openpnm 1.0.0__zip

OpenPNM-1.1/OpenPNM/Geometry/__GenericGeometry__.py

@@ -0,0 +1,106 @@
+# -*- coding: utf-8 -*-
+"""
+===============================================================================
+GenericGeometry -- Base class to manage pore scale geometry
+===============================================================================
+
+"""
+
+import scipy as sp
+from OpenPNM.Base import Core
+from OpenPNM.Base import logging
+from OpenPNM.Network import GenericNetwork
+logger = logging.getLogger(__name__)
+import OpenPNM.Geometry.models
+
+class GenericGeometry(Core):
+    r"""
+    GenericGeometry - Base class to construct a Geometry object
+
+    Parameters
+    ----------
+    network : OpenPNM Network Object
+
+    pores and/or throats : array_like
+        The list of pores and throats where this physics applies. If either are
+        left blank this will apply the physics nowhere.  The locations can be
+        change after instantiation using ``set_locations()``.
+
+    name : string
+        A unique name to apply to the object.  This name will also be used as a
+        label to identify where this this geometry applies.
+
+    Examples
+    --------
+    >>> pn = OpenPNM.Network.TestNet()
+    >>> Ps = pn.pores()  # Get all pores
+    >>> Ts = pn.throats()  # Get all throats
+    >>> geom = OpenPNM.Geometry.GenericGeometry(network=pn,pores=Ps,throats=Ts)
+    """
+
+    def __init__(self,network=None,pores=[],throats=[],seed=None,**kwargs):
+        r"""
+        Initialize
+        """
+        super(GenericGeometry,self).__init__(**kwargs)
+        logger.name = self.name
+
+        if network is None:
+            self._net = GenericNetwork()
+        else:
+            self._net = network  # Attach network to self
+            self._net._geometries.append(self)  # Register self with network.geometries
+
+        #Initialize a label dictionary in the associated network
+        self._net['pore.'+self.name] = False
+        self._net['throat.'+self.name] = False
+        self.set_locations(pores=pores,throats=throats)
+        self._seed = seed
+
+    def __getitem__(self,key):
+        element = key.split('.')[0]
+        # Convert self.name into 'all'
+        if key.split('.')[-1] == self.name:
+            key = element + '.all'
+
+        if key in self.keys():  # Look for data on self...
+            return super(GenericGeometry,self).__getitem__(key)
+        if key == 'throat.conns':  # Handle specifically
+            [P1,P2] = self._net['throat.conns'][self._net[element+'.'+self.name]].T
+            Pmap = sp.zeros((self._net.Np,),dtype=int)-1
+            Pmap[self._net.pores(self.name)] = self.Ps
+            conns = sp.array([Pmap[P1],Pmap[P2]]).T
+            # Replace -1's with nans
+            if sp.any(conns==-1):
+                conns = sp.array(conns,dtype=object)
+                conns[sp.where(conns==-1)] = sp.nan
+            return conns
+        else:  # ...Then check Network
+            return self._net[key][self._net[element+'.'+self.name]]
+
+    def set_locations(self,pores=[],throats=[],mode='add'):
+        r'''
+        Set the pore and throat locations of the Geometry object
+
+        Parameters
+        ----------
+        pores and throats : array_like
+            The list of pores and/or throats in the Network where the object 
+            should be applied
+        mode : string
+            Indicates whether list of pores or throats is to be added or removed
+            from the object.  Options are 'add' (default) or 'remove'.
+
+        '''
+        if len(pores) > 0:
+            pores = sp.array(pores,ndmin=1)
+            self._set_locations(element='pore',locations=pores,mode=mode)
+        if len(throats) > 0:
+            throats = sp.array(throats,ndmin=1)
+            self._set_locations(element='throat',locations=throats,mode=mode)
+
+if __name__ == '__main__':
+    #Run doc tests
+    import doctest
+    doctest.testmod(verbose=True)
+

