Post-development design review

[mattldawson]

• Did we use gamma correctly? It's an array, but we only ever use the first element #604
• Condense the first two arguments of the linear solver so that we don't need to make a copy #492
• review user interactions with multiple grid-cell solving to identify difficulties and easily made errors
• User defined rate constants have an easy API with the state to set their values. Maybe we can come up with something similar for the surface reaction rate constants so that the index of the values doesn't need to be remembered.
• Make sure copyright and license is included at the top of each source code file, and review approach for how to handle this header bock in the error.hpp file currently set up to allow inclusion in fortran code. #620
• Check if resetting the L and U matrices before solving with Rosenbrock is needed #587
• Remove nlohman::json in favor of yaml-cpp since it parses both yaml and json #619
• Allow solvers parameters to be modified after construction of the solver. May revisit how solver builder works - may not need to take parameters at construction time. #621
• Could we redesign the error schemes we have so that we don't need so much boilerplate code?
• Could we redesign the builders so that parameters don't need to be specified both in the template argument and then passes in a real instance later on?

CUDA-related things:

• Move Yerror construction outside of the inner solve loop for rosenbrock #622
• Change the storage of CUDA sparse matrix to leverage the CuSparse library (replacing the existing CUDA LU Decomposition and Linear Solver).
• Provide Allison an ill-conditioned matrix and see if she has a better suggestion of a different numerical solver (i.e., not LU).
• Change the CUDA class so that we only allocate device memory (no host memory allocation). This is specific for arrays of index or constants.
• Consider moving all temporary matrices onto the State so that memory for these temporary variables are only made once

  • micm/include/micm/solver/rosenbrock.inl

    Lines 14 to 25 in 6b1c58a

    	SolverResult result{};
    	result.state_ = SolverState::Running;
    	MatrixPolicy Y = state.variables_;
    	std::size_t num_rows = Y.NumRows();
    	std::size_t num_cols = Y.NumColumns();
    	MatrixPolicy Ynew(num_rows, num_cols, 0.0);
    	MatrixPolicy initial_forcing(num_rows, num_cols, 0.0);
    	MatrixPolicy forcing(num_rows, num_cols, 0.0);
    	std::vector<MatrixPolicy> K{};
    	const double h_max = parameters_.h_max_ == 0.0 ? time_step : std::min(time_step, parameters_.h_max_);
    	const double h_start =
    	parameters_.h_start_ == 0.0 ? std::max(parameters_.h_min_, DELTA_MIN) : std::min(h_max, parameters_.h_start_);