diff --git a/.gitignore b/.gitignore index 6546e1b543d3b10de9cc74afb7308016790a9eb8..72459251e36f6a738d628c56469c48aa162a176a 100644 --- a/.gitignore +++ b/.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 diff --git a/doc/boxmox_UserManual.tex b/boxmox/UserManual.tex similarity index 99% rename from doc/boxmox_UserManual.tex rename to boxmox/UserManual.tex index 0a81aa13baecef1ce29e2491dc596a0936b59295..55f24a77e77ff3d04e6dd5bb5f2d24b92cb8d53b 100644 --- a/doc/boxmox_UserManual.tex +++ b/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} diff --git a/drv/wrapper b/boxmox/wrapper similarity index 100% rename from drv/wrapper rename to boxmox/wrapper diff --git a/build_dist.sh b/build_dist.sh index dcb7fe60c5553e4dfb76875c1f161a5afdb09e64..b3240471f00c8e79301fe63cf264050bbd4cacc0 100755 --- a/build_dist.sh +++ b/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: diff --git a/configure.ac b/configure.ac index 923b8c1c23c68ad047e19677f19ca282c00edf22..48a5f1119b9391eff14a41de22dede30f9b382de 100644 --- a/configure.ac +++ b/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 diff --git a/examples/CB05TUCl_EPA.kpp b/examples/CB05TUCl_EPA.kpp index 055aff28e7e8a5a063fb804fb4ee8216b7a25b1f..6f838bb23b7303cec49ea0551d44c5937d1c55a7 100644 --- a/examples/CB05TUCl_EPA.kpp +++ b/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 diff --git a/examples/CB05TUCl_NCSU.kpp b/examples/CB05TUCl_NCSU.kpp index aa89ca3b5772ed9755d53e25535f8ba964557d0a..7fdc7cb9032646f1e3d1fb303c8234010d41acba 100644 --- a/examples/CB05TUCl_NCSU.kpp +++ b/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 diff --git a/examples/CBMZ.kpp b/examples/CBMZ.kpp index 24c3f203ea1500ed2206e613d14872ac4c733a6b..678b9d065ba093a9f763d955753e50625767d9e1 100644 --- a/examples/CBMZ.kpp +++ b/examples/CBMZ.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/HETCHEM.kpp b/examples/HETCHEM.kpp index d9e34ee9820fb2a72d3327f86636a8e24fa89726..f4738c87db3c243677d52f5646da49e6cb48e0cc 100644 --- a/examples/HETCHEM.kpp +++ b/examples/HETCHEM.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/MCMv3_3.kpp b/examples/MCMv3_3.kpp index 97218035d813997e3657fa1e22faff5bf624ea1a..a4024436a2f72c0fed78ebc04659229e9072746a 100644 --- a/examples/MCMv3_3.kpp +++ b/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 diff --git a/examples/MOZART_4.kpp b/examples/MOZART_4.kpp index ea637760961ae4ba627c26552a31e662db8960bc..ef211e12bee5ea2348e8580957f22b2c4a8f21cc 100644 --- a/examples/MOZART_4.kpp +++ b/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 diff --git a/examples/MOZART_T1.kpp b/examples/MOZART_T1.kpp index 985c57d3720bcc20d9849e4949635e79d1a6cb7d..052b163898b2a9882551e1a63ba71e46d7368528 100644 --- a/examples/MOZART_T1.kpp +++ b/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 diff --git a/examples/NO_NO2.kpp b/examples/NO_NO2.kpp index 28bf2605a392758f04e95e10058dc4d1ee882a83..cef26aa800ad79f202ad3fd9e17a9f4c316f8084 100644 --- a/examples/NO_NO2.kpp +++ b/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 diff --git a/examples/RACM.kpp b/examples/RACM.kpp index a8851e245229333ccbd94d35c77b237565bcb5ea..63e31d45fcb9aee15f070a1e01c16d6c7067237e 100644 --- a/examples/RACM.kpp +++ b/examples/RACM.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/RADM2.kpp b/examples/RADM2.kpp index 785be2e7fa5203ac3f3ffb8cb6a46708e745f65c..93d692f18f1e8b986509d14ea96453928aab2751 100644 --- a/examples/RADM2.kpp +++ b/examples/RADM2.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/RADMKA.kpp b/examples/RADMKA.kpp index ca7a9b7859dd7ea4a2db63973fa3ec3641c204e4..0a2f02161c3f0b67b5666ce5d1b345caeefddc4b 100644 --- a/examples/RADMKA.kpp +++ b/examples/RADMKA.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/SAPRC99.kpp b/examples/SAPRC99.kpp index d828cf535644f9ec2a59198f5df6e316b2cec9f0..5e30a88fece861aff004fc39f4696ec1831d6641 100644 --- a/examples/SAPRC99.kpp +++ b/examples/SAPRC99.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/examples/smog.kpp b/examples/smog.kpp index ed76a9d5ff108fd38775c0034868d8f3be049574..a0d0cb40109978044ca52d1ffadd4843649c361f 100644 --- a/examples/smog.kpp +++ b/examples/smog.kpp @@ -2,6 +2,6 @@ #LANGUAGE Fortran90 #DOUBLE ON #INTEGRATOR rosenbrock -#DRIVER ../boxmox/boxmox +#DRIVER boxmox #JACOBIAN SPARSE_LU_ROW #HESSIAN OFF diff --git a/scripts/list_BOXMOX_mechanisms b/scripts/list_BOXMOX_mechanisms index 28ada224c878600534051b003f31a06f2845d0d5..7113d8ca3638e2b7152d708e0b0fa69d61f7e5b5 100755 --- a/scripts/list_BOXMOX_mechanisms +++ b/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 $mech)) diff --git a/scripts/new_BOXMOX_experiment_from_example b/scripts/new_BOXMOX_experiment_from_example index 1b00e05086055d2ddc6bfee3853d7d6f2f478dc5..cf3c5805004494984083bbdb2e09046b758bf4cc 100755 --- a/scripts/new_BOXMOX_experiment_from_example +++ b/scripts/new_BOXMOX_experiment_from_example @@ -18,7 +18,7 @@ then echo "Call with ()." echo "If you omit , a subfolder with the name will be used." echo "Use -f to force removal of existing experiment folder." - echo "Examples available: "$(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} ]