Merge branch 'develop'

.gitignore

-boxmox/boxmox/README.aux
-boxmox/boxmox/README.log
-boxmox/boxmox/README.toc
-boxmox/boxmox/README.pdf
-boxmox/boxmox/compiled_mechs
-boxmox/bin/kpp
-boxmox/src/*.o
-boxmox/src/lex.yy.c
-boxmox/src/y.tab.c
-boxmox/src/y.tab.h
+bin/
+share
+build
+src/kpp
+boxmox*.tar.gz
+
+boxmox/UserManual.toc
+boxmox/UserManual.aux
+boxmox/UserManual.log
+boxmox/UserManual.pdf
+doc/boxmox_UserManual.pdf
+
+src/bison.c
+src/bison.h
+src/yacc.c
+
+**~
+
+# bc we create this automatically using build_dist.sh
+Makefile.am
+
+doc/boxmox_README.pdf
+
 **.DS_Store
+
+# http://www.gnu.org/software/automake
+
+Makefile.in
+/ar-lib
+/mdate-sh
+/py-compile
+/test-driver
+/ylwrap
+.deps/
+.dirstamp
+
+# http://www.gnu.org/software/autoconf
+
+autom4te.cache
+/autoscan.log
+/autoscan-*.log
+/aclocal.m4
+/compile
+/config.cache
+/config.guess
+/config.h.in
+/config.log
+/config.status
+/config.sub
+/configure
+/configure.scan
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+
+# https://www.gnu.org/software/libtool/
+
+/ltmain.sh
+
+# http://www.gnu.org/software/texinfo
+
+/texinfo.tex
+
+# http://www.gnu.org/software/m4/
+
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+
+# Generated Makefile
+# (meta build system like autotools,
+# can automatically generate from config.status script
+# (which is called by configure script))
+Makefile

.gitlab-ci.yml

-create_patch:
-  image: ubuntu:rolling
-  script:
-    - bash create_BOXMOX_patch.bash
-  tags:
-    - ehs_vm
-
-boxmox_latest:
-  image: ubuntu:rolling
-  script:
-    - cp -r boxmox boxmox_latest
-    - bash prep_BOXMOX_src_directory.bash boxmox_latest latest
-    - tar cvzf boxmox_latest.tar.gz boxmox_latest
-  tags:
-    - ehs_vm
-  artifacts:
-    paths:
-      - boxmox_latest.tar.gz
+image: ubuntu:rolling
 
-.compile:
-  script:
-    - bash install_BOXMOX.bash COMPILE_ONLY
-    - export KPP_HOME=$(pwd)/boxmox
-    - export PATH=$KPP_HOME/bin:$KPP_HOME/boxmox/bin:$PATH
-    - cd boxmox/models
-    - prepare_BOXMOX_mechanism MOZART_4
-    - new_BOXMOX_experiment_from_example chamber_experiment
-    - for mechpath in *def;
-      do
-        mech=${mechpath/.def/};
-        echo ${mech};
-        if [ "${mech}" != "CB05TUCl_EPA" ] && [ "${mech}" != "MCMv3_3" ];
-        then
-          prepare_BOXMOX_mechanism -f ${mech};
-          new_BOXMOX_experiment ${mech} chamber_experiment_${mech};
-          cp chamber_experiment/*csv chamber_experiment_${mech}/;
-          cd chamber_experiment_${mech};
-          ./${mech}.exe;
-          cd ..;
-        fi;
-      done
-  tags:
-    - ehs_vm
+cache:
+  paths:
+    - "$CI_PROJECT_DIR/build/"
 
-compile_ubuntu_latest:
-  image: ubuntu:rolling
-  extends: .compile
+build:
   before_script:
     - DEBIAN_FRONTEND=noninteractive apt-get -qq update
-    - DEBIAN_FRONTEND=noninteractive apt-get -qq install wget patch make gcc gfortran flex bison texlive
-  tags:
-    - ehs_vm
-
+    - DEBIAN_FRONTEND=noninteractive apt-get -qq install wget patch make gcc gfortran flex bison texlive autoconf autotools-dev
+    - "[ -f ./version ] && export VERSION=$(cat ./version)"
+  script:
+    - . build_dist.sh "$CI_PROJECT_DIR/build"
+  artifacts:
+    name: boxmox-latest
+    paths:
+      - boxmox-*.tar.gz

