From b68eff0e4847c560b1bd9dfa81ffe80831b4e38b Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 28 Jul 2019 10:42:28 +0200
Subject: [PATCH] Functionality for checking plumed include files has been done
in a neater way
---
developer-doc/usingDoxygen.md | 16 +++++----------
src/generic/Group.cpp | 5 +++--
src/generic/Include.cpp | 25 +++++++++++++---------
user-doc/Doxyfile | 2 --
user-doc/Makefile | 2 +-
user-doc/Miscelaneous.md | 5 +++--
user-doc/go-example-check | 33 ++++++++----------------------
user-doc/go-spelling | 4 ++--
user-doc/tutorials/aa-lugano-2.txt | 5 +++--
9 files changed, 41 insertions(+), 56 deletions(-)
diff --git a/developer-doc/usingDoxygen.md b/developer-doc/usingDoxygen.md
index 7ef8e8e69..e0dda8b7d 100644
--- a/developer-doc/usingDoxygen.md
+++ b/developer-doc/usingDoxygen.md
@@ -466,20 +466,14 @@ DISTANCE ATOMS=1,2 LABEL=dist
INCLUDE FILE=toBeIncluded.inc
\ endplumedfile /*** But with no space between the \ and the endplumedfile
-\plumedincludefile
-# this is toBeIncluded.inc
+\plumedfile
+#SETTINGS FILENAME=toBeIncluded.inc
RESTRAINT ARG=dist AT=2.0 KAPPA=1.0
-\ endplumedincludefile /*** But with no space between the \ and the endplumedincludefile
-\endverbatim
-
-Please note that it is essential that you write:
-
-\verbatim
-# this is <filename>
+\ endplumedfile /*** But with no space between the \ and the endplumedincludefile
\endverbatim
-on the second line in the plumedincludefile environment as this is where the script that builds the user documentation gets the name of the included file
-from. Also notice that if, as in the example above, the included file is not (by itself) a valid plumed input it CANNOT be called *.dat as the script that
+By including the FILENAME attribute on the SETTINGS line you can set the name of the plumed input file that is generated when the input is tested.
+Also notice that if, as in the example above, the included file is not (by itself) a valid plumed input it CANNOT be called *.dat as the script that
checks the input will complain.
\subsection molfileeg Using MOLFILE in your example input files
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 59b26c780..bdf44b223 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -79,11 +79,12 @@ PRINT ARG=c FILE=colvar
Groups can be conveniently stored in a separate file.
E.g. one could create a file named `groups.dat` which reads
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=groups.dat
# this is groups.dat
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
-\endplumedincludefile
+\endplumedfile
and then include it in the main 'plumed.dat' file
\plumedfile
INCLUDE FILE=groups.dat
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 950d6ef7e..d146678a5 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -54,11 +54,12 @@ d: DISTANCE ATOMS=c1,c2
PRINT ARG=d
\endplumedfile
where the content of file pippo.dat is
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=pippo.dat
# this is pippo.dat
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
-\endplumedincludefile
+\endplumedfile
The files in this example are rather short, but imagine a case like this one:
\plumedfile
@@ -67,7 +68,8 @@ c: COORDINATION GROUPA=groupa GROUPB=groupb R_0=0.5
METAD ARG=c HEIGHT=0.2 PACE=100 SIGMA=0.2 BIASFACTOR=5
\endplumedfile
Here `groups.dat` could be huge file containing group definitions such as
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=groups.dat
# this is groups.dat
groupa: GROUP ...
ATOMS={
@@ -91,17 +93,18 @@ groupb: GROUP ...
121
}
...
-\endplumedincludefile
+\endplumedfile
So, included files are the best place where one can store long definitions.
Another case where INCLUDE is very useful is when running multi-replica simulations.
