Skip to content

Commit

Permalink
Update C-I test table and add other fixes
Browse files Browse the repository at this point in the history 
docs/source/getting_started/02_running_kpp_sample_mech.rst
- Fix length of overline & underine for "1. Create a directory for the example"

docs/source/tech_info/06_info_for_kpp_developers.rst
- Updated the list of C-I tests

docs/source/tech_info/07_numerical_methods.rst
- Fix reference for Lin et al 2002

docs/source/tech_info/04_input_for_kpp.rst
- Fixed typo in MINVERSION reference ("_inversion-cmd" should be
  "_minversion-cmd")

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
  • Loading branch information
@yantosca
yantosca committed Jun 30, 2022
1 parent 7a7a519 commit ae9d778
Show file tree
Hide file tree
Showing 4 changed files with 62 additions and 62 deletions.
4 changes: 2 additions & 2 deletions docs/source/getting_started/02_running_kpp_sample_mech.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,9 @@ The sections below outline the steps necessary to build and run a

.. _example-step-1:

==================================
=====================================
1. Create a directory for the example
==================================
=====================================

Create a directory in which to build and run the example mechanism:

Expand Down
116 changes: 58 additions & 58 deletions docs/source/tech_info/06_info_for_kpp_developers.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -336,66 +336,66 @@ List of continuous integration tests
.. table:: Continuous integration tests
:align: center

+-----------------------+------------------------------------------------+
| C-I test | Description |
+=======================+================================================+
| :file:`radau90` | Uses the Runge-Kutta radau5 integrator |
| | with the SAPRC99 chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`rk` | Uses the Runge-Kutta integrator |
| | with the small_strato chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`rktlm` | Same as :file:`rk`, but uses the Runge-Kutta |
| | tangent-linear-model integrator. |
+-----------------------+------------------------------------------------+
| :file:`ros` | Uses the Rosenbrock integrator |
| | with the small_strato chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`ros_split` | Same as :file:`ros`, but tests the |
| | :command:`#FUNCTION SPLIT` command. |
+-----------------------+------------------------------------------------+
| :file:`rosadj` | Same as :file:`ros`, but uses the Rosenbrock |
| | adjoint integrator. |
+-----------------------+------------------------------------------------+
| :file:`rostlm` | Same as :file:`ros`, but uses the Rosenbrock |
| | tangent linear method integrator. |
+-----------------------+------------------------------------------------+
| :file:`rosenbrock90` | Uses the Rosenbrock integrator with the |
| | SAPRC99 chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`ros_minver` | Same as :file:`rosenbrock90`, but tests the |
| | :command:`#MINVERSION` command. This test |
| | is successful if the bulding of the |
| | mechanism fails with a "KPP version too old" |
| | error. |
+-----------------------+------------------------------------------------+
| :file:`ros_upcase` | Same as :file:`rosenbrock90`, but tests if |
| | KPP can generate Fortran90 code with the |
| | :file:`.F90` suffix (i.e. with |
| | :command:`#UPPERCASE ON`). |
+-----------------------+------------------------------------------------+
| :file:`saprc2006` | Uses the Rosenbrock integrator with the |
| | SAPRCNOV chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`sd` | Uses the Runge-Kutta SDIRK integrator |
| | with the small_strato chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`sdadj` | Same as :file:`sdadj`, but uses the |
| | Runge-Kutta SDIRK Adjoint integrator. |
+-----------------------+------------------------------------------------+
| :file:`small_f90` | Uses the LSODE integrator with the |
| | small_strato chemical mechanism. |
+-----------------------+------------------------------------------------+
| :file:`small_strato` | Uses the Rosenbrock integrator with the |
| | small_strato chemical mechanism. This uses |
| | the same options as the example described in |
| | :ref:`running-kpp-with-an-example-mechanism`. |
+-----------------------+------------------------------------------------+
+------------------------+-----------+-----------------+-----------------------+
| C-I test | Language | Model | Integrator |
+========================+===========+=================+=======================+
| ``C_rk`` | C | small_strato | runge_kutta |
+------------------------+-----------+-----------------+-----------------------+
| ``C_rosadj`` | C | small_strato | rosenbrock_adj |
+------------------------+-----------+-----------------+-----------------------+
| ``C_sd`` | C | small_strato | sdirk |
+------------------------+-----------+-----------------+-----------------------+
| ``C_sdadj`` | C | small_strato | sdirk_adj |
+------------------------+-----------+-----------------+-----------------------+
| ``C_small_strato`` | C | small_strato | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_lsode`` | Fortran90 | small_strato | lsode |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_radau`` | Fortran90 | saprc99 | radau5 |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_rk`` | Fortran90 | small_strato | runge_kutta |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_rktlm`` | Fortran90 | small_strato | runge_kutta_tlm |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_ros`` | Fortran90 | small_strato | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_ros_autoreduce`` | Fortran90 | saprc99 | rosenbrock_autoreduce |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_ros_split`` | Fortran90 | small_strato | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_ros_upcase`` | Fortran90 | saprc99 | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_rosadj`` | Fortran90 | small_strato | rosenbrock_adj |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_rosenbrock`` | Fortran90 | saprc99 | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_rostlm`` | Fortran90 | small_strato | rosenbrock_tlm |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_saprc_2006`` | Fortran90 | saprcnov | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_sd`` | Fortran90 | small_strato | sdirk |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_sdadj`` | Fortran90 | small_strato | sdirk_adj |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_seulex`` | Fortran90 | saprcnov | seulex |
+------------------------+-----------+-----------------+-----------------------+
| ``F90_small_strato`` | Fortran90 | small_strato | rosenbrock |
+------------------------+-----------+-----------------+-----------------------+
| ``X_minver`` | Fortran90 | small_strato | runge_kutta |
+------------------------+-----------+-----------------+-----------------------+

