Several typos in the documentation

CHANGES/v2.1.txt

@@ -80,7 +80,7 @@ character now has a special usage in component names.
     the configuration system falls back to an internal version which implements a minimal list
     of plugins (gromacs and dcd) (kindly provided by T. Giorgino).
   - \ref switchingfunction : added STRETCH flag.
-  - Negative strides in atom ranges (e.g. 10-1:-3).
+  - Negative strides in atom ranges (e.g. ATOMS=10-1:-3 is expanded to ATOMS=10,7,4,1).
   - \ref COORDINATION and \ref DHENERGY with NLIST now work correctly in replica exchange simulations.
   - Multicolvars with neighbor lists now work correctly in replica exchange simulations.
   - Improved multicolvar neighbor lists.

patches/namd-2.8.config

@@ -6,7 +6,7 @@ function plumed_preliminary_test(){
 }
 
 function plumed_patch_info(){
-  echo "WARNING: NAMD does not currently take into account virial contributions"
+  echo "\bug NAMD does not currently take into account virial contributions"
   echo "from PLUMED. Please use constant volume simulations only"
   echo ""
   echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"

patches/namd-2.9.config

@@ -6,7 +6,7 @@ function plumed_preliminary_test(){
 }
 
 function plumed_patch_info(){
-  echo "WARNING: NAMD does not currently take into account virial contributions"
+  echo "\bug NAMD does not currently take into account virial contributions"
   echo "from PLUMED. Please use constant volume simulations only"
   echo ""
   echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"

src/multicolvar/Torsions.cpp

@@ -31,7 +31,7 @@ using namespace std;
 namespace PLMD{
 namespace multicolvar{
 
-//+PLUMEDOC COLVAR TORSIONS
+//+PLUMEDOC MCOLVAR TORSIONS
 /*
 Calculate whether or not a set of torsional angles are within a particular range.
 

user-doc/Installation.txt

@@ -12,7 +12,7 @@ For those of you who are impatient, the following might do the job:
 > ./configure --prefix=/usr/local/lib
 > make -j 4
 > make doc # this is optional and requires doxygen installed
-> make install
+> make install # this is also optional - plumed can be used from the compilation directory
 \endverbatim
 
 Once the above is completed you can use PLUMED to analyze
@@ -87,7 +87,7 @@ in place so as to do some checking you can use
 > ./configure --enable-debug
 \endverbatim
 This will perform some extra check during execution (possibly slowing down PLUMED)
-and write full symbol tables in the executable (making the final executible  much larger).
+and write full symbol tables in the executable (making the final executable  much larger).
 
 The main goal of the automatic configure is to find the libraries.
 When they are stored in unconventional places it is thus sensible to tell autoconf where 
@@ -124,7 +124,8 @@ a specific version of a library by specifying it using the LIBS variable.
 if you have problems in linking the file 'src/lib/plumed-shared', try to set correctly
 the runtime path by using
 \verbatim
-> ./configure LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib" CPPFLAGS=-I/opt/local/include LIBS=-lmymatheval
+> ./configure LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib" \
+  CPPFLAGS=-I/opt/local/include LIBS=-lmymatheval
 \endverbatim
 Notice that although the file 'src/lib/plumed-shared' is not necessary, being
 able to produce it means that it will be possible to link PLUMED dynamically
@@ -193,12 +194,13 @@ Some simple to fix further problems include:
 - If the linker complains and suggests recompiling lapack with -fPIC, it means that you have static lapack libraries. Either install dynamic lapack libraries
 or switch to static compilation of PLUMED by unsetting the SOEXT variable
 in the configuration file.
-- If the linker complains that dsyevr_ cannot be found, try adding
-  -DF77_NO_UNDERSCORE to CPPFLAGS
 - If the linker complains about other missing functions (typically starting with
   "for_" prefix) then you should also link some Fortran libraries. PLUMED
   is written in C++ and often C++ linkers do not include Fortran libraries by default.
   These libraries are required for lapack and blas to work. Please check the documentation of your compiler.
+- If the linker complains that dsyevr_ cannot be found, try adding
+  -DF77_NO_UNDERSCORE to CPPFLAGS
+  Notice that "./configure" should automatically try this solution.
 
