diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index a81e6bf143aa0b2264ac9b1919684036c5f122a1..1f7d076a693b476807a6f812c25e5b4d2741d976 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -81,58 +81,76 @@ time to enable caching of the numerical approximation of the Jacobian matrix is selected. The following inputs can be specified using the prefix ``chemistry.integrator``: -+-----------------------+---------------------------------------------------------------------+--------+-----------+ -| | Description | Type | Default | -+=======================+=====================================================================+========+===========+ -| burner_verbose | Enable printing 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 solver. | String | Numerical | -| | This option is available for ``StiffSolver::BackwardEuler`` and | | | -| | ``StiffSolver::VODE``. | | | -| | | | | -| | Options (case-insensitive): | | | -| | | | | -| | * ``Numerical`` - first-order numerical approximation | | | -| | * ``Broyden`` - 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 | -| | enables 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``, enable 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 | Enable printing 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 solver. | String | Numerical | +| | This option is available for ``StiffSolver::BackwardEuler`` and | | | +| | ``StiffSolver::VODE``. | | | +| | | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``Numerical`` - first-order numerical approximation | | | +| | * ``Broyden`` - Broyden's method (only for ``BackwardEuler``) | | | ++------------------------+---------------------------------------------------------------------+--------+-----------+ +| broyden_type | When using the Broyden method in the Backward Euler ODE integrator, | String | Jacobian | +| | select whether to approximate the Jacobian or its inverse. | | | +| | This option is available only for ``StiffSolver::BackwardEuler``. | | | +| | | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``Jacobian`` | | | +| | * ``Inverse`` | | | ++------------------------+---------------------------------------------------------------------+--------+-----------+ +| broyden_initialization | When using the Broyden method in the Backward Euler ODE integrator, | String | Identity | +| | select whether to initialize the Jacobian or its inverse through the| | | +| | identity matrix or the numerical (finite-difference) approximation. | | | +| | | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``Identity`` | | | +| | * ``Numerical`` | | | ++------------------------+---------------------------------------------------------------------+--------+-----------+ +| 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 | +| | enables 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``, enable 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.