Final touches

README.md

@@ -16,6 +16,10 @@ We are looking forward to receiving your [new issue report](https://mbees.med.un
 
 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.
 
+## Building a distribution
+
+Once forked, you can create your own distributable archive using the `build_dist.sh` script, which takes the build directory as argument.
+
 ## Citation
 
 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).
@@ -26,7 +30,7 @@ Please cite our work when BOXMOX use constituted a relevant contribution to your
 
 KPP (adjoint) driver for BOXMOX.
 
-`drv/wrapper`
+`boxmox/wrapper`
 
 This is where all BOXMOX extension code lives.
 
@@ -34,7 +38,7 @@ This is where all BOXMOX extension code lives.
 
 Test cases for BOXMOX usage.
 
-`doc/boxmox_README.tex`
+`boxmox/boxmox_README.tex`
 
 BOXMOX documentation.
 

tools/create_BOXMOX_patch.bash

-#!/bin/bash
-
-boxmoxVersion=1.8
-kppVersion=2.2.3
-kppFile=kpp-2.2.3_Nov.2012.tar.gz
-
-boxmoxDir=boxmox
-kppDir=kpp-$kppVersion
-wrkDir=patch_wrk_dir
-
-prepScript=$(pwd)/prep_BOXMOX_src_directory.bash
-
-patchName=$(pwd)/boxmox_${boxmoxVersion}_${kppVersion}.patch
-
-tar xvzf $kppFile
-
-# copy both directories here to have relative paths
-rm -rf $wrkDir
-mkdir -p $wrkDir
-
-cp -r $boxmoxDir $wrkDir/boxmox
-mv $kppDir $wrkDir/kpp
-
-cd $wrkDir
-
-bash ${prepScript} boxmox ${boxmoxVersion}
-
-diff -rupwN kpp boxmox > ${patchName}
-
-exit 0