 \section CompilingPlumed Compiling PLUMED
 
@@ -337,7 +339,10 @@ do not want to set up modules, but we believe that using modules as described ab
 
 \section Patching Patching your MD code
 
-At the present times PLUMED can be added to the following list of codes:
+In case your MD code is not supporting PLUMED already, you should modify it.
+We provide scripts to adjust some of the most popular MD codes
+so as to provide PLUMED support.
+At the present times we support patching the following list of codes:
 
 @CODESL@
 
@@ -394,17 +399,18 @@ ALMOST 2.1 can be found in branches/almost-2.1/ and can be compiled:
 \warning ALMOST needs SQLITE3, GZIP and BZIP2 installed on your computer.
 
 \verbatim
-./configure --prefix="wherever you want it" 
-make
-make install
+> ./configure --prefix="wherever you want it" 
+> make
+> make install
 \endverbatim
 
 PLUMED will not use the RDCs module of ALMOST so you can ignore the warning about LAPACK.
 
-Once ALMOST is installeed, PLUMED 2 can then be configured with ALMOST enabled: 
+Once ALMOST is installed, PLUMED 2 can then be configured with ALMOST enabled: 
 
 \verbatim
-./configure --enable-almost CPPFLAGS="-I/ALMOST_INSTALL_PATH/include -I/ALMOST_INSTALL_PATH/include/almost" LDFLAGS="-L/ALMOST_INSTALL_PATH/lib"
+> ./configure --enable-almost CPPFLAGS="-I/ALMOST_INSTALL_PATH/include \
+  -I/ALMOST_INSTALL_PATH/include/almost" LDFLAGS="-L/ALMOST_INSTALL_PATH/lib"
 \endverbatim
 with ALMOST_INSTALL_PATH set to the full path to the ALMOST installation folder.
 

user-doc/Intro.txt

@@ -55,12 +55,16 @@ analsyis tools that come with PLUMED are given in:
 - \ref Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
 - \ref Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.
 
-PLUMED can be used in one of two ways.  It can be incorporated into any one of the MD codes listed below:
+PLUMED can be used in one of two ways.
+First, it can be incorporated into an MD code and used to analyse or bias a molecular dynamics run on the fly.
+Notice that some MD code could already include calls to the PLUMED library
+and be PLUMED-ready in its original distribution (check MD code documentation).
+Additionally, we provide patching procedures for the following codes:
 
 @CODESL@
 
-and used to analyse or bias a molecular dynamics run on the fly.  Alternatively, one
-can use it as a standalone tool for postprocessing the results from molecular dynamics 
+Alternatively, one
+can use PLUMED as a standalone tool for postprocessing the results from molecular dynamics 
 or enhanced sampling calculations.
 
 \page Changelog Change Log

user-doc/Misc.txt

@@ -21,7 +21,8 @@ erm... yes add lines of comments or trailing comments to your hearts content as
 \verbatim
 # This is the distance between two atoms:
 DISTANCE ATOM=1,2 LABEL=d1
-UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall. That I, one Snout by name, present a wall.
+UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall.
+# That I, one Snout by name, present a wall.
 \endverbatim
 (see \ref DISTANCE and \ref UPPER_WALLS)
 

user-doc/Syntax.txt

@@ -16,7 +16,7 @@ word in these lines specify what particular action is to be performed.  This is
 which provide PLUMED with more details as to how the action is to be performed.  These keywords are either single words
 (in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic
 bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated 
-list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in 
+list _with no spaces_ of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in 
 the calculation of a particular colvar). Space separated lists can be used instead of commma separated list if the entire list
 is enclosed in curly braces (e.g. ATOMS={1 2 3 4}).  Please note that you can split commands over multiple lines by using
 \ref ContinuationLines.