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KineticPreProcessor · Jul 3, 2022 · 57641d1 · 57641d1
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diff --git a/docs/source/bibtex.json b/docs/source/bibtex.json
@@ -13,7 +13,7 @@
         "tech_info/06_numerical_methods": [
             "Brown_Byrne_and_Hindmarsh_1989",
 	    "Hairer_and_Wanner_1991",
-	    "Hairer_Norsett_and_Wanner_1993",
+	    "Hairer_Norsett_and_Wanner_1987",
             "Sandu_et_al._1996",
             "Sandu_et_al._1997b",
             "Verwer_et_al._1999",
@@ -25,7 +25,7 @@
         "citations/10_kpp_references": [
             "Brown_Byrne_and_Hindmarsh_1989",
 	    "Hairer_and_Wanner_1991",
-	    "Hairer_Norsett_and_Wanner_1993",
+	    "Hairer_Norsett_and_Wanner_1987",
             "Damian-Iordache_1996",
             "Sandu_et_al._1996",
             "Sandu_et_al._1997b",

diff --git a/docs/source/citations/09_acknowledgments.rst b/docs/source/citations/09_acknowledgments.rst
@@ -22,12 +22,15 @@ This work has been supported by:
   <https://esto.nasa.gov/aist>`_ program (grant #
   `AIST-18-0011 <https://esto.nasa.gov/project-selections-for-aist-18/#martin>`_)
 
+We thank Jason Lander for his suggestions how
+to migrate from to :program:`yacc` to :program:`bison`.
+
+Shaddy Ahmed and Jennie Thomas helped us with the Matlab
+output of KPP.
+
 We would also like to thank Lucas Estrada for his assistance in
 setting up the :ref:`ci-tests` on `Azure DevOps Pipelines
 <https://azure.microsoft.com/en-us/services/devops/pipelines/>`_. and
 for assistance with debugging.
 
 Parts of this user manual are based on :cite:t:`Damian-Iordache_1996`.
-
-We thank Jason Lander for his suggestions how
-to migrate from to :program:`yacc` to :program:`bison`.
diff --git a/docs/source/citations/kpp.bib b/docs/source/citations/kpp.bib
@@ -300,11 +300,11 @@ @book{Hairer_and_Wanner_1996
  year         = {1996}
 }
 
-@book{Hairer_Norsett_and_Wanner_1993,
+@book{Hairer_Norsett_and_Wanner_1987,
  author       = {E. Hairer and S. P. Norsett and G. Wanner},
  title        = {Solving Ordinary Differential Equations I. Nonstiff Problems.},
  publisher    = {Springer-Verlag, Berlin},
- year         = {1993}
+ year         = {1987}
 }
 
 @article{Damian_et_al_2002,
@@ -440,3 +440,16 @@ @article{Lin_et_al._2022
  journal      = james,
  year         = {in prep., 2022}
 }
+
+@ARTICLE{Sandu_and_Sander_2006,
+  AUTHOR =       {A. Sandu and R. Sander},
+  TITLE =        {Technical note: Simulating chemical systems in
+                  Fortran90 and Matlab with the Kinetic PreProcessor
+                  KPP-2.1},
+  JOURNAL =      acp,
+  VOLUME =       6,
+  PAGES =        {187-195},
+  DOI =          {10.5194/ACP-6-187-2006},
+  YEAR =         2006
+}
+
diff --git a/docs/source/getting_started/00_revision_history.rst b/docs/source/getting_started/00_revision_history.rst
@@ -257,7 +257,7 @@ KPP 2.2.3
 
 - New Rosebrock method :code:`Rang3` was added.
 
-- The new KPP command :command:`#DECLARE` was added (see
+- The new KPP command :command:`#DECLARE` was added (see:
   :ref:`declare-cmd`).
 
 - Several vector and array functions from :program:`BLAS` (:code:`WCOPY`,
@@ -269,24 +269,29 @@ KPP 2.2.3
 KPP 2.1
 =======
 
-- Fortran90 output has been available since the preliminary version
-  “1.1-f90-alpha12” provided in :cite:t:`Sander_et_al._2005`.
+- Described by :cite:t:`Sandu_and_Sander_2006`.
 
-- Matlab is a new target language (see Sect. `4.4 <#sec:matlab>`__).
+- Matlab is a new target language (see: :ref:`matlab-code`).
 
 - The set of integrators has been extended with a general Rosenbrock
   integrator, and the corresponding tangent linear and adjoint methods.
 
