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4. Tools within

Th previous section describes how tools are used in

Help on the syntax for invoking a tool and using its methods and settings can be accessed interactively within itself by typing "? tool" or "?? tool". Typing "??" gives a one-line description of each tool.

These are the different categories of tools:

LAMMPS in/out files chain, data, dump, log, patch, bdump, ldump, tdump
ChemCell in/out files cdata, olog, dump
SPPARKS in/out files olog, dump
SPARTA in/out files sdata, olog, dump
Visualization gl, rasmol, raster, svg, vmd
File conversion cfg, ensight, pdbfile, vtk, xyz
GUI wrappers animate, image, plotview, vcr
Plotting gnu, matlab
Miscellaneous histo, mdump, pair, vec

Within the plotting and viz categories, individual tools share many common methods, so the tools can often be used interchangeably. For example, the same script can produce an animation using either Raster3d or SVG to generate the movie frames, by simply changing the line that creates the visualizer object, or by passing the object into the script as an argument.

This is the complete list of tools in; the link is to each tool's documentation page. Animate a series of image files Read LAMMPS dump local files with bond info Read, write, manipulate Chemcell data files Create bead-spring chains for LAMMPS input Convert LAMMPS snapshots to CFG format Read, write, manipulate LAMMPS data files Read, write, manipulate dump files and particle attributes Convert LAMMPS snapshots to Ensight format 3d interactive visualization via OpenGL Create plots via GnuPlot plotting program Particle density histogram from a dump View and manipulate images Read LAMMPS dump files with line info Read LAMMPS log files and extract thermodynamic data Create plots via MatLab numerical analysis program Read, write, manipulate mesh dump files Read other log files (ChemCell, SPPARKS, SPARTA) and extract time-series data Compute LAMMPS pairwise energies Create patchy Lennard-Jones particles for LAMMPS input Read, write PDB files in combo with LAMMPS snapshots Plot multiple vectors from a data set 3d visualization via RasMol program 3d visualization via Raster3d program Read, write, manipulate SPARTA surface files 3d visualization via SVG files Read LAMMPS dump files with triangle info VCR-style GUI for 3d interactive OpenGL visualization Create numeric vectors from columns in file or list of vecs Convert LAMMPS snapshots to VTK format Wrapper on VMD visualization package Convert LAMMPS snapshots to XYZ format

This diagram represents the different ways tools can be interconnected by Tools within the same red box are tools that are (roughly) interchangeable.