Final enhancements for rc.1 #52
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MikeHeiber
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Dec 8, 2018
MikeHeiber
commented
- Resolves Add Parameters base classes #35
- Resolves Add changelog file for documenting changes between versions #48
- Resolves Add contributor guidelines #49
- Resolves Update Object calculateDisplacement function to also allow calculation of displacement along a specified cardinal direction #50
- Resolves Add DOS vector creation functions that create vectors of floats #51
-Resolves #50 -Resolves #51 Object class: -updated calculateDisplacement function to allow user to specify a direction for when one wants to calculate the displacement only along a particular cardinal direction Utils: -added float variants of the createExponentialDOSVector and createGaussianDOSVector functions tests: -updated ExponentialDOSTests and GaussianDOSTests to also test the new float versions of DOS creation functions -updated ObjectTests to check the behavior of the updated Object calculateDisplacement function
Object class: -updated calculateDisplacement function to output the absolute value of the displacement
-applied formatting
-added Utils interpolateData test for case with nonlinear x-vals
General: -added CONTRIBUTING.md file with details about how people can contribute to the project
Utils: -corrected bug in interpolateData function that was occuring with small numbers for the x-vals
Utils: -added float versions of several calculateProbabilityHist functions to allow calculation of probability hists given a vector of float data -refactored createExponentialDOSVector functions to be simpler -fixed bug in new float version of the createExponentialDOSVector function by checking for the distribution generator outputing inf and trying again until a valid value is generated tests: -updated SimulationTest AlgorithmTests by increasing N_tests to get better statistics and reduce likelihood of test failure -updated UtilsTest ExponentialDOSTests to use the new float versions of the calculateProbabilityHist functions -re-enabled commnad line output during the tests
Utils: -refactored all MPI functions to replace usage of for loops where possible by simpler copy, assign, and accumulate functions
[skip ci] General -update copyright dates in Doxygen documentation for the Event, Lattice, Object, Simulation, and Site classes and also the Parameters_Simulation and Parameters_Lattice structs
[skip ci] General: -added CHANGELOG.md file with a detailed list of changes in this release -updated README by adding links to the Changelog and the Contributing instructions file
[skip ci] General: -updated Doxyfile with the next version number
Utils: -added missing float version of calculateProbabilityHist function that specifies the bin size tests: -updated Utils CalculateProbabilityHistTests by adding tests for the new float versions of the calculateProbabilityHist functions
General: -updated changelog with info about tests for the calculateProbabilityHist functions tests: -refactored CalculateProbabilityHist Tests to use generate function for filling vectors with random numbers
General: -updated Changelog to document these updates Utils: -Updated calculateProbabilityHist functions to filter input data vectors of any non finite numbers -Fixed rare bug in calculateProbabilityHist function where the index was being calculated wrong due to floating point rounding error -Updated vector_which_median function to cast the return of the distance function to int to prevent compiler warning -Updated createGaussianDOSVector function by refactoring the code and using the generate function to fill the ouput data vector tests: -Added tests to CalculateProbabilityHistTests to check that the data filtering for non finite values is working properly -Updated CalculateProbabilityHistTests by specifying the double version of the uniform_real_distribution, increasing the number of entries in the data vectors to increase stastically accuracy and reduce likelihood of test failure, and using the generate function to populate the data vectors -Updated all uses of count_if function by casting the return to int to prevent compiler warning
tests: -Updated CalculateProbabilityHistTests with tests of float verisions where the input data vector size is less than the number of bins
[skip ci] General: -updated Doxygen documentation
General: -Changed Parameters_Simulation and Parameters_Lattice structs into classes -Added more detailed building and testing instruction to README -Added info about the new parameters classes to README Lattice class: -Added call to check the input lattice parameters when calling init and throwing an invalid argument exception if they are not valid Parameters_Lattice class: -Added checkParameters function to check the validity of the parameter member variables Parameters_Lattice class: -Added checkParameters function to check the validity of the parameter member variables Parameters_Simulation class: -Added checkParameters function to check the validity of the parameter member variables Simulation class: -Added call to check the input lattice parameters when calling init and throwing an invalid argument exception if they are not valid -Updated init function lattice construction to use the Parameters_Lattice object within the Parameters_Simulation object tests: -Added new CheckParameters tests in SimulationTests and LatticeTests -Updated various params definition with the new parameter format -Added new test to InitializationTests in LatticeTests to check for exception when trying to initialize a Lattice object with invalid params -Added new test to SetupTests in SimulationTests to check for exception when trying to initialize a Simulation object with invalid params
[skip ci] -updated Doxygen documentation and Doxyfile -fixed bug where Doxygen was not including the main markdown files in the documentation
