code stringlengths 66 870k | docstring stringlengths 19 26.7k | func_name stringlengths 1 138 | language stringclasses 1
value | repo stringlengths 7 68 | path stringlengths 5 324 | url stringlengths 46 389 | license stringclasses 7
values |
|---|---|---|---|---|---|---|---|
def _validate_x0(self):
"""Ensures x0 doesn't contain any nans/infs."""
x0 = self["pore.initial_guess"]
if not np.isfinite(x0).all():
raise Exception("x0 contains inf/nan values") | Ensures x0 doesn't contain any nans/infs. | _validate_x0 | python | PMEAL/OpenPNM | openpnm/algorithms/_transport.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/algorithms/_transport.py | MIT |
def _validate_topology_health(self):
"""
Ensures the network is not clustered, and if it is, they're at
least connected to a boundary condition pore.
"""
Ps = ~np.isnan(self['pore.bc.rate']) + ~np.isnan(self['pore.bc.value'])
if not is_fully_connected(network=self.network... |
Ensures the network is not clustered, and if it is, they're at
least connected to a boundary condition pore.
| _validate_topology_health | python | PMEAL/OpenPNM | openpnm/algorithms/_transport.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/algorithms/_transport.py | MIT |
def _validate_linear_system(self):
"""Ensures the linear system Ax = b doesn't contain any nans/infs."""
if np.isfinite(self.A.data).all() and np.isfinite(self.b).all():
return
raise Exception("A or b contains inf/nan values") | Ensures the linear system Ax = b doesn't contain any nans/infs. | _validate_linear_system | python | PMEAL/OpenPNM | openpnm/algorithms/_transport.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/algorithms/_transport.py | MIT |
def rate(self, pores=[], throats=[], mode='group'):
"""
Calculates the net rate of material moving into a given set of
pores or throats
Parameters
----------
pores : array_like
The pores for which the rate should be calculated
throats : array_like
... |
Calculates the net rate of material moving into a given set of
pores or throats
Parameters
----------
pores : array_like
The pores for which the rate should be calculated
throats : array_like
The throats through which the rate should be calculate... | rate | python | PMEAL/OpenPNM | openpnm/algorithms/_transport.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/algorithms/_transport.py | MIT |
def add_phases(self, phases):
"""
Adds supplied phases to MultiPhase object and sets occupancy to 0.
Parameters
----------
phases : list[Phase] or Phase
"""
phases = np.array(phases, ndmin=1)
for phase in phases:
if phase.name in self.setting... |
Adds supplied phases to MultiPhase object and sets occupancy to 0.
Parameters
----------
phases : list[Phase] or Phase
| add_phases | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def set_occupancy(self, phase, *, pores=[], throats=[], values=1):
r"""
Specifies occupancy of a phase in each pore or throat. This
method doesn't return any value.
Parameters
----------
phase : Phase
The phase whose occupancy is being specified.
pore... |
Specifies occupancy of a phase in each pore or throat. This
method doesn't return any value.
Parameters
----------
phase : Phase
The phase whose occupancy is being specified.
pores : ndarray
The location of pores whose occupancy is to be set.
... | set_occupancy | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def regenerate_models(self, propnames=None, exclude=[]):
r"""
Regenerate models associated with the Multiphase object
This method works by first regenerating the models associated with
the constituent phases, and then regenerating Multiphase models.
Parameters
---------... |
Regenerate models associated with the Multiphase object
This method works by first regenerating the models associated with
the constituent phases, and then regenerating Multiphase models.
Parameters
----------
propnames : list[str] or str
The list of proper... | regenerate_models | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def set_binary_partition_coef(self, phases, model, **kwargs):
"""
Sets binary partition coefficient as defined by the interface
concentration ratio of phase 1 to phase 2.
Parameters
----------
phases : list[Phase]
List of the two phases for which the binary p... |
Sets binary partition coefficient as defined by the interface
concentration ratio of phase 1 to phase 2.
Parameters
----------
phases : list[Phase]
List of the two phases for which the binary partition
coefficient model is being added.
model : Op... | set_binary_partition_coef | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def _add_interface_prop(self, propname, phases, model, **kwargs):
"""
Adds an interface model to the MultiPhase object. See Notes.
Notes
-----
Let's say the two phases corresponding to the interface model are
named: 'air' and 'water', and the interface propname to be add... |
Adds an interface model to the MultiPhase object. See Notes.
Notes
-----
Let's say the two phases corresponding to the interface model are
named: 'air' and 'water', and the interface propname to be added
is 'throat.foo'. After augmentation, 'throat.foo.air:water' will
... | _add_interface_prop | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def _format_interface_prop(self, propname, phases):
"""Formats propname as {propname}.{phase[0].name}:{phase[1].name}"""
prefix = propname
suffix = ":".join(phase.name for phase in phases)
return f"{prefix}.{suffix}" | Formats propname as {propname}.{phase[0].name}:{phase[1].name} | _format_interface_prop | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def _build_K(self):
"""Updates the global partition coefficient array"""
prefix = self.settings["partition_coef_prefix"]
self._K = np.ones(self.Nt, dtype=float)
# Find all binary partition coefficient models
models = [k for k in self.models.keys() if k.startswith(prefix)]
... | Updates the global partition coefficient array | _build_K | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def _interleave_data(self, prop):
"""Gathers property values from component phases to build a single array."""
element = self._parse_element(prop)[0]
vals = np.zeros(self._count(element=element), dtype=float)
# Retrieve property from constituent phases (weight = occupancy)
for ph... | Gathers property values from component phases to build a single array. | _interleave_data | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def _set_automatic_throat_occupancy(self, mode="mean"):
"""
Automatically interpolates throat occupancy based on that in
adjacent pores. This method doesn't return any value.
