Joss edits (#63)

Resolves #59 and #62 
-Updated CHANGELOG with notes about the most recent changes
-Made several previous changelog notes more concise
-Corrected errors in the paper bibtex entry formatting and added some missing reference info 
-Fixed incorrect copyright statement years in test.cpp and test_mpi.cpp
-Added line to .gitignore file to ignore the x64 build directory
-Added default values for all parameters in Parameters_Simulation and Parameters_Lattice to avoid undefined behavior with uninitialized parameters
-Added tests that the default values for the Parameters_Simulation and Parameters_Lattice objects are invalid parameters
-Fixed several typos and spelling mistakes in the documentation source files
-Updated the Doxygen documentation files
-Updated changelog heading for the changes coming in v2.0.0
-Updated README by changing current status to note the release of a stable v2.0
-Updated README by modifying the acknowledgements for v2.0

.gitignore

@@ -31,4 +31,5 @@
 # Visual Studio files
 *.vcxproj*
 .vs*
+x64*
 *.sln

CHANGELOG.md

@@ -6,7 +6,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 --------------------------------------------------------------------------------------------------------------------------------
 
-## [Unreleased]
+## [v2.0.0] - 2019-01-22
+
+### Added
+- .gitignore - Ignore statement for the Visual Studio x64 build directory
+- paper.bib - Missing reference info to several of the book chapter bibtex entries
+- Parameters_Lattice - Default values for all parameters
+- Parameters_Simulation - Default values for all parameters
+- test.cpp (SimulationTest) - Test that default parameters object has invalid parameters
+- test.cpp (LatticeTest) - Test that default parameters object has invalid parameters
+
+### Changed
+- README.md - Current status to note release of stable v2.0.0
+
+### Fixed
+- docs - Several spelling mistakes and typos in the documentation
+- test.cpp - Copyright years in the Doxygen documentation block
+- test_mpi.cpp - Copyright years in the Doxygen documentation block
+- paper.md - Typos and formatting issues
+- paper.bib - Formatting problems in bibtex entries
 
 ## [v2.0.0-rc.2] - 2019-01-07 - Release Candidate 2
 
@@ -64,13 +82,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Utils (createGaussianDOSVector) - Refactored code to use generate function for filling the output data vector
 - Utils (MPI_*) - Refactored functions by replacing for loops with copy, assign, and accumulate functions to make code more concise
 - test.cpp (main) - Re-enabled command line output during the tests to make it easier to see when errors occur
-- test.cpp (CalculateProbabilityHistTests) - Replaced generic unform_real_distribution by specifying use of the double version
+- test.cpp (CalculateProbabilityHistTests) - Replaced generic uniform_real_distribution by specifying use of the double version
 - test.cpp (CalculateProbabilityHistTests) - Increasing the number of entries in the data vectors to increase statistical accuracy and reduce likelihood of test failure
 - test.cpp (CalculateProbabilityHistTests) - Refactored tests to use the generate function for filling a vector with random numbers
 
 ### Fixed
-- Event - Corrected the copyright years in the Doxygen documentation block for the class
-- Lattice - Corrected the copyright years in the Doxygen documentation block for the class
-- Object - Corrected the copyright years in the Doxygen documentation block for the class
-- Simulation - Corrected the copyright years in the Doxygen documentation block for the class
-- Site - Corrected the copyright years in the Doxygen documentation block for the class
+- Event - Copyright years in the Doxygen documentation block for the class
+- Lattice - Copyright years in the Doxygen documentation block for the class
+- Object - Copyright years in the Doxygen documentation block for the class
+- Simulation - Copyright years in the Doxygen documentation block for the class
+- Site - Copyright years in the Doxygen documentation block for the class

README.md

@@ -1,4 +1,4 @@
-# KMC_Lattice
+# KMC_Lattice 
 
 ## General Information
 
@@ -25,8 +25,7 @@ For further reading about kinetic Monte Carlo simulations, nice overviews of the
 
 ## Current Status
 
-The current release is KMC_Lattice [![GitHub (pre-)release](https://img.shields.io/github/release/MikeHeiber/KMC_Lattice/all.svg?style=flat-square)](https://github.com/MikeHeiber/KMC_Lattice/releases).
-All major planned features that are to be included in v2.0 are now implemented and have undergone significant testing. 
+The latest stable release is KMC_Lattice v2.0.0.
 Please report any remaining bugs or submit feature requests for future releases in the [Issues](https://github.com/MikeHeiber/KMC_Lattice/issues) section. 
 
