diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt index 2acf6db71f..316e661475 100644 --- a/doc/src/Intro_nonfeatures.txt +++ b/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