commit 80592c0da1cede071707d0aebb159a5b0781d2df Author: ckloss Date: Fri Feb 3 14:10:31 2012 +0100 Committer: ckloss On branch master Initial commit for lpp, version 2011-10-11 diff --git a/INSTALL.txt b/INSTALL.txt new file mode 100644 index 0000000..d0f3552 --- /dev/null +++ b/INSTALL.txt @@ -0,0 +1,8 @@ +to install liggghts post processing copy the following lines of code into your bashrc (please change the variable CFDEM_lppPath according to your system): + +============================================ +CFDEM_lppPath=/Users/s/work/parallelpizza/nightly_build + +alias lpp="python $CFDEM_lppPath/src/lpp.py" +alias pizza ="python $CFDEM_lppPath/src/pizza.py" +============================================ diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..a0c2723 --- /dev/null +++ b/LICENSE @@ -0,0 +1,350 @@ +GNU GENERAL PUBLIC LICENSE + +Version 2, June 1991 + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. +59 Temple Place - Suite 330, Boston, MA 02111-1307, USA + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +Preamble + +The licenses for most software are designed to take away your freedom +to share and change it. 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If this is what you want to do, use the +GNU Library General Public License instead of this License. diff --git a/README b/README new file mode 100644 index 0000000..d467e90 --- /dev/null +++ b/README @@ -0,0 +1,41 @@ +This is the Pizza.py (1 Oct 2006) software package. + +Copyright (2005) Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +certain rights in this software. This software is distributed under +the GNU General Public License. + +---------------------------------------------------------------------- + +Pizza.py is a loosely integrated collection of tools written in +Python, many of which provide pre- and post-processing capability for +the LAMMPS molecular dynamics package. There are tools to create +input files, convert between file formats, process log and dump files, +create plots, and visualize and animate simulation snapshots. + +Pizza.py was developed at Sandia National Laboratories, a US +Department of Energy facility, with funding from the DOE. It is an +open-source code, distributed freely under the terms of the GNU Public +License (GPL). + +The maintainer of Pizza.py is Steve Plimpton, who can be emailed at +sjplimp@sandia.gov. The Pizza.py WWW site +(www.cs.sandia.gov/~sjplimp/lammps.html) and LAMMPS WWW Site +(www.cs.sandia.gov/~sjplimp/lammps.html) have more information about +the code and its uses. + +The Pizza.py (1 Oct 2006) distribution includes the following files +and directories: + +README this file +LICENSE the GNU open-source license +doc HTML documentation for Pizza.py +examples scripts and data sets that exercise Pizza.py tools +scripts various Pizza.py script files +src source code for Pizza.py and its tools + +Point your browser at any of these files to get started: + +doc/Manual.html the Pizza.py manual +doc/Section_intro.html hi-level introduction to Pizza.py +doc/Section_install.html how to install Pizza.py diff --git a/README_GRANULAR b/README_GRANULAR new file mode 100644 index 0000000..649c995 --- /dev/null +++ b/README_GRANULAR @@ -0,0 +1,28 @@ +================================================================= +This is lpp (liggghts post processing), an update to pizza.py offering better visualization +of granular (DEM) LIGGGHTS or LAMMPS simulations using pizza.py + +LAMMPS=Large Atomic and Molecular Massively Parallel Simulator. +http://lammps.sandia.gov/ + +LIGGGHTS=LAMMPS Improved for General Granular and Granular + Heat Transfer Simulations +http://www.liggghts.com // www.cfdem.com + +pizza.py=LAMMPS post processor +http://www.sandia.gov/~sjplimp/pizza.html +================================================================= +Christoph Kloss, Linz, Aug. 2010 - +Stefan Amberger Linz, July 2011 - +Philippe Seil Linz, Sept 2011 - + +all +Christian-Doppler Laboratory on Particulate Flow Modelling +Institute of Fluid Mechanics and Heat Transfer +Johannes Kepler University, +Altenbergerstrasse 69, A-4040 Linz/Austria +www.particulate-flow.at +================================================================= + +For information on how to use the lpp tool, see doc/lpp.html + diff --git a/changelog_lpp.txt b/changelog_lpp.txt new file mode 100644 index 0000000..1f95bfa --- /dev/null +++ b/changelog_lpp.txt @@ -0,0 +1,18 @@ +2011-10-11 - Christoph Kloss ++ included pizza patches from Steve Plimpton (Sandia) until 2011-10-07 OK ++ changed the doc in pizza-style (removed readme_granular.txt, new lpp.txt/html file) OK ++ Automatic recognition of variables extended to computes (c_) and variables (v_) OK ++ included a new functionality written by Mark Bentley (Space Research Institute, Austrian Academy of Sciences) + to convert dump/local output into VTK to viz stress chains TODO ++ test+debug force chains TODO + +2011-09-27 - Philippe Seil ++ added LPP command line options that give control over things like output filenames, chunksizes etc. + +2011-08-10 - Stefan Amberger ++ bugfix for (dump.py, vtk.py) parallelpizza would crash if empty dumpfiles were processed (i.e. number of atoms == 0) + +2011-08-12 - Stefan Amberger ++ removed (vtk.py) the binding of variables to specific positions in liggghts dump files. + scalars / vectors are now recognized automatically (rules: x,y,z in the end --> vector; f_variable[i], f_variable[i+1], f_variable[i+2] --> vector) ++ lpp now uses command line arguments. new usage: User$ lpp dump* diff --git a/doc/Manual.html b/doc/Manual.html new file mode 100644 index 0000000..9910981 --- /dev/null +++ b/doc/Manual.html @@ -0,0 +1,205 @@ + + +Pizza.py Users Manual + + + + + + + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

+ +

Pizza.py Documentation +

+

Version info: +

+

The Pizza.py "version" is the date when it was released, such as 1 May +2010. Pizza.py is updated continuously. Whenever we fix a bug or add a +feature, we release it immediately, and post a notice on this page of +the WWW site. 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 and logfile every time you run +Pizza.py. It is also in the file src/version.h and in the Pizza.py +directory name created when you unpack a tarball. +

+ +

Pizza.py is a loosely integrated collection of tools written in +Python, many of which provide pre- and post-processing capability for +the LAMMPS molecular dynamics and ChemCell cell +simulator packages. There are tools to create input files, convert +between file formats, process log and dump files, create plots, and +visualize and animate simulation snapshots. +

+

The name Pizza.py is meant to evoke the aroma of a collection of +"toppings" that the user can combine in different ways on a "crust" of +basic functionality, with Python as the "cheese" that glues everything +together. +

+

The maintainer of Pizza.py is Steve +Plimpton at Sandia National +Laboratories, a US Department of Energy (DOE) +laboratory. Many of the tools were written by Matt Jones, a BYU +student who spent a summer at Sandia. The Pizza.py WWW Site at +www.cs.sandia.gov/~sjplimp/pizza.html has more information about +Pizza.py and its uses. +

+ + + + + + + + + + + + +
+ +

The Pizza.py documentation is organized into the following sections. +If you find errors or omissions in this manual or have suggestions for +useful information to add, please send an email to sjplimp@sandia.gov +so we can improve the Pizza.py documentation. +

+

PDF file of the entire manual, generated by +htmldoc +

+
  1. Introduction + + +
  2. Installing Pizza.py + + +
  3. Basics of using Pizza.py + + +
  4. Tools within Pizza.py + +
  5. Example scripts + +
  6. Extending Pizza.py + + +
+
+ +

List of tools in Pizza.py: +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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
clog.py Read ChemCell log files and extract species data
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
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
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 +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/doc/Manual.pdf b/doc/Manual.pdf new file mode 100644 index 0000000..ed26298 Binary files /dev/null and b/doc/Manual.pdf differ diff --git a/doc/Manual.txt b/doc/Manual.txt new file mode 100644 index 0000000..f24d4b1 --- /dev/null +++ b/doc/Manual.txt @@ -0,0 +1,156 @@ + +Pizza.py Users Manual + + + + + + + +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +

+ +Pizza.py Documentation :c,h3 + +Version info: :h4 + +The Pizza.py "version" is the date when it was released, such as 1 May +2010. Pizza.py is updated continuously. Whenever we fix a bug or add a +feature, we release it immediately, and post a notice on "this page of +the WWW site"_bug. 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 and logfile every time you run +Pizza.py. It is also in the file src/version.h and in the Pizza.py +directory name created when you unpack a tarball. + +If you browse the HTML or PDF doc pages on the Pizza.py WWW site, they +always describe the most current version of Pizza.py. :ulb,l + +If you browse the HTML or PDF doc pages included in your tarball, they +describe the version you have. :ule,l + +Pizza.py is a loosely integrated collection of tools written in +Python, many of which provide pre- and post-processing capability for +the "LAMMPS"_lammps molecular dynamics and "ChemCell"_cccell cell +simulator packages. There are tools to create input files, convert +between file formats, process log and dump files, create plots, and +visualize and animate simulation snapshots. + +The name Pizza.py is meant to evoke the aroma of a collection of +"toppings" that the user can combine in different ways on a "crust" of +basic functionality, with Python as the "cheese" that glues everything +together. + +The maintainer of Pizza.py is "Steve +Plimpton"_http://www.cs.sandia.gov/~sjplimp at "Sandia National +Laboratories"_sandia, a US Department of Energy ("DOE"_doe) +laboratory. Many of the tools were written by Matt Jones, a BYU +student who spent a summer at Sandia. The "Pizza.py WWW Site"_pws at +www.cs.sandia.gov/~sjplimp/pizza.html has more information about +Pizza.py and its uses. + +:link(sandia,http://www.sandia.gov) +:link(bug,http://www.cs.sandia.gov/pizza/bug.html) +:link(sjp,http://www.cs.sandia.gov/~sjplimp) +:link(doe,http://www.doe.gov) +:link(lammps,http://www.cs.sandia.gov/~sjplimp/lammps.html) +:link(ccell,http://www.cs.sandia.gov/~sjplimp/chemcell.html) + +:line + +The Pizza.py documentation is organized into the following sections. +If you find errors or omissions in this manual or have suggestions for +useful information to add, please send an email to sjplimp@sandia.gov +so we can improve the Pizza.py documentation. + +"PDF file"_Manual.pdf of the entire manual, generated by +"htmldoc"_http://www.easysw.com/htmldoc + +"Introduction"_Section_intro.html :olb,l + 1.1 "What is Pizza.py"_1_1 :ulb,b + 1.2 "Open source distribution"_1_2 :b + 1.3 "Acknowledgements"_1_3 :ule,b +"Installing Pizza.py"_Section_install.html :l + 2.1 "Installing Python"_2_1 :ulb,b + 2.2 "Running Pizza.py"_2_2 :b + 2.3 "Setting up the DEFAULTS.py file"_2_3 :b + 2.4 "Installing additional Python packages"_2_4 :b + 2.5 "Installing other software"_2_5 :ule,b +"Basics of using Pizza.py"_Section_basics.html :l + 3.1 "Python syntax"_3_1 :ulb,b + 3.2 "Pizza.py command line arguments"_3_2 :b + 3.3 "Pizza.py extensions to the Python interpreter"_3_3 :b + 3.4 "Using Pizza.py tools"_3_4 :b + 3.5 "Runnning Pizza.py and Python scripts"_3_5 :b + 3.6 "Error messages"_3_6 :ule,b +"Tools within Pizza.py"_Section_tools.html :l +"Example scripts"_Section_examples.html :l +"Extending Pizza.py"_Section_extend.html :l +:ole + +:line + +List of tools in Pizza.py: + +"animate.py"_animate.html; Animate a series of image files +"bdump.py"_bdump.html; Read LAMMPS dump local files with bond info +"cdata.py"_cdata.html; Read, write, manipulate "ChemCell"_ccell data files +"chain.py"_chain.html; Create bead-spring chains for LAMMPS input +"cfg.py"_cfg.html; Convert LAMMPS snapshots to CFG format +"clog.py"_clog.html; Read "ChemCell"_ccell log files and extract species data +"data.py"_data.html; Read, write, manipulate LAMMPS data files +"dump.py"_dump.html; Read, write, manipulate dump files and particle attributes +"ensight.py"_ensight.html; Convert LAMMPS snapshots to "Ensight"_ensight format +"gl.py"_gl.html; 3d interactive visualization via OpenGL +"gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program +"histo.py"_histo.html; Particle density histogram from a dump +"image.py"_image.html; View and manipulate images +"ldump.py"_ldump.html; Read LAMMPS dump files with line info +"log.py"_log.html; Read LAMMPS log files and extract thermodynamic data +"matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program +"mdump.py"_mdump.html; Read, write, manipulate mesh dump files +"pair.py"_pair.html; Compute LAMMPS pairwise energies +"patch.py"_patch.html; Create patchy Lennard-Jones particles for LAMMPS input +"pdbfile.py"_pdbfile.html; Read, write PDB files in combo with LAMMPS snapshots +"plotview.py"_plotview.html; Plot multiple vectors from a data set +"rasmol.py"_rasmol.html; 3d visualization via "RasMol"_rasmol program +"raster.py"_raster.html; 3d visualization via "Raster3d"_raster3d program +"svg.py"_svg.html; 3d visualization via "SVG"_svg files +"tdump.py"_tdump.html; Read LAMMPS dump files with triangle info +"vcr.py"_vcr.html; VCR-style GUI for 3d interactive OpenGL visualization +"vec.py"_vec.html; Create numeric vectors from columns in file or list of vecs +"vtk.py"_vtk.html; Convert LAMMPS snapshots to VTK format +"vmd.py"_vmd.html; Wrapper on "VMD visualization package"_vmd +"xyz.py"_xyz.html; Convert LAMMPS snapshots to XYZ format :tb(s=;) + +:link(gnuplot,http://www.gnuplot.info) +:link(matlab,http://www.mathworks.com) +:link(rasmol,http://www.openrasmol.org) +:link(raster3d,http://www.bmsc.washington.edu/raster3d/raster3d.html) +:link(svg,http://www.w3.org/Graphics/SVG) +:link(ensight,http://www.ensight.com) +:link(vmd,http://www.ks.uiuc.edu/Research/vmd) + +:link(1_1,Section_intro.html#1_1) +:link(1_2,Section_intro.html#1_2) +:link(1_3,Section_intro.html#1_3) + +:link(2_1,Section_install.html#2_1) +:link(2_2,Section_install.html#2_2) +:link(2_3,Section_install.html#2_3) +:link(2_4,Section_install.html#2_4) +:link(2_5,Section_install.html#2_5) + +:link(3_1,Section_basics.html#3_1) +:link(3_2,Section_basics.html#3_2) +:link(3_3,Section_basics.html#3_3) +:link(3_4,Section_basics.html#3_4) +:link(3_5,Section_basics.html#3_5) +:link(3_6,Section_basics.html#3_6) diff --git a/doc/Section_basics.html b/doc/Section_basics.html new file mode 100644 index 0000000..c086fcb --- /dev/null +++ b/doc/Section_basics.html @@ -0,0 +1,297 @@ + +
Previous Section - Pizza.py WWW Site - +Pizza.py Documentation - Pizza.py Tools - Next +Section +
+ + + + + + +
+ +

3. Basics of using Pizza.py +

+

The previous section describes how to install +and run Pizza.py and the various software it uses. After Pizza.py has +started you should see a ">" prompt. The following sections describe +what comes next: +

+3.1 Python syntax
+3.2 Pizza.py command line arguments
+3.3 Pizza.py extensions to the Python interpreter
+3.4 Using Pizza.py tools
+3.5 Runnning Pizza.py and Python scripts
+3.6 Error messages
+ +
+ +

3.1 Python syntax +

+

Aside from its tools, Pizza.py itself simply adds a bit of +functionality to the Python interpreter to enable it to more easily +launch shell commands and scripts and invoke its tools. Pizza.py's +">" prompt is different from Python's ">>>" prompt to indicate the +extra functionality is available, but you can type any Python command +you would type at the Python prompt. +

+

Python is a powerful scripting and programming language, similar in +scope and universality to Perl. This little Pizza.py manual cannot +attempt to teach you how to use Python, its syntax, or its rich set of +powerful built-in commands. If you only use the extra tools provided +by Pizza.py, you can think of Pizza.py as an application with a +self-contained set of commands. However, if you learn more about +Python, you will be able to write more powerful Pizza.py scripts, +access and manipulate data stored inside Pizza.py tools, or even add +your own commands and tools, which need not have anything to do with +LAMMPS or ChemCell. +

+

You can learn about Python at www.python.org. My most-used +Python book is Essential Python by Dave Beazley which +assumes some programming experience but covers both the basics of +Python and its many powerful libraries in a well-written, concise +manner. +

+ + +
+ +

3.2 Pizza.py command line arguments +

+

When running Pizza.py, several command-line options can be added +as switches, e.g. +

+
pizza.py switch args switch args ... 
+
+
+ + + + + +
-s silent (else print start-up help)
-t log dump raster load only these tools
-x raster rasmol load all tools except these
-f file arg1 arg2 run script file with args
-c "vec = range(100)" run Python command
-q quit (else interactive) +
+ +

Switches can appear in any order and be used multiple times. The -f +scripts and -c commands are executed in the order they appear. Script +files are Python files which can contain Python or Pizza.py tool +commands. Pizza.py looks for script files in 3 places: your current +working directory, the pizza/scripts directory, and any extra +directories you list in the src/DEFAULTS.py file. This means you can +add your own scripts to pizza/scripts or to directories of your +choosing. +

+

The argument of the -c switch will typically need to be enclosed in +quotes to avoid being interpreted by the shell. This also allows +multiple Python commands to be separated by semi-colons, e.g. +

+
-c "a = range(100); print a" 
+
+
+ +

3.3 Pizza.py extensions to the Python interpreter +

+

As mentioned above, the standard Python syntax is extended a bit at +the Pizza.py ">" interactive prompt. These options were inspired by +the LazyPython.py code of Nathan Gray, which taught me how to +extend the Python interpreter. These are the short-cuts: +

+
+ + + + + + + + +
? print help message
?? one-line for each tool and script
? raster list tool commands or script syntax
?? energy.py full documentation of tool or script
!ls -l shell command
@cd .. cd to a new directory
@log tmp.log log all commands typed so far to file
@run block.py arg1 arg2 run script file with args
@time d = dump("*.dump") time a command +
+ + + +

Shell commands begun with a "!" can include the redirection operators +"<" or ">". The shell command "!cd" will not change directories +permanently; use the "@cd" short-cut instead. Any short-cut command +starting with "@" can be abbreviated with one or more letters. +E.g. "@r" is the same as "@run". The @log command requires that the +Python readline library be available on your system. +

+

Each of the above short-cuts can be performed by native Python +commands; they are just not as simple to type. Here is how several of +the short-cuts can be written in Python, which is what you need to do +in a script, since the above short-cuts only work at the Pizza.py +interactive prompt: +

+
+ + + + +
Short-cut Native Python
!ls -l sys.command("ls -l")
@cd .. os.chdir("..")
@run myfile.py execfile("myfile.py")
CTRL-D sys.exit() +
+ +
+ +

3.4 Using Pizza.py tools +

+

The tools that Pizza.py adds to Python are each implemented as a +single Python class (e.g. dump, log, raster), so the first step in +using a tool is to create an instance of the class (an object). Each +class defines a set of methods (functions) that operate on the objects +you create and their associated data. Each method, including the +constructor, takes zero or more arguments, which may be previously +created objects. In practical terms, this means that you type +commands like this: +

+
d = dump("dump.*")
+p = pdb("my.pdb",d)
+p.many()
+dnew = dump("dump.all") 
+
+

The first 2 commands create dump and pdb objects named "d" and "p" +respectively. The "d" and "p" are Python variable names; you could +use any names you wish: "dump12" or "Dump_mine" or whatever. The 3rd +line invokes the "many" method within the pdb class for the pdb object +"p". This method writes out a series of PDB files using the snapshots +in "d" which was passed to "p" when it was created. The final command +creates a new dump object "dnew" from another dump file. You can +create and manage as many objects (of the same or different classes) +simultaneously as you wish. If the last line assigned the object to +"d", the original dump object with the same name would be deleted by +Python. +

+

Various Pizza.py tools create temporary files as they operate. These +are all named tmp.*. Pizza.py does not clean up all of these files, +since they are sometimes useful to look at for debugging or other +purposes. +

+

Python syntax allows for powerful combinations of tools to be invoked +in one or a few commands. For example +

+
lg = log("log.*")
+m = matlab()
+plotview(lg,m) 
+
+

could be abbreviated as +

+
plotview(log("log.*"),matlab()) 
+
+

With the -c command line switch, this one-liner could be specified +when Pizza.py is launched. This example also illustrates that created +objects (like the plotview object) do not need to be assigned to +variables if they will not be accessed in subsequent commands. +

+
+ +

3.5 Running Pizza.py and Python scripts +

+

A file containing Python and/or Pizza.py commands can be executed as a +script and arguments can be passed to it (if desired). The script can +be run in several different ways: +

+

(1) From the Pizza.py command line +

+
% pizza -f script.sample file.test 10 ... 
+
+

(2) From the Pizza.py interactive prompt +

+
> @run script.sample file.test 10 ... 
+
+

(3) From the Python command line +

+
% python -i script.sample file.test 10 ... 
+
+

(4) From a shell prompt with #!/usr/local/bin/python -i as 1st line of script +

+
% script.sample arg1 arg2 ... 
+
+

(5) From the Python interactive prompt +

+
>>> argv = 0,"file.test","10",...
+>>> execfile("script.sample") 
+
+

(6) As a nested script from within another Python or Pizza.py script file +

+
argv = 0,"file.test","10",...
+execfile("script.sample") 
+
+

The Pizza.py interpreter short-cut commands described +in the next section cannot be used in a script file. +

+

There are 2 additional issues to address in your script files. +

+

(A) First, if the script uses Pizza.py commands and you want to run it +from Python itself (methods 3,4,5,6), then your script should import +the necessary Pizza.py tools directly. E.g. if your script uses the +log and matlab tools, you would put these lines at the top: +

+
from log import log
+from matlab import matlab 
+
+

This is OK to do even if the script will be run by Pizza.py since it +doesn't matter that Pizza.py already imported the tools. Note that if +you do this, you can then give your script file and the Python tool +*.py files it uses to someone who doesn't have Pizza.py and they can +run your script with their Python. +

+

(B) Second, if your script takes arguments and you want the same +script to run identically for all 6 methods, then you need to include +this line at the beginning of the script: +

+
if not globals().has_key("argv"): argv = sys.argv 
+
+

This will enable the arguments to be accessed in the script as +argv1 for the 1st argument, argv2 for the 2nd, etc. +

+

This works because in methods 3,4 Python stores the script arguments +in sys.argv and the script name in sys.argv0. The above line of +Python code copies sys.argv to argv. When Pizza.py runs the script +(methods 1,2) it loads the arguments directly into the "argv" +variable. Methods 5,6 load the arguments into argv explicitly before +executing the script via execfile(). In this case argv0 is a dummy +argument to conform with the Python convention for sys.argv. +

+

Also note in methods 5,6 that all arguments such as "10" must be +strings even if they are numeric values, since this is the way they +are passed to the script in methods 1,2,3,4. +

+

As an example of the flexibility enabled by combining scripts, +arguments, and command-line options in Pizza.py, consider the 3-line +example of the previous sub-section. We modify the script as follows +and save it as logview.py: +

+
files = ' '.join(argv1:)   # create one string from list of filenames
+lg = log(files)
+m = matlab()
+plotview(lg,m) 
+
+

If an alias is defined in your shell start-up file, such as +

+
alias logview ~/pizza/src/pizza.py -f logview.py 
+
+

then you can type the following one-liner at the shell prompt to +invoke Pizza.py on the logview.py script with a list of files you +specfiy. +

+
% logview log.1 log.2 ... 
+
+

A set of plots and a control GUI will appear on your screen. +

+
+ +

3.6 Error messages +

+

If you mistype a Pizza.py or Python command or pass an invalid +argument to a tool method, an error message will be printed by Python. +Usually these will be self-explanatory. Sometimes they will point to +a line of code inside a tool which Python was unable to execute +successfully. This could be because you passed the wrong arguments to +the tool, the data the tool is operating on is invalid, or because +there's a bug in the tool. In the latter case, please figure out as +much as you can about the bug and email a description and the +necessary files to reproduce the bug in the simplest possible way to +sjplimp@sandia.gov. +

+ diff --git a/doc/Section_basics.txt b/doc/Section_basics.txt new file mode 100644 index 0000000..1af7219 --- /dev/null +++ b/doc/Section_basics.txt @@ -0,0 +1,286 @@ +"Previous Section"_Section_install.html - "Pizza.py WWW Site"_pws - +"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next +Section"_Section_tools.html :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +3. Basics of using Pizza.py :h3 + +The "previous section"_Section_install.txt describes how to install +and run Pizza.py and the various software it uses. After Pizza.py has +started you should see a ">" prompt. The following sections describe +what comes next: + +3.1 "Python syntax"_#3_1 +3.2 "Pizza.py command line arguments"_#3_2 +3.3 "Pizza.py extensions to the Python interpreter"_#3_3 +3.4 "Using Pizza.py tools"_#3_4 +3.5 "Runnning Pizza.py and Python scripts"_#3_5 +3.6 "Error messages"_#3_6 :all(b) + +:line + +3.1 Python syntax :h4,link(3_1) + +Aside from its tools, Pizza.py itself simply adds a bit of +functionality to the Python interpreter to enable it to more easily +launch shell commands and scripts and invoke its tools. Pizza.py's +">" prompt is different from Python's ">>>" prompt to indicate the +extra functionality is available, but you can type any Python command +you would type at the Python prompt. + +Python is a powerful scripting and programming language, similar in +scope and universality to Perl. This little Pizza.py manual cannot +attempt to teach you how to use Python, its syntax, or its rich set of +powerful built-in commands. If you only use the extra tools provided +by Pizza.py, you can think of Pizza.py as an application with a +self-contained set of commands. However, if you learn more about +Python, you will be able to write more powerful Pizza.py scripts, +access and manipulate data stored inside Pizza.py tools, or even add +your own commands and tools, which need not have anything to do with +LAMMPS or ChemCell. + +You can learn about Python at "www.python.org"_python. My most-used +Python book is "Essential Python"_beazley by Dave Beazley which +assumes some programming experience but covers both the basics of +Python and its many powerful libraries in a well-written, concise +manner. + +:link(beazley,http://www.amazon.com/exec/obidos/tg/detail/-/0735709017/104-4868532-2659916?v=glance) + +:line + +3.2 Pizza.py command line arguments :h4,link(3_2) + +When running Pizza.py, several command-line options can be added +as switches, e.g. + +pizza.py switch args switch args ... :pre + + -s, silent (else print start-up help) + -t log dump raster, load only these tools + -x raster rasmol, load all tools except these + -f file arg1 arg2, run script file with args + -c "vec = range(100)", run Python command + -q, quit (else interactive) :tb() + +Switches can appear in any order and be used multiple times. The -f +scripts and -c commands are executed in the order they appear. Script +files are Python files which can contain Python or Pizza.py tool +commands. Pizza.py looks for script files in 3 places: your current +working directory, the pizza/scripts directory, and any extra +directories you list in the src/DEFAULTS.py file. This means you can +add your own scripts to pizza/scripts or to directories of your +choosing. + +The argument of the -c switch will typically need to be enclosed in +quotes to avoid being interpreted by the shell. This also allows +multiple Python commands to be separated by semi-colons, e.g. + +-c "a = range(100); print a" :pre + +:line + +3.3 Pizza.py extensions to the Python interpreter :h4,link(3_3) + +As mentioned above, the standard Python syntax is extended a bit at +the Pizza.py ">" interactive prompt. These options were inspired by +the "LazyPython.py"_gray code of Nathan Gray, which taught me how to +extend the Python interpreter. These are the short-cuts: + + ?, print help message + ??, one-line for each tool and script + ? raster, list tool commands or script syntax + ?? energy.py, full documentation of tool or script + !ls -l, shell command + @cd .., cd to a new directory + @log tmp.log, log all commands typed so far to file + @run block.py arg1 arg2, run script file with args + @time d = dump("*.dump"), time a command :tb() + +:link(gray,http://www.idyll.org/~n8gray/code/index.html) + +Shell commands begun with a "!" can include the redirection operators +"<" or ">". The shell command "!cd" will not change directories +permanently; use the "@cd" short-cut instead. Any short-cut command +starting with "@" can be abbreviated with one or more letters. +E.g. "@r" is the same as "@run". The @log command requires that the +Python readline library be available on your system. + +Each of the above short-cuts can be performed by native Python +commands; they are just not as simple to type. Here is how several of +the short-cuts can be written in Python, which is what you need to do +in a script, since the above short-cuts only work at the Pizza.py +interactive prompt: + +Short-cut, Native Python +!ls -l, sys.command("ls -l") +@cd .., os.chdir("..") +@run myfile.py, execfile("myfile.py") +CTRL-D, sys.exit() :tb() + +:line + +3.4 Using Pizza.py tools :h4,link(3_4) + +The tools that Pizza.py adds to Python are each implemented as a +single Python class (e.g. dump, log, raster), so the first step in +using a tool is to create an instance of the class (an object). Each +class defines a set of methods (functions) that operate on the objects +you create and their associated data. Each method, including the +constructor, takes zero or more arguments, which may be previously +created objects. In practical terms, this means that you type +commands like this: + +d = dump("dump.*") +p = pdb("my.pdb",d) +p.many() +dnew = dump("dump.all") :pre + +The first 2 commands create dump and pdb objects named "d" and "p" +respectively. The "d" and "p" are Python variable names; you could +use any names you wish: "dump12" or "Dump_mine" or whatever. The 3rd +line invokes the "many" method within the pdb class for the pdb object +"p". This method writes out a series of PDB files using the snapshots +in "d" which was passed to "p" when it was created. The final command +creates a new dump object "dnew" from another dump file. You can +create and manage as many objects (of the same or different classes) +simultaneously as you wish. If the last line assigned the object to +"d", the original dump object with the same name would be deleted by +Python. + +Various Pizza.py tools create temporary files as they operate. These +are all named tmp.*. Pizza.py does not clean up all of these files, +since they are sometimes useful to look at for debugging or other +purposes. + +Python syntax allows for powerful combinations of tools to be invoked +in one or a few commands. For example + +lg = log("log.*") +m = matlab() +plotview(lg,m) :pre + +could be abbreviated as + +plotview(log("log.*"),matlab()) :pre + +With the -c command line switch, this one-liner could be specified +when Pizza.py is launched. This example also illustrates that created +objects (like the plotview object) do not need to be assigned to +variables if they will not be accessed in subsequent commands. + +:line + +3.5 Running Pizza.py and Python scripts :h4,link(3_5) + +A file containing Python and/or Pizza.py commands can be executed as a +script and arguments can be passed to it (if desired). The script can +be run in several different ways: + +(1) From the Pizza.py command line + +% pizza -f script.sample file.test 10 ... :pre + +(2) From the Pizza.py interactive prompt + +> @run script.sample file.test 10 ... :pre + +(3) From the Python command line + +% python -i script.sample file.test 10 ... :pre + +(4) From a shell prompt with #!/usr/local/bin/python -i as 1st line of script + +% script.sample arg1 arg2 ... :pre + +(5) From the Python interactive prompt + +>>> argv = [0,"file.test","10",...] +>>> execfile("script.sample") :pre + +(6) As a nested script from within another Python or Pizza.py script file + +argv = [0,"file.test","10",...] +execfile("script.sample") :pre + +The Pizza.py interpreter short-cut commands described +in the next section cannot be used in a script file. + +There are 2 additional issues to address in your script files. + +(A) First, if the script uses Pizza.py commands and you want to run it +from Python itself (methods 3,4,5,6), then your script should import +the necessary Pizza.py tools directly. E.g. if your script uses the +log and matlab tools, you would put these lines at the top: + +from log import log +from matlab import matlab :pre + +This is OK to do even if the script will be run by Pizza.py since it +doesn't matter that Pizza.py already imported the tools. Note that if +you do this, you can then give your script file and the Python tool +*.py files it uses to someone who doesn't have Pizza.py and they can +run your script with their Python. + +(B) Second, if your script takes arguments and you want the same +script to run identically for all 6 methods, then you need to include +this line at the beginning of the script: + +if not globals().has_key("argv"): argv = sys.argv :pre + +This will enable the arguments to be accessed in the script as +argv[1] for the 1st argument, argv[2] for the 2nd, etc. + +This works because in methods 3,4 Python stores the script arguments +in sys.argv and the script name in sys.argv[0]. The above line of +Python code copies sys.argv to argv. When Pizza.py runs the script +(methods 1,2) it loads the arguments directly into the "argv" +variable. Methods 5,6 load the arguments into argv explicitly before +executing the script via execfile(). In this case argv[0] is a dummy +argument to conform with the Python convention for sys.argv. + +Also note in methods 5,6 that all arguments such as "10" must be +strings even if they are numeric values, since this is the way they +are passed to the script in methods 1,2,3,4. + +As an example of the flexibility enabled by combining scripts, +arguments, and command-line options in Pizza.py, consider the 3-line +example of the previous sub-section. We modify the script as follows +and save it as logview.py: + +files = ' '.join(argv[1:]) # create one string from list of filenames +lg = log(files) +m = matlab() +plotview(lg,m) :pre + +If an alias is defined in your shell start-up file, such as + +alias logview ~/pizza/src/pizza.py -f logview.py :pre + +then you can type the following one-liner at the shell prompt to +invoke Pizza.py on the logview.py script with a list of files you +specfiy. + +% logview log.1 log.2 ... :pre + +A set of plots and a control GUI will appear on your screen. + +:line + +3.6 Error messages :h4,link(3_6) + +If you mistype a Pizza.py or Python command or pass an invalid +argument to a tool method, an error message will be printed by Python. +Usually these will be self-explanatory. Sometimes they will point to +a line of code inside a tool which Python was unable to execute +successfully. This could be because you passed the wrong arguments to +the tool, the data the tool is operating on is invalid, or because +there's a bug in the tool. In the latter case, please figure out as +much as you can about the bug and email a description and the +necessary files to reproduce the bug in the simplest possible way to +sjplimp@sandia.gov. diff --git a/doc/Section_examples.html b/doc/Section_examples.html new file mode 100644 index 0000000..554196a --- /dev/null +++ b/doc/Section_examples.html @@ -0,0 +1,57 @@ + +
Previous Section - Pizza.py WWW Site - +Pizza.py Documentation - Pizza.py Tools - Next +Section +
+ + + + + + +
+ +

5. Example scripts +

+

The Pizza.py distribution includes 2 sets of example scripts. A +listing of included scripts is given on the Pizza.py WWW +site. +

+ + +

(A) The examples directory has a README file and a variety of scripts. +For each tool in Pizza.py there is a test_tool.py script that invokes +the tool on a simple data set (from the files sub-directory) and +exercises various tool methods. These scripts are meant to illustrate +how the tool is used. +

+

Assuming pizza.py is in your path, each of the test scripts can be run +from within the examples directory by typing one of these lines (from +the shell or from within Pizza.py): +

+
% pizza.py -f test_animate.py
+> @run test_animate.py 
+
+

The remaining scripts in the examples directory illustrate how to do +various tasks in Pizza.py. They are not meant to be generically +useful nor are they well documented. Rather they are illustrations of +how to do some specific task quickly and straightforwardly. Most of +these scripts are not meant to be run by other users, since their data +files are not included. +

+

(B) The scripts directory contains several scripts you may find useful +either to use directly or to modify to create a new script for your +purposes. +

+

The top of each script file describes its purpose and syntax. That +information can be be accessed from within Pizza.py by typing "??" or +"? name.py" or "?? name.py". +

+

As explained in this section, any file in +the scripts directory can be run from the directory where your data +lives, by typing a line appropriate to the script's syntax, e.g. +

+
% pizza.py -f movie.py svg 60 135 dump.protein      from the shell
+> @run movie.py svg 60 135 dump.protein             from Pizza.py 
+
+ diff --git a/doc/Section_examples.txt b/doc/Section_examples.txt new file mode 100644 index 0000000..75401aa --- /dev/null +++ b/doc/Section_examples.txt @@ -0,0 +1,52 @@ +"Previous Section"_Section_tools.html - "Pizza.py WWW Site"_pws - +"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next +Section"_Section_extend.html :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +5. Example scripts :h3 + +The Pizza.py distribution includes 2 sets of example scripts. A +listing of included scripts is given on the "Pizza.py WWW +site"_scripts. + +:link(scripts,http://www.cs.sandia.gov/~sjplimp/pizza/scripts.html) + +(A) The examples directory has a README file and a variety of scripts. +For each tool in Pizza.py there is a test_tool.py script that invokes +the tool on a simple data set (from the files sub-directory) and +exercises various tool methods. These scripts are meant to illustrate +how the tool is used. + +Assuming pizza.py is in your path, each of the test scripts can be run +from within the examples directory by typing one of these lines (from +the shell or from within Pizza.py): + +% pizza.py -f test_animate.py +> @run test_animate.py :pre + +The remaining scripts in the examples directory illustrate how to do +various tasks in Pizza.py. They are not meant to be generically +useful nor are they well documented. Rather they are illustrations of +how to do some specific task quickly and straightforwardly. Most of +these scripts are not meant to be run by other users, since their data +files are not included. + +(B) The scripts directory contains several scripts you may find useful +either to use directly or to modify to create a new script for your +purposes. + +The top of each script file describes its purpose and syntax. That +information can be be accessed from within Pizza.py by typing "??" or +"? name.py" or "?? name.py". + +As explained in "this section"_Section_basics.html#3_5, any file in +the scripts directory can be run from the directory where your data +lives, by typing a line appropriate to the script's syntax, e.g. + +% pizza.py -f movie.py svg 60 135 dump.protein from the shell +> @run movie.py svg 60 135 dump.protein from Pizza.py :pre diff --git a/doc/Section_extend.html b/doc/Section_extend.html new file mode 100644 index 0000000..d24a344 --- /dev/null +++ b/doc/Section_extend.html @@ -0,0 +1,101 @@ + +
Previous Section - Pizza.py WWW Site - +Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

6. Extending Pizza.py +

+

Pizza.py can easily be extended in several ways: +

+
  1. fix a bug +
  2. make a tool method faster or cleaner +
  3. add a new method or setting to a tool +
  4. add a new tool +
  5. add a generically useful script to the scripts dir +
  6. add a script that does something interesting to the examples dir +
  7. send a picture or movie you made with Pizza.py for the WWW page. +
+

You might be able to do (2) because you're better with Python than we +are! Note that generally, we've opted for simplicity versus speed in +writing the tools, unless the operation is very costly. An example of +something I'd like to speed up is the reading of large dump files in +dump.py. +

+

Some of the ideas we've had for (3), but haven't gotten around to, are +listed at the top of the src/*.py files as ToDo items. +

+

If you think your addition will be useful to other Pizza.py users, +email it to sjplimp@sandia.gov and it can be added to the distribution +with an attribution to you, both in the source code and on the +Pizza.py WWW site. +