OpenPNM-1.1/OpenPNM/Geometry/__SGL10__.py

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+"""
+===============================================================================
+SGL10 -- A geometry model for SGL10 type Gas Diffusion Layers
+===============================================================================
+
+"""
+
+from OpenPNM.Geometry import models as gm
+from OpenPNM.Geometry import GenericGeometry
+
+class SGL10(GenericGeometry):
+    r"""
+    SGL10 subclass of GenericGeometry.
+
+    """
+
+    def __init__(self, **kwargs):
+        r"""
+        Initialize
+        """
+        super(SGL10,self).__init__(**kwargs)
+        self._generate()
+
+    def _generate(self):
+        r'''
+        '''
+        self.models.add(propname='pore.seed',
+                        model=gm.pore_misc.random,
+                        num_range=[0,0.8834],
+                        seed=self._seed,
+                        regen_mode='constant')
+        self.models.add(propname='throat.seed',
+                        model=gm.throat_misc.neighbor,
+                        pore_prop='pore.seed',
+                        mode='min')
+        self.models.add(propname='pore.diameter',
+                        model=gm.pore_diameter.sphere,
+                        psd_name='weibull_min',
+                        psd_shape=3.07,
+                        psd_loc=1.97e-6,
+                        psd_scale=1.6e-5,
+                        psd_offset=18e-6)
+        self.models.add(propname='pore.area',
+                        model=gm.pore_area.spherical)
+        self.models.add(propname='pore.volume',
+                        model=gm.pore_volume.sphere)
+        self.models.add(propname='throat.diameter',
+                        model=gm.throat_diameter.cylinder,
+                        tsd_name='weibull_min',
+                        tsd_shape=3.07,
+                        tsd_loc=1.97e-6,
+                        tsd_scale=1.6e-5,
+                        tsd_offset=18e-6)
+        self.models.add(propname='throat.length',
+                        model=gm.throat_length.straight)
+        self.models.add(propname='throat.volume',
+                        model=gm.throat_volume.cylinder)
+        self.models.add(propname='throat.area',
+                        model=gm.throat_area.cylinder)
+        self.models.add(propname='throat.surface_area',
+                        model=gm.throat_surface_area.cylinder)
+
+
+if __name__ == '__main__':
+    pn = OpenPNM.Network.TestNet()
+    pass

OpenPNM-1.1/OpenPNM/Geometry/__Stick_and_Ball__.py

@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+"""
+===============================================================================
+Stick_and_Ball -- A standard 'stick & ball' geometrical model
+===============================================================================
+
+"""
+
+from OpenPNM.Geometry import models as gm
+from OpenPNM.Geometry import GenericGeometry
+
+class Stick_and_Ball(GenericGeometry):
+    r"""
+    Stick and Ball subclass of GenericGeometry.  This subclass is meant as a
+    basic default geometry to get started quickly.
+
+    Parameters
+    ----------
+    name : string
+        The name of the object, which is also used as the label where this
+        geometry is defined.
+
+    """
+
+    def __init__(self, **kwargs):
+        r"""
+        Initialize
+        """
+        super(Stick_and_Ball,self).__init__(**kwargs)
+        self._generate()
+
+    def _generate(self):
+        self.models.add(propname='pore.seed',
+                        model=gm.pore_misc.random,
+                        regen_mode='constant',
+                        seed=self._seed)
+        self.models.add(propname='throat.seed',
+                        model=gm.throat_misc.neighbor,
+                        mode='min')
+        self.models.add(propname='pore.diameter',
+                        model=gm.pore_diameter.sphere,
+                        psd_name='weibull_min',
+                        psd_shape=2.5,
+                        psd_loc=0,
+                        psd_scale=0.5)
+        self.models.add(propname='pore.area',
+                        model=gm.pore_area.spherical)
+        self.models.add(propname='pore.volume',
+                        model=gm.pore_volume.sphere)
+        self.models.add(propname='throat.diameter',
+                        model=gm.throat_diameter.cylinder,
+                        tsd_name='weibull_min',
+                        tsd_shape=2.5,
+                        tsd_loc=0,
+                        tsd_scale=0.5)
+        self.models.add(propname='throat.length',
+                        model=gm.throat_length.straight)
+        self.models.add(propname='throat.volume',
+                        model=gm.throat_volume.cylinder)
+        self.models.add(propname='throat.area',
+                        model=gm.throat_area.cylinder)
+        self.models.add(propname='throat.surface_area',
+                        model=gm.throat_surface_area.cylinder)
+
+if __name__ == '__main__':
+    #Run doc tests
+    import doctest
+    doctest.testmod(verbose=True)