Parameters
----------
mode : str
Interpolation method. Options are:
===... |
Automatically interpolates throat occupancy based on that in
adjacent pores. This method doesn't return any value.
Parameters
----------
mode : str
Interpolation method. Options are:
=========== =====================================================
... | _set_automatic_throat_occupancy | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def multiphase_diffusion(phase,
pore_diffusivity="pore.diffusivity",
throat_diffusivity="throat.diffusivity",
size_factors="throat.diffusive_size_factors",
partition_coef_global="throat.partition_coef.global"):
r"""
... |
Calculates the diffusive conductance of conduits for multiphase systems.
Parameters
----------
%(phase)s
pore_diffusivity : str
%(dict_blurb)s pore diffusivity
throat_diffusivity : str
%(dict_blurb)s throat diffusivity
size_factors : str
%(dict_blurb)s conduit size ... | multiphase_diffusion | python | PMEAL/OpenPNM | openpnm/contrib/_multiphase.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_multiphase.py | MIT |
def run(self, x0, tspan, saveat=None, integrator=None):
"""
Runs all of the transient algorithms simultaneoulsy and returns the
solution.
Parameters
----------
x0 : ndarray or float
Array (or scalar) containing initial condition values.
tspan : array_... |
Runs all of the transient algorithms simultaneoulsy and returns the
solution.
Parameters
----------
x0 : ndarray or float
Array (or scalar) containing initial condition values.
tspan : array_like
Tuple (or array) containing the integration time s... | run | python | PMEAL/OpenPNM | openpnm/contrib/_transient_multiphysics.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_transient_multiphysics.py | MIT |
def _build_rhs(self):
"""
Returns a function handle, which calculates dy/dt = rhs(y, t).
Notes
-----
``y`` is a composite array that contains ALL the variables that
the multiphysics algorithm solves for, e.g., if the constituent
algorithms are ``TransientFickianD... |
Returns a function handle, which calculates dy/dt = rhs(y, t).
Notes
-----
``y`` is a composite array that contains ALL the variables that
the multiphysics algorithm solves for, e.g., if the constituent
algorithms are ``TransientFickianDiffusion``, and
``Transie... | _build_rhs | python | PMEAL/OpenPNM | openpnm/contrib/_transient_multiphysics.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/contrib/_transient_multiphysics.py | MIT |
def clear(self, mode=None):
r"""
Clears or deletes certain things from object. If no arguments are provided
it defaults to the normal `dict` behavior.
Parameters
----------
mode : str
Controls which things are to be deleted. Options are:
========... |
Clears or deletes certain things from object. If no arguments are provided
it defaults to the normal `dict` behavior.
Parameters
----------
mode : str
Controls which things are to be deleted. Options are:
=========== ====================================... | clear | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def keys(self, mode=None):
r"""
An overloaded version of ``keys`` that optionally accepts a ``mode``
Parameters
----------
mode : str
If given, optionally, it controls which type of keys are returned.
Options are:
========== =================... |
An overloaded version of ``keys`` that optionally accepts a ``mode``
Parameters
----------
mode : str
If given, optionally, it controls which type of keys are returned.
Options are:
========== =======================================================
... | keys | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def to_mask(self, pores=None, throats=None):
r"""
Generates a boolean mask with `True` values in the given locations
Parameters
----------
pores : array_like
The pore indices where `True` values will be placed. If `pores` is
given the `throats` is ignored... |
Generates a boolean mask with `True` values in the given locations
Parameters
----------
pores : array_like
The pore indices where `True` values will be placed. If `pores` is
given the `throats` is ignored.
throats : array_like
The throat ind... | to_mask | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def to_indices(self, mask):
r"""
Converts a boolean mask to pore or throat indices
Parameters
----------
mask : ndarray
A boolean mask with `True` values indicating either pore or
throat indices. This array must either be Nt or Np long, otherwise
... |
Converts a boolean mask to pore or throat indices
Parameters
----------
mask : ndarray
A boolean mask with `True` values indicating either pore or
throat indices. This array must either be Nt or Np long, otherwise
an Exception is raised.
Ret... | to_indices | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def props(self, element=['pore', 'throat']):
r"""
Retrieves a list of keys that contain numerical data (i.e. "properties")
Parameters
----------
element : str, list of strings
Indicates whether `'pore'` or `'throat'` properties should be returned.
The def... |
Retrieves a list of keys that contain numerical data (i.e. "properties")
Parameters
----------
element : str, list of strings
Indicates whether `'pore'` or `'throat'` properties should be returned.
The default is `['pore', 'throat']`, so both are returned.
... | props | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def interpolate_data(self, propname, mode='mean'):
r"""
Generates an array of the requested pore/throat data by interpolating
the neighboring throat/pore data.
Parameters
----------
propname : str
The data to be generated.
mode : str
Dicta... |
Generates an array of the requested pore/throat data by interpolating
the neighboring throat/pore data.
Parameters
----------
propname : str
The data to be generated.
mode : str
Dictate how the interpolation is done. Options are 'mean', 'min',
... | interpolate_data | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def get_conduit_data(self, propname):
r"""
Fetches an Nt-by-3 array of the requested property
Parameters
----------
propname : str
The dictionary key of the property to fetch.