+ + +
+ +

Here are ideas to consider when creating new Pizza.py tools or +scripts: +

+

(1) For tools, your *.py file should contain a Python class with the +same name as the *.py file since it will be imported into Pizza.py +with a statement like +

+
from dump import dump 
+
+

(2) Your scripts can use methods from Pizza.py classes to make data +analysis easier. E.g. scripts can be written that use the dump tool +to read dump files, then use the iterator calls and vecs() method from +dump.py to loop over snapshots and extract lists of particles for +further computation. See the scripts and examples directories for +examples of this. +

+

(3) To flag an error in your script or tool and exit back to the +Pizza.py prompt, use a line like: +

+
raise StandardError,"error message" 
+
+

(4) Document your tool be defining the "oneline" and "docstr" +variables at the top of the file. This is what will be printed when +you type "? dump", for example. +

+

(5) If you intend your tool to interact with other Pizza.py tools, you +should follow the Pizza.py philosophy of having objects be passed as +arguments to the tool methods. If you're creating a tool that is +similar to an existing tool, but a different flavor (e.g. wrapping +another plotting package in addition to MatLab or GnuPlot), then try +to make the interface similar to the others so all the related tools +can be used interchangeably. +

+

(6) From the Pizza.py perspective, the difference between a script and +a tool is as follows. A script typically does a specific operation +(with or without arguments). E.g. process a dump file and compute a +quantity. A tool version of the same operation would allow it to +store internal state and persist, or to be packaged in a way that +other tools or scripts can create instances of it and call its +methods. From the Python perspective the code for the 2 cases may not +look very different. The tool version might just be some Python +variables and methods stuck inside a Python class, which is what a +Pizza.py tool basically is. +

+

(7) The various Pizza.py tools are mostly related to the "LAMMPS" +molecular dynamics or ChemCell cell simulator packages. But +of course you can write Pizza.py tools that have nothing to do with +LAMMPS or ChemCell. If you think they will still be of general +interest to Pizza.py users, you can send them to us to include in the +Pizza.py distribution. Or you can keep the top-level pizza.py file, +throw away the LAMMPS and ChemCell tool files, build your own toolkit +for whatever application you wish, and use or even distribute it +yourself. That's the open-source philosophy. +

+ + + + + diff --git a/doc/Section_extend.txt b/doc/Section_extend.txt new file mode 100644 index 0000000..5d54805 --- /dev/null +++ b/doc/Section_extend.txt @@ -0,0 +1,95 @@ +"Previous Section"_Section_tools.html - "Pizza.py WWW Site"_pws - +"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +6. Extending Pizza.py :h3 + +Pizza.py can easily be extended in several ways: + +fix a bug +make a tool method faster or cleaner +add a new method or setting to a tool +add a new tool +add a generically useful script to the scripts dir +add a script that does something interesting to the examples dir +send a picture or movie you made with Pizza.py for the "WWW page"_pws. :ol + +You might be able to do (2) because you're better with Python than we +are! Note that generally, we've opted for simplicity versus speed in +writing the tools, unless the operation is very costly. An example of +something I'd like to speed up is the reading of large dump files in +dump.py. + +Some of the ideas we've had for (3), but haven't gotten around to, are +listed at the top of the src/*.py files as ToDo items. + +If you think your addition will be useful to other Pizza.py users, +email it to sjplimp@sandia.gov and it can be added to the distribution +with an attribution to you, both in the source code and on the +"Pizza.py WWW site"_thanks. + +:link(thanks,http://www.cs.sandia.gov/~sjplimp/pizza/thanks.html) + +:line + +Here are ideas to consider when creating new Pizza.py tools or +scripts: + +(1) For tools, your *.py file should contain a Python class with the +same name as the *.py file since it will be imported into Pizza.py +with a statement like + +from dump import dump :pre + +(2) Your scripts can use methods from Pizza.py classes to make data +analysis easier. E.g. scripts can be written that use the dump tool +to read dump files, then use the iterator calls and vecs() method from +dump.py to loop over snapshots and extract lists of particles for +further computation. See the scripts and examples directories for +examples of this. + +(3) To flag an error in your script or tool and exit back to the +Pizza.py prompt, use a line like: + +raise StandardError,"error message" :pre + +(4) Document your tool be defining the "oneline" and "docstr" +variables at the top of the file. This is what will be printed when +you type "? dump", for example. + +(5) If you intend your tool to interact with other Pizza.py tools, you +should follow the Pizza.py philosophy of having objects be passed as +arguments to the tool methods. If you're creating a tool that is +similar to an existing tool, but a different flavor (e.g. wrapping +another plotting package in addition to MatLab or GnuPlot), then try +to make the interface similar to the others so all the related tools +can be used interchangeably. + +(6) From the Pizza.py perspective, the difference between a script and +a tool is as follows. A script typically does a specific operation +(with or without arguments). E.g. process a dump file and compute a +quantity. A tool version of the same operation would allow it to +store internal state and persist, or to be packaged in a way that +other tools or scripts can create instances of it and call its +methods. From the Python perspective the code for the 2 cases may not +look very different. The tool version might just be some Python +variables and methods stuck inside a Python class, which is what a +Pizza.py tool basically is. + +(7) The various Pizza.py tools are mostly related to the "LAMMPS" +molecular dynamics or "ChemCell"_ccell cell simulator packages. But +of course you can write Pizza.py tools that have nothing to do with +LAMMPS or ChemCell. If you think they will still be of general +interest to Pizza.py users, you can send them to us to include in the +Pizza.py distribution. Or you can keep the top-level pizza.py file, +throw away the LAMMPS and ChemCell tool files, build your own toolkit +for whatever application you wish, and use or even distribute it +yourself. That's the open-source philosophy. + +:link(lammps,http://www.cs.sandia.gov/~sjplimp/lammps.html) +:link(ccell,http://www.cs.sandia.gov/~sjplimp/chemcell.html) diff --git a/doc/Section_install.html b/doc/Section_install.html new file mode 100644 index 0000000..73b5d32 --- /dev/null +++ b/doc/Section_install.html @@ -0,0 +1,548 @@ + +
Previous Section - Pizza.py WWW Site - +Pizza.py Documentation - Pizza.py Tools - Next +Section +
+ + + + + + +
+ +

2. Installing Pizza.py +

+

Unpack the Pizza.py distribution by typing the following: +

+
gunzip pizza.tar.gz
+tar xvf pizza.tar 
+
+

The Pizza.py main directory should then contain the following +directories: +

+
+ + + + + +
README initial instructions
LICENSE the GNU open-source license
doc HTML documentation for Pizza.py
examples scripts and data sets that exercise Pizza.py tools
scripts various Pizza.py script files
src source code for Pizza.py and its tools +
+ +

Because Python is an interpreted language, there is no need to compile +or "make" Pizza.py. You run Pizza.py by executing the src/pizza.py +file directly, as described below. However there are 3 issues to +consider: (a) you must have Python installed on your machine, (b) some +Pizza.py tools require your Python to be extended with additional +Python packages, and (c) some Pizza.py tools are wrappers on other +software which needs to be available on your system. +

+

If you don't plan to use a particular Pizza.py tool, you don't need to +install additional Python packages or other software it requires. +

+2.1 Installing Python
+2.2 Running Pizza.py
+2.3 Setting up the DEFAULTS.py file
+2.4 Installing additional Python packages
+2.5 Installing other software
+ +

Note that we cannot provide help on installing the various software +packages described here. If you have problems, you'll need to talk to +a local expert who can help you with your machine. If you find that +instructions on this page are incorrect or incomplete or you can +provide a better description of the install procedure, please send an +email to sjplimp@sandia.gov. +

+
+ +

Installing Python +

+

Python is open-source software available for Unix, Macintosh, and +Windows machines. If you have a Linux box or Mac it is probably +already installed. If the python executable is in your path, typing +"python" should give you a Python prompt ">>>" and tell you what +version you are running. Version 2.4 or newer is sufficiently current +to run Pizza.py, though older versions may work as well. +

+

If Python is not installed on your machine, go to +www.python.org to download a binary or +source-code version and then build and/or install it. +

+

On my Linux box, this was as easy as +

+
./configure; make; sudo make install 
+
+

To use the Pizza.py tools that have GUIs, you need to +insure your Python supports Tcl/Tk via the Tkinter module. This is +the case if you can type the following from your Python prompt: +

+
>>> import Tkinter
+>>> Tkinter._test() 
+
+

If this fails, see further instructions below for Tkinter. +

+

IMPORTANT NOTE: If you are installing a new version of Python, read +the Tkinter section first, since it describes how to make sure the +Tcl/Tk and Togl libraries are installed. If you want to use the +Pizza.py tools that require them, you need to do this step first +before building Python. +

+
+ +

Running Pizza.py +

+

Typically Pizza.py should be run from the directory where your LAMMPS +or other data files are. Like any Python program, Pizza.py can be run +in one of 2 ways, by typing either +

+
python -i ~/pizza/src/pizza.py
+~/pizza/src/pizza.py 
+
+

where the last argument is the full pathname of the pizza.py file. +

+

The -i switch leaves Python in interactive mode (instead of exiting) +after the pizza.py script is run. In the 2nd case, if the src dir is +in your path, just pizza.py could be typed. For the 2nd case, you +must also set src/pizza.py to be an executable file (chmod +x +pizza.py) and edit the 1st line of pizza.py to reflect where Python +lives on your system (find it by typing "which python"), e.g. +

+
#!/usr/local/bin/python -i 
+
+

Putting a definition like one of the following in your .cshrc file (or +equivalent syntax for other Unix shell start-up files) will let you +simply type "pizza" at the command-line to start Pizza.py. +

+

alias pizza python -i ~/pizza/src/pizza.py +alias pizza ~/pizza/src/pizza.py +

+

Pizza.py accepts several command-line options; they are described in +this section of the documentation. +

+

When Pizza.py starts, it reads a few values from the src/DEFAULTS.py +file (described below) and imports the *.py files from the src +directory as Python modules. These are the Pizza.py tools. Error +messages will be printed if your Python has not been extended with a +Python package that a tool requires. If you don't plan to use the +tool you can ignore the message, or exclude that tool via the +command-line switch "-x". +

+

Once all tools have been loaded and any initial scripts and commands +have been run (via command-line arguments) you should see the Pizza.py +">" prompt. From this point on, everything you type is a Python +command. Python interprets what you type, operates on your data, and +produces output or error messages, just as if you were typing in +response to Python's interactive prompt ">>>". +

+

You can also type special commands that have been added to the Python +interpreter by Pizza.py or commands that invoke Pizza.py tools. More +details about these options are explained in this +section of the documentation. +

+

As with Python, type Ctrl-D to exit Pizza.py at any time. +

+
+ +

Setting up the DEFAULTS.py file +

+

When Pizza.py starts it reads 3 values from the src/DEFAULTS.py file: +

+
+ + +
PIZZA_TOOLS directories that contain additional Pizza.py tools
PIZZA_SCRIPTS directories that contain additional Pizza.py scripts
PIZZA_EXCLUDE Python files that are not loaded, since they are not tools +
+ +

These are designed to allow users to augment Pizza.py with their own +tools and scripts, which need not be stored in the directories of the +Pizza.py pacakge. Follow the instructions in the DEFAULTS.py file for +using these options. +

+

The DEFAULTS.py files also contains various variables that specify the +name and path of programs that Pizza.py tools will execute on your +system. In some cases the variables contain settings that are used by +these programs. Read the comments in the DEFAULTS.py file for more +information. +

+

The following table lists the keywords in the DEFAULTS.py, the program +or setting that will be used by default if the keyword line is +commented out, and the Pizza.py tools that use the keyword. If the +program is not in your path or you wish to use an alternate program or +setting, you must edit the DEFAULTS.py file accordingly. If you don't +plan to use any tool that needs the keyword, you can ignore its +setting. +

+
+ + + + + + + + + + + + + + +
Keyword Default Value Purpose Tools that Use it
DISPLAY display display image files (ImageMagick) rasmol, raster, svg
CONVERT convert convert image files (ImageMagick) image
MONTAGE montage montage image files (ImageMagick) image
GNUPLOT gnuplot Gnu Plotting package gnu
GNUTERM x11 GnuPlot terminal gnu
GUNZIP gunzip unzip a compressed *.gz file dump, log
LABEL3D label3d put a label on a Raster3D image raster
MATLAB matlab MatLab numerical analysis & plotting package matlab
RASMOL rasmol RasMol molecular vizualization package rasmol
RENDER render Raster3D vizualization rendering engine raster
VMDNAME vmd VMD visualization package vmd
VMDDIR /usr/local/lib/vmd VMD visualization package vmd
VMDDEV win VMD visualization package vmd
VMDARCH LINUX VMD visualization package vmd +
+ +
+ +

Installing additional Python packages +

+

This is the list of extra Python packages various Pizza.py tools +require. If a tool is not listed it requires no extra packages. +Instructions on where to find the Python extensions and how to install +them are listed below. +

+
+ + + + + + + +
Package Tools that Use it
Numeric or Numpy dump, mdump, bdump, ldump, tdump
pexpect vmd
PIL animate, gl, image
Pmw image
PyOpenGL gl, vcr
readline Pizza.py itself
Tkinter animate, image, plotview, vcr +
+ +
+ +

Numeric or Numpy +

+

Numeric and its follow-on NumPy enables Python to +process vectors and arrays of numbers efficiently, both in terms of +memory and CPU speed. It's an extremely useful extension to have in +your Python if you do any numerical work on large data sets. Pizza.py +can use either Numeric or NumPy. +

+

If Numeric or NumPy is already installed in your Python, you should be +able to type one of the following without getting an error: +

+
>>> import Numeric
+>>> import numpy 
+
+

Numeric can be downloaded from this site on SourceForge and +NumPy from this site. Numeric version 24.2 is fine for +Pizza.py as is a current version of NumPy. Once unpacked, you can +type the following from the Numeric or NumPy directories to install it +in your Python. +

+
sudo python setup.py install 
+
+

Note: on my Linux box, when Numeric installed itself under the Python +lib in /usr/local, it did not set all file permsissions correctly to +allow a user to import it. So I also needed to do this: +

+
sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Numeric 
+
+ + + + +
+ +

pexpect +

+

Pexpect in a pure Python +implementation of the Expect capability of the Tcl language. It +allows Python to send commands to another program, and handshake the +interaction between them, one command at a time. +

+

If pexpect is already installed in your Python, you should be able to +type the following without getting an error: +

+
>>> import pexpect 
+
+

Pexpect can be downloaded from this +site. As of Nov 2010, Version +2.4 is fine. On my Linux box, this command installed it: +

+
sudo python setup.py install 
+
+
+ +

PIL +

+

The PIL (Python Imaging Library) allows Python to read image +files, manipulate them, and convert between several common image +formats. +

+ + + + +

If PIL is already installed in your Python, you should be able to type +the following without getting an error: +

+
>>> import Image,ImageTk 
+
+

PIL can be downloaded from this site. As of July 2007, +Version 1.1.6 is fine. On my Linux box, this command installed it: +

+
sudo python setup.py install 
+
+

with a notice that Tkinter and ZLIB (PNG) support were enabled. If +you want the Pizza.py tools to recognize other image formats +(e.g. JPEG), then look at the README for further details, if the PIL +build did not find the correct libraries. +

+
+ +

Pmw +

+

Pmw (Python mega-widgets) is a common Tkinter extension that +provides a host of more powerful GUI widgets. +

+ + +

If Pmw is already installed in your Python, you should be able to type +the following without getting an error: +

+
>>> import Pmw 
+
+

Pmw can be downloaded from this site. As of July 2007, Version +1.2 is fine. Pmw is installed by putting its files in your Python's +site-packages directory. After unpacking the tarball and +naming the resulting dir "pmw", I installed it on my Linux +box as follows: +

+
sudo cp -r pmw /usr/local/lib/python2.5/site-packages/Pmw
+sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Pmw 
+
+
+ +

PyOpenGL +

+

The PyOpenGL package is a wrapper on the ubiquitous OpenGL +graphics library and allows a Python program to make graphics calls in +standard OpenGL syntax. It also includes Togl support for opening a +Tk OpenGL widget, assuming your Python has Tkinter intstalled and that +Tkinter was built with Togl (read on!). The Pizza.py tools that use +PyOpenGL require this capability. +

+ + +

If PyOpenGL is already installed in your Python, you should be able to +type the following without getting an error: +

+
>>> import OpenGL 
+
+

If your PyOpenGL supports Togl, you should be able to type the +following without getting an error: +

+
>>> from OpenGL.Tk import *
+>>> from OpenGL.GLUT import * 
+
+

PyOpenGL can be downloaded from this site on SourceForge. +You want the latest PyOpenGL release (not OpenGLContext). As of July +2007, Version 3.0.0a6 is what I used. +

+

IMPORTANT NOTE: I had many problems installing earlier versions of +PyOpenGL on various boxes. But the 3.0 release was much easier to +install on my Linux box, as outlined here. Note that version 3.0 +requires Python 2.4 or later. +

+

IMPORTANT NOTE #2: By default, your Python may or may not have Tkinter +installed. Even if Tkinter is installed, it probably was not built +with Togl. If this is the case, you should install them first before +installing PyOpenGl, otherwise you will still get errors when you try +to use the Pizza.py tools that use PyOpenGL, because they require +Tkinter and Togl. See the Tkinter section below for instructions on +installing Tkinter and Togl in your Python. +

+

Installing 3.0 version of PyOpenGL requires the setuptools package be +part of your Python. As of July 2007, it can be downloaded from this +site. It is a single file, ez_setup.py, which can be +installed in your Python by typing: +

+
sudo python ez_setup.py 
+
+ + +

Once setuptools and Tkinter and Togl are in place, installing PyOpenGL +on my Linux box was as simple as: +

+
sudo python setup.py install 
+
+
+ +

readline +

+

The readline library is part of Python but is not supported +on all systems. If it works in your Python, then Pizza.py (and +Python) prompts are more shell-like and should support arrow keys, +Emacs-style editing, command history, etc. If you get an error "No +module named readline" when Pizza.py starts up, you can ignore it, or +comment out the line "import readline" in src/pizza.py. +

+

If readline is already installed in your Python, you should be able to +type the following without getting an error: +

+
>>> import readline 
+
+

The readline library can be downloaded from this site. +After building the library, I believe you then have to rebuild Python +itself. +

+ + + + +
+ +

Tkinter +

+

The Tkinter package is part of Python but is not always enabled when +Python is built, typically due to not finding the Tcl/Tk libraries. +If you can type the following without an error message in your Python, +then Tkinter is operational in your Python: +

+
>>> import Tkinter
+>>> Tkinter._test() 
+
+

If this fails, you need to rebuild Python and either insure it finds +the Tcl/Tk libraries or build those libraries first as described here. +Since I wanted a more current Python then was installed with Linux on +my box, I download the latest Python (Python 2.5.1 as of July 2007) +and installed it under /usr/local. +

+

IMPORTANT NOTE: If you want to use any of the Pizza.py tools that use +PyOpenGL, you also need the Togl library. You should install it +before building the Tcl/Tk libraries which you then build before +re-building Python, as described here. Unfortunately, if Tkinter is +already in your Python but without Togl support, I think you need to +go thru these 3 steps in order. +

+

(1) To intstall Togl, download it from this site on +SourceForge. As of July 2007, Version 1.7 is fine. +

+ + +

After unpacking the tarball, installing it on my Linux box was +as simple as: +

+
./configure; make; sudo make install 
+
+

(2) To build Tck/Tk libraries with Togl support, go to this +site on SourceForce to download the latest versions of Tcl and +Tk. +

+ + +

As of July 2007, I was unable to build version 8.4.15 on my Redhat +Linux box due to an odd error, but 8.4.7 built fine. After unpacking +the two tarballs I did the following: +

+
cd tcl8.4.7/unix
+./configure; make; sudo make install 
+cd tk8.4.7/unix
+./configure; make; sudo make install 
+
+

This build should find the Togl library previously installed under +/usr/local. +

+

(3) Now you can re-build Python and it should find the correct Tcl/Tk +libraries under /usr/local. Note that when you run ./configure as the +first step in building Python, it will tell you what it found for +Tcl/Tk. +

+
+ +

Installing other software +

+

Some Pizza.py tools invoke other software which must be installed on +your system for the tool to work. This is an alphabetic list of the +needed software. Except where noted, it is freely available for +download on the WWW. The Pizza.py tools that use this software are +listed above in this section. To see if you already have the +software on your box, type "which command", e.g. "which display". +

+

ImageMagick display, convert, montage commands +

+

Several Pizza.py tools display image files. The ImageMagick "display" +program can be used for this purpose. Likewise, the ImageMagick +"convert" and "montage" comands are used by the image tool. The +ImageMagick toolkit can be downloaded from this site and +contains a variety of useful image conversion and manipulation +software. +

+ + +

GnuPlot +

+

The Pizza.py gnu tool is a wrapper on the open-source GnuPlot program. +GnuPlot can be downloaded from this site. +

+ + +

Gunzip +

+

Gunzip is invoked by Python to read compressed (*.gz) data and dump +files. It is almost certainly on your Unix system. If not if can be +downloaded from this site. +

+ + +

Label3d +

+

The Pizza.py tool raster uses the label3d and render programs from the +Raster3d visualization package to produce high-quality ray-traced +images. See the description of "Render" below for information about +Raster3d. +

+

MatLab +

+

The Pizza.py matlab tool is a wrapper on MatLab which is a widely-used +commercial numerical analysis package that also produces nice plots. +Further information is available at the MathWorks WWW site. +When MatLab is installed on your system and the appropriate +environment variables are set, the command "matlab" should launch the +program. +

+ + +

RasMol +

+

The Pizza.py rasmol tool invokes the RasMol visualization package to +view molecular systems and produce nice images. RasMol can be +downloaded from this site, which is for the original +open-source version of RasMol, not the Protein Explorer derivative +version of RasMol. +

+ + +

Note that when using RasMol on a Mac, you will need to launch X11 +first (or run Pizza.py from an X11 xterm) to get RasMol to display +properly. +

+

Render +

+

The Pizza.py tool raster uses the render and label3d programs from the +Raster3d visualization package to produce high-quality ray-traced +images. Raster3d can be downloaded from this site. +

+ + +

For Macs, Raster3d is available for download via Fink as an +unstable package. +

+ + + + +

VMD +

+

The Pizza.py vmd tool is a simple wrapper on the VMD visualization +package which is a popular tool for visualizing the output of +molecular dynamics simulations. VMD can be downloaded from this +site. +

+ + + diff --git a/doc/Section_install.txt b/doc/Section_install.txt new file mode 100644 index 0000000..564ab05 --- /dev/null +++ b/doc/Section_install.txt @@ -0,0 +1,531 @@ +"Previous Section"_Section_intro.html - "Pizza.py WWW Site"_pws - +"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next +Section"_Section_basics.html :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +2. Installing Pizza.py :h3 + +Unpack the Pizza.py distribution by typing the following: + +gunzip pizza.tar.gz +tar xvf pizza.tar :pre + +The Pizza.py main directory should then contain the following +directories: + +README: initial instructions +LICENSE: the GNU open-source license +doc: HTML documentation for Pizza.py +examples: scripts and data sets that exercise Pizza.py tools +scripts: various Pizza.py script files +src: source code for Pizza.py and its tools :tb(s=:) + +Because Python is an interpreted language, there is no need to compile +or "make" Pizza.py. You run Pizza.py by executing the src/pizza.py +file directly, as described below. However there are 3 issues to +consider: (a) you must have Python installed on your machine, (b) some +Pizza.py tools require your Python to be extended with additional +Python packages, and (c) some Pizza.py tools are wrappers on other +software which needs to be available on your system. + +If you don't plan to use a particular Pizza.py tool, you don't need to +install additional Python packages or other software it requires. + +2.1 "Installing Python"_#2_1 +2.2 "Running Pizza.py"_#2_2 +2.3 "Setting up the DEFAULTS.py file"_#2_3 +2.4 "Installing additional Python packages"_#2_4 +2.5 "Installing other software"_#2_5 :all(b) + +Note that we cannot provide help on installing the various software +packages described here. If you have problems, you'll need to talk to +a local expert who can help you with your machine. If you find that +instructions on this page are incorrect or incomplete or you can +provide a better description of the install procedure, please send an +email to sjplimp@sandia.gov. + +:line + +Installing Python :h4,link(2_1) + +Python is open-source software available for Unix, Macintosh, and +Windows machines. If you have a Linux box or Mac it is probably +already installed. If the python executable is in your path, typing +"python" should give you a Python prompt ">>>" and tell you what +version you are running. Version 2.4 or newer is sufficiently current +to run Pizza.py, though older versions may work as well. + +If Python is not installed on your machine, go to +"www.python.org"_http://www.python.org to download a binary or +source-code version and then build and/or install it. + +On my Linux box, this was as easy as + +./configure; make; sudo make install :pre + +To use the Pizza.py tools that have GUIs, you need to +insure your Python supports Tcl/Tk via the Tkinter module. This is +the case if you can type the following from your Python prompt: + +>>> import Tkinter +>>> Tkinter._test() :pre + +If this fails, see further instructions below for Tkinter. + +IMPORTANT NOTE: If you are installing a new version of Python, read +the Tkinter section first, since it describes how to make sure the +Tcl/Tk and Togl libraries are installed. If you want to use the +Pizza.py tools that require them, you need to do this step first +before building Python. + +:line + +Running Pizza.py :h4,link(2_2) + +Typically Pizza.py should be run from the directory where your LAMMPS +or other data files are. Like any Python program, Pizza.py can be run +in one of 2 ways, by typing either + +python -i ~/pizza/src/pizza.py +~/pizza/src/pizza.py :pre + +where the last argument is the full pathname of the pizza.py file. + +The -i switch leaves Python in interactive mode (instead of exiting) +after the pizza.py script is run. In the 2nd case, if the src dir is +in your path, just pizza.py could be typed. For the 2nd case, you +must also set src/pizza.py to be an executable file (chmod +x +pizza.py) and edit the 1st line of pizza.py to reflect where Python +lives on your system (find it by typing "which python"), e.g. + +#!/usr/local/bin/python -i :pre + +Putting a definition like one of the following in your .cshrc file (or +equivalent syntax for other Unix shell start-up files) will let you +simply type "pizza" at the command-line to start Pizza.py. + +alias pizza python -i ~/pizza/src/pizza.py +alias pizza ~/pizza/src/pizza.py + +Pizza.py accepts several command-line options; they are described in +"this section"_Section_basics.html of the documentation. + +When Pizza.py starts, it reads a few values from the src/DEFAULTS.py +file (described below) and imports the *.py files from the src +directory as Python modules. These are the Pizza.py tools. Error +messages will be printed if your Python has not been extended with a +Python package that a tool requires. If you don't plan to use the +tool you can ignore the message, or exclude that tool via the +command-line switch "-x". + +Once all tools have been loaded and any initial scripts and commands +have been run (via command-line arguments) you should see the Pizza.py +">" prompt. From this point on, everything you type is a Python +command. Python interprets what you type, operates on your data, and +produces output or error messages, just as if you were typing in +response to Python's interactive prompt ">>>". + +You can also type special commands that have been added to the Python +interpreter by Pizza.py or commands that invoke Pizza.py tools. More +details about these options are explained in "this +section"_Section_basics.html of the documentation. + +As with Python, type Ctrl-D to exit Pizza.py at any time. + +:line + +Setting up the DEFAULTS.py file :h4,link(2_3) + +When Pizza.py starts it reads 3 values from the src/DEFAULTS.py file: + +PIZZA_TOOLS: directories that contain additional Pizza.py tools +PIZZA_SCRIPTS: directories that contain additional Pizza.py scripts +PIZZA_EXCLUDE: Python files that are not loaded, since they are not tools :tb(s=:) + +These are designed to allow users to augment Pizza.py with their own +tools and scripts, which need not be stored in the directories of the +Pizza.py pacakge. Follow the instructions in the DEFAULTS.py file for +using these options. + +The DEFAULTS.py files also contains various variables that specify the +name and path of programs that Pizza.py tools will execute on your +system. In some cases the variables contain settings that are used by +these programs. Read the comments in the DEFAULTS.py file for more +information. + +The following table lists the keywords in the DEFAULTS.py, the program +or setting that will be used by default if the keyword line is +commented out, and the Pizza.py tools that use the keyword. If the +program is not in your path or you wish to use an alternate program or +setting, you must edit the DEFAULTS.py file accordingly. If you don't +plan to use any tool that needs the keyword, you can ignore its +setting. + +Keyword: Default Value: Purpose: Tools that Use it +DISPLAY: display: display image files (ImageMagick): rasmol, raster, svg +CONVERT: convert: convert image files (ImageMagick): image +MONTAGE: montage: montage image files (ImageMagick): image +GNUPLOT: gnuplot: Gnu Plotting package: gnu +GNUTERM: x11: GnuPlot terminal: gnu +GUNZIP: gunzip: unzip a compressed *.gz file: dump, log +LABEL3D: label3d: put a label on a Raster3D image: raster +MATLAB: matlab: MatLab numerical analysis & plotting package: matlab +RASMOL: rasmol: RasMol molecular vizualization package: rasmol +RENDER: render: Raster3D vizualization rendering engine: raster +VMDNAME: vmd: VMD visualization package: vmd +VMDDIR: /usr/local/lib/vmd: VMD visualization package: vmd +VMDDEV: win: VMD visualization package: vmd +VMDARCH: LINUX: VMD visualization package: vmd :tb(s=:) + +:line + +Installing additional Python packages :h4,link(2_4) + +This is the list of extra Python packages various Pizza.py tools +require. If a tool is not listed it requires no extra packages. +Instructions on where to find the Python extensions and how to install +them are listed below. + +Package : Tools that Use it +Numeric or Numpy : dump, mdump, bdump, ldump, tdump +pexpect : vmd +PIL : animate, gl, image +Pmw : image +PyOpenGL: gl, vcr +readline: Pizza.py itself +Tkinter : animate, image, plotview, vcr :tb(s=:) + +:line + +Numeric or Numpy :h4 + +"Numeric"_numeric and its follow-on "NumPy"_numpy enables Python to +process vectors and arrays of numbers efficiently, both in terms of +memory and CPU speed. It's an extremely useful extension to have in +your Python if you do any numerical work on large data sets. Pizza.py +can use either Numeric or NumPy. + +If Numeric or NumPy is already installed in your Python, you should be +able to type one of the following without getting an error: + +>>> import Numeric +>>> import numpy :pre + +Numeric can be downloaded from "this site"_numdown on SourceForge and +NumPy from "this site"_numeric. Numeric version 24.2 is fine for +Pizza.py as is a current version of NumPy. Once unpacked, you can +type the following from the Numeric or NumPy directories to install it +in your Python. + +sudo python setup.py install :pre + +Note: on my Linux box, when Numeric installed itself under the Python +lib in /usr/local, it did not set all file permsissions correctly to +allow a user to import it. So I also needed to do this: + +sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Numeric :pre + +:link(numeric,http://numeric.scipy.org) +:link(numdown,http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351) + +:line + +pexpect :h4 + +"Pexpect"_http://pypi.python.org/pypi/pexpect in a pure Python +implementation of the Expect capability of the Tcl language. It +allows Python to send commands to another program, and handshake the +interaction between them, one command at a time. + +If pexpect is already installed in your Python, you should be able to +type the following without getting an error: + +>>> import pexpect :pre + +Pexpect can be downloaded from "this +site"_http://pypi.python.org/pypi/pexpect. As of Nov 2010, Version +2.4 is fine. On my Linux box, this command installed it: + +sudo python setup.py install :pre + +:line + +PIL :h4 + +The PIL ("Python Imaging Library"_pil) allows Python to read image +files, manipulate them, and convert between several common image +formats. + +:link(pil,http://www.pythonware.com/products/pil) +:link(pildown,http://effbot.org/zone/pil-index.htm) + +If PIL is already installed in your Python, you should be able to type +the following without getting an error: + +>>> import Image,ImageTk :pre + +PIL can be downloaded from "this site"_pildown. As of July 2007, +Version 1.1.6 is fine. On my Linux box, this command installed it: + +sudo python setup.py install :pre + +with a notice that Tkinter and ZLIB (PNG) support were enabled. If +you want the Pizza.py tools to recognize other image formats +(e.g. JPEG), then look at the README for further details, if the PIL +build did not find the correct libraries. + +:line + +Pmw :h4 + +Pmw ("Python mega-widgets"_pmw) is a common Tkinter extension that +provides a host of more powerful GUI widgets. + +:link(pmw,http://pmw.sourceforge.net) + +If Pmw is already installed in your Python, you should be able to type +the following without getting an error: + +>>> import Pmw :pre + +Pmw can be downloaded from "this site"_pmw. As of July 2007, Version +1.2 is fine. Pmw is installed by putting its files in your Python's +site-packages directory. After unpacking the tarball and +naming the resulting dir "pmw", I installed it on my Linux +box as follows: + +sudo cp -r pmw /usr/local/lib/python2.5/site-packages/Pmw +sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Pmw :pre + +:line + +PyOpenGL :h4 + +The "PyOpenGL"_pyopengl package is a wrapper on the ubiquitous OpenGL +graphics library and allows a Python program to make graphics calls in +standard OpenGL syntax. It also includes Togl support for opening a +Tk OpenGL widget, assuming your Python has Tkinter intstalled and that +Tkinter was built with Togl (read on!). The Pizza.py tools that use +PyOpenGL require this capability. + +:link(pyopengl,http://pyopengl.sourceforge.net) + +If PyOpenGL is already installed in your Python, you should be able to +type the following without getting an error: + +>>> import OpenGL :pre + +If your PyOpenGL supports Togl, you should be able to type the +following without getting an error: + +>>> from OpenGL.Tk import * +>>> from OpenGL.GLUT import * :pre + +PyOpenGL can be downloaded from "this site"_pyopengl on SourceForge. +You want the latest PyOpenGL release (not OpenGLContext). As of July +2007, Version 3.0.0a6 is what I used. + +IMPORTANT NOTE: I had many problems installing earlier versions of +PyOpenGL on various boxes. But the 3.0 release was much easier to +install on my Linux box, as outlined here. Note that version 3.0 +requires Python 2.4 or later. + +IMPORTANT NOTE #2: By default, your Python may or may not have Tkinter +installed. Even if Tkinter is installed, it probably was not built +with Togl. If this is the case, you should install them first before +installing PyOpenGl, otherwise you will still get errors when you try +to use the Pizza.py tools that use PyOpenGL, because they require +Tkinter and Togl. See the Tkinter section below for instructions on +installing Tkinter and Togl in your Python. + +Installing 3.0 version of PyOpenGL requires the setuptools package be +part of your Python. As of July 2007, it can be downloaded from "this +site"_setuptools. It is a single file, ez_setup.py, which can be +installed in your Python by typing: + +sudo python ez_setup.py :pre + +:link(setuptools,http://peak.telecommunity.com/DevCenter/setuptools) + +Once setuptools and Tkinter and Togl are in place, installing PyOpenGL +on my Linux box was as simple as: + +sudo python setup.py install :pre + +:line + +readline :h4 + +The "readline"_readline library is part of Python but is not supported +on all systems. If it works in your Python, then Pizza.py (and +Python) prompts are more shell-like and should support arrow keys, +Emacs-style editing, command history, etc. If you get an error "No +module named readline" when Pizza.py starts up, you can ignore it, or +comment out the line "import readline" in src/pizza.py. + +If readline is already installed in your Python, you should be able to +type the following without getting an error: + +>>> import readline :pre + +The readline library can be downloaded from "this site"_readdown. +After building the library, I believe you then have to rebuild Python +itself. + +:link(readline,http://cnswww.cns.cwru.edu/~chet/readline/rltop.html) +:link(readdown,http://cnswww.cns.cwru.edu/~chet/readline/rltop.html#Availability) + +:line + +Tkinter :h4 + +The Tkinter package is part of Python but is not always enabled when +Python is built, typically due to not finding the Tcl/Tk libraries. +If you can type the following without an error message in your Python, +then Tkinter is operational in your Python: + +>>> import Tkinter +>>> Tkinter._test() :pre + +If this fails, you need to rebuild Python and either insure it finds +the Tcl/Tk libraries or build those libraries first as described here. +Since I wanted a more current Python then was installed with Linux on +my box, I download the latest Python (Python 2.5.1 as of July 2007) +and installed it under /usr/local. + +IMPORTANT NOTE: If you want to use any of the Pizza.py tools that use +PyOpenGL, you also need the Togl library. You should install it +before building the Tcl/Tk libraries which you then build before +re-building Python, as described here. Unfortunately, if Tkinter is +already in your Python but without Togl support, I think you need to +go thru these 3 steps in order. + +(1) To intstall Togl, download it from "this site"_togl on +SourceForge. As of July 2007, Version 1.7 is fine. + +:link(togl,http://togl.sourceforge.net) + +After unpacking the tarball, installing it on my Linux box was +as simple as: + +./configure; make; sudo make install :pre + +(2) To build Tck/Tk libraries with Togl support, go to "this +site"_tcltk on SourceForce to download the latest versions of Tcl and +Tk. + +:link(tcltk,http://sourceforge.net/project/showfiles.php?group_id=10894) + +As of July 2007, I was unable to build version 8.4.15 on my Redhat +Linux box due to an odd error, but 8.4.7 built fine. After unpacking +the two tarballs I did the following: + +cd tcl8.4.7/unix +./configure; make; sudo make install +cd tk8.4.7/unix +./configure; make; sudo make install :pre + +This build should find the Togl library previously installed under +/usr/local. + +(3) Now you can re-build Python and it should find the correct Tcl/Tk +libraries under /usr/local. Note that when you run ./configure as the +first step in building Python, it will tell you what it found for +Tcl/Tk. + +:line + +Installing other software :h4,link(2_5) + +Some Pizza.py tools invoke other software which must be installed on +your system for the tool to work. This is an alphabetic list of the +needed software. Except where noted, it is freely available for +download on the WWW. The Pizza.py tools that use this software are +listed above in "this section"_#2_3. To see if you already have the +software on your box, type "which command", e.g. "which display". + +ImageMagick display, convert, montage commands :h4 + +Several Pizza.py tools display image files. The ImageMagick "display" +program can be used for this purpose. Likewise, the ImageMagick +"convert" and "montage" comands are used by the image tool. The +ImageMagick toolkit can be downloaded from "this site"_imagemagick and +contains a variety of useful image conversion and manipulation +software. + +:link(imagemagick,http://www.imagemagick.org/script/index.php) + +GnuPlot :h4 + +The Pizza.py gnu tool is a wrapper on the open-source GnuPlot program. +GnuPlot can be downloaded from "this site"_gnuplot. + +:link(gnuplot,http://www.gnuplot.info) + +Gunzip :h4 + +Gunzip is invoked by Python to read compressed (*.gz) data and dump +files. It is almost certainly on your Unix system. If not if can be +downloaded from "this site"_gzip. + +:link(gzip,http://www.gnu.org/software/gzip/gzip.html) + +Label3d :h4 + +The Pizza.py tool raster uses the label3d and render programs from the +Raster3d visualization package to produce high-quality ray-traced +images. See the description of "Render" below for information about +Raster3d. + +MatLab :h4 + +The Pizza.py matlab tool is a wrapper on MatLab which is a widely-used +commercial numerical analysis package that also produces nice plots. +Further information is available at "the MathWorks WWW site"_matlab. +When MatLab is installed on your system and the appropriate +environment variables are set, the command "matlab" should launch the +program. + +:link(matlab,http://www.mathworks.com) + +RasMol :h4 + +The Pizza.py rasmol tool invokes the RasMol visualization package to +view molecular systems and produce nice images. RasMol can be +downloaded from "this site"_rasmol, which is for the original +open-source version of RasMol, not the Protein Explorer derivative +version of RasMol. + +:link(rasmol,http://www.openrasmol.org) + +Note that when using RasMol on a Mac, you will need to launch X11 +first (or run Pizza.py from an X11 xterm) to get RasMol to display +properly. + +Render :h4 + +The Pizza.py tool raster uses the render and label3d programs from the +Raster3d visualization package to produce high-quality ray-traced +images. Raster3d can be downloaded from "this site"_raster. + +:link(raster,http://www.bmsc.washington.edu/raster3d/raster3d.html) + +For Macs, Raster3d is available for download via "Fink"_fink as an +"unstable package"_unstable. + +:link(fink,http://fink.sourceforge.net/pdb/package.php/raster3d) +:link(unstable,http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable) + +VMD :h4 + +The Pizza.py vmd tool is a simple wrapper on the "VMD visualization +package"_vmd which is a popular tool for visualizing the output of +molecular dynamics simulations. VMD can be downloaded from "this +site"_vmd. + +:link(vmd,http://www.ks.uiuc.edu/Research/vmd) diff --git a/doc/Section_intro.html b/doc/Section_intro.html new file mode 100644 index 0000000..a77227c --- /dev/null +++ b/doc/Section_intro.html @@ -0,0 +1,160 @@ + +
Previous Section - Pizza.py WWW Site - Pizza.py +Documentation - Pizza.py Tools - Next +Section +
+ + + + + + +
+ +

