 808, in _active_perspective_changed
    self._show_perspective(old, new)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/workbench_window.py", line 756, in _show_perspective
    new.create(self)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/perspective.py", line 97, in create
    self._add_contents(window, self.contents)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/perspective.py", line 134, in _add_contents
    self._add_perspective_item(window, item)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/perspective.py", line 155, in _add_perspective_item
    window.add_view(
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/workbench_window.py", line 297, in add_view
    self.layout.add_view(view, position, relative_to, size)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/workbench/workbench_window_layout.py", line 115, in add_view
    view.destroy_control()
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugins/python_shell/view/python_shell_view.py", line 149, in destroy_control
    self.window.application.unregister_service(self._service_id)
                                               ^^^^^^^^^^^^^^^^
AttributeError: 'PythonShellView' object has no attribute '_service_id'
ERROR|2024-02-14 15:15:08,316|getting extensions from Plugin(id='envisage.ui.workbench', name='Workbench'), trait <my_action_sets>
Traceback (most recent call last):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugin.py", line 326, in _get_extensions_from_trait
    extensions = getattr(self, trait_name)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/workbench_plugin.py", line 185, in _my_action_sets_default
    from .default_action_set import DefaultActionSet
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/default_action_set.py", line 21, in <module>
    class DefaultActionSet(ActionSet):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/default_action_set.py", line 25, in DefaultActionSet
    Menu(
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_types.py", line 2695, in validate
    return TraitListObject(self, object, name, value)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 584, in __init__
    super().__init__(
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in __init__
    super().__init__(self.item_validator(item) for item in iterable)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
    super().__init__(self.item_validator(item) for item in iterable)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 867, in _item_validator
    return trait_validator(object, self.name, value)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: Each element of the 'groups' trait of a Menu instance must be a Group or None, but a value of 'OpenGroup' <class 'str'> was specified.
ERROR|2024-02-14 15:15:08,348|Uncaught exception:
Traceback (most recent call last):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/mayaviViewer/mayaviDaemon.py", line 326, in <module>
    main(sys.argv[1:])
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/mayaviViewer/mayaviDaemon.py", line 322, in main
    m.main(argv)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/mayavi/plugins/app.py", line 197, in main
    app.run()
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/mayavi/plugins/mayavi_workbench_application.py", line 81, in run
    window.open()
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/workbench/workbench_window.py", line 159, in open
    self.create()
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/application_window.py", line 114, in create
    self._create_trim_widgets(self.control)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/i_application_window.py", line 161, in _create_trim_widgets
    self._create_menu_bar(parent)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/pyface/ui/qt/application_window.py", line 55, in _create_menu_bar
    if self.menu_bar_manager is not None:
       ^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/workbench_window.py", line 106, in _menu_bar_manager_default
    return self._action_manager_builder.create_menu_bar_manager("MenuBar")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/workbench_window.py", line 224, in __action_manager_builder_default
    window=self, action_sets=self.action_sets
                             ^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/workbench_window.py", line 168, in _action_sets_default
    return [factory(window=self) for factory in self._action_sets]
                                                ^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/extension_point.py", line 122, in get
    extensions = extension_registry.get_extensions(self.id)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/application.py", line 206, in get_extensions
    return self.extension_registry.get_extensions(extension_point_id)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/extension_registry.py", line 110, in get_extensions
    return self._get_extensions(extension_point_id)[:]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/provider_extension_registry.py", line 99, in _get_extensions
    extensions = self._initialize_extensions(extension_point_id)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/provider_extension_registry.py", line 279, in _initialize_extensions
    extensions.append(provider.get_extensions(extension_point_id)[:])
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugin.py", line 137, in get_extensions
    extensions = self._get_extensions_from_trait(trait_names[0])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/plugin.py", line 326, in _get_extensions_from_trait
    extensions = getattr(self, trait_name)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/workbench_plugin.py", line 185, in _my_action_sets_default
    from .default_action_set import DefaultActionSet
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/default_action_set.py", line 21, in <module>
    class DefaultActionSet(ActionSet):
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/envisage/ui/workbench/default_action_set.py", line 25, in DefaultActionSet
    Menu(
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_types.py", line 2695, in validate
    return TraitListObject(self, object, name, value)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 584, in __init__
    super().__init__(
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in __init__
    super().__init__(self.item_validator(item) for item in iterable)
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
    super().__init__(self.item_validator(item) for item in iterable)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/trait_list_object.py", line 867, in _item_validator
    return trait_validator(object, self.name, value)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: Each element of the 'groups' trait of a Menu instance must be a Group or None, but a value of 'OpenGroup' <class 'str'> was specified.

6 replies

agoncalvescoel Feb 14, 2024
Author

The output from python setup.py test is

python      3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
fipy        3.4.4+12.g3e38ff268
numpy       1.26.4
pysparse    not installed
scipy       1.12.0
matplotlib  3.8.2
mpi4py      3.1.5
petsc4py    3.20.4
pyamgx      not installed
PyTrilinos  not installed
mayavi      4.8.1
gmsh        4.12.2
solver      petsc

Solver suite is petsc
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/setuptools/command/test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  ir_d = dist.fetch_build_eggs(dist.install_requires)
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  tr_d = dist.fetch_build_eggs(dist.tests_require or [])
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  er_d = dist.fetch_build_eggs(
running egg_info
creating FiPy.egg-info
writing FiPy.egg-info/PKG-INFO
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
writing requirements to FiPy.egg-info/requires.txt
writing top-level names to FiPy.egg-info/top_level.txt
writing manifest file 'FiPy.egg-info/SOURCES.txt'
reading manifest file 'FiPy.egg-info/SOURCES.txt'
writing manifest file 'FiPy.egg-info/SOURCES.txt'
running build_ext

python      3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
fipy        3.4.4+12.g3e38ff268
numpy       1.26.4
pysparse    not installed
scipy       1.12.0
matplotlib  3.8.2
mpi4py      3.1.5
petsc4py    3.20.4
pyamgx      not installed
PyTrilinos  not installed
mayavi      4.8.1
gmsh        4.12.2
solver      petsc

