openpnm 1.4.6__zip → 1.5__zip

OpenPNM-1.5/OpenPNM/Base/__Controller__.py

@@ -0,0 +1,10 @@
+"""
+###############################################################################
+Controller:  Overall controller class
+###############################################################################
+"""
+from OpenPNM.Base import Workspace
+
+
+class Controller(Workspace):
+    pass

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Base/__Core__.py

@@ -3,7 +3,7 @@
 Core:  Core Data Class
 ###############################################################################
 """
-from OpenPNM.Base import Controller
+from OpenPNM.Base import Workspace
 import string
 import random
 import scipy as sp
@@ -11,7 +11,7 @@ import scipy.constants
 from OpenPNM.Base import logging, Tools
 from OpenPNM.Base import ModelsDict
 logger = logging.getLogger()
-ctrl = Controller()
+mgr = Workspace()
 
 
 class Core(dict):
@@ -107,20 +107,20 @@ class Core(dict):
                 # TODO: This should probably raise the following exception
                 # raise Exception('Cannot write vector of the wrong length')
 
-    def _get_ctrl(self):
-        if self in ctrl.values():
-            return ctrl
+    def _get_mgr(self):
+        if self in mgr.values():
+            return mgr
         else:
             return {}
 
-    def _set_ctrl(self, ctrl):
-        if self not in ctrl.values():
-            ctrl.update({self.name: self})
+    def _set_mgr(self, mgr):
+        if self not in mgr.values():
+            mgr.update({self.name: self})
 
-    controller = property(fget=_get_ctrl, fset=_set_ctrl)
+    workspace = property(fget=_get_mgr, fset=_set_mgr)
 
     def _set_name(self, name):
-        if name in ctrl.keys():
+        if name in mgr.keys():
             raise Exception('An object named '+name+' already exists')
         elif name is None:
             name = ''.join(random.choice(string.ascii_uppercase +
@@ -130,7 +130,7 @@ class Core(dict):
         elif self._name is not None:
             logger.info('Changing the name of '+self.name+' to '+name)
             # Check if name collides with any arrays in the simulation
-            if ctrl._validate_name(name):
+            if mgr._validate_name(name):
                 # Rename any label arrays
                 for item in self._simulation():
                     if 'pore.'+self.name in item.keys():
@@ -140,11 +140,11 @@ class Core(dict):
             else:
                 raise Exception('The provided name is already in use')
         # Remove reference to object under old name, if present
-        for item in list(ctrl.items()):
+        for item in list(mgr.items()):
             if item[1] is self:
-                ctrl.pop(item[0])
-        # Add object to controller under new name
-        ctrl.update({name: self})
+                mgr.pop(item[0])
+        # Add object to workspace under new name
+        mgr.update({name: self})
         self._name = name
 
     def _get_name(self):
@@ -425,7 +425,7 @@ class Core(dict):
         Returns
         -------
         A list containing the dictionary keys on the object limited by the
-        specified \'mode\'.
+        specified ``mode``.
 
         Examples
         --------
@@ -1294,8 +1294,21 @@ class Core(dict):
                        return_mapping=return_mapping)
         return Ts
 
-    Tnet = property(fget=map_throats)
-    Pnet = property(fget=map_pores)
+    @property
+    def Tnet(self):
+        r"""
+        A shortcut to retrieve the mapping of the current object's throats onto
+        the network.
+        """
+        return self.map_throats()
+
+    @property
+    def Pnet(self):
+        r"""
+        A shortcut to retrieve the mapping of the current object's pores onto
+        the network.
+        """
+        return self.map_pores()
 
     def _parse_locations(self, locations):
         r"""
@@ -1424,7 +1437,7 @@ class Core(dict):
              if parsed_labels.count(L) > 1]
         return parsed_labels
 
-    def _parse_mode(self, mode, allowed=None, single=None):
+    def _parse_mode(self, mode, allowed=None, single=False):
         r"""
         This private method is for checking the \'mode\' used in the calling
         method.