Returns
-------
data : ndarray
An Nt-by-3 array with e... |
Fetches an Nt-by-3 array of the requested property
Parameters
----------
propname : str
The dictionary key of the property to fetch.
Returns
-------
data : ndarray
An Nt-by-3 array with each column containing the requrested data
... | get_conduit_data | python | PMEAL/OpenPNM | openpnm/core/_base2.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_base2.py | MIT |
def _parse_indices(self, indices):
r"""
This private method accepts a list of pores or throats and returns a
properly structured Numpy array of indices.
Parameters
----------
indices : int or array_like
This argument can accept numerous different data types i... |
This private method accepts a list of pores or throats and returns a
properly structured Numpy array of indices.
Parameters
----------
indices : int or array_like
This argument can accept numerous different data types including
boolean masks, integers an... | _parse_indices | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _parse_element(self, element, single=False):
r"""
This private method is used to parse the keyword \'element\' in many
of the above methods.
Parameters
----------
element : str or List[str]
The element argument to check. If is None is recieved, then a li... |
This private method is used to parse the keyword \'element\' in many
of the above methods.
Parameters
----------
element : str or List[str]
The element argument to check. If is None is recieved, then a list
containing both \'pore\' and \'throat\' is ret... | _parse_element | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _parse_labels(self, labels, element):
r"""
This private method is used for converting \'labels\' to a proper
format, including dealing with wildcards (\*).
Parameters
----------
labels : str or List[str]
The label or list of labels to be parsed. Note that... |
This private method is used for converting \'labels\' to a proper
format, including dealing with wildcards (\*).
Parameters
----------
labels : str or List[str]
The label or list of labels to be parsed. Note that the \* can be
used as a wildcard.
... | _parse_labels | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _parse_mode(self, mode, allowed=None, single=False):
r"""
This private method is for checking the \'mode\' used in the calling
method.
Parameters
----------
mode : str or List[str]
The mode(s) to be parsed
allowed : List[str]
A list co... |
This private method is for checking the \'mode\' used in the calling
method.
Parameters
----------
mode : str or List[str]
The mode(s) to be parsed
allowed : List[str]
A list containing the allowed modes. This list is defined by the
... | _parse_mode | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _get_labels(self, element, locations, mode):
r"""
This is the actual label getter method, but it should not be called
directly. Use ``labels`` instead.
"""
# Parse inputs
locations = self._parse_indices(locations)
element = self._parse_element(element=element... |
This is the actual label getter method, but it should not be called
directly. Use ``labels`` instead.
| _get_labels | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def labels(self, pores=[], throats=[], element=None, mode='union'):
r"""
Returns a list of labels present on the object
Additionally, this function can return labels applied to a specified
set of pores or throats
Parameters
----------
element : str
C... |
Returns a list of labels present on the object
Additionally, this function can return labels applied to a specified
set of pores or throats
Parameters
----------
element : str
Controls whether pore or throat labels are returned. If empty then
b... | labels | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def set_label(self, label, pores=None, throats=None, mode='add'):
r"""
Creates or updates a label array
Parameters
----------
label : str
The label to apply to the specified locations
pores : array_like
A list of pore indices or a boolean mask of ... |
Creates or updates a label array
Parameters
----------
label : str
The label to apply to the specified locations
pores : array_like
A list of pore indices or a boolean mask of where given label
should be added or removed (see ``mode``)
... | set_label | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _get_indices(self, element, labels, mode='or'):
r"""
This is the actual method for getting indices, but should not be called
directly. Use ``pores`` or ``throats`` instead.
"""
# Parse and validate all input values.
element = self._parse_element(element, single=True)... |
This is the actual method for getting indices, but should not be called
directly. Use ``pores`` or ``throats`` instead.
| _get_indices | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def pores(self, labels=None, mode='or', asmask=False):
r"""
Returns pore indicies where given labels exist, according to the logic
specified by the ``mode`` argument.
Parameters
----------
labels : str or list[str]
The label(s) whose pores locations are reque... |
Returns pore indicies where given labels exist, according to the logic
specified by the ``mode`` argument.
Parameters
----------
labels : str or list[str]
The label(s) whose pores locations are requested. This argument
also accepts '*' for wildcard sear... | pores | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def filter_by_label(self, pores=[], throats=[], labels=None, mode='or'):
r"""
Returns which of the supplied pores (or throats) has the specified
label(s)
Parameters
----------
pores, or throats : array_like
List of pores or throats to be filtered
labe... |
Returns which of the supplied pores (or throats) has the specified
label(s)
Parameters
----------
pores, or throats : array_like
List of pores or throats to be filtered
labels : list of strings
The labels to apply as a filter
mode : str
... | filter_by_label | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def num_pores(self, labels='all', mode='or'):
r"""
Returns the number of pores of the specified labels
Parameters
----------
labels : list of strings, optional
The pore labels that should be included in the count.
If not supplied, all pores are counted.
... |
Returns the number of pores of the specified labels
Parameters
----------
labels : list of strings, optional
The pore labels that should be included in the count.
If not supplied, all pores are counted.
labels : list of strings
Label of pores... | num_pores | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def num_throats(self, labels='all', mode='union'):
r"""
Return the number of throats of the specified labels
Parameters
----------
labels : list of strings, optional
The throat labels that should be included in the count.