boxmox/src/Makefile → Makefile.am_BLUEPRINT

@@ -4,8 +4,7 @@
 #        Builds simulation code for chemical kinetic systems
 #
 #  Copyright (C) 1995-1996 Valeriu Damian and Adrian Sandu
-#  Copyright (C) 1997-2005 Adrian Sandu
-#      with contributions from: Mirela Damian, Rolf Sander 
+#  Copyright (C) 1997-2004 Adrian Sandu
 #
 #  KPP is free software; you can redistribute it and/or modify it under the
 #  terms of the GNU General Public License as published by the Free Software
@@ -30,58 +29,43 @@
 #
 #######################################################################################
 
-include ../Makefile.defs
+SUBDIRS = src
+EXTRA_DIST = src/bison.h	src/code.h	src/gdata.h	src/gdef.h	src/scan.h
 
-BISON=bison -d 
-CFLAGS=`cat ../cflags`
+dist_doc_DATA = README.md doc/kpp_UserManual.pdf doc/boxmox_UserManual.pdf
+dist_bin_SCRIPTS = scripts/list_BOXMOX_mechanisms \
+				   scripts/new_BOXMOX_experiment \
+				   scripts/new_BOXMOX_experiment_from_example \
+				   scripts/prepare_BOXMOX_mechanism \
+				   scripts/validate_BOXMOX_installation
 
-all: kpp
+install-data-local:
+	$(MKDIR_P) $(DESTDIR)$(pkgdatadir)/compiled_mechs
 
-.c.o:
-	@echo "  "$(CC) $(CC_FLAGS) $(CFLAGS) -c $*.c
-	@$(CC) $(CC_FLAGS) $(CFLAGS) -I$(INCLUDE_DIR) -c $*.c
+uninstall-local:
+	rmdir $(DESTDIR)$(pkgdatadir)/compiled_mechs 2>/dev/null || :
 
-OBJS  = \
-	y.tab.o \
-	lex.yy.o \
-	scanner.o \
-	scanutil.o \
-	kpp.o \
-	gen.o \
-	code.o \
-	code_c.o \
-	code_f77.o \
-	code_f90.o \
-	code_matlab.o \
-	debug.o
+dist-hook:
+	chmod u+w $(distdir)/boxmox/wrapper
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/boxmox/wrapper > tmp; mv tmp $(distdir)/boxmox/wrapper
+	chmod u+w $(distdir)/drv/boxmox.f90
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/drv/boxmox.f90 > tmp; mv tmp $(distdir)/drv/boxmox.f90
+	chmod u+w $(distdir)/drv/boxmox_adjoint.f90
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/drv/boxmox_adjoint.f90 > tmp; mv tmp $(distdir)/drv/boxmox_adjoint.f90
+	chmod u+w $(distdir)/scripts/new_BOXMOX_experiment
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/scripts/new_BOXMOX_experiment > tmp; mv tmp $(distdir)/scripts/new_BOXMOX_experiment
+	chmod u+w $(distdir)/scripts/new_BOXMOX_experiment_from_example
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/scripts/new_BOXMOX_experiment_from_example > tmp; mv tmp $(distdir)/scripts/new_BOXMOX_experiment_from_example
 
-kpp:    $(OBJS)
-	@echo "  "$(CC) $(CC_FLAGS) $(CFLAGS) $(OBJS) -L$(FLEX_LIB_DIR) -lfl -o kpp
-	@$(CC) $(CC_FLAGS) $(CFLAGS) $(OBJS) -L$(FLEX_LIB_DIR) -lfl -o kpp
-	@mv kpp ../bin
+install-data-hook:
+	@echo " "
+	@echo " --- YOU ARE GOOD TO GO ---"
+	@echo " "
+	@echo "To use BOXMOX, you need to add the following lines to"
+	@echo "your .bashrc, .profile (a hidden file in your home directory)"
+	@echo "or similar, so they are executed upon login:"
+	@echo " "
+	@echo "export KPP_HOME=${prefix}/share/boxmox"
+	@echo "export PATH=${prefix}/bin:\$$PATH"
+	@echo " "
 
