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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[v2.1.0] - 2020-08-09 - Build and Bugfix Update

Added

  • .travis.yml - Test builds for GCC 9
  • .travis.yml - Test builds for clang 7
  • makefile - Detection of versioned g++ compilers
  • makefile - Detection of clang compiler and setting the compiler flags
  • README.md - Information about clang compiler support

Changed

  • .travis.yml - Copyright years up to 2020
  • .travis.yml - Test build OS from Ubuntu trusty to Ubuntu xenial and bionic
  • .travis.yml - Simplified how GCC versions are installed and configured
  • docs - Updated Doxygen documentation for v2.1.0 using Doxygen v1.8.18
  • Doxyfile - Project version to v2.1.0 and other adjustments for Doxygen version v1.8.18
  • LICENSE - Copyright years up to 2020
  • makefile - Copyright years up to 2020
  • makefile - Updated how the underlying compiler is detected now using 'mpicxx -show'
  • Object - Copyright years up to 2020
  • Object - Updated calculateDisplacement method to calculate net displacement when specifying a direction instead of the absolute displacement
  • README.md - Latest stable release version to v2.1.0
  • README.md - Updated description of testing configurations
  • test.cpp (CalculateDisplacementTests) - Updated tests to check for negative net displacement when specifying a direction
  • Version - Copyright years up to 2020
  • Version - Current version string to v2.1.0

Removed

  • .travis.yml - Test builds for GCC 4.7, 4.8, and 4.9
  • .travis.yml - Test builds for mpich with GCC 6 and 8
  • README.md - Mention of MVAPICH MPI package

Fixed

  • README.md - Typo in test command

[v2.1.0-beta.1] - 2019-02-10 - MPI Calculate Pair Vector Average Update

Added

  • README.md - Citation info and links for the JOSS paper
  • .gitignore - Statement to ignore the packages directory created by MS Visual Studio
  • Utils (MPI_calculatePairVectorAvg) - new function for calculating the average of x-y distribution data
  • test_mpi.cpp (CalculatePairVectorAvgTests) - new test case with units tests for the Utils::MPI_calculatePairVectorAvg function
  • test_mpi.cpp (CalculateProbabilityHistTests) - new units tests to check for the output histogram range and to check exception throwing when input histograms are too small or have different bin sizes

Changed

  • Doxyfile - Documentation version to v2.1.0-beta.1
  • docs - Updated Doxygen documentation for v2.1.0-beta.1
  • Utils (MPI_calculateProbHistAvg) - Updated function to throw invalid_argument exception on all processors if the input histogram on any proc is too small or if bin sizes do not match
  • Version - Current version string to v2.1.0-beta.1

[v2.0.1] - 2019-01-29 - JOSS Paper Correction

Changed

  • Version - Current version string to v2.0.1
  • Doxyfile - Documentation version to v2.0.1
  • docs - Updated Doxygen documentation for v2.0.1
  • README.md - Information about latest stable release to v2.0.1

Fixed

  • CHANGELOG.md - v2.0.0 release date
  • papers/v2_paper/paper.md - Fixed typo

[v2.0.0] - 2019-01-23 - First Stable Release

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

Added

  • README.md - Information about the BKL algorithm and the Gillespie first-reaction method implemented in the tools with link to the original papers
  • README.md - Information about and link to the KMC_Lattice_example repo
  • README.md - Major features list
  • README.md - Section heading for the API documentation, citation instructions, and acknowledgments
  • papers/v2_paper/paper.md - Initial draft of v2.0 JOSS paper text
  • papers/v2_paper/paper.bib - Initial draft of v2.0 JOSS paper references
  • .gitignore - Ignore statements for Visual Studio project files

Changed

  • Many files - Copyright statement to show years 2017-2019
  • README.md - Rearranged sections and moved the build instructions to the end of the usage instructions sections
  • Version.cpp - Version string to v2.0.0
  • Doxyfile - project version number to v2.0.0 and brief project description
  • docs - Re-generated documentation using latest Doxygen v1.8.15

Removed

  • docs - Repository markdown files from the documentation build

[v2.0.0-rc.1] - 2018-12-11 - Release Candidate 1

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
  • README.md - More detailed instructions for building and testing KMC_Lattice
  • Object (calculateDisplacement) - New optional direction parameter that allows users to tell the function to calculate the displacement along a specific Cartesian direction
  • Simulation (getN_events) - Cast return of count_if function to int to prevent compiler warning
  • Utils (calculateProbabilityHist) - Float versions of several calculateProbabilityHist functions
  • Utils (calculateProbabilityHist) - Filtering of input data vectors to remove inf and nan entries
  • Utils (calculateProbabilityHist) - Check for and correct index calculation error due to floating point rounding
  • Utils (createExponentialDOSVector) - Float version of the createExponentialDOSVector function to allow the user to conserve memory
  • Utils (createGaussianDOSVector) - Float version of the createExponentialDOSVector function to allow the user to conserve memory
  • Utils (vector_which_median) - Cast return of distance function to int to prevent compiler warning
  • test.cpp (BKL_determinePathwayTests) - Cast return of count_if function to int to prevent compiler warning
  • test.cpp (CalculateProbabilityHistTests) - Tests of the float versions of calculateProbabilityHist
  • test.cpp (CalculateProbabilityHistTests) - Tests of both double and float versions of calculateProbabilityHist where the input data vectors contain some non finite entries = test.cpp (EventExecutionTests) - Cast return of count_if function to int to prevent compiler warning
  • test.cpp (ExponentialDOSTests) - Test of the float version of the createExponentialDOSVector
  • test.cpp (ExponentialDOSTests) - Cast return of count_if function to int to prevent compiler warning
  • test.cpp (GaussianDOSTests) - Test of the float version of the createGaussianDOSVector
  • test.cpp (LatticeTests) - Cast return of count_if functions to int to prevent compiler warning
  • test.cpp (ObjectTests) - Tests of the new calculateDisplacement function behavior

Changed

  • Doxyfile - Updated the version number to v2.0.0-rc.1
  • docs - Generated updated Doxygen documentation
  • Parameters_Lattice - Refactored struct into a new class
  • test.cpp (AlgorithmTests) - Increased N_tests to gather more statistics and reduce likelihood of test failure
  • Utils (createExponentialDOSVector) - Refactored code to make selection of the Gaussian side or the exponential side of the dist more simple
  • 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 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 - 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