This page is a continuous listing of new features and bug fixes for the Pizza.py toolkit.
To stay up-to-date with the current Pizza.py, you can download the current tarball from the download page at any time, which will include all the features/fixes listed below.
A Pizza.py "version" is the date when it was released, such as 1 Sept 2010. Pizza.py is updated continuously. Every time we fix a bug or add a feature, we release it immediately, as listed below. Each dated copy of Pizza.py contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen every time you run Pizza.py. It is also in the file src/pizza.py and in the Pizza.py directory name created when you unpack a tarball.
9 Oct 2015
Maintentance patch. A few small feature updates and bug fixes.
This is the list of changed files from the 2 Jul 2014 version.
2 Jul 2014
Changed the name of the clog tool to olog to stand for reading of other log files. This is because the log files can now come from a variety of other programs: ChemCell, SPPARKS, SPARTA.
This is the list of changed files from the 30 Jun 2014 version.
30 Jun 2014
New sdata tool for reading, creating, and writing out surface files used as input to the SPARTA Direct Simulation Monte Carlo (DSMC) code.
This is the list of changed files from the 7 Feb 2013 version.
7 Feb 2014
Added some logic to the dump tool to deal more correctly with empty snapshots that have no atoms.
This is the list of changed files from the 11 Sep 2013 version.
11 Sep 2013
One additional change to the data tool, to support the changes to the patch tool.
This is the list of changed files from the 10 Sep 2013 version.
10 Sep 2013
Added some options to the patch tool, for different kinds of patchy and rigid-body particles.
This is the list of changed files from the 6 Aug 2012 version.
6 Aug 2012
Made the dump tool backward compatible with the dump file format produced by other codes besides LAMMPS, specifically with respect to the BOX BOUNDS info in the dump file.
This is the list of changed files from the 14 Jun 2012 version.
14 Jun 2012
Added more support to the dump tool for triclinic (non-orthogonal) boxes. Removed the size() method from the gl tool, and made it part of the constructor, so that the window size can be selected one time at launch. Dynamic resizing does not seem to work in some windowing systems.
This is the list of changed files from the 22 May 2012 version.
22 May 2012
Forgot to include some data files used by the example scripts in yesterday's patch.
This is the list of changed files from the 21 May 2012 version.
21 May 2012
Made some updates to the test scripts in the examples dir, to make them compatible with the current version of Pizza.py.
This is the list of changed files from the 9 Feb 2012 version.
9 Feb 2012
Made the dump tool scale and unscale atom coordinates correctly for triclinic geometries, which is indicated by extra BOX BOUNDS fields in the dump file.
Also made some minor changes for how mesh dump files and the mdump tool are treated by the dump tool.
This is the list of changed files from the 8 Dec 2011 version.
8 Dec 2011
Upgraded the write commmand for the dump tool to write out ints for the "id" and "type" columns of dump data, but floats for everything else. Previously it assumed the 1st 2 columns were int and the rest float, but custom dump files are often not formatted that way.
This is the list of changed files from the 7 Oct 2011 version.
7 Oct 2011
Added a glutInit() call to the gl tool since some versions of freeglut seem to require this.
This is the list of changed files from the 15 Sep 2011 version.
15 Sep 2011
Added the tdump tool which can work with the dump tool to visualze triangles from a LAMMPS simulation. Also added some options to the patch tool to enable creation of rigid bodies built out of triangles.
Also made the auto-unscaling feature of the dump tool be up-to-date with the current self-documenting format of LAMMPS dump files.
This is the list of changed files from the 27 May 2011 version.
27 May 2011
Updated the PDF manual.
This is the list of changed files from the 19 May 2011 version.
19 May 2011
David Hart (Sandia) added some start-up logic to insure the GL tool does not cause problems when running without a display.
This is the list of changed files from the 18 May 2011 version.
18 May 2011
Changed to continuous updating of versions, rather than increments to an occasionally released version.
This is the list of changed files from the 24 Nov 2010 version.
24 Nov 2010
Axel Kohlmeyer (Temple U) added a vmd tool that is a wrapper on the popular VMD visualization package, which allows it to be controlled from Python and Pizza.py scripts. In particular it allows the interactive visualization of molecular dynamics snapshots as generated from LAMMPS. See the python directory in the LAMMPS distribution for examples of scripts that do this.
This is the list of changed files from the 23 Nov 2010 version.
23 Nov 2010
Added the ldump and bdump tools which can work with the dump tool to visualze line segments and bonds from a LAMMPS simulation. Also added some options to the patch tool to enable creation of 2d rigid bodies built out of line segments.
This is the list of changed files from the 1 Oct 2010 version.
1 Oct 2010
Jeff Greathouse (Sandia) added a density_area.py script to the scripts dir, which allows integrating the area under the density profile.
This is the list of changed files from the 19 Apr 2010 version.
19 Apr 2010
Added setv() method to dump tool, and new options on write() method. This is to allow easier manipulation of a set of dump files for nudged elastic band (NEB) calculation in LAMMPS, to produce snapshots that contain atoms from multiple replicas.
This is the list of changed files from the 8 Dec 2009 version.
8 Dec 2009
David Hart (Sandia) added a density2d.py script. He also added an error check for running without a display, so that Tkinter will do the right thing and not try to create GUI windows for certain tools.
This is the list of changed files from the 7 Dec 2009 version.
7 Dec 2009
David Hart (Sandia) enhanced the dump and mdump tools to allow use of the NumPy Python package. This means Pizza.py can now use either NumPy or the older Numeric pacakge.
This is the list of changed files from the 22 Nov 2009 version.
22 Nov 2009
Enhanced the dump tool write and scatter commands to write self-describing LAMMPS dump files, with atom column info.
This is the list of changed files from the 21 Nov 2009 version.
21 Nov 2009
Changed some file opens to include a binary-mode flag, so that they will open and can be seeked correctly under Windows. Never saw this issue on Linux or a Mac.
This is the list of changed files from the 3 Jun 2009 version.
Thanks to Ting Li (KULeuven) for flagging this issue.
3 Jun 2009
Another upgrade to the dump tool to allow it to read self-describing LAMMPS (or other) dump files that have the names of the per-atom columns embedded in the file. This one insures that all versions of coordinates (x,xs,xu) are recognized by the dump tool, so you don't have to use the dump.map() method.
This is the list of changed files from the 16 Mar 2009 version.
Thanks to Carolyn Phillips (U Mich) for pointing this out.
16 Mar 2009
Upgraded the dump tool to allow it to read self-describing LAMMPS (or other) dump files that have the names of the per-atom columns embedded in the file. If reading this format of file, it means you don't have to label the columns yourself with the dump.map() method.
This is the list of changed files from the 1 Dec 2008 version.
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:
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:
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.