tools/install_BOXMOX.bash

-#!/bin/bash
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# BOXMOX extensions to KPP - installation script
-#
-# execute as
-# me@mymachine> bash install_BOXMOX.bash
-#
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-#
-# 1.0 Christoph Knote - NCAR/ACD - knote@ucar.edu - 06/2014
-# 1.1 Christoph Knote - NCAR/ACD - knote@ucar.edu - 07/2014
-#     updates to the MOZART mechanism
-# 1.2 Christoph Knote - LMU - christoph.knote@lmu.de - 08/2015
-#     various updates to BOXMOX
-# 1.3 Christoph Knote - LMU - christoph.knote@lmu.de - 11/2015
-#     new Namelist feature, various code updates
-# 1.4 Christoph Knote - LMU - christoph.knote@lmu.de - 09/2016
-#     included MCM and other mechanisms, code updates
-# 1.5 Christoph Knote - LMU - christoph.knote@lmu.de - 11/2016
-#     new commands included for simplified usage, code updates
-# 1.6 Christoph Knote - LMU - christoph.knote@lmu.de - 02/2017
-#     ability to create adjoint using prepare_BOXMOX_mechanism
-# 1.6.1 Christoph Knote - LMU - christoph.knote@lmu.de - 02/2017
-#     bugfix release
-# 1.7 Christoph Knote - LMU - christoph.knote@lmu.de - 12/2017
-#     new file format, heterogeneous reactions/aerosol, dilution
-# 1.8 Christoph Knote - UniA - christoph.knote@med.uni-augsburg.de - 11/2021
-#     first release from new website at University Augsburg
-#
-# USER SECTION
-
-# This is where your BOXMOX will be
-boxmoxDir=$(pwd)/boxmox
-
-# your C compiler - gcc should be fine on most systems
-CC=gcc
-
-# the FLEX lexical analyzer - check via "which flex"
-FLEX=$(which flex 2> /dev/null)
-
-# the FLEX library directory - on Linux try via "type -a libfl.a",
-# if this fails it is usually somewhere close to the binary (e.g. in ../lib)
-FLEX_LIB_DIR=/usr/lib/x86_64-linux-gnu
-
-# your C compiler flags (if any). Note: separate multiple arguments by spaces and enclose in quotation marks.
-CC_FLAGS="-g -Wall"
-
-# standard headers
-INCLUDE_DIR=/usr/include
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# nothing to be changed beyond this point...
-
-boxmoxVersion=1.8
-
-# see if we have everything we need
-hash sed >/dev/null 2>&1      || { echo "BOXMOX installer needs 'sed'"; exit 1; }
-hash make >/dev/null 2>&1     || { echo "BOXMOX installer needs 'make'"; exit 1; }
-hash bison >/dev/null 2>&1    || { echo "BOXMOX installer needs 'bison'"; exit 1; }
-
-# see if the given options make sense
-hash $CC >/dev/null 2>&1      || { echo "C compiler $CC unknown"; exit 1; }
-[ -f $FLEX ]                  || { echo "No FLEX executable found at $FLEX"; exit 1; }
-[ -f $FLEX_LIB_DIR/libfl.a ]  || { echo "No FLEX library found in $FLEX_LIB_DIR"; exit 1; }
-[ -d $INCLUDE_DIR ]           || { echo "No include directory found at $INCLUDE_DIR"; exit 1; }
-
-hash gfortran >/dev/null 2>&1 || { echo "Note: BOXMOX will need 'gfortran' or another Fortran compiler.";  }
-
-# let's go - describe what's gonna happen
-echo " "
-echo "BOXMOX extension to KPP (${boxmoxVersion})"
-echo " "
-echo "Output directory: $boxmoxDir"
-echo "C compiler:       $CC"
-echo "C compiler flags: $CC_FLAGS"
-echo "FLEX binary:      $FLEX"
-echo "FLEX library:     $FLEX_LIB_DIR/libfl.a"
-echo " "
-
-[ -z $KPP_HOME ] || { echo "The KPP_HOME variable is set (to '${KPP_HOME}'), it seems there is already another KPP/BOXMOX installation. Make sure to update your \$KPP_HOME and \$PATH variables after this new installation."; echo ""; }
-
-mkdir -p $boxmoxDir || { echo "Could not create BOXMOX directory $boxmoxDir"; exit 1; }
-
-cd $boxmoxDir
-
-# make (missing) bin subfolder
-mkdir -p bin
-
-mv Makefile.defs Makefile.defs.BACK
-
-sed "s|CC=.*|CC=$CC|;s|CC_FLAGS=.*|CC_FLAGS=$CC_FLAGS|;s|FLEX=.*|FLEX=$FLEX|;s|FLEX_LIB_DIR=.*|FLEX_LIB_DIR=$FLEX_LIB_DIR|;s|INCLUDE_DIR = .*|INCLUDE_DIR = $INCLUDE_DIR|" Makefile.defs.BACK > Makefile.defs
-[[ $? ]] || { echo "Could not patch Makefile.defs"; exit 1; }
-
-make &> compile.log
-
-[ -f bin/kpp ] || { echo "Could not compile BOXMOX - see compile.log"; exit 1; }
-
-export KPP_HOME=$boxmoxDir
-export PATH=$KPP_HOME/bin:$KPP_HOME/boxmox/bin:$PATH
-
-echo " "
-echo " --- YOU ARE GOOD TO GO ---"
-echo " "
-echo "Remember to copy the following lines into"
-echo "your .bashrc (a hidden file in your home directory)"
-echo "so they are executed upon login:"
-echo " "
-echo "export KPP_HOME=$boxmoxDir"
-echo "export PATH=\$KPP_HOME/bin:\$KPP_HOME/boxmox/bin:\$PATH"
-echo " "
-
-

tools/prep_BOXMOX_src_directory.bash

-#!/bin/bash
-
-boxmoxDir=$1
-boxmoxVersion=$2
-
-# now clean up the superfluous directories and files
-rm -rf ${boxmoxDir}/boxmox/compiled_mechs
-find . -name "*.DS_Store" -delete
-find . -name "*~" -delete
-find . -name "*.log" -delete
-find . -name "*.aux" -delete
-find . -name "*.o" -delete
-find . -name "*.dvi" -delete
-find . -name "*synctex*" -delete
-find . -name "*_CSIRO*" -delete
-find . -name "*NO_NO2*" -delete
-
-# replace BOXMOX version strings
-sed -i 's/__BOXMOX_VERSION__/'${boxmoxVersion}'/g' ${boxmoxDir}/boxmox/wrapper
-sed -i 's/__BOXMOX_VERSION__/'${boxmoxVersion}'/g' ${boxmoxDir}/boxmox/boxmox.f90
-sed -i 's/__BOXMOX_VERSION__/'${boxmoxVersion}'/g' ${boxmoxDir}/boxmox/boxmox_adjoint.f90
-sed -i 's/__BOXMOX_VERSION__/'${boxmoxVersion}'/g' ${boxmoxDir}/boxmox/bin/new_BOXMOX_experiment
-sed -i 's/__BOXMOX_VERSION__/'${boxmoxVersion}'/g' ${boxmoxDir}/boxmox/bin/new_BOXMOX_experiment_from_example