diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt index 5d4b556e7c..079d25ed54 100644 --- a/doc/src/Intro_nonfeatures.txt +++ b/doc/src/Intro_nonfeatures.txt @@ -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