Merge branch 'dev'

.travis.yml

@@ -1,5 +1,8 @@
 sudo: false
 
+os:
+  - linux
+
 language: python
 
 python:

appveyor.yml

@@ -0,0 +1,23 @@
+build: false
+
+environment:
+  matrix:
+    - PYTHON_VERSION: 3.6
+      MINICONDA: C:\Miniconda3
+
+init:
+  - "ECHO %PYTHON_VERSION% %MINICONDA%"
+
+install:
+  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - "conda create -q -n test-environment python=%PYTHON_VERSION% numpy==1.14"
+  - conda install --file conda_requirements.txt
+  - activate test-environment
+  - pip install -r test_requirements.txt
+  - python setup.py install
+
+test_script:
+  - python ./bin/test pep8 cov

bin/test

@@ -2,6 +2,8 @@
 
 import sys
 import pytest
+import numpy
+numpy.warnings.filterwarnings('ignore')
 
 args = ['-v']
 

example_script.py

@@ -1,6 +1,5 @@
 import openpnm as op
 ws = op.Workspace()
-ws.settings['loglevel'] = 40
 proj = ws.new_project()
 
 pn = op.network.Cubic(shape=[10, 10, 10], spacing=1e-4, project=proj)
@@ -36,7 +35,7 @@
                    prefactor='pore.A', exponent='pore.n',
                    regen_mode='deferred')
 rxn = op.algorithms.FickianDiffusion(network=pn)
-rxn.setup(phase=air)
+rxn.setup(phase=air, solver='spsolve')
 Ps = pn.find_nearby_pores(pores=50, r=5e-4, flatten=True)
 rxn.set_source(propname='pore.2nd_order_rxn', pores=Ps)
 rxn.set_value_BC(pores=pn.pores('top'), values=1)

openpnm/__init__.py

@@ -13,11 +13,60 @@
 **OpenPNM**
 
 OpenPNM is a package for performing pore network simulations of transport in
-porous materials
+porous materials.
+
+It consists of the following submodules:
+
++----------------+------------------------------------------------------------+
+| Submodule      | Contents and Description                                   |
++================+============================================================+
+| ``core``       | Houses the ``Base`` & ``Subdomain`` classes, & model       |
+|                | related mixins                                             |
++----------------+------------------------------------------------------------+
+| ``network``    | ``GenericNetwork`` class plus various network generators   |
++----------------+------------------------------------------------------------+
+| ``geometry``   | ``GenericGeometry`` class plus some subclasses containing a|
+|                | predefined set of pore-scale models                        |
++----------------+------------------------------------------------------------+
+| ``phases``     | ``GenericPhase`` class plus some subclasses containing     |
+|                | predefined models for common fluids like Water             |
++----------------+------------------------------------------------------------+
+| ``physics``    | ``GenericPhysics`` class plus some subclasses containing a |
+|                | predefined set of pore-scale models                        |
++----------------+------------------------------------------------------------+
+| ``algorithms`` | Algorithms for simulating transport and percolation        |
++----------------+------------------------------------------------------------+
+| ``materials``  | A collection of predefined projects consisting of a network|
+|                | with suitable topology and a geometry with necessary models|
++----------------+------------------------------------------------------------+
+| ``topotools``  | Tools for querying and manipulating network topology       |
++----------------+------------------------------------------------------------+
+| ``io``         | Import from and export to various common data formats      |
++----------------+------------------------------------------------------------+
+| ``utils``      | Helper utilites & classes, including ``Workspace`` and     |
+|                |  ``Project``                                               |
++----------------+------------------------------------------------------------+
+| ``models``     | Library of pore-scale models for calculating geometric,    |
+|                | thermodynamic, and physical properties                     |
++----------------+------------------------------------------------------------+
 
 """
+import os
+from pathlib import Path
+from git import Repo
+
+__version__ = '2.0.2'
 
