Works, builds, runs.

.gitignore

@@ -4,10 +4,11 @@ build
 src/kpp
 boxmox*.tar.gz
 
-doc/boxmox*toc
-doc/boxmox*aux
-doc/boxmox*log
-doc/boxmox*pdf
+boxmox/UserManual.toc
+boxmox/UserManual.aux
+boxmox/UserManual.log
+boxmox/UserManual.pdf
+doc/boxmox_UserManual.pdf
 
 src/bison.c
 src/bison.h

doc/boxmox_UserManual.tex → boxmox/UserManual.tex

@@ -758,7 +758,7 @@ 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}

build_dist.sh

@@ -9,7 +9,7 @@ echo
 cp Makefile.am_BLUEPRINT Makefile.am
 
 # list all files in these subdirectories
-distFiles=$(find drv examples case_studies int models util -type f)
+distFiles=$(find boxmox drv examples case_studies int models util -type f)
 
 #pretty print them                                        45 char wide    dd tab, backslash at end    remove backslash last line  remove tab first line
 printf 'nobase_dist_pkgdata_DATA = %s\n' "${distFiles[*]}" | fmt -w 45 | sed -e 's/\(.*\)$/\t\1 \\/g' | sed '$ s/\\//g' | sed '1 s/\t//g' >> Makefile.am
@@ -18,9 +18,10 @@ echo
 echo " --- build documentation ---"
 echo
 
-cd doc
-pdflatex boxmox_UserManual
-pdflatex boxmox_UserManual
+cd boxmox
+pdflatex UserManual
+pdflatex UserManual
+cp UserManual.pdf ../doc/boxmox_UserManual.pdf
 cd ..
 
 # now standard:

configure.ac

@@ -6,8 +6,21 @@ AC_INIT([boxmox], [1.8], [christoph.knote@med.uni-augsburg.de])
 dnl we use the build type foreign here instead of gnu because I do not have a NEWS file and similar, yet.
 AM_INIT_AUTOMAKE([-Wall foreign tar-pax])
 AC_PROG_CC
+if test x$CC = "x" ; then
+    AC_MSG_ERROR([C compiler is required to build KPP.])
+fi
 AC_PROG_LEX(noyywrap)
+if test x$LEX = "x" ; then
+    AC_MSG_ERROR([flex is required to build KPP.])
+fi
 AC_PROG_YACC
+if test x$YACC = "x" ; then
+    AC_MSG_ERROR([bison or yacc is required to build KPP.])
+fi
+AC_PROG_FC
+if test x$FC = "x" ; then
+    AC_MSG_ERROR([Fortran compiler is required to build BOXMOX mechanisms.])
+fi
 AC_PROG_MKDIR_P
 AC_CONFIG_FILES([
     Makefile

examples/CB05TUCl_EPA.kpp

@@ -2,7 +2,7 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF
 #FUNCTION AGGREGATE

examples/CB05TUCl_NCSU.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/CBMZ.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/HETCHEM.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/MCMv3_3.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/MOZART_4.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/MOZART_T1.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/NO_NO2.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/RACM.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/RADM2.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/RADMKA.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/SAPRC99.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

examples/smog.kpp

@@ -2,6 +2,6 @@
 #LANGUAGE Fortran90
 #DOUBLE ON
 #INTEGRATOR rosenbrock
-#DRIVER ../boxmox/boxmox
+#DRIVER boxmox
 #JACOBIAN SPARSE_LU_ROW
 #HESSIAN OFF

scripts/list_BOXMOX_mechanisms

@@ -28,9 +28,7 @@ validate_BOXMOX_installation || { echo "Validating BOXMOX installation failed";
 
 BOXMOX_MECH_PATH=${KPP_HOME}/compiled_mechs
 
-if [ -z $(ls -A ${BOXMOX_MECH_PATH}) ]; then
-    echo No mechanisms compiled yet.
-else
+if [ ! -z $(ls -A ${BOXMOX_MECH_PATH}) ]; then
   for mech in $(find ${BOXMOX_MECH_PATH}/*)
   do
     mechList+=($(basename $mech))

scripts/new_BOXMOX_experiment_from_example

@@ -18,7 +18,7 @@ then
   echo "Call with <example name> (<experiment path>)."
   echo "If you omit <experiment path>, a subfolder with the name <example name> will be used."
   echo "Use -f to force removal of existing experiment folder."
-  echo "Examples available: "$(find ${KPP_HOME}/examples/* -maxdepth 1 -type d -exec basename {} \;)
+  echo "Examples available: "$(find ${KPP_HOME}/case_studies/* -maxdepth 1 -type d -exec basename {} \;)
   exit 1
 fi
 
@@ -28,7 +28,7 @@ example_req=$1
 # check if BOXMOX is correctly set up
 validate_BOXMOX_installation || { echo "Validating BOXMOX installation failed"; exit 1; }
 
-example_dir=${KPP_HOME}/examples/${example_req}
+example_dir=${KPP_HOME}/case_studies/${example_req}
 
 # check if example exists
 if [ ! -d ${example_dir} ]