If not supplied, all throats are ... |
Return the number of throats of the specified labels
Parameters
----------
labels : list of strings, optional
The throat labels that should be included in the count.
If not supplied, all throats are counted.
mode : str, optional
Specifies how... | num_throats | python | PMEAL/OpenPNM | openpnm/core/_mixins.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_mixins.py | MIT |
def _find_target(self):
"""
Finds and returns the target object to which this ModelsDict is
associated.
"""
for proj in ws.values():
for obj in proj:
if hasattr(obj, "models"):
if obj.models is self:
return o... |
Finds and returns the target object to which this ModelsDict is
associated.
| _find_target | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def dependency_list(self):
r"""
Returns a list of dependencies in the order with which they should
be called to ensure data is calculated by one model before it's
asked for by another.
Notes
-----
This raises an exception if the graph has cycles which means the
... |
Returns a list of dependencies in the order with which they should
be called to ensure data is calculated by one model before it's
asked for by another.
Notes
-----
This raises an exception if the graph has cycles which means the
dependencies are unresolvable (i... | dependency_list | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def dependency_graph(self, deep=False):
"""
Returns a NetworkX graph object of the dependencies
Parameters
----------
deep : bool, optional
Defines whether intra- or inter-object dependency graph is
desired. Default is False, i.e. only returns dependencie... |
Returns a NetworkX graph object of the dependencies
Parameters
----------
deep : bool, optional
Defines whether intra- or inter-object dependency graph is
desired. Default is False, i.e. only returns dependencies
within the object.
See Also
... | dependency_graph | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def dependency_map(self,
ax=None,
figsize=None,
deep=False,
style='shell'): # pragma: no cover
"""
Create a graph of the dependency graph in a decent format
Parameters
----------
ax : ma... |
Create a graph of the dependency graph in a decent format
Parameters
----------
ax : matplotlib.axis, optional
Matplotlib axis object on which dependency map is to be drawn.
figsize : tuple, optional
Tuple containing frame size.
See Also
... | dependency_map | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def _info(self): # Pragma: no cover
r"""
Prints a nicely formatted list of model names and the domain to which
they apply.
Notes
-----
This is a hidden function for now, but could be exposed if useful.
"""
names = {}
for item in self:
... |
Prints a nicely formatted list of model names and the domain to which
they apply.
Notes
-----
This is a hidden function for now, but could be exposed if useful.
| _info | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def target(self):
"""
Finds and returns the object to which this model is assigned
"""
for proj in ws.values():
for obj in proj:
if hasattr(obj, "models"):
for mod in obj.models.values():
if mod is self:
... |
Finds and returns the object to which this model is assigned
| target | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def add_model(self, propname, model, domain='all', regen_mode='normal',
**kwargs):
r"""
Add a pore-scale model to the object, along with the desired arguments
Parameters
----------
propname : str
The name of the property being computed. E.g. if
... |
Add a pore-scale model to the object, along with the desired arguments
Parameters
----------
propname : str
The name of the property being computed. E.g. if
``propname='pore.diameter'`` then the computed results will be stored
in ``obj['pore.diameter... | add_model | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def add_model_collection(self, models, domain='all', regen_mode='deferred'):
r"""
Add a ``collection`` of several models at once
Parameters
----------
models : dict
The collection of models to add.
regen_mode : str
By default the models are not re... |
Add a ``collection`` of several models at once
Parameters
----------
models : dict
The collection of models to add.
regen_mode : str
By default the models are not regenerated upon addition. See the
docstring for ``add_model`` for more informa... | add_model_collection | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def regenerate_models(self, propnames=None, exclude=[]):
r"""
Runs all the models stored in the object's ``models`` attribute
Parameters
----------
propnames : list of strings
If given then only the specified models are run
exclude : list of strings
... |
Runs all the models stored in the object's ``models`` attribute
Parameters
----------
propnames : list of strings
If given then only the specified models are run
exclude : list of strings
If given then these models will *not* be run
Notes
... | regenerate_models | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def run_model(self, propname, domain=None):
r"""
Runs the requested model and places the result into the correct
locations
Parameters
----------
propname : str
The name of the model to run.
domain : str
The label of the domain for which th... |
Runs the requested model and places the result into the correct
locations
Parameters
----------
propname : str
The name of the model to run.
domain : str
The label of the domain for which the model should be run. Passing
``propname='p... | run_model | python | PMEAL/OpenPNM | openpnm/core/_models.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/core/_models.py | MIT |
def solve(self, rhs, x0, tspan, saveat, **kwargs):
"""
Solves the system of ODEs defined by dy/dt = rhs(t, y).
Parameters
----------
rhs : function handle
RHS vector in the system of ODEs defined by dy/dt = rhs(t, y)
x0 : array_like
Initial value ... |
Solves the system of ODEs defined by dy/dt = rhs(t, y).
Parameters
----------
rhs : function handle
RHS vector in the system of ODEs defined by dy/dt = rhs(t, y)
x0 : array_like
Initial value for the system of ODEs
tspan : array_like
... | solve | python | PMEAL/OpenPNM | openpnm/integrators/_scipy.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/integrators/_scipy.py | MIT |
def network_to_comsol(network, filename=None):
r"""
Saves the network and geometry data from the given objects into the
specified file. This exports in 2D only where throats and pores
have rectangular and circular shapes, respectively.
Parameters
----------
network : Network
The net... |
Saves the network and geometry data from the given objects into the
specified file. This exports in 2D only where throats and pores
have rectangular and circular shapes, respectively.
