KPP 3.1.1 release

This is the release commit for KPP version 3.1.1.
Please see CHANGELOG.md for a list of updates.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

.readthedocs.yaml

@@ -14,7 +14,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.7"
+    python: "3.12"
     nodejs: "14"
     rust:   "1.55"
     golang: "1.17"

CHANGELOG.md

@@ -8,6 +8,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.1.1] - 2024-04-30
+### Changed
+- Updated Python package versions for ReadTheDocs in `docs/requirements.txt`
+- Now request Python 3.12 for ReadTheDocs builds in `.readthedocs.yaml`
+- Updated `MAX_NO_OF_LINES` to 2000 to parse the MCM mechanism
+- Updaeed `MAX_EQN` to 18000 to parse the MCM mechanism
+
+### Fixed
+- Now only add tha extra `Aout` argument to `Fun` and `Fun_Split` for F90 (see issues #56, #96)
+
 <!-- Version numbers must be synchronized in CHANGELOG.md, -->
 <!-- src/gdata.h, and docs/source/conf.py-->
 ## [3.1.0] - 2023-12-20

docs/requirements.txt

@@ -1,10 +1,15 @@
-# Requirements for building the KPP documentation
+# ======================================================================
+# ReadTheDocs requirements file
 #
-# These Python package versions have been proven to work:
+# If you wish to install the dependencies for building the ReadTheDocs
+# ReadTheDocs documentation from PyPI (the Python Package Index), use:
 #
-sphinx==3.5.4
-sphinx_rtd_theme==0.5.2
-sphinxcontrib-bibtex==2.2.0
-recommonmark
-docutils==0.16
-jinja2==3.0.3
+# $ pip install -r requirements.txt
+# ======================================================================
+sphinx==7.2.6
+sphinx_rtd_theme==2.0.0
+sphinxcontrib-bibtex==2.6.2
+sphinx-autobuild==2021.3.14
+recommonmark==0.7.1
+docutils==0.20.1
+jinja2==3.1.3

docs/source/conf.py

@@ -25,7 +25,7 @@
 # The full version, including alpha/beta/rc tags
 # (version numbers must be synchronized in CHANGELOG.md, src/gdata.h,
 # and docs/source/conf.py)
-release = "3.1.0"
+release = "3.1.1"
 
 
 # -- General configuration ---------------------------------------------------

docs/source/getting_started/00_revision_history.rst

@@ -8,6 +8,31 @@ Only the major new features are listed here. For a detailed description
 of the changes, read `CHANGELOG.md
 <https://github.com/KineticPreProcessor/KPP/blob/main/CHANGELOG.md>`_.
 
+.. _kpp311:
+
+=========
+KPP 3.1.1
+=========
+
+.. _kpp310:
+- Use newer Python packages to build ReadTheDocs documentation (see
+  :file:`docs/requirements.txt`)
+- Increased :code:`MAX_NO_OF_LINES` and :code:`MAX_EQN` in order to
+  parse the entire MCM mechanism
+- Now only add the extra `Aout` argument to `Fun` and `Fun_Split` for
+  target language :literal:`Fortran90`.  This fixes a Matlab build error.
+
+=========
+KPP 3.1.0
+=========
+
+- Added :literal:`#AUTOREDUCE` to the list of KPP commands in the
+  ReadTheDocs documentaton
+- Added :file:`examples/mcm` folder with minimal example for the
+  Master Chemical Mechanism
+- Added C-I test for MCM, based on the minimal example
+- Removed obsolete input options from the code and documentation
+
 .. _kpp302:
 
 =========

docs/source/using_kpp/04_input_for_kpp.rst

@@ -929,8 +929,8 @@ or define variables directly, e.g.:
 Note that the :code:`USE` statements must precede any variable
 definitions.
 
-The inlined code will be placed directly into the :code:`UPDATE_RCONST`
-routine in the :ref:`Rates` function.
+The inlined code will be placed directly into the subroutines
+:code:`UPDATE_RCONST` and :code:`UPDATE_PHOTO` in the :ref:`Rates` file.
 
 .. _f90-util:
 

examples/mcm/README.md

@@ -12,8 +12,8 @@ degradation mechanism is used as an example.
 1. Browse through the [MCM](https://mcm.york.ac.uk/MCM/browse) and
    select a Subset of the mechanism.
 
-2. Go  to the [export page](https://mcm.york.ac.uk/MCM/export) and
-   choose KPP as the output format.
+2. Go to the [export page](https://mcm.york.ac.uk/MCM/export) and choose
+   KPP as the output format.
 
