Merge branch 'v2.3'

.travis.yml

@@ -118,12 +118,14 @@ install:
   - if test -n "$PLUMED_MACPORTS" ; then ./.travis/config.macports.sh ; fi
 
 script:
-# we enable crystallization and manyrestraints modules
-  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=crystallization:manyrestraints:adjmat"
+# make sure all modules are enabled
+  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=all"
 # we enable fftw, which is off by default
   - CONFIG_FLAGS="$CONFIG_FLAGS --enable-fftw"
   - if test "$MAKEDOC" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-pdfdoc" ; fi
   - if test "$MAKEDOC" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-gcov" ; fi
+# when running lcov plumed should be compiled with -O0
+  - if test "$MAKEDOC" == yes ; then PLUMED_CXXFLAGS=-O0 ; fi
 
 # BUILD:
 # this is done only if PLUMED_CXX is defined

src/colvar/ContactMap.cpp

@@ -46,7 +46,7 @@ The following example calculates switching functions based on the distances betw
 to a file named colvar.
 
 \verbatim
-CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH=(RATIONAL R_0=1.5) LABEL=f1
+CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH={RATIONAL R_0=1.5} LABEL=f1
 PRINT ARG=f1.* FILE=colvar
 \endverbatim
 
@@ -61,7 +61,7 @@ ATOMS1=1,2 REFERENCE1=0.1 WEIGHT1=0.5
 ATOMS2=3,4 REFERENCE2=0.5 WEIGHT2=1.0 
 ATOMS3=4,5 REFERENCE3=0.25 WEIGHT3=1.0 
 ATOMS4=5,6 REFERENCE4=0.0 WEIGHT4=0.5 
-SWITCH=(RATIONAL R_0=1.5) 
+SWITCH={RATIONAL R_0=1.5} 
 LABEL=cmap
 CMDIST
 ... CONTACTMAP