Continue updating the ReadTheDocs documentation

(1) Split files across docs/source/getting_started, docs/source/using_kpp, docs/source/tech_info, docs/source/citations, and docs/source/reference (2) Updated conf.py to remove the rubric for references (3) Updated content in "Input for KPP" and "Output from KPP" (4) Added figures and table titles (5) Trimmed trailing whitespace Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KineticPreProcessor · May 13, 2022 · df1bae4 · df1bae4
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diff --git a/docs/source/_static/small_hess1.png b/docs/source/_static/small_hess1.png
diff --git a/docs/source/_static/small_hess2.png b/docs/source/_static/small_hess2.png
diff --git a/docs/source/_static/small_jac.png b/docs/source/_static/small_jac.png
diff --git a/docs/source/bibtex.json b/docs/source/bibtex.json
@@ -1,10 +1,14 @@
 {
     "cited": {
+        "using_kpp/04_input_for_kpp": [
+            "1996:Sandu_Potra_Damian_and_Carmichael",
+        ],
         "citations/09_acknowledgments": [
             "1996:Damian-Iordache",
         ],
-        "citations/10_kpp_references": [
+        "citations/10_kpp_kreferences": [
             "1996:Damian-Iordache",
+            "1996:Sandu_Potra_Damian_and_Carmichael",
         ],
     }
 }
diff --git a/docs/source/citations/adrian.bib b/docs/source/citations/adrian.bib
@@ -230,7 +230,7 @@ @TECHREPORT{1995:KPP-GUIDE
 INSTITUTION  = {The University of Iowa, Iowa City, IA 52246},
 YEAR         = 1995}
 
-@ARTICLE{1996:IMPLEMENTATION,
+@ARTICLE{1996:Sandu_Potra_Damian_and_Carmichael,
 AUTHOR       = {A. Sandu and F. A. Potra and V. Damian and G. R. Carmichael},
 TITLE        = {Efficient implementation of fully implicit methods for
 atmospheric chemistry},
@@ -239,7 +239,7 @@ @ARTICLE{1996:IMPLEMENTATION
 PAGES        = {101-110},
 YEAR         = 1996}
 
- 
+
 @book{1993::HW1,
  author = "E.~ Hairer and S.P.~ Norsett and G.~ Wanner",
  title = " Solving Ordinary Differential Equations I.
@@ -279,7 +279,7 @@ @book{1993:LSODE
  publisher = {NASA reference publication 1327},
  year = {1993}
 }
- 
+
 @article{1989:VODE,
  author = "P.N.~ Brown and G.D.~ Byrne and A.C.~ Hindmarsh",
  title = "VODE: A Variable Step ODE Solver",

diff --git a/docs/source/citations/rolf.bib b/docs/source/citations/rolf.bib
@@ -187,9 +187,9 @@ @ARTICLE{2002:vonGlasow
 
 @ARTICLE{2003:vonKuhlmann,
 KEYWORD      = {model},
-AUTHOR       = {R. von Kuhlmann and M. G. Lawrence and P. J. Crutzen and P. J. 
+AUTHOR       = {R. von Kuhlmann and M. G. Lawrence and P. J. Crutzen and P. J.
 Rasch},
-TITLE        = {A model for studies of tropospheric ozone and nonmethane 
+TITLE        = {A model for studies of tropospheric ozone and nonmethane
 hydrocarbons: Model description and ozone results},
 JOURNAL      = jgr,
 VOLUME       = {108D},
@@ -291,4 +291,3 @@ @BOOK{1996:Hairer-Wanner
 Differential-Algebraic Problems},
 PUBLISHER    = {Springer-Verlag},
 YEAR         = 1996}
-
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -66,7 +66,6 @@ def format_web_refs(self, e):
 register_plugin("pybtex.style.formatting", "refstyle", RefStyle)
 
