else:
return None
elif 'FIPY_LSM' in os.environ:
return os.environ['FIPY_LSM'].lower()
elif _checkForLSMLIB():
return 'lsmlib'
elif _checkForSKFMM():
return 'skfmm'
else:
return None
LSM_SOLVER = _parseLSMSolver()
register_skipper(flag="LSM",
test=lambda: LSM_SOLVER is not None,
why="neither `lsmlib` nor `skfmm` can be found on the $PATH")
register_skipper(flag="LSMLIB",
test=lambda: LSM_SOLVER == 'lsmlib',
why="`lsmlib` must be used to run some tests")
register_skipper(flag="SKFMM",
test=lambda: LSM_SOLVER == 'skfmm',
why="`skfmm` must be used to run some tests")
__all__ = ["DistanceVariable"]
class DistanceVariable(CellVariable):
r"""
except ImportError:
from fipy.tools.comms.dummyComm import DummyComm
serialComm, parallelComm = DummyComm(), DummyComm()
else:
from fipy.tools.comms.dummyComm import DummyComm
serialComm, parallelComm = DummyComm(), DummyComm()
return serialComm, parallelComm
serial, parallel = serialComm, parallelComm = _getComms()
from fipy.tests.doctestPlus import register_skipper
register_skipper(flag="SERIAL",
test=lambda: parallelComm.Nproc == 1,
why="more than one processor found",
skipWarning=False)
register_skipper(flag="PARALLEL",
test=lambda: parallelComm.Nproc > 1,
why="only one processor found",
skipWarning=False)
register_skipper(flag="PROCESSOR_0",
test=lambda: parallelComm.procID == 0,
why="not running on processor 0",
skipWarning=False)
for M in (2, 3):
for N in range(M):
register_skipper(flag="PROCESSOR_%d_OF_%d" % (N, M),
except ImportError:
from fipy.tools.comms.dummyComm import DummyComm
serialComm, parallelComm = DummyComm(), DummyComm()
else:
from fipy.tools.comms.dummyComm import DummyComm
serialComm, parallelComm = DummyComm(), DummyComm()
return serialComm, parallelComm
serial, parallel = serialComm, parallelComm = _getComms()
from fipy.tests.doctestPlus import register_skipper
register_skipper(flag="SERIAL",
test=lambda: parallelComm.Nproc == 1,
why="more than one processor found",
skipWarning=False)
register_skipper(flag="PARALLEL",
test=lambda: parallelComm.Nproc > 1,
why="only one processor found",
skipWarning=False)
register_skipper(flag="PROCESSOR_0",
test=lambda: parallelComm.procID == 0,
why="not running on processor 0",
skipWarning=False)
for M in (2, 3):
for N in range(M):
register_skipper(flag="PROCESSOR_%d_OF_%d" % (N, M),
except (ImportError, SerialSolverError) as inst:
exceptions.append(inst)
try:
if _parallelComm.Nproc > 1:
raise SerialSolverError('scipy')
from fipy.solvers.scipy import *
__all__.extend(scipy.__all__)
solver = "scipy"
from fipy.matrices.scipyMatrix import _ScipyMeshMatrix
_MeshMatrix = _ScipyMeshMatrix
except (ImportError, SerialSolverError) as inst:
exceptions.append(inst)
import warnings
warnings.warn(
"Could not import any solver package. If you are using Trilinos, make sure you have all of the necessary Trilinos packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK."