/home/anacoelho/fipy/fipy/tests/test.py:228: PkgResourcesDeprecationWarning: Parameters to load are deprecated.  Call .resolve and .require separately.
  loader_class = loader_ep.load(require=False)
import fipy.solvers.test ... ok
import fipy.terms.test ... ok
import fipy.tools.test ... ok
import fipy.matrices.test ... ok
import fipy.meshes.test ... ok
import fipy.variables.test ... ok
import fipy.viewers.test ... ok
import fipy.boundaryConditions.test ... ok
import fipy.terms.cellTerm ... ok
import fipy.terms.abstractDiffusionTerm ... ok
import fipy.terms.diffusionTerm ... ok
import fipy.terms.term ... ok
import fipy.terms.abstractConvectionTerm ... ok
import fipy.terms.transientTerm ... ok
import fipy.terms.powerLawConvectionTerm ... ok
import fipy.terms.exponentialConvectionTerm ... ok
import fipy.terms.upwindConvectionTerm ... ok
import fipy.terms.implicitSourceTerm ... ok
import fipy.terms.coupledBinaryTerm ... ok
import fipy.terms.abstractBinaryTerm ... ok
import fipy.terms.unaryTerm ... ok
import fipy.terms.nonDiffusionTerm ... ok
import fipy.terms.asymmetricConvectionTerm ... ok
import fipy.terms.binaryTerm ... ok
import fipy.terms.firstOrderAdvectionTerm ... ok
import fipy.terms.advectionTerm ... ok
import fipy.terms.vanLeerConvectionTerm ... ok
_test (fipy.terms.cellTerm.CellTerm)
Doctest: fipy.terms.cellTerm.CellTerm._test ... ok
_buildMatrix (fipy.terms.abstractDiffusionTerm._AbstractDiffusionTerm)
Doctest: fipy.terms.abstractDiffusionTerm._AbstractDiffusionTerm._buildMatrix ... ok
_test (fipy.terms.diffusionTerm.DiffusionTerm)
Doctest: fipy.terms.diffusionTerm.DiffusionTerm._test ... ok
_test (fipy.terms.term.Term)
Doctest: fipy.terms.term.Term._test ... ok
justErrorVector (fipy.terms.term.Term)
Doctest: fipy.terms.term.Term.justErrorVector ... ok
justResidualVector (fipy.terms.term.Term)
Doctest: fipy.terms.term.Term.justResidualVector ... ok
__init__ (fipy.terms.abstractConvectionTerm._AbstractConvectionTerm)
Doctest: fipy.terms.abstractConvectionTerm._AbstractConvectionTerm.__init__ ... ok
_getWeight (fipy.terms.abstractConvectionTerm._AbstractConvectionTerm)
Doctest: fipy.terms.abstractConvectionTerm._AbstractConvectionTerm._getWeight ... ok
_test (fipy.terms.abstractConvectionTerm._AbstractConvectionTerm)
Doctest: fipy.terms.abstractConvectionTerm._AbstractConvectionTerm._test ... ok
TransientTerm (fipy.terms.transientTerm)
Doctest: fipy.terms.transientTerm.TransientTerm ... ok
_getTransientGeomCoeff (fipy.terms.transientTerm.TransientTerm)
Doctest: fipy.terms.transientTerm.TransientTerm._getTransientGeomCoeff ... ok
_test (fipy.terms.transientTerm.TransientTerm)
Doctest: fipy.terms.transientTerm.TransientTerm._test ... ok
_PowerLawConvectionTermAlpha (fipy.terms.powerLawConvectionTerm)
Doctest: fipy.terms.powerLawConvectionTerm._PowerLawConvectionTermAlpha ... /home/anacoelho/fipy/fipy/terms/powerLawConvectionTerm.py:76: RuntimeWarning: overflow encountered in multiply
  alpha = numerix.where(  (10. >= P) & (P > eps),  ((P-1.) + tmpSqr*tmpSqr*tmp) / P, alpha)
/home/anacoelho/fipy/fipy/terms/powerLawConvectionTerm.py:80: RuntimeWarning: overflow encountered in multiply
  alpha = numerix.where((-eps >  P) & (P >= -10.),     (tmpSqr*tmpSqr*tmp - 1.) / P, alpha)
ok
_calcValue (fipy.terms.exponentialConvectionTerm._ExponentialConvectionTermAlpha)
Doctest: fipy.terms.exponentialConvectionTerm._ExponentialConvectionTermAlpha._calcValue ... ok
_testPecletSign (fipy.terms.upwindConvectionTerm.UpwindConvectionTerm)
Doctest: fipy.terms.upwindConvectionTerm.UpwindConvectionTerm._testPecletSign ... ok
_getWeight (fipy.terms.implicitSourceTerm.ImplicitSourceTerm)
Doctest: fipy.terms.implicitSourceTerm.ImplicitSourceTerm._getWeight ... ok
_CoupledBinaryTerm (fipy.terms.coupledBinaryTerm)
Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm ... ok
_calcVars (fipy.terms.coupledBinaryTerm._CoupledBinaryTerm)
Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm._calcVars ... ok
_test (fipy.terms.coupledBinaryTerm._CoupledBinaryTerm)
Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm._test ... ok
__neg__ (fipy.terms.abstractBinaryTerm._AbstractBinaryTerm)
Doctest: fipy.terms.abstractBinaryTerm._AbstractBinaryTerm.__neg__ ... ok
__repr__ (fipy.terms.unaryTerm._UnaryTerm)
Doctest: fipy.terms.unaryTerm._UnaryTerm.__repr__ ... ok
_buildAndAddMatrices (fipy.terms.unaryTerm._UnaryTerm)
Doctest: fipy.terms.unaryTerm._UnaryTerm._buildAndAddMatrices ... ok
_test (fipy.terms.unaryTerm._UnaryTerm)
Doctest: fipy.terms.unaryTerm._UnaryTerm._test ... ok
__mul__ (fipy.terms.nonDiffusionTerm._NonDiffusionTerm)
Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm.__mul__ ... ok
__neg__ (fipy.terms.nonDiffusionTerm._NonDiffusionTerm)
Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm.__neg__ ... ok
_test (fipy.terms.nonDiffusionTerm._NonDiffusionTerm)
Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm._test ... ok
_getDefaultSolver (fipy.terms.asymmetricConvectionTerm._AsymmetricConvectionTerm)
Doctest: fipy.terms.asymmetricConvectionTerm._AsymmetricConvectionTerm._getDefaultSolver ... ok
_test (fipy.terms.binaryTerm._BinaryTerm)
Doctest: fipy.terms.binaryTerm._BinaryTerm._test ... ok
FirstOrderAdvectionTerm (fipy.terms.firstOrderAdvectionTerm)
Doctest: fipy.terms.firstOrderAdvectionTerm.FirstOrderAdvectionTerm ... ok
AdvectionTerm (fipy.terms.advectionTerm)
Doctest: fipy.terms.advectionTerm.AdvectionTerm ... ok
_test (fipy.terms.vanLeerConvectionTerm.VanLeerConvectionTerm)
Doctest: fipy.terms.vanLeerConvectionTerm.VanLeerConvectionTerm._test ... ok
import fipy.tools.dimensions.physicalField ... ok
import fipy.tools.numerix ... ok
import fipy.tools.dump ... ok
import fipy.tools.vector ... ok
import fipy.tools.sharedtempfile ... ok
import fipy.tools.timer ... ok
__abs__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__abs__ ... ok
__add__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__add__ ... ok
__array__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__array__ ... ok
__array_wrap__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ ... ok
__float__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__float__ ... ok
__getitem__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__getitem__ ... ok
__gt__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__gt__ ... ok
__init__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__init__ ... ok
__mod__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__mod__ ... ok
__mul__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__mul__ ... ok
__neg__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__neg__ ... ok
__pow__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__pow__ ... ok
__repr__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__repr__ ... ok
__setitem__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__setitem__ ... ok
__str__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__str__ ... ok
__sub__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__sub__ ... ok
__truediv__ (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__truediv__ ... ok
_getUnit (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField._getUnit ... ok
_setUnit (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField._setUnit ... ok
arccos (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arccos ... ok
arccosh (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arccosh ... ok
arcsin (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arcsin ... ok
arctan (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctan ... ok
arctan2 (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctan2 ... ok
