Merge remote-tracking branch 'origin/docs' into docs

docs/source/getting_started/00_revision_history.rst

@@ -123,9 +123,9 @@ NOTE: Contains KPP modifications specific to GEOS-Chem
 
 - Now create Fortran-90 source code files with :file:`*.F90` instead
   of :file:`*.f90`. (NOTE: In :ref:`kpp250`, this can specified with
-  the :ref:`uppercasef90` command.)
+  the :ref:`uppercasef90-cmd` command.)
 
-- Remove calls to UPDATE_SUN and UPDATE_RCONST from all *.f90
+- Remove calls to UPDATE_SUN and UPDATE_RCONST from all :code:`*.f90`
   integrators. (NOTE: This has been restored in :ref:`kpp250`.)
 
 .. _kpp225gc:
@@ -171,7 +171,7 @@ NOTE: Contains KPP modifications specific to GEOS-Chem
 
 - Added :code:`OMPThreadPrivate` function for F77.
 
-- Added declaration of :code:`A` in :ref:`ROOT_Function`
+- Added declaration of :code:`A` in :ref:`Function`
 
 - Added :code:`OMP THREADPRIVATE` Functionality to F90 output.
 
@@ -212,7 +212,7 @@ KPP 2.2.3
 
 - New Rosebrock method :code:`Rang3` was added.
 
-- The new KPP command :code:`#DECLARE` was added (see :ref:`declare`).
+- The new KPP command :code:`#DECLARE` was added (see :ref:`declare-cmd`).
 
 - Several vector and array functions from :program:`BLAS` (:code:`WCOPY`,
   :code:`WAXPY`, etc.) were replaced by Fortran90 expressions.
@@ -241,6 +241,6 @@ KPP 2.1
   reactions (see :ref:`lookat-and-monitor`.
 
 - The dummy index allows to test if a certain species occurs in the
-  current chemistry mechanism. (see :ref:`dummyindex`)
+  current chemistry mechanism. (see :ref:`dummyindex-cmd`)
 
 - Lines starting with :code:`//` are comment lines.

docs/source/getting_started/02_running_kpp_sample_mech.rst

@@ -125,7 +125,7 @@ code in the KPP language (cf. :ref:`bnf-description`):
    #CHECK O; N;                    { Check Mass Balance of oxygen & nitrogen }
 
    #INITVALUES                     { Set initial values of species           }
-     CFACTOR = 1.    ;             { and et units conversion factor to 1     }
+     CFACTOR = 1.    ;             { and set units conversion factor to 1    }
      O1D = 9.906E+01 ;
      O   = 6.624E+08 ;
      O3  = 5.326E+11 ;

docs/source/index.rst

@@ -16,7 +16,7 @@ The Kinetic PreProcessor: KPP
    <p>
    <a href="https://github.com/KineticPreProcessor/KPP/blob/main/LICENSE.txt"><img
    src="https://img.shields.io/badge/License-GPLv3-blue.svg"></a>
-   <a href="https://doi.org/10.5281/zenodo.4552707"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4552707.svg"></a>
+   <a href="https://doi.org/10.5281/zenodo.6563908"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6563908.svg"></a>
    <a href="https://kpp.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/kpp?label=ReadTheDocs"></a>
    </p>
 

docs/source/reference/editing_these_docs.rst

@@ -5,8 +5,8 @@
 Editing this User Guide
 #######################
 
-This user guide is generated with `Sphinx <https://www.sphinx-doc.org/>`_. 
-Sphinx is an open-source Python project designed to make writing software documentation easier. 
+This user guide is generated with `Sphinx <https://www.sphinx-doc.org/>`_.
+Sphinx is an open-source Python project designed to make writing software documentation easier.
 The documentation is written in a reStructuredText (it's similar to markdown), which Sphinx extends for software documentation.
 The source for the documentation is the :file:`docs/source` directory in top-level of the source code.
 
@@ -15,14 +15,17 @@ Quick start
 ===========
 
 To build this user guide on your local machine, you need to install Sphinx. Sphinx is a Python 3 package and
-it is available via :program:`pip`. This user guide uses the Read The Docs theme, so you will also need to 
+it is available via :program:`pip`. This user guide uses the Read The Docs theme, so you will also need to
 install :literal:`sphinx-rtd-theme`. It also uses the `sphinxcontrib-bibtex <https://pypi.org/project/sphinxcontrib-bibtex/>`_
 and `recommonmark <https://recommonmark.readthedocs.io/>`_ extensions, which you'll need to install.
 
 .. code-block:: console
 
-   $ pip install sphinx sphinx-rtd-theme sphinxcontrib-bibtex recommonmark
+   $ cd $KPP_HOME/docs
+   $ pip install -r requirements.txt
 
+Installing with :file:`requirements.txt` will make sure that the
+proper versions of Sphinx and its dependencies will be installed.
 
 To build this user guide locally, navigate to the :file:`docs/` directory and make the :literal:`html` target.
 
@@ -34,7 +37,7 @@ To build this user guide locally, navigate to the :file:`docs/` directory and ma
 
 This will build the user guide in :file:`docs/build/html`, and you can
 open :file:`index.html` in your  web-browser. The source files for the
-user guide are found in :file:`docs/source`.   
+user guide are found in :file:`docs/source`.
 