OpenPNM-1.1/OpenPNM/Geometry/__TestGeometry__.py

@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+"""
+===============================================================================
+TestGeometry -- A Geomery for Toray TGPH090 gas diffusion layers
+===============================================================================
+
+"""
+
+import scipy as _sp
+from OpenPNM.Geometry import models as gm
+from OpenPNM.Geometry import GenericGeometry
+
+class TestGeometry(GenericGeometry):
+    r"""
+    Toray090 subclass of GenericGeometry
+
+    """
+
+    def __init__(self, **kwargs):
+        r"""
+        Initialize
+        """
+        super(TestGeometry,self).__init__(**kwargs)
+        self._generate()
+
+    def _generate(self):
+        r'''
+        '''
+        self.models.add(propname='pore.seed',
+                        model=gm.pore_misc.random,
+                        regen_mode='constant',
+                        seed=1)
+        self.models.add(propname='throat.seed',
+                        model=gm.throat_misc.neighbor,
+                        pore_prop='pore.seed',
+                        mode='min')
+        self['pore.diameter'] = self['pore.seed']
+        self['throat.diameter'] = self['throat.seed']
+        self['pore.volume']=_sp.pi/6*self['pore.diameter']**3
+        self['pore.area']=_sp.constants.pi/4*self['pore.diameter']**2
+
+        self.models.add(propname='throat.length',
+                        model=gm.throat_length.straight)
+        self['throat.volume'] = _sp.pi/4*self['throat.length']*self['throat.diameter']**2
+        self['throat.area'] = _sp.constants.pi/4*(self['throat.diameter'])**2
+        self['throat.surface_area'] = _sp.constants.pi/(self['throat.diameter'])*self['throat.length']
+
+if __name__ == '__main__':
+    import OpenPNM
+    pn = OpenPNM.Network.TestNet()
+    pass

OpenPNM-1.1/OpenPNM/Geometry/__Toray090__.py

@@ -0,0 +1,68 @@
+"""
+module __Toray090__: Subclass of GenericGeometry for a standard Toray TGPH090
+gas diffusion layer.s
+===============================================================================
+
+.. warning:: The classes of this module should be loaded through the 'Geometry.__init__.py' file.
+
+"""
+
+from OpenPNM.Geometry import models as gm
+from OpenPNM.Geometry import GenericGeometry
+
+class Toray090(GenericGeometry):
+    r"""
+    Toray090 subclass of GenericGeometry
+
+    """
+
+    def __init__(self, **kwargs):
+        r"""
+        Initialize
+        """
+        super(Toray090,self).__init__(**kwargs)
+        self._generate()
+
+    def _generate(self):
+        r'''
+        '''
+        self.models.add(propname='pore.seed',
+                        model=gm.pore_misc.random,
+                        num_range=[0,0.95],
+                        seed=self._seed,
+                        regen_mode='constant')
+        self.models.add(propname='throat.seed',
+                        model=gm.throat_misc.neighbor,
+                        pore_prop='pore.seed',
+                        mode='min')
+        self.models.add(propname='pore.diameter',
+                        model=gm.pore_diameter.sphere,
+                        psd_name='weibull_min',
+                        psd_shape=2.77,
+                        psd_loc=6.9e-7,
+                        psd_scale=9.8e-6,
+                        psd_offset=10e-6)
+        self.models.add(propname='pore.area',
+                        model=gm.pore_area.spherical)
+        self.models.add(propname='pore.volume',
+                        model=gm.pore_volume.sphere)
+        self.models.add(propname='throat.diameter',
+                        model=gm.throat_diameter.cylinder,
+                        tsd_name='weibull_min',
+                        tsd_shape=2.77,
+                        tsd_loc=6.9e-7,
+                        tsd_scale=9.8e-6,
+                        tsd_offset=10e-6)
+        self.models.add(propname='throat.length',
+                        model=gm.throat_length.straight)
+        self.models.add(propname='throat.volume',
+                        model=gm.throat_volume.cylinder)
+        self.models.add(propname='throat.area',
+                        model=gm.throat_area.cylinder)
+        self.models.add(propname='throat.surface_area',
+                        model=gm.throat_surface_area.cylinder)
+
+if __name__ == '__main__':
+    import OpenPNM
+    pn = OpenPNM.Network.TestNet()
+    pass