 To keep track of upcoming changes or review prior changes to the codebase, please see the [Changelog](./CHANGELOG.md).
@@ -133,4 +132,4 @@ If you find KMC_Lattice to be helpful for your research, please cite the forthco
 
 ## Acknowledgments
 
-Development of v2.0 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).
+Development of v2.0.0 was 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).

docs/_event_8h_source.html

@@ -108,12 +108,12 @@
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_a6bb050f23b507f7e6a403be92ff2a978"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#a6bb050f23b507f7e6a403be92ff2a978">KMC_Lattice::Event::getExecutionTime</a></div><div class="ttdeci">double getExecutionTime() const</div><div class="ttdoc">Gets the currently planned execution time of the event.</div><div class="ttdef"><b>Definition:</b> Event.cpp:43</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_ae5896cedb18cf8aab168b8fe650366e8"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#ae5896cedb18cf8aab168b8fe650366e8">KMC_Lattice::Event::getObjectTargetPtr</a></div><div class="ttdeci">Object * getObjectTargetPtr() const</div><div class="ttdoc">Gets a pointer to the Object object that is designated as the target of the event.</div><div class="ttdef"><b>Definition:</b> Event.cpp:51</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_afce20092596b97529c44f492e6500223"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#afce20092596b97529c44f492e6500223">KMC_Lattice::Event::setRateConstant</a></div><div class="ttdeci">void setRateConstant(double val)</div><div class="ttdoc">Sets the value of the rate constant for the event.</div><div class="ttdef"><b>Definition:</b> Event.cpp:81</div></div>
-<div class="ttc" id="class_k_m_c___lattice_1_1_event_html_ad930fb3e106af7dd05990517aafeb511"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#ad930fb3e106af7dd05990517aafeb511">KMC_Lattice::Event::sim_ptr</a></div><div class="ttdeci">Simulation * sim_ptr</div><div class="ttdoc">Points to the Simulation object that the Event is asociated with.</div><div class="ttdef"><b>Definition:</b> Event.h:109</div></div>
+<div class="ttc" id="class_k_m_c___lattice_1_1_event_html_ad930fb3e106af7dd05990517aafeb511"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#ad930fb3e106af7dd05990517aafeb511">KMC_Lattice::Event::sim_ptr</a></div><div class="ttdeci">Simulation * sim_ptr</div><div class="ttdoc">Points to the Simulation object that the Event is associated with.</div><div class="ttdef"><b>Definition:</b> Event.h:109</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_abbe835876bab01e0aee6089660ffd8b1"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#abbe835876bab01e0aee6089660ffd8b1">KMC_Lattice::Event::~Event</a></div><div class="ttdeci">virtual ~Event()</div><div class="ttdoc">Default virtual destructor needed by the base class.</div><div class="ttdef"><b>Definition:</b> Event.cpp:15</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_a27e523a6b00ac1a1af98c4fd0d604cb2"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#a27e523a6b00ac1a1af98c4fd0d604cb2">KMC_Lattice::Event::calculateRateConstant</a></div><div class="ttdeci">void calculateRateConstant(const double input_rate)</div><div class="ttdoc">Default virtual function that can be overloaded by derived Event classes.</div><div class="ttdef"><b>Definition:</b> Event.cpp:31</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_a33013c3d2725dfc65c809fbb3352c914"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#a33013c3d2725dfc65c809fbb3352c914">KMC_Lattice::Event::getEventType</a></div><div class="ttdeci">virtual std::string getEventType() const</div><div class="ttdoc">Gets the name of event class.</div><div class="ttdef"><b>Definition:</b> Event.cpp:39</div></div>
 <div class="ttc" id="class_k_m_c___lattice_1_1_event_html_ab6822c45f54c2c4c93d10fd26760ecb1"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#ab6822c45f54c2c4c93d10fd26760ecb1">KMC_Lattice::Event::Event</a></div><div class="ttdeci">Event()</div><div class="ttdoc">The default constructor that creates an empty Event object.</div><div class="ttdef"><b>Definition:</b> Event.cpp:19</div></div>
-<div class="ttc" id="class_k_m_c___lattice_1_1_event_html_a5700c065682318ddd26e3f1d07c9a165"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#a5700c065682318ddd26e3f1d07c9a165">KMC_Lattice::Event::setDestCoords</a></div><div class="ttdeci">void setDestCoords(const Coords &amp;coords)</div><div class="ttdoc">Sets the desination coordinates of the event.</div><div class="ttdef"><b>Definition:</b> Event.cpp:59</div></div>
+<div class="ttc" id="class_k_m_c___lattice_1_1_event_html_a5700c065682318ddd26e3f1d07c9a165"><div class="ttname"><a href="class_k_m_c___lattice_1_1_event.html#a5700c065682318ddd26e3f1d07c9a165">KMC_Lattice::Event::setDestCoords</a></div><div class="ttdeci">void setDestCoords(const Coords &amp;coords)</div><div class="ttdoc">Sets the destination coordinates of the event.</div><div class="ttdef"><b>Definition:</b> Event.cpp:59</div></div>
 <div class="ttc" id="namespace_k_m_c___lattice_html"><div class="ttname"><a href="namespace_k_m_c___lattice.html">KMC_Lattice</a></div><div class="ttdef"><b>Definition:</b> Event.cpp:10</div></div>
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