New Features and Bug Fixes in Pizza.py

This page lists new features and bug fixes in the Pizza.py toolkit since the current version was released.

To add these features/fixes to your version of Pizza.py, download the upgraded version from the download page, that includes all these features/fixes.

The current version of Pizza.py is 1 Oct 2006.

1 Dec 2008

Added a reorder command to the data tool to allow data files for different LAMMPS atom styles to more easily be created.

Also added some options to the patch tool to allow it to create 2d systems, and 2d stars and boxes and dimers as output composite particles.

This is the list of changed files from the 17 Nov 2007 version.

17 Nov 2007

Fixed a one-line glitch in the 15Nov07 patch.

This is the list of changed files from the 15 Nov 2007 version.

15 Nov 2007

Added support to the data tool for non-orthogonal triclinic boxes in LAMMPS via the "xy xz yz" keyword that can appear in the header portion of the data file.

This is the list of changed files from the 10 Aug 2007 version.

Thanks to Krishna Iyengar (Cornell U) for identifying the problem.

10 Aug 2007

Added some sync logic to the gl and vcr tools to insure GL screenshots are captured correctly to files. Was having trouble with this on a faster graphics box.

Also updated the Pizza.py install directions substantially, to give details of how to install all the various Python packages used by all the Pizza.py tools on a Linux box.

In particular, the latest 3.0 version of PyOpenGL and the Tkinter graphics lib seem much easier to install, so if that was a problem for you before, try out the new instructions.

This is the list of changed files from the 17 Jun 2007 version.

17 June 2007

Fixed some one-line bugs with opening gzipped files by various tools.

This is the list of changed files from the 3 May 2007 version.

Thanks to Vladimir Stegailov for identifying the problem.

3 May 2007

Added class 2 fields to the data tool so it can deal with LAMMPS data files that contain class 2 potential info.

Also added an option to the plotview tool to set which vector is treated as the x-axis.

This is the list of changed files from the 14 Apr 2007 version.

Thanks to James Palko for pointing out the data tool deficiency.

14 Apr 2007

Added a mdump tool to read in mesh files and allow them to be converted to Ensight format or visualized directly with other Pizza.py tools such as the gl and raster tools.

The mesh file format is described on the mdump doc page. 2d triangular and 3d tetrahedral meshes are currently supported. Meshes can be static or dynamic and have nodal and/or element quantities defined.

This is the list of changed files from the 13 Apr 2007 version.

13 Apr 2007

Added a sort option to the dump tool to allow sorting of atom snapshots by any column (e.g. x or type) rather than the default which is by atom ID.

This is the list of changed files from the 12 Apr 2007 version.

12 Apr 2007

Aidan Thompson (Sandia) has written a new file conversion tool, called cfg, which converts LAMMPS snapshots to the CFG format used by the AtomEye visualization package.

This is the list of changed files from the 16 Mar 2007 version.

16 Mar 2007

Upgraded the ensight tool to allow for empty snapshots and consistency of the number of particle types across snapshots, which Ensight seems to like.

This is the list of changed files from the 31 Jan 2007 version.

31 Jan 2007

Fixed a couple bugs in the new ensight tool, as well as made some other minor tweaks to various files.

This is the list of changed files from the 3 Nov 2006 version.

3 Nov 2006

Added a capability for the vec tool to accept a list of numeric vectors as input. They can then be plotted interactively via the plotview tool.

This is the list of changed files from the 10 Oct 2006 version.

10 Oct 2006

Added an ensight tool that can convert LAMMPS or ChemCell data/dump files to the file format used as input to the Ensight visualization package. Ensight is a widely-used commercial package with a GUI front-end that can perform high-quality viz and animation.

This is the list of changed files from the 1 Oct 2006 version.

Thanks to Greg Wagner and Jon Zimmerman (SNL) for explaining the Ensight format and testing out this new tool.

New release of Pizza.py. 12367 lines of code in src dir.

These are the most significant features added since the 7 Nov 2005 version. People who contributed to the features are listed in parentheses:

• clog tool which reads ChemCell log files for plotting
• cdata tool which creates ChemCell geometries and populates them with particles
• histo tool which can create histograms of particle densities from dump snapshots
• changed name of pdb tool to pdbfile to avoid conflicts with another Python internal
• new scripts: distance.py, bond_distribute.py, angle_distribute.py (Paul Crozier, SNL)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of Pizza.py. 9129 lines of code in src dir. These are the most significant features added since the 7 Sept 2005 version:

• added a gl tool which enables 3d interactive viz of LAMMPS snapshots via OpenGL
• added a vcr tool which provides a VCR-style GUI wrapper for the gl tool
• added a color table with 140 pre-defined colors to viz tools (gl, raster, svg)
• multiple incremental plots option for gnu and matlab tools
• added convert and montage methods to image tool
• allow type=0 setting for atom/bond/etc color/radii/etc in viz tools (gl, raster, svg)
• set default view to (60,30) in viz tools (gl, raster, svg)
• changed trans() method to shift() in viz tools and its arguments are now pixels (gl, raster, svg)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

7 Sept 2005

Initial public release of Pizza.py. 6896 lines of Python code in src dir.