CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[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)

[3.1.0] - 2023-12-20

Added

• #AUTOREDUCE has been added to the list of KPP commands in the ReadTheDocs documentaton
• Added examples/mcm folder with minimal example for the Master Chemical Mechanism
• Added C-I test for MCM, based on the minimal example

Removed

• TRANSPORT and TRANSPORTALL input options; these were obsolete
• LUMP input option; this was obsolete
• DEFRAD, SETRAD, INITIALIZE, XGRID, YGRID, ZGRID, WRITE_OPT, RUN, USE, USES; these were obsolete

[3.0.2] - 2023-06-02

Added

• Added .readthedocs.yaml for configuring ReadTheDocs builds
• Added a ReadTheDocs badge in README.md
• State that #INTEGRATOR none statements should be removed in RTD documentation

Changed

• Added pybtex and pybtex-docutils to the docs/requirements.txt

Fixed

• Minor issues in site-lisp/kpp.el file for Emacs

[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

• C-language updates
  • Restored driver programs general.c and general_adj.c
  • Updated rate-law functions in util/UserRateLaws.c
  • Added C-I tests for C-language integrators (using the small_strato mechanism
  • Now use // instead of /* */ comment strings
• ReadTheDocs documentation updates:
  • Authors in the reference page are now listed alphabetically
  • In-text citations now use the :cite:t style (e.g. "Smith et al [2000]")
  • Corrected several omissions
  • Removed table numbers from tables (to reduce confusion)
  • Now document additional installation steps for MacOS X
  • Added documentation about KPP_FLEX_LIB_DIR
  • Added badges for release, release date, and Azure pipelines to index.rst
  • All authors from the Lin et al [2022] paper about KPP 3.0.0 have been added to the front page of ReadTheDocs and .zenodo.json
• C-I test additions
  • Added a C-I test for the rosenbrock_autoreduce integrator

Changed

• C-I test updates
  • Renamed CI-test folders for clarity (C_*, F90_*, 'X_*')
  • Abstracted reusable code into the ci-common-defs.sh script
  • Replaced ci-manual-testing-script.sh with ci-testing-script.sh (which now works both locally and on Azure Dev Pipelines)
  • Renamed ci-manual-cleanup-script.sh to ci-cleanup-script.sh
  • Updated docs accordingly
• Makefile changes
  • Makefile.defs now uses environment variable KPP_FLEX_LIB_DIR when it cannot find the flex library file in standard locations v
  • Removed host-specific if blocks from Makefile.defs
• Other changes
  • DOUBLE_COMPLEX is now replaced by COMPLEX(kind=dp)
  • Fixed incorrect license string in .zenodo.json
  • Added extra free() statements in src/gen.c to avoid memory leaks
• Bug fix in int/feuler.f90: FIX must be the 2nd argument passed to routine Fun (from routine FunTemplate)

Removed

• 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] - 2022-06-24

Added

• New integrator: rosenbrock_autoreduce.f90
  • Also added corresponding documentation for ReadTheDocs

Changed

• The ICNTRL(5) option in the LSODE integrator is now ICNTRL(10).

[2.5.0] - 2022-05-18

Added

• New integrators
  • feuler.f90
• New C-I tests
  • ros_minver
  • ros_upcase
  • Added scripts to run C-I tests manually (for development/debugging)
• Brought updates for GEOS-Chem into the main line of development
  • Added #MINVERSION switch to force KPP to stop unless a minimum version is used
  • Added #UPPERCASEF90 to generate F90 code with the .F90 suffixes
  • Removed EQUIVALENCE statements from F90-generated code; VAR and FIX now point to C witihin integrators. This is to ensure thread-safe operation when using KPP-generated code in an OpenMP parallel environment.
• Bug fixes:
  • Make sure to inline parameter "sp" into the _Global.F90 file when the "#DOUBLE off" option is used.

