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add pmpl files
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‎src/common/pmpl.hpp‎

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#pragma once
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#include "ShivaMacros.hpp"
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namespace shiva
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{
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#if defined(HPCREACT_USE_DEVICE)
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#if defined(HPCREACT_USE_CUDA)
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#define deviceMalloc( PTR, BYTES ) cudaMalloc( PTR, BYTES );
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#define deviceMallocManaged( PTR, BYTES ) cudaMallocManaged( PTR, BYTES );
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#define deviceDeviceSynchronize() cudaDeviceSynchronize();
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#define deviceMemCpy( DST, SRC, BYTES, KIND ) cudaMemcpy( DST, SRC, BYTES, KIND );
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#define deviceFree( PTR ) cudaFree( PTR );
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#elif defined(HPCREACT_USE_HIP)
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#define deviceMalloc( PTR, BYTES ) hipMalloc( PTR, BYTES );
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#define deviceMallocManaged( PTR, BYTES ) hipMallocManaged( PTR, BYTES );
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#define deviceDeviceSynchronize() hipDeviceSynchronize();
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#define deviceMemCpy( DST, SRC, BYTES, KIND ) hipMemcpy( DST, SRC, BYTES, KIND );
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#define deviceFree( PTR ) hipFree( PTR );
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#endif
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#endif
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/**
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* @namespace shiva::pmpl
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* @brief The pmpl namespace contains all of the pmpl classes and functions
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* used to provide a portablity layer in unit testing.
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*/
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namespace pmpl
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{
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/**
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* @brief This function checks if two floating point numbers are equal within a
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* tolerance.
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* @tparam REAL_TYPE This is the type of the floating point numbers to compare.
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* @param a This is the first floating point number to compare.
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* @param b This is the second floating point number to compare.
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* @param tolerance This is the tolerance to use when comparing the two numbers.
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* @return This returns true if the two numbers are equal within the tolerance.
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*/
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template< typename REAL_TYPE >
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static constexpr bool check( REAL_TYPE const a, REAL_TYPE const b, REAL_TYPE const tolerance )
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{
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return ( a - b ) * ( a - b ) < tolerance * tolerance;
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}
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/**
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* @brief This function provides a generic kernel execution mechanism that can
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* be called on either host or device.
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* @tparam LAMBDA The type of the lambda function to execute.
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* @param func The lambda function to execute.
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*/
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template< typename LAMBDA >
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HPCREACT_GLOBAL void genericKernel( LAMBDA func )
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{
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func();
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}
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/**
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* @brief This function provides a wrapper to the genericKernel function.
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* @tparam LAMBDA The type of the lambda function to execute.
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* @param func The lambda function to execute.
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*
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* This function will execute the lambda through a kernel launch of
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* genericKernel.
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*/
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template< typename LAMBDA >
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void genericKernelWrapper( LAMBDA && func )
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{
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#if defined(HPCREACT_USE_DEVICE)
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genericKernel << < 1, 1 >> > ( std::forward< LAMBDA >( func ) );
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#else
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genericKernel( std::forward< LAMBDA >( func ) );
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#endif
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}
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/**
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* @brief This function provides a generic kernel execution mechanism that can
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* be called on either host or device.
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* @tparam DATA_TYPE The type of the data pointer.
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* @tparam LAMBDA The type of the lambda function to execute.
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* @param func The lambda function to execute.
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* @param data A general data pointer to pass to the lambda function that should
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* hold all data required to execute the lambda function, aside from what is
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* captured.
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*/
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template< typename DATA_TYPE, typename LAMBDA >
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HPCREACT_GLOBAL void genericKernel( LAMBDA func, DATA_TYPE * const data )
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{
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func( data );
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}
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/**
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* @brief This function provides a wrapper to the genericKernel function.
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* @tparam DATA_TYPE The type of the data pointer.
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* @tparam LAMBDA The type of the lambda function to execute.
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* @param N The size of the data array.
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* @param hostData The data pointer to pass to the lambda function.
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* @param func The lambda function to execute.
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*
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* This function will allocate the data pointer on the device, execute the
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* lambda through a kernel launch of genericKernel, and then synchronize the
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* device.
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*/
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template< typename DATA_TYPE, typename LAMBDA >
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void genericKernelWrapper( int const N, DATA_TYPE * const hostData, LAMBDA && func )
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{
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#if defined(HPCREACT_USE_DEVICE)
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DATA_TYPE * deviceData;
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deviceMalloc( &deviceData, N * sizeof(DATA_TYPE) );
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genericKernel <<< 1, 1 >>> ( std::forward< LAMBDA >( func ), deviceData );
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deviceDeviceSynchronize();
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deviceMemCpy( hostData, deviceData, N * sizeof(DATA_TYPE), cudaMemcpyDeviceToHost );
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deviceFree( deviceData );
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#else
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HPCREACT_UNUSED_VAR( N );
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genericKernel( std::forward< LAMBDA >( func ), hostData );
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#endif
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}
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/**
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* @brief convenience function for allocating data allocated on a pointer
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* @tparam DATA_TYPE The type of the data pointer.
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* @param data The data pointer to deallocate.
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*/
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template< typename DATA_TYPE >
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HPCREACT_CONSTEXPR_HOSTDEVICE_FORCEINLINE void deallocateData( DATA_TYPE * data )
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{
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#if defined(HPCREACT_USE_DEVICE)
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deviceFree( data );
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#else
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delete[] data;
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#endif
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}
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} // namespace pmpl
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} // namespace shiva