-__version__ = '2.0.1'
+try:
+    path = Path(os.path.realpath(__file__), '../../').resolve()
+    repo = Repo(str(path))
+    if repo.active_branch.name != 'master':
+        commit_id = repo.active_branch.commit.hexsha[:6]
+        __commit__ = ''+str(commit_id)
+    else:
+        __commit__ = None
+except:
+    pass
 
 from . import utils
 from .utils import Workspace, Project

openpnm/algorithms/AdvectionDiffusion.py

@@ -71,19 +71,68 @@ def _build_A(self, force=False):
         Qij = -gh*np.diff(P[conns], axis=1).squeeze()
         Qij = np.append(Qij, -Qij)
 
+        Peij = Qij/gd
+        Peij[(Peij < 1e-10) & (Peij >= 0)] = 1e-10
+        Peij[(Peij > -1e-10) & (Peij <= 0)] = -1e-10
+        Qij = Peij*gd
+
         if force:
             self._pure_A = None
         if self._pure_A is None:
-            if (s_dis == 'upwind'):
+            if s_dis == 'upwind':
                 w = gd + np.maximum(0, -Qij)
                 A = network.create_adjacency_matrix(weights=w)
-            elif (s_dis == 'hybrid'):
+            elif s_dis == 'hybrid':
                 w = np.maximum(0, np.maximum(-Qij, gd-Qij/2))
                 A = network.create_adjacency_matrix(weights=w)
-            elif (s_dis == 'powerlaw'):
-                Peij = np.absolute(Qij/gd)
-                w = gd*np.maximum(0, (1-0.1*Peij)**5) + np.maximum(0, -Qij)
+            elif s_dis == 'powerlaw':
+                w = gd * np.maximum(0, (1 - 0.1*np.abs(Peij))**5) + \
+                    np.maximum(0, -Qij)
+                A = network.create_adjacency_matrix(weights=w)
+            elif s_dis == 'exponential':
+                w = -Qij / (1 - np.exp(Peij))
                 A = network.create_adjacency_matrix(weights=w)
+            else:
+                raise Exception('Unrecognized discretization scheme: ' + s_dis)
             A = laplacian(A)
             self._pure_A = A
         self.A = self._pure_A.copy()
+
+    def set_outflow_BC(self, pores, mode='merge'):
+        r"""
+        Adds outflow boundary condition to the selected pores.
+
+        Outflow condition simply means that the gradient of the solved
+        quantity does not change, i.e. is 0.
+
+        """
+        # Hijack the parse_mode function to verify mode/pores argument
+        mode = self._parse_mode(mode, allowed=['merge', 'overwrite', 'remove'],
+                                single=True)
+        pores = self._parse_indices(pores)
+        # Calculating A[i,i] values to ensure the outflow condition
+        network = self.project.network
+        phase = self.project.phases()[self.settings['phase']]
+        throats = network.find_neighbor_throats(pores=pores)
+        C12 = network['throat.conns'][throats]
+        P12 = phase[self.settings['pressure']][C12]
+        gh = phase[self.settings['hydraulic_conductance']][throats]
+        Q12 = -gh * np.diff(P12, axis=1).squeeze()
+        Qp = np.zeros(self.Np)
+        np.add.at(Qp, C12[:, 0], -Q12)
+        np.add.at(Qp, C12[:, 1], Q12)
+        # Store boundary values
+        if ('pore.bc_outflow' not in self.keys()) or (mode == 'overwrite'):
+            self['pore.bc_outflow'] = np.nan
+        self['pore.bc_outflow'][pores] = Qp[pores]
+
+    def _apply_BCs(self):
+        # Apply Dirichlet and rate BCs
+        ReactiveTransport._apply_BCs(self)
+        if 'pore.bc_outflow' not in self.keys():
+            return
+        # Apply outflow BC
+        diag = self.A.diagonal()
+        ind = np.isfinite(self['pore.bc_outflow'])
+        diag[ind] += self['pore.bc_outflow'][ind]
+        self.A.setdiag(diag)