Changed

• Code updates
  • Rewrote code to remove compiler warnings
  • Fortran-90 makefiles now use GFORTRAN as the default compiler option
  • Added ReadTheDocs output
  • Updated top-of-file comment headers to point to the KPP Github site and to acknowledge new authors
  • Routine Fun() now returns optional arguments Aout and Vdotout
• Updates for building on MacOS
  • Reduce size of MAX_EQN and MAX_SPECIES to get KPP to run within 65532 kb of stack memory

[2.4.0] - 2022-04-25

Added

• Brought updates from the MECCA branch into the main line of development:
  • new integrators: beuler.f90, rosenbrock_mz.f90, rosenbrock_posdef.f90, rosenbrock_posdef_h211b_qssa.f90
  • several memory sizes (MAX_EQN, ...) increased to allow large chemical mechanisms
  • new Makefile target: list
  • LaTeX User Manual added
• Now use ICNTRL(15) to decide whether or not to toggle calling the Update_SUN, Update_RCONST, and Update_PHOTO routines from within the integrator

[2.3.2_gc]

Added

• Workaround for F90 derived-type objects in inlined code (i.e. properly parse State_Het%xArea, etc).
• Write global variables NUMDEN, MW, SR_MW, SR_TEMP, TEMP_OVER_K300, K300_OVER_TEMP to gckpp_Global.F90
• Documentation for ReadTheDocs (in the docs folder)
• Github issue templates

Changed

• MAX_INLINE (max # of inlined code lines to read) is now 200000
• Version number in gdata.h is now 2.3.2
• README.md now contains the ReadTheDocs badge
• README.md now points to kpp.readthedocs.io for documentation

Removed

• Comment out the Update_Sun() functions in update_sun.F90, update_sun.F
• Default rate law functions are no longer written to gckpp_Rates.F90

[2.3.1_gc]

Added

• Documentation for ReadTheDocs (in the docs folder)
• Github issue templates

Changed

• Version number in gdata.h is now 2.3.1
• README.md now contains the ReadTheDocs badge
• README.md now points to kpp.readthedocs.io for documentation

[2.3.0_gc]

Added

• Added README.md for the GC_updates branch
• Added MIT license for the GC_updates branch
• Add Aout argument to return reaction rates from SUBROUTINE Fun

Changed

• Rename KPP/kpp_2.2.3_01 folder to KPP/kpp-code
• Now write gckpp_Model.F90 and gckpp_Precision.F90 from gen.c
• Do not write file creation & time to KPP-generated files
• Now create Fortran-90 source code files with *.F90 instead of *.f90

Removed

• Remove calls to UPDATE_SUN and UPDATE_RCONST from all *.f90 integrators

[2.2.5_gc]

Changed

• Increase MAX_INLINE from 20000 to 50000

[2.2.4_gc]

Added

• Add MIT license files and update README.md accordingly
• Create README.md for main branch
• Set FLEX_LIB_DIR using FLEX_HOME env variable if it is defined
• Added an exponential integrator
• Added array to *_Monitor for family names (FAM_NAMES) string vector
• Added functionality for Prod/Loss families using FAMILY token
• Add scripts necessary to build a new mechanism for GEOS-Chem
• Completed the prod/loss option (token: #FLUX [on/off])
• Added OMP THREADPRIVATE to LinearAlgebra.F90
• Added rosenbrock_split.def integrator definition
• Added OMPThreadPrivate function for F77
• Added declaration of "A" in *_Function.F90
• Added OMPThreadPrivate Functionality to F90 output
• Completed the split-form Function for f90

Changed

• Increase maximum number of equations
• Increase MAX_FAMILIES parameter from 50 to 300
• Extend equation length limit to 200 characters.
• Also changed the species name for a family to the family name itself.
• Modified Families to minimize the number of additional species created
• Rename and change indexing convention

Removed

• Remove unnecessary files
• Remove files for GEOS-Chem from top-level directory; these are now in the GEOS-Chem source code
• Delete the old name directory

Fixed

• Fix to add coefficients to *_Monitor.f90
• Fixed a pad processing of terms leading to LOSS fam also generating PROD terms.
• Fix input argument to ComputeFamilies() from VAR to V - MSL
• Parameter NFAM was not defined. This is fixed. (MSL)
• Added fix to camculate NET rather than GROSS prod/loss families - MSL
• Add fix to calculate NET rather than GROSS prod/loss families - MSL
• Re-fixed the equivalence statement needed for GEOS-Chem to work. MSL
• Corrected miniterpretation of the split-form Function for f90.