)
for inst in exceptions:
warnings.warn(inst.__class__.__name__ + ': ' +
inst.message)
else:
raise ImportError('Unknown solver package %s' % solver)
from fipy.tests.doctestPlus import register_skipper
register_skipper(flag='PYSPARSE_SOLVER',
test=lambda: solver == 'pysparse',
why="the PySparse solvers are not being used.",
skipWarning=True)
return "skfmm"
else:
return None
elif 'FIPY_LSM' in os.environ:
return os.environ['FIPY_LSM'].lower()
elif _checkForLSMLIB():
return 'lsmlib'
elif _checkForSKFMM():
return 'skfmm'
else:
return None
LSM_SOLVER = _parseLSMSolver()
register_skipper(flag="LSM",
test=lambda : LSM_SOLVER is not None,
why="neither `lsmlib` nor `skfmm` can be found on the $PATH")
register_skipper(flag="LSMLIB",
test=lambda : LSM_SOLVER == 'lsmlib',
why="`lsmlib` must be used to run some tests")
register_skipper(flag="SKFMM",
test=lambda : LSM_SOLVER == 'skfmm',
why="`skfmm` must be used to run some tests")
__all__ = ["DistanceVariable"]
class DistanceVariable(CellVariable):
r"""
def _checkForTVTK():
hasTVTK = True
try:
try:
from tvtk.api import tvtk
except ImportError as e:
from enthought.tvtk.api import tvtk
except Exception:
hasTVTK = False
return hasTVTK
register_skipper(flag="TVTK",
test=_checkForTVTK,
why="the `tvtk` package cannot be imported")
class VTKViewer(AbstractViewer):
"""Renders `_MeshVariable` data in VTK format
"""
def __init__(self, vars, title=None, limits={}, **kwlimits):
"""Creates a VTKViewer
:Parameters:
vars
a `_MeshVariable` or a tuple of them
title
displayed at the top of the `Viewer` window
limits : dict
from fipy.viewers.viewer import AbstractViewer
from fipy.tests.doctestPlus import register_skipper
def _checkForTVTK():
hasTVTK = True
try:
try:
from tvtk.api import tvtk
except ImportError as e:
from enthought.tvtk.api import tvtk
except Exception:
hasTVTK = False
return hasTVTK
register_skipper(flag="TVTK",
test=_checkForTVTK,
why="the `tvtk` package cannot be imported")
class VTKViewer(AbstractViewer):
"""Renders `_MeshVariable` data in VTK format
"""
def __init__(self, vars, title=None, limits={}, **kwlimits):
"""Creates a VTKViewer
:Parameters:
vars
a `_MeshVariable` or a tuple of them
title
displayed at the top of the `Viewer` window
limits : dict
a (deprecated) alternative to limit keyword arguments
if _parallelComm.Nproc > 1:
raise SerialSolverError('scipy')
from fipy.solvers.scipy import *
__all__.extend(scipy.__all__)
solver = "scipy"
from fipy.matrices.scipyMatrix import _ScipyMeshMatrix
_MeshMatrix = _ScipyMeshMatrix
except (ImportError, SerialSolverError) as inst:
exceptions.append(inst)
import warnings
warnings.warn("Could not import any solver package. If you are using Trilinos, make sure you have all of the necessary Trilinos packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.")
for inst in exceptions:
warnings.warn(inst.__class__.__name__ + ': ' + inst.message)
else:
raise ImportError('Unknown solver package %s' % solver)
from fipy.tests.doctestPlus import register_skipper
register_skipper(flag='PYSPARSE_SOLVER',
test=lambda: solver == 'pysparse',
why="the Pysparse solvers are not being used.",
skipWarning=True)
register_skipper(flag='NOT_PYAMGX_SOLVER',
test=lambda: solver != 'pyamgx',
why="the PyAMGX solver is being used.",
skipWarning=True)
__docformat__ = 'restructuredtext'
import platform
from fipy.terms.implicitSourceTerm import ImplicitSourceTerm
from fipy.variables.variable import Variable
from fipy.terms.explicitUpwindConvectionTerm import ExplicitUpwindConvectionTerm
from fipy.variables.surfactantConvectionVariable import SurfactantConvectionVariable
from fipy.terms.transientTerm import TransientTerm
from fipy.tests.doctestPlus import register_skipper
from fipy.solvers import solver
register_skipper(
flag="NOTLINUXSCIPY",
test=lambda: platform.system() != "Linux" or solver != 'scipy',
why="`scipy` solvers on Linux fail intermittently: #575")
class AdsorbingSurfactantEquation():
r"""
The `AdsorbingSurfactantEquation` object solves the
`SurfactantEquation` but with an adsorbing species from some bulk
value. The equation that describes the surfactant adsorbing is
given by,
.. math::
\dot{\theta} = J v \theta + k c (1 - \theta - \theta_{\text{other}}) - \theta c_{\text{other}} k_{\text{other}} - k^- \theta
where :math:`\theta`, :math:`J`, :math:`v`, :math:`k`, :math:`c`,
except (ImportError, SerialSolverError) as inst:
exceptions.append(inst)
try:
if _parallelComm.Nproc > 1:
raise SerialSolverError('scipy')
from fipy.solvers.scipy import *
__all__.extend(scipy.__all__)
solver = "scipy"
from fipy.matrices.scipyMatrix import _ScipyMeshMatrix
_MeshMatrix = _ScipyMeshMatrix
except (ImportError, SerialSolverError) as inst:
exceptions.append(inst)
import warnings
warnings.warn("Could not import any solver package. If you are using Trilinos, make sure you have all of the necessary Trilinos packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.")
for inst in exceptions:
warnings.warn(inst.__class__.__name__ + ': ' + inst.message)
else:
raise ImportError, 'Unknown solver package %s' % solver
from fipy.tests.doctestPlus import register_skipper
register_skipper(flag='PYSPARSE_SOLVER',
test=lambda: solver == 'pysparse',
why="the PySparse solvers are not being used.",
skipWarning=True)