OpenPNM-1.1/OpenPNM/Geometry/__Voronoi__.py

@@ -0,0 +1,98 @@
+# -*- coding: utf-8 -*-
+"""
+===============================================================================
+Voronoi --Subclass of GenericGeometry for a standard Geometry created from a
+Voronoi Diagram Used with Delaunay Network but could work for others (not tested)
+===============================================================================
+
+
+"""
+
+import scipy as sp
+from OpenPNM.Geometry import models as gm
+from OpenPNM.Geometry import GenericGeometry
+
+class Voronoi(GenericGeometry):
+    r"""
+    Voronoi subclass of GenericGeometry.
+
+    Parameters
+    ----------
+
+
+    """
+
+    def __init__(self, fibre_rad = 3e-06, load_gen='gen', **kwargs):
+        r"""
+        Initialize
+        """
+        if int(sp.__version__.split('.')[1]) < 13:
+            raise Exception('The installed version of Scipy is too old, Voronoi cannot run')
+        super(Voronoi,self).__init__(**kwargs)
+        if load_gen == 'gen':
+            self._generate(fibre_rad)
+        
+
+    def _generate(self,fibre_rad):
+        r'''
+        '''
+
+        self.models.add(propname='pore.vertices',
+                        model=gm.pore_vertices.voronoi)
+        self.models.add(propname='throat.vertices',
+                        model=gm.throat_vertices.voronoi)
+        self.models.add(propname='throat.normal',
+                        model=gm.throat_normal.voronoi)
+        self.models.add(propname='throat.offset_vertices',
+                        model=gm.throat_offset_vertices.distance_transform,
+                        offset=fibre_rad,
+                        set_dependent = True)
+        "Remove throats that are fully occluded and pores with no connections"
+        self._net.trim_occluded_throats()
+        
+        self.models.add(propname='pore.seed',
+                        model=gm.pore_misc.random,
+                        seed=self._seed)
+        self.models.add(propname='throat.seed',
+                        model=gm.throat_misc.neighbor,
+                        pore_prop='pore.seed',
+                        mode='min')
+        self.models.add(propname='pore.volume',
+                        model=gm.pore_volume.voronoi)
+        self.models.add(propname='pore.diameter',
+                        model=gm.pore_diameter.voronoi)
+        self.models.add(propname='pore.area',
+                        model=gm.pore_area.spherical)          
+        self.models.add(propname='throat.diameter',
+                        model=gm.throat_diameter.voronoi)
+        self.models.add(propname='throat.length',
+                        model=gm.throat_length.constant,
+                        const=fibre_rad*2)
+        self.models.add(propname='throat.volume',
+                        model=gm.throat_volume.extrusion)
+        self.models.add(propname='throat.surface_area',
+                        model=gm.throat_surface_area.extrusion)
+                       
+        "Old Methods Replaced by Distance Transform"
+        #self.add_model(propname='throat.area',
+        #               model=gm.throat_area.voronoi)
+        #self.add_model(propname='throat.perimeter',
+        #               model=gm.throat_perimeter.voronoi)
+        #self.add_model(propname='throat.centroid',
+        #               model=gm.throat_centroid.centre_of_mass)
+        #self.add_model(propname='pore.centroid',
+        #               model=gm.pore_centroid.centre_of_mass)
+        #self.add_model(propname='pore.indiameter',
+        #               model=gm.pore_diameter.insphere)
+        #self.add_model(propname='throat.indiameter',
+        #               model=gm.throat_diameter.incircle) 
+        "Shift the pore coords to the centroids"
+        #vo.pore2centroid(self._net)
+    
+if __name__ == '__main__':
+    import OpenPNM
+    pn = OpenPNM.Network.Delaunay(name='test_net')
+    pn.generate(num_pores=100, domain_size=[0.0001,0.0001,0.0001])
+    pn.add_boundaries()
+    test = OpenPNM.Geometry.Voronoi(pores=pn.Ps,throats=pn.Ts,network=pn)
+    pn.regenerate_geometries()