1. Introduction +

+

These sections describe what Pizza.py is, what it means to be +open-source software, and acknowledge the funding and people who have +contributed to Pizza.py. +

+1.1 What is Pizza.Py
+1.2 Open source distribution
+1.3 Acknowledgements
+ +
+ +

1.1 What is Pizza.py +

+

Pizza.py is a loosely integrated collection of tools, many of which +provide pre- and post-processing capabilities for the LAMMPS +molecular dynamics and ChemCell cell simulator packages. +

+ + + + +

There are tools to create input files, convert between file formats to +connect to other codes, process log and dump files, plot output, and +visualize and animate simulation snapshots. +

+

Python is used in Pizza.py in 3 ways: +

+ +

Python makes it easy for users of Pizza.py to: +

+ +

The topmost level of Pizza.py adds a modest bit of functionality to +the Python interpreter to make it easier to invoke tools and pass data +between them. As such, Python is an ideal "framework" or "glue" +language that enables various tools to be hooked together, while also +providing a rich programming environment of its own. +

+
+ +

1.2 Open source distribution +

+

Pizza.py comes with no warranty of any kind. As each source file +states in its header, it is distributed free-of-charge, under the +terms of the GNU Public License (GPL). This is often referred +to as open-source distribution - see www.gnu.org or +www.opensource.org for more details. The legal text of +the GPL is in the LICENSE file that is included in the Pizza.py +distribution. +

+ + + + + + +

Here is a summary of what the GPL means for Pizza.py users: +

+

(1) Anyone is free to use, modify, or extend Pizza.py in any way they +choose, including for commercial purposes. +

+

(2) If you distribute a modified version of Pizza.py, it must remain +open-source, meaning you distribute it under the terms of the GPL. +You should clearly annotate such a code as a derivative version of +Pizza.py. +

+

(3) If you release any code that includes Pizza.py source code, then +it must also be open-sourced, meaning you distribute it under the +terms of the GPL. +

+

(4) If you give Pizza.py to someone else, the GPL LICENSE file and +source file headers (including the GPL notices) should remain part of +the code. +

+

In the spirit of an open-source code, these are various ways you can +contribute to making Pizza.py better. You can send email to +sjplimp@sandia.gov on any of these items. +

+ +
+ +

1.3 Acknowledgements +

+

Pizza.py has been developed at Sandia National Laboratories +which is a multiprogram laboratory operated by Sandia Corporation, a +Lockheed Martin Company, for the United States Department of Energy's +National Nuclear Security Administration under contract +DE-AC04-94AL85000. +

+

Funding for Pizza.py development has come from the US Department of +Energy (DOE), through its LDRD and Genomes-to-Life programs. +The latter effort has been funded by DOE's OASCR and +OBER offices as part of the US Department of Energy's +Genomics:GTL program (www.doegenomestolife.org) under the +project, "Carbon Sequestration in Synechococcus Sp.: From +Molecular Machines to Hierarchical Modeling". +

+ + + + + + + + + + + + +

The maintainer of Pizza.py is Steve Plimpton. +

+ + +

Matt Jones, a BYU student who was a summer intern at Sandia, wrote +several of the coolest tools in Pizza.py and about half the code in +the initial version. +

+

Others who have written tools or scripts that are part of the Pizza.py +distribution are listed on the Pizza.py WWW site. +

+ + + diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt new file mode 100644 index 0000000..f80f25b --- /dev/null +++ b/doc/Section_intro.txt @@ -0,0 +1,147 @@ +"Previous Section"_Manual.html - "Pizza.py WWW Site"_pws - "Pizza.py +Documentation"_pd - "Pizza.py Tools"_pt - "Next +Section"_Section_install.html :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +1. Introduction :h3 + +These sections describe what Pizza.py is, what it means to be +open-source software, and acknowledge the funding and people who have +contributed to Pizza.py. + +1.1 "What is Pizza.Py"_#1_1 +1.2 "Open source distribution"_#1_2 +1.3 "Acknowledgements"_#1_3 :all(b) + +:line + +1.1 What is Pizza.py :link(1_1),h4 + +Pizza.py is a loosely integrated collection of tools, many of which +provide pre- and post-processing capabilities for the "LAMMPS"_lammps +molecular dynamics and "ChemCell"_ccell cell simulator packages. + +:link(lammps,http://www.cs.sandia.gov/~sjplimp/lammps.html) +:link(ccell,http://www.cs.sandia.gov/~sjplimp/chemcell.html) + +There are tools to create input files, convert between file formats to +connect to other codes, process log and dump files, plot output, and +visualize and animate simulation snapshots. + +Python is used in Pizza.py in 3 ways: + +to provide an interactive and scripting interface to the tools +as a language for writing tools +to wrap existing stand-alone codes :ul + +Python makes it easy for users of Pizza.py to: + +experiment with tools interactively +automate tasks as script files of commands +extend tools or create new ones :ul + +The topmost level of Pizza.py adds a modest bit of functionality to +the Python interpreter to make it easier to invoke tools and pass data +between them. As such, Python is an ideal "framework" or "glue" +language that enables various tools to be hooked together, while also +providing a rich programming environment of its own. + +:line + +1.2 Open source distribution :link(1_2),h4 + +Pizza.py comes with no warranty of any kind. As each source file +states in its header, it is distributed free-of-charge, under the +terms of the "GNU Public License"_gnu (GPL). This is often referred +to as open-source distribution - see "www.gnu.org"_gnuorg or +"www.opensource.org"_opensource for more details. The legal text of +the GPL is in the LICENSE file that is included in the Pizza.py +distribution. + +:link(gnu,http://www.gnu.org/copyleft/gpl.html) +:link(gnuorg,http://www.gnu.org) +:link(opensource,http://www.opensource.org) + +Here is a summary of what the GPL means for Pizza.py users: + +(1) Anyone is free to use, modify, or extend Pizza.py in any way they +choose, including for commercial purposes. + +(2) If you distribute a modified version of Pizza.py, it must remain +open-source, meaning you distribute it under the terms of the GPL. +You should clearly annotate such a code as a derivative version of +Pizza.py. + +(3) If you release any code that includes Pizza.py source code, then +it must also be open-sourced, meaning you distribute it under the +terms of the GPL. + +(4) If you give Pizza.py to someone else, the GPL LICENSE file and +source file headers (including the GPL notices) should remain part of +the code. + +In the spirit of an open-source code, these are various ways you can +contribute to making Pizza.py better. You can send email to +sjplimp@sandia.gov on any of these items. + +If you write a Pizza.py script that is generally useful or illustrates +how to do something cool with Pizza.py, it can be added to the +Pizza.py distribution. Ditto for a picture or movie that can be added +to the "Pizza.py WWW site"_pws. :ulb,l + +If you add a new method to one of the tools or create a new tool that +is useful for Pizza.py or LAMMPS or ChemCell users, it can be added to +the Pizza.py distribution. See the ToDo list at the beginning of the +src/*.py files for features that haven't yet been implemented. :l + +If you find a bug, report it. :l + +Report if you find an error or omission in the "Pizza.py +documentation"_pd or on the "Pizza.py WWW Site"_pws, or have a +suggestion for something to clarify or include. :l + +Point prospective users to the "Pizza.py WWW Site"_pws or link to it +from your WWW site. :ule,l + +:line + +1.3 Acknowledgements :h4,link(1_3) + +Pizza.py has been developed at "Sandia National Laboratories"_sandia +which is a multiprogram laboratory operated by Sandia Corporation, a +Lockheed Martin Company, for the United States Department of Energy's +National Nuclear Security Administration under contract +DE-AC04-94AL85000. + +Funding for Pizza.py development has come from the US Department of +Energy ("DOE"_doe), through its LDRD and Genomes-to-Life programs. +The latter effort has been funded by DOE's "OASCR"_oascr and +"OBER"_ober offices as part of the US Department of Energy's +Genomics:GTL program ("www.doegenomestolife.org"_gtl) under the +"project"_ourgtl, "Carbon Sequestration in Synechococcus Sp.: From +Molecular Machines to Hierarchical Modeling". + +:link(sandia,http://www.sandia.gov) +:link(doe,http://www.doe.gov) +:link(gtl,http://www.doegenomestolife.org) +:link(ourgtl,http://www.genomes2life.org) +:link(oascr,http://www.sc.doe.gov/ascr/home.html) +:link(ober,http://www.er.doe.gov/production/ober/ober_top.html) + +The maintainer of Pizza.py is "Steve Plimpton"_sjp. + +:link(sjp,http://www.cs.sandia.gov/~sjplimp) + +Matt Jones, a BYU student who was a summer intern at Sandia, wrote +several of the coolest tools in Pizza.py and about half the code in +the initial version. + +Others who have written tools or scripts that are part of the Pizza.py +distribution are listed on the "Pizza.py WWW site"_authors. + +:link(authors,http://www.cs.sandia.gov/~sjplimp/pizza/thanks.html) diff --git a/doc/Section_tools.html b/doc/Section_tools.html new file mode 100644 index 0000000..352d288 --- /dev/null +++ b/doc/Section_tools.html @@ -0,0 +1,101 @@ + +
Previous Section - Pizza.py WWW Site - +Pizza.py Documentation - Pizza.py Tools - Next +Section +
+ + + + + + +
+ +

4. Tools within Pizza.py +

+

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, clog, 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
clog.py Read ChemCell log files and extract species data
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
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
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. +

+
+
+ diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt new file mode 100644 index 0000000..10181f6 --- /dev/null +++ b/doc/Section_tools.txt @@ -0,0 +1,85 @@ +"Previous Section"_Section_basics.html - "Pizza.py WWW Site"_pws - +"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next +Section"_Section_examples.html :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pt,Section_tools.html) + +:line + +4. Tools within Pizza.py :h3 + +"Th previous section"_Section_basics.html#3_4 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, clog, 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 :tb(s=:) + +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.html; Animate a series of image files +"bdump.py"_bdump.html; Read LAMMPS dump local files with bond info +"cdata.py"_data.html; Read, write, manipulate "Chemcell"_ccell data files +"chain.py"_chain.html; Create bead-spring chains for LAMMPS input +"cfg.py"_cfg.html; Convert LAMMPS snapshots to CFG format +"clog.py"_clog.html; Read "ChemCell"_ccell log files and extract species data +"data.py"_data.html; Read, write, manipulate LAMMPS data files +"dump.py"_dump.html; Read, write, manipulate dump files and particle attributes +"ensight.py"_ensight.html; Convert LAMMPS snapshots to "Ensight"_ensight format +"gl.py"_gl.html; 3d interactive visualization via OpenGL +"gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program +"histo.py"_histo.html; Particle density histogram from a dump +"image.py"_image.html; View and manipulate images +"ldump.py"_ldump.html; Read LAMMPS dump files with line info +"log.py"_log.html; Read LAMMPS log files and extract thermodynamic data +"matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program +"mdump.py"_mdump.html; Read, write, manipulate mesh dump files +"pair.py"_pair.html; Compute LAMMPS pairwise energies +"patch.py"_patch.html; Create patchy Lennard-Jones particles for LAMMPS input +"pdbfile.py"_pdbfile.html; Read, write PDB files in combo with LAMMPS snapshots +"plotview.py"_plotview.html; Plot multiple vectors from a data set +"rasmol.py"_rasmol.html; 3d visualization via "RasMol"_rasmol program +"raster.py"_raster.html; 3d visualization via "Raster3d"_raster3d program +"svg.py"_svg.html; 3d visualization via "SVG"_svg files +"tdump.py"_tdump.html; Read LAMMPS dump files with triangle info +"vcr.py"_vcr.html; VCR-style GUI for 3d interactive OpenGL visualization +"vec.py"_vec.html; Create numeric vectors from columns in file or list of vecs +"vtk.py"_vtk.html; Convert LAMMPS snapshots to VTK format +"vmd.py"_vmd.html; Wrapper on "VMD visualization package"_vmd +"xyz.py"_xyz.html; Convert LAMMPS snapshots to XYZ format :tb(s=;) + +:link(gnuplot,http://www.gnuplot.info) +:link(matlab,http://www.mathworks.com) +:link(rasmol,http://www.openrasmol.org) +:link(raster3d,http://www.bmsc.washington.edu/raster3d/raster3d.html) +:link(svg,http://www.w3.org/Graphics/SVG) +:link(ensight,http://www.ensight.com) +:link(ccell,http://www.cs.sandia.gov/~sjplimp/cell.html) +:link(vmd,http://www.ks.uiuc.edu/Research/vmd) + +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. + +:c,image(tools.jpg) diff --git a/doc/animate.html b/doc/animate.html new file mode 100644 index 0000000..336582e --- /dev/null +++ b/doc/animate.html @@ -0,0 +1,61 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

animate tool +

+

Purpose: +

+

Animate a series of image files. +

+

Description: +

+

The animate tool displays a GUI to view and animate a series of image +files. +

+

The animate constructor creates the GUI. The animation can be +controlled by the GUI widgets or by invoking the tool methods: play(), +stop(), next(), etc. The frame slider can be dragged to view a +desired frame. +

+

Image files can be in any format (PNG, GIF, BMP, etc) recognized by +the Python Image Library (PIL) installed in your Python. Various +Pizza.py visualization tools (raster, rasmol, etc) create such image +files. If a particular image format fails to load, your PIL +installation was linked without support for that format. Rebuild PIL, +and follow its install instructions. +

+

Usage: +

+
a = animate("image*.png")     create GUI to animate set of image files 
+
+
Actions (same as GUI widgets): 
+
+
a.first()		      go to first frame
+a.prev()                      go to previous frame
+a.back()                      play backwards from current frame to start
+a.stop()         	      stop on current frame		
+a.play()                      play from current frame to end
+a.next()		      go to next frame
+a.last()		      go to last frame 
+
+
a.frame(31)    	              set frame slider
+a.delay(0.4)     	      set delay slider 
+
+

Related tools: +

+

gl, raster, rasmol, +svg, vcr +

+

Prerequisites: +

+

Python Tkinter and PIL packages. +

+ diff --git a/doc/animate.txt b/doc/animate.txt new file mode 100644 index 0000000..b2507c1 --- /dev/null +++ b/doc/animate.txt @@ -0,0 +1,56 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +animate tool :h3 + +[Purpose:] + +Animate a series of image files. + +[Description:] + +The animate tool displays a GUI to view and animate a series of image +files. + +The animate constructor creates the GUI. The animation can be +controlled by the GUI widgets or by invoking the tool methods: play(), +stop(), next(), etc. The frame slider can be dragged to view a +desired frame. + +Image files can be in any format (PNG, GIF, BMP, etc) recognized by +the Python Image Library (PIL) installed in your Python. Various +Pizza.py visualization tools (raster, rasmol, etc) create such image +files. If a particular image format fails to load, your PIL +installation was linked without support for that format. Rebuild PIL, +and follow its install instructions. + +[Usage:] + +a = animate("image*.png") create GUI to animate set of image files :pre + +Actions (same as GUI widgets): :pre + +a.first() go to first frame +a.prev() go to previous frame +a.back() play backwards from current frame to start +a.stop() stop on current frame +a.play() play from current frame to end +a.next() go to next frame +a.last() go to last frame :pre + +a.frame(31) set frame slider +a.delay(0.4) set delay slider :pre + +[Related tools:] + +"gl"_gl.html, "raster"_raster.html, "rasmol"_rasmol.html, +"svg"_svg.html, "vcr"_vcr.html + +[Prerequisites:] + +Python Tkinter and PIL packages. diff --git a/doc/bdump.html b/doc/bdump.html new file mode 100644 index 0000000..61587ea --- /dev/null +++ b/doc/bdump.html @@ -0,0 +1,109 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

bdump tool +

+

Purpose: +

+

Read dump files with bond info. +

+

Description: +

+

The bdump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each entry contains info for a bond in a LAMMPS +simulation as is typically written by the dump local command in +LAMMPS. Other tools use bdump objects to extract bond info for +visualization, like the dump tool via its extra() method. +

+

The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. +

+

The map() method assigns names to columns of attributes. The +id,type,atom1,atom2 names must be assigned in order for bond info to +be extracted. +

+

The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). +

+
+ +

Normally, LAMMPS creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump local files is simple. Each snapshot is formatted as +follows: +

+
ITEM: TIMESTEP
+100
+ITEM: NUMBER OF ENTRIES
+32
+ITEM: ENTRIES
+1 1 5 10
+2 1 11 45
+3 2 6 8
+...
+N -3 23 456 
+
+

There are N lines following "ITEM: ENTRIES" where N is the number of +entries. Entries do not have to be listed in any particular order. +There can be a different number of entries in each snapshot. Each +line must contain the bond ID, type, and the 2 atom IDs of the atoms +in the bond, as specified by the map() command. +

+
+ +

Usage: +

+
b = bdump("dump.one")             read in one or more dump files
+b = bdump("dump.1 dump.2.gz")	  can be gzipped
+b = bdump("dump.*")		  wildcard expands to multiple files
+b = bdump("dump.*",0)		  two args = store filenames, but don't read 
+
+
  incomplete and duplicate snapshots are deleted
+  no column name assignment is performed 
+
+
time = b.next()             	  read next snapshot from dump files 
+
+
  used with 2-argument constructor to allow reading snapshots one-at-a-time
+  snapshot will be skipped only if another snapshot has same time stamp
+  return time stamp of snapshot read
+  return -1 if no snapshots left or last snapshot is incomplete
+  no column name assignment is performed 
+
+
b.map(1,"id",3,"x")               assign names to atom columns (1-N) 
+
+
  must assign id,type,atom1,atom2 
+
+
time,box,atoms,bonds,tris,lines = b.viz(index)   return list of viz objects 
+
+
  viz() returns line info for specified timestep index
+    can also call as viz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = NULL
+    atoms = NULL
+    bonds = id,type,atom1,atom2 for each line as 2d array
+    tris = NULL
+    lines = NULL 
+
+

Related tools: +

+

dump, gl, raster, svg +

+

Prerequisites: +

+

Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). +

+ diff --git a/doc/bdump.txt b/doc/bdump.txt new file mode 100644 index 0000000..cd736f7 --- /dev/null +++ b/doc/bdump.txt @@ -0,0 +1,104 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +bdump tool :h3 + +[Purpose:] + +Read dump files with bond info. + +[Description:] + +The bdump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each entry contains info for a bond in a LAMMPS +simulation as is typically written by the dump local command in +LAMMPS. Other tools use bdump objects to extract bond info for +visualization, like the dump tool via its extra() method. + +The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. + +The map() method assigns names to columns of attributes. The +id,type,atom1,atom2 names must be assigned in order for bond info to +be extracted. + +The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). + +:line + +Normally, "LAMMPS"_http://lammps.sandia.gov creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump local files is simple. Each snapshot is formatted as +follows: + +ITEM: TIMESTEP +100 +ITEM: NUMBER OF ENTRIES +32 +ITEM: ENTRIES +1 1 5 10 +2 1 11 45 +3 2 6 8 +... +N -3 23 456 :pre + +There are N lines following "ITEM: ENTRIES" where N is the number of +entries. Entries do not have to be listed in any particular order. +There can be a different number of entries in each snapshot. Each +line must contain the bond ID, type, and the 2 atom IDs of the atoms +in the bond, as specified by the map() command. + +:line + +[Usage:] + +b = bdump("dump.one") read in one or more dump files +b = bdump("dump.1 dump.2.gz") can be gzipped +b = bdump("dump.*") wildcard expands to multiple files +b = bdump("dump.*",0) two args = store filenames, but don't read :pre + + incomplete and duplicate snapshots are deleted + no column name assignment is performed :pre + +time = b.next() read next snapshot from dump files :pre + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed :pre + +b.map(1,"id",3,"x") assign names to atom columns (1-N) :pre + + must assign id,type,atom1,atom2 :pre + +time,box,atoms,bonds,tris,lines = b.viz(index) return list of viz objects :pre + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = NULL + atoms = NULL + bonds = id,type,atom1,atom2 for each line as 2d array + tris = NULL + lines = NULL :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). diff --git a/doc/cdata.html b/doc/cdata.html new file mode 100644 index 0000000..a1a5993 --- /dev/null +++ b/doc/cdata.html @@ -0,0 +1,224 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

cdata tool +

+

Purpose: +

+

Read, create, manipulate ChemCell data files. +

+

Description: +

+

The cdata tool reads and writes ChemCell data files which contain +particle and surface information. It enables the creation of +geometric models of cells for input to ChemCell. +

+

The cdata constructor reads in the specified LAMMPS data file. With +no argument, an empty cdata object is created which can have objects +added to it later, and then be written out. +

+

A cdata object or file contains "objects" of different types. Each +object has a unique user-assigned ID. Objects can be of several +types: "group", "triangles", "region", "facets", or "lines". A group +is a list of particles, all of the same type. Triangles define a +surface and include a list of vertices, triangle definitions, and +adjacent edge connections. A region is a geometric object that +defines a surface, such as a sphere. Facets are a CUBIT meshing +format that defines a set of vertices and triangles; it is converted +into a triangles entry. Lines are a collection of line segments. +

+

The box(), sphere(), shell(), cyl(), and cap() methods create a new +"region" object. The q() method sets triangulations factors that are +used when the region is converted into a triangulated surface for +output or visualization. +

+

The line() and ibox() methods create a "lines" object. +

+

The surf() method creates a "triangles" object from a region, using +the q() parameters. The surftri() method creats a new "triangles" +object from a list of triangle indices belonging to another surface. +The surfselect() method applies an if test to vertices and triangles +in another surface to choose a subset of them to form a new +"triangles" object. The bins() method sets the number of bins in x,y +when surfaces are binned for the purpose of creating particles +inside/outside the surface. +

+

The part(), part2d(), partarray(), and partring() methods create a +"group" of particles inside, outside, or on regions or triangulated +surfaces. Particles are 3d by default, or 2d if created on a surface. +The partsurf() method can be used to change the name of the surface 2d +particles are on, since that attribute is written to a file when the +particles are output. The creation of particles uses a random # +generator whose initial seed can be set via the seed() method. +

+

The random() method can be used to pick a random point on the surface +of a "region" or "triangles" object. The project() method maps +particles to the surface of a "region" or "triangulate" object. +

+

The center(), trans(), rotate(), and scale() methods are used to +perform a geometric transformation on a "group" of particles or a +"triangles" object. The union() method creates a new object of +"union" type from a list of objects. The join() method does the same +thing except all objects in the list must be of the same type and the +new object is also of that type. A join() can only be done for +"group", "triangles", or "line" objects. The delete(), rename(), and +copy() methods manipulate the IDs of previously defined objects. +

+

Be default all objects are selected when created. The select() and +unselect() methods can be used to select a subset of existing objects. +The write() and append() methods write out selected objects to a file. +

+

The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. gl, raster, svg tools). Only +selected objects are returned to the caller. A cdata file can be +visualzed similarly to a snapshots from a dump file. In the case of a +cdata file, there is only a single snapshot with index 0. +

+

Usage: +

+
c = cdata()			   create a datafile object
+c = cdata("mem.surf")              read in one or more ChemCell data files
+c = cdata("mem.part.gz mem.surf")  can be gzipped
+c = cdata("mem.*")		   wildcard expands to multiple files
+c.read("mem.surf")		   read in one or more data files 
+
+
  read() has same argument options as constructor
+  files contain the following kinds of entries, each of which becomes an object
+    particles, triangles, region, facets
+    particles is a list of particles -> becomes a group
+    triangles is 3 lists of vertices, triangles, connections -> becomes a surf
+    region is a ChemCell command defining a region -> becomes a region
+    facets is a CUBIT format of vertices and triangles -> becomes a surf
+  each object is assigned an ID = name in file
+  ID can be any number or string, must be unique 
+
+
c.box(ID,xlo,ylo,zlo,xhi,yhi,zhi)  create a box region
+c.sphere(ID,x,y,z,r)		   create a sphere region
+c.shell(ID,x,y,z,r,rinner)	   create a shell region
+c.cyl(ID,'x',c1,c2,r,lo,hi)	   create a axis-aligned cylinder region
+c.cap(ID,'x',c1,c2,r,lo,hi)	   create a axis-aligned capped-cylinder region
+c.q(ID,q1,q2,...)                  set region triangulation quality factors 
+
+
  box() can create an axis-aligned plane, line, or point if lo=hi
+  cyl() can create an axis-aligned circle if lo=hi
+  for cyl() and cap(): 'x' c1,c2 = y,z; 'y' c1,c2 = x,z; 'z' c,c2 = x,y
+  q's are size factors for region triangulation
+    for box, q1,q2,q3 = # of divisions per xyz of box
+    for sphere or shell, q1 = # of divisions per face edge of embedded cube
+    for cyl or cap, q1 = # of divisions per face edge of end cap, must be even
+                    q2 = # of divisions along length of cylinder 
+
+
c.line(ID,x1,y1,z1,x2,y2,z2)       create a line object with one line
+c.lbox(ID,xlo,ylo,zlo,xhi,yhi,zhi) create a line object with 12 box lines 
+
+
c.surf(ID,id-region)               create a triangulated surf from a region
+c.surftri(ID,id-surf,t1,t2,...)    create a tri surf from list of id-surf tris
+c.surfselect(ID,id-surf,test)      create a tri surf from test on id-surf tris
+c.bins(ID,nx,ny)                   set binning parameters for a surf 
+
+
  triangulation of a shell is just done for the outer sphere
+  for surftri(), one or more tri indices (1-N) must be listed
+  for surfselect(), test is string like "$x < 2.0 and $y > 0.0"
+  bins are used when particles are created inside/outside a surf 
+
+
c.part(ID,n,id_in)  	           create N particles inside object id_in
+c.part(ID,n,id_in,id_out)	   particles are also outside object id_out
+c.part2d(ID,n,id_on)               create 2d particles on object id_on
+c.partarray(ID,nx,nz,nz,x,y,z,dx,dy,dz)   create 3d grid of particles
+c.partring(ID,n,x,y,z,r,'x')              create ring of particles
+c.partsurf(ID,id_on)               change surf of existing 2d particle group
+c.seed(43284)			   set random # seed (def = 12345) 
+
+
  generate particle positions randomly (unless otherwise noted)
+  for part(), id_in and id_out must be IDs of a surf, region, or union object
+    inside a union object means inside any of the lower-level objects
+    outside a union object means outside all of the lower-level objects
+  for part2d(), id_on must be ID of a surf, region, or union object
+  for part2d(), particles will be written as 2d assigned to surf id_on
+  for partring(), ring axis is in 'x','y', or 'z' direction
+  partsurf() changes surf id_on for an existing 2d particle group 
+
+
x,n = c.random(ID)                 pick a random pt on surf of object ID
+c.project(ID,ID2,dx,dy,dz,eps,fg)  project particles in ID to surf of obj ID2 
+
+
  random() returns pt = [x,y,z] and normal vec n [nx,ny,nz]
+  for random(), ID can be surf or region obj
+  project() remaps particle coords in group ID
+    moves each particle along dir until they are within eps of surface
+    if no fg arg, dir = (dx,dy,dz)
+    if fg arg, dir = line from particle coord to (dx,dy,dz)
+    ID2 can be surf or region obj
+    particles are converted to 2d assigned to surf ID2 
+
+
c.center(ID,x,y,z)                 set center point of object
+c.trans(ID,dx,dy,dz)   	 	   translate an object
+c.rotate(ID,'x',1,1,0,'z',-1,1,0)  rotate an object
+c.scale(ID,sx,sy,sz)		   scale an object 
+
+
  objects must be surface or particle group, regions cannot be changed
+  for center(), default is middle of bounding box (set when obj is created)
+  for rotate(), set any 2 axes, must be orthogonal, 3rd is inferred
+    object is rotated so that it's current xyz axes point along new ones
+  rotation and scaling occur relative to center point 
+
+
c.union(ID,id1,id2,...)		   create a new union object from id1,id2,etc
+c.join(ID,id1,id2,...)             create a new object by joining id1,id2,etc
+c.delete(id1,id2,...)              delete one or more objects
+c.rename(ID,IDnew)                 rename an object
+c.copy(ID,IDnew) 	           create a new object as copy of old object 
+
+
  for union, all lower-level objects must be of surface, region, or union style
+  for join, all joined objects must be of same style: group, surf, line
+    new object is the same style 
+
+
c.select(id1,id2,...)              select one or more objects
+c.select()                         select all objects
+c.unselect(id1,id2,...)            unselect one or more objects
+c.unselect()                       unselect all objects 
+
+
  selection applies to write() and viz() 
+
+
c.write("file")			   write all selected objs to ChemCell file
+c.write("file",id1,id2,...)	   write only listed & selected objects to file
+c.append("file")		   append all selected objs to ChemCell file
+c.append("file",id1,id2,...)	   append only listed & selected objects 
+
+
  union objects are skipped, not written to file 
+
+
index,time,flag = c.iterator(0/1)          loop over single snapshot
+time,box,atoms,bonds,tris,lines = c.viz(index)   return list of viz objects 
+
+
  iterator() and viz() are compatible with equivalent dump calls
+  iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
+    index = timestep index within dump object (only 0 for data file)
+    time = timestep value (only 0 for data file)
+    flag = -1 when iteration is done, 1 otherwise
+  viz() returns info for selected objs for specified timestep index (must be 0)
+    time = 0
+    box = [xlo,ylo,zlo,xhi,yhi,zhi]
+    atoms = id,type,x,y,z for each atom as 2d array
+      NULL if atoms do not exist
+    bonds = NULL
+    tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array
+      regions are triangulated according to q() settings by viz()
+      NULL if surfaces do not exist
+    lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
+      NULL if lines do not exist
+    types are assigned to each object of same style in ascending order 
+
+

Related tools: +

+

clog, data, gl, +raster, svg +

+

Prerequisites: none +

+ diff --git a/doc/cdata.txt b/doc/cdata.txt new file mode 100644 index 0000000..e3ebbbf --- /dev/null +++ b/doc/cdata.txt @@ -0,0 +1,219 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +cdata tool :h3 + +[Purpose:] + +Read, create, manipulate ChemCell data files. + +[Description:] + +The cdata tool reads and writes ChemCell data files which contain +particle and surface information. It enables the creation of +geometric models of cells for input to ChemCell. + +The cdata constructor reads in the specified LAMMPS data file. With +no argument, an empty cdata object is created which can have objects +added to it later, and then be written out. + +A cdata object or file contains "objects" of different types. Each +object has a unique user-assigned ID. Objects can be of several +types: "group", "triangles", "region", "facets", or "lines". A group +is a list of particles, all of the same type. Triangles define a +surface and include a list of vertices, triangle definitions, and +adjacent edge connections. A region is a geometric object that +defines a surface, such as a sphere. Facets are a CUBIT meshing +format that defines a set of vertices and triangles; it is converted +into a triangles entry. Lines are a collection of line segments. + +The box(), sphere(), shell(), cyl(), and cap() methods create a new +"region" object. The q() method sets triangulations factors that are +used when the region is converted into a triangulated surface for +output or visualization. + +The line() and ibox() methods create a "lines" object. + +The surf() method creates a "triangles" object from a region, using +the q() parameters. The surftri() method creats a new "triangles" +object from a list of triangle indices belonging to another surface. +The surfselect() method applies an if test to vertices and triangles +in another surface to choose a subset of them to form a new +"triangles" object. The bins() method sets the number of bins in x,y +when surfaces are binned for the purpose of creating particles +inside/outside the surface. + +The part(), part2d(), partarray(), and partring() methods create a +"group" of particles inside, outside, or on regions or triangulated +surfaces. Particles are 3d by default, or 2d if created on a surface. +The partsurf() method can be used to change the name of the surface 2d +particles are on, since that attribute is written to a file when the +particles are output. The creation of particles uses a random # +generator whose initial seed can be set via the seed() method. + +The random() method can be used to pick a random point on the surface +of a "region" or "triangles" object. The project() method maps +particles to the surface of a "region" or "triangulate" object. + +The center(), trans(), rotate(), and scale() methods are used to +perform a geometric transformation on a "group" of particles or a +"triangles" object. The union() method creates a new object of +"union" type from a list of objects. The join() method does the same +thing except all objects in the list must be of the same type and the +new object is also of that type. A join() can only be done for +"group", "triangles", or "line" objects. The delete(), rename(), and +copy() methods manipulate the IDs of previously defined objects. + +Be default all objects are selected when created. The select() and +unselect() methods can be used to select a subset of existing objects. +The write() and append() methods write out selected objects to a file. + +The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. gl, raster, svg tools). Only +selected objects are returned to the caller. A cdata file can be +visualzed similarly to a snapshots from a dump file. In the case of a +cdata file, there is only a single snapshot with index 0. + +[Usage:] + +c = cdata() create a datafile object +c = cdata("mem.surf") read in one or more ChemCell data files +c = cdata("mem.part.gz mem.surf") can be gzipped +c = cdata("mem.*") wildcard expands to multiple files +c.read("mem.surf") read in one or more data files :pre + + read() has same argument options as constructor + files contain the following kinds of entries, each of which becomes an object + particles, triangles, region, facets + particles is a list of particles -> becomes a group + triangles is 3 lists of vertices, triangles, connections -> becomes a surf + region is a ChemCell command defining a region -> becomes a region + facets is a CUBIT format of vertices and triangles -> becomes a surf + each object is assigned an ID = name in file + ID can be any number or string, must be unique :pre + +c.box(ID,xlo,ylo,zlo,xhi,yhi,zhi) create a box region +c.sphere(ID,x,y,z,r) create a sphere region +c.shell(ID,x,y,z,r,rinner) create a shell region +c.cyl(ID,'x',c1,c2,r,lo,hi) create a axis-aligned cylinder region +c.cap(ID,'x',c1,c2,r,lo,hi) create a axis-aligned capped-cylinder region +c.q(ID,q1,q2,...) set region triangulation quality factors :pre + + box() can create an axis-aligned plane, line, or point if lo=hi + cyl() can create an axis-aligned circle if lo=hi + for cyl() and cap(): 'x' c1,c2 = y,z; 'y' c1,c2 = x,z; 'z' c,c2 = x,y + q's are size factors for region triangulation + for box, q1,q2,q3 = # of divisions per xyz of box + for sphere or shell, q1 = # of divisions per face edge of embedded cube + for cyl or cap, q1 = # of divisions per face edge of end cap, must be even + q2 = # of divisions along length of cylinder :pre + +c.line(ID,x1,y1,z1,x2,y2,z2) create a line object with one line +c.lbox(ID,xlo,ylo,zlo,xhi,yhi,zhi) create a line object with 12 box lines :pre + +c.surf(ID,id-region) create a triangulated surf from a region +c.surftri(ID,id-surf,t1,t2,...) create a tri surf from list of id-surf tris +c.surfselect(ID,id-surf,test) create a tri surf from test on id-surf tris +c.bins(ID,nx,ny) set binning parameters for a surf :pre + + triangulation of a shell is just done for the outer sphere + for surftri(), one or more tri indices (1-N) must be listed + for surfselect(), test is string like "$x < 2.0 and $y > 0.0" + bins are used when particles are created inside/outside a surf :pre + +c.part(ID,n,id_in) create N particles inside object id_in +c.part(ID,n,id_in,id_out) particles are also outside object id_out +c.part2d(ID,n,id_on) create 2d particles on object id_on +c.partarray(ID,nx,nz,nz,x,y,z,dx,dy,dz) create 3d grid of particles +c.partring(ID,n,x,y,z,r,'x') create ring of particles +c.partsurf(ID,id_on) change surf of existing 2d particle group +c.seed(43284) set random # seed (def = 12345) :pre + + generate particle positions randomly (unless otherwise noted) + for part(), id_in and id_out must be IDs of a surf, region, or union object + inside a union object means inside any of the lower-level objects + outside a union object means outside all of the lower-level objects + for part2d(), id_on must be ID of a surf, region, or union object + for part2d(), particles will be written as 2d assigned to surf id_on + for partring(), ring axis is in 'x','y', or 'z' direction + partsurf() changes surf id_on for an existing 2d particle group :pre + +x,n = c.random(ID) pick a random pt on surf of object ID +c.project(ID,ID2,dx,dy,dz,eps,fg) project particles in ID to surf of obj ID2 :pre + + random() returns pt = \[x,y,z\] and normal vec n \[nx,ny,nz\] + for random(), ID can be surf or region obj + project() remaps particle coords in group ID + moves each particle along dir until they are within eps of surface + if no fg arg, dir = (dx,dy,dz) + if fg arg, dir = line from particle coord to (dx,dy,dz) + ID2 can be surf or region obj + particles are converted to 2d assigned to surf ID2 :pre + +c.center(ID,x,y,z) set center point of object +c.trans(ID,dx,dy,dz) translate an object +c.rotate(ID,'x',1,1,0,'z',-1,1,0) rotate an object +c.scale(ID,sx,sy,sz) scale an object :pre + + objects must be surface or particle group, regions cannot be changed + for center(), default is middle of bounding box (set when obj is created) + for rotate(), set any 2 axes, must be orthogonal, 3rd is inferred + object is rotated so that it's current xyz axes point along new ones + rotation and scaling occur relative to center point :pre + +c.union(ID,id1,id2,...) create a new union object from id1,id2,etc +c.join(ID,id1,id2,...) create a new object by joining id1,id2,etc +c.delete(id1,id2,...) delete one or more objects +c.rename(ID,IDnew) rename an object +c.copy(ID,IDnew) create a new object as copy of old object :pre + + for union, all lower-level objects must be of surface, region, or union style + for join, all joined objects must be of same style: group, surf, line + new object is the same style :pre + +c.select(id1,id2,...) select one or more objects +c.select() select all objects +c.unselect(id1,id2,...) unselect one or more objects +c.unselect() unselect all objects :pre + + selection applies to write() and viz() :pre + +c.write("file") write all selected objs to ChemCell file +c.write("file",id1,id2,...) write only listed & selected objects to file +c.append("file") append all selected objs to ChemCell file +c.append("file",id1,id2,...) append only listed & selected objects :pre + + union objects are skipped, not written to file :pre + +index,time,flag = c.iterator(0/1) loop over single snapshot +time,box,atoms,bonds,tris,lines = c.viz(index) return list of viz objects :pre + + iterator() and viz() are compatible with equivalent dump calls + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = timestep index within dump object (only 0 for data file) + time = timestep value (only 0 for data file) + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected objs for specified timestep index (must be 0) + time = 0 + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = id,type,x,y,z for each atom as 2d array + NULL if atoms do not exist + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + regions are triangulated according to q() settings by viz() + NULL if surfaces do not exist + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + NULL if lines do not exist + types are assigned to each object of same style in ascending order :pre + +[Related tools:] + +"clog"_clog.html, "data"_data.html, "gl"_gl.html, +"raster"_raster.html, "svg"_svg.html + +[Prerequisites:] none diff --git a/doc/cfg.html b/doc/cfg.html new file mode 100644 index 0000000..5a99847 --- /dev/null +++ b/doc/cfg.html @@ -0,0 +1,60 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

cfg tool +

+

Purpose: +

+

Convert LAMMPS snapshots to AtomEye CFG format. +

+

Description: +

+

The cfg tool converts atom snapshots in a LAMMPS dump or data file to +the CFG format used by the AtomEye visualization tool. +

