Remove solver_.parameters_

[montythind]

This PR includes moving Parameters
absolute tolerance and relative tolearnce to state from solver

Note:
I have left
std::vector absolute_tolerance_;
double relative_tolerance_{ 1e-6 };

in rosenbrock_solver_prarameter.hpp as the CUDA tests are failing because tolerance doesnt get copied over to the device. Issue occurs in CudaRosenbrockSolver constructor when doing this->parameters_.absolute_tolerance_.size(); it comes out as zero

We can potential get rid of this line in solver_builder.inl. This is also a temporary. solution.
options.absolute_tolerance_ = state_parameters.absolute_tolerance_;

Along with that i have commented out unit tests till we don't have a solution how to deal with tolerance.

closes #621

[montythind]

I do see some calls where solver.solver_.parameters_ is not being modifiedbut rather the value is getting used. Example:

EXPECT_EQ(solver.solver_.parameters_.absolute_tolerance_[state.variable_map_["Ar"]], 1.0e-12);
std::vector atol = gpu_solver.solver_.parameters_.absolute_tolerance_;

I am unsure if we need to change these as well?

@K20shores @mattldawson

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.38%. Comparing base (faf21bd) to head (757e613).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #668      +/-   ##
==========================================
+ Coverage   94.09%   94.38%   +0.29%     
==========================================
  Files          63       63              
  Lines        4281     4294      +13     
==========================================
+ Hits         4028     4053      +25     
+ Misses        253      241      -12     

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[K20shores]

Right direction, but we still have some more work to do. Any mechanism-specific thing (like tolerances) need to be moved somewhere else. We should spend some time figuring out where they need to go. Also, the parameters need to be any set of paramters (rosenbrock, backward euler, etc.)

[sjsprecious]

Thanks @montythind for working on this PR. I observed the following failures on Derecho:

         15 - cuda_rosenbrock (SEGFAULT)
         31 - rosenbrock (SEGFAULT)
         45 - regression_test_solve (NUMERICAL)
         46 - chapman_integration (SEGFAULT)
         47 - analytical_rosenbrock_integration (NUMERICAL)
         48 - analytical_backward_euler (NUMERICAL)
         49 - terminator (NUMERICAL)
         50 - integrated_reaction_rates (NUMERICAL)
         52 - README_example (NUMERICAL)
         53 - solve_results (NUMERICAL)
         54 - multiple_grid_cells (NUMERICAL)
         55 - rate_constants_no_user_defined_example_by_hand (NUMERICAL)
         56 - rate_constants_user_defined_example_by_hand (NUMERICAL)
         57 - solver_configuration (NUMERICAL)
         59 - rate_constants_no_user_defined_example_with_config (NUMERICAL)
         60 - rate_constants_user_defined_example_with_config (NUMERICAL)
         61 - carbon_bond_5_example (NUMERICAL)
         62 - chapman_example (NUMERICAL)
         63 - robertson_example (NUMERICAL)
         64 - ts1_example (NUMERICAL)

[montythind]

I am not sure what happened but after my latest pull and merge- lot of tests failed. I am looking what caused the test failures

[sjsprecious]

Thanks @K20shores and @montythind for working on this and addressing all my comments. It looks great to me and I could confirm that all the CPU & GPU tests pass on Derecho.

[mattldawson]

Looks great! Just one minor question, but nothing that should hold up merging

[boulderdaze]

Looks good! I just have a couple questions and suggestions.