Joss edits (#12)

- Resolves #9 
- Resolves #10 
- Resolves #11 

General:
-added missing references info to the paper.bib file
-updated Acknowledgements section of paper.md file to acknowledge TEM tomo data from Andy
-updated paper.md to remove potential conflicts with math symbols
-fixed use of underscores in paper.md
-corrected some formatting errors and typos in paper.md
-added further explanation to the figure caption in paper.md
-corrected mistake in the testing instructions for the mpi tests in README
-added CONTRIBUTING.md file with some more detailed instructions for how others can contribute to the project
-updated README current status to highlight that v4.0 is now stable
-added link to the Changelog in the Current Status section of README
-added link to CONTRIBUTING.md file in README
-add initial changelog file with changes for the v4.0 release
-added link to the CHANGELOG.md file in CONTRIBUTING.md
-generated updated Doxygen documentation
-updated Doxyfile version to v4.0.0
-updated Changelog by adding changes in this commit

Version class:
-updated the version string to v4.0.0

Author: MikeHeiber

CHANGELOG.md

@@ -0,0 +1,33 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+--------------------------------------------------------------------------------------------------------------------------------
+
+## [Unreleased]
+
+## [v4.0.0] - 2018-11-29 - Final Release
+
+This release only changes documentation files and does not contain modifications to the source code.
+
+### Added
+- CONTRIBUTING.md - New file with instructions for how others can contribute to the project
+- README.md - Link to new CONTRIBUTING file
+- CHANGELOG.md - New file detailing the changes for each release
+- README.md - Link to new CHANGELOG file
+- papers/v4_paper/paper.bib - Several missing reference entries
+- papers/v4_paper/paper.md - Acknowledgement of Dr. Andrew A. Herzing for TEM tomo data
+
+### Changed
+- README.md - Current release status to note that v4.0 is now stable
+- papers/v4_paper/paper.md - Image alt text to be more descriptive
+- papers/v4_paper/paper.md - Formating of plus signs using \texttt command
+- Version.cpp - Current_version namespace variable to v4.0.0
+- Doxyfile - updated the version number to v4.0.0
+- docs - generated updated Doxygen documentation
+
+### Fixed
+- README.md - Instructions for running the MPI tests
+- papers/v4_paper/paper.md - Problem with underscore by adding a backslash

CONTRIBUTING.md

@@ -0,0 +1,96 @@
+# Contributing to Ising_OPV
+
+We welcome new contributors to this project to help make the Ising_OPV morphology tool better and more effective for our scientific and educational users. Contributions can take on a variety of forms, such as bug reports, feature requests, code documentation updates, user tutorials, feature implementations, bugfixes, and more.
+
+## Ground Rules
+
+- To maintain an inclusive and welcoming environment, all community members must follow the [Code of Conduct](./CODE_OF_CONDUCT.md).
+- To keep project development organized, all new features and bugfixes must be proposed and discussed using [issues](https://github.com/MikeHeiber/Ising_OPV/issues) before changes are implemented.
+- C++ code should follow the [C++11 standard](https://en.wikipedia.org/wiki/C%2B%2B11) and should be written to be simple and largely self-documenting with self-descriptive names.
+
+## Filing Issues
+
+One of the easiest ways to contribute is by using the software and submitting bug reports and feature requests as issues in the [Issues section](https://github.com/MikeHeiber/Ising_OPV/issues). 
+Before filing a new issue please check that your issue has not already been submitted. 
+If it has, 'like' the issue and add any additional feedback you have to the issue thread in a comment.
+If your issue has not already been filed, create a new issue and provide a detailed description of the problem or new idea/suggestion. 
+The code owners will review new issues, provide feedback, and decide if and when to implement the changes needed to resolve the issue.
+
+## Working on an Issue
+
+1. Before you set out to tackle an issue, discuss your implementation plans with the code owners on the issue page.
+    
+    Especially for code additions needed to add new features, it is important to discuss your implementation ideas with the code owners to ensure that the software design is relatively well thought out and fits with the rest of the codebase.
+    
+2. Create fork of the Ising_OPV repo on your account.
+
+    Click the "Fork" button near the top of any Ising_OPV Github webpage.
+
+3. Connect your fork to the upstream repo
+
+    ```
+    git remote add upstream https://github.com/MikeHeiber/Ising_OPV.git
+    ```
+
+4. Clone your forked Ising_OPV repo to your local machine.
+
+    ```
+    git clone --recurse-submodules https://github.com/YOUR_USERNAME/Ising_OPV
+    ```
+
+5. Create a new feature branch from the development branch.
+
+    ```
+    git checkout development
+    git branch feature-new-thing
+    git checkout feature-new-thing
+    ```
+
+6. Implement your changes keeping the scope of changes limited to the specified issue.
+
+7. Document your changes by adding to the [Changelog](./CHANGELOG.md).
+
+8. Update your new branch with any upstream changes and resolve any conflicts.
+
+    ```
+    git fetch upstream
+    git checkout development
+    git merge upstream/development
+    git checkout feature-new-thing
+    git rebase development
+    ```
+
+9. Make sure your changes do not break any of the existing functionality by running the tests locally.
+
+    ```
+    make test
+    ./test/Ising_OPV_tests.exe
+    mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe
+    ```
+    
+10. Push your local changes to your forked Ising_OPV repo.
+
+    ```
+    git push origin feature-new-thing
+    ```
+
+11. Submit a pull request
+
+    See below for details about how to submit a pull request.
+
+## Code Testing and Documentation Standards
+
+Unit tests using the [googletest framework](https://github.com/abseil/googletest/blob/master/googletest/docs/primer.md) must be created for all new/modified functions and added to the test/test.cpp or test/test_mpi.cpp file as appropriate. Tests should include comments that describe what functionality each test code section is testing for.
+
+All new/modified classes and functions must be documented using the [Doxygen style](https://www.stack.nl/~dimitri/doxygen/manual/docblocks.html).
+
+## Submitting A Pull Request
+
+The pull request must reference the issue that is being resolved.
+Merging of feature branches into the development branch will be done using a squash merge operation to keep a tidy Git history.
+The squash merge will be done by a code owner, so you must provide a single overall commit message that details all changes in the pull request body text for the code owner the use with the merge.
+The pull request version of the code must pass all [TravisCI tests](https://travis-ci.org/MikeHeiber/Ising_OPV) and must not reduce code testing coverage on [Coveralls](https://coveralls.io/github/MikeHeiber/Ising_OPV).
+Code will be formatted during the code review stage to the Microsoft Visual Studio 2017 standard format.
+Updated documentation files will also be generated by Doxygen during the code review stage as needed.
+Code owners may add new commits to your pull request branch in order to help you fix any problems.
+

