adjust wording of non-features discussion to be more in-sync with recent developments

doc/src/Intro_nonfeatures.txt

@@ -13,15 +13,19 @@ LAMMPS is designed to be a fast, parallel engine for molecular
 dynamics (MD) simulations.  It provides only a modest amount of
 functionality for setting up simulations and analyzing their output.
 
-Specifically, LAMMPS does not:
+Specifically, LAMMPS was not conceived and designed for:
 
-run thru a GUI
-build molecular systems
+being run thru a GUI
+build molecular systems, or building molecular topologies
 assign force-field coefficients automagically
-perform sophisticated analyses of your MD simulation
+perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
 plot your output data :ul
 
+Although over the years these limitations have been somewhat
+reduced through features added to LAMMPS or external tools
+that either interface with LAMMPS or extend LAMMPS.
+
 Here are suggestions on how to perform these tasks:
 
 GUI: LAMMPS can be built as a library and a Python wrapper that wraps
@@ -29,7 +33,7 @@ the library interface is provided.  Thus, GUI interfaces can be
 written in Python (or C or C++ if desired) that run LAMMPS and
 visualize or plot its output.  Examples of this are provided in the
 python directory and described on the "Python"_Python_head.html doc
-page. :ulb,l
+page.  Also, there are several external wrappers or GUI frontends.:ulb,l
 
 Builder: Several pre-processing tools are packaged with LAMMPS.  Some
 of them convert input files in formats produced by other MD codes such
@@ -40,28 +44,36 @@ molecular builder that will generate complex molecular models.  See
 the "Tools"_Tools.html doc page for details on tools packaged with
 LAMMPS.  The "Pre/post processing
 page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
-describes a variety of 3rd party tools for this task. :l
+describes a variety of 3rd party tools for this task.  Furthermore,
+some LAMMPS internal commands to reconstruct topology, as well as
+the option to insert molecule templates instead of atoms.:l
 
 Force-field assignment: The conversion tools described in the previous
 bullet for CHARMM, AMBER, and Insight will also assign force field
 coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
 or Accelerys force field files. :l
 
-Simulation analyses: If you want to perform analyses on-the-fly as
+Simulation analysis: If you want to perform analysis on-the-fly as
 your simulation runs, see the "compute"_compute.html and
 "fix"_fix.html doc pages, which list commands that can be used in a
 LAMMPS input script.  Also see the "Modify"_Modify.html doc page for
 info on how to add your own analysis code or algorithms to LAMMPS.
 For post-processing, LAMMPS output such as "dump file
 snapshots"_dump.html can be converted into formats used by other MD or
-post-processing codes.  Some post-processing tools packaged with
+post-processing codes.  To some degree, that conversion can be done
+directly inside of LAMMPS by interfacing to the VMD molfile plugins.
+The "rerun"_rerun.html command also allows to do some post-processing
+of existing trajectories, and through being able to read a variety
+of file formats, this can also be used for analysing trajectories
+from other MD codes.  Some post-processing tools packaged with
 LAMMPS will do these conversions.  Scripts provided in the
 tools/python directory can extract and massage data in dump files to
 make it easier to import into other programs.  See the
 "Tools"_Tools.html doc page for details on these various options. :l
 
 Visualization: LAMMPS can produce JPG or PNG snapshot images
-on-the-fly via its "dump image"_dump_image.html command.  For
+on-the-fly via its "dump image"_dump_image.html command and pass
+them to an external program FFmpeg to generate movies from them.  For
 high-quality, interactive visualization there are many excellent and
 free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for