-clean:  
-	@rm -f *~ *.o cflags 
-
-maintainer-clean: clean
-	@rm -f lex.yy.c y.tab.c y.tab.h
-
-lex.yy.c: scan.l scan.h
-	@echo "  "$(FLEX) scan.l
-	@$(FLEX) -olex.yy.c scan.l 
-
-y.tab.c: scan.y scan.h
-	@echo "  "$(BISON) scan.y
-	@$(BISON) -o y.tab.c scan.y
-
-flex: lex.yy.c y.tab.c
-
-scanner.o: scan.h gdata.h
-scanutil.o: scan.h
-kpp.o: gdata.h
-gen.o: gdata.h code.h
-debug.o: gdata.h
-code.o: gdata.h code.h
-
-code_c.o: gdata.h code.h
-code_f.o: gdata.h code.h

README.md

@@ -4,35 +4,51 @@
 
 Documentation, user downloads, online tools and further information can be found [here](https://mbees.med.uni-augsburg.de/boxmodeling/).
 
-This is the development repository. BOXMOX is an extension to KPP, hence it lives as part of KPP. For distribution, a patch against standard KPP is created, KPP is downloaded from the original location, and the code is patched. For testing, each commit creates a [downloadable distribution](https://git.rz.uni-augsburg.de/knotechr/boxmox/-/jobs/artifacts/master/download?job=boxmox_latest) which can used directly for testing.
+This is the development repository.
 
-Feel free to push merge requests and add issues if you should encounter any.
+## Latest distributable archive
 
-Please cite our work when BOXMOX use constituted a relevant contribution to your scientific work. The citation for BOXMOX is [Knote et al., Atm. Env., 2015](http://dx.doi.org/10.1016/j.atmosenv.2014.11.066).
-
-## Code structure
+The most current BOXMOX distribution .tar.gz can be found [here](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox/-/jobs/artifacts/master/download?job=build).
 
-`boxmox/`
+## Contributing
 
-Main KPP directory, patched and extended for BOXMOX.
+We are looking forward to receiving your [new issue report](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox/-/issues/new).
 
-`boxmox/boxmox/`
+If you'd like to contribute source code directly, please [create a fork](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox), make your changes and then [submit a merge request](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox/-/merge_requests/new) to the original project.
 
-Additional data and code for BOXMOX.
+## Citation
 
-`boxmox/boxmox/wrapper`
+Please cite our work when BOXMOX use constituted a relevant contribution to your scientific work. The citation for BOXMOX is [Knote et al., Atm. Env., 2015](http://dx.doi.org/10.1016/j.atmosenv.2014.11.066).
 
-Main BOXMOX user code file.
+## Where does BOXMOX extend KPP?
 
-`boxmox/boxmox/boxmox(_adjoint).f90`
+`drv/boxmox.f90`/ `drv/boxmox_adjoint.f90`
 
 KPP (adjoint) driver for BOXMOX.
 
-`boxmox/boxmox/examples`
+`drv/wrapper`
+
+This is where all BOXMOX extension code lives.
+
+`case_studies/`
 
 Test cases for BOXMOX usage.
 
-[Christoph Knote](mailto:christoph.knote@med.uni-augsburg.de), [MBEES, Faculty of Medicine, University of Augsburg](https://mbees.med.uni-augsburg.de), Germany
+`doc/boxmox_README.tex`
+
+BOXMOX documentation.
+
+`models/`
+
+Additional chemistry mechanisms included with BOXMOX.
+
+`scripts/`
+
+Command-line scripts to drive BOXMOX.
+
+`util/UserRateLaws_BOXMOX.f90`
+
+Rate constant equations for BOXMOX.
 
 ## License statement
 
@@ -49,3 +65,7 @@ GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+## Contact
+
+[Christoph Knote](mailto:christoph.knote@med.uni-augsburg.de), [MBEES, Faculty of Medicine, University of Augsburg](https://mbees.med.uni-augsburg.de), Germany
+

