Merge pull request #6 from MikeHeiber/development

Code Cleanup, Documentation, and Testing Update
- updated README with more information about installing and using Ising_OPV and details about the morphology analysis data that is generated
- performed major reorganization of the code and streamlined the API
- updated how users import morphology files or tomogram data so that all options are in the parameter file and not passed as command line arguments
- added Parameters class to handle importing parameters from the parameter file and checking the validity of the parameters
- added Version class to keep track of the current version and compare parameter files and morphology files from different versions
- updated format of output for many of the morphology analysis files to be more consistent
- added API documentation for all public functions and class members
- added tests for all functional features and many cases of users attempting to use invalid parameters or input data
- updated format of the parameter file
- corrected bugs in the calculation of histograms for the morphology analysis
- added and implemented new utility MPI functions to make it easier to gather result values from each processor
- simplified tomogram analysis options and now allow users to specify the mixed phase volume fraction
- updated treatment of imported morphologies; when importing morphologies and then modifying them, the final morphologies will overwrite the morphologies in the current working directory

Author: MikeHeiber

.travis.yml

@@ -13,7 +13,7 @@ compiler:
     - gcc
 
 env:
-    - OPTIONS="GCC_VERSION=5 && MPI=openmpi && TARGET=test_coverage"
+    - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_coverage"
     - OPTIONS="GCC_VERSION=4.7 && MPI=mpich2 && TARGET=test"
     - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test"
     - OPTIONS="GCC_VERSION=4.8 && MPI=mpich2 && TARGET=test"
@@ -42,9 +42,6 @@ before_install:
     - if [[ "$TARGET" = test_coverage ]]; then pip install --user cpp-coveralls; fi
 
 script:
-    - make -j10 $TARGET
-    - cd test
-    - travis_wait ./Ising_OPV_tests.exe
-    - cd ..
+    - make -j10 $TARGET && travis_wait ./test/Ising_OPV_tests.exe && travis_wait mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe
     - if [[ "$TARGET" = test_coverage ]]; then coveralls --include src --exclude "googletest/*" --gcov-options '\-lp'; fi
     - if [[ "$TARGET" = test ]]; then make -j10 && mpiexec -n 4 ./Ising_OPV.exe parameters_default.txt; fi

README.md

@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Ising_OPV
-   &#160;<span id="projectnumber">v4.0-beta.1</span>
+   &#160;<span id="projectnumber">v4.0-beta.2</span>
    </div>
    <div id="projectbrief">Generates and analyzes model bulk heterojunction morphologies in a parallel computing environment</div>
   </td>
@@ -87,12 +87,20 @@
 </div>
 
 <div class="header">
+  <div class="summary">
+<a href="#namespaces">Namespaces</a>  </div>
   <div class="headertitle">
 <div class="title">Lattice.cpp File Reference</div>  </div>
 </div><!--header-->
 <div class="contents">
 <div class="textblock"><code>#include &quot;<a class="el" href="_lattice_8h_source.html">Lattice.h</a>&quot;</code><br />
-</div></div><!-- contents -->
+</div><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
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@@ -30,7 +30,7 @@
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+<code>#include &lt;ctime&gt;</code><br />
 <code>#include &lt;functional&gt;</code><br />
+<code>#include &lt;stdexcept&gt;</code><br />
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@@ -30,7 +30,7 @@
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+   &#160;<span id="projectnumber">v4.0-beta.2</span>
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    <div id="projectbrief">Generates and analyzes model bulk heterojunction morphologies in a parallel computing environment</div>
   </td>
@@ -87,12 +87,20 @@
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+  <div class="summary">
+<a href="#namespaces">Namespaces</a>  </div>
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-</div></div><!-- contents -->
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+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
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 <div class="contents">
 <div class="textblock"><code>#include &quot;<a class="el" href="_lattice_8h_source.html">Lattice.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="_parameters_8h_source.html">Parameters.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="_utils_8h_source.html">Utils.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="_version_8h_source.html">Version.h</a>&quot;</code><br />
 <code>#include &quot;tinyxml2/tinyxml2.h&quot;</code><br />
 <code>#include &lt;algorithm&gt;</code><br />
+<code>#include &lt;array&gt;</code><br />
+<code>#include &lt;cstdio&gt;</code><br />
 <code>#include &lt;ctime&gt;</code><br />
 <code>#include &lt;fstream&gt;</code><br />
 <code>#include &lt;functional&gt;</code><br />
 <code>#include &lt;numeric&gt;</code><br />
 <code>#include &lt;sstream&gt;</code><br />
+<code>#include &lt;stdexcept&gt;</code><br />
 </div>
 <p><a href="_morphology_8h_source.html">Go to the source code of this file.</a></p>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">This class contains a lattice representation of a materials blend with the ability to simulate phase separation and perform a variety of structural analyses.  <a href="class_ising___o_p_v_1_1_morphology.html#details">More...</a><br /></td></tr>
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