Th previous section describes how Pizza.py tools are used in Pizza.py.
Help on the syntax for invoking a tool and using its methods and settings can be accessed interactively within Pizza.py itself by typing "? tool" or "?? tool". Typing "??" gives a one-line description of each tool.
These are the different categories of Pizza.py 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 Pizza.py; the link is to each tool's documentation page.
| animate.py | Animate a series of image files |
| bdump.py | Read LAMMPS dump local files with bond info |
| cdata.py | Read, write, manipulate Chemcell data files |
| chain.py | Create bead-spring chains for LAMMPS input |
| cfg.py | Convert LAMMPS snapshots to CFG format |
| data.py | Read, write, manipulate LAMMPS data files |
| dump.py | Read, write, manipulate dump files and particle attributes |
| ensight.py | Convert LAMMPS snapshots to Ensight format |
| gl.py | 3d interactive visualization via OpenGL |
| gnu.py | Create plots via GnuPlot plotting program |
| histo.py | Particle density histogram from a dump |
| image.py | View and manipulate images |
| ldump.py | Read LAMMPS dump files with line info |
| log.py | Read LAMMPS log files and extract thermodynamic data |
| matlab.py | Create plots via MatLab numerical analysis program |
| mdump.py | Read, write, manipulate mesh dump files |
| olog.py | Read other log files (ChemCell, SPPARKS, SPARTA) and extract time-series data |
| pair.py | Compute LAMMPS pairwise energies |
| patch.py | Create patchy Lennard-Jones particles for LAMMPS input |
| pdbfile.py | Read, write PDB files in combo with LAMMPS snapshots |
| plotview.py | Plot multiple vectors from a data set |
| rasmol.py | 3d visualization via RasMol program |
| raster.py | 3d visualization via Raster3d program |
| sdata.py | Read, write, manipulate SPARTA surface files |
| svg.py | 3d visualization via SVG files |
| tdump.py | Read LAMMPS dump files with triangle info |
| vcr.py | VCR-style GUI for 3d interactive OpenGL visualization |
| vec.py | Create numeric vectors from columns in file or list of vecs |
| vtk.py | Convert LAMMPS snapshots to VTK format |
| vmd.py | Wrapper on VMD visualization package |
| xyz.py | Convert LAMMPS snapshots to XYZ format |
This diagram represents the different ways tools can be interconnected by Pizza.py. Tools within the same red box are tools that are (roughly) interchangeable.