 3. Click on the `Download` button and rename the downloaded file to
    `mcm_isoprene.eqn`.

src/code_f90.c

@@ -120,7 +120,7 @@ int first;
 int crtident;
 
 /* if MAX_NO_OF_LINES is too small, KPP will split lines incorrectly */
-int number_of_lines = 1, MAX_NO_OF_LINES = 250;
+int number_of_lines = 1, MAX_NO_OF_LINES = 2000;
 
 /*  Operator Mapping: 0xaa = '*' | 0xab = '+' | 0xac = ','
                       0xad = '-' | 0xae ='.' | 0xaf = '/' */

src/gdata.h

@@ -31,7 +31,7 @@
 
 // Version numbers must be synchronized in CHANGELOG.md, src/gdata.h,
 // and docs/source/conf.py
-#define KPP_VERSION "3.1.0"
+#define KPP_VERSION "3.1.1"
 
 #ifndef _GDATA_H_
 #define _GDATA_H_
@@ -57,11 +57,14 @@
 //       problems on MacOS then consider reducing MAX_EQN and MAX_SPECIES
 //       to smaller values than are listed below.
 //         -- Bob Yantosca (03 May 2022)
+//   (3) The large value of MAX_EQN = 18000 is necessary to run the
+//       complete MCM mechanism in KPP.
+//         -- Rolf Sander (2024-01-03)
 #ifdef MACOS
 #define MAX_EQN        2000     // Max number of equations (MacOS only)
 #define MAX_SPECIES    1000     // Max number of species   (MacOS only)
 #else
-#define MAX_EQN       11000     // Max number of equations
+#define MAX_EQN       18000     // Max number of equations
 #define MAX_SPECIES    6000     // Max number of species
 #endif
 #define MAX_SPNAME       30     // Max char length of species name

src/gen.c

@@ -652,24 +652,42 @@ int F_VAR, FSPLIT_VAR;
   // Note: When changing the FunctionBegin declarations below,
   // the number of arguments minus one must be changed in DefFnc here
   // as well. (hplin, 7/6/22)
-  F_VAR = DefFnc( "Fun", 5,
-                  "time derivatives of variables - Aggregate form");
-
-  FSPLIT_VAR = DefFnc( "Fun_SPLIT", 7,
-                       "time derivatives of variables - Split form");
-
+  // 
+  // For F90, add an extra argument to Fun and Fun_Split to return
+  // the Aout array. (hplin, bmy, 30 Apr 2024)
+  if (useLang == F90_LANG) {
+    F_VAR = DefFnc("Fun", 5,
+		   "time derivatives of variables - Aggregate form");
+    FSPLIT_VAR = DefFnc("Fun_SPLIT", 7,
+			"time derivatives of variables - Split form");
+  } else {
+    F_VAR = DefFnc("Fun", 4,
+                   "time derivatives of variables - Aggregate form");
+    FSPLIT_VAR = DefFnc("Fun_SPLIT", 6,
+                        "time derivatives of variables - Split form");
+  }
 
   // We have added the capability to return equation rates and the
   // time derivative of variable species from Fun via optional arguments
   // Aout and VdotOut (when z_useAggregate=1)
   //   -- Bob Yantosca (03 May 2022)
   //
   // Vdotout functionality can be accomplished using Vdot (hplin, 7/6/22)
+  //
+  // F90 needs Fun to have an extra argument for Aout (hplin, bmy, 30 Apr 2024)
   if( z_useAggregate ) {
-    FunctionBegin( F_VAR, V, F, RCT, Vdot, Aout );
+    if (useLang == F90_LANG) {
+      FunctionBegin( F_VAR, V, F, RCT, Vdot, Aout );\
+    } else {
+      FunctionBegin( F_VAR, V, F, RCT, Vdot );
+    }
   }
   else {
-    FunctionBegin( FSPLIT_VAR, V, F, RCT, Vdot, P_VAR, D_VAR, Aout );
+    if (useLang == F90_LANG) {
+      FunctionBegin( FSPLIT_VAR, V, F, RCT, Vdot, P_VAR, D_VAR, Aout );
+    } else {
+      FunctionBegin( FSPLIT_VAR, V, F, RCT, Vdot, P_VAR, D_VAR );
+    }
   }
 
   if ( (useLang==MATLAB_LANG)&&(!z_useAggregate) )

util/Makefile_f90

@@ -36,7 +36,7 @@ FC_HPUX    = f90
 FOPT_HPUX  = -O -u +Oall +check=on
 
 FC_GFORTRAN     = gfortran
-FOPT_GFORTRAN   = -cpp -O -g
+FOPT_GFORTRAN   = -cpp -O -g -frecursive
 
 # define FULL_ALGEBRA for non-sparse integration
 FC   = $(FC_$(COMPILER))