[2.2.3_rs3] - 2018-11-30

CHANGES by Rolf Sander:

• several int/*.f90: TABs converted to spaces
• several dvode files converted to unix file format
• kpp/int/beuler.f90:
  • factor 101 added to Hstart
  • description of the error numbers IERR added
• kpp/int/rosenbrock_posdef_h211b_qssa.f90: USE KPP_ROOT_Function, ONLY: Fun_Split

CHANGES by Sergey Gromov and Rolf Sander:

• several limits increased:
  • src/gdata.h: #define MAX_K 1000
  • src/scan.l: char crtToken[1000]; char nextToken[1000]; char crtFile[1000]; char crt_rate[1000];
  • src/scan.y: %union{char str[1000];};

CHANGES by Adrian Sandu:

• new integrator beuler.f90 (based on sdirk.f90)

[2.2.3_rs2] - 2016-11-21

CHANGES by Rolf Sander:

• src/gen.c: bug fix in GenerateParamHeader(): char name[MAX_SPNAME] instead of name[20]
• kpp.el updated: #REPLACE, #ENDREPLACE, uncertainty of rate coefficient
• Makefile.defs.Linux: compiler option -Wno-implicit-function-declaration

[2.2.3_rs1] - 2016-08-28

CHANGES by Rolf Sander:

• upgrade to the official KPP version 2.2.3

[2.2.1_rs7] - 2016-02-09

CHANGES by Rolf Sander:

• rosenbrock_mz.f90-orig deleted
• new function StoichNum to get stoichiometric numbers:
  • src/gen.c: new function GenerateFun_Split()
  • kp4.sh: GenerateStoichNum added to KPP_SUBROUTINE_LIST

[2.2.1_rs6] - 2016-01-07

CHANGES by Rolf Sander:

• src/code_f90.c: Maximum number of continuation lines MAX_NO_OF_LINES increased again, now to 250
• src/gdata.h: info adjusted
• src/gen.c: "USE kpp_Parameters" added to SUBROUTINE Initialize to allow species-specific code in #INLINE F90_INIT
• several int/*.f90: TABs converted to spaces

CHANGES by Patrick Joeckel:

• int/rosenbrock_mz.f90: loop fusion according to BULL
• new file Makefile.m

Changes by Domenico Taraborrelli:

• option for faster chemistry calculation by alternative time stepping (integrator rosenbrock_posdef_h211b_qssa)
  • modified files:
    • src/gen.c: new function GenerateFun_Split
    • kp4.sh: GenerateFun_Split added to KPP_SUBROUTINE_LIST
  • new integrator files: rosenbrock_posdef_h211b_qssa.def, rosenbrock_posdef_h211b_qssa.f90

[2.2.1_rs5] - since caaba_2.5n, 2010-02-22

CHANGES by Rolf Sander:

• src/gdata.h: several limits increased to allow larger mechanisms: #define MAX_EQN 11000 #define MAX_SPECIES 3500 #define MAX_EQNTAG 32 #define MAX_K 300
• src/gen.c:
  • crow and diag deleted because they are not used
  • Fortran90 double precision changed to SELECTED_REAL_KIND(12,307)
• src/Makefile: PHONY target list added to list the configuration
• src/scan.h: MAX_INLINE increased to 100000
• src/scan.l: several limits increased to allow larger mechanisms: char crtToken[300]; char nextToken[300]; char crtFile[300]; char crt_rate[300];
• src/scan.y:
  • "char" increased to 300 (must be the same as MAX_K)
• util/sutil.f90: TABs converted to spaces

[2.2.1_rs4] - since caaba_2.5m, 2009-11-27

CHANGES by Patrick Joeckel:

• Makefile, Makefile.defs, Makefile.defs.*, src/Makefile: changes to allow compilation on different machines