+ + +

The cfg constructor takes an object that stores atom snapshots +(dump, data) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. +

+

The one(), many(), and single() methods convert specific snapshots to +the CFG format and write them out. Optionally, a file prefix for the +CFG output files can also be specified. A ".cfg" suffix will be +appended to all output files. +

+

If your atom snapshots are not sorted by atom ID (e.g. because they +were written out by a parallel LAMMPS run), then you may want to sort +them before converting them to CFG files with this tool. This can be +done by "d = dump("tmp.dump"); d.sort()". This is because AtomEye +does not use atom IDs directly but infers an ID by the order of atoms +as they appear in the CFG file. +

+

Usage: +

+
c = cfg(d)		d = object containing atom coords (dump, data) 
+
+
c.one()                 write all snapshots to tmp.cfg
+c.one("new")            write all snapshots to new.cfg
+c.many()                write snapshots to tmp0000.cfg, tmp0001.cfg, etc
+c.many("new")           write snapshots to new0000.cfg, new0001.cfg, etc
+c.single(N)             write snapshot for timestep N to tmp.cfg 
+c.single(N,"file")      write snapshot for timestep N to file.cfg  
+
+

Related tools: +

+

data, dump, ensight, +vtk, xyz +

+

Prerequisites: none +

+ diff --git a/doc/cfg.txt b/doc/cfg.txt new file mode 100644 index 0000000..22efaeb --- /dev/null +++ b/doc/cfg.txt @@ -0,0 +1,55 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +cfg tool :h3 + +[Purpose:] + +Convert LAMMPS snapshots to AtomEye CFG format. + +[Description:] + +The cfg tool converts atom snapshots in a LAMMPS dump or data file to +the CFG format used by the "AtomEye"_atomeye visualization tool. + +:link(atomeye,http://164.107.79.177/Archive/Graphics/A) + +The cfg constructor takes an object that stores atom snapshots +("dump"_dump.html, "data"_data.html) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. + +The one(), many(), and single() methods convert specific snapshots to +the CFG format and write them out. Optionally, a file prefix for the +CFG output files can also be specified. A ".cfg" suffix will be +appended to all output files. + +If your atom snapshots are not sorted by atom ID (e.g. because they +were written out by a parallel LAMMPS run), then you may want to sort +them before converting them to CFG files with this tool. This can be +done by "d = dump("tmp.dump"); d.sort()". This is because AtomEye +does not use atom IDs directly but infers an ID by the order of atoms +as they appear in the CFG file. + +[Usage:] + +c = cfg(d) d = object containing atom coords (dump, data) :pre + +c.one() write all snapshots to tmp.cfg +c.one("new") write all snapshots to new.cfg +c.many() write snapshots to tmp0000.cfg, tmp0001.cfg, etc +c.many("new") write snapshots to new0000.cfg, new0001.cfg, etc +c.single(N) write snapshot for timestep N to tmp.cfg +c.single(N,"file") write snapshot for timestep N to file.cfg :pre + +[Related tools:] + +"data"_data.html, "dump"_dump.html, "ensight"_ensight.html, +"vtk"_vtk.html, "xyz"_xyz.html + +[Prerequisites:] none diff --git a/doc/chain.html b/doc/chain.html new file mode 100644 index 0000000..22857f2 --- /dev/null +++ b/doc/chain.html @@ -0,0 +1,72 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

chain tool +

+

Purpose: +

+

Create bead-spring chains for LAMMPS input. +

+

Description: +

+

The chain tool creates random, overlapping bead-spring (FENE) chains +and writes them out as a LAMMPS data file. They need to be simulated +with a soft potential in LAMMPS to un-overlap them before they form +a proper melt. +

+

The chain constructor uses the total number of monomers and the +Lennard-Jones reduced density to create a simulation box of the +appropriate size. Optionally, the box shape can also be specified. +

+

The build() method creates N chains, each with M monomers. It can be +invoked multiple times to create sets of chains with different +properties. The starting point of each chain is chosen randomly, as +is the position of subsequent monomers. The seed value sets the +random number generator used for coordinate generation. +

+

The mtype, btype, blen, and dmin settings affect how the chain and its +monomers are created. Dmin is the minimum distance allowed between a +new monomer and the monomer two before it, so it determines the +stiffness of the chain. Each monomer is assigned a molecule ID as it +is created, in accord with the id setting. +

+

Once N total monomers have been created, the ensemble of chains is +written to a LAMMPS data file via the write() method. +

+

Usage: +

+
c = chain(N,rho)            setup box with N monomers at reduced density rho
+c = chain(N,rho,1,1,2)	    x,y,z = aspect ratio of box (def = 1,1,1) 
+
+
c.seed = 48379              set random # seed (def = 12345)
+c.mtype = 2    		    set type of monomers (def = 1)
+c.btype = 1           	    set type of bonds (def = 1)
+c.blen = 0.97               set length of bonds (def = 0.97)
+c.dmin = 1.02               set min dist from i-1 to i+1 site (def = 1.02) 
+
+
c.id = "chain"              set molecule ID to chain # (default)
+c.id = "end1"               set molecule ID to count from one end of chain
+c.id = "end2"               set molecule ID to count from either end of chain 
+
+
c.build(100,10)		    create 100 chains, each of length 10 
+
+
  can be invoked multiple times interleaved with different settings
+  must fill box with total of N monomers 
+
+
c.write("data.file")        write out all built chains to LAMMPS data file 
+
+

Related tools: +

+

data, patch +

+

Prerequisites: none +

+ diff --git a/doc/chain.txt b/doc/chain.txt new file mode 100644 index 0000000..1b53589 --- /dev/null +++ b/doc/chain.txt @@ -0,0 +1,67 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +chain tool :h3 + +[Purpose:] + +Create bead-spring chains for LAMMPS input. + +[Description:] + +The chain tool creates random, overlapping bead-spring (FENE) chains +and writes them out as a LAMMPS data file. They need to be simulated +with a soft potential in LAMMPS to un-overlap them before they form +a proper melt. + +The chain constructor uses the total number of monomers and the +Lennard-Jones reduced density to create a simulation box of the +appropriate size. Optionally, the box shape can also be specified. + +The build() method creates N chains, each with M monomers. It can be +invoked multiple times to create sets of chains with different +properties. The starting point of each chain is chosen randomly, as +is the position of subsequent monomers. The seed value sets the +random number generator used for coordinate generation. + +The mtype, btype, blen, and dmin settings affect how the chain and its +monomers are created. Dmin is the minimum distance allowed between a +new monomer and the monomer two before it, so it determines the +stiffness of the chain. Each monomer is assigned a molecule ID as it +is created, in accord with the id setting. + +Once N total monomers have been created, the ensemble of chains is +written to a LAMMPS data file via the write() method. + +[Usage:] + +c = chain(N,rho) setup box with N monomers at reduced density rho +c = chain(N,rho,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1) :pre + +c.seed = 48379 set random # seed (def = 12345) +c.mtype = 2 set type of monomers (def = 1) +c.btype = 1 set type of bonds (def = 1) +c.blen = 0.97 set length of bonds (def = 0.97) +c.dmin = 1.02 set min dist from i-1 to i+1 site (def = 1.02) :pre + +c.id = "chain" set molecule ID to chain # (default) +c.id = "end1" set molecule ID to count from one end of chain +c.id = "end2" set molecule ID to count from either end of chain :pre + +c.build(100,10) create 100 chains, each of length 10 :pre + + can be invoked multiple times interleaved with different settings + must fill box with total of N monomers :pre + +c.write("data.file") write out all built chains to LAMMPS data file :pre + +[Related tools:] + +"data"_data.html, "patch"_patch.html + +[Prerequisites:] none diff --git a/doc/clog.html b/doc/clog.html new file mode 100644 index 0000000..61eca3f --- /dev/null +++ b/doc/clog.html @@ -0,0 +1,62 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

clog tool +

+

Purpose: +

+

Read ChemCell and SPPARKS log files and extract time-series data. +

+

Description: +

+

Read one or more ChemCell log files and combine their species +statistical data into long, named vectors (versus time). The vectors +can be used in Python for further processing and plotting, or they can +be output to a file. +

+

The log constructor reads one or more log files. If 2 arguments are +specified, a single file is specified, and it is assumed to contain +data for multiple runs, which are averaged. +

+

The nvec, nlen, and names values give the # of vectors, their length, +and names. The get() method returns one of more vectors as a Python +list. The write() method outputs the numeric vectors to a file. +

+

Usage: +

+
c = clog("file1")                    read in one or more log files
+c = clog("log1 log2.gz")             can be gzipped
+c = clog("file*")                    wildcard expands to multiple files
+c = clog("log.cell","Time")          2nd arg = start string for time section
+c = clog("log.cell","",0)            3rd arg = average all runs 
+
+
  incomplete and duplicate thermo entries are deleted
+  if specify 2nd arg, it delimits a time section
+  no 2nd arg or empty string, use default which is ChemCell specific
+  if specify any 3rd arg, average all runs, assume all start at time 0 
+
+
nvec = c.nvec                        # of vectors of thermo info
+nlen = c.nlen                        length of each vectors
+names = c.names                      list of vector names
+a,b,... = c.get("A","B",...)         return one or more vectors of values
+c.write("file.txt")	 	     write all vectors to a file
+c.write("file.txt","A","B",...)      write listed vectors to a file 
+
+
  get and write allow abbreviated (uniquely) vector names 
+
+

Related tools: +

+

plotview, gnu, log, +matlab +

+

Prerequisites: none +

+ diff --git a/doc/clog.txt b/doc/clog.txt new file mode 100644 index 0000000..9a175a0 --- /dev/null +++ b/doc/clog.txt @@ -0,0 +1,57 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +clog tool :h3 + +[Purpose:] + +Read ChemCell and SPPARKS log files and extract time-series data. + +[Description:] + +Read one or more ChemCell log files and combine their species +statistical data into long, named vectors (versus time). The vectors +can be used in Python for further processing and plotting, or they can +be output to a file. + +The log constructor reads one or more log files. If 2 arguments are +specified, a single file is specified, and it is assumed to contain +data for multiple runs, which are averaged. + +The nvec, nlen, and names values give the # of vectors, their length, +and names. The get() method returns one of more vectors as a Python +list. The write() method outputs the numeric vectors to a file. + +[Usage:] + +c = clog("file1") read in one or more log files +c = clog("log1 log2.gz") can be gzipped +c = clog("file*") wildcard expands to multiple files +c = clog("log.cell","Time") 2nd arg = start string for time section +c = clog("log.cell","",0) 3rd arg = average all runs :pre + + incomplete and duplicate thermo entries are deleted + if specify 2nd arg, it delimits a time section + no 2nd arg or empty string, use default which is ChemCell specific + if specify any 3rd arg, average all runs, assume all start at time 0 :pre + +nvec = c.nvec # of vectors of thermo info +nlen = c.nlen length of each vectors +names = c.names list of vector names +a,b,... = c.get("A","B",...) return one or more vectors of values +c.write("file.txt") write all vectors to a file +c.write("file.txt","A","B",...) write listed vectors to a file :pre + + get and write allow abbreviated (uniquely) vector names :pre + +[Related tools:] + +"plotview"_plotview.html, "gnu"_gnu.html, "log"_log.html, +"matlab"_matlab.html + +[Prerequisites:] none diff --git a/doc/data.html b/doc/data.html new file mode 100644 index 0000000..f6ec222 --- /dev/null +++ b/doc/data.html @@ -0,0 +1,107 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

data tool +

+

Purpose: +

+

Read, write, manipulate LAMMPS data files. +

+

Description: +

+

The data tool reads and writes LAMMPS data files. It also allows +their content to be accessed or modified. +

+

The data constructor reads in the specified LAMMPS data file. With no +argument, an empty data object is created which can have fields added +to it later, and then be written out. +

+

The map() method assigns names to different atom attributes by their +column number (1-N). The get() method extracts columns of information +from the specified section of the data file. +

+

The title, headers, and sections variables can be set directly. The +header values correspond to one-line definition that appear at the top +of the data file. The box size values should be set to a Python +tuple, e.g. +

+
d.headers["xlo xhi"] = (-30, 30) 
+
+

The section value should be a list of text lines, each of which +includes a newline at the end. +

+

The delete() method deletes a header or entire section of the data +file. The replace() method allows one column of a section to be +replaced with a vector of new values. The newxyz() methods replaces +the xyz coords of the "Atoms" section of the data file with xyz values +from the Nth snapshot of a dump object containing snapshots. +

+

The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. raster, svg tools). A data file +can be visualzed similarly to snapshots from a dump file. In the case +of a data file, there is only a single snapshot with index 0. +

+

The write() method outputs a LAMMPS data file. +

+

Usage: +

+
d = data("data.poly")            read a LAMMPS data file, can be gzipped
+d = data()			 create an empty data file 
+
+
d.map(1,"id",3,"x")              assign names to atom columns (1-N) 
+
+
coeffs = d.get("Pair Coeffs")    extract info from data file section
+q = d.get("Atoms",4) 
+
+
  1 arg = all columns returned as 2d array of floats
+  2 args = Nth column returned as vector of floats 
+
+
d.reorder("Atoms",1,3,2,4,5)     reorder columns (1-N) in a data file section 
+
+
  1,3,2,4,5 = new order of previous columns, can delete columns this way 
+
+
d.title = "My LAMMPS data file"	 set title of the data file
+d.headers["atoms"] = 1500        set a header value
+d.sections["Bonds"] = lines      set a section to list of lines (with newlines)
+d.delete("bonds")		 delete a keyword or section of data file
+d.delete("Bonds")
+d.replace("Atoms",5,vec)      	 replace Nth column of section with vector
+d.newxyz(dmp,1000)		 replace xyz in Atoms with xyz of snapshot N 
+
+
  newxyz assumes id,x,y,z are defined in both data and dump files
+    also replaces ix,iy,iz if they are defined 
+
+
index,time,flag = d.iterator(0/1)          loop over single data file snapshot
+time,box,atoms,bonds,tris,lines = d.viz(index)   return list of viz objects 
+
+
  iterator() and viz() are compatible with equivalent dump calls
+  iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
+    index = timestep index within dump object (only 0 for data file)
+    time = timestep value (only 0 for data file)
+    flag = -1 when iteration is done, 1 otherwise
+  viz() returns info for specified timestep index (must be 0)
+    time = 0
+    box = [xlo,ylo,zlo,xhi,yhi,zhi]
+    atoms = id,type,x,y,z for each atom as 2d array
+    bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array
+      NULL if bonds do not exist
+    tris = NULL
+    lines = NULL 
+
+
d.write("data.new")             write a LAMMPS data file 
+
+

Related tools: +

+

gl, raster, svg +

+

Prerequisites: none +

+ diff --git a/doc/data.txt b/doc/data.txt new file mode 100644 index 0000000..ac1c970 --- /dev/null +++ b/doc/data.txt @@ -0,0 +1,102 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +data tool :h3 + +[Purpose:] + +Read, write, manipulate LAMMPS data files. + +[Description:] + +The data tool reads and writes LAMMPS data files. It also allows +their content to be accessed or modified. + +The data constructor reads in the specified LAMMPS data file. With no +argument, an empty data object is created which can have fields added +to it later, and then be written out. + +The map() method assigns names to different atom attributes by their +column number (1-N). The get() method extracts columns of information +from the specified section of the data file. + +The title, headers, and sections variables can be set directly. The +header values correspond to one-line definition that appear at the top +of the data file. The box size values should be set to a Python +tuple, e.g. + +d.headers\["xlo xhi"\] = (-30, 30) :pre + +The section value should be a list of text lines, each of which +includes a newline at the end. + +The delete() method deletes a header or entire section of the data +file. The replace() method allows one column of a section to be +replaced with a vector of new values. The newxyz() methods replaces +the xyz coords of the "Atoms" section of the data file with xyz values +from the Nth snapshot of a dump object containing snapshots. + +The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. raster, svg tools). A data file +can be visualzed similarly to snapshots from a dump file. In the case +of a data file, there is only a single snapshot with index 0. + +The write() method outputs a LAMMPS data file. + +[Usage:] + +d = data("data.poly") read a LAMMPS data file, can be gzipped +d = data() create an empty data file :pre + +d.map(1,"id",3,"x") assign names to atom columns (1-N) :pre + +coeffs = d.get("Pair Coeffs") extract info from data file section +q = d.get("Atoms",4) :pre + + 1 arg = all columns returned as 2d array of floats + 2 args = Nth column returned as vector of floats :pre + +d.reorder("Atoms",1,3,2,4,5) reorder columns (1-N) in a data file section :pre + + 1,3,2,4,5 = new order of previous columns, can delete columns this way :pre + +d.title = "My LAMMPS data file" set title of the data file +d.headers\["atoms"\] = 1500 set a header value +d.sections\["Bonds"\] = lines set a section to list of lines (with newlines) +d.delete("bonds") delete a keyword or section of data file +d.delete("Bonds") +d.replace("Atoms",5,vec) replace Nth column of section with vector +d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N :pre + + newxyz assumes id,x,y,z are defined in both data and dump files + also replaces ix,iy,iz if they are defined :pre + +index,time,flag = d.iterator(0/1) loop over single data file snapshot +time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects :pre + + iterator() and viz() are compatible with equivalent dump calls + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = timestep index within dump object (only 0 for data file) + time = timestep value (only 0 for data file) + flag = -1 when iteration is done, 1 otherwise + viz() returns info for specified timestep index (must be 0) + time = 0 + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = id,type,x,y,z for each atom as 2d array + bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array + NULL if bonds do not exist + tris = NULL + lines = NULL :pre + +d.write("data.new") write a LAMMPS data file :pre + +[Related tools:] + +"gl"_gl.html, "raster"_raster.html, "svg"_svg.html + +[Prerequisites:] none diff --git a/doc/dump.html b/doc/dump.html new file mode 100644 index 0000000..d176805 --- /dev/null +++ b/doc/dump.html @@ -0,0 +1,236 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

dump tool +

+

Purpose: +

+

Read, write, manipulate dump files and particle attributes. +

+

Description: +

+

The dump tool reads one or more LAMMPS dump files, stores their +contents as a series of snapshots with 2d arrays of atom attributes, +and allows the values to be accessed and manipulated. Other tools use +dump objects to convert LAMMPS files to other formats or visualize the +atoms. +

+

The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. +

+

The map() method assigns names to columns of atom attributes. The +tselect() methods select one or more snapshots by their time stamp. +The delete() method deletes unselected timesteps so their memory is +freed up. This can be useful to do when reading snapshots +one-at-a-time for huge data sets. The aselect() methods selects atoms +within selected snapshots. The write() and scatter() methods write +selected snapshots and atoms to one or more files. +

+

The scale(), unscale(), wrap(), unwrap(), and owrap() methods change +the coordinates of all atoms with respect to the simulation box size. +The sort() method sorts atoms within snapshots by their ID or another +specified column. +

+

The set() method enables new or existing columns to be set to new +values. The minmax() method sets a column to an integer value between +the min and max values in another column; it can be used to create a +color map. The clone() method copies that column values at one +timestep to other timesteps on a per-atom basis. +

+

The time(), atom(), and vecs() methods return time or atom data as +vectors of values. +

+

The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. gl, raster, svg tools). You can +also use the iterator() method in your scripts to loop over selected +snapshots. The atype setting determines what atom column is returned +as the atom "type" by the viz() method. The bonds() method can be +used to create a static list of bonds that are returned by the viz() +method. +

+
+ +

Normally, LAMMPS creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: +

+
ITEM: TIMESTEP
+100
+ITEM: NUMBER OF ATOMS
+32
+ITEM: BOX BOUNDS
+0 3.35919
+0 3.35919
+0 7.50
+ITEM: ATOMS
+1 1 0 0 0
+2 1 0.25 0.25 0
+3 1 0.25 0 0.25
+...
+N 3 0.7 0.5 0.6 
+
+

The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. As the dump tool commands +indicate, atoms do not have to be listed in any particular order. +There can be a different number of atoms in each snapshot. The values +on each atom line are "ID type x y z" by default, but other quantities +can be listed in any desired order. The map() command can be used to +specify the ordering if it is not the default. +

+
+ +

Usage: +

+
d = dump("dump.one")              read in one or more dump files
+d = dump("dump.1 dump.2.gz")	  can be gzipped
+d = dump("dump.*")		  wildcard expands to multiple files
+d = dump("dump.*",0)		  two args = store filenames, but don't read 
+
+
  incomplete and duplicate snapshots are deleted
+  atoms will be unscaled if stored in files as scaled 
+
+
time = d.next()             	  read next snapshot from dump files 
+
+
  used with 2-argument constructor to allow reading snapshots one-at-a-time
+  snapshot will be skipped only if another snapshot has same time stamp
+  return time stamp of snapshot read
+  return -1 if no snapshots left or last snapshot is incomplete
+  no column name assignment or unscaling is performed 
+
+
d.map(1,"id",3,"x")               assign names to atom columns (1-N) 
+
+
  not needed if dump file is self-describing 
+
+
d.tselect.all()			  select all timesteps
+d.tselect.one(N)		  select only timestep N
+d.tselect.none()		  deselect all timesteps
+d.tselect.skip(M)		  select every Mth step
+d.tselect.test("$t >= 100 and $t < 10000")      select matching timesteps
+d.delete()	      	      	  delete non-selected timesteps 
+
+
  selecting a timestep also selects all atoms in the timestep
+  skip() and test() only select from currently selected timesteps
+  test() uses a Python Boolean expression with $t for timestep value
+    Python comparison syntax: == != < > <= >= and or 
+
+
d.aselect.all()	      	                      select all atoms in all steps
+d.aselect.all(N)      	                      select all atoms in one step
+d.aselect.test("$id > 100 and $type == 2")    select match atoms in all steps
+d.aselect.test("$id > 100 and $type == 2",N)  select matching atoms in one step 
+
+
  all() with no args selects atoms from currently selected timesteps
+  test() with one arg selects atoms from currently selected timesteps
+  test() sub-selects from currently selected atoms
+  test() uses a Python Boolean expression with $ for atom attributes
+    Python comparison syntax: == != < > <= >= and or
+    $name must end with a space 
+
+
d.write("file")	   	           write selected steps/atoms to dump file
+d.write("file",head,app)	   write selected steps/atoms to dump file
+d.scatter("tmp")		   write selected steps/atoms to multiple files 
+
+
  write() can be specified with 2 additional flags
+    headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
+  scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc 
+
+
d.scale() 	    	  	   scale x,y,z to 0-1 for all timesteps
+d.scale(100)			   scale atom coords for timestep N
+d.unscale()			   unscale x,y,z to box size to all timesteps
+d.unscale(1000)			   unscale atom coords for timestep N
+d.wrap()			   wrap x,y,z into periodic box via ix,iy,iz
+d.unwrap()			   unwrap x,y,z out of box via ix,iy,iz
+d.owrap("other")		   wrap x,y,z to same image as another atom
+d.sort()              	  	   sort atoms by atom ID in all selected steps
+d.sort("x")            	  	   sort atoms by column value in all steps
+d.sort(1000)			   sort atoms in timestep N 
+
+
  scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
+  wrap(), unwrap(), owrap() require ix,iy,iz be defined
+  owrap() requires a column be defined which contains an atom ID
+    name of that column is the argument to owrap()
+    x,y,z for each atom is wrapped to same image as the associated atom ID
+    useful for wrapping all molecule's atoms the same so it is contiguous 
+
+
m1,m2 = d.minmax("type")               find min/max values for a column
+d.set("$ke = $vx * $vx + $vy * $vy")   set a column to a computed value
+d.setv("type",vector)                  set a column to a vector of values
+d.spread("ke",N,"color")	       2nd col = N ints spread over 1st col
+d.clone(1000,"color")	       	       clone timestep N values to other steps 
+
+
  minmax() operates on selected timesteps and atoms
+  set() operates on selected timesteps and atoms
+    left hand side column is created if necessary
+    left-hand side column is unset or unchanged for non-selected atoms
+    equation is in Python syntax
+    use $ for column names, $name must end with a space
+  setv() operates on selected timesteps and atoms
+    if column label does not exist, column is created
+    values in vector are assigned sequentially to atoms, so may want to sort()
+    length of vector must match # of selected atoms
+  spread() operates on selected timesteps and atoms
+    min and max are found for 1st specified column across all selected atoms
+    atom's value is linear mapping (1-N) between min and max
+    that is stored in 2nd column (created if needed)
+    useful for creating a color map
+  clone() operates on selected timesteps and atoms
+    values at every timestep are set to value at timestep N for that atom ID
+    useful for propagating a color map 
+
+
t = d.time()  	     	       	   return vector of selected timestep values
+fx,fy,... = d.atom(100,"fx","fy",...)   return vector(s) for atom ID N
+fx,fy,... = d.vecs(1000,"fx","fy",...)  return vector(s) for timestep N 
+
+
  atom() returns vectors with one value for each selected timestep
+  vecs() returns vectors with one value for each selected atom in the timestep 
+
+
index,time,flag = d.iterator(0/1)          loop over dump snapshots
+time,box,atoms,bonds,tris,lines = d.viz(index)   return list of viz objects
+d.atype = "color"                          set column returned as "type" by viz
+d.extra(obj)				   extract bond/tri/line info from obj 
+
+
  iterator() loops over selected timesteps
+  iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
+    index = index within dump object (0 to # of snapshots)
+    time = timestep value
+    flag = -1 when iteration is done, 1 otherwise
+  viz() returns info for selected atoms for specified timestep index
+    can also call as viz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
+    atoms = id,type,x,y,z for each atom as 2d array
+    bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array
+      if extra() used to define bonds, else NULL
+    tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array
+      if extra() used to define tris, else NULL
+    lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
+      if extra() used to define lines, else NULL
+  atype is column name viz() will return as atom type (def = "type")
+  extra() extracts bonds/tris/lines from obj each time viz() is called
+    obj can be data object for bonds, cdata object for tris and lines, 
+      bdump object for bonds, mdump object for tris, ldump object for lines 
+
+

Related tools: +

+

data, gl, mdump, tdump, +raster, svg +

+

Prerequisites: +

+

Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). +

+ diff --git a/doc/dump.txt b/doc/dump.txt new file mode 100644 index 0000000..a10f8b2 --- /dev/null +++ b/doc/dump.txt @@ -0,0 +1,231 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +dump tool :h3 + +[Purpose:] + +Read, write, manipulate dump files and particle attributes. + +[Description:] + +The dump tool reads one or more LAMMPS dump files, stores their +contents as a series of snapshots with 2d arrays of atom attributes, +and allows the values to be accessed and manipulated. Other tools use +dump objects to convert LAMMPS files to other formats or visualize the +atoms. + +The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. + +The map() method assigns names to columns of atom attributes. The +tselect() methods select one or more snapshots by their time stamp. +The delete() method deletes unselected timesteps so their memory is +freed up. This can be useful to do when reading snapshots +one-at-a-time for huge data sets. The aselect() methods selects atoms +within selected snapshots. The write() and scatter() methods write +selected snapshots and atoms to one or more files. + +The scale(), unscale(), wrap(), unwrap(), and owrap() methods change +the coordinates of all atoms with respect to the simulation box size. +The sort() method sorts atoms within snapshots by their ID or another +specified column. + +The set() method enables new or existing columns to be set to new +values. The minmax() method sets a column to an integer value between +the min and max values in another column; it can be used to create a +color map. The clone() method copies that column values at one +timestep to other timesteps on a per-atom basis. + +The time(), atom(), and vecs() methods return time or atom data as +vectors of values. + +The iterator() and viz() methods are called by Pizza.py tools that +visualize snapshots of atoms (e.g. gl, raster, svg tools). You can +also use the iterator() method in your scripts to loop over selected +snapshots. The atype setting determines what atom column is returned +as the atom "type" by the viz() method. The bonds() method can be +used to create a static list of bonds that are returned by the viz() +method. + +:line + +Normally, "LAMMPS"_http://lammps.sandia.gov creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: + +ITEM: TIMESTEP +100 +ITEM: NUMBER OF ATOMS +32 +ITEM: BOX BOUNDS +0 3.35919 +0 3.35919 +0 7.50 +ITEM: ATOMS +1 1 0 0 0 +2 1 0.25 0.25 0 +3 1 0.25 0 0.25 +... +N 3 0.7 0.5 0.6 :pre + +The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. As the dump tool commands +indicate, atoms do not have to be listed in any particular order. +There can be a different number of atoms in each snapshot. The values +on each atom line are "ID type x y z" by default, but other quantities +can be listed in any desired order. The map() command can be used to +specify the ordering if it is not the default. + +:line + +[Usage:] + +d = dump("dump.one") read in one or more dump files +d = dump("dump.1 dump.2.gz") can be gzipped +d = dump("dump.*") wildcard expands to multiple files +d = dump("dump.*",0) two args = store filenames, but don't read :pre + + incomplete and duplicate snapshots are deleted + atoms will be unscaled if stored in files as scaled :pre + +time = d.next() read next snapshot from dump files :pre + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment or unscaling is performed :pre + +d.map(1,"id",3,"x") assign names to atom columns (1-N) :pre + + not needed if dump file is self-describing :pre + +d.tselect.all() select all timesteps +d.tselect.one(N) select only timestep N +d.tselect.none() deselect all timesteps +d.tselect.skip(M) select every Mth step +d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps +d.delete() delete non-selected timesteps :pre + + selecting a timestep also selects all atoms in the timestep + skip() and test() only select from currently selected timesteps + test() uses a Python Boolean expression with $t for timestep value + Python comparison syntax: == != < > <= >= and or :pre + +d.aselect.all() select all atoms in all steps +d.aselect.all(N) select all atoms in one step +d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps +d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step :pre + + all() with no args selects atoms from currently selected timesteps + test() with one arg selects atoms from currently selected timesteps + test() sub-selects from currently selected atoms + test() uses a Python Boolean expression with $ for atom attributes + Python comparison syntax: == != < > <= >= and or + $name must end with a space :pre + +d.write("file") write selected steps/atoms to dump file +d.write("file",head,app) write selected steps/atoms to dump file +d.scatter("tmp") write selected steps/atoms to multiple files :pre + + write() can be specified with 2 additional flags + headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append + scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc :pre + +d.scale() scale x,y,z to 0-1 for all timesteps +d.scale(100) scale atom coords for timestep N +d.unscale() unscale x,y,z to box size to all timesteps +d.unscale(1000) unscale atom coords for timestep N +d.wrap() wrap x,y,z into periodic box via ix,iy,iz +d.unwrap() unwrap x,y,z out of box via ix,iy,iz +d.owrap("other") wrap x,y,z to same image as another atom +d.sort() sort atoms by atom ID in all selected steps +d.sort("x") sort atoms by column value in all steps +d.sort(1000) sort atoms in timestep N :pre + + scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms + wrap(), unwrap(), owrap() require ix,iy,iz be defined + owrap() requires a column be defined which contains an atom ID + name of that column is the argument to owrap() + x,y,z for each atom is wrapped to same image as the associated atom ID + useful for wrapping all molecule's atoms the same so it is contiguous :pre + +m1,m2 = d.minmax("type") find min/max values for a column +d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value +d.setv("type",vector) set a column to a vector of values +d.spread("ke",N,"color") 2nd col = N ints spread over 1st col +d.clone(1000,"color") clone timestep N values to other steps :pre + + minmax() operates on selected timesteps and atoms + set() operates on selected timesteps and atoms + left hand side column is created if necessary + left-hand side column is unset or unchanged for non-selected atoms + equation is in Python syntax + use $ for column names, $name must end with a space + setv() operates on selected timesteps and atoms + if column label does not exist, column is created + values in vector are assigned sequentially to atoms, so may want to sort() + length of vector must match # of selected atoms + spread() operates on selected timesteps and atoms + min and max are found for 1st specified column across all selected atoms + atom's value is linear mapping (1-N) between min and max + that is stored in 2nd column (created if needed) + useful for creating a color map + clone() operates on selected timesteps and atoms + values at every timestep are set to value at timestep N for that atom ID + useful for propagating a color map :pre + +t = d.time() return vector of selected timestep values +fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N +fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N :pre + + atom() returns vectors with one value for each selected timestep + vecs() returns vectors with one value for each selected atom in the timestep :pre + +index,time,flag = d.iterator(0/1) loop over dump snapshots +time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects +d.atype = "color" set column returned as "type" by viz +d.extra(obj) extract bond/tri/line info from obj :pre + + iterator() loops over selected timesteps + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = index within dump object (0 to # of snapshots) + time = timestep value + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected atoms for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\] + atoms = id,type,x,y,z for each atom as 2d array + bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array + if extra() used to define bonds, else NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + if extra() used to define tris, else NULL + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + if extra() used to define lines, else NULL + atype is column name viz() will return as atom type (def = "type") + extra() extracts bonds/tris/lines from obj each time viz() is called + obj can be data object for bonds, cdata object for tris and lines, + bdump object for bonds, mdump object for tris, ldump object for lines :pre + +[Related tools:] + +"data"_data.html, "gl"_gl.html, "mdump"_mdump.html, "tdump"_tdump.html, +"raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). diff --git a/doc/ensight.html b/doc/ensight.html new file mode 100644 index 0000000..c93dd51 --- /dev/null +++ b/doc/ensight.html @@ -0,0 +1,78 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

ensight tool +

+

Purpose: +

+

Convert LAMMPS snapshots or meshes to Ensight format. +

+

Description: +

+

The ensight tool converts atom snapshots in a LAMMPS dump or data file +or mesh data from a mesh file to the format used by the Ensight +visualization package. See the dump or +mdump tools for info about the format of these files and +what data they contain. +

+ + +

The ensight constructor takes an object that stores atom or mesh +snapshots (dump, data) as its first argument. +The atom snapshots must have "id", "type", "x", "y", and "z" defined; +see the map() methods of those tools. +

+

The one(), many(), and single() methods convert specific snapshots to +Ensight format and write them out. These methods take a file prefix +as an optional first argument; the prefix "tmp" will be used if not +specified. These methods all create a prefix.case file which is used +by Ensight to define the format and list all associated files. One or +more prefix*.xyz files are also produced which contain atom +coordinates sorted by atom type. If additional pairs of arguments are +specified, attributes from the shapshot data (atoms or elements) can +be written into Ensight variable files, and used by Ensight as display +attributes for the atoms or mesh elements. +

+

Usage: +

+
e = ensight(d)	     d = object with atoms or elements (dump,data,mdump)
+e.change = 1         set to 1 if element nodal xyz change with time (def = 0)
+e.maxtype = 10       max particle type, set if query to data will be bad 
+
+
e.one()
+e.one("new")
+e.one("cns","Centro","eng","Energy")
+e.one("new","cns","Centro","eng","Energy")
+                     write all snapshots as an Ensight data set
+                     Ensight header file = tmp.case (no 1st arg) or new.case
+                     Ensight coord file = tmp.xyz or new.xyz
+                     additional pairs of args create auxiliary files:
+                       tmp.cns, tmp.eng or new.cns, new.eng
+                     cns,eng = column name in dump file and file name suffix
+                     Centro,Energy = Ensight name for the variable 
+
+
e.increment()        same args as one(), but process dump out-of-core 
+
+
e.many()             same args as one(), but create multiple Ensight files
+                     tmp0000.xyz, tmp0001.xyz, etc
+                     new0000.cns, new0001.cns, etc
+                     new0000.eng, new0001.eng, etc 
+
+
e.single(N)          same args as one() prepended by N, but write a single snap 
+
+