arctanh (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctanh ... ok
ceil (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.ceil ... ok
conjugate (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.conjugate ... ok
convertToUnit (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.convertToUnit ... ok
copy (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.copy ... ok
cos (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.cos ... ok
cosh (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.cosh ... ok
dot (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.dot ... ok
floor (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.floor ... ok
getsctype (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.getsctype ... ok
inBaseUnits (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inBaseUnits ... ok
inDimensionless (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inDimensionless ... ok
inRadians (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inRadians ... ok
inSIUnits (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inSIUnits ... ok
inUnitsOf (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inUnitsOf ... ok
itemset (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.itemset ... ok
log (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.log ... ok
log10 (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.log10 ... ok
numericValue (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.numericValue ... ok
put (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.put ... ok
reshape (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.reshape ... ok
sign (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sign ... ok
sin (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sin ... ok
sinh (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sinh ... ok
sqrt (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sqrt ... ok
sum (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sum ... ok
take (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.take ... ok
tan (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tan ... ok
tanh (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tanh ... ok
tostring (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tostring ... ok
unit (fipy.tools.dimensions.physicalField.PhysicalField)
Doctest: fipy.tools.dimensions.physicalField.PhysicalField.unit ... ok
__eq__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__eq__ ... ok
__mul__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__mul__ ... ok
__pow__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__pow__ ... ok
__repr__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__repr__ ... ok
__rtruediv__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__rtruediv__ ... ok
__truediv__ (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__truediv__ ... ok
conversionFactorTo (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.conversionFactorTo ... ok
conversionTupleTo (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.conversionTupleTo ... ok
isAngle (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isAngle ... ok
isCompatible (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isCompatible ... ok
isDimensionless (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isDimensionless ... ok
isDimensionlessOrAngle (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isDimensionlessOrAngle ... ok
isInverseAngle (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isInverseAngle ... ok
name (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.name ... ok
setName (fipy.tools.dimensions.physicalField.PhysicalUnit)
Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.setName ... ok
_Scale (fipy.tools.dimensions.physicalField)
Doctest: fipy.tools.dimensions.physicalField._Scale ... ok
_findUnit (fipy.tools.dimensions.physicalField)
Doctest: fipy.tools.dimensions.physicalField._findUnit ... ok
numerix (fipy.tools)
Doctest: fipy.tools.numerix ... ok
_broadcastShapes (fipy.tools.numerix)
Doctest: fipy.tools.numerix._broadcastShapes ... ok
_indexShape (fipy.tools.numerix)
Doctest: fipy.tools.numerix._indexShape ... ok
_invert_indices (fipy.tools.numerix)
Doctest: fipy.tools.numerix._invert_indices ... ok
dot (fipy.tools.numerix)
Doctest: fipy.tools.numerix.dot ... ok
getShape (fipy.tools.numerix)
Doctest: fipy.tools.numerix.getShape ... ok
nearest (fipy.tools.numerix)
Doctest: fipy.tools.numerix.nearest ... ok
put (fipy.tools.numerix)
Doctest: fipy.tools.numerix.put ... ok
tostring (fipy.tools.numerix)
Doctest: fipy.tools.numerix.tostring ... ok
write (fipy.tools.dump)
Doctest: fipy.tools.dump.write ... ok
prune (fipy.tools.vector)
Doctest: fipy.tools.vector.prune ... ok
SharedTemporaryFile (fipy.tools.sharedtempfile)
Doctest: fipy.tools.sharedtempfile.SharedTemporaryFile ... ok
Timer (fipy.tools.timer)
Doctest: fipy.tools.timer.Timer ... ok
import fipy.matrices.petscMatrix ... ok
__init__ (fipy.matrices.petscMatrix._PETScIdentityMatrix)
Doctest: fipy.matrices.petscMatrix._PETScIdentityMatrix.__init__ ... ok
__init__ (fipy.matrices.petscMatrix._PETScIdentityMeshMatrix)
Doctest: fipy.matrices.petscMatrix._PETScIdentityMeshMatrix.__init__ ... ok
CSR (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.CSR ... ok
LIL (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.LIL ... ok
T (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.T ... ok
__add__ (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.__add__ ... ok
__mul__ (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.__mul__ ... ok
addAt (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.addAt ... ok
put (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.put ... ok
putDiagonal (fipy.matrices.petscMatrix._PETScMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMatrix.putDiagonal ... ok
__mul__ (fipy.matrices.petscMatrix._PETScMeshMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMeshMatrix.__mul__ ... ok
_test (fipy.matrices.petscMatrix._PETScMeshMatrix)
Doctest: fipy.matrices.petscMatrix._PETScMeshMatrix._test ... ok
import fipy.meshes.mesh ... ok
import fipy.meshes.mesh2D ... ok
import fipy.meshes.nonUniformGrid1D ... ok
import fipy.meshes.nonUniformGrid2D ... ok
import fipy.meshes.nonUniformGrid3D ... ok
import fipy.meshes.tri2D ... ok
import fipy.meshes.gmshMesh ... ok
import fipy.meshes.periodicGrid1D ... ok
import fipy.meshes.periodicGrid2D ... ok
import fipy.meshes.periodicGrid3D ... ok
import fipy.meshes.uniformGrid1D ... ok
import fipy.meshes.uniformGrid2D ... ok
import fipy.meshes.uniformGrid3D ... ok
import fipy.meshes.cylindricalUniformGrid1D ... ok
import fipy.meshes.cylindricalUniformGrid2D ... ok
import fipy.meshes.cylindricalNonUniformGrid1D ... ok
import fipy.meshes.cylindricalNonUniformGrid2D ... ok
import fipy.meshes.sphericalUniformGrid1D ... ok
import fipy.meshes.sphericalNonUniformGrid1D ... ok
import fipy.meshes.factoryMeshes ... ok
import fipy.meshes.abstractMesh ... ok
import fipy.meshes.representations.gridRepresentation ... ok
__mul__ (fipy.meshes.mesh.Mesh)
Doctest: fipy.meshes.mesh.Mesh.__mul__ ... ok
_getNearestCellID (fipy.meshes.mesh.Mesh)
Doctest: fipy.meshes.mesh.Mesh._getNearestCellID ... ok
_handleFaceConnection (fipy.meshes.mesh.Mesh)
Doctest: fipy.meshes.mesh.Mesh._handleFaceConnection ... ok
_test (fipy.meshes.mesh.Mesh)
Doctest: fipy.meshes.mesh.Mesh._test ... ok
_test (fipy.meshes.mesh2D.Mesh2D)
Doctest: fipy.meshes.mesh2D.Mesh2D._test ... ok
extrude (fipy.meshes.mesh2D.Mesh2D)
Doctest: fipy.meshes.mesh2D.Mesh2D.extrude ... ok