Notes about C-I tests:

#. :file:`F90_ros_split` also uses :command:`#FUNCTION SPLIT`.
#. :file:`F90_ros_upcase` also uses :command:`#UPPERCASEF90 ON`.
#. :file:`F90_small_strato` is the example from
:ref:`running-kpp-with-an-example-mechanism`.
#. :file:`X_minver` tests if the :ref:`minversion-cmd` command works
properly.

Each continuous integration test is contained in a subdirectory of
:file:`$KPP_HOME/ci-tests` in a KPP definition file (ending in
:file:`.kpp`) from :file:`$KPP_HOME/models/` or
:file:`$KPP_HOME/examples/`.
:file:`$KPP_HOME/ci-tests`. In each subdirectory is a KPP definition
file (ending in :file:`.kpp`).

.. _running-ci-tests-on-azure:

Expand Down
2 changes: 1 addition & 1 deletion docs/source/tech_info/07_numerical_methods.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -343,7 +343,7 @@ Rosenbrock with mechanism auto-reduction

**Integrator file:** :file:`int/rosenbrock_autoreduce.f90`

Mechanism auto-reduction (described in :cite:t:`2022:Lin_et_al`) expands
Mechanism auto-reduction (described in :cite:t:`Lin_et_al._2022`) expands
previous work by :cite:t:`Santillana_et_al._2010` and
:cite:t:`Shen_et_al._2020` to a computationally efficient implementation
in KPP, avoiding memory re-allocation, re-compile of the code, and
Expand Down
2 changes: 1 addition & 1 deletion docs/source/using_kpp/04_input_for_kpp.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -684,7 +684,7 @@ ODE function, Jacobian, and Hessian, for the target languages C,
Fortran77, and Fortran90. The default is :command:`#MEX ON`. With
:command:`#MEX OFF`, no Mex files are generated.

.. _inversion-cmd:
.. _minversion-cmd:

#MINVERSION
-----------
Expand Down

0 comments on commit ae9d778

Please sign in to comment.