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         = v4.0.0-rc.2
+PROJECT_NUMBER         = v4.0.0
 
 # 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

README.md

@@ -1,4 +1,4 @@
-Ising_OPV
+Ising_OPV 
 =========
 
 This C++ software package can be used to create and analyze bulk heterojunction morphologies for further use in kinetic Monte Carlo simulation tools, such as [Excimontec](https://github.com/MikeHeiber/Excimontec). 
@@ -18,11 +18,12 @@ Generated or imported morphologies are then rigorously analyzed to determine imp
 
 ## 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)
+v4.0 is now stable. 
+Please report any bugs or submit feature requests for future releases in the [Issues](https://github.com/MikeHeiber/Ising_OPV/issues) section. 
 
-All major planned features for v4.0 are now implemented and have undergone significant testing. 
-However, there may still be bugs that need to be fixed. 
-Please report any bugs or submit feature requests in the [Issues](https://github.com/MikeHeiber/Ising_OPV/issues) section. 
+Latest pre-release:  [![GitHub Pre-release](https://img.shields.io/github/release-pre/MikeHeiber/Ising_OPV/all.svg?style=flat-square)](https://github.com/MikeHeiber/Ising_OPV/releases)
+
+To keep track of upcoming changes or review prior changes to the codebase, please see the [Changelog](./CHANGELOG.md).
 
 #### Continuous Integration and Testing Status:
 
@@ -40,9 +41,10 @@ Code is being tested using [googletest](https://github.com/google/googletest) wi
 | 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
+## Contributing
 
-If you would like to contribute to the development of this project or would like some help in using the tool for your research, please contact me ([email protected]) to discuss a collaboration. 
+If you would like to contribute to the development of this project, please see the [contributing instructions](./CONTRIBUTING.md).
+If you would like some help in using or customizing the tool for your research, please contact me ([email protected]) to discuss a collaboration. 
 You can check out my research using this tool and other work on [Researchgate](https://www.researchgate.net/profile/Michael_Heiber).
 
 ## Using Ising_OPV
@@ -71,7 +73,14 @@ Once you have an MPI library installed and have an appropriate compiler, to buil
 Then, navigate to the Ising_OPV directory and run `make`. 
 Once the normal build is successful, you should test Ising_OPV on your own hardware using the unit and system tests provided before you use the tool. 
 Build the testing executable by running `make test`. 
-Once the test build is complete, run the two test executables `./test/Ising_OPV_tests.exe` and `./test/Ising_OPV_MPI_tests.exe`.
+Once the test build is complete, run the two test executables
+
+```./test/Ising_OPV_tests.exe```
+
+and
+
+```mpiexec -n 4 ./test/Ising_OPV_MPI_tests.exe```.
+
 Please report any build or testing errors in the [Issues](https://github.com/MikeHeiber/Ising_OPV/issues) section. If you do not have any build or testing errors, then you are ready to go!
 
 #### Running Simulations

docs/Thumbs.db

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