NonUniformGrid1D (fipy.meshes.nonUniformGrid1D)
Doctest: fipy.meshes.nonUniformGrid1D.NonUniformGrid1D ... ok
_test (fipy.meshes.nonUniformGrid1D.NonUniformGrid1D)
Doctest: fipy.meshes.nonUniformGrid1D.NonUniformGrid1D._test ... ok
_test (fipy.meshes.nonUniformGrid2D.NonUniformGrid2D)
Doctest: fipy.meshes.nonUniformGrid2D.NonUniformGrid2D._test ... ok
_test (fipy.meshes.nonUniformGrid3D.NonUniformGrid3D)
Doctest: fipy.meshes.nonUniformGrid3D.NonUniformGrid3D._test ... ok
_test (fipy.meshes.tri2D.Tri2D)
Doctest: fipy.meshes.tri2D.Tri2D._test ... ok
Gmsh2D (fipy.meshes.gmshMesh)
Doctest: fipy.meshes.gmshMesh.Gmsh2D ... ok
_test (fipy.meshes.gmshMesh.Gmsh2D)
Doctest: fipy.meshes.gmshMesh.Gmsh2D._test ... ok
_test (fipy.meshes.gmshMesh.Gmsh2DIn3DSpace)
Doctest: fipy.meshes.gmshMesh.Gmsh2DIn3DSpace._test ... ok
_test (fipy.meshes.gmshMesh.Gmsh3D)
Doctest: fipy.meshes.gmshMesh.Gmsh3D._test ... ok
_test (fipy.meshes.gmshMesh.GmshGrid2D)
Doctest: fipy.meshes.gmshMesh.GmshGrid2D._test ... ok
_test (fipy.meshes.gmshMesh.GmshGrid3D)
Doctest: fipy.meshes.gmshMesh.GmshGrid3D._test ... ok
_test (fipy.meshes.gmshMesh.MSHFile)
Doctest: fipy.meshes.gmshMesh.MSHFile._test ... ok
PeriodicGrid1D (fipy.meshes.periodicGrid1D)
Doctest: fipy.meshes.periodicGrid1D.PeriodicGrid1D ... ok
_translate (fipy.meshes.periodicGrid1D.PeriodicGrid1D)
Doctest: fipy.meshes.periodicGrid1D.PeriodicGrid1D._translate ... ok
PeriodicGrid2D (fipy.meshes.periodicGrid2D)
Doctest: fipy.meshes.periodicGrid2D.PeriodicGrid2D ... ok
_translate (fipy.meshes.periodicGrid2D._BasePeriodicGrid2D)
Doctest: fipy.meshes.periodicGrid2D._BasePeriodicGrid2D._translate ... ok
PeriodicGrid3D (fipy.meshes.periodicGrid3D)
Doctest: fipy.meshes.periodicGrid3D.PeriodicGrid3D ... ok
_test (fipy.meshes.periodicGrid3D.PeriodicGrid3D)
Doctest: fipy.meshes.periodicGrid3D.PeriodicGrid3D._test ... ok
_translate (fipy.meshes.periodicGrid3D._BasePeriodicGrid3D)
Doctest: fipy.meshes.periodicGrid3D._BasePeriodicGrid3D._translate ... ok
UniformGrid1D (fipy.meshes.uniformGrid1D)
Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D ... ok
_getNearestCellID (fipy.meshes.uniformGrid1D.UniformGrid1D)
Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D._getNearestCellID ... ok
_test (fipy.meshes.uniformGrid1D.UniformGrid1D)
Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D._test ... ok
_getNearestCellID (fipy.meshes.uniformGrid2D.UniformGrid2D)
Doctest: fipy.meshes.uniformGrid2D.UniformGrid2D._getNearestCellID ... ok
_test (fipy.meshes.uniformGrid2D.UniformGrid2D)
Doctest: fipy.meshes.uniformGrid2D.UniformGrid2D._test ... ok
_test (fipy.meshes.uniformGrid3D.UniformGrid3D)
Doctest: fipy.meshes.uniformGrid3D.UniformGrid3D._test ... ok
CylindricalUniformGrid1D (fipy.meshes.cylindricalUniformGrid1D)
Doctest: fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D ... ok
_test (fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D)
Doctest: fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D._test ... ok
_test (fipy.meshes.cylindricalUniformGrid2D.CylindricalUniformGrid2D)
Doctest: fipy.meshes.cylindricalUniformGrid2D.CylindricalUniformGrid2D._test ... ok
CylindricalNonUniformGrid1D (fipy.meshes.cylindricalNonUniformGrid1D)
Doctest: fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D ... ok
_test (fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D)
Doctest: fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D._test ... ok
_test (fipy.meshes.cylindricalNonUniformGrid2D.CylindricalNonUniformGrid2D)
Doctest: fipy.meshes.cylindricalNonUniformGrid2D.CylindricalNonUniformGrid2D._test ... ok
SphericalUniformGrid1D (fipy.meshes.sphericalUniformGrid1D)
Doctest: fipy.meshes.sphericalUniformGrid1D.SphericalUniformGrid1D ... ok
_test (fipy.meshes.sphericalUniformGrid1D.SphericalUniformGrid1D)
Doctest: fipy.meshes.sphericalUniformGrid1D.SphericalUniformGrid1D._test ... ok
SphericalNonUniformGrid1D (fipy.meshes.sphericalNonUniformGrid1D)
Doctest: fipy.meshes.sphericalNonUniformGrid1D.SphericalNonUniformGrid1D ... ok
_test (fipy.meshes.sphericalNonUniformGrid1D.SphericalNonUniformGrid1D)
Doctest: fipy.meshes.sphericalNonUniformGrid1D.SphericalNonUniformGrid1D._test ... ok
Grid2D (fipy.meshes.factoryMeshes)
Doctest: fipy.meshes.factoryMeshes.Grid2D ... ok
_dnl (fipy.meshes.factoryMeshes)
Doctest: fipy.meshes.factoryMeshes._dnl ... ok
__add__ (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.__add__ ... /home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/doctest.py:1353: UserWarning: Vertices are not aligned
  exec(compile(example.source, filename, "single",
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/doctest.py:1353: UserWarning: Faces are not aligned
  exec(compile(example.source, filename, "single",
ok
__sub__ (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.__sub__ ... ok
__truediv__ (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.__truediv__ ... ok
_connectFaces (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh._connectFaces ... ok
_vertexCellIDs (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh._vertexCellIDs ... ok
_vertexFaceIDs (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh._vertexFaceIDs ... ok
facesBack (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesBack ... ok
facesBottom (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesBottom ... ok
facesFront (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesFront ... ok
facesLeft (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesLeft ... ok
facesRight (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesRight ... ok
facesTop (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesTop ... ok
x (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.x ... ok
y (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.y ... ok
z (fipy.meshes.abstractMesh.AbstractMesh)
Doctest: fipy.meshes.abstractMesh.AbstractMesh.z ... ok
_test (fipy.meshes.representations.gridRepresentation._GridRepresentation)
Doctest: fipy.meshes.representations.gridRepresentation._GridRepresentation._test ... ok
import fipy.variables.variable ... ok
import fipy.variables.meshVariable ... ok
import fipy.variables.cellVariable ... ok
import fipy.variables.faceVariable ... ok
import fipy.variables.operatorVariable ... ok
import fipy.variables.betaNoiseVariable ... ok
import fipy.variables.exponentialNoiseVariable ... ok
import fipy.variables.gammaNoiseVariable ... ok
import fipy.variables.gaussianNoiseVariable ... ok
import fipy.variables.uniformNoiseVariable ... ok
import fipy.variables.modularVariable ... ok
import fipy.variables.binaryOperatorVariable ... ok
import fipy.variables.unaryOperatorVariable ... ok
import fipy.variables.coupledCellVariable ... ok
import fipy.variables.cellToFaceVariable ... ok
import fipy.variables.faceGradVariable ... ok
import fipy.variables.gaussCellGradVariable ... ok
import fipy.variables.faceGradContributionsVariable ... ok
import fipy.variables.surfactantConvectionVariable ... ok
import fipy.variables.surfactantVariable ... ok
import fipy.variables.levelSetDiffusionVariable ... ok
import fipy.variables.distanceVariable ... ok
Variable (fipy.variables.variable)
Doctest: fipy.variables.variable.Variable ... ok
_UnaryOperatorVariable (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._UnaryOperatorVariable ... ok
