table with default values of KPP commands, and more

docs/source/tech_info/06_info_for_kpp_developers.rst

@@ -280,39 +280,40 @@ To add a new KPP command, the source code has to be edited at several
 locations. A short summary is presented here, using the new command as
 an example:
 
--  Add to several files in the directory:
+* Add the new command to several files in the :file:`src/` directory:
+
+  - :file:`scan.h`: add :code:`void CmdNEWCMD( char *cmd );`
 
-.. code-block:: C
+  - :file:`scan.l`: add :code:`{ "NEWCMD", PRM_STATE, NEWCMD },`
 
-   void CmdNEWCMD( char *cmd );
-   -  : ``{ "NEWCMD", PRM_STATE, NEWCMD },``
+  - :file:`scanner.c`: add :code:`void CmdNEWCMD( char *cmd )`
 
-   -  : ``void CmdNEWCMD( char *cmd )``
+  - :file:`scan.y`:
 
-   -  :
+    - add :code:`%token NEWCMD`
 
-      -  ``%token NEWCMD``
+    - add :code:`| NEWCMD PARAMETER`
 
-      -  ``NEWCMD PARAMETER``
+    - add :code:`{ CmdNEWCMD( $2 ); }`
 
-      -  ``{ CmdNEWCMD( $2 ); }``
+* Add :ref:`ci-tests`:
 
--  Add a :ref:`ci-tests`:
+  - Create a new directory :file:`ci-tests/ros_newcmd/ros_newcmd.kpp`
 
-   -  Create a new directory
+  - Add new :ref:`ci-tests` to the :file:`ci-tests` folder and
+    update the scripts in the :file:`.ci-pipelines` folder.
 
-   -  Add new :ref:`ci-tests` to the :file:`ci-tests` folder and
-      update the scripts in :file:`.ci-pipelines` folder.
+* Other:
 
--  Other:
+  - explain in user manual :file:`manual/kpp_UserManual.tex`:
 
-   -  Explain in user manual:
+    - add to table :code:`tab:commands`
 
-      -  Add to table
+    - add a section :code:`sec:command-newcmd`
 
-      -  Add a section
+    - add to BNF description table :code:`sec:bnf`
 
-      -  Add to BNF description table
+  - add to :file:`site-lisp/kpp.el`
 
 .. _ci-tests:
 

docs/source/tech_info/07_numerical_methods.rst

@@ -373,7 +373,7 @@ Fully implicit 3-stage Runge-Kutta methods.  Several variants are available:
 
 RADAU5
 ------
-**Integrator files:** :file:`int/kpp_radau5.f90`
+**Integrator files:** :file:`int/radau5.f90`
 
 This Runge-Kutta method of order 5 based on RADAU-IIA quadrature
 is stiffly accurate. The KPP implementation follows the original
@@ -396,14 +396,14 @@ variants are available:
 
 SDIRK4
 ------
-**Integrator file:** :file:`int/kpp_sdirk4.f90`
+**Integrator file:** :file:`int/sdirk4.f90`
 
 SDIRK4 is an L-stable, singly-diagonally-implicit Runge-Kutta method
 of order 4. The implementation is based on :cite:`1991:Hairer_and_Wanner`.
 
 SEULEX
 ------
-**Integrator file:** :file:`int/kpp_seulex.f90`
+**Integrator file:** :file:`int/seulex.f90`
 
 SEULEX is a variable  order stiff extrapolation code able to produce
 highly accurate solutions. The KPP implementation is based on the
@@ -484,21 +484,35 @@ implementations of BDF methods, described in the following sections:
 
 LSODE
 -----
-**Integrator file:** :file:`int/kpp_lsode.f90`
+**Integrator file:** :file:`int/lsode.f90`
 
 LSODE, the Livermore ODE solver :cite:`1993:LSODE`, implements backward
 differentiation formula (BDF) methods for stiff problems.  LSODE has
 been translated to Fortran90 for the incorporation into the KPP library.
 
