reformatting and simplification of fix plumed docs

doc/src/fix_plumed.txt

@@ -25,33 +25,32 @@ fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
 
 [Description:]
 
-This fix instructs LAMMPS to call the PLUMED library, which allows one
-to perform various forms of trajectory analysis on the fly and to also
-use methods such as umbrella sampling and metadynamics to enhance the
-sampling of phase space.
-
-The documentation included here only describes the fix plumed command.
-This command is LAMMPS specific whereas most of the functionality
-implemented in PLUMED will work with a range of MD codes and also when
-PLUMED is used as a stand alone code.  The full documentation for PLUMED
-is available at "this website"_http://www.plumed.org/documentation
-
-The PLUMED library is developed at
-"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2 A
-detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
-
-There are some example scripts for using this package with LAMMPS in the
+This fix instructs LAMMPS to call the "PLUMED"_plumedhome library, which
+allows one to perform various forms of trajectory analysis on the fly
+and to also use methods such as umbrella sampling and metadynamics to
+enhance the sampling of phase space.
+
+The documentation included here only describes the fix plumed command
+itself.  This command is LAMMPS specific, whereas most of the
+functionality implemented in PLUMED, however, will work with a range of
+MD codes, and when PLUMED is used as a stand alone code for analysis.
+The full "documentation for PLUMED"_plumeddocs is available online and
+included in the PLUMED source code.  The PLUMED library development is
+hosted at
+"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
+A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
+
+There is an example input for using this package with LAMMPS in the
 examples/USER/plumed directory.
 
 :line
 
-The command to call PLUMED above is reasonably self explanatory.  Within
-the input file for lammps the user is required to specify the input file
-for PLUMED and a file on which to output the PLUMED log.  The user must
-specify both of these arguments every time PLUMED is to be used.
-Furthermore, the fix plumed command should appear in the LAMMPS input
-file after the relevant input paramters (e.g. the timestep) have been
-set.
+The command to make LAMMPS call PLUMED during a run requires two keyword
+value pairs pointing to the PLUMED input file and an output file for the
+PLUMED log. The user must specify these arguments every time PLUMED is
+to be used.  Furthermore, the fix plumed command should appear in the
+LAMMPS input file [after] relevant input paramters (e.g. the timestep)
+have been set.
 
 The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
 to PLUMED and there can only be one instance of the plumed fix at a
@@ -64,10 +63,10 @@ functionality by only allowing only one plumed fix in the LAMMPS input.
 The {plumedfile} keyword allows the user to specify the name of the
 PLUMED input file.  Instructions as to what should be included in a
 plumed input file can be found in the "documentation for
-PLUMED"_http://www.plumed.org/documentation.
+PLUMED"_plumeddocs
 
 The {outfile} keyword allows the user to specify the name of a file on
-which to output the PLUMED log.  This log file normally just parots the
+which to output the PLUMED log.  This log file normally just parrots the
 information that is contained in the input file.  The names of the files
 on which the results from the various analyses that have been performed
 using PLUMED will be specified by the user in the PLUMED input file.
@@ -76,12 +75,13 @@ using PLUMED will be specified by the user in the PLUMED input file.
 
 When performing a restart of a calculation that involves PLUMED you must
 include a RESTART command in the PLUMED input file as detailed in the
-"PLUMED documentation"_http://www.plumed.org/documentation.  When the
-restart command is found in the PLUMED input PLUMED will append to the
-files that were generated in the run that was performed previously.
-Furthermore, any history dependent bias potentials that were accumulated
-in previous calculations will be read in when the restart command is
-included in the PLUMED input.
+"PLUMED documentation"_plumeddocs.  When the restart command is found in
+the PLUMED input PLUMED will append to the files that were generated in
+the run that was performed previously.  No part of the PLUMED restart
+data is included in the LAMMPS restart files.  Furthermore, any history
+dependent bias potentials that were accumulated in previous calculations
+will be read in when the RESTART command is included in the PLUMED
+input.
 
 The "fix_modify"_fix_modify.html {energy} option is not supported by
 this fix.
@@ -97,10 +97,7 @@ This fix is part of the USER-PLUMED package.  It is only enabled if
 LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.
 
-There can only be one plumed fix active at a time. Since the interface
-communicates only the minimum amount of information and since the PLUMED
-module itself can handle an arbitrary number of analysis and biasing
-methods, this is not a limitation of functionality.
+There can only be one plumed fix active at a time.
 
 [Related commands:]
 
@@ -115,3 +112,6 @@ The default options are plumedfile = NULL and outfile = NULL
 
 :link(PLUMED)
 [(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
+:link(plumeddocs,http://www.plumed.org/documentation)
+:link(plumedhome,http://www.plumed.org/)