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Base/__ModelsDict__.py

@@ -5,7 +5,7 @@ ModelsDict:  Abstract Class for Containing Models
 """
 import inspect
 from collections import OrderedDict
-from OpenPNM.Base import logging, Controller
+from OpenPNM.Base import logging, Workspace
 logger = logging.getLogger()
 
 
@@ -81,13 +81,13 @@ class ModelWrapper(dict):
         return self['model'](**kwargs)
 
     def _find_master(self):
-        ctrl = Controller()
+        mgr = Workspace()
         master = []
-        for item in list(ctrl.keys()):
-            if ctrl[item].models is not None:
-                for model in list(ctrl[item].models.keys()):
-                    if ctrl[item].models[model] is self:
-                        master.append(ctrl[item])
+        for item in list(mgr.keys()):
+            if mgr[item].models is not None:
+                for model in list(mgr[item].models.keys()):
+                    if mgr[item].models[model] is self:
+                        master.append(mgr[item])
         if len(master) > 1:
             raise Exception('More than one master found! This model dictionary '
                             'has been associated with multiple objects. To use '
@@ -360,11 +360,11 @@ class ModelsDict(OrderedDict):
             self.move_to_end(item)
 
     def _find_master(self):
-        ctrl = Controller()
+        mgr = Workspace()
         master = []
-        for item in list(ctrl.keys()):
-            if ctrl[item].models is self:
-                master.append(ctrl[item])
+        for item in list(mgr.keys()):
+            if mgr[item].models is self:
+                master.append(mgr[item])
         if len(master) > 1:
             raise Exception('More than one master found! This model dictionary '
                             'has been associated with multiple objects. To use the '

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Base/__Tools__.py

@@ -17,6 +17,10 @@ class PrintableList(list):
         lines.append(horizontal_rule)
         return '\n'.join(lines)
 
+    def __repr__(self):
+        self.sort()
+        return super().__repr__()
+
 
 class ObjectContainer(dict):
     r"""
@@ -98,7 +102,7 @@ class SetLocations():
     def add(obj, element, locations):
         net = obj._net
         element = obj._parse_element(element, single=True)
-        locations = obj._parse_locations(locations)
+        locations = net._parse_locations(locations)
 
         # Adapt the method depending on type of object received
         if obj._isa('Physics'):

OpenPNM-1.4.6/OpenPNM/Base/__Controller__.py → OpenPNM-1.5/OpenPNM/Base/__Workspace__.py

@@ -1,9 +1,9 @@
 """
 ###############################################################################
-Controller:  Overall controller class
+Workspace:  A class for managing the workspace of all objects
 ###############################################################################
 """
-import pickle as _pickle
+import dill as _pickle
 import copy as _copy
 import time
 import random
@@ -13,16 +13,16 @@ from OpenPNM.Base import logging
 logger = logging.getLogger()
 
 
-class Controller(dict):
+class Workspace(dict):
     # The following __instance__ class variable and subclassed __new__ method
-    # makes the Controller class a 'Singleton'.  This way, any instantiation
-    # of a controller object anywhere in the code will return the same object.
+    # makes the Workspace class a 'Singleton'.  This way, any instantiation
+    # of a workspace object anywhere in the code will return the same object.
     __instance__ = None
 
     def __new__(cls, *args, **kwargs):
-        if Controller.__instance__ is None:
-            Controller.__instance__ = dict.__new__(cls)
-        return Controller.__instance__
+        if Workspace.__instance__ is None:
+            Workspace.__instance__ = dict.__new__(cls)
+        return Workspace.__instance__
 
     def __init__(self):
         self.comments = 'Using OpenPNM ' + OpenPNM.__version__
@@ -48,7 +48,7 @@ class Controller(dict):
                 else:
                     lines.append(str.format('ERROR: ',
                                             geom.name,
-                                            'Object Not in Controller'))
+                                            'Object Not in Workspace'))
             for phase in net._phases:
                 if len(phase._phases) == 0:
                     str = '+ {0:<13} {1:<20} ({2})'
@@ -75,7 +75,7 @@ class Controller(dict):
                     else:
                         lines.append(str.format('ERROR: ',
                                                 phys.name,
-                                                'Object Not in Controller'))
+                                                'Object Not in Workspace'))
         return '\n'.join(lines)
 
     def _setloglevel(self, level):
@@ -149,7 +149,7 @@ class Controller(dict):
         Examples
         --------
         >>> import OpenPNM
-        >>> ctrl = OpenPNM.Base.Controller()
+        >>> mgr = OpenPNM.Base.Workspace()
         >>> pn = OpenPNM.Network.TestNet()
         >>> geom = OpenPNM.Geometry.GenericGeometry(network=pn,
         ...                                         pores=pn.Ps,
@@ -158,10 +158,10 @@ class Controller(dict):
         # Label entries are added to the Network where geom is defined
         >>> 'pore.'+geom.name in pn.keys()
         True
-        >>> ctrl.purge_object(geom)
+        >>> mgr.purge_object(geom)
 