Parameters
----------
network : Network
The network containing the desired data
Notes
-----
... | network_to_comsol | python | PMEAL/OpenPNM | openpnm/io/_comsol.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_comsol.py | MIT |
def project_to_csv(project, filename=''):
r"""
Save all the pore and throat data on the Network and Phase objects to a CSV
file
Parameters
----------
project : list
An openpnm ``project`` object
filename : str or path object
The name of the file to store the data
"""
... |
Save all the pore and throat data on the Network and Phase objects to a CSV
file
Parameters
----------
project : list
An openpnm ``project`` object
filename : str or path object
The name of the file to store the data
| project_to_csv | python | PMEAL/OpenPNM | openpnm/io/_csv.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_csv.py | MIT |
def project_to_dict(project, categorize_by=['name'], flatten=False, element=None,
delim=' | '):
r"""
Returns a single dictionary object containing data from the given
OpenPNM project, with the keys organized differently depending on
optional arguments.
Parameters
----------
... |
Returns a single dictionary object containing data from the given
OpenPNM project, with the keys organized differently depending on
optional arguments.
Parameters
----------
project : list
An OpenPNM project object
categorize_by : str or list[str]
Indicates how the dictiona... | project_to_dict | python | PMEAL/OpenPNM | openpnm/io/_dict.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_dict.py | MIT |
def project_to_hdf5(project, filename=''):
r"""
Creates an HDF5 file containing data from the specified objects
Parameters
----------
network : Network
The network containing the desired data
phases : list[Phase]s (optional, default is none)
A list of phase objects whose data a... |
Creates an HDF5 file containing data from the specified objects
Parameters
----------
network : Network
The network containing the desired data
phases : list[Phase]s (optional, default is none)
A list of phase objects whose data are to be included
Returns
-------
f : ... | project_to_hdf5 | python | PMEAL/OpenPNM | openpnm/io/_hdf5.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_hdf5.py | MIT |
def print_hdf5(f, flat=False):
r"""
Given an hdf5 file handle, prints to console in a human readable manner
Parameters
----------
f : file handle
The hdf5 file to print
flat : bool
Flag to indicate if print should be nested or flat. The default is
``flat==False`` result... |
Given an hdf5 file handle, prints to console in a human readable manner
Parameters
----------
f : file handle
The hdf5 file to print
flat : bool
Flag to indicate if print should be nested or flat. The default is
``flat==False`` resulting in a nested view.
| print_hdf5 | python | PMEAL/OpenPNM | openpnm/io/_hdf5.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_hdf5.py | MIT |
def network_to_jsongraph(network, filename=''):
r"""
Write the network to disk as a JGF file.
Parameters
----------
network : Network
filename : str
Desired file name, defaults to network name if not given
"""
# Ensure output file is valid
filename = _parse_filename(filena... |
Write the network to disk as a JGF file.
Parameters
----------
network : Network
filename : str
Desired file name, defaults to network name if not given
| network_to_jsongraph | python | PMEAL/OpenPNM | openpnm/io/_jsongraph.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_jsongraph.py | MIT |
def network_from_jsongraph(filename):
r"""
Loads the JGF file onto the given project.
Parameters
----------
filename : str
The name of the file containing the data to import. The formatting
of this file is outlined below.
Returns
-------
network : dict
An OpenP... |
Loads the JGF file onto the given project.
Parameters
----------
filename : str
The name of the file containing the data to import. The formatting
of this file is outlined below.
Returns
-------
network : dict
An OpenPNM Network dictionary
| network_from_jsongraph | python | PMEAL/OpenPNM | openpnm/io/_jsongraph.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_jsongraph.py | MIT |
def network_from_marock(filename, voxel_size=1):
r"""
Load data from a 3DMA-Rock extracted network.
Parameters
----------
filename : str
The location of the 'np2th' and 'th2np' files. This can be an
absolute path or relative to the current working directory.
voxel_size : scalar
... |
Load data from a 3DMA-Rock extracted network.
Parameters
----------
filename : str
The location of the 'np2th' and 'th2np' files. This can be an
absolute path or relative to the current working directory.
voxel_size : scalar
The resolution of the image on which 3DMA-Rock wa... | network_from_marock | python | PMEAL/OpenPNM | openpnm/io/_marock.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_marock.py | MIT |
def network_from_networkx(G):
r"""
Creates an OpenPNM Network from a undirected NetworkX graph object
Parameters
----------
G : networkx.classes.graph.Graph Object
The NetworkX graph. G should be undirected. The numbering of nodes
should be numeric (int's), zero-based and should not... |
Creates an OpenPNM Network from a undirected NetworkX graph object
Parameters
----------
G : networkx.classes.graph.Graph Object
The NetworkX graph. G should be undirected. The numbering of nodes
should be numeric (int's), zero-based and should not contain any
gaps, i.e. ``G.no... | network_from_networkx | python | PMEAL/OpenPNM | openpnm/io/_networkx.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_networkx.py | MIT |
def network_to_networkx(network):
r"""
Write OpenPNM Network to a NetworkX object.
Parameters
----------
network : dict
The OpenPNM Network to be converted to a NetworkX object
Returns
-------
G : undirected graph object
A NetworkX object with all pore/throat properties... |
Write OpenPNM Network to a NetworkX object.