__abs__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__abs__ ... ok
__and__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__and__ ... ok
__array__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__array__ ... ok
__array_wrap__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__array_wrap__ ... ok
__bool__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__bool__ ... ok
__call__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__call__ ... ok
__eq__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__eq__ ... ok
__ge__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__ge__ ... ok
__getitem__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__getitem__ ... ok
__gt__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__gt__ ... ok
__init__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__init__ ... ok
__invert__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__invert__ ... ok
__le__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__le__ ... ok
__lt__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__lt__ ... ok
__ne__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__ne__ ... ok
__or__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__or__ ... ok
__pow__ (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.__pow__ ... ok
_execInline (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._execInline ... ok
_getCIndexString (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._getCIndexString ... ok
_getCstring (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._getCstring ... ok
_getShape (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._getShape ... ok
_getUnit (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._getUnit ... ok
_getValue (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._getValue ... ok
_setUnit (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._setUnit ... ok
_test (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable._test ... ok
all (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.all ... ok
allclose (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.allclose ... ok
any (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.any ... ok
constrain (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.constrain ... ok
copy (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.copy ... ok
getsctype (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.getsctype ... ok
inBaseUnits (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.inBaseUnits ... ok
inUnitsOf (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.inUnitsOf ... ok
release (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.release ... ok
setValue (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.setValue ... ok
shape (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.shape ... ok
unit (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.unit ... ok
value (fipy.variables.variable.Variable)
Doctest: fipy.variables.variable.Variable.value ... ok
_MeshVariable__dot (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable._MeshVariable__dot ... ok
_shapeClassAndOther (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable._shapeClassAndOther ... ok
constraintMask (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable.constraintMask ... ok
min (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable.min ... ok
shape (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable.shape ... ok
std (fipy.variables.meshVariable.MeshVariable)
Doctest: fipy.variables.meshVariable.MeshVariable.std ... ok
_testDot (fipy.variables.meshVariable)
Doctest: fipy.variables.meshVariable._testDot ... ok
CellVariable (fipy.variables.cellVariable)
Doctest: fipy.variables.cellVariable.CellVariable ... ok
_OperatorVariableClass (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable._OperatorVariableClass ... ok
__call__ (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.__call__ ... ok
_test (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable._test ... ok
arithmeticFaceValue (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.arithmeticFaceValue ... ok
cellVolumeAverage (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.cellVolumeAverage ... ok
constrain (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.constrain ... ok
harmonicFaceValue (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.harmonicFaceValue ... ok
leastSquaresGrad (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.leastSquaresGrad ... ok
minmodFaceValue (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.minmodFaceValue ... ok
old (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.old ... ok
release (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.release ... ok
updateOld (fipy.variables.cellVariable.CellVariable)
Doctest: fipy.variables.cellVariable.CellVariable.updateOld ... ok
divergence (fipy.variables.faceVariable.FaceVariable)
Doctest: fipy.variables.faceVariable.FaceVariable.divergence ... ok
_testBinOp (fipy.variables.operatorVariable)
Doctest: fipy.variables.operatorVariable._testBinOp ... /home/anacoelho/fipy/fipy/variables/variable.py:1143: RuntimeWarning: invalid value encountered in scalar divide
  return self._BinaryOperatorVariable(lambda a, b: a / b, other)
ok
BetaNoiseVariable (fipy.variables.betaNoiseVariable)
Doctest: fipy.variables.betaNoiseVariable.BetaNoiseVariable ... ok
ExponentialNoiseVariable (fipy.variables.exponentialNoiseVariable)
Doctest: fipy.variables.exponentialNoiseVariable.ExponentialNoiseVariable ... ok
GammaNoiseVariable (fipy.variables.gammaNoiseVariable)
Doctest: fipy.variables.gammaNoiseVariable.GammaNoiseVariable ... ok
GaussianNoiseVariable (fipy.variables.gaussianNoiseVariable)
Doctest: fipy.variables.gaussianNoiseVariable.GaussianNoiseVariable ... ok
UniformNoiseVariable (fipy.variables.uniformNoiseVariable)
Doctest: fipy.variables.uniformNoiseVariable.UniformNoiseVariable ... ok
ModularVariable (fipy.variables.modularVariable)
Doctest: fipy.variables.modularVariable.ModularVariable ... ok
_setValueInternal (fipy.variables.modularVariable.ModularVariable)
Doctest: fipy.variables.modularVariable.ModularVariable._setValueInternal ... ok
updateOld (fipy.variables.modularVariable.ModularVariable)
Doctest: fipy.variables.modularVariable.ModularVariable.updateOld ... ok
_BinaryOperatorVariable (fipy.variables.binaryOperatorVariable)
Doctest: fipy.variables.binaryOperatorVariable._BinaryOperatorVariable ... ok
_UnaryOperatorVariable (fipy.variables.unaryOperatorVariable)
Doctest: fipy.variables.unaryOperatorVariable._UnaryOperatorVariable ... ok
__array__ (fipy.variables.coupledCellVariable._CoupledCellVariable)
Doctest: fipy.variables.coupledCellVariable._CoupledCellVariable.__array__ ... ok
release (fipy.variables.cellToFaceVariable._CellToFaceVariable)
Doctest: fipy.variables.cellToFaceVariable._CellToFaceVariable.release ... ok
_FaceGradVariable (fipy.variables.faceGradVariable)
Doctest: fipy.variables.faceGradVariable._FaceGradVariable ... ok
_GaussCellGradVariable (fipy.variables.gaussCellGradVariable)
Doctest: fipy.variables.gaussCellGradVariable._GaussCellGradVariable ... ok
_FaceGradContributions (fipy.variables.faceGradContributionsVariable)
Doctest: fipy.variables.faceGradContributionsVariable._FaceGradContributions ... ok
__init__ (fipy.variables.surfactantConvectionVariable.SurfactantConvectionVariable)
Doctest: fipy.variables.surfactantConvectionVariable.SurfactantConvectionVariable.__init__ ... ok
__init__ (fipy.variables.surfactantVariable.SurfactantVariable)
Doctest: fipy.variables.surfactantVariable.SurfactantVariable.__init__ ... ok
_LevelSetDiffusionVariable (fipy.variables.levelSetDiffusionVariable)
Doctest: fipy.variables.levelSetDiffusionVariable._LevelSetDiffusionVariable ... ok
DistanceVariable (fipy.variables.distanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable ... ok