-        # geom is removed from Controller object
-        >>> geom.name in ctrl.keys()
+        # geom is removed from Workspace object
+        >>> geom.name in mgr.keys()
         False
 
         # geom's labels are removed from the Network too
@@ -186,7 +186,7 @@ class Controller(dict):
                 self[item].geometries.pop(name, None)
                 self[item].physics.pop(name, None)
                 self[item].phases.pop(name, None)
-            # Remove object from Controller dict
+            # Remove object from Workspace dict
             self.pop(name, None)
 
     def ghost_object(self, obj):
@@ -210,14 +210,14 @@ class Controller(dict):
         Examples
         --------
         >>> import OpenPNM
-        >>> ctrl = OpenPNM.Base.Controller()
+        >>> mgr = OpenPNM.Base.Workspace()
         >>> pn = OpenPNM.Network.TestNet()
-        >>> pn2 = ctrl.ghost_object(pn)
+        >>> pn2 = mgr.ghost_object(pn)
         >>> pn is pn2  # A copy of pn is created
         False
         >>> pn2.keys() == pn.keys()  # They have otherwise identical data
         True
-        >>> pn2 in ctrl.values() # pn2 is not associated with existing Controller
+        >>> pn2 in mgr.values() # pn2 is not associated with existing Workspace
         False
 
         It can also be used to create ghosts of other object types:
@@ -225,7 +225,7 @@ class Controller(dict):
         >>> geom = OpenPNM.Geometry.TestGeometry(network=pn,
         ...                                      pores=pn.Ps,
         ...                                      throats=pn.Ts)
-        >>> geo2 = ctrl.ghost_object(geom)
+        >>> geo2 = mgr.ghost_object(geom)
         >>> geom is geo2
         False
 
@@ -234,11 +234,11 @@ class Controller(dict):
         True
 
         # But they are not the same object
-        >>> geo2 is ctrl[geo2.name]
+        >>> geo2 is mgr[geo2.name]
         False
 
-        # The ghost is not registered with the Controller
-        >>> geo2 in ctrl.values()
+        # The ghost is not registered with the Workspace
+        >>> geo2 in mgr.values()
         False
 
         # The following comparisons look at some 'behind the scenes' information
@@ -279,7 +279,7 @@ class Controller(dict):
     def load_simulation(self, filename):
         r"""
         Loads a Network simulation fromt the specified 'net' file and adds it
-        to the Controller
+        to the Workspace
 
         Parameters
         ----------
@@ -300,11 +300,11 @@ class Controller(dict):
                 raise Exception('An object with that name is already present')
         # If no exceptions, then transfer objects to self
         for item in temp_dict.values():
-            item.controller = self
+            item.workspace = self
 
     def save(self, filename=''):
         r"""
-        Save the entire state of the Controller to a 'pnm' file.
+        Save the entire state of the Workspace to a 'pnm' file.
 
         Parameters
         ----------
@@ -318,17 +318,17 @@ class Controller(dict):
         .. code-block:: python
 
             import OpenPNM
-            ctrl = OpenPNM.Base.Controller()
-            ctrl.clear()  # Ensure no previous objects are present
+            mgr = OpenPNM.Base.Workspace()
+            mgr.clear()  # Ensure no previous objects are present
             pn = OpenPNM.Network.TestNet()
-            ctrl.save('test.pnm')
-            pn.name in ctrl.keys()
+            mgr.save('test.pnm')
+            pn.name in mgr.keys()
             #=> True
-            ctrl.clear()
-            ctrl.keys()
+            mgr.clear()
+            mgr.keys()
             dict_keys([])
-            ctrl.load('test.pnm')
-            pn.name in ctrl.keys()
+            mgr.load('test.pnm')
+            pn.name in mgr.keys()
             #=> True
 
         """
@@ -344,25 +344,36 @@ class Controller(dict):
 
     def load(self, filename):
         r"""
-        Load an entire Controller from a 'pnm' file.
+        Load an entire Workspace from a 'pnm' file.
 