 
-#bibtex_bibliography_header = ".. rubric:: References"
 bibtex_bibliography_header = ""
 bibtex_footbibliography_header = bibtex_bibliography_header
 

diff --git a/docs/source/getting_started/00_revision_history.rst b/docs/source/getting_started/00_revision_history.rst
@@ -30,12 +30,12 @@ KPP-2.4.0
 
 - New integrators: :file:`beuler.f90`, :file:`rosenbrock_mz.f90`,
   :file:`rosenbrock_posdef.f90,  :file:`rosenbrock_posdef_h211b_qssa.f90`
-  
+
 - Several memory sizes (:code:`MAX_EQN`, ...) increased to allow large
-  chemical mechanisms 
-  
+  chemical mechanisms
+
 - new Makefile target: :code:`list`
-  
+
 - LaTeX User Manual added
 
 - Now use :code:`ICNTRL(15)` to decide whether or not to toggle calling the

diff --git a/docs/source/getting_started/01_installation.rst b/docs/source/getting_started/01_installation.rst
@@ -11,13 +11,13 @@ Download KPP from Github
 ========================
 
 Clone the KPP source code from the `KPP Github repository
-<(https://github.com/KineticPreProcessor/KPP>`_: 
+<(https://github.com/KineticPreProcessor/KPP>`_:
 
 .. code-block:: console
 
    $ git clone https://github.com/KineticPreProcessor/KPP.git
 
-This will create folder named KPP in your disk space. 
+This will create folder named KPP in your disk space.
 
 ========================================
 Define the KPP_HOME environment variable
@@ -104,7 +104,7 @@ Change to the KPP/src directory:
    $ cd $KPP_HOME/src
 
 To clean a previously-built KPP installation, delete the KPP object
-files and all the examples with:    
+files and all the examples with:
 
 .. code-block:: console
 
@@ -118,7 +118,7 @@ To delete a previoulsy-built KPP executable as well, type:
 
 If necessary, edit and enter the name of your C compiler in
 :file:`src/Makefile`.  The default setting is :program:`gcc` (aka the
-GNU Compiler Collection).  
+GNU Compiler Collection).
 
 Create the kpp executable with:
 

diff --git a/docs/source/getting_started/02_running_kpp_sample_mech.rst b/docs/source/getting_started/02_running_kpp_sample_mech.rst
@@ -27,16 +27,15 @@ capabilities. However, the software tools are general and can be applied
 to virtually any kinetic mechanism.
 
 We focus on Fortran90. Particularities of the C, Fortran77, and Matlab
-languages are discussed in `Target language selection
-<language_>`_. 
+languages are discussed in the :ref:`#LANGUAGE` section.
 
 The KPP input files (with suffix :file:`.kpp`) specify the model, the
 target language, the precision, the integrator and the driver, etc. The file
 name (without the suffix :file:`.kpp`) serves as the root name for the
 simulation. In this paper we will refer to this name as root. Since
 the root name will be incorporated into Fortran90 module names, it can
 only contain valid Fortran90 characters, i.e. letters, numbers, and the
-underscore. To specify a KPP model, write a root file with the following lines: 
+underscore. To specify a KPP model, write a root file with the following lines:
 
 .. code-block:: console
 
@@ -57,7 +56,7 @@ by KPP) is selected with the command:
    #LANGUAGE Fortran90
 
 Here, we have chosen Fortran90. See `Target language selection
-<target-language-selection_>`_ for other options. 
+<target-language-selection_>`_ for other options.
 
 The data type of the generated model can be switched between
 single/double precision with the command . The command selects a

diff --git a/docs/source/tech_info/06_info_for_kpp_developers.rst b/docs/source/tech_info/06_info_for_kpp_developers.rst
@@ -44,7 +44,7 @@ KPP directory structure
          \    evaluate parsed input
          \    flex/bison-generated file
          \    flex/bison-generated header file
-         \    
+         \
          ==== =================================
 
 The KPP distribution will unfold a directory ``$KPP_HOME`` with the
@@ -99,7 +99,7 @@ KPP environment variables
 In order for KPP to find its components, it has to know the path to the
 location where the KPP distribution is installed. This is achieved by
 requiring the :envvar:`$KPP_HOME` environment variable to be set to the path
-where KPP is installed. 
+where KPP is installed.
 
