Merge pull request #7 from MikeHeiber/development

Everything look good!

.travis.yml

@@ -14,6 +14,8 @@ compiler:
 
 env:
     - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_coverage"
+    - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_default"
+    - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_example1"
     - 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"
@@ -41,7 +43,10 @@ before_install:
     - if [[ "$MPI" = openmpi ]]; then sudo apt-get -y install -qq openmpi-bin libopenmpi-dev; fi
     - if [[ "$TARGET" = test_coverage ]]; then pip install --user cpp-coveralls; fi
 
-script:
-    - make -j10 $TARGET && travis_wait ./test/Ising_OPV_tests.exe && travis_wait mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe
+script: 
+    - if [[ "$TARGET" = test ]]; then make -j10 test && travis_wait ./test/Ising_OPV_tests.exe && travis_wait mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe; fi
+    - if [[ "$TARGET" = test_default ]]; then make -j10 && travis_wait mpiexec -n 4 ./Ising_OPV.exe parameters_default.txt; fi
+    - if [[ "$TARGET" = test_example1 ]]; then make -j10 && travis_wait mpiexec -n 4 ./Ising_OPV.exe ./examples/example1/parameters_ex1.txt; fi
+    - if [[ "$TARGET" = test_coverage ]]; then make -j10 test_coverage && travis_wait ./test/Ising_OPV_tests.exe && travis_wait mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe; fi
     - if [[ "$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
+

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = Ising_OPV
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.0-beta.1
+PROJECT_NUMBER         = v4.0.0-rc.2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -2203,7 +2203,7 @@ PERL_PATH              = /usr/bin/perl
 # powerful graphs.
 # The default value is: YES.
 
-CLASS_DIAGRAMS         = YES
+CLASS_DIAGRAMS         = NO
 
 # You can define message sequence charts within doxygen comments using the \msc
 # command. Doxygen will then run the mscgen tool (see:
@@ -2412,7 +2412,7 @@ INTERACTIVE_SVG        = NO
 # found. If left blank, it is assumed the dot tool can be found in the path.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_PATH               = 
+DOT_PATH               = "C:/Program Files (x86)/Graphviz2.38/bin"
 
 # The DOTFILE_DIRS tag can be used to specify one or more directories that
 # contain dot files that are included in the documentation (see the \dotfile

README.md

@@ -14,6 +14,8 @@ Generated or imported morphologies are then rigorously analyzed to determine imp
 - Create morphology sets from imported experimental three-dimensional tomograms
 - Calculate detailed structural analysis of the morphology set
 
+<img src="./papers/v4_paper/tomogram_analysis.png" alt="Tomography data import and analysis workflow" width="650">
+
 ## Current Status
 
 Latest release:  [![GitHub (pre-)release](https://img.shields.io/github/release/MikeHeiber/Ising_OPV/all.svg?style=flat-square)](https://github.com/MikeHeiber/Ising_OPV/releases)
@@ -35,8 +37,8 @@ Code is being tested using [googletest](https://github.com/google/googletest) wi
 
 | Branch | Status |
 | :------: | ------ |
-| Master | [![Coveralls github branch](https://img.shields.io/coveralls/github/MikeHeiber/Ising_OPV/master.svg?style=for-the-badge)](https://coveralls.io/github/MikeHeiber/Ising_OPV?branch=master) |
-| Development | [![Coveralls github branch](https://img.shields.io/coveralls/github/MikeHeiber/Ising_OPV/development.svg?style=for-the-badge)](https://coveralls.io/github/MikeHeiber/Ising_OPV?branch=development) |
+| Master | [![Coveralls Github branch](https://img.shields.io/coveralls/github/MikeHeiber/Ising_OPV/master.svg?style=for-the-badge)](https://coveralls.io/github/MikeHeiber/Ising_OPV?branch=master) |
+| Development | [![Coveralls Github branch](https://img.shields.io/coveralls/github/MikeHeiber/Ising_OPV/development.svg?style=for-the-badge)](https://coveralls.io/github/MikeHeiber/Ising_OPV?branch=development) |
 
 ## Contact
 
@@ -81,7 +83,7 @@ Similar batch scripts can also be written for TORQUE or other job schedulers.
 