_cellInterfaceFlag (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._cellInterfaceFlag ... ok
_cellInterfaceNormals (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._cellInterfaceNormals ... ok
_cellValueOverFaces (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._cellValueOverFaces ... ok
_interfaceFlag (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._interfaceFlag ... ok
_interfaceNormals (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._interfaceNormals ... ok
_levelSetNormals (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable._levelSetNormals ... ok
cellInterfaceAreas (fipy.variables.distanceVariable.DistanceVariable)
Doctest: fipy.variables.distanceVariable.DistanceVariable.cellInterfaceAreas ... ok
import fipy.viewers.vtkViewer.test ... ok
import fipy.viewers.tsvViewer ... ok
import fipy.viewers.vtkViewer.vtkCellViewer ... /home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/observation/_generated_parser.py:258: DeprecationWarning: module 'sre_parse' is deprecated
  import sre_parse
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/traits/observation/_generated_parser.py:259: DeprecationWarning: module 'sre_constants' is deprecated
  import sre_constants
ok
import fipy.viewers.vtkViewer.vtkFaceViewer ... ok
_test (fipy.viewers.vtkViewer.vtkCellViewer.VTKCellViewer)
Doctest: fipy.viewers.vtkViewer.vtkCellViewer.VTKCellViewer._test ... ok
_test (fipy.viewers.vtkViewer.vtkFaceViewer.VTKFaceViewer)
Doctest: fipy.viewers.vtkViewer.vtkFaceViewer.VTKFaceViewer._test ... ok
plot (fipy.viewers.tsvViewer.TSVViewer)
Doctest: fipy.viewers.tsvViewer.TSVViewer.plot ... ok
import fipy.boundaryConditions.boundaryCondition ... ok
import fipy.boundaryConditions.fixedFlux ... ok
_test (fipy.boundaryConditions.boundaryCondition.BoundaryCondition)
Doctest: fipy.boundaryConditions.boundaryCondition.BoundaryCondition._test ... ok
_test (fipy.boundaryConditions.fixedFlux.FixedFlux)
Doctest: fipy.boundaryConditions.fixedFlux.FixedFlux._test ... ok
import examples.diffusion.test ... ok
import examples.chemotaxis.test ... ok
import examples.phase.test ... ok
import examples.convection.test ... ok
import examples.elphf.test ... ok
import examples.levelSet.test ... ok
import examples.cahnHilliard.test ... ok
import examples.flow.test ... ok
import examples.meshing.test ... ok
import examples.reactiveWetting.test ... ok
import examples.riemann.test ... ok
import examples.diffusion.steadyState.test ... ok
import examples.diffusion.explicit.test ... ok
import examples.diffusion.nthOrder.test ... ok
import examples.diffusion.mesh1D ... ok
import examples.diffusion.mesh20x20 ... ok
import examples.diffusion.circle ... ok
import examples.diffusion.circleQuad ... ok
import examples.diffusion.electrostatics ... ok
import examples.diffusion.variable ... ok
import examples.diffusion.anisotropy ... ok
import examples.diffusion.mesh20x20Coupled ... ok
import examples.diffusion.steadyState.mesh1D.tri2Dinput ... ok
import examples.diffusion.steadyState.mesh1D.inputPeriodic ... ok
import examples.diffusion.steadyState.mesh20x20.tri2Dinput ... ok
import examples.diffusion.steadyState.mesh50x50.input ... ok
import examples.diffusion.steadyState.mesh50x50.tri2Dinput ... ok
import examples.diffusion.steadyState.otherMeshes.grid3Dinput ... ok
import examples.diffusion.steadyState.otherMeshes.prism ... ok
import examples.diffusion.steadyState.mesh20x20.modifiedMeshInput ... ok
import examples.diffusion.steadyState.mesh20x20.isotropy ... ok
tri2Dinput (examples.diffusion.steadyState.mesh1D)
Doctest: examples.diffusion.steadyState.mesh1D.tri2Dinput ... ok
inputPeriodic (examples.diffusion.steadyState.mesh1D)
Doctest: examples.diffusion.steadyState.mesh1D.inputPeriodic ... ok
tri2Dinput (examples.diffusion.steadyState.mesh20x20)
Doctest: examples.diffusion.steadyState.mesh20x20.tri2Dinput ... ok
input (examples.diffusion.steadyState.mesh50x50)
Doctest: examples.diffusion.steadyState.mesh50x50.input ... ok
tri2Dinput (examples.diffusion.steadyState.mesh50x50)
Doctest: examples.diffusion.steadyState.mesh50x50.tri2Dinput ... ok
grid3Dinput (examples.diffusion.steadyState.otherMeshes)
Doctest: examples.diffusion.steadyState.otherMeshes.grid3Dinput ... ok
prism (examples.diffusion.steadyState.otherMeshes)
Doctest: examples.diffusion.steadyState.otherMeshes.prism ... ok
modifiedMeshInput (examples.diffusion.steadyState.mesh20x20)
Doctest: examples.diffusion.steadyState.mesh20x20.modifiedMeshInput ... ok
isotropy (examples.diffusion.steadyState.mesh20x20)
Doctest: examples.diffusion.steadyState.mesh20x20.isotropy ... ok
import examples.diffusion.explicit.tri2D ... ok
import examples.diffusion.explicit.mesh1D ... ok
import examples.diffusion.explicit.mixedelement ... ok
tri2D (examples.diffusion.explicit)
Doctest: examples.diffusion.explicit.tri2D ... ok
mesh1D (examples.diffusion.explicit)
Doctest: examples.diffusion.explicit.mesh1D ... ok
mixedelement (examples.diffusion.explicit)
Doctest: examples.diffusion.explicit.mixedelement ... ok
import examples.diffusion.nthOrder.input4thOrder1D ... ok
import examples.diffusion.nthOrder.input4thOrder_line ... ok
input4thOrder1D (examples.diffusion.nthOrder)
Doctest: examples.diffusion.nthOrder.input4thOrder1D ... ok
input4thOrder_line (examples.diffusion.nthOrder)
Doctest: examples.diffusion.nthOrder.input4thOrder_line ... ok
mesh1D (examples.diffusion)
Doctest: examples.diffusion.mesh1D ... ok
mesh20x20 (examples.diffusion)
Doctest: examples.diffusion.mesh20x20 ... ok
circle (examples.diffusion)
Doctest: examples.diffusion.circle ... ok
circleQuad (examples.diffusion)
Doctest: examples.diffusion.circleQuad ... ok
electrostatics (examples.diffusion)
Doctest: examples.diffusion.electrostatics ... ok
variable (examples.diffusion)
Doctest: examples.diffusion.variable ... ok
anisotropy (examples.diffusion)
Doctest: examples.diffusion.anisotropy ... ok
mesh20x20Coupled (examples.diffusion)
Doctest: examples.diffusion.mesh20x20Coupled ... ok
import examples.chemotaxis.input ... ok
import examples.chemotaxis.input2D ... ok
input (examples.chemotaxis)
Doctest: examples.chemotaxis.input ... ok
input2D (examples.chemotaxis)
Doctest: examples.chemotaxis.input2D ... ok
import examples.phase.impingement.test ... ok
import examples.phase.missOrientation.test ... ok
import examples.phase.binary ... ok
import examples.phase.anisotropyOLD ... ok
import examples.phase.anisotropy ... ok
import examples.phase.quaternary ... ok
import examples.phase.simple ... ok
import examples.phase.symmetry ... ok
import examples.phase.binary ... ok
import examples.phase.binaryCoupled ... ok
import examples.phase.polyxtal ... ok
import examples.phase.polyxtalCoupled ... ok
import examples.phase.impingement.mesh40x1 ... ok
import examples.phase.impingement.mesh20x20 ... ok
mesh40x1 (examples.phase.impingement)
Doctest: examples.phase.impingement.mesh40x1 ... ok
mesh20x20 (examples.phase.impingement)
Doctest: examples.phase.impingement.mesh20x20 ... ok
import examples.phase.missOrientation.mesh1D ... ok
import examples.phase.missOrientation.circle ... ok
import examples.phase.missOrientation.modCircle ... ok
mesh1D (examples.phase.missOrientation)
Doctest: examples.phase.missOrientation.mesh1D ... ok
circle (examples.phase.missOrientation)
Doctest: examples.phase.missOrientation.circle ... ok
modCircle (examples.phase.missOrientation)
Doctest: examples.phase.missOrientation.modCircle ... ok
binary (examples.phase)
Doctest: examples.phase.binary ... /home/anacoelho/fipy/fipy/variables/variable.py:1143: RuntimeWarning: divide by zero encountered in scalar divide