         Parameters
         ----------
         filename : string
-            The file name of the Controller to load.
+            The file name of the Workspace to load.
 
         Notes
         -----
-        This calls the ``clear`` method of the Controller object, so it will
+        This calls the ``clear`` method of the Workspace object, so it will
         remove all existing objects in the current workspace.
         """
         filename = filename.rsplit('.pnm', 1)[0]
         if self != {}:
-            logger.warn('Loading data onto non-empty controller object,' +
+            logger.warn('Loading data onto non-empty workspace object,' +
                         ' existing data will be lost')
             self.clear()
 
         self = _pickle.load(open(filename+'.pnm', 'rb'))
+        for item in self._comments.values():
+            if 'Using OpenPNM' in item:
+                version = item.lstrip('Using OpenPNM ')
+                if version < OpenPNM.__version__:
+                    logger.warning('File was created with an earlier version ' +
+                                   'OpenPNM: \n' +
+                                   '--> File saved with version: ' +
+                                   str(version) +
+                                   '\n' +
+                                   '--> Current version: ' +
+                                   str(OpenPNM.__version__))
 
     def export(self, network=None, filename='', fileformat='VTK'):
         logger.warning("This method is deprecated, use \'export_data\'.")
@@ -379,7 +390,7 @@ class Controller(dict):
         network : OpenPNM Network Object
             This Network and all of its phases will be written to the specified
             file.  If no Network is given it will check to ensure that only one
-            Network exists on the Controller and use that.  If there is more
+            Network exists on the Workspace and use that.  If there is more
             than one Network an error is thrown.
         filename : string, optional
             The file name to save as.  If no name is given then the name of
@@ -487,7 +498,7 @@ class Controller(dict):
         r"""
         Accepts a Network object and creates a complete clone including all
         associated objects.  All objects in the cloned simulation are
-        registered with the Controller object and are fully functional.
+        registered with the Workspace object and are fully functional.
 
         Parameters
         ----------
@@ -517,9 +528,9 @@ class Controller(dict):
         Examples
         --------
         >>> import OpenPNM
-        >>> ctrl = OpenPNM.Base.Controller()
+        >>> mgr = OpenPNM.Base.Workspace()
         >>> pn = OpenPNM.Network.TestNet()
-        >>> pn2 = ctrl.clone_simulation(pn, name='cloned')
+        >>> pn2 = mgr.clone_simulation(pn, name='cloned')
         >>> pn2 is pn
         False
         """

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Base/__init__.py

@@ -3,7 +3,7 @@ r"""
 :mod:`OpenPNM.Base` -- Abstract Base Class, and Core Data Class
 ###############################################################################
 
-.. autoclass:: OpenPNM.Base.Controller
+.. autoclass:: OpenPNM.Base.Workspace
    :members:
    :undoc-members:
    :show-inheritance:
@@ -20,11 +20,13 @@ r"""
 
 """
 import logging as logging
+from .__Workspace__ import Workspace
 from .__Controller__ import Controller
 from .__ModelsDict__ import ModelsDict
 from . import __Tools__ as Tools
 from .__Core__ import Core
 
+
 # Set up logging to file - see previous section for more details
 log_format = \
     '%(asctime)s | %(levelname)-8s | %(name)s.%(funcName)s | %(message)s'

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Geometry/__Boundary__.py

@@ -47,10 +47,11 @@ class Boundary(GenericGeometry):
                         pore_prop='pore.diameter',
                         mode='max')
         self['pore.volume'] = 0.0
+        self['pore.seed'] = 1.0
+        self['throat.seed'] = 1.0
         self['throat.volume'] = 0.0
         self.models.add(propname='throat.length',
                         model=gm.throat_length.straight)
-        self['pore.area'] = 1.0
         if shape == 'spheres':
             self.models.add(propname='throat.area',
                             model=gm.throat_area.cylinder)

{OpenPNM-1.4.6 → OpenPNM-1.5}/OpenPNM/Geometry/__GenericGeometry__.py

@@ -57,7 +57,7 @@ class GenericGeometry(Core):
         try:
             self.set_locations(pores=pores, throats=throats)
         except:
-            self.controller.purge_object(self)
+            self.workspace.purge_object(self)
             raise Exception('Provided locations are in use, instantiation cancelled')
 
     def __getitem__(self, key):