 VODE
------
+----
 
-**Integrator file:** :file:`int/kpp_dvode.f90`
+**Integrator file:** :file:`int/dvode.f90`
 
 VODE :cite:`1989:VODE` uses another formulation of backward
 differentiation formulas. The version of VODE present in the KPP
 library uses directly the KPP sparse linear algebra routines.
 
+BEULER
+------
+
+**Integrator file:** :file:`int/beuler.f90`
+
+=====
+Other
+=====
+
+FEULER
+------
+
+**Integrator file:** :file:`int/feuler.f90`
+
 .. _integrator-input-output:
 
 =============================

docs/source/using_kpp/04_input_for_kpp.rst

@@ -368,10 +368,61 @@ included in the transport calculations.
 KPP commands
 ============
 
-A command begins on a new line with a :code:`#` sign, followed by a
+A KPP command begins on a new line with a :code:`#` sign, followed by a
 command name and one or more parameters.  Details about each command
 are given in the following subsections.
 
+.. table:: 
+   :align: center
+
+   +--------------------------+-----------------------+
+   | KPP command              | default value         |
+   +==========================+=======================+
+   | :command:`#CHECKALL`     |                       |
+   +--------------------------+-----------------------+
+   | :command:`#DECLARE`      | :code:`SYMBOL`        |
+   +--------------------------+-----------------------+
+   | :command:`#DOUBLE`       | :code:`ON`            |
+   +--------------------------+-----------------------+
+   | :command:`#DRIVER`       | :code:`none`          |
+   +--------------------------+-----------------------+
+   | :command:`#DUMMYINDEX`   | :code:`OFF`           |
+   +--------------------------+-----------------------+
+   | :command:`#EQNTAGS`      | :code:`OFF`           |
+   +--------------------------+-----------------------+
+   | :command:`#FUNCTION`     | :code:`AGGREGATE`     |
+   +--------------------------+-----------------------+
+   | :command:`#HESSIAN`      | :code:`ON`            |
+   +--------------------------+-----------------------+
+   | :command:`#INCLUDE`      |                       |
+   +--------------------------+-----------------------+
+   | :command:`#INTEGRATOR`   |                       |
+   +--------------------------+-----------------------+
+   | :command:`#INTFILE`      |                       |
+   +--------------------------+-----------------------+
+   | :command:`#JACOBIAN`     | :code:`SPARSE_LU_ROW` |
+   +--------------------------+-----------------------+
+   | :command:`#LANGUAGE`     |                       |
+   +--------------------------+-----------------------+
+   | :command:`#LOOKATALL`    |                       |
+   +--------------------------+-----------------------+
+   | :command:`#MEX`          | :code:`ON`            |
+   +--------------------------+-----------------------+
+   | :command:`#MINVERSION`   |                       |
+   +--------------------------+-----------------------+
+   | :command:`#MODEL`        |                       |
+   +--------------------------+-----------------------+
+   | :command:`#REORDER`      | :code:`ON`            |
+   +--------------------------+-----------------------+
+   | :command:`#STOCHASTIC`   | :code:`OFF`           |
+   +--------------------------+-----------------------+
+   | :command:`#STOICMAT`     | :code:`ON`            |
+   +--------------------------+-----------------------+
+   | :command:`#TRANSPORTALL` |                       |
+   +--------------------------+-----------------------+
+   | :command:`#UPPERCASEF90` | :code:`OFF`           |
+   +--------------------------+-----------------------+
+
 .. _declare-cmd:
 
 #DECLARE
@@ -544,8 +595,18 @@ is similar to:
 
    #INCLUDE $KPP_HOME/int/integrator-name.def
 
-If the :command:`#INTEGRATOR` the command occurs twice, the second
-replaces the first.
+The :command:`#INTEGRATOR` command allows the use of different
+integration techniques on the same model. If it occurs twice, the second
+replaces the first. Normally, KPP tries to find the selected integrator
+files in the directory :file:`$KPP_HOME/int/`. However, if the supplied
+file name contains a slash, it is assumed to be absolute. To access an
+integrator in the current directory, the prefix :file:`./` can be used,
+e.g.:
+
+.. code-block:: console
+
+   #INTEGRATOR ./mydeffile
+   #INTFILE ./myintegrator
 