 .. note::
 
@@ -50,27 +53,27 @@ can be easily miswritten. Two important things you should know right away are:
 * Indents are 3-spaces
 * "Things" are separated by 1 blank line. For example, a list or
   code-block following a paragraph should be separated from the
-  paragraph by 1 blank line. 
+  paragraph by 1 blank line.
 
 You should keep these in mind when you're first getting
 started. Dedicating an hour to learning reST will save you time in the
 long-run.  Below are some good resources for learning reST.
 
 * `reStructuredText primer
   <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_:
-  (single best resource; however, it's better read than skimmed) 
+  (single best resource; however, it's better read than skimmed)
 * Official `reStructuredText reference
   <https://docutils.sourceforge.io/docs/user/rst/quickref.html>`_
-  (there is *a lot* of information here) 
+  (there is *a lot* of information here)
 * `Presentation by Eric Holscher
   <https://www.youtube.com/watch?v=eWNiwMwMcr4>`_ (co-founder of Read
   The Docs) at DjangoCon US 2015 (the entire presentation is good, but
-  reST is described from 9:03 to 21:04) 
+  reST is described from 9:03 to 21:04)
 * `YouTube tutorial by Audrey Tavares's
-  <https://www.youtube.com/watch?v=DSIuLnoKLd8>`_ 
+  <https://www.youtube.com/watch?v=DSIuLnoKLd8>`_
 
 A good starting point would be Eric Holscher's presentations followed
-by the reStructuredText primer. 
+by the reStructuredText primer.
 
 ================
 Style guidelines
@@ -96,19 +99,19 @@ For **titles and headers**:
 the :literal:`:file:` role.
 
 **Program names** (e.g. :program:`cmake`) occuring in the text should
-use the :literal:`:program:` role. 
+use the :literal:`:program:` role.
 
 **OS-level commands** (e.g. :command:`rm`) occuring in the text should
-use the :literal:`:command:` role. 
+use the :literal:`:command:` role.
 
 **Environment variables** occuring in the text should use the
-:literal:`:envvar:` role. 
+:literal:`:envvar:` role.
 
 **Inline code** or code variables occuring in the text should use the
-:literal:`:code:` role. 
+:literal:`:code:` role.
 
 **Code snippets** should use :literal:`.. code-block:: <language>`
-directive like so 
+directive like so
 
 .. code-block:: none
 
@@ -117,7 +120,7 @@ directive like so
       import gcpy
       print("hello world")
 
-The language can be "none" to omit syntax highlighting. 
+The language can be "none" to omit syntax highlighting.
 
 For command line instructions, the "console" language should be
 used. The :literal:`$` should be used to denote the console's
@@ -126,4 +129,4 @@ instructions, a prompt like :literal:`gcuser:~/path1/path2$` should be
 used.
 
 **Inline literals** (e.g. the :literal:`$` above) should use the
-:literal:`:literal:` role. 
+:literal:`:literal:` role.

docs/source/tech_info/07_numerical_methods.rst

@@ -665,7 +665,7 @@ Details can be found in the comment lines of the individual integrator files
 
     Number of function calls.
 
-.. option:: ISTATUS_U(2)`
+.. option:: ISTATUS_U(2)
 
    Number of Jacobian calls.
 

docs/source/using_kpp/04_input_for_kpp.rst

@@ -372,9 +372,9 @@ 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:: 
+.. table::
    :align: center
-           
+
    +--------------------------+-----------------------+
    | KPP command              | default value         |
    +==========================+=======================+
@@ -651,6 +651,12 @@ for the fill-in due to the LU decomposition.
 #LANGUAGE
 ---------
 
+.. attention::
+
+   The :command:`Fortran77` language option is deprecated in
+   :ref:`kpp250` and  later versions. All further KPP development will
+   only support Fortran90.
+
 The :command:`#LANGUAGE` command selects the target language in which the
 code file is to be generated. Available options are :command:`Fortran90`,
 :command:`C`, or :command:`matlab`.

docs/source/using_kpp/05_output_from_kpp.rst

@@ -180,7 +180,7 @@ initialized in :file:`ROOT_Parameters.f90` (or :file:`.F90`).
    +----------------+---------------------------------------------+--------+
    | Parameter      | Represents                                  | Value  |
    +================+=============================================+========+
-   | ``NSPEC``      | No. chemical species (:code:`NVAR+NFIX`)    | 7      |
+   | ``NSPEC``      | No. chemical species (``NVAR`` + ``NFIX``)  | 7      |
    +----------------+---------------------------------------------+--------+
    | ``NVAR``       | No. variable species                        | 5      |
    +----------------+---------------------------------------------+--------+
@@ -203,9 +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
+Values listed the 3rd column of Table 5 are from the
 :command:`small_strato` mechanism
-(cf. :ref:`running-kpp-with-an-example-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

models/small_strato.def

@@ -7,7 +7,7 @@
 #CHECK O; N;                    { Check Mass Balance of oxygen & nitrogen }
 
 #INITVALUES                     { Set initial values of species           }
-  CFACTOR = 1.    ;             { and et units conversion factor to 1     }
+  CFACTOR = 1.    ;             { and set units conversion factor to 1    }
   O1D = 9.906E+01 ;
   O   = 6.624E+08 ;
   O3  = 5.326E+11 ;