Fix the Jacobian possible inputs for the chemistry section

This MR updates the inputs for the chemistry section, to be consistent with the changes in MR1397

docs/source_docs/user_guide/inputs/chemical_reactions.rst

@@ -52,55 +52,55 @@ time to enable caching of the numerical approximation of the Jacobian matrix
 is selected. The following inputs can be specified using the
 ``chemistry.integrator`` prefix:
 
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-|                                | Description                                                   |   Type   | Default |
-+================================+===============================================================+==========+=========+
-| burner_verbose                 | Enables the printing on screen of some integration statistics | int      | 0       |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| ode_max_steps                  | The maximum number of substeps for the ODE integration        | int      | 150000  |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| jacobian_type                  | Select how to compute the jacobian for the ODE iterative      | int      | 0       |
-|                                | solver. Available choices are:                                |          |         |
-|                                |                                                               |          |         |
-|                                | * 0 for a first-order numerical approximation                 |          |         |
-|                                | * 1 for the analytical jacobian (not available yet)           |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| atol                           | Absolute tolerance for the ODE integration error test between | Real     | 1.e-6   |
-|                                | the solution and the fine-step solution                       |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| rtol                           | Relative tolerance for the ODE integration error test between | Real     | 1.e-6   |
-|                                | the solution and the fine-step solution                       |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| retry_atol                     | Overwrites the absolute tolerance value atol in case the ODE  | Real     | -1      |
-|                                | integration fails                                             |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| retry_rtol                     | Overwrites the relative tolerance value rtol in case the ODE  | Real     | -1      |
-|                                | integration fails                                             |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| retry_swap_jacobian            | Swaps the type of jacobian (from 1 to 0 or vice versa) in     | int      | 1       |
-|                                | case the ODE integration fails                                |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| ode_max_dt                     | Maximum timestep size for the ODE integration substeps        | Real     | 1.e30   |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| maximum_timestep_change_factor | Only for StiffSolver::ForwardEuler, sets a maximum factor     | Real     | 1.001   |
-|                                | for the change of the timestep for the internal substeps      |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| max_iter                       | Maximum number of iterations for the internal Newton solver   | int      | 100     |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| linalg_do_pivoting             | Only for StiffSolver::BackwardEuler and StiffSolver::VODE,    | int      | 1       |
-|                                | switches on/off the pivoting when solving the linear algebra  |          |         |
-|                                | problem associated to the internal Newton solver              |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| rp_rtol                        | Relative tolerance for the convergence test of the internal   | Real     | 1.e-6   |
-|                                | Newton solver. Valid only for StiffSolver::BackwardEuler      |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| use_jacobian_caching           | Only for StiffSolver::VODE, enables caching the numerical     | int      | 1       |
-|                                | jacobian                                                      |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
-| X_reject_buffer                | Only for StiffSolver::VODE, constrain species abundances      | Real     | 1.0     |
-|                                | such that they don't change by more than a certain factor in  |          |         |
-|                                | a given step                                                  |          |         |
-+--------------------------------+---------------------------------------------------------------+----------+---------+
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+|                       | Description                                                         |   Type | Default   |
++=======================+=====================================================================+========+===========+
+| burner_verbose        | Enables the printing on screen of some integration statistics       | int    | 0         |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| ode_max_steps         | The maximum number of substeps for the ODE integration              | int    | 150000    |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| jacobian_type         | Select how to compute the jacobian for the ODE iterative            | string | Numerical |
+|                       | solver. Available choices are:                                      |        |           |
+|                       |                                                                     |        |           |
+|                       | * ``Numerical`` for a first-order numerical approximation           |        |           |
+|                       | * ``Broyden`` for Broyden's method (only for BackwardEuler)         |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| atol                  | Absolute tolerance for the ODE integration error test between       | Real   | 1.e-6     |
+|                       | the solution and the fine-step solution                             |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| rtol                  | Relative tolerance for the ODE integration error test between       | Real   | 1.e-6     |
+|                       | the solution and the fine-step solution                             |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| retry_atol            | Overwrites the absolute tolerance value atol in case the ODE        | Real   | -1        |
+|                       | integration fails                                                   |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| retry_rtol            | Overwrites the relative tolerance value rtol in case the ODE        | Real   | -1        |
+|                       | integration fails                                                   |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| retry_swap_jacobian   | Swaps the type of jacobian (from 1 to 0 or vice versa) in           | int    | 1         |
+|                       | case the ODE integration fails                                      |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| ode_max_dt            | Maximum timestep size for the ODE integration substeps              | Real   | 1.e30     |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| max_dt_change_factor  | Only for StiffSolver::ForwardEuler, sets a maximum factor           | Real   | 1.001     |
+|                       | for the change of the timestep for the internal substeps            |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| max_iter              | Maximum number of iterations for the internal Newton solver         | int    | 100       |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| linalg_do_pivoting    | Only for StiffSolver::BackwardEuler and StiffSolver::VODE,          | int    | 1         |
+|                       | switches on/off the pivoting when solving the linear algebra        |        |           |
+|                       | problem associated to the internal Newton solver                    |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| rp_rtol               | Relative tolerance for the convergence test of the internal         | Real   | 1.e-6     |
+|                       | Newton solver. Valid only for StiffSolver::BackwardEuler            |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| use_jacobian_caching  | Only for StiffSolver::VODE, enables caching the numerical           | int    | 1         |
+|                       | jacobian                                                            |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
+| X_reject_buffer       | Only for StiffSolver::VODE, constrain species abundances            | Real   | 1.0       |
+|                       | such that they don't change by more than a certain factor in        |        |           |
+|                       | a given step                                                        |        |           |
++-----------------------+---------------------------------------------------------------------+--------+-----------+
 
 
 Below is an example for specifying chemical reactions for MFIX-Exa.