CHANGES by Rolf Sander:

• src/code_matlab.c: "#include <time.h>" added because it is necessary for time_t, see: http://en.wikipedia.org/wiki/Time_t
• src/scanutil.c:
  • "#include <malloc.h>" removed because it comes from <stdlib.h> (this had caused a problem on MAC-OSX)
• src/scan.y:
  • "#include <malloc.h>" removed because it comes from <stdlib.h> (this had caused a problem on MAC-OSX)
• using GNU Bison 2.3 now instead of 2.1

[2.2.1_rs3] - since caaba_2.5c, 2008-07-17

CHANGES by Patrick Joeckel and Rolf Sander:

• src/code_f90.c and src/gdata.h: changes in MAX_EQNTAG etc. to avoid problems with long equation tags

[2.2.1_rs2] - since caaba_2.4, 2008-02-18

CHANGES by Rolf Sander:

• kpp_lsode.f90, kpp_seulex.f90, rosenbrock.f90, rosenbrock_posdef.f90, runge_kutta.f90, and sdirk.f90: IERR_NAMES (for error messages) adapted to correct syntax
• src/code_f90.c:
  • Maximum number of continuation lines increased to 100. If MAX_NO_OF_LINES is too small, kpp may split lines incorrectly.

[2.2.1_rs] - 2007-08-22

CHANGES by Rolf Sander:

• code_f90.c: added FlushBuf() to F90_DeclareData (otherwise MAX_OUTBUF would have to be very large for large reaction mechanisms)
• gen.c: The declaration of RTOLS was deleted because it is not needed by the integrators. If the driver programs need it, they can define it themselves.
• Makefile: new option maintainer-clean is now consistent with src/Makefile

CHANGES by Astrid Kerkweg:

• src/code_f90.c: string length of F90_types and in subroutine F90_DeclareData increased from 12 to 32 to avoid problems with long species names and long equation tags

CHANGES by Adrian Sandu and Rolf Sander:

• It looks like the model is hypersensitive to negative concentrations; many times when small negative concentrations are produced the entire future trajectory is put in jeopardy. In the new integrator rosenbrock_posdef.f90, this is fixed by changing "CALL WCOPY(N,Ynew,1,Y,1)" to "Y = MAX(Ynew,ZERO)".

[2.2.1] - 2006-12-01

CHANGES by Adrian Sandu:

• rosenbrock_soa deleted
• util/sutil.c: new subroutine KppDecompCmplxR
• new files: examples/cell.kpp, examples/saprc2006.kpp, int/runge_kutta.c, and int/sdirk.c

CHANGES by Rolf Sander:

• int/kpp_lsode.f90: like all other integrators, kpp_lsode now also returns IERR==1 after successful completion

CHANGES by Adrian Sandu and Rolf Sander:

• src/Makefile, scan.l, scan.y: yacc replaced by bison, implementing the bug fixes suggested by Jason Lander

[2.2_July2006] - 2006-07-23

CHANGES by Adrian Sandu:

• models/CMAQ added
• changes in int/runge_kutta_adj.f90 and int/runge_kutta_tlm.f90
• util/blas.c: new subroutines Set2Zero and WADD
• util/blas.f90: new subroutines WGEFA and WGESL
• util/sutil.f90: new subroutines KppDecompCmplxR, KppSolveCmplxR, and KppSolveTRCmplxR

[2.2.June2006] - 2006-06-06

CHANGES by Philipp Miehe and Adrian Sandu:

• new integrators kpp_sdirk4, rosenbrock_soa, runge_kutta, and sdirk
• integrators rosenbrock, rosenbrock_tlm, and rosenbrock_adj: completely revised
• new kpp command #DECLARE [SYMBOL|VALUE]
• util/blas.f90: new subroutine WADD
• util/sutil.f90: new subroutines KppSolveTRIndirect and KppSolveTRCmplx
• several files examples/* added
• changes in drv/general_adj.f90 and drv/general_tlm.f90
• examples/mimi* deleted

[2.1] - 2005-07-19