Parameters
----------
network : dict
The OpenPNM Network to be converted to a NetworkX object
Returns
-------
G : undirected graph object
A NetworkX object with all pore/throat properties attached to it
| network_to_networkx | python | PMEAL/OpenPNM | openpnm/io/_networkx.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_networkx.py | MIT |
def network_to_pandas(network, join=False, delim='.'):
"""Converts network data to a Pandas DataFrame."""
proj = Project()
proj.append(network)
# Initialize pore and throat data dictionary using Dict class
pdata = project_to_dict(project=proj, element='pore',
flatten=True... | Converts network data to a Pandas DataFrame. | network_to_pandas | python | PMEAL/OpenPNM | openpnm/io/_pandas.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_pandas.py | MIT |
def project_to_pandas(project, join=False, delim='.'):
r"""
Convert the Network and Phase data to a Pandas DataFrame(s)
Parameters
----------
project : list
An OpenPNM ``project`` object
join : bool
If ``False`` (default), two DataFrames are returned with *pore*
data in ... |
Convert the Network and Phase data to a Pandas DataFrame(s)
Parameters
----------
project : list
An OpenPNM ``project`` object
join : bool
If ``False`` (default), two DataFrames are returned with *pore*
data in one, and *throat* data in the other. If ``True`` the pore
... | project_to_pandas | python | PMEAL/OpenPNM | openpnm/io/_pandas.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_pandas.py | MIT |
def project_to_paraview(project, filename): # pragma: no cover
r"""
Exports an OpenPNM network to a paraview state file.
Parameters
----------
network : Network
The network containing the desired data.
filename : str
Path to saved .vtp file.
Notes
-----
Outputs a p... |
Exports an OpenPNM network to a paraview state file.
Parameters
----------
network : Network
The network containing the desired data.
filename : str
Path to saved .vtp file.
Notes
-----
Outputs a pvsm file that can be opened in Paraview. The pvsm file will
be saved... | project_to_paraview | python | PMEAL/OpenPNM | openpnm/io/_paraview.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_paraview.py | MIT |
def network_from_pergeos(filename):
r"""
Loads a network from a PerGeos file.
Notes
-----
PerGeos is the format used by the Avizo software. See `here for more
details <https://cases.pergeos.com/>`_.
"""
net = {}
# --------------------------------------------------------------------... |
Loads a network from a PerGeos file.
Notes
-----
PerGeos is the format used by the Avizo software. See `here for more
details <https://cases.pergeos.com/>`_.
| network_from_pergeos | python | PMEAL/OpenPNM | openpnm/io/_pergeos.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_pergeos.py | MIT |
def network_from_porespy(filename):
r"""
Load a network extracted using the PoreSpy package
Parameters
----------
filename : str or dict
Can either be a filename pointing to a pickled dictionary, or a
handle to a dictionary in memory. The second option lets users
avoid the s... |
Load a network extracted using the PoreSpy package
Parameters
----------
filename : str or dict
Can either be a filename pointing to a pickled dictionary, or a
handle to a dictionary in memory. The second option lets users
avoid the step of saving the dictionary to a file.
... | network_from_porespy | python | PMEAL/OpenPNM | openpnm/io/_porespy.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_porespy.py | MIT |
def network_to_salome(network, filename=None, explicit=False):
r"""
Saves the network data and writes a Salome .py instruction file.
Parameters
----------
network : Network
The network containing the desired data
Notes
-----
This method only saves the data, not any of the pore-... |
Saves the network data and writes a Salome .py instruction file.
Parameters
----------
network : Network
The network containing the desired data
Notes
-----
This method only saves the data, not any of the pore-scale models
or other attributes. To save an actual OpenPNM Project... | network_to_salome | python | PMEAL/OpenPNM | openpnm/io/_salome.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_salome.py | MIT |
def network_from_statoil(path, prefix):
r"""
Load data from the \'dat\' files located in specified folder.
Parameters
----------
path : str
The full path to the folder containing the set of \'dat\' files.
prefix : str
The file name prefix on each file. The data files are stored
... |
Load data from the \'dat\' files located in specified folder.
Parameters
----------
path : str
The full path to the folder containing the set of \'dat\' files.
prefix : str
The file name prefix on each file. The data files are stored
as \<prefix\>_node1.dat.
network : N... | network_from_statoil | python | PMEAL/OpenPNM | openpnm/io/_statoil.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_statoil.py | MIT |
def network_to_stl(network, filename=None, maxsize='auto',
fileformat='STL Format', logger_level=0):
r"""
Saves (transient/steady-state) data from the given objects into the
specified file.
Parameters
----------
network : Network.
The network containing the desired da... |
Saves (transient/steady-state) data from the given objects into the
specified file.
Parameters
----------
network : Network.
The network containing the desired data.
phases : list[Phase] (place holder, default is None).
List of phases containing the desired data.
filename :... | network_to_stl | python | PMEAL/OpenPNM | openpnm/io/_stl.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_stl.py | MIT |
def project_to_vtk(project, filename="",
fill_nans=None, fill_infs=None):
r"""
Save network and phase data to a single vtp file for visualizing in
Paraview.
Parameters
----------
network : Network
The Network containing the data to be written
phases : list, option... |
Save network and phase data to a single vtp file for visualizing in
Paraview.
Parameters
----------
network : Network
The Network containing the data to be written
phases : list, optional
A list containing Phase(s) containing data to be
written
filename : str, optio... | project_to_vtk | python | PMEAL/OpenPNM | openpnm/io/_vtk.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_vtk.py | MIT |
def project_to_xdmf(project, filename=''):
r"""
Saves (transient/steady-state) data from the given objects into
the specified file.
