diff --git a/patches/gromacs-4.5.5.config b/patches/gromacs-4.5.5.config index c4c96cc70c23ae5ce30c003563e8c5e5a23acc93..aee30f437e1685b78b0c7ce3d03099470d297529 100644 --- a/patches/gromacs-4.5.5.config +++ b/patches/gromacs-4.5.5.config @@ -18,3 +18,10 @@ function plumed_after_revert(){ mv src/kernel/Makefile.plumedbck src/kernel/Makefile } +function plumed_patch_info(){ + echo "" + echo "PLUMED can be incorperated into gromacs using a simple patching procedure." + echo "Patching must be done after gromacs has been configured." + echo + echo "For more information on gromacs you should visit http://www.gromacs.org" +} diff --git a/patches/gromacs-4.6.3.config b/patches/gromacs-4.6.3.config index a5d00fcea22295d52544fcd345e60947ff7553ef..844164555a79af13afefcad5ee9d2e3dcf258a5b 100644 --- a/patches/gromacs-4.6.3.config +++ b/patches/gromacs-4.6.3.config @@ -4,3 +4,11 @@ function plumed_preliminary_test(){ # check if the README contains the word GROMACS and if gromacs has been already configured grep -q GROMACS README 1>/dev/null 2>/dev/null } + +function plumed_patch_info(){ + echo "" + echo "PLUMED can be incorperated into gromacs using a simple patching procedure." + echo "Patching must be done after gromacs has been configured." + echo + echo "For more information on gromacs you should visit http://www.gromacs.org" +} diff --git a/patches/lammps-6Apr13.config b/patches/lammps-6Apr13.config index 7aa1e453acc89b3e771728925a4620caa2836edd..d7a729858589a931ce3c6132be0c20e38aaf60af 100644 --- a/patches/lammps-6Apr13.config +++ b/patches/lammps-6Apr13.config @@ -14,3 +14,9 @@ function plumed_after_revert(){ rm -fr src/USER-PLUMED/ } +function plumed_patch_info(){ + echo "" + echo "PLUMED can be incorperated into LAMMPS using a simple patching procedure." + echo + echo "For more information on LAMMPS you should visit http://lammps.sandia.gov/" +} diff --git a/patches/namd-2.8.config b/patches/namd-2.8.config index 3eff738a2fc6ae97add7a847e49352c15fcbe335..3bef46c3c5a3bd83f44e12caf867f063f2b40df4 100644 --- a/patches/namd-2.8.config +++ b/patches/namd-2.8.config @@ -4,3 +4,9 @@ function plumed_preliminary_test(){ # check if the README.txt contains the word NAMD grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config } + +function plumed_patch_info(){ + echo "" + echo "" + echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/" +} diff --git a/patches/patch.sh b/patches/patch.sh index fc77435c8b6ca6db9b5eff1b8972fcafa9b3c6a4..434d832650517a988cd9160a714495f69d7a9813 100755 --- a/patches/patch.sh +++ b/patches/patch.sh @@ -17,6 +17,8 @@ Actions (choose one): same as save, but save also original files -n NEWENGINE, --new NEWENGINE create a new patch named NEWENGINE (*) + -i, --info + output information on the patching procedure for a particular code Options: -e ENGINE, --engine ENGINE set MD engine to ENGINE (default: choose interactively) @@ -64,6 +66,7 @@ do (--save-originals) test -n "$action" && multiple_actions=yes ; action=save ; save_originals=yes ;; (--revert|-R|-r) test -n "$action" && multiple_actions=yes ; action=revert ;; (--list-engines|-l) test -n "$action" && multiple_actions=yes ; action=list ;; + (--info|-i) test -n "$action" && multiple_actions=yes ; action=info ;; (--new=*) test -n "$action" && multiple_actions=yes ; action=new ; newpatch="${prefix_option#--new=}" ;; (--description) echo "patch an MD engine" ; exit ;; (--engine=*) engine="${prefix_option#--engine=}" ;; @@ -250,6 +253,9 @@ case "$action" in plumed_after_patch fi ;; + (info) + plumed_patch_info + ;; (save) if [ ! -L Plumed.h -o ! -L Plumed.inc ] then diff --git a/patches/qespresso-5.0.2.config b/patches/qespresso-5.0.2.config index 84c8e48453a9c74b3998ecf58c1ef6fe42d95a5d..f7c7b6ff5255426bf2178facfc72cc428d32e120 100644 --- a/patches/qespresso-5.0.2.config +++ b/patches/qespresso-5.0.2.config @@ -15,3 +15,9 @@ awk '{if($1=="LIBS" && $2=="="){print $0" $(PLUMED_LOAD) "}else{print }}' make.s function plumed_after_revert(){ mv make.sys.old make.sys } + +function plumed_patch_info(){ + echo "" + echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org" +} + diff --git a/user-doc/extract b/user-doc/extract index a8944b12da30f8012ff7142319503e497fd1ff0c..5a0b96e2e65d4220bced30dea18889db7e7c3c1a 100755 --- a/user-doc/extract +++ b/user-doc/extract @@ -18,7 +18,13 @@ done # Create the list of codes that plumed works with from the set of available patches for file in ../patches/*.diff do - echo "- $file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///' >> automatic/codes.list + myengine=`echo "$file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///'` + mytag=`echo "$myengine" | sed -e 's/\./\_/g'` + echo "- \subpage $mytag" >> automatic/codes.list + echo "/**" >> automatic/$myengine.txt + echo "\page $mytag $myengine" >> automatic/$myengine.txt + plumed patch -e $myengine -i | grep -v "PLUMED patching tool" | grep -v "PLUMED location:" | grep -v "extra files located in:" | grep -v "MD engine:" | grep -v "diff file:" | grep -v "sourcing config file:" >> automatic/$myengine.txt + echo "*/" >> automatic/$myengine.txt done ## Check for utilities that register actions with no documentation