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correct broken formatting and add explicit links to ParmEd and InterMol, a few tweaks

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Axel Kohlmeyer
2018-12-28 00:24:58 -05:00
parent 685ed827d7
commit cc1c93a3d9
1 changed files with 21 additions and 16 deletions
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37
doc/src/Intro_nonfeatures.txt
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@ -16,7 +16,7 @@ functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS was not conceived and designed for:
being run thru a GUI
build molecular systems, or building molecular topologies
building molecular systems, or building molecular topologies
assign force-field coefficients automagically
perform sophisticated analysis of your MD simulation
visualize your MD simulation interactively
@ -24,18 +24,18 @@ 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.
that either closely 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
[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
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. Also, there are several external wrappers or GUI front ends.:ulb,l
page. Also, there are several external wrappers or GUI front ends. :ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
[Builder:] Several pre-processing tools are packaged with LAMMPS. Some
of them convert input files in formats produced by other MD codes such
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
are simple programs that will build simple molecular systems, such as
@ -45,15 +45,20 @@ 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. Furthermore,
some LAMMPS internal commands to reconstruct topology, as well as
the option to insert molecule templates instead of atoms.:l
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems. :l
Force-field assignment: The conversion tools described in the previous
[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 BIOVIA (formerly Accelrys) force field files. :l
or BIOVIA (formerly Accelrys) force field files. The tools
"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
powerful and flexible in converting force field and topology data
between various MD simulation programs. :l
Simulation analysis: If you want to perform analysis 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
@ -71,22 +76,22 @@ 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
[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
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
them to an external program, "FFmpeg"_https://www.ffmpeg.org 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
visualization packages that can use LAMMPS output data. :l
Plotting: See the next bullet about Pizza.py as well as the
[Plotting:] See the next bullet about Pizza.py as well as the
"Python"_Python_head.html doc page for examples of plotting LAMMPS
output. Scripts provided with the {python} tool in the tools
directory will extract and massage data in log and dump files to make
it easier to analyze and plot. See the "Tools"_Tools.html doc page
for more discussion of the various tools. :l
Pizza.py: Our group has also written a separate toolkit called
[Pizza.py:] Our group has also written a separate toolkit called
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the