 - The KPP-generated Fortran90 code has a different file structure than
-  the C or Fortran77 output (see :ref:`f90-code`).
+  the C or Fortran77 output (see: :ref:`f90-code`).
 
 - An automatically generated Makefile facilitates the compilation of
-  the KPP-generated code (see :ref:`Makefile`).
+  the KPP-generated code (see: :ref:`Makefile`).
 
 - Equation tags provide a convenient way to refer to specific chemical
-  reactions (see :ref:`lookat-and-monitor`.
+  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-cmd`)
+  current chemistry mechanism. (see: :ref:`dummyindex-cmd`)
 
 - Lines starting with :code:`//` are comment lines.
+
+===================
+KPP 1.1-f90-alpha12
+===================
+
+- First KPP version with Fortran90 :cite:p:`Sander_et_al._2005`.
diff --git a/docs/source/getting_started/01_installation.rst b/docs/source/getting_started/01_installation.rst
@@ -186,10 +186,14 @@ You should see output similar to:
    gcc -g -Wall -Wno-unused-function -I/usr/include -c debug.c
    gcc -g -Wall -Wno-unused-function -I/usr/include -c gen.c
    gcc -g -Wall -Wno-unused-function -I/usr/include -c kpp.c
+   flex -olex.yy.c scan.l 
+   bison -d -o y.tab.c scan.y
    gcc -g -Wall -Wno-unused-function -I/usr/include -c lex.yy.c
    gcc -g -Wall -Wno-unused-function -I/usr/include -c scanner.c
    gcc -g -Wall -Wno-unused-function -I/usr/include -c scanutil.c
    gcc -g -Wall -Wno-unused-function -I/usr/include -c y.tab.c
-   gcc -g -Wall -Wno-unused-function code.o code_c.o code_f77.o code_f90.o code_matlab.o debug.o gen.o kpp.o lex.yy.o scanner.o scanutil.o y.tab.o -L/usr/lib -lfl -o kpp
+   gcc -g -Wall -Wno-unused-function code.o code_c.o
+       code_f77.o code_f90.o code_matlab.o debug.o gen.o kpp.o
+       lex.yy.o scanner.o scanutil.o y.tab.o -L/usr/lib -lfl -o kpp
 
 This will create the executable file :file:`$KPP_HOME/bin/kpp`.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,7 +8,7 @@ The Kinetic PreProcessor: KPP
    <p><strong>Adrian Sandu<sup>1</sup>, Rolf Sander<sup>2</sup>, Michael Long<sup>3</sup>, Haipeng Lin<sup>4</sup>, and Robert Yantosca<sup>4</sup></strong></p>
    <p><em>
      <sup>1</sup> Virginia Polytechnic Institute and State University, Blacksburg, VA, USA<br/>
-     <sup>2</sup> Max-Planck Institute of Chemistry, Mainz, Germany<br/>
+     <sup>2</sup> Max-Planck Institute for Chemistry, Mainz, Germany<br/>
      <sup>3</sup> Renaissance Fiber, LLC, North Carolina, USA<br/>
      <sup>4</sup> Harvard University, Cambridge, MA, USA</em>
    </p>

diff --git a/docs/source/tech_info/07_numerical_methods.rst b/docs/source/tech_info/07_numerical_methods.rst
@@ -380,7 +380,7 @@ Runge-Kutta (aka RK) methods
 ============================
 
 A general :math:`s`-stage Runge-Kutta method is defined as (see
-Section II.1 of :cite:t:`Hairer_Norsett_and_Wanner_1993`)
+Section II.1 of :cite:t:`Hairer_Norsett_and_Wanner_1987`)
 
 .. math::
 

diff --git a/docs/source/using_kpp/05_output_from_kpp.rst b/docs/source/using_kpp/05_output_from_kpp.rst
@@ -980,14 +980,6 @@ the sections entitled :ref:`Function` ,
 m-function-files are the same as the names of the functions (prefixed
 by the model name :code:`ROOT`.
 
-The Matlab syntax for calling each function is
-
-.. code-block:: matlab
-
-   [Vdot] = Fun    (V, F, RCT);
-   [JVS ] = Jac_SP (V, F, RCT);
-   [HESS] = Hessian(V, F, RCT);
-
 The variables of :ref:`table-par` are defined as Matlab :code:`global`
 variables and initialized in the file
 :file:`ROOT_parameter_defs.m`. The variables of :ref:`table-glob` are