boxmox/Makefile.defs

-# -*- sh -*-
-##############################################################################
-#
-#  KPP - The Kinetic PreProcessor
-#        Builds simulation code for chemical kinetic systems
-#
-#  Copyright (C) 1995-1997 Valeriu Damian and Adrian Sandu
-#  Copyright (C) 1997-2005 Adrian Sandu
-#
-#  KPP is free software; you can redistribute it and/or modify it under the
-#  terms of the GNU General Public License as published by the Free Software
-#  Foundation (http://www.gnu.org/copyleft/gpl.html); either version 2 of the
-#  License, or (at your option) any later version.
-#
-#  KPP is distributed in the hope that it will be useful, but WITHOUT ANY
-#  WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-#  FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-#  details.
-#
-#  You should have received a copy of the GNU General Public License along
-##  with this program; if not, consult http://www.gnu.org/copyleft/gpl.html or
-#  write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-#  Boston, MA  02111-1307,  USA.
-#
-#  Adrian Sandu
-#  Computer Science Department
-#  Virginia Polytechnic Institute and State University
-#  Blacksburg, VA 24060
-#  E-mail: sandu@cs.vt.edu
-#
-##############################################################################
-
-# In order to compile KPP you have to provide the following information:
-
-# 1. The name of the compiler you want to use. Normaly this 
-#    is either GNU C compiler (gcc) or the native compiler (cc)
-#    You can use the complete pathname if the compiler is not in $PATH 
-#    Note that for SUN machines is better to use gcc.
-#    For GNU C compiler use:
-#      CC=gcc
-#    For the native compiler use:
-#      CC=cc
-
-CC=gcc 
-
-# 2. The name of your lexical analizer. KPP requires FLEX to be used.
-#    FLEX is a public domain lexical analizer and you can download it from
-#    http://www.gnu.org/software/flex/ or any other mirror site. If flex
-#    directory is not included in your path use the complete pathname.
-
-FLEX=flex
-
-# 3. The complete pathname of the FLEX library (libfl.a).
-#    On many systems this is either: 
-#    /usr/lib, /usr/lib64, /usr/local/util/lib/flex
-
-FLEX_LIB_DIR=/usr/lib
-
-# 4. Platform independent C compiler flags. By default "-O" is used which 
-#    turns on optimization. If you are experiencing problems you may try 
-#    "-g" to include debuging informations.
-
-CC_FLAGS= -g -Wall
-
-# 5. Path to include additional directories
-#    Typically: /usr/include on Linux
-#               /usr/include/sys on Mac OS X
-INCLUDE_DIR = /usr/include
-
-##############################################################################

boxmox/boxmox/README.tex → boxmox/UserManual.tex

@@ -15,11 +15,11 @@
 \ \\[8cm]
 
 {\LARGE BOXMOX extensions to KPP} \\[1cm]
-Christoph Knote (christoph.knote@lmu.de)\\
-Meteorological Institute, LMU Munich, Germany
+Christoph Knote (christoph.knote@med.uni-augsburg.de)\\
+Model-Based Environmental Exposure Science, Faculty of Medicine, University of Augsburg, Germany
 \\[1cm]
-Version 1.8a\\
-09/2019
+Version 1.8\\
+03/2022
 
 % version   name  comment
 % 0.9       CK    initial release
@@ -34,6 +34,7 @@ Version 1.8a\\
 % 1.7       CK    revamped mixing process options, included simple aerosol as
 %                 surface density area and radius
 % 1.8a      CK    implemented NOx fixing
+% 1.8       CK    move to GNU autotools for distribution
 \end{center}
 
 \thispagestyle{empty}
@@ -46,11 +47,20 @@ Version 1.8a\\
 
 \section*{Version history}
 
-\subsection*{1.8a}
+\subsection*{1.8}
 \textit{not released yet}
 
 New features
 
+\begin{itemize}
+  \item Move to GNU autotools for distribution
+\end{itemize}
+
+\subsection*{1.8a}
+\textit{not released}
+
+New features
+
 \begin{itemize}
   \item Implemented NO$_x$ fixing method for steady state calculations
 \end{itemize}
@@ -200,49 +210,22 @@ doi:10.5194/acp-6-187-2006, 2006.
 \emph{BOXMOX is a Linux program, we assume you are working on a reasonably
 recent Linux distribution.}
 
-You should have received or downloaded the \emph{install\_BOXMOX.bash} shell
-script. The script is written in {\tt bash}, a shell that is installed on most
-*nix machines, but might not be your default. Do not worry. Open the script in
-your favorite text editor and adapt the user section to your machine. You need
-to set
+Requirements for installing and running BOXMOX:
 
 \begin{itemize}
-  \item absolute path to the location you want BOXMOX to be
   \item C compiler (usually {\tt gcc} or {\tt cc})
-  \item C compile flags (if any)
-  \item absolute path to the FLEX binary (test with {\tt which flex})
-  \item absolute path to the FLEX library (libfl.a, try {\tt type -a libfl.a})
+  \item Fortran compiler ({\tt gfortran} is assumed)
+  \item flex (test with {\tt which flex})
+  \item flex library (libfl.a, try {\tt type -a libfl.a})
+  \item yacc or bison
 \end{itemize}
 