Related tools: +

+

cfg, data, dump, +mdump, vtk, xyz +

+

Prerequisites: none +

+ diff --git a/doc/ensight.txt b/doc/ensight.txt new file mode 100644 index 0000000..be66162 --- /dev/null +++ b/doc/ensight.txt @@ -0,0 +1,73 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +ensight tool :h3 + +[Purpose:] + +Convert LAMMPS snapshots or meshes to Ensight format. + +[Description:] + +The ensight tool converts atom snapshots in a LAMMPS dump or data file +or mesh data from a mesh file to the format used by the "Ensight +visualization package"_ensight. See the "dump"_dump.html or +"mdump"_mdump.html tools for info about the format of these files and +what data they contain. + +:link(ensight,http://www.ensight.com) + +The ensight constructor takes an object that stores atom or mesh +snapshots ("dump"_dump.html, "data"_data.html) as its first argument. +The atom snapshots must have "id", "type", "x", "y", and "z" defined; +see the map() methods of those tools. + +The one(), many(), and single() methods convert specific snapshots to +Ensight format and write them out. These methods take a file prefix +as an optional first argument; the prefix "tmp" will be used if not +specified. These methods all create a prefix.case file which is used +by Ensight to define the format and list all associated files. One or +more prefix*.xyz files are also produced which contain atom +coordinates sorted by atom type. If additional pairs of arguments are +specified, attributes from the shapshot data (atoms or elements) can +be written into Ensight variable files, and used by Ensight as display +attributes for the atoms or mesh elements. + +[Usage:] + +e = ensight(d) d = object with atoms or elements (dump,data,mdump) +e.change = 1 set to 1 if element nodal xyz change with time (def = 0) +e.maxtype = 10 max particle type, set if query to data will be bad :pre + +e.one() +e.one("new") +e.one("cns","Centro","eng","Energy") +e.one("new","cns","Centro","eng","Energy") + write all snapshots as an Ensight data set + Ensight header file = tmp.case (no 1st arg) or new.case + Ensight coord file = tmp.xyz or new.xyz + additional pairs of args create auxiliary files: + tmp.cns, tmp.eng or new.cns, new.eng + cns,eng = column name in dump file and file name suffix + Centro,Energy = Ensight name for the variable :pre + +e.increment() same args as one(), but process dump out-of-core :pre + +e.many() same args as one(), but create multiple Ensight files + tmp0000.xyz, tmp0001.xyz, etc + new0000.cns, new0001.cns, etc + new0000.eng, new0001.eng, etc :pre + +e.single(N) same args as one() prepended by N, but write a single snap :pre + +[Related tools:] + +"cfg"_cfg.html, "data"_data.html, "dump"_dump.html, +"mdump"_mdump.html, "vtk"_vtk.html, "xyz"_xyz.html + +[Prerequisites:] none diff --git a/doc/gl.html b/doc/gl.html new file mode 100644 index 0000000..4e2f20e --- /dev/null +++ b/doc/gl.html @@ -0,0 +1,187 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

gl tool +

+

Purpose: +

+

3d interactive visualization via OpenGL. +

+

Description: +

+

The gl tool does visualizes LAMMPS or ChemCell snapshots or data files +and mesh files via OpenGL graphics calls. The interface to OpenGL is +provided to Python by the open-source PyOpenGL +toolkit. To do interactive +visualization, consider using this tool in conjunction with the +vcr tool. +

+

The gl constructor takes a data object containing atom or mesh +snapshots as an argument (dump, data, +cdata, mdump). +

+

The show() method displays a single image of the selected atoms or +triangles of snapshot N and saves it as image.png. While an image is +displayed, the view can be changed directly by using the mouse buttons +in the OpenGl window to translate (left), rotate (middle), or zoom +(right) the image. However, these mouse changes are not permanent, +unless the corresponding trans(), rotate(), and zoom() methods are +invoked. The all() method loops thru all selected snapshots, +displaying each one in turn. The resulting image files are saved to +image0000.png, image0001.png, etc. The prefix "image" can be changed +via the file setting. +

+

The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the GL image should roughly +fill the window and be centered. +

+

Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. +

+

The acol(), arad(), bcol(), brad(), tcol(), and tfill() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the dump tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. +

+

Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from this WWW page which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. +

+ + +

The visual quality of atom spheres can be set via the q() method. The +axis() method toggles whether xyz axes are displayed in the OpenGL +window. Red is the +x axis, green is +y, and blue is +z. The ortho() +method toggles between an orthographic and perspective display of the +snapshot. The clip() method can be used to narrow the amount of data +that is visualized. The reload() method is needed if you change the +selection attributes of the underlying data assigned to the +gl tool, such as via the dump tool's methods. +These changes will not be visible in the OpenGL window until the data +is reloaded. +

+

Usage: +

+
g = gl(d)                   create OpenGL display for data in d 
+
+
  d = atom snapshot object (dump, data) 
+
+
g.bg("black")               set background color (def = "black")
+g.size(N)		    set image size to NxN
+g.size(N,M)		    set image size to NxM
+g.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
+g.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
+g.zoom(0.5)                 scale image by factor (def = 1)
+g.box(0/1/2)                0/1/2 = none/variable/fixed box
+g.box(0/1/2,"green")        set box color
+g.box(0/1/2,"red",4)        set box edge thickness
+g.file = "image"            file prefix for created images (def = "image") 
+
+
g.show(N)                   show image of snapshot at timestep N 
+
+
g.all()                     make images of all selected snapshots
+g.all(P)                    images of all, start file label at P
+g.all(N,M,P)                make M images of snapshot N, start label at P 
+
+
g.pan(60,135,1.0,40,135,1.5)    pan during all() operation
+g.pan()                         no pan during all() (default) 
+
+
  args = z theta, azimuthal phi, zoom factor at beginning and end
+  values at each step are interpolated between beginning and end values 
+
+
g.select = "$x > %g*3.0"    string to pass to d.aselect.test() during all()
+g.select = ""               no extra aselect (default) 
+
+
  %g varies from 0.0 to 1.0 from beginning to end of all() 
+
+
g.acol(2,"green")		   set atom colors by atom type (1-N)
+g.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+g.acol(0,"blue")	           2nd arg = one color or list of colors
+g.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
+g.acol(range(10),"loop")           assign colors in loop, randomly ordered 
+
+
  if 1st arg is 0, set all types to 2nd arg
+  if list of types has a 0 (e.g. range(10)), +1 is added to each value
+  interpolate means colors blend smoothly from one value to the next 
+
+
g.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol() 
+
+
g.bcol()			   set bond color, same args as acol()
+g.brad()			   set bond thickness, same args as arad() 
+
+
g.tcol()			   set triangle color, same args as acol()
+g.tfill()			   set triangle fill, 0 fill, 1 line, 2 both 
+
+
g.lcol()                           set line color, same args as acol()
+g.lrad()                           set line thickness, same args as arad() 
+
+
g.adef()                           set atom/bond/tri/line properties to default
+g.bdef()			   default = "loop" for colors, 0.45 for radii
+g.tdef()  			   default = 0.25 for bond/line thickness
+g.ldef()  			   default = 0 fill 
+
+
  by default 100 types are assigned
+  if atom/bond/tri/line has type > # defined properties, is an error 
+
+
from vizinfo import colors         access color list
+print colors                       list defined color names and RGB values
+colors["nickname"] = [R,G,B]       set new RGB values from 0 to 255 
+
+
  140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc 
+
+
Settings specific to gl tool: 
+
+
g.q(10)                     set quality of image (def = 5)
+g.axis(0/1)                 turn xyz axes off/on
+g.ortho(0/1)                perspective (0) vs orthographic (1) view
+g.clip('xlo',0.25)          clip in xyz from lo/hi at box fraction (0-1)
+g.reload()                  force all data to be reloaded
+g.cache = 0/1               turn off/on GL cache lists (def = on)
+theta,phi,x,y,scale,up = g.gview()   grab all current view parameters
+g.sview(theta,phi,x,y,scale,up)      set all view parameters 
+
+
  data reload is necessary if dump selection is used to change the data
+  cache lists usually improve graphics performance
+  gview returns values to use in other commands:
+    theta,phi are args to rotate()
+    x,y are args to shift()
+    scale is arg to zoom()
+    up is a 3-vector arg to sview() 
+
+

Related tools: +

+

dump, rasmol, raster, +svg, vcr, vmd +

+

Prerequisites: +

+

Python PyOpenGL and PIL packages. +

+ diff --git a/doc/gl.txt b/doc/gl.txt new file mode 100644 index 0000000..a7a1ba8 --- /dev/null +++ b/doc/gl.txt @@ -0,0 +1,182 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +gl tool :h3 + +[Purpose:] + +3d interactive visualization via OpenGL. + +[Description:] + +The gl tool does visualizes LAMMPS or ChemCell snapshots or data files +and mesh files via OpenGL graphics calls. The interface to OpenGL is +provided to Python by the open-source "PyOpenGL +toolkit"_http://pyopengl.sourceforge.net. To do interactive +visualization, consider using this tool in conjunction with the +"vcr"_vcr.html tool. + +The gl constructor takes a data object containing atom or mesh +snapshots as an argument ("dump"_dump.html, "data"_data.html, +"cdata"_cdata.html, "mdump"_mdump.html). + +The show() method displays a single image of the selected atoms or +triangles of snapshot N and saves it as image.png. While an image is +displayed, the view can be changed directly by using the mouse buttons +in the OpenGl window to translate (left), rotate (middle), or zoom +(right) the image. However, these mouse changes are not permanent, +unless the corresponding trans(), rotate(), and zoom() methods are +invoked. The all() method loops thru all selected snapshots, +displaying each one in turn. The resulting image files are saved to +image0000.png, image0001.png, etc. The prefix "image" can be changed +via the file setting. + +The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the GL image should roughly +fill the window and be centered. + +Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. + +The acol(), arad(), bcol(), brad(), tcol(), and tfill() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the "dump"_dump.html tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. + +Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from "this WWW page"_colortable which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. + +:link(colortable,http://www.oreilly.com/catalog/wdnut/excerpt/color_names.html) + +The visual quality of atom spheres can be set via the q() method. The +axis() method toggles whether xyz axes are displayed in the OpenGL +window. Red is the +x axis, green is +y, and blue is +z. The ortho() +method toggles between an orthographic and perspective display of the +snapshot. The clip() method can be used to narrow the amount of data +that is visualized. The reload() method is needed if you change the +selection attributes of the underlying data assigned to the +"gl"_gl.html tool, such as via the "dump"_dump.html tool's methods. +These changes will not be visible in the OpenGL window until the data +is reloaded. + +[Usage:] + +g = gl(d) create OpenGL display for data in d :pre + + d = atom snapshot object (dump, data) :pre + +g.bg("black") set background color (def = "black") +g.size(N) set image size to NxN +g.size(N,M) set image size to NxM +g.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +g.shift(x,y) translate by x,y pixels in view window (def = 0,0) +g.zoom(0.5) scale image by factor (def = 1) +g.box(0/1/2) 0/1/2 = none/variable/fixed box +g.box(0/1/2,"green") set box color +g.box(0/1/2,"red",4) set box edge thickness +g.file = "image" file prefix for created images (def = "image") :pre + +g.show(N) show image of snapshot at timestep N :pre + +g.all() make images of all selected snapshots +g.all(P) images of all, start file label at P +g.all(N,M,P) make M images of snapshot N, start label at P :pre + +g.pan(60,135,1.0,40,135,1.5) pan during all() operation +g.pan() no pan during all() (default) :pre + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values :pre + +g.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +g.select = "" no extra aselect (default) :pre + + %g varies from 0.0 to 1.0 from beginning to end of all() :pre + +g.acol(2,"green") set atom colors by atom type (1-N) +g.acol(\[2,4\],\["red","blue"\]) 1st arg = one type or list of types +g.acol(0,"blue") 2nd arg = one color or list of colors +g.acol(range(20),\["red","blue"\]) if list lengths unequal, interpolate +g.acol(range(10),"loop") assign colors in loop, randomly ordered :pre + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next :pre + +g.arad(\[1,2\],\[0.5,0.3\]) set atom radii, same rules as acol() :pre + +g.bcol() set bond color, same args as acol() +g.brad() set bond thickness, same args as arad() :pre + +g.tcol() set triangle color, same args as acol() +g.tfill() set triangle fill, 0 fill, 1 line, 2 both :pre + +g.lcol() set line color, same args as acol() +g.lrad() set line thickness, same args as arad() :pre + +g.adef() set atom/bond/tri/line properties to default +g.bdef() default = "loop" for colors, 0.45 for radii +g.tdef() default = 0.25 for bond/line thickness +g.ldef() default = 0 fill :pre + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error :pre + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors\["nickname"\] = \[R,G,B\] set new RGB values from 0 to 255 :pre + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc :pre + +Settings specific to gl tool: :pre + +g.q(10) set quality of image (def = 5) +g.axis(0/1) turn xyz axes off/on +g.ortho(0/1) perspective (0) vs orthographic (1) view +g.clip('xlo',0.25) clip in xyz from lo/hi at box fraction (0-1) +g.reload() force all data to be reloaded +g.cache = 0/1 turn off/on GL cache lists (def = on) +theta,phi,x,y,scale,up = g.gview() grab all current view parameters +g.sview(theta,phi,x,y,scale,up) set all view parameters :pre + + data reload is necessary if dump selection is used to change the data + cache lists usually improve graphics performance + gview returns values to use in other commands: + theta,phi are args to rotate() + x,y are args to shift() + scale is arg to zoom() + up is a 3-vector arg to sview() :pre + +[Related tools:] + +"dump"_dump.html, "rasmol"_rasmol.html, "raster"_raster.html, +"svg"_svg.html, "vcr"_vcr.html, "vmd"_vmd.html + +[Prerequisites:] + +Python PyOpenGL and PIL packages. diff --git a/doc/gnu.html b/doc/gnu.html new file mode 100644 index 0000000..f45bcf5 --- /dev/null +++ b/doc/gnu.html @@ -0,0 +1,116 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

gnu tool +

+

Purpose: +

+

Create plots via GnuPlot plotting program. +

+

Description: +

+

The gnu tool is a wrapper on the GnuPlot +plotting package. GnuPlot is open source software and runs on any +platform. +

+

The gnu constructor launches GnuPlot as a process which the gnu tool +sends commands to. The GnuPlot process can be killed via the stop() +method, though this is typically unnecessary. +

+

The plot() method plots a single vector against a linear index or +pairs of vectors against each other. The pairs of vectors are written +to files and read-in by GnuPlot's plot command. +

+

The mplot() method creates a series of plots and saves them each to a +numbered file. Each file is a plot of an increasing portion of the +vector(s). This can be used to make an animation of a plot. +

+

The enter() method can be used to interact with GnuPlot directly. +Each subsequent line you type is a GnuPlot command, until you type +"quit" or "exit" to return to Pizza.py. Single GnuPlot commands can +be issued as string arguments to the gnu tool. +

+

The export() method writes numeric data as columns to text files, so +that GnuPlot can read them via its "plot" command. +

+

Mutliple windows can be displayed, plotted to, and manipulated using +the select() and hide() methods. The save() method writes the +currently selected plot to a PostScript file. +

+

The remaining methods (aspect, title, xrange, etc) set attributes of +the currently selected plot. The erase() method resets all attributes +to their default values. +

+

Usage: +

+
g = gnu()		       start up GnuPlot
+g.stop()		       shut down GnuPlot process 
+
+
g.plot(a)                      plot vector A against linear index
+g.plot(a,b)	 	       plot B against A
+g.plot(a,b,c,d,...)	       plot B against A, D against C, etc
+g.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc 
+
+
  each plot argument can be a tuple, list, or Numeric/NumPy vector
+  mplot loops over range(M,N,S) and create one plot per iteration
+    last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
+    each plot is made from a portion of the vectors, depending on loop index i
+      Ith plot is of b[0:i] vs a[0:i], etc
+    series of plots saved as file0000.eps, file0001.eps, etc
+    if use xrange(),yrange() then plot axes will be same for all plots 
+
+
g("plot 'file.dat' using 2:3 with lines")      execute string in GnuPlot 
+
+
g.enter()	   	                enter GnuPlot shell
+gnuplot> plot sin(x) with lines         type commands directly to GnuPlot
+gnuplot> exit, quit	      	        exit GnuPlot shell 
+
+
g.export("data",range(100),a,...)       create file with columns of numbers 
+
+
  all vectors must be of equal length
+  could plot from file with GnuPlot command: plot 'data' using 1:2 with lines 
+
+
g.select(N)  	               figure N becomes the current plot 
+
+
  subsequent commands apply to this plot 
+
+
g.hide(N)  	               delete window for figure N
+g.save("file")	               save current plot as file.eps 
+
+
Set attributes for current plot: 
+
+
g.erase()                      reset all attributes to default values
+g.aspect(1.3)                  aspect ratio
+g.xtitle("Time")               x axis text
+g.ytitle("Energy")             y axis text
+g.title("My Plot")             title text
+g.title("title","x","y")       title, x axis, y axis text
+g.xrange(xmin,xmax)            x axis range
+g.xrange()                     default x axis range
+g.yrange(ymin,ymax)            y axis range
+g.yrange()                     default y axis range
+g.xlog()                       toggle x axis between linear and log
+g.ylog()                       toggle y axis between linear and log
+g.label(x,y,"text")            place label at x,y coords
+g.curve(N,'r')                 set color of curve N 
+
+
  colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue
+          'm' = magenta, 'c' = cyan, 'y' = yellow 
+
+

Related tools: +

+

matlab, plotview +

+

Prerequisites: +

+

GnuPlot plotting package. +

+ diff --git a/doc/gnu.txt b/doc/gnu.txt new file mode 100644 index 0000000..439bd0f --- /dev/null +++ b/doc/gnu.txt @@ -0,0 +1,111 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +gnu tool :h3 + +[Purpose:] + +Create plots via GnuPlot plotting program. + +[Description:] + +The gnu tool is a wrapper on the "GnuPlot"_http://www.gnuplot.info/ +plotting package. GnuPlot is open source software and runs on any +platform. + +The gnu constructor launches GnuPlot as a process which the gnu tool +sends commands to. The GnuPlot process can be killed via the stop() +method, though this is typically unnecessary. + +The plot() method plots a single vector against a linear index or +pairs of vectors against each other. The pairs of vectors are written +to files and read-in by GnuPlot's plot command. + +The mplot() method creates a series of plots and saves them each to a +numbered file. Each file is a plot of an increasing portion of the +vector(s). This can be used to make an animation of a plot. + +The enter() method can be used to interact with GnuPlot directly. +Each subsequent line you type is a GnuPlot command, until you type +"quit" or "exit" to return to Pizza.py. Single GnuPlot commands can +be issued as string arguments to the gnu tool. + +The export() method writes numeric data as columns to text files, so +that GnuPlot can read them via its "plot" command. + +Mutliple windows can be displayed, plotted to, and manipulated using +the select() and hide() methods. The save() method writes the +currently selected plot to a PostScript file. + +The remaining methods (aspect, title, xrange, etc) set attributes of +the currently selected plot. The erase() method resets all attributes +to their default values. + +[Usage:] + +g = gnu() start up GnuPlot +g.stop() shut down GnuPlot process :pre + +g.plot(a) plot vector A against linear index +g.plot(a,b) plot B against A +g.plot(a,b,c,d,...) plot B against A, D against C, etc +g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc :pre + + each plot argument can be a tuple, list, or Numeric/NumPy vector + mplot loops over range(M,N,S) and create one plot per iteration + last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors + each plot is made from a portion of the vectors, depending on loop index i + Ith plot is of b\[0:i\] vs a\[0:i\], etc + series of plots saved as file0000.eps, file0001.eps, etc + if use xrange(),yrange() then plot axes will be same for all plots :pre + +g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot :pre + +g.enter() enter GnuPlot shell +gnuplot> plot sin(x) with lines type commands directly to GnuPlot +gnuplot> exit, quit exit GnuPlot shell :pre + +g.export("data",range(100),a,...) create file with columns of numbers :pre + + all vectors must be of equal length + could plot from file with GnuPlot command: plot 'data' using 1:2 with lines :pre + +g.select(N) figure N becomes the current plot :pre + + subsequent commands apply to this plot :pre + +g.hide(N) delete window for figure N +g.save("file") save current plot as file.eps :pre + +Set attributes for current plot: :pre + +g.erase() reset all attributes to default values +g.aspect(1.3) aspect ratio +g.xtitle("Time") x axis text +g.ytitle("Energy") y axis text +g.title("My Plot") title text +g.title("title","x","y") title, x axis, y axis text +g.xrange(xmin,xmax) x axis range +g.xrange() default x axis range +g.yrange(ymin,ymax) y axis range +g.yrange() default y axis range +g.xlog() toggle x axis between linear and log +g.ylog() toggle y axis between linear and log +g.label(x,y,"text") place label at x,y coords +g.curve(N,'r') set color of curve N :pre + + colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue + 'm' = magenta, 'c' = cyan, 'y' = yellow :pre + +[Related tools:] + +"matlab"_matlab.html, "plotview"_plotview.html + +[Prerequisites:] + +GnuPlot plotting package. diff --git a/doc/histo.html b/doc/histo.html new file mode 100644 index 0000000..5374232 --- /dev/null +++ b/doc/histo.html @@ -0,0 +1,45 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

histo tool +

+

Purpose: +

+

Particle density histogram from a dump. +

+

Description: +

+

The histo tool creates spatial histograms of particle snapshots in +a dump file. +

+

The histo constructor takes an object that stores atom snapshots +(dump, data) as its argument. +

+

The compute() method creates a histogram in a specific dimension at a +desired resolution, averaged across all selected snapshots and atoms +in the dump. The returned vectors can be plotted; x is the distance +along the chosen dimension, y is the histogram counts. +

+

Usage: +

+
h = histo(d)                        d = dump/cdump object 
+
+
x,y = h.compute('x',N,lo,hi)        compute histogram in dim with N bins 
+
+
  lo/hi are optional, if not used histo will be over entire box 
+
+

Related tools: +

+

dump +

+

Prerequisites: none +

+ diff --git a/doc/histo.txt b/doc/histo.txt new file mode 100644 index 0000000..dc8688a --- /dev/null +++ b/doc/histo.txt @@ -0,0 +1,40 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +histo tool :h3 + +[Purpose:] + +Particle density histogram from a dump. + +[Description:] + +The histo tool creates spatial histograms of particle snapshots in +a dump file. + +The histo constructor takes an object that stores atom snapshots +("dump"_dump.html, "data"_data.html) as its argument. + +The compute() method creates a histogram in a specific dimension at a +desired resolution, averaged across all selected snapshots and atoms +in the dump. The returned vectors can be plotted; x is the distance +along the chosen dimension, y is the histogram counts. + +[Usage:] + +h = histo(d) d = dump/cdump object :pre + +x,y = h.compute('x',N,lo,hi) compute histogram in dim with N bins :pre + + lo/hi are optional, if not used histo will be over entire box :pre + +[Related tools:] + +"dump"_dump.html + +[Prerequisites:] none diff --git a/doc/image.html b/doc/image.html new file mode 100644 index 0000000..51cf785 --- /dev/null +++ b/doc/image.html @@ -0,0 +1,91 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

image tool +

+

Purpose: +

+

View and manipulate images. +

+

Description: +

+

The image tool can be used to display image files or convert them to +other formats via the ImageMagick tools (or alternate tools if +specified in the DEFAULTS.py file). +

+

The image constructor creates a GUI to view a set of image files as a +palette of thumbnail-size images. Each thumbnail can be clicked on to +view the full-size image. Clicking on the full-size image removes it. +The view() method does the same operation for a new set of files. +

+

The convert() method invokes the ImageMagick "convert" command to +convert an image file to a different format. If both arguments have a +wildcard character, one conversion is done for each file in the 1st +argument to create a file in the 2nd argument, e.g. "convert +image0012.svg new0012.png". If either argument has no wildcard, one +"convert" command is issued using both arguments. This form can be +used to create a movie file, e.g. "convert *.png ligand.mpg". +

+

The montage() method invokes the ImageMagick "montage" command to +combine 2 image files to create a 3rd. If all 3 arguments have a +wildcard character, one montage is created for each file in the 1st +argument, paired with one file in the 2nd argument, e.g. "montage +image0012.svg plot0012.eps combine0012.png". For this to work, the +1st arguments must each expand to the same number of files. If any of +the 3 arguments does not have a wildcard, one "montage" command is +issued using all 3 arguements. +

+

Image files can be in any format (PNG, GIF, JPG, etc) recognized by +the Python Image Library (PIL) installed in your Python or by +ImageMagick. Various Pizza.py visualization tools (raster, deja, +rasmol, etc) create such image files. If a particular image format +fails to load, your PIL installation was linked without support for +that format. Rebuild PIL, and follow the install instructions +included in its top directory. +

+

Usage: +

+
i = image("my1.gif my2.gif")    display thumbnails of matching images
+i = image("*.png *.gif")        wildcards allowed
+i = image("")	   		blank string matches all image suffixes
+i = image()			no display window opened if no arg 
+
+
  image suffixes for blank string = *.png, *.bmp, *.gif, *.tiff, *.tif
+  click on a thumbnail to view it full-size
+  click on thumbnail again to remove full-sized version 
+
+
i.view("*.png *.gif")	        display thumbnails of matching images 
+
+
  view arg is same as constructor arg 
+
+
i.convert("image*.svg","new*.png")                      each SVG file to PNG
+i.convert("image*.svg","new*.jpg","-quality 50")        3rd arg is switch
+i.convert("image*.png","movie.mpg")                     all PNGs to MPG movie
+i.convert("image*.png","movie.mpg","-resize 128x128")   3rd arg is switch
+i.montage("","image*.png","plot*.png","two*.png")       image + plot = two
+i.montage("-geometry 512x512","i*.png","new.png")       1st arg is switch 
+
+
  convert with 2 wildcard args loops over 1st set of files to make 2nd set
+  convert with not all wildcard args will issue single convert command
+  montage with all wildcard args loops over 1st set of files,
+    combines with one file from other sets, to make last set of files
+  montage with not all wildcard args will issue single montage command 
+
+

Related tools: +

+

raster, rasmol, animate +

+

Prerequisites: +

+

Python Tkinter, Pmw, and PIL packages. ImageMagick convert and +montage commands or equivalent. +

+ diff --git a/doc/image.txt b/doc/image.txt new file mode 100644 index 0000000..bd9d4f7 --- /dev/null +++ b/doc/image.txt @@ -0,0 +1,86 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +image tool :h3 + +[Purpose:] + +View and manipulate images. + +[Description:] + +The image tool can be used to display image files or convert them to +other formats via the ImageMagick tools (or alternate tools if +specified in the DEFAULTS.py file). + +The image constructor creates a GUI to view a set of image files as a +palette of thumbnail-size images. Each thumbnail can be clicked on to +view the full-size image. Clicking on the full-size image removes it. +The view() method does the same operation for a new set of files. + +The convert() method invokes the ImageMagick "convert" command to +convert an image file to a different format. If both arguments have a +wildcard character, one conversion is done for each file in the 1st +argument to create a file in the 2nd argument, e.g. "convert +image0012.svg new0012.png". If either argument has no wildcard, one +"convert" command is issued using both arguments. This form can be +used to create a movie file, e.g. "convert *.png ligand.mpg". + +The montage() method invokes the ImageMagick "montage" command to +combine 2 image files to create a 3rd. If all 3 arguments have a +wildcard character, one montage is created for each file in the 1st +argument, paired with one file in the 2nd argument, e.g. "montage +image0012.svg plot0012.eps combine0012.png". For this to work, the +1st arguments must each expand to the same number of files. If any of +the 3 arguments does not have a wildcard, one "montage" command is +issued using all 3 arguements. + +Image files can be in any format (PNG, GIF, JPG, etc) recognized by +the Python Image Library (PIL) installed in your Python or by +ImageMagick. Various Pizza.py visualization tools (raster, deja, +rasmol, etc) create such image files. If a particular image format +fails to load, your PIL installation was linked without support for +that format. Rebuild PIL, and follow the install instructions +included in its top directory. + +[Usage:] + +i = image("my1.gif my2.gif") display thumbnails of matching images +i = image("*.png *.gif") wildcards allowed +i = image("") blank string matches all image suffixes +i = image() no display window opened if no arg :pre + + image suffixes for blank string = *.png, *.bmp, *.gif, *.tiff, *.tif + click on a thumbnail to view it full-size + click on thumbnail again to remove full-sized version :pre + +i.view("*.png *.gif") display thumbnails of matching images :pre + + view arg is same as constructor arg :pre + +i.convert("image*.svg","new*.png") each SVG file to PNG +i.convert("image*.svg","new*.jpg","-quality 50") 3rd arg is switch +i.convert("image*.png","movie.mpg") all PNGs to MPG movie +i.convert("image*.png","movie.mpg","-resize 128x128") 3rd arg is switch +i.montage("","image*.png","plot*.png","two*.png") image + plot = two +i.montage("-geometry 512x512","i*.png","new.png") 1st arg is switch :pre + + convert with 2 wildcard args loops over 1st set of files to make 2nd set + convert with not all wildcard args will issue single convert command + montage with all wildcard args loops over 1st set of files, + combines with one file from other sets, to make last set of files + montage with not all wildcard args will issue single montage command :pre + +[Related tools:] + +"raster"_raster.html, "rasmol"_rasmol.html, "animate"_animate.html + +[Prerequisites:] + +Python Tkinter, Pmw, and PIL packages. ImageMagick convert and +montage commands or equivalent. diff --git a/doc/ldump.html b/doc/ldump.html new file mode 100644 index 0000000..c5f0e21 --- /dev/null +++ b/doc/ldump.html @@ -0,0 +1,121 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

ldump tool +

+

Purpose: +

+

Read dump files with line segment info. +

+

Description: +

+

The ldump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each atom contains line segment info from a 2d +LAMMPS simulation using atom_style line. Other tools use ldump +objects to extract line segment info for visualization, like the dump +tool via its extra() method. +

+

The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. +

+

The map() method assigns names to columns of atom attributes. +The id,type,end1x,end1y,end2x,end2y names must be assigned +in order for line segment info to be extracted. +

+

The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). +

+
+ +

Normally, LAMMPS creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: +

+
ITEM: TIMESTEP
+100
+ITEM: NUMBER OF ATOMS
+32
+ITEM: BOX BOUNDS
+0 3.35919
+0 3.35919
+0 7.50
+ITEM: ATOMS
+1 1 0 0 0 
+2 1 0.25 0.25 0
+3 1 0.25 0 0.25
+...
+N 3 0.7 0.5 0.6 
+
+

The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. Atoms do not have to be listed +in any particular order. There can be a different number of atoms in +each snapshot. Each line must contain the atom ID, type, and the end +points of the associated line segment, as specified by the map() +command. +

+
+ +

Usage: +

+
l = ldump("dump.one")             read in one or more dump files
+l = ldump("dump.1 dump.2.gz")	  can be gzipped
+l = ldump("dump.*")		  wildcard expands to multiple files
+l = ldump("dump.*",0)		  two args = store filenames, but don't read 
+
+
  incomplete and duplicate snapshots are deleted
+  no column name assignment is performed 
+
+
time = l.next()             	  read next snapshot from dump files 
+
+
  used with 2-argument constructor to allow reading snapshots one-at-a-time
+  snapshot will be skipped only if another snapshot has same time stamp
+  return time stamp of snapshot read
+  return -1 if no snapshots left or last snapshot is incomplete
+  no column name assignment is performed 
+
+
l.map(1,"id",3,"x")               assign names to atom columns (1-N) 
+
+
  must assign id,type,end1x,end1y,end2x,end2y 
+
+
time,box,atoms,bonds,tris,lines = l.viz(index)   return list of viz objects 
+
+
  viz() returns line info for specified timestep index
+    can also call as viz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
+    atoms = NULL
+    bonds = NULL
+    tris = NULL
+    lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
+      id,type are from associated atom 
+
+
l.owrap(...)		          wrap lines to same image as their atoms 
+
+
  owrap() is called by dump tool's owrap()
+  useful for wrapping all molecule's atoms/lines the same so it is contiguous 
+
+

Related tools: +

+

dump, gl, raster, svg +

+

Prerequisites: +

+

Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). +

+ diff --git a/doc/ldump.txt b/doc/ldump.txt new file mode 100644 index 0000000..6b51bb8 --- /dev/null +++ b/doc/ldump.txt @@ -0,0 +1,116 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +ldump tool :h3 + +[Purpose:] + +Read dump files with line segment info. + +[Description:] + +The ldump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each atom contains line segment info from a 2d +LAMMPS simulation using atom_style line. Other tools use ldump +objects to extract line segment info for visualization, like the dump +tool via its extra() method. + +The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. + +The map() method assigns names to columns of atom attributes. +The id,type,end1x,end1y,end2x,end2y names must be assigned +in order for line segment info to be extracted. + +The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). + +:line + +Normally, "LAMMPS"_http://lammps.sandia.gov creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: + +ITEM: TIMESTEP +100 +ITEM: NUMBER OF ATOMS +32 +ITEM: BOX BOUNDS +0 3.35919 +0 3.35919 +0 7.50 +ITEM: ATOMS +1 1 0 0 0 +2 1 0.25 0.25 0 +3 1 0.25 0 0.25 +... +N 3 0.7 0.5 0.6 :pre + +The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. Atoms do not have to be listed +in any particular order. There can be a different number of atoms in +each snapshot. Each line must contain the atom ID, type, and the end +points of the associated line segment, as specified by the map() +command. + +:line + +[Usage:] + +l = ldump("dump.one") read in one or more dump files +l = ldump("dump.1 dump.2.gz") can be gzipped +l = ldump("dump.*") wildcard expands to multiple files +l = ldump("dump.*",0) two args = store filenames, but don't read :pre + + incomplete and duplicate snapshots are deleted + no column name assignment is performed :pre + +time = l.next() read next snapshot from dump files :pre + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed :pre + +l.map(1,"id",3,"x") assign names to atom columns (1-N) :pre + + must assign id,type,end1x,end1y,end2x,end2y :pre + +time,box,atoms,bonds,tris,lines = l.viz(index) return list of viz objects :pre + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\] + atoms = NULL + bonds = NULL + tris = NULL + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + id,type are from associated atom :pre + +l.owrap(...) wrap lines to same image as their atoms :pre + + owrap() is called by dump tool's owrap() + useful for wrapping all molecule's atoms/lines the same so it is contiguous :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). diff --git a/doc/log.html b/doc/log.html new file mode 100644 index 0000000..8208309 --- /dev/null +++ b/doc/log.html @@ -0,0 +1,64 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +
+ +

log tool +

+

Purpose: +

+

Read LAMMPS log files and extract thermodynamic data. +

+

Description: +

+

Read one or more LAMMPS log files and combine their thermodynamic data +into long, named vectors (versus time). The vectors can be used in +Python for further processing and plotting, or they can be output to a +file. +

+

The log constructor reads one or more log files. If 2 arguments are +specified, a single file is specified, and it can be read +incrementally (e.g. as it is created) by the next() method. +

+

The nvec, nlen, and names values give the # of vectors, their length, +and names. The get() method returns one of more vectors as a Python +list. The write() method outputs the numeric vectors to a file. +

+

Usage: +

+
l = log("file1")                     read in one or more log files
+l = log("log1 log2.gz")              can be gzipped
+l = log("file*")                     wildcard expands to multiple files
+l = log("log.lammps",0)              two args = store filename, but don't read 
+
+
  incomplete and duplicate thermo entries are deleted 
+
+
time = l.next()                      read new thermo info from file 
+
+
  used with 2-argument constructor to allow reading thermo incrementally
+  return time stamp of last thermo read
+  return -1 if no new thermo since last read 
+
+
nvec = l.nvec                        # of vectors of thermo info
+nlen = l.nlen                        length of each vectors
+names = l.names                      list of vector names
+t,pe,... = l.get("Time","KE",...)    return one or more vectors of values
+l.write("file.txt")	 	     write all vectors to a file
+l.write("file.txt","Time","PE",...)  write listed vectors to a file 
+
+
  get and write allow abbreviated (uniquely) vector names 
+
+

Related tools: +

+

clog, plotview, gnu, +matlab +

+

Prerequisites: none +

+ diff --git a/doc/log.txt b/doc/log.txt new file mode 100644 index 0000000..54a9465 --- /dev/null +++ b/doc/log.txt @@ -0,0 +1,59 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +log tool :h3 + +[Purpose:] + +Read LAMMPS log files and extract thermodynamic data. + +[Description:] + +Read one or more LAMMPS log files and combine their thermodynamic data +into long, named vectors (versus time). The vectors can be used in +Python for further processing and plotting, or they can be output to a +file. + +The log constructor reads one or more log files. If 2 arguments are +specified, a single file is specified, and it can be read +incrementally (e.g. as it is created) by the next() method. + +The nvec, nlen, and names values give the # of vectors, their length, +and names. The get() method returns one of more vectors as a Python +list. The write() method outputs the numeric vectors to a file. + +[Usage:] + +l = log("file1") read in one or more log files +l = log("log1 log2.gz") can be gzipped +l = log("file*") wildcard expands to multiple files +l = log("log.lammps",0) two args = store filename, but don't read :pre + + incomplete and duplicate thermo entries are deleted :pre + +time = l.next() read new thermo info from file :pre + + used with 2-argument constructor to allow reading thermo incrementally + return time stamp of last thermo read + return -1 if no new thermo since last read :pre + +nvec = l.nvec # of vectors of thermo info +nlen = l.nlen length of each vectors +names = l.names list of vector names +t,pe,... = l.get("Time","KE",...) return one or more vectors of values +l.write("file.txt") write all vectors to a file +l.write("file.txt","Time","PE",...) write listed vectors to a file :pre + + get and write allow abbreviated (uniquely) vector names :pre + +[Related tools:] + +"clog"_clog.html, "plotview"_plotview.html, "gnu"_gnu.html, +"matlab"_matlab.html + +[Prerequisites:] none diff --git a/doc/lpp.html b/doc/lpp.html new file mode 100644 index 0000000..be3e841 --- /dev/null +++ b/doc/lpp.html @@ -0,0 +1,135 @@ + +
Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
+ + + + + + +

lpp tool +

+

Purpose: +

+

This is lpp (liggghts post processing), an update to pizza.py offering better visualization +of granular (DEM) LIGGGHTS or LAMMPS simulations using pizza.py via VTK files +

+
+ +

Description: +

+

This update provides the possibilty to convert LIGGGHTS/LAMMPS dump files to VTK exporting: +

+
  • particle radius, + +
  • particle velocity and rotational velocity vector, + +
  • particle force and torque vector, + +
  • customized vectors (e.g. calculated by a fix, compute or variable) + +
  • customized scalars (e.g. calculated by a fix, compute or variable) + +

    where the names are automatically assigned. +

    +

    The lpp tool runs in parallel (shared-memory) using the python "multiprocessing" tool. The number of processors can be controlled via command line args (see below). +

    +

    Additionally, the simulation box is also exported into VTK format +and stored in an "*_boundingBox.vtk" file +

    +
    + +

    Prerequisites for Usage: +

    +

    To be able to use the lpp tool, please use a dump custom command like the +following in your LIGGGHTS/LAMMPS input script: +

    +
    dump d0 all custom 100 dump*.example id type x y z ix iy iz vx vy vz fx fy fz 
+omegax omegay omegaz radius (customScalars) (customVectors) 
+
    +

    It is mandatory to use "x y z" in the dump custom command. The dump file +generated by LIGGGHTS/LAMMPS will look like this: +

    +
    ITEM: TIMESTEP
+5000
+ITEM: NUMBER OF ATOMS
+2988
+ITEM: BOX BOUNDS
+-0.05 0.05
+-0.05 0.05
+0 0.6
+ITEM: ATOMS id type x y z vx vy vz fx fy fz omegax omegay omegaz radius 
+
    +

