KPP 3.0.1 release

This release contains the following updates since KPP 3.0.0

1. PR #67 (change arrays from static allocation to dynamic)
2. PR #74 (Add CITATION.cff to activate "Cite this Repository" on GitHub)
3. Minor updates for ReadTheDocs

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

CHANGELOG.md

@@ -10,7 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 <!-- Version numbers must be synchronized in CHANGELOG.md, -->
 <!-- src/gdata.h, and docs/source/conf.py-->
-## [3.0.0]
+## [3.0.1] - 2023-03-21
+### Added
+- `CITATION.cff` file which will activate the "Cite this repository" option.
+
+### Fixed
+- Fixed a segmentation fault when using #STOICHMAT by using dynamically-sized variables `EqnNr` and `VarNr` rather than static variables `MAX_EQN` and `MAX_SPECIES`. 
+
+## [3.0.0] - 2022-11-09
 
 ### Added
 
@@ -58,7 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - bibtex.json (no longer needed w/ Sphinx 3.5.4)
 - Fun() no longer uses Vdotout since it can be retrieved from `Vdot`
 
-## [2.6.0]
+## [2.6.0] - 2022-06-24
 
 ### Added
 
@@ -69,7 +76,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - The `ICNTRL(5)` option in the LSODE integrator is now `ICNTRL(10)`.
 
-## [2.5.0]
+## [2.5.0] - 2022-05-18
 
 ### Added
 - New integrators
@@ -103,7 +110,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Reduce size of MAX_EQN and MAX_SPECIES to get KPP to run within
     65532 kb of stack memory
 
-## [2.4.0]
+## [2.4.0] - 2022-04-25
 
 ### Added
 

CITATION.cff

@@ -0,0 +1,109 @@
+cff-version: 1.2.0
+title: 'The Kinetic PreProcessor: KPP'
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Adrian
+    family-names: Sandu
+    affiliation: >-
+      Virginia Polytechnic Institute and State University,
+      Blacksburg, VA, USA
+  - given-names: Rolf
+    family-names: Sander
+    affiliation: 'Max-Planck Institute for Chemistry, Mainz, Germany'
+  - given-names: Michael S.
+    family-names: Long
+    affiliation: 'Renaissance Fiber, LLC, NC, USA'
+  - given-names: Haipeng
+    family-names: Lin
+    affiliation: >-
+      Harvard John A. Paulson School of Engineering and
+      Applied Sciences, Cambridge, MA, USA
+  - given-names: Robert M.
+    family-names: Yantosca
+    affiliation: >-
+      Harvard John A. Paulson School of Engineering and
+      Applied Sciences, Cambridge, MA, USA
+  - given-names: Lucas
+    family-names: Estrada
+    affiliation: >-
+      Harvard John A. Paulson School of Engineering and
+      Applied Sciences, Cambridge, MA, USA
+  - given-names: Lu
+    family-names: Shen
+    affiliation: 'School of Physics, Peking University, Bejing, China'
+  - given-names: Daniel J.
+    family-names: Jacob
+    affiliation: >-
+      Harvard John A. Paulson School of Engineering and
+      Applied Sciences, Cambridge, MA, USA
+identifiers:
+  - type: doi
+    value: 10.1029/2022MS003293
+    description: Paper
+  - type: doi
+    value: 10.5281/zenodo.6828025
+    description: Code archive (Zenodo)
+repository-code: 'https://github.com/KineticPreProcessor/KPP'
+url: 'https://kpp.readthedocs.io'
+abstract: >-
+  The KPP kinetic preprocessor is a software tool that
+  assists the computer simulation of chemical kinetic
+  systems.
+keywords:
+  - chemistry
+  - chemical-solver
+  - numerical-methods
+  - atmospheric-chemistry
+  - scientific-computing
+license: GPL-3.0
+preferred-citation:
+  type: article
+  authors:
+    - given-names: Haipeng
+      family-names: Lin
+      affiliation: >-
+        Harvard John A. Paulson School of Engineering and
+        Applied Sciences, Cambridge, MA, USA
+    - given-names: Michael S.
+      family-names: Long
+      affiliation: 'Renaissance Fiber, LLC, NC, USA'
+    - given-names: Rolf
+      family-names: Sander
+      affiliation: 'Max-Planck Institute for Chemistry, Mainz, Germany'
+    - given-names: Adrian
+      family-names: Sandu
+      affiliation: >-
+        Virginia Polytechnic Institute and State University,
+        Blacksburg, VA, USA
+    - given-names: Robert M.
+      family-names: Yantosca
+      affiliation: >-
+        Harvard John A. Paulson School of Engineering and
+        Applied Sciences, Cambridge, MA, USA
+    - given-names: Lucas
+      family-names: Estrada
+      affiliation: >-
+        Harvard John A. Paulson School of Engineering and
+        Applied Sciences, Cambridge, MA, USA
+    - given-names: Lu
+      family-names: Shen
+      affiliation: 'School of Physics, Peking University, Bejing, China'
+    - given-names: Daniel J.
+      family-names: Jacob
+      affiliation: >-
+        Harvard John A. Paulson School of Engineering and
+        Applied Sciences, Cambridge, MA, USA
+  title: >-
+    An adaptive auto-reduction solver for speeding up
+    integration of chemical kinetics in atmospheric
+    chemistry models: implementation and evaluation within
+    the Kinetic Pre-Processor (KPP) version 3.0.0
+  journal: JAMES
+  year: 2023
+  month: 2
+  volume: 15
+  issue: 2
+  doi: 10.1029/2022MS003293