  return self._BinaryOperatorVariable(lambda a, b: a / b, other)
ok
anisotropyOLD (examples.phase)
Doctest: examples.phase.anisotropyOLD ... ok
anisotropy (examples.phase)
Doctest: examples.phase.anisotropy ... ok
quaternary (examples.phase)
Doctest: examples.phase.quaternary ... ok
simple (examples.phase)
Doctest: examples.phase.simple ... ok
symmetry (examples.phase)
Doctest: examples.phase.symmetry ... ok
binary (examples.phase)
Doctest: examples.phase.binary ... ok
binaryCoupled (examples.phase)
Doctest: examples.phase.binaryCoupled ... ok
polyxtal (examples.phase)
Doctest: examples.phase.polyxtal ... ok
polyxtalCoupled (examples.phase)
Doctest: examples.phase.polyxtalCoupled ... ok
import examples.convection.exponential1D.mesh1D ... ok
import examples.convection.exponential1D.cylindricalMesh1D ... ok
import examples.convection.exponential1D.cylindricalMesh1DNonUniform ... ok
import examples.convection.exponential1D.tri2D ... ok
import examples.convection.exponential2D.mesh2D ... ok
import examples.convection.exponential2D.cylindricalMesh2D ... ok
import examples.convection.exponential2D.cylindricalMesh2DNonUniform ... ok
import examples.convection.exponential1DBack.mesh1D ... ok
import examples.convection.powerLaw1D.mesh1D ... ok
import examples.convection.exponential1DSource.mesh1D ... ok
import examples.convection.exponential2D.tri2D ... ok
import examples.convection.exponential1DSource.tri2D ... ok
import examples.convection.powerLaw1D.tri2D ... ok
import examples.convection.advection.vanLeerUpwind ... ok
import examples.convection.peclet ... ok
import examples.convection.robin ... ok
import examples.convection.source ... ok
mesh1D (examples.convection.exponential1D)
Doctest: examples.convection.exponential1D.mesh1D ... ok
cylindricalMesh1D (examples.convection.exponential1D)
Doctest: examples.convection.exponential1D.cylindricalMesh1D ... ok
cylindricalMesh1DNonUniform (examples.convection.exponential1D)
Doctest: examples.convection.exponential1D.cylindricalMesh1DNonUniform ... ok
tri2D (examples.convection.exponential1D)
Doctest: examples.convection.exponential1D.tri2D ... ok
mesh2D (examples.convection.exponential2D)
Doctest: examples.convection.exponential2D.mesh2D ... ok
cylindricalMesh2D (examples.convection.exponential2D)
Doctest: examples.convection.exponential2D.cylindricalMesh2D ... ok
cylindricalMesh2DNonUniform (examples.convection.exponential2D)
Doctest: examples.convection.exponential2D.cylindricalMesh2DNonUniform ... ok
mesh1D (examples.convection.exponential1DBack)
Doctest: examples.convection.exponential1DBack.mesh1D ... ok
mesh1D (examples.convection.powerLaw1D)
Doctest: examples.convection.powerLaw1D.mesh1D ... ok
mesh1D (examples.convection.exponential1DSource)
Doctest: examples.convection.exponential1DSource.mesh1D ... ok
tri2D (examples.convection.exponential2D)
Doctest: examples.convection.exponential2D.tri2D ... ok
tri2D (examples.convection.exponential1DSource)
Doctest: examples.convection.exponential1DSource.tri2D ... ok
tri2D (examples.convection.powerLaw1D)
Doctest: examples.convection.powerLaw1D.tri2D ... ok
vanLeerUpwind (examples.convection.advection)
Doctest: examples.convection.advection.vanLeerUpwind ... ok
peclet (examples.convection)
Doctest: examples.convection.peclet ... ok
robin (examples.convection)
Doctest: examples.convection.robin ... /home/anacoelho/fipy/fipy/variables/variable.py:1143: RuntimeWarning: invalid value encountered in divide
  return self._BinaryOperatorVariable(lambda a, b: a / b, other)
ok
source (examples.convection)
Doctest: examples.convection.source ... ok
import examples.elphf.diffusion.mesh1D ... ok
import examples.elphf.diffusion.mesh2D ... ok
import examples.elphf.phase ... ok
import examples.elphf.phaseDiffusion ... ok
import examples.elphf.poisson ... ok
mesh1D (examples.elphf.diffusion)
Doctest: examples.elphf.diffusion.mesh1D ... ok
mesh2D (examples.elphf.diffusion)
Doctest: examples.elphf.diffusion.mesh2D ... ok
phase (examples.elphf)
Doctest: examples.elphf.phase ... ok
phaseDiffusion (examples.elphf)
Doctest: examples.elphf.phaseDiffusion ... ok
poisson (examples.elphf)
Doctest: examples.elphf.poisson ... ok
import examples.levelSet.distanceFunction.test ... ok
import examples.levelSet.advection.test ... ok
import examples.levelSet.surfactant.test ... ok
import examples.levelSet.distanceFunction.mesh1D ... ok
import examples.levelSet.distanceFunction.circle ... ok
import examples.levelSet.distanceFunction.square ... ok
import examples.levelSet.distanceFunction.interior ... ok
mesh1D (examples.levelSet.distanceFunction)
Doctest: examples.levelSet.distanceFunction.mesh1D ... ok
circle (examples.levelSet.distanceFunction)
Doctest: examples.levelSet.distanceFunction.circle ... ok
square (examples.levelSet.distanceFunction)
Doctest: examples.levelSet.distanceFunction.square ... ok
interior (examples.levelSet.distanceFunction)
Doctest: examples.levelSet.distanceFunction.interior ... ok
import examples.levelSet.advection.mesh1D ... ok
import examples.levelSet.advection.circle ... ok
import examples.levelSet.advection.trench ... ok
mesh1D (examples.levelSet.advection)
Doctest: examples.levelSet.advection.mesh1D ... ok
circle (examples.levelSet.advection)
Doctest: examples.levelSet.advection.circle ... ok
trench (examples.levelSet.advection)
Doctest: examples.levelSet.advection.trench ... ok
import examples.levelSet.surfactant.circle ... ok
import examples.levelSet.surfactant.square ... ok
import examples.levelSet.surfactant.expandingCircle ... ok
circle (examples.levelSet.surfactant)
Doctest: examples.levelSet.surfactant.circle ... ok
square (examples.levelSet.surfactant)
Doctest: examples.levelSet.surfactant.square ... ok
expandingCircle (examples.levelSet.surfactant)
Doctest: examples.levelSet.surfactant.expandingCircle ... ok
import examples.cahnHilliard.tanh1D ... ok
import examples.cahnHilliard.mesh2D ... ok
import examples.cahnHilliard.mesh3D ... ok
import examples.cahnHilliard.sphere ... ok
tanh1D (examples.cahnHilliard)
Doctest: examples.cahnHilliard.tanh1D ... ok
mesh2D (examples.cahnHilliard)
Doctest: examples.cahnHilliard.mesh2D ... ok
mesh3D (examples.cahnHilliard)
Doctest: examples.cahnHilliard.mesh3D ... ok
sphere (examples.cahnHilliard)
Doctest: examples.cahnHilliard.sphere ... ok
import examples.flow.stokesCavity ... ok
stokesCavity (examples.flow)
Doctest: examples.flow.stokesCavity ... ok
import examples.meshing.sphere ... ok
sphere (examples.meshing)
Doctest: examples.meshing.sphere ... ok
import examples.reactiveWetting.liquidVapor1D ... ok
import examples.reactiveWetting.liquidVapor2D ... ok
liquidVapor1D (examples.reactiveWetting)
Doctest: examples.reactiveWetting.liquidVapor1D ... <doctest examples.reactiveWetting.liquidVapor1D[9]>:3: RuntimeWarning: divide by zero encountered in log
  numerix.log(rho / (molarWeight - vbar * rho))
<doctest examples.reactiveWetting.liquidVapor1D[47]>:18: RuntimeWarning: divide by zero encountered in scalar divide
  dt = min(dt, dx / max(abs(velocity)) * cfl)
ok
liquidVapor2D (examples.reactiveWetting)
Doctest: examples.reactiveWetting.liquidVapor2D ... <doctest examples.reactiveWetting.liquidVapor2D[9]>:3: RuntimeWarning: divide by zero encountered in log
  numerix.log(rho / (molarWeight - vbar * rho))
<doctest examples.reactiveWetting.liquidVapor2D[54]>:22: RuntimeWarning: divide by zero encountered in scalar divide
  dt = min(dt, dx / max(abs(velocityVector.mag)) * cfl)
ok
import examples.riemann.acoustics ... ok
acoustics (examples.riemann)
Doctest: examples.riemann.acoustics ... ok