 Regardless of the job scheduler, the program execution command is essentially the same. 
 Ising_OPV.exe takes one required input argument, which is the filename of the input parameter file. 
-An annotated example parameter file is provided with this package (parameters_default.txt).
+An annotated default parameter file is provided with this package (parameters_default.txt).
 
 For example, to create 10 morphologies using 10 processors with the default parameters, the command is:
 
@@ -91,11 +93,13 @@ Users can also import morphology sets previously generated by the Ising_OPV tool
 This will import the morphologies (morphology_0.txt, morphology_1.txt, etc) and assign one to each processor.
 The morphology files must be located in the working directory to be found and imported.
 
-Finally, users can also import experimental tomogram image data, generate a morphology set from the data, and then perform further operations by enabling tomogram import in the parameter file and specifying the name of tomogram dataset. 
+Finally, users can also import experimental 3D tomography image data, generate a morphology set from the data, and then perform further operations by enabling tomogram import in the parameter file and specifying the name of tomogram dataset. 
 The tomogram metadata is imported from an XML metadata file and then that is used for interpreting a RAW binary data file that contains the image data. 
+The metadata format required by Ising_OPV is defined in XML schema definition file, tomogram_metadata.xsd.
 Once the tomogram data is loaded, the morphology can be segmented into a number of equally size sub-volumes to form a new morphology set, and then the rest of the analysis is performed. 
 Again, the tomogram dataset files must be located in the working directory to be found and imported. 
-Also, the metadata format required by Ising_OPV is defined in XML schema definition file, tomogram_metadata.xsd.
+
+For more detailed examples, please see the [Examples](./examples/examples.md) file.
 
 #### Simulation Output
 
@@ -124,11 +128,15 @@ While this tool is designed to be primarily controlled through the parameter fil
 ## Citing this Work
 
 If you find Ising_OPV to be helpful for your research, please cite the original study:
+
 [M. C. Heiber and A. Dhinojwala, Phys. Rev. Appl. **2**, 014008 (2014).](http://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.2.014008) [[ResearchGate]](https://www.researchgate.net/publication/264419218_Efficient_Generation_of_Model_Bulk_Heterojunction_Morphologies_for_Organic_Photovoltaic_Device_Modeling)
 
 If your work involves investigating the effects of morphological tortuosity, please also cite the study that introduced the tortuosity features:
+
 [M.C. Heiber, K. Kister, A. Baumann, V. Dyakonov, C. Deibel, and T.-Q. Nguyen, Phys. Rev. Appl. **8**, 054043 (2017).](https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.8.054043) [[ResearchGate]](https://www.researchgate.net/publication/321226076_Impact_of_Tortuosity_on_Charge-Carrier_Transport_in_Organic_Bulk_Heterojunction_Blends)
 
+In addition, please also cite the DOI for the specific version that you used from [Zenodo.org](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%22592959%22&sort=-version&all_versions=True).
+
 ## Additional Reference List
 Several peer-reviewed publications discuss the development and application of this software tool:
 
@@ -140,7 +148,7 @@ Several peer-reviewed publications discuss the development and application of th
 - [M.C. Heiber, K. Kister, A. Baumann, V. Dyakonov, C. Deibel, and T.-Q. Nguyen, Phys. Rev. Appl. **8**, 054043 (2017).](https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.8.054043) [[ResearchGate]](https://www.researchgate.net/publication/321226076_Impact_of_Tortuosity_on_Charge-Carrier_Transport_in_Organic_Bulk_Heterojunction_Blends)
 
 ## Acknowledgments
-Thank you to Dr. Dean DeLongchamp at NIST for providing access to computing resources that support the ongoing development of v4.0. 
+Thank you to Dr. Dean M. DeLongchamp at NIST for providing access to computing resources that support the ongoing development of v4.0. 
 Development of v4.0 is supported by financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).
 
 Thank you to Klaus Kister for contributing to the development of the updated domain smoothing algorithm and the simplified morphology import procedure in v2.0 and help with testing for v3.0.

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