    The last line contains the name strings for the per-atom quanitites. +If the syntax of a name string triple of names meets one of the following +specifications this triple is recognized as a vector: +

    +
  • f_vectorname[i] f_vectorname[i+1] f_vectorname[i+2] + +
  • c_vectorname[i] c_vectorname[i+1] c_vectorname[i+2] + +
  • v_vectorname[i] v_vectorname[i+1] v_vectorname[i+2] + +
  • vectornamex vectornamey vectornamez + +

    "vectorname" can be any name (e.g. "v" for velocity, "tq" for torque, +etc., a fix or compute id, or a per-atom variable name.) +

    +

    All other quantities are recognized as scalars. +

    +
    + +

    Usage: +

    +

    After the simulation is finished, type "lpp dump.mySimulation" where "dump.mySimulation" +has to be replaced the name of your dump file or type "lpp dump*.mySimulation" +

    +

    For more command line options, see below. +

    +

    Now open paraview (www.paraview.org) and import the VTK files. To display the +particles correctly, you should first create a glyph by clicking on the "glyph" +button and then in the object inspector: +

    +
  • Choose Scalars -->"radius" + +
  • Glyph type -->"Sphere" + +
  • Radius -->"1" + +
  • Scale mode -->"Scalar" + +
  • Set Scale Factor -->"1" + +

    In a similar fashion, you can set up vector glyphs to visualize velocity etc. +

    +
    + +

    Command Line Options: +

    +

    A few command line options are avaliable to control lpp: +

    +

    -o fname : define output file names (default is liggghts + timestep number). This option can also be used to write to a specified folder, eg. "lpp -o foo/bar dump*" will create files bar1000.vtk, bar2000.vtk etc. in the directory ./foo while "lpp -o foo/ dump*" will create files named liggghts1000.vtk, ligggghts2000.vtk etc. in ./foo (providing the directory exists, lpp will not create any directories for you!) +

    +

    --chunksize : sets the amount of dumpfiles processed per chunk, the default is 8. Increasing the chunksize can improve performance, but the chunksize is limited by the amount of RAM on your system. Also keep in mind that multiple chunks may be processed depending on your --cpunum settings, and thus RAM demand is multiplied. +

    +

    --cpunum : sets the number of processes to start, default (and maximum) is the amount of cpu cores avaliable at your system. +

    +

    --debug : prints debug information, usually not needed +

    +

    --quiet : suppresses all output but error messages (also discards --debug) +

    +

    --help : writes a help message and exits +

    +
    + +

    Related tools: +

    +

    vtk, dump, +

    +
    + +

    Prerequisites: +

    +

    Python "multiprocessing" tool +

    + diff --git a/doc/lpp.txt b/doc/lpp.txt new file mode 100644 index 0000000..c877a74 --- /dev/null +++ b/doc/lpp.txt @@ -0,0 +1,119 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +lpp tool :h3 + +[Purpose:] + +This is lpp (liggghts post processing), an update to pizza.py offering better visualization +of granular (DEM) LIGGGHTS or LAMMPS simulations using pizza.py via VTK files + +:line + +[Description:] + +This update provides the possibilty to convert LIGGGHTS/LAMMPS dump files to VTK exporting: + +particle radius, :l +particle velocity and rotational velocity vector, :l +particle force and torque vector, :l +customized vectors (e.g. calculated by a fix, compute or variable) :l +customized scalars (e.g. calculated by a fix, compute or variable) :l + +where the names are automatically assigned. + +The lpp tool runs in parallel (shared-memory) using the python "multiprocessing" tool. The number of processors can be controlled via command line args (see below). + +Additionally, the simulation box is also exported into VTK format +and stored in an "*_boundingBox.vtk" file + +:line + +[Prerequisites for Usage:] + +To be able to use the lpp tool, please use a dump custom command like the +following in your LIGGGHTS/LAMMPS input script: + +dump d0 all custom 100 dump*.example id type x y z ix iy iz vx vy vz fx fy fz +omegax omegay omegaz radius (customScalars) (customVectors) :pre + +It is mandatory to use "x y z" in the dump custom command. The dump file +generated by LIGGGHTS/LAMMPS will look like this: + +ITEM: TIMESTEP +5000 +ITEM: NUMBER OF ATOMS +2988 +ITEM: BOX BOUNDS +-0.05 0.05 +-0.05 0.05 +0 0.6 +ITEM: ATOMS id type x y z vx vy vz fx fy fz omegax omegay omegaz radius :pre + +The last line contains the name strings for the per-atom quanitites. +If the syntax of a name string triple of names meets one of the following +specifications this triple is recognized as a vector: + +f_vectorname\[i\] f_vectorname\[i+1\] f_vectorname\[i+2\] :l +c_vectorname\[i\] c_vectorname\[i+1\] c_vectorname\[i+2\] :l +v_vectorname\[i\] v_vectorname\[i+1\] v_vectorname\[i+2\] :l +vectornamex vectornamey vectornamez :l + +"vectorname" can be any name (e.g. "v" for velocity, "tq" for torque, +etc., a fix or compute id, or a per-atom variable name.) + +All other quantities are recognized as scalars. + +:line + +[Usage:] + +After the simulation is finished, type "lpp dump.mySimulation" where "dump.mySimulation" +has to be replaced the name of your dump file or type "lpp dump*.mySimulation" + +For more command line options, see below. + +Now open paraview (www.paraview.org) and import the VTK files. To display the +particles correctly, you should first create a glyph by clicking on the "glyph" +button and then in the object inspector: + +Choose Scalars -->"radius" :l +Glyph type -->"Sphere" :l +Radius -->"1" :l +Scale mode -->"Scalar" :l +Set Scale Factor -->"1" :l + +In a similar fashion, you can set up vector glyphs to visualize velocity etc. + +:line + +[Command Line Options:] + +A few command line options are avaliable to control lpp: + +-o fname : define output file names (default is liggghts + timestep number). This option can also be used to write to a specified folder, eg. "lpp -o foo/bar dump*" will create files bar1000.vtk, bar2000.vtk etc. in the directory ./foo while "lpp -o foo/ dump*" will create files named liggghts1000.vtk, ligggghts2000.vtk etc. in ./foo (providing the directory exists, lpp will not create any directories for you!) + +--chunksize : sets the amount of dumpfiles processed per chunk, the default is 8. Increasing the chunksize can improve performance, but the chunksize is limited by the amount of RAM on your system. Also keep in mind that multiple chunks may be processed depending on your --cpunum settings, and thus RAM demand is multiplied. + +--cpunum : sets the number of processes to start, default (and maximum) is the amount of cpu cores avaliable at your system. + +--debug : prints debug information, usually not needed + +--quiet : suppresses all output but error messages (also discards --debug) + +--help : writes a help message and exits + +:line + +[Related tools:] + +"vtk"_vtk.html, "dump"_dump.html, + +:line + +[Prerequisites:] + +Python "multiprocessing" tool diff --git a/doc/matlab.html b/doc/matlab.html new file mode 100644 index 0000000..a58dd4c --- /dev/null +++ b/doc/matlab.html @@ -0,0 +1,128 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    matlab tool +

    +

    Purpose: +

    +

    Create plots via MatLab numerical analysis program. +

    +

    Description: +

    +

    The matlab tool is a wrapper on the MatLab +numerical analysis package, primarily designed to use its plotting +capabilities. MatLab is commercial software available on a variety +of platforms. +

    +

    The matlab constructor launches MatLab as a process which the matlab +tool sends commands to. The MatLab process can be killed via the +stop() method, though this is typically unnecessary. +

    +

    The plot() method plots a single vector against a linear index or +pairs of vectors against each other. The pairs of vectors are written +to files and read-in by MatLab. The Nth curve in a plot is stored in +the MatLab variable pizzaN, so the 2 vectors can be accessed within +MatLab as pizzaN(:,1) and pizzaN(:,2). +

    +

    The mplot() method creates a series of plots and saves them each to a +numbered file. Each file is a plot of an increasing portion of the +vector(s). This can be used to make an animation of a plot. +

    +

    The enter() method can be used to interact with MatLab directly. +Each subsequent line you type is a MatLab command, until you type +"quit" or "exit" to return to Pizza.py. Single MatLab commands can +be issued as string arguments to the gnu tool. +

    +

    The export() method writes numeric data as columns to text files, so +that MatLab can read them via its "importdata" command. +

    +

    Mutliple windows can be displayed, plotted to, and manipulated using +the select() and hide() methods. The save() method writes the +currently selected plot to a PostScript file. +

    +

    The remaining methods (aspect, title, xrange, etc) set attributes of +the currently selected plot. The erase() method resets all attributes +to their default values. +

    +

    Usage: +

    +
    m = matlab()		       start up MatLab
+m.stop()		       shut down MatLab process 
+
    +
    m.plot(a)                      plot vector A against linear index
+m.plot(a,b)	 	       plot B against A
+m.plot(a,b,c,d,...)	       plot B against A, D against C, etc
+m.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc 
+
    +
      each plot argument can be a tuple, list, or Numeric/NumPy vector
+  mplot loops over range(M,N,S) and create one plot per iteration
+    last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
+    each plot is made from a portion of the vectors, depending on loop index i
+      Ith plot is of b[0:i] vs a[0:i], etc
+    series of plots saved as file0000.eps, file0001.eps, etc
+    if use xrange(),yrange() then plot axes will be same for all plots 
+
    +
    m("c = a + b")                 execute string in MatLab 
+
    +
    m.enter()	   	       enter MatLab shell
+matlab> c = a + b              type commands directly to MatLab
+matlab> exit, quit	       exit MatLab shell 
+
    +
    m.export("data",range(100),a,...)       create file with columns of numbers 
+
    +
      all vectors must be of equal length
+  could plot from file with MatLab commands:
+    cols = importdata('data')
+    plot(cols(:,1),cols(:,2)) 
+
    +
    m.select(N)  	               figure N becomes the current plot 
+
    +
      subsequent commands apply to this plot 
+
    +
    m.hide(N)  	               delete window for figure N
+m.save("file")	               save current plot as file.eps 
+
    +
    Set attributes for current plot: 
+
    +
    m.erase()                      reset all attributes to default values
+m.aspect(1.3)                  aspect ratio
+m.xtitle("Time")               x axis text
+m.ytitle("Energy")             y axis text
+m.title("My Plot")             title text
+m.title("title","x","y")       title, x axis, y axis text
+m.xrange(xmin,xmax)            x axis range
+m.xrange()                     default x axis range
+m.yrange(ymin,ymax)            y axis range
+m.yrange()                     default y axis range
+m.xlog()                       toggle x axis between linear and log
+m.ylog()                       toggle y axis between linear and log
+m.label(x,y,"text")            place label at x,y coords
+m.curve(N,'r')                 set color of curve N
+m.curve(N,'g','--')            set color and line style of curve N
+m.curve(N,'b','-','v')         set color, line style, symbol of curve N 
+
    +
      colors:  'k' = black, 'r' = red, 'g' = green, 'b' = blue
+           'm' = magenta, 'c' = cyan, 'y' = yellow
+  styles:  '-' = solid, '--' = dashed, ':' = dotted, '-.' = dash-dot
+  symbols: '+' = plus, 'o' = circle, '*' = asterik, 'x' = X,
+           's' = square, 'd' = diamond, '^' = up triangle,
+           'v' = down triangle, '>' = right triangle,
+           '<' = left triangle, 'p' = pentagram, 'h' = hexagram 
+
    +

    Related tools: +

    +

    gnu, plotview +

    +

    Prerequisites: +

    +

    The MatLab numerical analysis package. +

    + diff --git a/doc/matlab.txt b/doc/matlab.txt new file mode 100644 index 0000000..7212258 --- /dev/null +++ b/doc/matlab.txt @@ -0,0 +1,123 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +matlab tool :h3 + +[Purpose:] + +Create plots via MatLab numerical analysis program. + +[Description:] + +The matlab tool is a wrapper on the "MatLab"_http://www.mathworks.com +numerical analysis package, primarily designed to use its plotting +capabilities. MatLab is commercial software available on a variety +of platforms. + +The matlab constructor launches MatLab as a process which the matlab +tool sends commands to. The MatLab process can be killed via the +stop() method, though this is typically unnecessary. + +The plot() method plots a single vector against a linear index or +pairs of vectors against each other. The pairs of vectors are written +to files and read-in by MatLab. The Nth curve in a plot is stored in +the MatLab variable pizzaN, so the 2 vectors can be accessed within +MatLab as pizzaN(:,1) and pizzaN(:,2). + +The mplot() method creates a series of plots and saves them each to a +numbered file. Each file is a plot of an increasing portion of the +vector(s). This can be used to make an animation of a plot. + +The enter() method can be used to interact with MatLab directly. +Each subsequent line you type is a MatLab command, until you type +"quit" or "exit" to return to Pizza.py. Single MatLab commands can +be issued as string arguments to the gnu tool. + +The export() method writes numeric data as columns to text files, so +that MatLab can read them via its "importdata" command. + +Mutliple windows can be displayed, plotted to, and manipulated using +the select() and hide() methods. The save() method writes the +currently selected plot to a PostScript file. + +The remaining methods (aspect, title, xrange, etc) set attributes of +the currently selected plot. The erase() method resets all attributes +to their default values. + +[Usage:] + +m = matlab() start up MatLab +m.stop() shut down MatLab process :pre + +m.plot(a) plot vector A against linear index +m.plot(a,b) plot B against A +m.plot(a,b,c,d,...) plot B against A, D against C, etc +m.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc :pre + + each plot argument can be a tuple, list, or Numeric/NumPy vector + mplot loops over range(M,N,S) and create one plot per iteration + last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors + each plot is made from a portion of the vectors, depending on loop index i + Ith plot is of b\[0:i\] vs a\[0:i\], etc + series of plots saved as file0000.eps, file0001.eps, etc + if use xrange(),yrange() then plot axes will be same for all plots :pre + +m("c = a + b") execute string in MatLab :pre + +m.enter() enter MatLab shell +matlab> c = a + b type commands directly to MatLab +matlab> exit, quit exit MatLab shell :pre + +m.export("data",range(100),a,...) create file with columns of numbers :pre + + all vectors must be of equal length + could plot from file with MatLab commands: + cols = importdata('data') + plot(cols(:,1),cols(:,2)) :pre + +m.select(N) figure N becomes the current plot :pre + + subsequent commands apply to this plot :pre + +m.hide(N) delete window for figure N +m.save("file") save current plot as file.eps :pre + +Set attributes for current plot: :pre + +m.erase() reset all attributes to default values +m.aspect(1.3) aspect ratio +m.xtitle("Time") x axis text +m.ytitle("Energy") y axis text +m.title("My Plot") title text +m.title("title","x","y") title, x axis, y axis text +m.xrange(xmin,xmax) x axis range +m.xrange() default x axis range +m.yrange(ymin,ymax) y axis range +m.yrange() default y axis range +m.xlog() toggle x axis between linear and log +m.ylog() toggle y axis between linear and log +m.label(x,y,"text") place label at x,y coords +m.curve(N,'r') set color of curve N +m.curve(N,'g','--') set color and line style of curve N +m.curve(N,'b','-','v') set color, line style, symbol of curve N :pre + + colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue + 'm' = magenta, 'c' = cyan, 'y' = yellow + styles: '-' = solid, '--' = dashed, ':' = dotted, '-.' = dash-dot + symbols: '+' = plus, 'o' = circle, '*' = asterik, 'x' = X, + 's' = square, 'd' = diamond, '^' = up triangle, + 'v' = down triangle, '>' = right triangle, + '<' = left triangle, 'p' = pentagram, 'h' = hexagram :pre + +[Related tools:] + +"gnu"_gnu.html, "plotview"_plotview.html + +[Prerequisites:] + +The MatLab numerical analysis package. diff --git a/doc/mdump.html b/doc/mdump.html new file mode 100644 index 0000000..da7a880 --- /dev/null +++ b/doc/mdump.html @@ -0,0 +1,287 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    mdump tool +

    +

    Purpose: +

    +

    Read, write, manipulate mesh dump files. +

    +

    Description: +

    +

    The mdump tool reads one or more mesh dump files, stores their +contents as a series of snapshots with node and element values, and +allows the values to be accessed and manipulated. Other tools use +mdump objects to convert mesh files to other formats or visualize the +mesh. +

    +

    The constructor method is passed a string containing one or more mesh +dump filenames. They can be listed in any order since snapshots are +sorted by timestep after they are read and duplicate snapshots (with +the same time stamp) are deleted. If a 2nd argument is specified, the +files are not immediately read, but snapshots can be read +one-at-a-time by the next() method. +

    +

    The map() method assigns names to columns of element values. The +tselect() methods select one or more snapshots by their time stamp. +The delete() method deletes unselected timesteps so their memory is +freed up. This can be useful to do when reading snapshots +one-at-a-time for huge data sets. The eselect() methods selects +elements within selected snapshots. +

    +

    The time() and vecs() methods return time or element values as vectors +of values. +

    +

    The iterator() and viz() methods are called by Pizza.py tools that +visualize triangles (e.g. gl, raster, svg tools). You can also use +the iterator() method in your scripts to loop over selected snapshots. +The etype setting determines what element value is returned as the +element "type" by the viz() method. The mviz() method is called by +the ensight tool to extract per-node and per-element data to include +in Ensight files it outputs, so that it can visualized in the Ensight +package. +

    +
    + +

    The format of mesh dump files read in by this tool is simple. There +are 4 kinds of entries that can appear within each timestep, in any +order. These are a list of node coordinates, a list of element +topologies (trianglular, tetrahedral, square, and cubic elements are +currently supported), a list of nodal values, and a list of element +values. Note that a mesh file does not need to include all 4 entries +every timestep. For example, if the file only defines a mesh, but no +nodal or element values, then those two entries need not appear. If +the mesh is static, then the nodal coordinates and element topologies +only need to be defined once (e.g. for timestep 0). If the mesh +moves, but its topology is static, then the element topology will be +defined once (timestep 0), but new nodal coordinates could be defined +every timestamp. +

    +

    A single mesh file can contain multiple snapshots, listed one after +the other. +

    +

    The format of a nodal coordinates entry is as follows: +

    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF NODES
+121
+ITEM: BOX BOUNDS
+0 10
+0 10
+0 0
+ITEM: NODES
+1 1 0 0 0
+2 1 0 1 0
+3 1 0 2 0
+...
+N 3 7.5 3 2.5 
+
    +

    The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +NODES" where N is the number of nodes. The nodes do not need to be +listed in any particular order. There can be a different number of +nodes in each snapshot. The values on each node line are "ID type x y +z". +

    +

    The format of an element topology entry is in one of the following +styles (triangles, tetrahedra, squares, cubes): +

    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF TRIANGLES
+200
+ITEM: TRIANGLES
+1 1 1 13 12
+2 1 1 2 13
+3 1 2 14 13
+...
+N 3 259 340 432 
+
    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF TETS
+200
+ITEM: TETS
+1 1 1 13 12 27
+2 1 1 2 13 35
+3 1 2 14 13 103
+...
+N 3 259 340 432 1005 
+
    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF SQUARES
+200
+ITEM: SQUARES
+1 1 1 13 12 4
+2 1 1 2 13 6
+3 1 2 14 13 11
+...
+N 3 259 340 432 500 
+
    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF CUBES
+200
+ITEM: CUBES
+1 1 1 13 12 5 3 6 10 20
+2 1 1 2 13 10 3 4 5 6
+3 1 2 14 13 15 10 18 19
+...
+N 3 259 340 432 200 456 918 1002 988 
+
    +

    There are N lines following "ITEM: TRIANGLES" or "ITEM: TETS" or +"ITEM: SQUARES" or "ITEM: CUBES" where N is the number of elements. +The elements do not need to be listed in any particular order. There +can be a different number of elements in each snapshot. The values on +each element line are "ID type node1 node2 ... nodeN", where N depends +on the type of element. For triangles, N = 3, and the order should +give an outward normal via the right-hand rule. For tets, N = 4, and +the order should give a right-hand rule for the first 3 nodes that +points towards the 4th node. For squares, N = 4, and the nodes should +be listed in counter-clockwise order around the square. For cubes, N += 8, and the first 4 nodes are the lower face (ordered same as a +square), and the last 4 nodes are directly above the lower 4 as the +upper face. +

    +

    The format of a nodal values entry is as follows: +

    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF NODE VALUES
+200
+ITEM: NODE VALUES
+1 1
+2 1
+3 9
+...
+N 32 
+
    +

    There are N lines following "ITEM: NODE VALUES" where N is the number +of nodes. The nodes do not need to be listed in any particular order. +There can be a different number of nodes in each snapshot, but it +should be consistent with the current nodal coordinates entry. The +values on each node line are "ID value1 value2 ..." where there are +as many columns as desired. Each line should have the same number of +values. +

    +

    The format of an element values entry is as follows: +

    +
    ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ELEMENT VALUES
+200
+ITEM: ELEMENT VALUES
+1 1
+2 1
+3 9
+...
+N 32 
+
    +

    There are N lines following "ITEM: ELEMENT VALUES" where N is the +number of elements. The elements do not need to be listed in any +particular order. There can be a different number of elements in each +snapshot, but it should be consistent with the current element +topology entry. The values on each element line are "ID value1 value2 +..." where there are as many columns as desired. Each line should +have the same number of values. The map() command can be used to +assign names to each of these columns of values. +

    +
    + +

    Usage: +

    +
    m = mdump("mesh.one")             read in one or more mesh dump files
+m = mdump("mesh.1 mesh.2.gz")	  can be gzipped
+m = mdump("mesh.*")		  wildcard expands to multiple files
+m = mdump("mesh.*",0)		  two args = store filenames, but don't read 
+
    +
      incomplete and duplicate snapshots are deleted 
+
    +
    time = m.next()             	  read next snapshot from dump files 
+
    +
      used with 2-argument constructor to allow reading snapshots one-at-a-time
+  snapshot will be skipped only if another snapshot has same time stamp
+  return time stamp of snapshot read
+  return -1 if no snapshots left or last snapshot is incomplete
+  no column name assignment or unscaling is performed 
+
    +
    m.map(2,"temperature")            assign names to element value columns (1-N) 
+
    +
    m.tselect.all()			  select all timesteps
+m.tselect.one(N)		  select only timestep N
+m.tselect.none()		  deselect all timesteps
+m.tselect.skip(M)		  select every Mth step
+m.tselect.test("$t >= 100 and $t < 10000")      select matching timesteps
+m.delete()	      	      	  delete non-selected timesteps 
+
    +
      selecting a timestep also selects all elements in the timestep
+  skip() and test() only select from currently selected timesteps
+  test() uses a Python Boolean expression with $t for timestep value
+    Python comparison syntax: == != < > <= >= and or 
+
    +
    m.eselect.all()	      	                      select all elems in all steps
+m.eselect.all(N)      	                      select all elems in one step
+m.eselect.test("$id > 100 and $type == 2")    select match elems in all steps
+m.eselect.test("$id > 100 and $type == 2",N)  select matching elems in one step 
+
    +
      all() with no args selects atoms from currently selected timesteps
+  test() with one arg selects atoms from currently selected timesteps
+  test() sub-selects from currently selected elements
+  test() uses a Python Boolean expression with $ for atom attributes
+    Python comparison syntax: == != < > <= >= and or
+    $name must end with a space 
+
    +
    t = m.time()  	     	       	   return vector of selected timestep values
+fx,fy,... = m.vecs(1000,"fx","fy",...)  return vector(s) for timestep N 
+
    +
      vecs() returns vectors with one value for each selected elem in the timestep 
+
    +
    index,time,flag = m.iterator(0/1)          loop over mesh dump snapshots
+time,box,atoms,bonds,tris,lines = m.viz(index)  return list of viz objects
+nodes,elements,nvalues,evalues = m.mviz(index)  return list of mesh viz objects
+m.etype = "color"                          set column returned as "type" by viz 
+
    +
      iterator() loops over selected timesteps
+  iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
+    index = index within dump object (0 to # of snapshots)
+    time = timestep value
+    flag = -1 when iteration is done, 1 otherwise
+  viz() returns info for selected elements for specified timestep index
+    can also call as viz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
+    atoms = NULL
+    bonds = NULL
+    tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array
+      each element is decomposed into tris
+    lines = NULL
+  mviz() returns info for all elements for specified timestep index
+    can also call as mviz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
+    nodes = list of nodes = id,type,x,y,z
+    elements = list of elements = id,type,node1,node2,...
+    nvalues = list of node values = id,type,value1,value2,...
+    evalues = list of element values = id,type,value1,value2,...
+  etype is column name viz() will return as element type (def = "" = elem type) 
+
    +

    Related tools: +

    +

    dump, gl, raster, svg +

    +

    Prerequisites: +

    +

    Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). +

    + diff --git a/doc/mdump.txt b/doc/mdump.txt new file mode 100644 index 0000000..46ea7be --- /dev/null +++ b/doc/mdump.txt @@ -0,0 +1,282 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +mdump tool :h3 + +[Purpose:] + +Read, write, manipulate mesh dump files. + +[Description:] + +The mdump tool reads one or more mesh dump files, stores their +contents as a series of snapshots with node and element values, and +allows the values to be accessed and manipulated. Other tools use +mdump objects to convert mesh files to other formats or visualize the +mesh. + +The constructor method is passed a string containing one or more mesh +dump filenames. They can be listed in any order since snapshots are +sorted by timestep after they are read and duplicate snapshots (with +the same time stamp) are deleted. If a 2nd argument is specified, the +files are not immediately read, but snapshots can be read +one-at-a-time by the next() method. + +The map() method assigns names to columns of element values. The +tselect() methods select one or more snapshots by their time stamp. +The delete() method deletes unselected timesteps so their memory is +freed up. This can be useful to do when reading snapshots +one-at-a-time for huge data sets. The eselect() methods selects +elements within selected snapshots. + +The time() and vecs() methods return time or element values as vectors +of values. + +The iterator() and viz() methods are called by Pizza.py tools that +visualize triangles (e.g. gl, raster, svg tools). You can also use +the iterator() method in your scripts to loop over selected snapshots. +The etype setting determines what element value is returned as the +element "type" by the viz() method. The mviz() method is called by +the ensight tool to extract per-node and per-element data to include +in Ensight files it outputs, so that it can visualized in the Ensight +package. + +:line + +The format of mesh dump files read in by this tool is simple. There +are 4 kinds of entries that can appear within each timestep, in any +order. These are a list of node coordinates, a list of element +topologies (trianglular, tetrahedral, square, and cubic elements are +currently supported), a list of nodal values, and a list of element +values. Note that a mesh file does not need to include all 4 entries +every timestep. For example, if the file only defines a mesh, but no +nodal or element values, then those two entries need not appear. If +the mesh is static, then the nodal coordinates and element topologies +only need to be defined once (e.g. for timestep 0). If the mesh +moves, but its topology is static, then the element topology will be +defined once (timestep 0), but new nodal coordinates could be defined +every timestamp. + +A single mesh file can contain multiple snapshots, listed one after +the other. + +The format of a nodal coordinates entry is as follows: + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF NODES +121 +ITEM: BOX BOUNDS +0 10 +0 10 +0 0 +ITEM: NODES +1 1 0 0 0 +2 1 0 1 0 +3 1 0 2 0 +... +N 3 7.5 3 2.5 :pre + +The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +NODES" where N is the number of nodes. The nodes do not need to be +listed in any particular order. There can be a different number of +nodes in each snapshot. The values on each node line are "ID type x y +z". + +The format of an element topology entry is in one of the following +styles (triangles, tetrahedra, squares, cubes): + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF TRIANGLES +200 +ITEM: TRIANGLES +1 1 1 13 12 +2 1 1 2 13 +3 1 2 14 13 +... +N 3 259 340 432 :pre + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF TETS +200 +ITEM: TETS +1 1 1 13 12 27 +2 1 1 2 13 35 +3 1 2 14 13 103 +... +N 3 259 340 432 1005 :pre + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF SQUARES +200 +ITEM: SQUARES +1 1 1 13 12 4 +2 1 1 2 13 6 +3 1 2 14 13 11 +... +N 3 259 340 432 500 :pre + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF CUBES +200 +ITEM: CUBES +1 1 1 13 12 5 3 6 10 20 +2 1 1 2 13 10 3 4 5 6 +3 1 2 14 13 15 10 18 19 +... +N 3 259 340 432 200 456 918 1002 988 :pre + +There are N lines following "ITEM: TRIANGLES" or "ITEM: TETS" or +"ITEM: SQUARES" or "ITEM: CUBES" where N is the number of elements. +The elements do not need to be listed in any particular order. There +can be a different number of elements in each snapshot. The values on +each element line are "ID type node1 node2 ... nodeN", where N depends +on the type of element. For triangles, N = 3, and the order should +give an outward normal via the right-hand rule. For tets, N = 4, and +the order should give a right-hand rule for the first 3 nodes that +points towards the 4th node. For squares, N = 4, and the nodes should +be listed in counter-clockwise order around the square. For cubes, N += 8, and the first 4 nodes are the lower face (ordered same as a +square), and the last 4 nodes are directly above the lower 4 as the +upper face. + +The format of a nodal values entry is as follows: + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF NODE VALUES +200 +ITEM: NODE VALUES +1 1 +2 1 +3 9 +... +N 32 :pre + +There are N lines following "ITEM: NODE VALUES" where N is the number +of nodes. The nodes do not need to be listed in any particular order. +There can be a different number of nodes in each snapshot, but it +should be consistent with the current nodal coordinates entry. The +values on each node line are "ID value1 value2 ..." where there are +as many columns as desired. Each line should have the same number of +values. + +The format of an element values entry is as follows: + +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ELEMENT VALUES +200 +ITEM: ELEMENT VALUES +1 1 +2 1 +3 9 +... +N 32 :pre + +There are N lines following "ITEM: ELEMENT VALUES" where N is the +number of elements. The elements do not need to be listed in any +particular order. There can be a different number of elements in each +snapshot, but it should be consistent with the current element +topology entry. The values on each element line are "ID value1 value2 +..." where there are as many columns as desired. Each line should +have the same number of values. The map() command can be used to +assign names to each of these columns of values. + +:line + +[Usage:] + +m = mdump("mesh.one") read in one or more mesh dump files +m = mdump("mesh.1 mesh.2.gz") can be gzipped +m = mdump("mesh.*") wildcard expands to multiple files +m = mdump("mesh.*",0) two args = store filenames, but don't read :pre + + incomplete and duplicate snapshots are deleted :pre + +time = m.next() read next snapshot from dump files :pre + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment or unscaling is performed :pre + +m.map(2,"temperature") assign names to element value columns (1-N) :pre + +m.tselect.all() select all timesteps +m.tselect.one(N) select only timestep N +m.tselect.none() deselect all timesteps +m.tselect.skip(M) select every Mth step +m.tselect.test("$t >= 100 and $t < 10000") select matching timesteps +m.delete() delete non-selected timesteps :pre + + selecting a timestep also selects all elements in the timestep + skip() and test() only select from currently selected timesteps + test() uses a Python Boolean expression with $t for timestep value + Python comparison syntax: == != < > <= >= and or :pre + +m.eselect.all() select all elems in all steps +m.eselect.all(N) select all elems in one step +m.eselect.test("$id > 100 and $type == 2") select match elems in all steps +m.eselect.test("$id > 100 and $type == 2",N) select matching elems in one step :pre + + all() with no args selects atoms from currently selected timesteps + test() with one arg selects atoms from currently selected timesteps + test() sub-selects from currently selected elements + test() uses a Python Boolean expression with $ for atom attributes + Python comparison syntax: == != < > <= >= and or + $name must end with a space :pre + +t = m.time() return vector of selected timestep values +fx,fy,... = m.vecs(1000,"fx","fy",...) return vector(s) for timestep N :pre + + vecs() returns vectors with one value for each selected elem in the timestep :pre + +index,time,flag = m.iterator(0/1) loop over mesh dump snapshots +time,box,atoms,bonds,tris,lines = m.viz(index) return list of viz objects +nodes,elements,nvalues,evalues = m.mviz(index) return list of mesh viz objects +m.etype = "color" set column returned as "type" by viz :pre + + iterator() loops over selected timesteps + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = index within dump object (0 to # of snapshots) + time = timestep value + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected elements for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\] + atoms = NULL + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + each element is decomposed into tris + lines = NULL + mviz() returns info for all elements for specified timestep index + can also call as mviz(time,1) and will find index of preceding snapshot + time = timestep value + box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\] + nodes = list of nodes = id,type,x,y,z + elements = list of elements = id,type,node1,node2,... + nvalues = list of node values = id,type,value1,value2,... + evalues = list of element values = id,type,value1,value2,... + etype is column name viz() will return as element type (def = "" = elem type) :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). diff --git a/doc/pair.html b/doc/pair.html new file mode 100644 index 0000000..ddc3b52 --- /dev/null +++ b/doc/pair.html @@ -0,0 +1,68 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    pair tool +

    +

    Purpose: +

    +

    Compute LAMMPS pairwise energies. +

    +

    Description: +

    +

    The pair tool computes a pairwise energy between 2 particles using a +LAMMPS molecular dynamics force field. Thus it can be used in an +analysis script to compute energies between groups of atoms from a +LAMMPS snapshot file. +

    +

    The pair constructor specifies the force field style. Only some of +the LAMMPS pair styles are currently included in this tool, but new +styles can easily be added. Code from the LAMMPS pair*.cpp file needs +to be re-coded in Python to make this work. +

    +

    The coeff() method reads the pairwise coefficients for the force field +from a data file object (see the data tool). The init() +method does pre-computations for the force field parameters needed by +the single() method which does a pairwise computation between two +atoms of type = itype,jtype separated by a squared distance rsq. The +arguments for init() and single() can be different for a particular +force field style. When you write the init() and single() methods for +a new style, you can define what arguments are needed. +

    +

    Usage: +

    +
    p = pair("lj/charmm/coul/charmm")   create pair object for specific pair style 
+
    +
      available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm 
+
    +
    p.coeff(d)			    extract pairwise coeffs from data object
+p.init(cut1,cut2,...)		    setup based on coeffs and cutoffs 
+
    +
      init args are specific to pair style:
+    lj/cut = cutlj
+    lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional)
+    lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul
+      (last 2 optional) 
+
    +
    e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...)   compute LJ/Coul energy 
+
    +
      pairwise energy between 2 atoms at distance rsq with their attributes
+  args are specific to pair style:
+    lj/cut = rsq,itype,jtype
+    lj/cut/coul/cut = rsq,itype,jtype,q1,q2
+    lj/charmm/coul/charmm = rsq,itype,jtype,q1,q2 
+
    +

    Related tools: +

    +

    data +

    +

    Prerequisites: none +

    + diff --git a/doc/pair.txt b/doc/pair.txt new file mode 100644 index 0000000..3c83085 --- /dev/null +++ b/doc/pair.txt @@ -0,0 +1,63 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +pair tool :h3 + +[Purpose:] + +Compute LAMMPS pairwise energies. + +[Description:] + +The pair tool computes a pairwise energy between 2 particles using a +LAMMPS molecular dynamics force field. Thus it can be used in an +analysis script to compute energies between groups of atoms from a +LAMMPS snapshot file. + +The pair constructor specifies the force field style. Only some of +the LAMMPS pair styles are currently included in this tool, but new +styles can easily be added. Code from the LAMMPS pair*.cpp file needs +to be re-coded in Python to make this work. + +The coeff() method reads the pairwise coefficients for the force field +from a data file object (see the "data"_data.html tool). The init() +method does pre-computations for the force field parameters needed by +the single() method which does a pairwise computation between two +atoms of type = itype,jtype separated by a squared distance rsq. The +arguments for init() and single() can be different for a particular +force field style. When you write the init() and single() methods for +a new style, you can define what arguments are needed. + +[Usage:] + +p = pair("lj/charmm/coul/charmm") create pair object for specific pair style :pre + + available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm :pre + +p.coeff(d) extract pairwise coeffs from data object +p.init(cut1,cut2,...) setup based on coeffs and cutoffs :pre + + init args are specific to pair style: + lj/cut = cutlj + lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional) + lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul + (last 2 optional) :pre + +e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy :pre + + pairwise energy between 2 atoms at distance rsq with their attributes + args are specific to pair style: + lj/cut = rsq,itype,jtype + lj/cut/coul/cut = rsq,itype,jtype,q1,q2 + lj/charmm/coul/charmm = rsq,itype,jtype,q1,q2 :pre + +[Related tools:] + +"data"_data.html + +[Prerequisites:] none diff --git a/doc/patch.html b/doc/patch.html new file mode 100644 index 0000000..cedef79 --- /dev/null +++ b/doc/patch.html @@ -0,0 +1,107 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    patch tool +

    +

    Purpose: +

    +

    Create patchy Lennard-Jones particles for LAMMPS input. +

    +

    Description: +

    +

    The patch tool creates large multi-atom particles and writes them out +as a LAMMPS data file. They need to be simulated with a soft +potential in LAMMPS to un-overlap them before they form a proper +ensemble. +

    +

    The individual particles consist of a collection of Lennard-Jones +atoms of various types. By defining force field coefficients +appropriately, specific atoms can be made attractive or repulsive, so +that "patches" of atoms on the particle surface are reactive. The +Pizza.py WWW site has example images and movies of simulations +using such particles. A paper by Sharon Glotzer's +group at U Michigan describing a variety of patchy particle +models was the motivation for this tool. +

    + + +

    The patch constructor takes a volume fraction as an argument to determine +how densely to fill the simulation box. Optionally, the box shape can +also be specified. +

    +

    The build() method creates N particles, each of speficied style and +with specified atom types. Several styles are available and new ones +can easily be added to patch.py. You will need to look in patch.py +for the details of what each style represents. For example, "hex2" +uses a C60 bucky ball as a template and creates hexagonal 6-atom +patches (atoms of a different type) on either side of the ball. +

    +

    The build() method can be invoked multiple times to create collections +of particles. The position and orientation of each particle is chosen +randomly. The seed value sets the random number generator used for +coordinate generation. +

    +

    The ensemble of chains is written to a LAMMPS data file via the +write() method. +