‎src/reactions/unitTests/CMakeLists.txt‎

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# Specify list of tests
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set( testSourceFiles
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testReactionsParameterData.cpp )
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set( dependencyList hpcReact gtest )
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# Add gtest C++ based tests
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foreach(test ${testSourceFiles})
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get_filename_component( test_name ${test} NAME_WE )
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blt_add_executable( NAME ${test_name}
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SOURCES ${test}
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OUTPUT_DIR ${TEST_OUTPUT_DIRECTORY}
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DEPENDS_ON ${dependencyList} )
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blt_add_test( NAME ${test_name}
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COMMAND ${test_name} )
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endforeach()

‎src/reactions/unitTests/testReactionsParameterData.cpp‎

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#include "../ReactionsBase_impl.hpp"
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#include "MultiVector.hpp"
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#include "common/CArrayWrapper.hpp"
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#include "../ReactionsParameterDataPredefined.hpp"
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#include <gtest/gtest.h>
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using namespace hpcReact;
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template< typename T >
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constexpr bool nearEqual( T a, T b, T tol = 1e-7 )
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{
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return ( a - b ) * ( a - b ) < tol * tol;
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}
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TEST( testReactionsBase, testParamsInitialization )
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{
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static_assert( chemicalReactionsParams.numPrimarySpecies == 7, "Number of primary species is not 7" );
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static_assert( chemicalReactionsParams.numSecondarySpecies == 11, "Number of secondary species is not 11" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[0], 9.00 ), "Ion size for primary species 0 is not 9.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[1], 4.00 ), "Ion size for primary species 1 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[2], 6.00 ), "Ion size for primary species 2 is not 6.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[3], 4.00 ), "Ion size for primary species 3 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[4], 3.00 ), "Ion size for primary species 4 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[5], 8.00 ), "Ion size for primary species 5 is not 8.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[6], 4.00 ), "Ion size for primary species 6 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[0] , 3.50 ), "Ion size for secondary species 0 is not 3.50" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[1] , 3.00 ), "Ion size for secondary species 1 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[2] , 4.50 ), "Ion size for secondary species 2 is not 4.50" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[3] , 3.00 ), "Ion size for secondary species 3 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[4] , 4.00 ), "Ion size for secondary species 4 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[5] , 3.00 ), "Ion size for secondary species 5 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[6] , 3.00 ), "Ion size for secondary species 6 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[7] , 4.00 ), "Ion size for secondary species 7 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[8] , 3.00 ), "Ion size for secondary species 8 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[9] , 3.00 ), "Ion size for secondary species 9 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[10], 4.00 ), "Ion size for secondary species 10 is not 4.00" );
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static_assert( chemicalReactionsParams.m_chargePrimary[0] == 1, "Charge for primary species 0 is not 1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[1] == -1, "Charge for primary species 1 is not -1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[2] == 2, "Charge for primary species 2 is not 2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[3] == -2, "Charge for primary species 3 is not -2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[4] == -1, "Charge for primary species 4 is not -1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[5] == 2, "Charge for primary species 5 is not 2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[6] == 1, "Charge for primary species 6 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[0] == -1, "Charge for secondary species 0 is not -1" );
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static_assert( chemicalReactionsParams.m_chargeSec[1] == 0, "Charge for secondary species 1 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[2] == -2, "Charge for secondary species 2 is not -2" );
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static_assert( chemicalReactionsParams.m_chargeSec[3] == 0, "Charge for secondary species 3 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[4] == 1, "Charge for secondary species 4 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[5] == 0, "Charge for secondary species 5 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[6] == 0, "Charge for secondary species 6 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[7] == 1, "Charge for secondary species 7 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[8] == 0, "Charge for secondary species 8 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[9] == 0, "Charge for secondary species 9 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[10] == -1, "Charge for secondary species 10 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_DebyeHuckelA, 0.5465 ), "Debye Huckel A is not 0.5465" );
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static_assert( nearEqual( chemicalReactionsParams.m_DebyeHuckelB, 0.3346 ), "Debye Huckel B is not 0.3346" );