 The :envvar:`PATH` variable should be updated to contain the
 :file:`$KPP_HOME/bin` directory.
@@ -117,7 +117,7 @@ Default setting: none
 KPP_MODEL
 ---------
 Optional, specifies additional places where KPP will look for model
-files before searching the default location.  
+files before searching the default location.
 
 Default setting: :file:`$KPP_HOME/models`.
 
@@ -222,7 +222,7 @@ an example:
 -  Add to several files in the directory:
 
 .. code-block:: C
-   
+
    void CmdNEWCMD( char *cmd );
    -  : ``{ "NEWCMD", PRM_STATE, NEWCMD },``
 

diff --git a/docs/source/tech_info/07_numerical_methods.rst b/docs/source/tech_info/07_numerical_methods.rst
@@ -346,23 +346,23 @@ This Runge-Kutta method of order 5 based on RADAU-IIA quadrature
 is stiffly accurate. The KPP implementation follows the original
 implementation of :raw-latex:`\citet`.    While RADAU5 is  relatively
 expensive (when compared to the  Rosenbrock methods), it  is more
-robust and is useful to obtain accurate reference solutions.                  
+robust and is useful to obtain accurate reference solutions.
 
 RK SDIRK
 --------
-**Integrator files:**  :file:`int/sdirk.f`,          
+**Integrator files:**  :file:`int/sdirk.f`,
 
-SDIRK is an L-stable, singly-diagonally-implicit Runge-Kutta method. The    
-implementation is based on :raw-latex:`\citet`. Several variants are       
-available: 
+SDIRK is an L-stable, singly-diagonally-implicit Runge-Kutta method. The
+implementation is based on :raw-latex:`\citet`. Several variants are
+available:
 
-  - Sdirk 2a, 2b: 2 stages, order 2                
+  - Sdirk 2a, 2b: 2 stages, order 2
   - Sdirk 3a: 3 stages, order 2
   - Sdirk 4a, 4b: 5 stages, order 4
 
 RK SDIRK4
 ----------
-**Integrator files:** :file:`int/kpp_sdirk4.f`,  :file:`int/kpp_sdirk4.f90` 
+**Integrator files:** :file:`int/kpp_sdirk4.f`,  :file:`int/kpp_sdirk4.f90`
 
 SDIRK4 is an L-stable, singly-diagonally-implicit Runge-Kutta method
 of order 4. The implementation is based on :raw-latex:`\citet`.
@@ -452,18 +452,18 @@ Table `[tab:BDF] <#tab:BDF>`__.
 
 LSODE
 -----
-**Integrator file:** :file:`int/kpp_lsode.f90` 
+**Integrator file:** :file:`int/kpp_lsode.f90`
 
 LSODE, the Livermore ODE solver (:cite:`LSODE`), implements backward
 differentiation formula (BDF) methods for stiff problems.  LSODE has
-been translated to Fortran90 for the incorporation into the KPP library.  
+been translated to Fortran90 for the incorporation into the KPP library.
 
 LSODES
 -------
 **Integrator file:** :file:`int/atm_lsodes.f`
 
  LSODES, the sparse version of the Livermore ODE  solver LSODE, is
- modified to interface directly with the KPP generated code. 
+ modified to interface directly with the KPP generated code.
 
 VODE
 -----
@@ -610,4 +610,3 @@ Details can be found in the comment lines of the individual integrator files
 |                      | taken.  For multiple restarts, use :code:`Hnew` as |
 |                      | :code:`Hstart` in the subsequent run.              |
 +----------------------+----------------------------------------------------+
-