README.md

@@ -1,7 +1,7 @@
 [![Latest
 Release](https://img.shields.io/github/v/release/KineticPreProcessor/KPP?label=Latest%20Release)](https://kpp.readthedocs.io) [![License: GPL
 v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/KineticPreProcessor/KPP/blob/main/LICENSE.txt) [![C-I
-tests](https://img.shields.io/azure-devops/build/KineticPreProcessor/KPP/1/main?label=C-I%20Tests)](https://dev.azure.com/KineticPreProcessor/KPP/_build) [![ReadTheDocs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://kpp.readthedocs.io/en/latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6563908.svg)](https://doi.org/10.5281/zenodo.6563908)
+tests](https://img.shields.io/azure-devops/build/KineticPreProcessor/KPP/1/main?label=C-I%20Tests)](https://dev.azure.com/KineticPreProcessor/KPP/_build) [![ReadTheDocs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://kpp.readthedocs.io/en/latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7308373.svg)](https://doi.org/10.5281/zenodo.7308373)
 
 # The Kinetic PreProcessor: KPP
 This is the repository for the The Kinetic PreProcessor (KPP) source code.

docs/source/conf.py

@@ -19,13 +19,13 @@
 # -- Project information -----------------------------------------------------
 
 project = "KPP: The Kinetic PreProcessor"
-copyright = "2022, The KPP Development Team"
-author = "A. Sandu, R. Sander, M. Long, H. Lin, and R. Yantosca"
+copyright = "2023, The KPP Development Team"
+author = "A. Sandu, R. Sander, M. Long, H. Lin, R. Yantosca, L. Estrada, L. Shen, and D. J. Jacob"
 
 # 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 = "3.0.0"
+release = "3.0.1"
 
 
 # -- General configuration ---------------------------------------------------

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 "3.0.0"
+#define KPP_VERSION "3.0.1"
 
 #ifndef _GDATA_H_
 #define _GDATA_H_

src/gen.c

@@ -1071,8 +1071,8 @@ void GenerateJacReactantProd()
 {
 int i, j, k, l, m, JVRP_NZ, newrow;
 int F_STOIC;
-int crow_JVRP[MAX_EQN], icol_JVRP[MAX_EQN*MAX_SPECIES];
-int irow_JVRP[MAX_EQN*MAX_SPECIES];
+int crow_JVRP[EqnNr], icol_JVRP[EqnNr*VarNr];
+int irow_JVRP[EqnNr*VarNr];
 
   if( VarNr == 0 ) return;