    +

    Usage: +

    +
    p = patch(vfrac)           setup box with a specified volume fraction
+p = patch(vfrac,1,1,2)     x,y,z = aspect ratio of box (def = 1,1,1) 
+
    +
    p.seed = 48379		   set random # seed (def = 12345)
+p.randomized = 0	   1 = choose next particle randomly, 0 = as generated
+p.dim = 2		   set dimension of created box (def = 3)
+p.blen = 0.97              set length of tether bonds (def = 0.97)
+p.dmin = 1.02              set min r from i-1 to i+1 tether site (def = 1.02)
+p.lattice = [Nx,Ny,Nz]     generate Nx by Ny by Nz lattice of particles 
+
    +
      if lattice is set, Nx*Ny*Nz must equal N for build
+  lattice = [0,0,0] = generate N particles randomly, default 
+
    +
    p.build(100,"hex2",1,2,3)  create 100 "hex2" particles with types 1,2,3 
+
    +
      can be invoked multiple times
+  keywords:
+    c60hex2: diam,1,2,3 = C-60 with 2 hex patches and ctr part, types 1,2,3
+    hex2: diam,1,2 = one large particle with 2 7-mer hex patches, types 1,2
+    hex4: diam,1,2 = one large particle with 4 7-mer hex patches, types 1,2
+    ring: diam,N,1,2 = one large part with equatorial ring of N, types 1,2
+    ball: diam,m1,m2,1,2,3 = large ball with m12-len tethers, types 1,2,3
+    tri5: 1,2 = 3-layer 5-size hollow tri, types 1,2
+    rod: N,m1,m2,1,2,3 = N-length rod with m12-len tethers, types 1,2,3
+    tri: N,m1,m2,m3,1,2,3,4 = N-size tri with m123-len tethers, types 1-4
+    hex: m1,m2,m3,m4,m5,m6,1,2,3,4,5,6,7 = 7-atom hex with m-len tethers, t 1-7
+    dimer: r,1 = two particles r apart, type 1, no bond
+    star2d: N,r,1 = 2d star of length N (odd), beads r apart, type 1, no bonds
+    box2d: N,M,r,1 = 2d NxM box, beads r apart, type 1, no bonds
+    tritet: A,m = 4-tri tet with edge length A, tri type m
+    tribox: Alo,Ahi,Blo,Bhi,Clo,Chi,m = 12-tri box with side lengths A,B,C & m
+    linebox: Alo,Ahi,Blo,Bhi,m = 4-line 2d rectangle with random side lengths
+                                 from Alo to Ahi and Blo to Bhi, line type m
+    linetri: Alo,Ahi,Blo,Bhi,m = 3-line 2d triangle with random base
+                                 from Alo to Ahi and height Blo to Bhi, type m 
+
    +
    p.write("data.patch")      write out system to LAMMPS data file 
+
    +

    Related tools: +

    +

    chain, data +

    +

    Prerequisites: none +

    +
    + + + +

    (Glotzer) Zhang and Glotzer, NanoLetters, 4, 1407-1413 (2004). +

    + diff --git a/doc/patch.txt b/doc/patch.txt new file mode 100644 index 0000000..a5e1783 --- /dev/null +++ b/doc/patch.txt @@ -0,0 +1,101 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +patch tool :h3 + +[Purpose:] + +Create patchy Lennard-Jones particles for LAMMPS input. + +[Description:] + +The patch tool creates large multi-atom particles and writes them out +as a LAMMPS data file. They need to be simulated with a soft +potential in LAMMPS to un-overlap them before they form a proper +ensemble. + +The individual particles consist of a collection of Lennard-Jones +atoms of various types. By defining force field coefficients +appropriately, specific atoms can be made attractive or repulsive, so +that "patches" of atoms on the particle surface are reactive. The +"Pizza.py WWW site"_pws has example images and movies of simulations +using such particles. A "paper"_#Glotzer by "Sharon Glotzer's +group"_glotzer at U Michigan describing a variety of patchy particle +models was the motivation for this tool. + +:link(glotzer,http://www.engin.umich.edu/dept/che/research/glotzer) + +The patch constructor takes a volume fraction as an argument to determine +how densely to fill the simulation box. Optionally, the box shape can +also be specified. + +The build() method creates N particles, each of speficied style and +with specified atom types. Several styles are available and new ones +can easily be added to patch.py. You will need to look in patch.py +for the details of what each style represents. For example, "hex2" +uses a C60 bucky ball as a template and creates hexagonal 6-atom +patches (atoms of a different type) on either side of the ball. + +The build() method can be invoked multiple times to create collections +of particles. The position and orientation of each particle is chosen +randomly. The seed value sets the random number generator used for +coordinate generation. + +The ensemble of chains is written to a LAMMPS data file via the +write() method. + +[Usage:] + +p = patch(vfrac) setup box with a specified volume fraction +p = patch(vfrac,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1) :pre + +p.seed = 48379 set random # seed (def = 12345) +p.randomized = 0 1 = choose next particle randomly, 0 = as generated +p.dim = 2 set dimension of created box (def = 3) +p.blen = 0.97 set length of tether bonds (def = 0.97) +p.dmin = 1.02 set min r from i-1 to i+1 tether site (def = 1.02) +p.lattice = \[Nx,Ny,Nz\] generate Nx by Ny by Nz lattice of particles :pre + + if lattice is set, Nx*Ny*Nz must equal N for build + lattice = \[0,0,0\] = generate N particles randomly, default :pre + +p.build(100,"hex2",1,2,3) create 100 "hex2" particles with types 1,2,3 :pre + + can be invoked multiple times + keywords: + c60hex2: diam,1,2,3 = C-60 with 2 hex patches and ctr part, types 1,2,3 + hex2: diam,1,2 = one large particle with 2 7-mer hex patches, types 1,2 + hex4: diam,1,2 = one large particle with 4 7-mer hex patches, types 1,2 + ring: diam,N,1,2 = one large part with equatorial ring of N, types 1,2 + ball: diam,m1,m2,1,2,3 = large ball with m12-len tethers, types 1,2,3 + tri5: 1,2 = 3-layer 5-size hollow tri, types 1,2 + rod: N,m1,m2,1,2,3 = N-length rod with m12-len tethers, types 1,2,3 + tri: N,m1,m2,m3,1,2,3,4 = N-size tri with m123-len tethers, types 1-4 + hex: m1,m2,m3,m4,m5,m6,1,2,3,4,5,6,7 = 7-atom hex with m-len tethers, t 1-7 + dimer: r,1 = two particles r apart, type 1, no bond + star2d: N,r,1 = 2d star of length N (odd), beads r apart, type 1, no bonds + box2d: N,M,r,1 = 2d NxM box, beads r apart, type 1, no bonds + tritet: A,m = 4-tri tet with edge length A, tri type m + tribox: Alo,Ahi,Blo,Bhi,Clo,Chi,m = 12-tri box with side lengths A,B,C & m + linebox: Alo,Ahi,Blo,Bhi,m = 4-line 2d rectangle with random side lengths + from Alo to Ahi and Blo to Bhi, line type m + linetri: Alo,Ahi,Blo,Bhi,m = 3-line 2d triangle with random base + from Alo to Ahi and height Blo to Bhi, type m :pre + +p.write("data.patch") write out system to LAMMPS data file :pre + +[Related tools:] + +"chain"_chain.html, "data"_data.html + +[Prerequisites:] none + +:line + +:link(Glotzer) +[(Glotzer)] Zhang and Glotzer, NanoLetters, 4, 1407-1413 (2004). diff --git a/doc/pdbfile.html b/doc/pdbfile.html new file mode 100644 index 0000000..3160988 --- /dev/null +++ b/doc/pdbfile.html @@ -0,0 +1,98 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    pdbfile tool +

    +

    Purpose: +

    +

    Read, write PDB files in combo with LAMMPS snapshots. +

    +

    Description: +

    +

    The pdbfile tool reads in PDB (Protein Data Bank) files of protein +coordinates and uses them in conjunction with LAMMPS snapshots in +various ways. The PDB format is commonly used by various +vizualization and analysis programs. +

    +

    The pdbfile constructor takes a string argument listing one or more +PDB filenames and a data argument with LAMMPS atom information +(data or dump object). The atom snapshots +must have "id", "type", "x", "y", and "z" defined; see the map() +methods of those tools. +

    +

    Both arguments to the constructor are optional, as described below. +If a single PDB file is given as a constructor argument, and it is 4 +letters long, and it does not exist on your system, then it is treated +as a PDB identifier and the matching PDB file is downloaded from a PDB +repository on the WWW to your machine. +

    +

    The one(), many(), and single() methods write out PDB files in various +manners, depending on the 1 or 2 arguments used in the constructor. +If only a string was specified (no data object), the specified PDB +files are written out as-is. Thus the one() method concatenates the +files together. If only a data object was specified (no string of PDB +files), then PDB files in a generic format (Lennard-Jones atoms) are +created. If both arguments are specified, then only a single PDB file +can be listed. It is treated as a template file, and the atom +coordinates in the data object replace the atom coordinates in the +template PDB file to create a series of new PDB files. This +replacement is only done for selected atoms (in the dump object) and +for atom IDs that appear in the PDB file. +

    +

    The iterator() method is called by the rasmol tool to +create a series of PDB files for visualization purposes. +

    +

    Usage: +

    +
    p = pdbfile("3CRO")         create pdb object from PDB file or WWW
+p = pdbfile("pep1 pep2")    read in multiple PDB files
+p = pdbfile("pep*")         can use wildcards
+p = pdbfile(d)              read in snapshot data with no PDB file
+p = pdbfile("3CRO",d)       read in single PDB file with snapshot data 
+
    +
      string arg contains one or more PDB files
+    don't need .pdb suffix except wildcard must expand to file.pdb
+    if only one 4-char file specified and it is not found,
+      it will be downloaded from http://www.rcsb.org as 3CRO.pdb
+  d arg is object with atom coordinates (dump, data) 
+
    +
    p.one()                     write all output as one big PDB file to tmp.pdb
+p.one("mine")               write to mine.pdb
+p.many()                    write one PDB file per snapshot: tmp0000.pdb, ...
+p.many("mine")              write as mine0000.pdb, mine0001.pdb, ...
+p.single(N)                 write timestamp N as tmp.pdb
+p.single(N,"new")           write as new.pdb 
+
    +
      how new PDB files are created depends on constructor inputs:
+    if no d: one new PDB file for each file in string arg (just a copy)
+    if only d specified: one new PDB file per snapshot in generic format
+    if one file in str arg and d: one new PDB file per snapshot
+      using input PDB file as template
+    multiple input PDB files with a d is not allowed 
+
    +
    index,time,flag = p.iterator(0)
+index,time,flag = p.iterator(1) 
+
    +
      iterator = loop over number of PDB files
+    call first time with arg = 0, thereafter with arg = 1
+    N = length = # of snapshots or # of input PDB files
+    index = index of snapshot or input PDB file (0 to N-1)
+    time = timestep value (time stamp for snapshot, index for multiple PDB)
+    flag = -1 when iteration is done, 1 otherwise
+  typically call p.single(time) in iterated loop to write out one PDB file 
+
    +

    Related tools: +

    +

    data, dump, rasmol +

    +

    Prerequisites: none +

    + diff --git a/doc/pdbfile.txt b/doc/pdbfile.txt new file mode 100644 index 0000000..f4bc92e --- /dev/null +++ b/doc/pdbfile.txt @@ -0,0 +1,93 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +pdbfile tool :h3 + +[Purpose:] + +Read, write PDB files in combo with LAMMPS snapshots. + +[Description:] + +The pdbfile tool reads in PDB (Protein Data Bank) files of protein +coordinates and uses them in conjunction with LAMMPS snapshots in +various ways. The PDB format is commonly used by various +vizualization and analysis programs. + +The pdbfile constructor takes a string argument listing one or more +PDB filenames and a data argument with LAMMPS atom information +("data"_data.html or "dump"_dump.html object). The atom snapshots +must have "id", "type", "x", "y", and "z" defined; see the map() +methods of those tools. + +Both arguments to the constructor are optional, as described below. +If a single PDB file is given as a constructor argument, and it is 4 +letters long, and it does not exist on your system, then it is treated +as a PDB identifier and the matching PDB file is downloaded from a PDB +repository on the WWW to your machine. + +The one(), many(), and single() methods write out PDB files in various +manners, depending on the 1 or 2 arguments used in the constructor. +If only a string was specified (no data object), the specified PDB +files are written out as-is. Thus the one() method concatenates the +files together. If only a data object was specified (no string of PDB +files), then PDB files in a generic format (Lennard-Jones atoms) are +created. If both arguments are specified, then only a single PDB file +can be listed. It is treated as a template file, and the atom +coordinates in the data object replace the atom coordinates in the +template PDB file to create a series of new PDB files. This +replacement is only done for selected atoms (in the dump object) and +for atom IDs that appear in the PDB file. + +The iterator() method is called by the "rasmol"_rasmol.html tool to +create a series of PDB files for visualization purposes. + +[Usage:] + +p = pdbfile("3CRO") create pdb object from PDB file or WWW +p = pdbfile("pep1 pep2") read in multiple PDB files +p = pdbfile("pep*") can use wildcards +p = pdbfile(d) read in snapshot data with no PDB file +p = pdbfile("3CRO",d) read in single PDB file with snapshot data :pre + + string arg contains one or more PDB files + don't need .pdb suffix except wildcard must expand to file.pdb + if only one 4-char file specified and it is not found, + it will be downloaded from http://www.rcsb.org as 3CRO.pdb + d arg is object with atom coordinates (dump, data) :pre + +p.one() write all output as one big PDB file to tmp.pdb +p.one("mine") write to mine.pdb +p.many() write one PDB file per snapshot: tmp0000.pdb, ... +p.many("mine") write as mine0000.pdb, mine0001.pdb, ... +p.single(N) write timestamp N as tmp.pdb +p.single(N,"new") write as new.pdb :pre + + how new PDB files are created depends on constructor inputs: + if no d: one new PDB file for each file in string arg (just a copy) + if only d specified: one new PDB file per snapshot in generic format + if one file in str arg and d: one new PDB file per snapshot + using input PDB file as template + multiple input PDB files with a d is not allowed :pre + +index,time,flag = p.iterator(0) +index,time,flag = p.iterator(1) :pre + + iterator = loop over number of PDB files + call first time with arg = 0, thereafter with arg = 1 + N = length = # of snapshots or # of input PDB files + index = index of snapshot or input PDB file (0 to N-1) + time = timestep value (time stamp for snapshot, index for multiple PDB) + flag = -1 when iteration is done, 1 otherwise + typically call p.single(time) in iterated loop to write out one PDB file :pre + +[Related tools:] + +"data"_data.html, "dump"_dump.html, "rasmol"_rasmol.html + +[Prerequisites:] none diff --git a/doc/plotview.html b/doc/plotview.html new file mode 100644 index 0000000..7604d40 --- /dev/null +++ b/doc/plotview.html @@ -0,0 +1,69 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    plotview tool +

    +

    Purpose: +

    +

    Plot multiple vectors from a data set. +

    +

    Description: +

    +

    The plotview tool displays a GUI for showing a series of plots of +vectors stored in another Pizza.py tool. Individual plots can be +displayed or hidden or saved to a file. +

    +

    The plotview constructor creates the GUI and takes a data object +(log, vec) and a plot object (gnu, +matlab) as arguments. +

    +

    The vectors in the data object are converted to individual plots. The +2nd thru Nth vectors are each plotted against the 1st vector to create +N-1 plots. One or more plots can be displayed simultaneously (right +buttons in GUI), but only one is selected at a time (left buttons in +GUI). The yes(), no(), and select() methods perform the same function +as the GUI buttons. +

    +

    The currently selected plot can be modified (title, range, etc) +by the methods of the plot object. +

    +

    The file() and save() methods (or corresponding GUI widgets) save the +currently selected plot to a PostScript file. +

    +

    Usage: +

    +
    p = plotview(d,pl)      create GUI for viewing plots 
+
    +
      d = Pizza.py object that contains vectors (log, vec)
+  pl = Pizza.py plotting object (gnu, matlab) 
+
    +
    p.select(2)             select one plot as current (1-N)
+p.yes(3)                toggle one plot's visibility
+p.no(3) 
+
    +
      only one plot is selected at a time
+  multiple plots can be visible at same time
+  select is same as clicking on left-side radio-button
+  yes/no is same as clicking on right-side checkbox 
+
    +
    p.x = "Time"            which vector is X vector (1st vec by default)
+p.file("pressure")      filename prefix for saving a plot
+p.save()                save currently selected plot to file.eps 
+
    +

    Related tools: +

    +

    log, gnu, matlab +

    +

    Prerequisites: +

    +

    Python Tkinter package. +

    + diff --git a/doc/plotview.txt b/doc/plotview.txt new file mode 100644 index 0000000..689eb6c --- /dev/null +++ b/doc/plotview.txt @@ -0,0 +1,64 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +plotview tool :h3 + +[Purpose:] + +Plot multiple vectors from a data set. + +[Description:] + +The plotview tool displays a GUI for showing a series of plots of +vectors stored in another Pizza.py tool. Individual plots can be +displayed or hidden or saved to a file. + +The plotview constructor creates the GUI and takes a data object +("log"_log.html, "vec"_vec.html) and a plot object ("gnu"_gnu.html, +"matlab"_matlab.html) as arguments. + +The vectors in the data object are converted to individual plots. The +2nd thru Nth vectors are each plotted against the 1st vector to create +N-1 plots. One or more plots can be displayed simultaneously (right +buttons in GUI), but only one is selected at a time (left buttons in +GUI). The yes(), no(), and select() methods perform the same function +as the GUI buttons. + +The currently selected plot can be modified (title, range, etc) +by the methods of the plot object. + +The file() and save() methods (or corresponding GUI widgets) save the +currently selected plot to a PostScript file. + +[Usage:] + +p = plotview(d,pl) create GUI for viewing plots :pre + + d = Pizza.py object that contains vectors (log, vec) + pl = Pizza.py plotting object (gnu, matlab) :pre + +p.select(2) select one plot as current (1-N) +p.yes(3) toggle one plot's visibility +p.no(3) :pre + + only one plot is selected at a time + multiple plots can be visible at same time + select is same as clicking on left-side radio-button + yes/no is same as clicking on right-side checkbox :pre + +p.x = "Time" which vector is X vector (1st vec by default) +p.file("pressure") filename prefix for saving a plot +p.save() save currently selected plot to file.eps :pre + +[Related tools:] + +"log"_log.html, "gnu"_gnu.html, "matlab"_matlab.html + +[Prerequisites:] + +Python Tkinter package. diff --git a/doc/rasmol.html b/doc/rasmol.html new file mode 100644 index 0000000..0ff9cb2 --- /dev/null +++ b/doc/rasmol.html @@ -0,0 +1,77 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    rasmol tool +

    +

    Purpose: +

    +

    3d visualization via RasMol program. +

    +

    Description: +

    +

    The rasmol tool is a wrapper on the RasMol +visualization program. RasMol is open source software and runs on +many platforms. The link above is for the Open Rasmol WWW site, not +the Protein Explorer WWW site. Protein Explorer is a derivative of +RasMol and runs primarily on Windows machines within a browser. This +Pizza.py tool wraps the original RasMol program, not Protein Explorer. +

    +

    The rasmol constructor takes a pdbfile object as its +argument which produces PDB files that RasMol reads in. The pdbfile +object can produce PDB files from a LAMMPS dump or data file, as well +as in other ways. +

    +

    The show() method runs RasMol on the atoms of snapshot N (converted to +a PDB file) and displays the resulting image stored as image.gif. +Either a default RasMol script or one you specify is used to format +the RasMol image. The all() method loops thru all selected snapshots +and runs RasMol on each one. The resulting image files are saved to +image0000.gif, image0001.gif, etc. The prefix "image" can be changed +via the file setting. +

    +

    A RasMol script can be created by running RasMol itself (outside of +Pizza.py), typing commands or choosing menu options to format the +display as desired, then typing "write script filename". +Alternatively the run() method will do this for you. It runs RasMol +on snapshot N and lets you interact with RasMol directly either via +typing or mouse operations in the RasMol window. When you type "quit" +or "exit" the script file will be saved (do not exit via the Rasmol +menu). +

    +

    Usage: +

    +
    r = rasmol(p)           create RasMol wrapper for pdb object p 
+
    +
    r.file = "image"        file prefix for created images (def = "image") 
+
    +
    r.show(N)               show snapshot at timestep N with default script
+r.show(N,"my.rasmol")   use file as RasMol script 
+
    +
    r.all()                 make images of all selected snapshots with def script
+r.all("my.rasmol")      use file as RasMol script 
+
    +
    r.run(N)                run RasMol interactivly on snapshot N
+r.run(N,"new.rasmol")                 adjust via mouse or RasMol commands
+r.run(N,"new.rasmol","old.rasmol")    type quit to save RasMol script file 
+
    +
      if 2 args, 2nd arg is new script file, else save to "tmp.rasmol"
+  if 3 args, 3rd arg is initial script file, else use default script 
+
    +

    Related tools: +

    +

    dump, gl, pdbfile, +raster, svg +

    +

    Prerequisites: +

    +

    The RasMol program. +

    + diff --git a/doc/rasmol.txt b/doc/rasmol.txt new file mode 100644 index 0000000..f937d3c --- /dev/null +++ b/doc/rasmol.txt @@ -0,0 +1,72 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +rasmol tool :h3 + +[Purpose:] + +3d visualization via RasMol program. + +[Description:] + +The rasmol tool is a wrapper on the "RasMol"_http://www.openrasmol.org +visualization program. RasMol is open source software and runs on +many platforms. The link above is for the Open Rasmol WWW site, not +the Protein Explorer WWW site. Protein Explorer is a derivative of +RasMol and runs primarily on Windows machines within a browser. This +Pizza.py tool wraps the original RasMol program, not Protein Explorer. + +The rasmol constructor takes a "pdbfile"_pdbfile.html object as its +argument which produces PDB files that RasMol reads in. The pdbfile +object can produce PDB files from a LAMMPS dump or data file, as well +as in other ways. + +The show() method runs RasMol on the atoms of snapshot N (converted to +a PDB file) and displays the resulting image stored as image.gif. +Either a default RasMol script or one you specify is used to format +the RasMol image. The all() method loops thru all selected snapshots +and runs RasMol on each one. The resulting image files are saved to +image0000.gif, image0001.gif, etc. The prefix "image" can be changed +via the file setting. + +A RasMol script can be created by running RasMol itself (outside of +Pizza.py), typing commands or choosing menu options to format the +display as desired, then typing "write script filename". +Alternatively the run() method will do this for you. It runs RasMol +on snapshot N and lets you interact with RasMol directly either via +typing or mouse operations in the RasMol window. When you type "quit" +or "exit" the script file will be saved (do not exit via the Rasmol +menu). + +[Usage:] + +r = rasmol(p) create RasMol wrapper for pdb object p :pre + +r.file = "image" file prefix for created images (def = "image") :pre + +r.show(N) show snapshot at timestep N with default script +r.show(N,"my.rasmol") use file as RasMol script :pre + +r.all() make images of all selected snapshots with def script +r.all("my.rasmol") use file as RasMol script :pre + +r.run(N) run RasMol interactivly on snapshot N +r.run(N,"new.rasmol") adjust via mouse or RasMol commands +r.run(N,"new.rasmol","old.rasmol") type quit to save RasMol script file :pre + + if 2 args, 2nd arg is new script file, else save to "tmp.rasmol" + if 3 args, 3rd arg is initial script file, else use default script :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "pdbfile"_pdbfile.html, +"raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +The RasMol program. diff --git a/doc/raster.html b/doc/raster.html new file mode 100644 index 0000000..da1f420 --- /dev/null +++ b/doc/raster.html @@ -0,0 +1,156 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    raster tool +

    +

    Purpose: +

    +

    3d visualization via Raster3d program. +

    +

    Description: +

    +

    The raster tool is a wrapper on the +Raster3d +visualization program. Raster3d is open source software and runs on +many platforms. +

    +

    The raster constructor takes a data object containing atom or mesh +snapshots as an argument (dump, data, +cdata, mdump). +

    +

    The show() method runs Raster3d on the selected atoms or triangles of +snapshot N and displays the resulting image stored as image.png. The +all() method loops thru all selected snapshots and runs Raster3d on +each one. The resulting image files are saved to image0000.png, +image0001.png, etc. The prefix "image" can be changed via the file +setting. +

    +

    The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the Raster3d image should +roughly fill the window and be centered. +

    +

    Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. +

    +

    The acol(), arad(), bcol(), brad(), and tcol() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the dump tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. +

    +

    Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from this WWW page which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. +

    + + +

    Usage: +

    +
    r = raster(d)               create Raster3d wrapper for data in d 
+
    +
      d = atom snapshot object (dump, data) 
+
    +
    r.bg("black")               set background color (def = "black")
+r.size(N)		    set image size to NxN
+r.size(N,M)		    set image size to NxM
+r.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
+r.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
+r.zoom(0.5)                 scale image by factor (def = 1)
+r.box(0/1/2)                0/1/2 = none/variable/fixed box
+r.box(0/1/2,"green")        set box color
+r.box(0/1/2,"red",4)        set box edge thickness
+r.file = "image"            file prefix for created images (def = "image") 
+
    +
    r.show(N)                   show image of snapshot at timestep N 
+
    +
    r.all()                     make images of all selected snapshots
+r.all(P)                    images of all, start file label at P
+r.all(N,M,P)                make M images of snapshot N, start label at P 
+
    +
    r.pan(60,135,1.0,40,135,1.5)    pan during all() operation
+r.pan()                         no pan during all() (default) 
+
    +
      args = z theta, azimuthal phi, zoom factor at beginning and end
+  values at each step are interpolated between beginning and end values 
+
    +
    r.select = "$x > %g*3.0"    string to pass to d.aselect.test() during all()
+r.select = ""               no extra aselect (default) 
+
    +
      %g varies from 0.0 to 1.0 from beginning to end of all() 
+
    +
    r.label(x,y,"h",size,"red","This is a label")    add label to each image
+r.nolabel()                                      delete all labels 
+
    +
      x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font
+  size = fontsize (e.g. 10), "red" = color of text 
+
    +
    r.acol(2,"green")		   set atom colors by atom type (1-N)
+r.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+r.acol(0,"blue")	           2nd arg = one color or list of colors
+r.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
+r.acol(range(10),"loop")           assign colors in loop, randomly ordered 
+
    +
      if 1st arg is 0, set all types to 2nd arg
+  if list of types has a 0 (e.g. range(10)), +1 is added to each value
+  interpolate means colors blend smoothly from one value to the next 
+
    +
    r.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol() 
+
    +
    r.bcol()			   set bond color, same args as acol()
+r.brad()			   set bond thickness, same args as arad() 
+
    +
    r.tcol()			   set triangle color, same args as acol()
+r.tfill()			   set triangle fill, 0 fill, 1 line, 2 both 
+
    +
    r.lcol()                           set line color, same args as acol()
+r.lrad()                           set line thickness, same args as arad() 
+
    +
    r.adef()                           set atom/bond/tri/line properties to default
+r.bdef()			   default = "loop" for colors, 0.45 for radii
+r.tdef()  			   default = 0.25 for bond/line thickness
+r.ldef()  			   default = 0 fill 
+
    +
      by default 100 types are assigned
+  if atom/bond/tri/line has type > # defined properties, is an error 
+
    +
    from vizinfo import colors         access color list
+print colors                       list defined color names and RGB values
+colors["nickname"] = [R,G,B]       set new RGB values from 0 to 255 
+
    +
      140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc 
+
    +

    Related tools: +

    +

    dump, gl, rasmol, svg +

    +

    Prerequisites: +

    +

    The Raster3d render and label3d programs. +

    + diff --git a/doc/raster.txt b/doc/raster.txt new file mode 100644 index 0000000..6f4ef64 --- /dev/null +++ b/doc/raster.txt @@ -0,0 +1,151 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +raster tool :h3 + +[Purpose:] + +3d visualization via Raster3d program. + +[Description:] + +The raster tool is a wrapper on the +"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html +visualization program. Raster3d is open source software and runs on +many platforms. + +The raster constructor takes a data object containing atom or mesh +snapshots as an argument ("dump"_dump.html, "data"_data.html, +"cdata"_cdata.html, "mdump"_mdump.html). + +The show() method runs Raster3d on the selected atoms or triangles of +snapshot N and displays the resulting image stored as image.png. The +all() method loops thru all selected snapshots and runs Raster3d on +each one. The resulting image files are saved to image0000.png, +image0001.png, etc. The prefix "image" can be changed via the file +setting. + +The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the Raster3d image should +roughly fill the window and be centered. + +Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. + +The acol(), arad(), bcol(), brad(), and tcol() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the "dump"_dump.html tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. + +Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from "this WWW page"_colortable which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. + +:link(colortable,http://www.oreilly.com/catalog/wdnut/excerpt/color_names.html) + +[Usage:] + +r = raster(d) create Raster3d wrapper for data in d :pre + + d = atom snapshot object (dump, data) :pre + +r.bg("black") set background color (def = "black") +r.size(N) set image size to NxN +r.size(N,M) set image size to NxM +r.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +r.shift(x,y) translate by x,y pixels in view window (def = 0,0) +r.zoom(0.5) scale image by factor (def = 1) +r.box(0/1/2) 0/1/2 = none/variable/fixed box +r.box(0/1/2,"green") set box color +r.box(0/1/2,"red",4) set box edge thickness +r.file = "image" file prefix for created images (def = "image") :pre + +r.show(N) show image of snapshot at timestep N :pre + +r.all() make images of all selected snapshots +r.all(P) images of all, start file label at P +r.all(N,M,P) make M images of snapshot N, start label at P :pre + +r.pan(60,135,1.0,40,135,1.5) pan during all() operation +r.pan() no pan during all() (default) :pre + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values :pre + +r.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +r.select = "" no extra aselect (default) :pre + + %g varies from 0.0 to 1.0 from beginning to end of all() :pre + +r.label(x,y,"h",size,"red","This is a label") add label to each image +r.nolabel() delete all labels :pre + + x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font + size = fontsize (e.g. 10), "red" = color of text :pre + +r.acol(2,"green") set atom colors by atom type (1-N) +r.acol(\[2,4\],\["red","blue"\]) 1st arg = one type or list of types +r.acol(0,"blue") 2nd arg = one color or list of colors +r.acol(range(20),\["red","blue"\]) if list lengths unequal, interpolate +r.acol(range(10),"loop") assign colors in loop, randomly ordered :pre + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next :pre + +r.arad(\[1,2\],\[0.5,0.3\]) set atom radii, same rules as acol() :pre + +r.bcol() set bond color, same args as acol() +r.brad() set bond thickness, same args as arad() :pre + +r.tcol() set triangle color, same args as acol() +r.tfill() set triangle fill, 0 fill, 1 line, 2 both :pre + +r.lcol() set line color, same args as acol() +r.lrad() set line thickness, same args as arad() :pre + +r.adef() set atom/bond/tri/line properties to default +r.bdef() default = "loop" for colors, 0.45 for radii +r.tdef() default = 0.25 for bond/line thickness +r.ldef() default = 0 fill :pre + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error :pre + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors\["nickname"\] = \[R,G,B\] set new RGB values from 0 to 255 :pre + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "rasmol"_rasmol.html, "svg"_svg.html + +[Prerequisites:] + +The Raster3d render and label3d programs. diff --git a/doc/svg.html b/doc/svg.html new file mode 100644 index 0000000..a317725 --- /dev/null +++ b/doc/svg.html @@ -0,0 +1,158 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    svg tool +

    +

    Purpose: +

    +

    3d visualization via SVG files. +

    +

    Description: +

    +

    The svg tool creates Scalable Vector Graphics +(SVG) files from atom or mesh +snapshots. The SVG format can be displayed or animated by various +tools and is a popular format for viewing solid state lattices. +

    +

    The svg constructor takes a data object containing atom or mesh +snapshots as an argument (dump, data, +cdata, mdump). +

    +

    The show() method creates an image.svg file for snapshot N. The all() +method loops thru all selected snapshots and creates the image files +image0000.svg, image0001.svg, etc. The prefix "image" can be changed +via the file setting. +

    +

    The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the Raster3d image should +roughly fill the window and be centered. +

    +

    Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. +

    +

    The acol(), arad(), bcol(), brad(), and tcol() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the dump tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. +

    +

    Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from this WWW page which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. +

    + + +

    Usage: +

    +
    s = svg(d)                  create SVG object for data in d 
+
    +
      d = atom snapshot object (dump, data) 
+
    +
    s.bg("black")               set background color (def = "black")
+s.size(N)		    set image size to NxN
+s.size(N,M)		    set image size to NxM
+s.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
+s.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
+s.zoom(0.5)                 scale image by factor (def = 1)
+s.box(0/1/2)                0/1/2 = none/variable/fixed box
+s.box(0/1/2,"green")        set box color
+s.box(0/1/2,"red",4)        set box edge thickness
+s.file = "image"            file prefix for created images (def = "image") 
+
    +
    s.show(N)                   show image of snapshot at timestep N 
+
    +
    s.all()                     make images of all selected snapshots
+s.all(P)                    images of all, start file label at P
+s.all(N,M,P)                make M images of snapshot N, start label at P 
+
    +
    s.pan(60,135,1.0,40,135,1.5)    pan during all() operation
+s.pan()                         no pan during all() (default) 
+
    +
      args = z theta, azimuthal phi, zoom factor at beginning and end
+  values at each step are interpolated between beginning and end values 
+
    +
    s.select = "$x > %g*3.0"    string to pass to d.aselect.test() during all()
+s.select = ""               no extra aselect (default) 
+
    +
      %g varies from 0.0 to 1.0 from beginning to end of all() 
+
    +
    s.label(x,y,"h",size,"red","This is a label")    add label to each image
+s.nolabel()                                      delete all labels 
+
    +
      x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font
+  size = fontsize (e.g. 10), "red" = color of text 
+
    +
    s.acol(2,"green")		   set atom colors by atom type (1-N)
+s.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+s.acol(0,"blue")          	   2nd arg = one color or list of colors
+s.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
+s.acol(range(10),"loop")           assign colors in loop, randomly ordered 
+
    +
      if 1st arg is 0, set all types to 2nd arg
+  if list of types has a 0 (e.g. range(10)), +1 is added to each value
+  interpolate means colors blend smoothly from one value to the next 
+
    +
    s.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol() 
+
    +
    s.bcol()			   set bond color, same args as acol()
+s.brad()			   set bond thickness, same args as arad() 
+
    +
    s.tcol()			   set triangle color, same args as acol()
+s.tfill()			   set triangle fill, 0 fill, 1 line, 2 both 
+
    +
    s.lcol()                           set line color, same args as acol()
+s.lrad()                           set line thickness, same args as arad() 
+
    +
    s.adef()                           set atom/bond/tri/line properties to default
+s.bdef()			   default = "loop" for colors, 0.45 for radii
+s.tdef()  			   default = 0.25 for bond/line thickness
+s.ldef()  			   default = 0 fill 
+
    +
      by default 100 types are assigned
+  if atom/bond/tri/line has type > # defined properties, is an error 
+
    +
    from vizinfo import colors         access color list
+print colors                       list defined color names and RGB values
+colors["nickname"] = [R,G,B]       set new RGB values from 0 to 255 
+
    +
      140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc 
+
    +
    Settings specific to svg tool: 
+
    +
    s.thick = 2.0               pixel thickness of black atom border 
+
    +

    Related tools: +

    +

    dump, gl, raster, rasmol +

    +

    Prerequisites: +

    +

    Display program for viewing *.svg image files. +

    + diff --git a/doc/svg.txt b/doc/svg.txt new file mode 100644 index 0000000..770a064 --- /dev/null +++ b/doc/svg.txt @@ -0,0 +1,153 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +svg tool :h3 + +[Purpose:] + +3d visualization via SVG files. + +[Description:] + +The svg tool creates Scalable Vector Graphics +("SVG"_http://www.w3.org/Graphics/SVG) files from atom or mesh +snapshots. The SVG format can be displayed or animated by various +tools and is a popular format for viewing solid state lattices. + +The svg constructor takes a data object containing atom or mesh +snapshots as an argument ("dump"_dump.html, "data"_data.html, +"cdata"_cdata.html, "mdump"_mdump.html). + +The show() method creates an image.svg file for snapshot N. The all() +method loops thru all selected snapshots and creates the image files +image0000.svg, image0001.svg, etc. The prefix "image" can be changed +via the file setting. + +The bg(), size(), rotate(), trans(), zoom(), box(), label(), and +nolabel() methods control various aspects of the images produced. +Without the trans() and zoom() settings, the Raster3d image should +roughly fill the window and be centered. + +Additional movie effects can be produced using the pan() and select() +methods. The pan() method specifies an initial and final viewpoint +that is applied to the images produced by the all() method. For +intermediate images, the view parameters will be interpolated between +their initial and final values. The pan() method can thus be used to +rotate a single image or fly-by the simulation as it animates. The +select() method performs additional atom selection for each image of +the all() sequence. An image-dependent %g variable can be used in the +select() string. The select() method can thus be used to slice thru +the data set. + +The acol(), arad(), bcol(), brad(), and tcol() methods change +attributes of the atoms, bonds, and triangles displayed. Each atom or +bond returned from the data object has an integer "type" from 1 to N. +The type is used to index into a list of RGB colors or radii for atoms +and bond thickness. The adef(), bdef(), and tdef() methods setup +default mappings of types to colors/radii. The other methods enable +specific assignments to be made. The interpolation option (e.g. many +types assigned to a few colors), enables a smooth rainbow of colors to +be assigned to a range of types. Note that the "dump"_dump.html tool +allows any vector to be returned as an atom "type" via its atype +setting. Thus displayed colors can be keyed to atom velocity or other +properties. + +Colors are specified with a string, e.g. "red". There are 140 +pre-defined colors from "this WWW page"_colortable which can be +examined by importing the "colors" variable from "vizinfo". New +colors can be defined by assigning a nickname of your choice to an RGB +triplet, as described below. + +:link(colortable,http://www.oreilly.com/catalog/wdnut/excerpt/color_names.html) + +[Usage:] + +s = svg(d) create SVG object for data in d :pre + + d = atom snapshot object (dump, data) :pre + +s.bg("black") set background color (def = "black") +s.size(N) set image size to NxN +s.size(N,M) set image size to NxM +s.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +s.shift(x,y) translate by x,y pixels in view window (def = 0,0) +s.zoom(0.5) scale image by factor (def = 1) +s.box(0/1/2) 0/1/2 = none/variable/fixed box +s.box(0/1/2,"green") set box color +s.box(0/1/2,"red",4) set box edge thickness +s.file = "image" file prefix for created images (def = "image") :pre + +s.show(N) show image of snapshot at timestep N :pre + +s.all() make images of all selected snapshots +s.all(P) images of all, start file label at P +s.all(N,M,P) make M images of snapshot N, start label at P :pre + +s.pan(60,135,1.0,40,135,1.5) pan during all() operation +s.pan() no pan during all() (default) :pre + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values :pre + +s.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +s.select = "" no extra aselect (default) :pre + + %g varies from 0.0 to 1.0 from beginning to end of all() :pre + +s.label(x,y,"h",size,"red","This is a label") add label to each image +s.nolabel() delete all labels :pre + + x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font + size = fontsize (e.g. 10), "red" = color of text :pre + +s.acol(2,"green") set atom colors by atom type (1-N) +s.acol(\[2,4\],\["red","blue"\]) 1st arg = one type or list of types +s.acol(0,"blue") 2nd arg = one color or list of colors +s.acol(range(20),\["red","blue"\]) if list lengths unequal, interpolate +s.acol(range(10),"loop") assign colors in loop, randomly ordered :pre + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next :pre + +s.arad(\[1,2\],\[0.5,0.3\]) set atom radii, same rules as acol() :pre + +s.bcol() set bond color, same args as acol() +s.brad() set bond thickness, same args as arad() :pre + +s.tcol() set triangle color, same args as acol() +s.tfill() set triangle fill, 0 fill, 1 line, 2 both :pre + +s.lcol() set line color, same args as acol() +s.lrad() set line thickness, same args as arad() :pre + +s.adef() set atom/bond/tri/line properties to default +s.bdef() default = "loop" for colors, 0.45 for radii +s.tdef() default = 0.25 for bond/line thickness +s.ldef() default = 0 fill :pre + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error :pre + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors\["nickname"\] = \[R,G,B\] set new RGB values from 0 to 255 :pre + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc :pre + +Settings specific to svg tool: :pre + +s.thick = 2.0 pixel thickness of black atom border :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "rasmol"_rasmol.html + +[Prerequisites:] + +Display program for viewing *.svg image files. diff --git a/doc/tdump.html b/doc/tdump.html new file mode 100644 index 0000000..fa23862 --- /dev/null +++ b/doc/tdump.html @@ -0,0 +1,122 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    tdump tool +