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static_assert( nearEqual( chemicalReactionsParams.m_WATEQBDot, 0.0438 ), "WATEQBDot is not 0.0438" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][0], -1.0 ), "Stoichiometry matrix for species 0 and 0 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][1], 0.0 ), "Stoichiometry matrix for species 0 and 1 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][2], 0.0 ), "Stoichiometry matrix for species 0 and 2 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][3], 0.0 ), "Stoichiometry matrix for species 0 and 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][4], 0.0 ), "Stoichiometry matrix for species 0 and 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][5], 0.0 ), "Stoichiometry matrix for species 0 and 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][6], 0.0 ), "Stoichiometry matrix for species 0 and 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][0], 1.0 ), "Stoichiometry matrix for species 1 and 0 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][1], 1.0 ), "Stoichiometry matrix for species 1 and 1 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][2], 0.0 ), "Stoichiometry matrix for species 1 and 2 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][3], 0.0 ), "Stoichiometry matrix for species 1 and 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][4], 0.0 ), "Stoichiometry matrix for species 1 and 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][5], 0.0 ), "Stoichiometry matrix for species 1 and 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][6], 0.0 ), "Stoichiometry matrix for species 1 and 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[0], 13.99 ), "Log10 equilibrium constant for species 0 is not 13.99" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[1], -6.36 ) , "Log10 equilibrium constant for species 1 is not -6.36" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[2], 10.33 ), "Log10 equilibrium constant for species 2 is not 10.33" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[3], -3.77 ) , "Log10 equilibrium constant for species 3 is not -3.77" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[4], -1.09 ) , "Log10 equilibrium constant for species 4 is not -1.09" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[5], 7.07 ) , "Log10 equilibrium constant for species 5 is not 7.07" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[6], - 2.16 ) , "Log10 equilibrium constant for species 6 is not -2.16" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[7], + 0.67 ) , "Log10 equilibrium constant for species 7 is not 0.67" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[8], + 0.60 ) , "Log10 equilibrium constant for species 8 is not 0.60" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[9], - 2.43 ) , "Log10 equilibrium constant for species 9 is not -2.43" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[10], - 0.82 ), "Log10 equilibrium constant for species 10 is not -0.82" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][0],-2.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 0 is not -2" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][1], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 1 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][2], 1.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 2 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][3], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][4], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][5], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][6], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][0],-1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 0 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][1], 1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 1 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][2], 1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 2 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][3], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][4], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][5], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][6], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticlog10EqConst[0], 20.19 ), "Log10 equilibrium constant for kinetic reaction 0 is not 20.19" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticlog10EqConst[1], 1.32 ), "Log10 equilibrium constant for kinetic reaction 1 is not 1.32" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticReactionRateConstant[0], 9.95e-1 ), "Reaction rate constant for kinetic reaction 0 is not 9.95e-1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticReactionRateConstant[1], 9.95e-3 ), "Reaction rate constant for kinetic reaction 1 is not 9.95e-3" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticSpecificSurfaceArea, 1.0 ), "Specific surface area is not 1.0" );
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}
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TEST( testReactionsBase, testEquilibriumParamsExtraction )
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{
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constexpr auto eqParams = chemicalReactionsParams.equilibriumReactions();
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static_assert( eqParams.numPrimarySpecies == 7, "Number of primary species is not 7" );
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static_assert( eqParams.numSecondarySpecies == 11, "Number of secondary species is not 11" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[0], 9.00 ), "Ion size for primary species 0 is not 9.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[1], 4.00 ), "Ion size for primary species 1 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[2], 6.00 ), "Ion size for primary species 2 is not 6.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[3], 4.00 ), "Ion size for primary species 3 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[4], 3.00 ), "Ion size for primary species 4 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[5], 8.00 ), "Ion size for primary species 5 is not 8.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[6], 4.00 ), "Ion size for primary species 6 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[0] , 3.50 ), "Ion size for secondary species 0 is not 3.50" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[1] , 3.00 ), "Ion size for secondary species 1 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[2] , 4.50 ), "Ion size for secondary species 2 is not 4.50" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[3] , 3.00 ), "Ion size for secondary species 3 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[
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}
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int main( int argc, char * * argv )
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{
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::testing::InitGoogleTest( &argc, argv );
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int const result = RUN_ALL_TESTS();
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return result;
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}

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