From 032612dbdf0f27ac4896173288e57f111a196b95 Mon Sep 17 00:00:00 2001 From: Roberto Porcu <robbberto88@gmail.com> Date: Wed, 22 Jan 2025 14:54:10 +0000 Subject: [PATCH] Fix the Jacobian possible inputs for the chemistry section (exa/docs!109) --- .../user_guide/inputs/chemical_reactions.rst | 98 +++++++++---------- 1 file changed, 49 insertions(+), 49 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 0306be9..0e2dc6b 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/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. -- GitLab