----------------------------------------------------------------------
Ran 543 tests in 82.921s

OK
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Skipped 2 doctest examples because the Pysparse solvers are not being used.
Skipped 38 doctest examples because neither `lsmlib` nor `skfmm` can be found on the $PATH
Skipped 1 doctest examples because `skfmm` must be used to run some tests
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

agoncalvescoel Feb 14, 2024
Author

And with the second suggestion:

(MYFIPYENV) anacoelho@HYHNB053:~/fipy$ FIPY_VIEWER=matplotlib python examples/diffusion/circle.py
Uncaught exception:
Traceback (most recent call last):
  File "/home/anacoelho/fipy/examples/diffusion/circle.py", line 178, in <module>
    exec(fipy.tests.doctestPlus._getScript())
  File "<string>", line 55, in <module>
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/__init__.py", line 131, in Viewer
    raise ImportError("Failed to import a viewer: %s" % str(errors))
ImportError: Failed to import a viewer: ['matplotlib: Unable to determine Axes to steal space for Colorbar. Either provide the *cax* argument to use as the Axes for the Colorbar, provide the *ax* argument to steal space from it, or add *mappable* to an Axes.']

guyer Feb 14, 2024
Maintainer

OK, thank you. I see this, too (#1009). For the moment, you can either downgrade Matplotlib to 3.7.x or solve on regular grids. The issue only seems to happen when using an irregular mesh.

agoncalvescoel Feb 14, 2024
Author

Okay, thanks! Will try to work with it!

agoncalvescoel Feb 14, 2024
Author

Downgrading works for the circle problem :)

agoncalvescoel · 2024-02-14T15:39:07Z

agoncalvescoel
Feb 14, 2024
Author

For the example coupled.py, I also have:

(MYFIPYENV) anacoelho@HYHNB053:~/fipy$ python examples/diffusion/coupled.py
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/matplotlibViewer/__init__.py:122: UserWarning: Matplotlib1DViewer efficiency is improved by setting the 'datamax' and 'datamin' keys
  return Matplotlib1DViewer(vars=vars, title=title, axes=axes, **kwlimits)
Killed

It crashed my wsl window, I have to restart the pc to recconect. I also had another error using the FIPY_VIEWER=matplotlib
on this one, related to strings in matplotlib.

I also noted that for the mesh1D.py, everything works well until you get to the following part of the code:

The blue line does not show up at zero, and the validation from numerix gives false...

4 replies

guyer Feb 14, 2024
Maintainer

This is a separate problem. Can you please open a new issue?

agoncalvescoel Feb 14, 2024
Author

Of course!

agoncalvescoel Feb 14, 2024
Author

The other error I mentioned with the coupled.py persists. Let me know if I should create a new issue with that

(MYFIPYENV) anacoelho@HYHNB053:~/fipy$ FIPY_VIEWER=matplotlib python examples/diffusion/coupled.py
QStandardPaths: wrong permissions on runtime directory /run/user/1000/, 0755 instead of 0700
/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/matplotlibViewer/__init__.py:122: UserWarning: Matplotlib1DViewer efficiency is improved by setting the 'datamax' and 'datamin' keys
  return Matplotlib1DViewer(vars=vars, title=title, axes=axes, **kwlimits)
Uncaught exception:
Traceback (most recent call last):
  File "/home/anacoelho/fipy/examples/diffusion/coupled.py", line 125, in <module>
    exec(fipy.tests.doctestPlus._getScript())
  File "<string>", line 103, in <module>
  File "/home/anacoelho/miniconda3/envs/MYFIPYENV/lib/python3.11/site-packages/fipy/viewers/__init__.py", line 131, in Viewer
    raise ImportError("Failed to import a viewer: %s" % str(errors))
ImportError: Failed to import a viewer: ['matplotlib: can only concatenate str (not "int") to str']

guyer Feb 14, 2024
Maintainer

The other error I mentioned with the coupled.py persists. Let me know if I should create a new issue with that

Yes, please

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Errors running examples #1006

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Errors running examples #1006

agoncalvescoel Feb 9, 2024

Replies: 4 comments · 11 replies

wd15 Feb 9, 2024 Collaborator

agoncalvescoel Feb 12, 2024 Author

guyer Feb 12, 2024 Maintainer

agoncalvescoel Feb 14, 2024 Author

agoncalvescoel Feb 14, 2024 Author

agoncalvescoel Feb 14, 2024 Author

guyer Feb 14, 2024 Maintainer

agoncalvescoel Feb 14, 2024 Author

agoncalvescoel Feb 14, 2024 Author

agoncalvescoel Feb 14, 2024 Author

guyer Feb 14, 2024 Maintainer

agoncalvescoel Feb 14, 2024 Author

agoncalvescoel Feb 14, 2024 Author

guyer Feb 14, 2024 Maintainer

agoncalvescoel
Feb 9, 2024

Replies: 4 comments 11 replies

wd15
Feb 9, 2024
Collaborator

agoncalvescoel
Feb 12, 2024
Author

guyer Feb 12, 2024
Maintainer

agoncalvescoel
Feb 14, 2024
Author

agoncalvescoel Feb 14, 2024
Author

agoncalvescoel Feb 14, 2024
Author

guyer Feb 14, 2024
Maintainer

agoncalvescoel Feb 14, 2024
Author

agoncalvescoel Feb 14, 2024
Author

agoncalvescoel
Feb 14, 2024
Author

guyer Feb 14, 2024
Maintainer

agoncalvescoel Feb 14, 2024
Author

agoncalvescoel Feb 14, 2024
Author

guyer Feb 14, 2024
Maintainer