Parameters
----------
network : Network
The network containing the desired data
phases : list[Phase] (optional, default is None)
A list of phas... |
Saves (transient/steady-state) data from the given objects into
the specified file.
Parameters
----------
network : Network
The network containing the desired data
phases : list[Phase] (optional, default is None)
A list of phase objects whose data are to be included
Notes
... | project_to_xdmf | python | PMEAL/OpenPNM | openpnm/io/_xdmf.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/io/_xdmf.py | MIT |
def spheres_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Calculates conduit lengths in the network assuming pores are spheres
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
--... |
Calculates conduit lengths in the network assuming pores are spheres
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
lengths : ndarray
Array (Nt by 3) contain... | spheres_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def circles_and_rectangles(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are circles
and throats are rectangles.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
---------... |
Calculates conduit lengths in the network assuming pores are circles
and throats are rectangles.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be u... | circles_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def cones_and_cylinders(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are cones
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
... |
Calculates conduit lengths in the network assuming pores are cones
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
| cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def intersecting_cones(network, pore_coords="pore.coords", throat_coords="throat.coords"):
r"""
Calculates conduit lengths in the network assuming pores are cones
that intersect. Therefore, the throat is the cross sectional plane where
two pores meet and has negligible/zero volume.
A conduit is def... |
Calculates conduit lengths in the network assuming pores are cones
that intersect. Therefore, the throat is the cross sectional plane where
two pores meet and has negligible/zero volume.
A conduit is defined as ( 1/2 pore - 1/2 pore ).
Parameters
----------
%(network)s
%(Pcoords)s
... | intersecting_cones | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def hybrid_cones_and_cylinders(
network, pore_diameter="pore.diameter", throat_coords="throat.coords"
):
r"""
Calculates conduit lengths in the network assuming pores are cones
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
... |
Calculates conduit lengths in the network assuming pores are cones
and throats are cylinders.
A conduit is defined as ( 1/2 pore - full throat - 1/2 pore ).
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
| hybrid_cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def trapezoids_and_rectangles(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-----... |
Calculates conduit lengths in the network assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| trapezoids_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def intersecting_trapezoids(
network, pore_coords="pore.coords", throat_coords="throat.coords"
):
r"""
Calculates conduit lengths in the network assuming pores are
intersecting trapezoids.
Parameters
----------
%(network)s
%(Pcoords)s
%(Tcoords)s
Returns
-------
Notes
... |
Calculates conduit lengths in the network assuming pores are
intersecting trapezoids.
Parameters
----------
%(network)s
%(Pcoords)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| intersecting_trapezoids | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def hybrid_trapezoids_and_rectangles(
network, pore_diameter="pore.diameter", throat_coords="throat.coords"
):
r"""
Calculates conduit lengths in the network assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
... |
Calculates conduit lengths in the network assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
... | hybrid_trapezoids_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def pyramids_and_cuboids(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are truncated
pyramids and throats are cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-----... |
Calculates conduit lengths in the network assuming pores are truncated
pyramids and throats are cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
| pyramids_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def intersecting_pyramids(
network, pore_coords="pore.coords", throat_coords="throat.coords"
):
r"""
Calculates conduit lengths in the network assuming pores are
intersecting pyramids.
Parameters
----------
%(network)s
%(Pcoords)s
%(Tcoords)s
Returns
-------
"""
re... |
Calculates conduit lengths in the network assuming pores are
intersecting pyramids.
Parameters
----------
%(network)s
%(Pcoords)s
%(Tcoords)s
Returns
-------
| intersecting_pyramids | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def hybrid_pyramids_and_cuboids(
network, pore_diameter="pore.diameter", throat_coords="throat.coords"
):
r"""
Calculates conduit lengths in the network assuming pores are truncated
pyramids that intersect. Therefore, the throat is the cross sectional plane where
two pores meet and has negligible/ze... |
Calculates conduit lengths in the network assuming pores are truncated
pyramids that intersect. Therefore, the throat is the cross sectional plane where
two pores meet and has negligible/zero volume.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
| hybrid_pyramids_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def cubes_and_cuboids(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are cubes
and throats are cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
"""
... |
Calculates conduit lengths in the network assuming pores are cubes
and throats are cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
| cubes_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def squares_and_rectangles(
network, pore_diameter="pore.diameter", throat_diameter="throat.diameter"
):
r"""
Calculates conduit lengths in the network assuming pores are squares
and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
... |
Calculates conduit lengths in the network assuming pores are squares
and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| squares_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def _get_L_ctc(network):
"""Returns throat spacing if it exists, otherwise calculates it."""