General: -Updated makefile to build the new parameters classes and added output of compiler warnings to the PGI compiler flags
General: -Updated Changelog with new estimated release date tests: -Fixed typo in CalculateProbabilityHistTests causing the tests not to check float data with less data entries than number of bins
Parameters_Simulation class: -Added nullptr as the default value for the Logfile pointer -Updated checkParameters function to check if the logfile ofstream has not been set and still has a nullptr value tests: -Updated SimulationTests CheckParameters function with tests for unassigned or unopened logfile ofstream parameter
[skip ci] General: -Updated Changelog to have an Unreleased heading where new changes will be logged before they are released
tests: -Updated UtilsTests GaussianDOSTests with comments to explain each test and increased the number of data entries to reduce the likelihood of test failure
tests: -Updated ExponentialDOSTests with better descriptions for each test and more concise calculation of the prob dist peak height -Updated GaussianDOSTests with better method for determining the peak height, reducing the need for larger data entries and allowing a smaller test tolerance
tests: -Updated GaussianDOSTest by increasing the tolerance for the peak height tests
MikeHeiber
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Dec 9, 2018
* Final enhancements for rc.1 (#52) * Enhancements Update - Resolves #35 - Resolves #48 - Resolves #49 - Resolves #50 - Resolves #51 General: -Added more detailed building and testing instruction to README -Added CONTRIBUTING.md file with details about how people can contribute to the project -Added CHANGELOG.md file with a detailed list of changes in this release -Updated README by adding links to the Changelog and the Contributing instructions file -Changed Parameters_Simulation and Parameters_Lattice structs into classes -Update copyright dates in Doxygen documentation for the Event, Lattice, Object, Simulation, Site, Parameters_Simulation, and Parameters_Lattice classes -Added info about the new parameters classes to README -Updated makefile to build the new parameters classes and added output of compiler warnings to the PGI compiler flags -Updated Doxyfile with the next version number -Fixed bug where Doxygen was not including the main markdown files in the documentation -Updated Doxygen documentation Lattice class: -Updated init function to check the input lattice parameters and throw an invalid argument exception if they are not valid Object class: -Updated calculateDisplacement function to allow user to specify a direction for when one wants to calculate the absolute displacement only along a particular Cartesian direction Parameters_Lattice class: -Added checkParameters function to check the validity of the parameter member variables Parameters_Simulation class: -Added checkParameters function to check the validity of the parameter member variables -Added nullptr as the default value for the Logfile pointer Simulation class: -Updated init function to check the input parameters and throw an invalid argument exception if they are not valid -Updated init function lattice construction to use the Parameters_Lattice object within the Parameters_Simulation object Utils: -Added float variants of the createExponentialDOSVector and createGaussianDOSVector functions -Added float versions of the calculateProbabilityHist functions to allow calculation of probability hists given a vector of float data -Refactored createExponentialDOSVector and createGaussianDOSVector functionc to make them simpler and use the generate function to fill the ouput data vector -Updated calculateProbabilityHist functions to filter input data vectors of any non finite numbers -Fixed rare bug in calculateProbabilityHist function where the index was being calculated wrong due to floating point rounding error -Updated vector_which_median function to cast the return of the distance function to int to prevent compiler warning -Refactored all MPI functions to replace usage of for loops where possible by simpler copy, assign, and accumulate functions tests: -Updated ObjectTests to check the behavior of the updated Object calculateDisplacement function -Updated SimulationTest AlgorithmTests by increasing N_tests to get better statistics and reduce likelihood of test failure -Updated UtilsTests ExponentialDOSTests and GaussianDOSTests functions to also test the new float versions of DOS creation functions and calculateProbabilityHist functions -Updated UtilsTests ExponentialDOSTests and GaussianDOSTests functions with comments to explain each test and more concise, accurate calculation of the prob dist peak height -Updated Utils CalculateProbabilityHistTests by adding tests for the new float versions of the calculateProbabilityHist functions -Refactored CalculateProbabilityHist Tests to use generate function for filling vectors with random numbers -Added tests to CalculateProbabilityHistTests to check that the data filtering for non finite values is working properly -Updated CalculateProbabilityHistTests by specifying the double version of the uniform_real_distribution, increasing the number of entries in the data vectors to increase statistically accuracy and reduce likelihood of test failure, and using the generate function to populate the data vectors -Updated main by re-enabling command line output during the tests -Updated all uses of count_if function by casting the return to int to prevent compiler warning -Added new CheckParameters tests in SimulationTests and LatticeTests -Updated various params definitions with the new parameter format -Added new test to InitializationTests in LatticeTests to check for exception when trying to initialize a Lattice object with invalid params -Added new test to SetupTests in SimulationTests to check for exception when trying to initialize a Simulation object with invalid params
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