OpenPNM-1.1/OpenPNM/Geometry/__init__.py

@@ -0,0 +1,47 @@
+r"""
+###############################################################################
+:mod:`OpenPNM.Geometry`: Classes related to the creation of pore-scale geometry
+###############################################################################
+
+Contents
+--------
+GenericGeometry: The init statement performs the important tasks of registering
+itself with the network and creating data dictionaries of the necessary size
+
+Subclasses: These can be custom made by users to represent specfic geometries.
+It is necessary for their init's to call the init of the GenericGeometry class
+in order to be properly instantiated.  OpenPNM comes with a few basic 
+pre-written materials.  New classes added to this directory will be 
+automatically imported and available.
+
+Classes
+-------
+
+.. autoclass:: GenericGeometry
+   :members:
+
+.. autoclass:: Stick_and_Ball
+   :members:
+
+.. autoclass:: Cube_and_Cuboid
+   :members:
+   
+.. autoclass:: Boundary
+   :members:
+   
+.. autoclass:: Voronoi
+   :members:
+   
+"""
+
+from .__GenericGeometry__ import GenericGeometry
+from .__Cube_and_Cuboid__ import Cube_and_Cuboid
+from .__Stick_and_Ball__ import Stick_and_Ball
+from .__TestGeometry__ import TestGeometry
+from .__Boundary__ import Boundary
+from .__Voronoi__ import Voronoi
+from .__Toray090__ import Toray090
+from .__SGL10__ import SGL10
+from . import models
+
+        

OpenPNM-1.1/OpenPNM/Geometry/models/__init__.py

@@ -0,0 +1,33 @@
+r"""
+*******************************************************************************
+models -- Classes for calculating pore-scale properties
+*******************************************************************************
+
+Contents
+--------
+Contains Models for applying pore and throat geometry
+
+"""
+
+from . import pore_area
+from . import pore_centroid
+from . import pore_diameter
+from . import pore_misc
+from . import pore_seed
+from . import pore_volume
+from . import pore_surface_area
+from . import pore_vertices
+from . import throat_vertices
+from . import throat_normal
+from . import throat_offset_vertices
+from . import throat_area
+from . import throat_centroid
+from . import throat_diameter
+from . import throat_length
+from . import throat_misc
+from . import throat_perimeter
+from . import throat_seed
+from . import throat_surface_area
+from . import throat_vector
+from . import throat_volume
+from . import throat_shape_factor

OpenPNM-1.1/OpenPNM/Geometry/models/pore_area.py

@@ -0,0 +1,27 @@
+r"""
+===============================================================================
+pore_area -- Models for cross-sectional area of a pore body
+===============================================================================
+
+"""
+import scipy as _sp
+
+def spherical(geometry,
+              pore_diameter='pore.diameter',
+              **kwargs):
+    r"""
+    Calculate cross-sectional area for a spherical pore
+    """
+    diams = geometry[pore_diameter]
+    value = _sp.constants.pi/4*(diams)**2
+    return value
+
+def cubic(geometry,
+          pore_diameter='pore.diameter',
+          **kwargs):
+    r"""
+    Calculate cross-sectional pore area for a cubic pore
+    """
+    diams = geometry[pore_diameter]
+    value = (diams)**2
+    return value

OpenPNM-1.1/OpenPNM/Geometry/models/pore_centroid.py

@@ -0,0 +1,35 @@
+r"""
+===============================================================================
+pore_centroid -- N.B Neither method is accurate but is quicker than that implemented in pore.volume
+===============================================================================
+
+"""
+import scipy as _sp
+
+
+def voronoi(geometry,
+            pore_vertices='pore.vertices',
+            **kwargs):
+    r"""
+    Calculate the centroid of the pore from the voronoi vertices - C.O.M
+    """
+    verts = geometry[pore_vertices]
+    value = _sp.ndarray([len(verts),3])
+    for i,vert in enumerate(verts):
+        value[i] = _sp.array([vert[:,0].mean(),vert[:,1].mean(),vert[:,2].mean()])
+    return value
+
+def voronoi2(geometry,
+             vertices='throat.centroid',
+             **kwargs):
+    r"""
+    Calculate the centroid from the mean of the throat centroids
+    """
+    value = _sp.ndarray([geometry.num_pores(),3])
+    pore_map = geometry.map_pores(geometry.pores(),geometry._net)
+    for geom_pore,net_pore in pore_map:
+        net_throats = geometry._net.find_neighbor_throats(net_pore)
+        geom_throats = geometry._net.map_throats(net_throats,geometry)[:,1]
+        verts = geometry[vertices][geom_throats]
+        value[geom_pore]=_sp.array([verts[:,0].mean(),verts[:,1].mean(),verts[:,2].mean()])
+    return value