try:
L_ctc = network["throat.spacing"]
except KeyError:
P12 = network["throat.conns"]
C1 = network["pore.coords"][P12[:, 0]]
C2 = network["pore.coords"][P12[:, 1]]
L_ctc = np.... | Returns throat spacing if it exists, otherwise calculates it. | _get_L_ctc | python | PMEAL/OpenPNM | openpnm/models/geometry/conduit_lengths/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/conduit_lengths/_funcs.py | MIT |
def spheres_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes diffusive shape coefficient for conduits assuming pores are
spheres and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
... |
Computes diffusive shape coefficient for conduits assuming pores are
spheres and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
size_factors : ndarray
Array (Nt by 3) containing conduit values for each element
of the pore... | spheres_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def circles_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes diffusive shape coefficient for conduits assuming pores are
circles and throats are rectangles
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns... |
Computes diffusive shape coefficient for conduits assuming pores are
circles and throats are rectangles
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
... | circles_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def cones_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes diffusive shape coefficient assuming pores are truncated cones
and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
---... |
Computes diffusive shape coefficient assuming pores are truncated cones
and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def intersecting_cones(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes diffusive shape coefficient assuming pores are intersecting cones.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
... |
Computes diffusive shape coefficient assuming pores are intersecting cones.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| intersecting_cones | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def hybrid_cones_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes diffusive shape coefficient assuming pores are truncated cones
and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
... |
Computes diffusive shape coefficient assuming pores are truncated cones
and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
... | hybrid_cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def trapezoids_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Compute diffusive shape coefficient for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
R... |
Compute diffusive shape coefficient for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
... | trapezoids_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def intersecting_trapezoids(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes diffusive shape coefficient for conduits of intersecting
trapezoids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
... |
Computes diffusive shape coefficient for conduits of intersecting
trapezoids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| intersecting_trapezoids | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def hybrid_trapezoids_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Compute diffusive shape coefficient for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s... |
Compute diffusive shape coefficient for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmet... | hybrid_trapezoids_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def pyramids_and_cuboids(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes diffusive size factor for conduits of truncated pyramids and
cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
... |
Computes diffusive size factor for conduits of truncated pyramids and
cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| pyramids_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def hybrid_pyramids_and_cuboids(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes diffusive size factor for conduits of truncated pyramids and
cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
No... |
Computes diffusive size factor for conduits of truncated pyramids and
cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| hybrid_pyramids_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def intersecting_pyramids(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes diffusive size factor for conduits of pores with intersecting pyramids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
... |
Computes diffusive size factor for conduits of pores with intersecting pyramids.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| intersecting_pyramids | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def cubes_and_cuboids(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
pore_aspect=[1, 1, 1],
throat_aspect=[1, 1, 1],
):
r"""
Computes diffusive shape coefficient for conduits assuming pores are
cubes and throats are cuboids.
Parameters
----------
... |
Computes diffusive shape coefficient for conduits assuming pores are
cubes and throats are cuboids.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
pore_aspect : list
Aspect ratio of the pores
throat_aspect : list
Aspect ratio of the throats
Returns
-------... | cubes_and_cuboids | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def squares_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
pore_aspect=[1, 1],
throat_aspect=[1, 1],
):
r"""
Computes diffusive size factor for conduits assuming pores are squares
and throats are rectangles.
Parameters
----------
%... |
Computes diffusive size factor for conduits assuming pores are squares
and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
pore_aspect : list
Aspect ratio of the pores
throat_aspect : list
Aspect ratio of the throats
Returns
-------
... | squares_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def ncylinders_in_series(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
n=5
):
r"""
Computes diffusive size factors for conduits of spheres and cylinders
with the spheres approximated as N cylinders in series.
Parameters
----------
%(network)s
%(... |
Computes diffusive size factors for conduits of spheres and cylinders
with the spheres approximated as N cylinders in series.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
n : int
Number of cylindrical divisions for each pore and throat
Returns
-------
Notes
... | ncylinders_in_series | python | PMEAL/OpenPNM | openpnm/models/geometry/diffusive_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/diffusive_size_factors/_funcs.py | MIT |
def spheres_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes hydraulic size factors for conduits assuming pores are
spheres and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-... |
Computes hydraulic size factors for conduits assuming pores are
spheres and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
size_factors : ndarray
Array (Nt by 3) containing conduit values for each element
of the pore-thro... | spheres_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
def circles_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes hydraulic size factors for conduits assuming pores are
circles and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
... |
Computes hydraulic size factors for conduits assuming pores are
circles and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
| circles_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
def cones_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes hydraulic size factors for conduits assuming pores are
truncated cones and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns... |
Computes hydraulic size factors for conduits assuming pores are
truncated cones and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
| cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
def intersecting_cones(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes hydraulic size factors of intersecting cones.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
"""
D1, Dt, D2 = ne... |
Computes hydraulic size factors of intersecting cones.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
| intersecting_cones | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
def hybrid_cones_and_cylinders(
network,
pore_diameter="pore.diameter",
throat_coords="throat.coords"
):
r"""
Computes hydraulic size factors for conduits assuming pores are
truncated cones and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
... |
Computes hydraulic size factors for conduits assuming pores are
truncated cones and throats are cylinders.
Parameters
----------
%(network)s
%(Dp)s
%(Tcoords)s
Returns
-------
Notes
-----
| hybrid_cones_and_cylinders | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
def trapezoids_and_rectangles(
network,
pore_diameter="pore.diameter",
throat_diameter="throat.diameter",
):
r"""
Computes hydraulic size factors for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Retur... |
Computes hydraulic size factors for conduits assuming pores are
trapezoids and throats are rectangles.
Parameters
----------
%(network)s
%(Dp)s
%(Dt)s
Returns
-------
Notes
-----
This model should only be used for true 2D networks, i.e. with planar
symmetry.
| trapezoids_and_rectangles | python | PMEAL/OpenPNM | openpnm/models/geometry/hydraulic_size_factors/_funcs.py | https://github.com/PMEAL/OpenPNM/blob/master/openpnm/models/geometry/hydraulic_size_factors/_funcs.py | MIT |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.