 .. _intfile-cmd:
 
@@ -561,22 +622,12 @@ replaces the first.
 The integrator definition file selects an integrator file with
 :command:`#INTFILE` and also defines some suitable options for it. The
 :command:`#INTFILE` command selects the file that contains the integrator
-routine. This command allows the use of different integration
-techniques on the same model. The parameter of the
+routine. The parameter of the
 command is a file name, without suffix. The appropriate suffix
 (:code:`.f90`, :code:`.F90`, :code:`.c`, or :code:`.m` is appended and
 the result selects the file from which the integrator
 is taken. This file will be copied into the code file in the appropriate
-place. All integrators have to conform to the same specific calling
-sequence. Normally, KPP tries to find the selected integrator file in
-the directory :file:`$KPP_HOME/int/`. However, if the supplied file name
-contains a slash, it is assumed to be absolute. To access an integrator
-in the current directory, the prefix :file:`./` can be used, e.g.:
-
-.. code-block:: console
-
-   #INTEGRATOR ./mydeffile
-   #INTFILE ./myintegrator
+place.
 
 .. _jacobian-cmd:
 

docs/source/using_kpp/05_output_from_kpp.rst

@@ -31,15 +31,13 @@ is contained in the following sections.
    are only produced under certain circumstances.
 
 All subroutines and functions, global parameters, variables, and
-sparsity data structures  are encapsulated in modules. There is
-exactly one module in each file, and the name of the module is
-identical to the file name but without  the suffix :code:`.f90` or
-:code:`.F90`. `Figure 1 (above) <The Fortran90 code_>`_ shows how these modules
-are related to  each other. The generated code is consistent with the
-Fortran90 standard. It will not exceed the maximum number of 39 continuation
-lines. If KPP cannot properly split an expression to keep the number
-of continuation lines below the threshold then it will generate a
-warning message pointing to the location of this expression.
+sparsity data structures are encapsulated in modules. There is exactly
+one module in each file, and the name of the module is identical to the
+file name but without the suffix :code:`.f90` or :code:`.F90`. `Figure 1
+(above) <The Fortran90 code_>`_ shows how these modules are related to
+each other. The generated code is consistent with the Fortran90
+standard. It may, however, exceed the official maximum number of 39
+continuation lines.
 
 .. tip::
 
@@ -182,7 +180,7 @@ initialized in :file:`ROOT_Parameters.f90` (or :file:`.F90`).
    +----------------+---------------------------------------------+--------+
    | Parameter      | Represents                                  | Value  |
    +================+=============================================+========+
-   | ``NSPEC``      | No. chemical species (``NVAR``+``NFIX``)    | 7      |
+   | ``NSPEC``      | No. chemical species (:code:`NVAR+NFIX`)    | 7      |
    +----------------+---------------------------------------------+--------+
    | ``NVAR``       | No. variable species                        | 5      |
    +----------------+---------------------------------------------+--------+
@@ -205,9 +203,9 @@ initialized in :file:`ROOT_Parameters.f90` (or :file:`.F90`).
    | ``indf_spc``   | Index of fixed species *spc* in :code:`FIX` |        |
    +----------------+---------------------------------------------+--------+
 
-   NOTE: Values listed the 3rd column of Table 5 are from the
-   :command:`small_strato` mechanism
-   (cf. :ref:`running-kpp-with-an-example-mechanism`). 
+NOTE: Values listed the 3rd column of Table 5 are from the
+:command:`small_strato` mechanism
+(cf. :ref:`running-kpp-with-an-example-mechanism`). 
 
 KPP orders the variable species such that the sparsity pattern of the
 Jacobian is maintained after an LU decomposition. For our example there