Here different replicas might have different input files, but perhaps a large part of the
input is shared. This part can be put in a common included file. For instance you could have
`common.dat`:
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=common.dat
# this is common.dat
t: TORSION ATOMS=1,2,3,4
-\endplumedincludefile
+\endplumedfile
Then `plumed.0.dat`:
\plumedfile
# this is plumed.0.dat
@@ -128,15 +131,17 @@ t: TORSION ATOMS=1,2,3,4
INCLUDE FILE=other.inc
\endplumedfile
Then `other.0.inc`:
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=other.0.inc
# this is other.0.inc
RESTRAINT ARG=t AT=1.0 KAPPA=10
-\endplumedincludefile
+\endplumedfile
And `other.1.inc`:
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=other.1.inc
# this is other.1.inc
RESTRAINT ARG=t AT=1.2 KAPPA=10
-\endplumedincludefile
+\endplumedfile
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 571e3ad3b..26134d62f 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -238,8 +238,6 @@ ALIASES = \
"tarball{1}=\htmlonly<span style=\"background-color:yellow\">\endhtmlonly<a href=\"tutorial-resources/\1.tar.gz\" style=\"font-weight:bold\" style=\"color:green\" download=\"\1.tar.gz\"> TARBALL </a>\htmlonly</span>\endhtmlonly" \
"plumedfile=\verbatim BEGIN_PLUMED_FILE" \
"endplumedfile=\endverbatim" \
- "plumedincludefile=\verbatim BEGIN_PLUMED_FILE" \
- "endplumedincludefile=\endverbatim" \
"auxfile{1}=\verbatim" \
"endauxfile=\endverbatim" \
"plumednotmaintained=\warning This branch is not maintained. Users are invited to upgrade to a newer version"
diff --git a/user-doc/Makefile b/user-doc/Makefile
index 9e869587a..9e35d3c8e 100644
--- a/user-doc/Makefile
+++ b/user-doc/Makefile
@@ -17,7 +17,7 @@ else
all:
ifeq ($(make_doc),yes)
make_pdfdoc=$(make_pdfdoc) ./extract
- # temporarily removed for travis to build:
+ # check examples in input file:
./go-example-check
make_pdfdoc=$(make_pdfdoc) ./go-doxygen
cp *png html/
diff --git a/user-doc/Miscelaneous.md b/user-doc/Miscelaneous.md
index a1a452d41..01e9712f2 100644
--- a/user-doc/Miscelaneous.md
+++ b/user-doc/Miscelaneous.md
@@ -482,10 +482,11 @@ DISTANCE ATOMS=1,2 LABEL=dist
INCLUDE FILE=toBeIncluded.inc
\endplumedfile
plus a "toBeIncluded.inc" file
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=toBeIncluded.inc
# this is toBeIncluded.inc
RESTRAINT ARG=dist AT=2.0 KAPPA=1.0
-\endplumedincludefile
+\endplumedfile
However, when you do this it is important to recognize that \ref INCLUDE is a real directive that is only resolved
after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
diff --git a/user-doc/go-example-check b/user-doc/go-example-check
index bd5232592..846bedfdf 100755
--- a/user-doc/go-example-check
+++ b/user-doc/go-example-check
@@ -5,7 +5,7 @@ mkdir example-check
# This generates plumed.dat files for each of the documentation pages in the manual
for file in *PP.md automatic/*.txt ../CHANGES/*.md tutorials/*.txt tutorials/*.site tutorials/others/*.txt ; do
- # echo Generating examples to check for file $file
+ #echo Generating examples to check for file $file
# Single replica examples
splits=`echo $file | sed -e 's/\// /g'`
nf=`echo $splits | awk '{print NF}'`
@@ -29,31 +29,16 @@ for file in *PP.md automatic/*.txt ../CHANGES/*.md tutorials/*.txt tutorials/*.s
wrongc=`grep "this is wrong" example-check/$fname/$i.dat | wc -l | awk '{print $1}'`
if [ $wrongc -gt 0 ] ; then
rm example-check/$fname/$i.dat
+ else
+ # This deals with include files
+ hasname=`grep "#SETTINGS" example-check/$fname/$i.dat | grep "FILENAME=" | wc -l | awk '{print $1}'`
+ if [ $hasname -gt 0 ] ; then
+ filename=`grep "#SETTINGS" example-check/$fname/$i.dat | awk '{for(i=1;i<=NF;++i){if(match($i,"FILENAME=")){print $i}}}' | sed -e 's/FILENAME=//'`
