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[CL] New Phreeqc Interface #2640

Merged
merged 41 commits into from Sep 18, 2019
Merged

[CL] New Phreeqc Interface #2640

merged 41 commits into from Sep 18, 2019

Commits on Sep 17, 2019

  1. [T] KineticReactantBlockTest using PhreeqcKernel.

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  2. [CL] Add types of chemical solvers supported.

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  3. [CL] move Output into folder PhreeqcIOData.

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  4. [CL] Add namespace scope.

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  5. [CL] Move creation of solution components into a new function.

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  6. [CL] Extract parsing means of adjusting charge.

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  7. [CL] Create base class ChemicalSolverInterface.

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  8. [CL] Create derived class PhreeqcIO and PhreeqcKernel.

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  9. [CL] Instantiate object of Aqueous Solution.

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  10. [CL] Instantiate object of initial aqueous solution.

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  11. [CL] Instantiate object of kinetic reactant.

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  12. [CL] Create reaction rate.

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  13. [AP|PL] Replace with chemical solver interface instead.

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  14. [CMake] Make phreeqc keywords public.

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  15. [CMake] Include subdirectory PhreeqcKernelData.

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  16. [PL] Add time record for chemical calculation by Phreeqc.

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  17. [CL] Add methods of class PhreeqcKernel.

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  18. [CMake] Include subdirectory Common.

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  19. [CL] Instantiate object of reaction rate.

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  20. [CL] Extract creation of reaction rate.

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  21. [CL] Initialize array of Phreeqc::rates.

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  22. [CL] PhreeqcKernel ctor.

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  23. [CL] renamed virtual class method as setTimeStepSize

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  24. [CL] Add small private class methods.

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  25. [CL/PhreeqcIO] Replaced header files with forward-decls.

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  26. [CL/PhreeqcKernel] Replaced header files with forward-decls.

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  27. [CL] Extract parsing path to database. 

    Signed-off-by: renchao_lu <renchao.lu@gmail.com>
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  28. [CL] Set private inheritance for derived class Kinetics. 

    Signed-off-by: renchao_lu <renchao.lu@gmail.com>
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  29. [CL] Set private inheritance for class AqueousSolution.

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  30. [CL] Create unique_ptr to an instance of Class kinetic_reactant.

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  31. [CL] Allocate memory for rate.commands.

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  32. [CL] Parameter renamed as _initial_aqueous_solution.

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  33. [CMake] Set C++ standard as c++14.

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  34. [CL] Drop structure binding feature.

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  35. [CL] Add doxygen docu headers.

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  36. [CL] Dropped time step size setter.

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  37. [CL] Load database.

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  38. [CL] Initialize Phreeqc general settings.

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  39. [CL] Fix clang-tidy warnings.

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  40. [CL] Solve doxygen warnings.

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  41. [Jenkins] Changed quality gate threshold, because of Phreeqc.

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