-Save the file. Now execute it:
+BOXMOX installation is then straightforward:
 
 \begin{verbatim}
-me@mymachine> bash install_BOXMOX.bash
-
-BOXMOX extension to KPP (1.7)
-
-Output directory: /glade/u/home/knote/testy
-C compiler:       gcc
-C compiler flags: -O
-FLEX binary:      /usr/bin/flex
-FLEX library:     /usr/lib64/libfl.a
-
-Downloading BOXMOX
-Downloading KPP
-Unpacking KPP
-Patching KPP
-Compiling KPP
-Tex'ing BOXMOX readme (boxmox/README.pdf)
-
- --- YOU ARE GOOD TO GO ---
-
-Remember to set the following env. variables and
-add them to your .bashrc. to remember them permanently:
-
-export KPP_HOME=/glade/u/home/knote/boxmox
-export PATH=$KPP_HOME/bin:$PATH
-
-me@mymachine>
+./configure --prefix=<absolue path to where BOXMOX should be installed>
+make
+make install
 \end{verbatim}
 
 Once you see the message ``YOU ARE GOOD TO GO'', everything should have worked
@@ -288,7 +271,7 @@ me@mymachine>
 
 This creates a box model executable for the chosen mechanism (in this case,
 MOZART-4) which you can now use for your experiments. The executables can be
-found in \emph{\$KPP\_HOME/boxmox/compiled\_mechs/\mech}.
+found in \emph{\$KPP\_HOME/compiled\_mechs/\mech}.
 
 \subsubsection{{\tt new\_BOXMOX\_experiment}}
 
@@ -343,7 +326,7 @@ values.
 A typical \emph{BOXMOX.nml} file looks like this:
 
 \begin{alltt}
-\input{examples/BOXMOX.nml}
+\input{../case_studies/BOXMOX.nml}
 \end{alltt}
 
 
@@ -758,7 +741,7 @@ Make sure the following variables are set:
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF
 \end{verbatim}

boxmox/cflags

- 

boxmox/cflags.guess

-#!/bin/sh
-UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
-UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
-UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
-UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-
-CC=cc
-if [ x$1 != x ]; then CC=$1; fi
-
-exec 5>./cflags
-
-# Note: order is significant - the case branches are not exclusive.
-
-case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}:${CC}" in
-
-    *:HP-UX:*:*:cc*) # For HP-UX workstations
-        echo " -Aa -D_HPUX_SOURCE " 1>&5; exit 0 ;;
-
-    *:AIX:*:*:cc*) # For machines running AIX
-        echo " -Aa " 1>&5; exit 0 ;;
-
-    *:IRIX:*:*:cc*) # For machines running IRIX
-        echo " " 1>&5; exit 0 ;;
-
-    *:IRIX64:*:*:cc*) # For machines running IRIX64 
-        echo " " 1>&5; exit 0 ;;
-
-    *:Linux:*:*:cc*) # For Linux machines
-        echo " " 1>&5; exit 0 ;;
-
-    *:SunOS:*:*:cc*) # For SUN machines
-        echo " Please use gcc compiler on SUN machines."; exit 1 ;;
-
-    *:*:*:*:gcc*) # this is the default case, for gcc
-        echo " " 1>&5; exit 0 ;;
-
-    *:*:*:*:*) # this is the default case
-        echo " " 1>&5; exit 0 ;;
-esac

boxmox/int.modified_WCOPY/rosenbrock_soa.def

- 
-#FUNCTION AGGREGATE
-#JACOBIAN SPARSE_LU_ROW
-
-#DOUBLE ON 
-#INTFILE rosenbrock_soa
-
-#INLINE F90_GLOBAL
-      INTEGER Autonomous
-      COMMON /INTGDATA/ Autonomous
-      REAL*8 STEPSTART
-      COMMON /GDATA/ STEPSTART
-#ENDINLINE
-
-#INLINE F90_INIT
-       STEPMIN=0.0001
-       STEPMAX=3600.
-       Autonomous = 1 
-       STEPSTART=STEPMIN
-#ENDINLINE
-
-
-