+ mv example-check/$fname/$i.dat example-check/$fname/$filename
+ fi
fi
sline=$eline
done
- # Check for plumed include files
- cat $file |
- awk 'BEGIN{inp=0;}{
- if( $1=="\\endplumedincludefile" ){ print ">>END OF EXAMPLE>>"; inp=0; }
- else if( $1=="\\plumedincludefile" ){ inp=1; }
- else if( inp==1 ){ print $0; }
- }' > example-check/$fname.inc
- ninc=`grep ">>END OF EXAMPLE>>" example-check/$fname.inc | wc -l | awk '{print $1}'`
- # And split the set of include files
- sline=0
- for ((i=1;i<=$ninc;++i)) ; do
- checks=`grep -A 1 "plumedincludefile" $file | head -n $((($i-1)*6+2)) | tail -n 1 | awk '{match($0,"# this is")}'`
- ifname=`grep -A 1 "plumedincludefile" $file | head -n $((($i-1)*6+2)) | tail -n 1 | awk '{if(match($0,"# this is")){ print $4; } else { print "ERROR";}}'`
- if [ $ifname == "ERROR" ] ; then
- echo ERROR in specification of include file for $file
- exit 1
- fi
- eline=`grep -n ">>END OF EXAMPLE>>" example-check/$fname.inc | head -n $i | tail -n 1 | awk '{print $1}' | sed -e 's/:>>END//g'`
- head -n $(($eline-1)) example-check/$fname.inc | tail -n $(($eline-1-$sline)) > example-check/$fname/$ifname
- sline=$eline
- done
- rm example-check/$fname.inc
# Check for auxiliary files
cat $file |
awk 'BEGIN{inp=0;}{
@@ -145,7 +130,7 @@ for dir in * ; do
fi
nerr=`grep "PLUMED error" check.log | wc -l | awk '{print $1}'`
if [ $nerr -gt 0 ] ; then
- echo Found mistakes for examples $file
+ echo Found mistakes for examples in $dir example $file
cat check.log
exit 1
fi
diff --git a/user-doc/go-spelling b/user-doc/go-spelling
index 6b9ced05d..e01ae4b2f 100755
--- a/user-doc/go-spelling
+++ b/user-doc/go-spelling
@@ -29,8 +29,8 @@ for file in *PP.md automatic/*.txt ../CHANGES/*.md tutorials/*.txt tutorials/*.s
# This is some stuff to get rid of stuff that trips up the spell checker: the equations and the plumed examples
cat $file | grep -v "\\image" | grep -v "anchor" | sed -e 's/psi-1//' | sed -e 's/-#//' | sed -e 's/@//' | sed -e 's/&//' | sed -e 's/\vdots//' |
awk 'BEGIN{inp=0}{
- if($1=="\\endplumedfile" || $1=="\\f]" || $1=="\\f}" || $1=="\\endauxfile" || $1=="\\endplumedincludefile" || $1=="\\endverbatim" || $1=="\\endcode"){inp=0;}
- else if($1=="\\plumedfile" || $1=="\\f[" || $1=="\\f{eqnarray*}{" || match($1,"\\auxfile") || $1=="\\plumedincludefile" || $1=="\\verbatim" || index($1,"\\code{")!=0 ){inp=1;}
+ if($1=="\\endplumedfile" || $1=="\\f]" || $1=="\\f}" || $1=="\\endauxfile" || $1=="\\endverbatim" || $1=="\\endcode"){inp=0;}
+ else if($1=="\\plumedfile" || $1=="\\f[" || $1=="\\f{eqnarray*}{" || match($1,"\\auxfile") || $1=="\\verbatim" || index($1,"\\code{")!=0 ){inp=1;}
else if(inp==0){
skip=0;
for(i=1;i<=NF;++i){
diff --git a/user-doc/tutorials/aa-lugano-2.txt b/user-doc/tutorials/aa-lugano-2.txt
index 9235e1311..4c92988a1 100644
--- a/user-doc/tutorials/aa-lugano-2.txt
+++ b/user-doc/tutorials/aa-lugano-2.txt
@@ -390,7 +390,8 @@ is presented in the following but the exercise is possible only if plumed is com
Here we use the "replica" syntax of plumed to write a single plumed input file for all the windows:
-\plumedincludefile
+\plumedfile
+#SETTINGS FILENAME=plumed.dat
# this is plumed.dat
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
@@ -413,7 +414,7 @@ restraint-phi: RESTRAINT ...
} ...
# monitor the two variables and the bias potential from the restraint
PRINT STRIDE=20 ARG=phi,psi,restraint-phi.bias FILE=COLVAR
-\endplumedincludefile
+\endplumedfile
The \@replicas syntax allow to define different values for a variable for the different replicas.
--
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