    +

    Purpose: +

    +

    Read dump files with triangle info. +

    +

    Description: +

    +

    The tdump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each atom contains triangle segment info from a +LAMMPS simulation using atom_style tri. Other tools use tdump objects +to extract triangle info for visualization, like the dump tool via its +extra() method. +

    +

    The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. +

    +

    The map() method assigns names to columns of atom attributes. The +id,type, corner1x,corner1y,corner1z, corner2x,corner2y,corner2z, +corner3x,corner3y,corner3z names must be assigned in order for line +segment info to be extracted. +

    +

    The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). +

    +
    + +

    Normally, LAMMPS creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: +

    +
    ITEM: TIMESTEP
+100
+ITEM: NUMBER OF ATOMS
+32
+ITEM: BOX BOUNDS
+0 3.35919
+0 3.35919
+0 7.50
+ITEM: ATOMS
+1 1 0 0 0 
+2 1 0.25 0.25 0
+3 1 0.25 0 0.25
+...
+N 3 0.7 0.5 0.6 
+
    +

    The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. Atoms do not have to be listed +in any particular order. There can be a different number of atoms in +each snapshot. Each line must contain the atom ID, type, and the end +points of the associated line segment, as specified by the map() +command. +

    +
    + +

    Usage: +

    +
    t = tdump("dump.one")             read in one or more dump files
+t = tdump("dump.1 dump.2.gz")	  can be gzipped
+t = tdump("dump.*")		  wildcard expands to multiple files
+t = tdump("dump.*",0)		  two args = store filenames, but don't read 
+
    +
      incomplete and duplicate snapshots are deleted
+  no column name assignment is performed 
+
    +
    time = t.next()             	  read next snapshot from dump files 
+
    +
      used with 2-argument constructor to allow reading snapshots one-at-a-time
+  snapshot will be skipped only if another snapshot has same time stamp
+  return time stamp of snapshot read
+  return -1 if no snapshots left or last snapshot is incomplete
+  no column name assignment is performed 
+
    +
    t.map(1,"id",3,"x")               assign names to atom columns (1-N) 
+
    +
      must assign id,type,corner1x,corner1y,corner1z,corner2x,corner2y,corner2z,corner3x,corner3y,corner3z 
+
    +
    time,box,atoms,bonds,tris,lines = t.viz(index)   return list of viz objects 
+
    +
      viz() returns line info for specified timestep index
+    can also call as viz(time,1) and will find index of preceding snapshot
+    time = timestep value
+    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
+    atoms = NULL
+    bonds = NULL
+    tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3 for each tri as 2d array
+      id,type are from associated atom
+    lines = NULL 
+
    +
    t.owrap(...)		          wrap tris to same image as their atoms 
+
    +
      owrap() is called by dump tool's owrap()
+  useful for wrapping all molecule's atoms/tris the same so it is contiguous 
+
    +

    Related tools: +

    +

    dump, gl, raster, svg +

    +

    Prerequisites: +

    +

    Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). +

    + diff --git a/doc/tdump.txt b/doc/tdump.txt new file mode 100644 index 0000000..4e7ecd6 --- /dev/null +++ b/doc/tdump.txt @@ -0,0 +1,117 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +tdump tool :h3 + +[Purpose:] + +Read dump files with triangle info. + +[Description:] + +The tdump tool reads one or more LAMMPS dump files, and stores their +contents as a series of snapshots with 2d arrays of atom attributes. +It is assumed that each atom contains triangle segment info from a +LAMMPS simulation using atom_style tri. Other tools use tdump objects +to extract triangle info for visualization, like the dump tool via its +extra() method. + +The constructor method is passed a string containing one or more dump +filenames. They can be listed in any order since snapshots are sorted +by timestep after they are read and duplicate snapshots (with the same +time stamp) are deleted. If a 2nd argument is specified, the files +are not immediately read, but snapshots can be read one-at-a-time by +the next() method. + +The map() method assigns names to columns of atom attributes. The +id,type, corner1x,corner1y,corner1z, corner2x,corner2y,corner2z, +corner3x,corner3y,corner3z names must be assigned in order for line +segment info to be extracted. + +The viz() method is called by Pizza.py tools that visualize snapshots +of atoms (e.g. gl, raster, svg tools). + +:line + +Normally, "LAMMPS"_http://lammps.sandia.gov creates the dump files +read in by this tool. If you want to create them yourself, the format +of LAMMPS dump files is simple. Each snapshot is formatted as +follows: + +ITEM: TIMESTEP +100 +ITEM: NUMBER OF ATOMS +32 +ITEM: BOX BOUNDS +0 3.35919 +0 3.35919 +0 7.50 +ITEM: ATOMS +1 1 0 0 0 +2 1 0.25 0.25 0 +3 1 0.25 0 0.25 +... +N 3 0.7 0.5 0.6 :pre + +The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the +next line, zlo zhi on the last. There are N lines following "ITEM: +ATOMS" where N is the number of atoms. Atoms do not have to be listed +in any particular order. There can be a different number of atoms in +each snapshot. Each line must contain the atom ID, type, and the end +points of the associated line segment, as specified by the map() +command. + +:line + +[Usage:] + +t = tdump("dump.one") read in one or more dump files +t = tdump("dump.1 dump.2.gz") can be gzipped +t = tdump("dump.*") wildcard expands to multiple files +t = tdump("dump.*",0) two args = store filenames, but don't read :pre + + incomplete and duplicate snapshots are deleted + no column name assignment is performed :pre + +time = t.next() read next snapshot from dump files :pre + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed :pre + +t.map(1,"id",3,"x") assign names to atom columns (1-N) :pre + + must assign id,type,corner1x,corner1y,corner1z,corner2x,corner2y,corner2z,corner3x,corner3y,corner3z :pre + +time,box,atoms,bonds,tris,lines = t.viz(index) return list of viz objects :pre + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\] + atoms = NULL + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3 for each tri as 2d array + id,type are from associated atom + lines = NULL :pre + +t.owrap(...) wrap tris to same image as their atoms :pre + + owrap() is called by dump tool's owrap() + useful for wrapping all molecule's atoms/tris the same so it is contiguous :pre + +[Related tools:] + +"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "svg"_svg.html + +[Prerequisites:] + +Numeric or NumPy Python packages. Gunzip command (if you want to read +gzipped files). diff --git a/doc/tools.jpg b/doc/tools.jpg new file mode 100644 index 0000000..d1ed2d0 Binary files /dev/null and b/doc/tools.jpg differ diff --git a/doc/vcr.html b/doc/vcr.html new file mode 100644 index 0000000..e8d10a5 --- /dev/null +++ b/doc/vcr.html @@ -0,0 +1,94 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    vcr tool +

    +

    Purpose: +

    +

    VCR-style GUI for 3d interactive OpenGL visualization. +

    +

    Description: +

    +

    The vcr tool displays a GUI to do 3d interactive visualization of +LAMMPS snapshots or data files. It is a wrapper on the gl +tool which draws the individual images in OpenGL windows +

    +

    The vcr constructor creates the GUI. Note that multiple OpenGL +windows can be run by the same GUI so that multiple views of the same +data set can be manipulated simultaneously (or views of different data +sets so long as they have the same # of snapshots). +

    +

    The view can be controlled by the GUI widgets or by invoking the tool +methods: play(), stop(), axis(), etc. The frame slider can be dragged +to view a desired frame. The mouse can also be used in the OpenGL +window to translage, rotate, or zoom the scene. The clipping sliders +or methods can be used to narrow the view of displayed data, though +their interactivity can be slow for scenes with lots of data. +

    +

    The reload() method is needed if you change the selection attributes +of the underlying data assigned to the gl tool, such as via +the dump tool's methods. These changes will not be +visible in the OpenGL windows until the data is reloaded. +

    +

    The save() method will save the current OpenGL window contents +to a PNG file. If multiple OpenGL windows are being used, multiple +files will be created. The save-all checkbox or method will store one +file per snapshot if the Play or Back buttons are used to start an +animation. +

    +

    Usage: +

    +
    v = vcr(gl1,gl2,...)       start vcr GUI with one or more gl windows
+v.add(gl)                  add a gl window to vcr GUI 
+
    +
    Actions (same as GUI widgets): 
+
    +
    v.first()		   go to first frame
+v.prev()                   go to previous frame
+v.back()                   play backwards from current frame to start
+v.stop()         	   stop on current frame		
+v.play()                   play from current frame to end
+v.next()		   go to next frame
+v.last()		   go to last frame 
+
    +
    v.frame(31)    	           set frame slider
+v.delay(0.4)     	   set delay slider
+v.q(5)          	   set quality slider 
+
    +
    v.xaxis()		   view scene from x axis
+v.yaxis()  		   view scene from y axis
+v.zaxis()		   view scene from z axis
+v.box()		 	   toggle bounding box
+v.axis() 	           toggle display of xyz axes
+v.norm()	           recenter and resize the view
+v.ortho()	           toggle ortho/perspective button
+v.reload()           	   reload all frames from gl viewer data files 
+
    +
    v.clipxlo(0.2)             clip scene at x lo fraction of box
+v.clipxhi(1.0)             clip at x hi
+v.clipylo(0.2)             clip in y
+v.clipyhi(1.0)
+v.clipzlo(0.2)             clip in z
+v.clipzhi(1.0) 
+
    +
    v.save()		   save current scene to file.png
+v.file("image")		   set filename
+v.saveall()		   toggle save-all checkbox 
+
    +

    Related tools: +

    +

    animate, gl +

    +

    Prerequisites: +

    +

    Python Tkinter package. +

    + diff --git a/doc/vcr.txt b/doc/vcr.txt new file mode 100644 index 0000000..cee15a4 --- /dev/null +++ b/doc/vcr.txt @@ -0,0 +1,89 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +vcr tool :h3 + +[Purpose:] + +VCR-style GUI for 3d interactive OpenGL visualization. + +[Description:] + +The vcr tool displays a GUI to do 3d interactive visualization of +LAMMPS snapshots or data files. It is a wrapper on the "gl"_gl.html +tool which draws the individual images in OpenGL windows + +The vcr constructor creates the GUI. Note that multiple OpenGL +windows can be run by the same GUI so that multiple views of the same +data set can be manipulated simultaneously (or views of different data +sets so long as they have the same # of snapshots). + +The view can be controlled by the GUI widgets or by invoking the tool +methods: play(), stop(), axis(), etc. The frame slider can be dragged +to view a desired frame. The mouse can also be used in the OpenGL +window to translage, rotate, or zoom the scene. The clipping sliders +or methods can be used to narrow the view of displayed data, though +their interactivity can be slow for scenes with lots of data. + +The reload() method is needed if you change the selection attributes +of the underlying data assigned to the "gl"_gl.html tool, such as via +the "dump"_dump.html tool's methods. These changes will not be +visible in the OpenGL windows until the data is reloaded. + +The save() method will save the current OpenGL window contents +to a PNG file. If multiple OpenGL windows are being used, multiple +files will be created. The save-all checkbox or method will store one +file per snapshot if the Play or Back buttons are used to start an +animation. + +[Usage:] + +v = vcr(gl1,gl2,...) start vcr GUI with one or more gl windows +v.add(gl) add a gl window to vcr GUI :pre + +Actions (same as GUI widgets): :pre + +v.first() go to first frame +v.prev() go to previous frame +v.back() play backwards from current frame to start +v.stop() stop on current frame +v.play() play from current frame to end +v.next() go to next frame +v.last() go to last frame :pre + +v.frame(31) set frame slider +v.delay(0.4) set delay slider +v.q(5) set quality slider :pre + +v.xaxis() view scene from x axis +v.yaxis() view scene from y axis +v.zaxis() view scene from z axis +v.box() toggle bounding box +v.axis() toggle display of xyz axes +v.norm() recenter and resize the view +v.ortho() toggle ortho/perspective button +v.reload() reload all frames from gl viewer data files :pre + +v.clipxlo(0.2) clip scene at x lo fraction of box +v.clipxhi(1.0) clip at x hi +v.clipylo(0.2) clip in y +v.clipyhi(1.0) +v.clipzlo(0.2) clip in z +v.clipzhi(1.0) :pre + +v.save() save current scene to file.png +v.file("image") set filename +v.saveall() toggle save-all checkbox :pre + +[Related tools:] + +"animate"_animate.html, "gl"_gl.html + +[Prerequisites:] + +Python Tkinter package. diff --git a/doc/vec.html b/doc/vec.html new file mode 100644 index 0000000..8b72ec9 --- /dev/null +++ b/doc/vec.html @@ -0,0 +1,60 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    vec tool +

    +

    Purpose: +

    +

    Create numeric vectors from columns in file or list of vecs. +

    +

    Description: +

    +

    The vec tool creates numeric vectors that can be extracted, written to +files, or imported into other tools like plotview for +plotting. +

    +

    The vec constructor takes either a file or list argument. For a file +argument, columns of numeric data are read from the file. Blank lines +or lines that do not start with a numeric character (0123456789.-) are +skipped. Each column must have the same number of values. For a list +argument, each element of the list is assumed to be a vector of values +(i.e. the list is a list of lists), as shown in the example below. +

    +

    The columns of data may be accessed by number (1-N) or by name ("col1" +thru "colN"). +

    +

    The get() and write() methods extract the numeric vectors of data. +

    +

    Usage: +

    +
    v = vec("file1")                    read in numeric vectors from a file
+v = vec(array)                      array = list of numeric vectors 
+
    +
      skip blank lines and lines that start with non-numeric characters
+  example array with 2 vecs = [[1,2,3,4,5], [10,20,30,40,50]]
+  assigns names = "col1", "col2", etc 
+
    +
    nvec = v.nvec                       # of vectors
+nlen = v.nlen		            lengths of vectors
+names = v.names		            list of vector names
+x,y,... = l.get(1,"col2",...)       return one or more vectors of values
+l.write("file.txt")	            write all vectors to a file
+l.write("file.txt","col1",7,...)    write listed vectors to a file 
+
    +
      get and write allow abbreviated (uniquely) vector names or digits (1-Nvec) 
+
    +

    Related tools: +

    +

    data, dump +

    +

    Prerequisites: none +

    + diff --git a/doc/vec.txt b/doc/vec.txt new file mode 100644 index 0000000..4196352 --- /dev/null +++ b/doc/vec.txt @@ -0,0 +1,55 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +vec tool :h3 + +[Purpose:] + +Create numeric vectors from columns in file or list of vecs. + +[Description:] + +The vec tool creates numeric vectors that can be extracted, written to +files, or imported into other tools like "plotview"_plotview.html for +plotting. + +The vec constructor takes either a file or list argument. For a file +argument, columns of numeric data are read from the file. Blank lines +or lines that do not start with a numeric character (0123456789.-) are +skipped. Each column must have the same number of values. For a list +argument, each element of the list is assumed to be a vector of values +(i.e. the list is a list of lists), as shown in the example below. + +The columns of data may be accessed by number (1-N) or by name ("col1" +thru "colN"). + +The get() and write() methods extract the numeric vectors of data. + +[Usage:] + +v = vec("file1") read in numeric vectors from a file +v = vec(array) array = list of numeric vectors :pre + + skip blank lines and lines that start with non-numeric characters + example array with 2 vecs = \[\[1,2,3,4,5\], \[10,20,30,40,50\]\] + assigns names = "col1", "col2", etc :pre + +nvec = v.nvec # of vectors +nlen = v.nlen lengths of vectors +names = v.names list of vector names +x,y,... = l.get(1,"col2",...) return one or more vectors of values +l.write("file.txt") write all vectors to a file +l.write("file.txt","col1",7,...) write listed vectors to a file :pre + + get and write allow abbreviated (uniquely) vector names or digits (1-Nvec) :pre + +[Related tools:] + +"data"_data.html, "dump"_dump.html + +[Prerequisites:] none diff --git a/doc/vmd.html b/doc/vmd.html new file mode 100644 index 0000000..e67c543 --- /dev/null +++ b/doc/vmd.html @@ -0,0 +1,60 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    vmd tool +

    +

    Purpose: +

    +

    Control VMD from python. +

    +

    Description: +

    +

    The vmd tool is a simple wrapper on the VMD visualization +package, a popular tool for visualizing snapshots from molecular +dynamics simulations. +

    + + +

    The vmd constructor invokes VMD in its own window. Data can be passed +to it for visualization via the new(), data(), replace(), and append() +methods. The other methods permit more specialized interactions with +VMD through its command syntax. +

    +

    Usage: +

    +
    v = vmd()		       start up VMD
+v.stop()		       shut down VMD instance
+v.clear()		       delete all visualizations 
+
    +
    v.rep(style)		       set default representation style. One of
+			       (Lines|VDW|Licorice|DynamicBonds|Points|CPK) 
+v.new(file[,type])   	       load new file (default file type 'lammpstrj')
+v.data(file[,atomstyle])       load new data file (default atom style 'full')
+v.replace(file[,type])	       replace current frames with new file
+v.append(file[,type]) 	       append file to current frame(s)
+v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame 
+
    +
    v.frame(frame)		       set current frame
+v.flush()		       flush pending input to VMD and update GUI
+v.read(file)		       read Tcl script file (e.g. saved state) 
+
    +
    v.enter()		       enter interactive shell
+v.debug([True|False])	       display generated VMD script commands? 
+
    +

    Related tools: +

    +

    gl +

    +

    Prerequisites: +

    +

    Python pexpect package. +

    + diff --git a/doc/vmd.txt b/doc/vmd.txt new file mode 100644 index 0000000..b19211d --- /dev/null +++ b/doc/vmd.txt @@ -0,0 +1,55 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +vmd tool :h3 + +[Purpose:] + +Control VMD from python. + +[Description:] + +The vmd tool is a simple wrapper on the "VMD visualization +package"_vmd, a popular tool for visualizing snapshots from molecular +dynamics simulations. + +:link(vmd,http://www.ks.uiuc.edu/Research/vmd) + +The vmd constructor invokes VMD in its own window. Data can be passed +to it for visualization via the new(), data(), replace(), and append() +methods. The other methods permit more specialized interactions with +VMD through its command syntax. + +[Usage:] + +v = vmd() start up VMD +v.stop() shut down VMD instance +v.clear() delete all visualizations :pre + +v.rep(style) set default representation style. One of + (Lines|VDW|Licorice|DynamicBonds|Points|CPK) +v.new(file\[,type\]) load new file (default file type 'lammpstrj') +v.data(file\[,atomstyle\]) load new data file (default atom style 'full') +v.replace(file\[,type\]) replace current frames with new file +v.append(file\[,type\]) append file to current frame(s) +v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame :pre + +v.frame(frame) set current frame +v.flush() flush pending input to VMD and update GUI +v.read(file) read Tcl script file (e.g. saved state) :pre + +v.enter() enter interactive shell +v.debug(\[True|False\]) display generated VMD script commands? :pre + +[Related tools:] + +"gl"_gl.html + +[Prerequisites:] + +Python pexpect package. diff --git a/doc/vtk.html b/doc/vtk.html new file mode 100644 index 0000000..f6ea78c --- /dev/null +++ b/doc/vtk.html @@ -0,0 +1,54 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    vtk tool +

    +

    Purpose: +

    +

    Convert LAMMPS snapshots to VTK format. +

    +

    Description: +

    +

    The vtk tool converts atom snapshots in a LAMMPS dump or data file to +the VTK format used by various visualization packages. +

    +

    The vtk constructor takes an object that stores atom snapshots +(dump, data) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. +

    +

    The one(), many(), and single() methods convert specific snapshots to +the VTK format and write them out. Optionally, a file prefix for the +XYZ output files can also be specified. A ".xyz" suffix will be +appended to all output files. +

    +

    Usage: +

    +
    v = vtk(d)	        d = object containing atom coords (dump, data) 
+
    +
    v.one()                 write all snapshots to tmp.vtk
+v.one("new")            write all snapshots to new.vtk
+v.many()                write snapshots to tmp0000.vtk, tmp0001.vtk, etc
+v.many("new")           write snapshots to new0000.vtk, new0001.vtk, etc
+v.single(N)             write snapshot for timestep N to tmp.vtk 
+v.single(N,"file")      write snapshot for timestep N to file.vtk 
+
    +
      surfaces in snapshot will be written to SURF1.vtk, SURF2.vtk, etc
+    where each surface (triangle type) is in a different file 
+
    +

    Related tools: +

    +

    cfg, data, dump, +ensight, xyz +

    +

    Prerequisites: none +

    + diff --git a/doc/vtk.txt b/doc/vtk.txt new file mode 100644 index 0000000..af3e9fe --- /dev/null +++ b/doc/vtk.txt @@ -0,0 +1,49 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +vtk tool :h3 + +[Purpose:] + +Convert LAMMPS snapshots to VTK format. + +[Description:] + +The vtk tool converts atom snapshots in a LAMMPS dump or data file to +the VTK format used by various visualization packages. + +The vtk constructor takes an object that stores atom snapshots +("dump"_dump.html, "data"_data.html) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. + +The one(), many(), and single() methods convert specific snapshots to +the VTK format and write them out. Optionally, a file prefix for the +XYZ output files can also be specified. A ".xyz" suffix will be +appended to all output files. + +[Usage:] + +v = vtk(d) d = object containing atom coords (dump, data) :pre + +v.one() write all snapshots to tmp.vtk +v.one("new") write all snapshots to new.vtk +v.many() write snapshots to tmp0000.vtk, tmp0001.vtk, etc +v.many("new") write snapshots to new0000.vtk, new0001.vtk, etc +v.single(N) write snapshot for timestep N to tmp.vtk +v.single(N,"file") write snapshot for timestep N to file.vtk :pre + + surfaces in snapshot will be written to SURF1.vtk, SURF2.vtk, etc + where each surface (triangle type) is in a different file :pre + +[Related tools:] + +"cfg"_cfg.html, "data"_data.html, "dump"_dump.html, +"ensight"_ensight.html, "xyz"_xyz.html + +[Prerequisites:] none diff --git a/doc/xyz.html b/doc/xyz.html new file mode 100644 index 0000000..e77987d --- /dev/null +++ b/doc/xyz.html @@ -0,0 +1,51 @@ + +
    Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools +
    + + + + + + +
    + +

    xyz tool +

    +

    Purpose: +

    +

    Convert LAMMPS snapshots to XYZ format. +

    +

    Description: +

    +

    The xyz tool converts atom snapshots in a LAMMPS dump or data file to +the XYZ format used by various visualization packages. +

    +

    The xyz constructor takes an object that stores atom snapshots +(dump, data) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. +

    +

    The one(), many(), and single() methods convert specific snapshots to +the XYZ format and write them out. Optionally, a file prefix for the +XYZ output files can also be specified. A ".xyz" suffix will be +appended to all output files. +

    +

    Usage: +

    +
    x = xyz(d)		d = object containing atom coords (dump, data) 
+
    +
    x.one()                 write all snapshots to tmp.xyz
+x.one("new")            write all snapshots to new.xyz
+x.many()                write snapshots to tmp0000.xyz, tmp0001.xyz, etc
+x.many("new")           write snapshots to new0000.xyz, new0001.xyz, etc
+x.single(N)             write snapshot for timestep N to tmp.xyz 
+x.single(N,"file")      write snapshot for timestep N to file.xyz  
+
    +

    Related tools: +

    +

    cfg, data, dump, +ensight, vtk +

    +

    Prerequisites: none +

    + diff --git a/doc/xyz.txt b/doc/xyz.txt new file mode 100644 index 0000000..e8d210d --- /dev/null +++ b/doc/xyz.txt @@ -0,0 +1,46 @@ +"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c + +:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pd,Manual.html) +:link(pc,Section_tools.html) + +:line + +xyz tool :h3 + +[Purpose:] + +Convert LAMMPS snapshots to XYZ format. + +[Description:] + +The xyz tool converts atom snapshots in a LAMMPS dump or data file to +the XYZ format used by various visualization packages. + +The xyz constructor takes an object that stores atom snapshots +("dump"_dump.html, "data"_data.html) as its first argument. The atom +snapshots must have "id", "type", "x", "y", and "z" defined; see the +map() methods of those tools. + +The one(), many(), and single() methods convert specific snapshots to +the XYZ format and write them out. Optionally, a file prefix for the +XYZ output files can also be specified. A ".xyz" suffix will be +appended to all output files. + +[Usage:] + +x = xyz(d) d = object containing atom coords (dump, data) :pre + +x.one() write all snapshots to tmp.xyz +x.one("new") write all snapshots to new.xyz +x.many() write snapshots to tmp0000.xyz, tmp0001.xyz, etc +x.many("new") write snapshots to new0000.xyz, new0001.xyz, etc +x.single(N) write snapshot for timestep N to tmp.xyz +x.single(N,"file") write snapshot for timestep N to file.xyz :pre + +[Related tools:] + +"cfg"_cfg.html, "data"_data.html, "dump"_dump.html, +"ensight"_ensight.html, "vtk"_vtk.html + +[Prerequisites:] none diff --git a/examples/README b/examples/README new file mode 100644 index 0000000..ca30508 --- /dev/null +++ b/examples/README @@ -0,0 +1,21 @@ +This directory contains a collection of example scripts. There is one +test_*.py script for each tool in Pizza.py. These illustrate how to +use the tool. The small data sets used by these scripts are in the +files sub-directly. + +A test_*.py script can be run by launching Pizza.py from this +directory, e.g. + +% pizza.py -f test_animate.py from the shell +> @run test_animtate.py from Pizza.py + +The other scripts in this directory perform specific tasks. Read the +comments at the top of the script file for an explanation. Most of +these scripts require a data set to operate on, which is not provided. +These scripts are included simply to illustrate how a particular task +can be done in Pizza.py. + +These scripts create output and temporary files as they operate. +These are all named tmp*. Pizza.py does not clean up all the +temporary files, since they are sometimes useful to look at for +debugging or other purposes. diff --git a/examples/files/bucky0000.png b/examples/files/bucky0000.png new file mode 100644 index 0000000..0c13a88 Binary files /dev/null and b/examples/files/bucky0000.png differ diff --git a/examples/files/bucky0001.png b/examples/files/bucky0001.png new file mode 100644 index 0000000..c7ffdf9 Binary files /dev/null and b/examples/files/bucky0001.png differ diff --git a/examples/files/bucky0002.png b/examples/files/bucky0002.png new file mode 100644 index 0000000..cecec07 Binary files /dev/null and b/examples/files/bucky0002.png differ diff --git a/examples/files/bucky0003.png b/examples/files/bucky0003.png new file mode 100644 index 0000000..cf7f7d6 Binary files /dev/null and b/examples/files/bucky0003.png differ diff --git a/examples/files/data.micelle b/examples/files/data.micelle new file mode 100644 index 0000000..afd5f42 --- /dev/null +++ b/examples/files/data.micelle @@ -0,0 +1,1530 @@ + LAMMPS 2d micelle data file + + 1200 atoms + 300 bonds + 0 angles + 0 dihedrals + 0 impropers + + 4 atom types + 1 bond types + 0 angle types + 0 dihedral types + 0 improper types + + 0.000000E+00 35.85686 xlo xhi + 0.000000E+00 35.85686 ylo yhi + -0.1000000 0.1000000 zlo zhi + + Masses + + 1 1.000000 + 2 1.000000 + 3 1.000000 + 4 1.000000 + + Atoms + + 1 139 2 0.000 0.000 0.000 + 2 0 1 1.195 0.000 0.000 + 3 0 1 2.390 0.000 0.000 + 4 0 1 3.586 0.000 0.000 + 5 0 1 4.781 0.000 0.000 + 6 0 1 5.976 0.000 0.000 + 7 0 1 7.171 0.000 0.000 + 8 0 1 8.367 0.000 0.000 + 9 0 1 9.562 0.000 0.000 + 10 114 2 10.757 0.000 0.000 + 11 0 1 11.952 0.000 0.000 + 12 52 2 13.148 0.000 0.000 + 13 0 1 14.343 0.000 0.000 + 14 0 1 15.538 0.000 0.000 + 15 0 1 16.733 0.000 0.000 + 16 0 1 17.928 0.000 0.000 + 17 0 1 19.124 0.000 0.000 + 18 0 1 20.319 0.000 0.000 + 19 0 1 21.514 0.000 0.000 + 20 0 1 22.709 0.000 0.000 + 21 0 1 23.905 0.000 0.000 + 22 0 1 25.100 0.000 0.000 + 23 0 1 26.295 0.000 0.000 + 24 110 2 27.490 0.000 0.000 + 25 128 2 28.685 0.000 0.000 + 26 0 1 29.881 0.000 0.000 + 27 0 1 31.076 0.000 0.000 + 28 0 1 32.271 0.000 0.000 + 29 0 1 33.466 0.000 0.000 + 30 0 1 34.662 0.000 0.000 + 31 0 1 0.000 1.195 0.000 + 32 0 1 1.195 1.195 0.000 + 33 113 2 2.390 1.195 0.000 + 34 0 1 3.586 1.195 0.000 + 35 75 2 4.781 1.195 0.000 + 36 0 1 5.976 1.195 0.000 + 37 0 1 7.171 1.195 0.000 + 38 89 2 8.367 1.195 0.000 + 39 0 1 9.562 1.195 0.000 + 40 94 2 10.757 1.195 0.000 + 41 0 1 11.952 1.195 0.000 + 42 35 2 13.148 1.195 0.000 + 43 0 1 14.343 1.195 0.000 + 44 0 1 15.538 1.195 0.000 + 45 0 1 16.733 1.195 0.000 + 46 0 1 17.928 1.195 0.000 + 47 0 1 19.124 1.195 0.000 + 48 0 1 20.319 1.195 0.000 + 49 0 1 21.514 1.195 0.000 + 50 0 1 22.709 1.195 0.000 + 51 0 1 23.905 1.195 0.000 + 52 0 1 25.100 1.195 0.000 + 53 0 1 26.295 1.195 0.000 + 54 0 1 27.490 1.195 0.000 + 55 0 1 28.685 1.195 0.000 + 56 0 1 29.881 1.195 0.000 + 57 0 1 31.076 1.195 0.000 + 58 0 1 32.271 1.195 0.000 + 59 0 1 33.466 1.195 0.000 + 60 0 1 34.662 1.195 0.000 + 61 0 1 0.000 2.390 0.000 + 62 0 1 1.195 2.390 0.000 + 63 119 2 2.390 2.390 0.000 + 64 0 1 3.586 2.390 0.000 + 65 24 2 4.781 2.390 0.000 + 66 0 1 5.976 2.390 0.000 + 67 0 1 7.171 2.390 0.000 + 68 0 1 8.367 2.390 0.000 + 69 0 1 9.562 2.390 0.000 + 70 0 1 10.757 2.390 0.000 + 71 0 1 11.952 2.390 0.000 + 72 0 1 13.148 2.390 0.000 + 73 0 1 14.343 2.390 0.000 + 74 0 1 15.538 2.390 0.000 + 75 0 1 16.733 2.390 0.000 + 76 0 1 17.928 2.390 0.000 + 77 0 1 19.124 2.390 0.000 + 78 0 1 20.319 2.390 0.000 + 79 0 1 21.514 2.390 0.000 + 80 0 1 22.709 2.390 0.000 + 81 0 1 23.905 2.390 0.000 + 82 74 2 25.100 2.390 0.000 + 83 0 1 26.295 2.390 0.000 + 84 0 1 27.490 2.390 0.000 + 85 0 1 28.685 2.390 0.000 + 86 47 2 29.881 2.390 0.000 + 87 0 1 31.076 2.390 0.000 + 88 0 1 32.271 2.390 0.000 + 89 0 1 33.466 2.390 0.000 + 90 0 1 34.662 2.390 0.000 + 91 0 1 0.000 3.586 0.000 + 92 0 1 1.195 3.586 0.000 + 93 0 1 2.390 3.586 0.000 + 94 0 1 3.586 3.586 0.000 + 95 0 1 4.781 3.586 0.000 + 96 0 1 5.976 3.586 0.000 + 97 0 1 7.171 3.586 0.000 + 98 0 1 8.367 3.586 0.000 + 99 0 1 9.562 3.586 0.000 + 100 121 2 10.757 3.586 0.000 + 101 0 1 11.952 3.586 0.000 + 102 0 1 13.148 3.586 0.000 + 103 129 2 14.343 3.586 0.000 + 104 0 1 15.538 3.586 0.000 + 105 0 1 16.733 3.586 0.000 + 106 0 1 17.928 3.586 0.000 + 107 0 1 19.124 3.586 0.000 + 108 0 1 20.319 3.586 0.000 + 109 117 2 21.514 3.586 0.000 + 110 0 1 22.709 3.586 0.000 + 111 0 1 23.905 3.586 0.000 + 112 0 1 25.100 3.586 0.000 + 113 0 1 26.295 3.586 0.000 + 114 0 1 27.490 3.586 0.000 + 115 0 1 28.685 3.586 0.000 + 116 49 2 29.881 3.586 0.000 + 117 0 1 31.076 3.586 0.000 + 118 0 1 32.271 3.586 0.000 + 119 0 1 33.466 3.586 0.000 + 120 0 1 34.662 3.586 0.000 + 121 0 1 0.000 4.781 0.000 + 122 0 1 1.195 4.781 0.000 + 123 0 1 2.390 4.781 0.000 + 124 0 1 3.586 4.781 0.000 + 125 38 2 4.781 4.781 0.000 + 126 0 1 5.976 4.781 0.000 + 127 67 2 7.171 4.781 0.000 + 128 0 1 8.367 4.781 0.000 + 129 3 2 9.562 4.781 0.000 + 130 0 1 10.757 4.781 0.000 + 131 41 2 11.952 4.781 0.000 + 132 0 1 13.148 4.781 0.000 + 133 131 2 14.343 4.781 0.000 + 134 0 1 15.538 4.781 0.000 + 135 0 1 16.733 4.781 0.000 + 136 0 1 17.928 4.781 0.000 + 137 0 1 19.124 4.781 0.000 + 138 0 1 20.319 4.781 0.000 + 139 0 1 21.514 4.781 0.000 + 140 0 1 22.709 4.781 0.000 + 141 0 1 23.905 4.781 0.000 + 142 0 1 25.100 4.781 0.000 + 143 0 1 26.295 4.781 0.000 + 144 0 1 27.490 4.781 0.000 + 145 0 1 28.685 4.781 0.000 + 146 0 1 29.881 4.781 0.000 + 147 0 1 31.076 4.781 0.000 + 148 0 1 32.271 4.781 0.000 + 149 0 1 33.466 4.781 0.000 + 150 0 1 34.662 4.781 0.000 + 151 53 2 0.000 5.976 0.000 + 152 0 1 1.195 5.976 0.000 + 153 0 1 2.390 5.976 0.000 + 154 0 1 3.586 5.976 0.000 + 155 0 1 4.781 5.976 0.000 + 156 0 1 5.976 5.976 0.000 + 157 48 2 7.171 5.976 0.000 + 158 0 1 8.367 5.976 0.000 + 159 30 2 9.562 5.976 0.000 + 160 0 1 10.757 5.976 0.000 + 161 0 1 11.952 5.976 0.000 + 162 104 2 13.148 5.976 0.000 + 163 0 1 14.343 5.976 0.000 + 164 136 2 15.538 5.976 0.000 + 165 0 1 16.733 5.976 0.000 + 166 0 1 17.928 5.976 0.000 + 167 0 1 19.124 5.976 0.000 + 168 116 2 20.319 5.976 0.000 + 169 0 1 21.514 5.976 0.000 + 170 0 1 22.709 5.976 0.000 + 171 0 1 23.905 5.976 0.000 + 172 0 1 25.100 5.976 0.000 + 173 40 2 26.295 5.976 0.000 + 174 0 1 27.490 5.976 0.000 + 175 145 2 28.685 5.976 0.000 + 176 33 2 29.881 5.976 0.000 + 177 0 1 31.076 5.976 0.000 + 178 0 1 32.271 5.976 0.000 + 179 0 1 33.466 5.976 0.000 + 180 0 1 34.662 5.976 0.000 + 181 0 1 0.000 7.171 0.000 + 182 0 1 1.195 7.171 0.000 + 183 0 1 2.390 7.171 0.000 + 184 0 1 3.586 7.171 0.000 + 185 0 1 4.781 7.171 0.000 + 186 0 1 5.976 7.171 0.000 + 187 0 1 7.171 7.171 0.000 + 188 0 1 8.367 7.171 0.000 + 189 0 1 9.562 7.171 0.000 + 190 0 1 10.757 7.171 0.000 + 191 0 1 11.952 7.171 0.000 + 192 15 2 13.148 7.171 0.000 + 193 0 1 14.343 7.171 0.000 + 194 0 1 15.538 7.171 0.000 + 195 0 1 16.733 7.171 0.000 + 196 0 1 17.928 7.171 0.000 + 197 0 1 19.124 7.171 0.000 + 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a/examples/files/peptide.pdb b/examples/files/peptide.pdb new file mode 100644 index 0000000..be1146e --- /dev/null +++ b/examples/files/peptide.pdb @@ -0,0 +1,86 @@ +ATOM 1 CY ACE 1 63.789 58.632 49.746 1.00 2.20 C +ATOM 2 CAY ACE 1 37.255 59.802 50.242 1.00 2.20 C +ATOM 3 OY ACE 1 62.889 58.775 48.923 1.00 2.20 O +ATOM 4 1HY ACE 1 37.725 60.385 49.421 1.00 2.20 H +ATOM 5 2HY ACE 1 38.052 59.394 50.899 1.00 2.20 H +ATOM 6 3HY ACE 1 63.987 60.414 50.913 1.00 2.20 H +ATOM 7 N TYR 2 64.074 57.490 50.302 1.00 2.20 N +ATOM 8 CA TYR 2 63.647 56.203 49.941 1.00 2.20 C +ATOM 9 C TYR 2 62.333 55.902 50.564 1.00 2.20 C +ATOM 10 O TYR 2 61.418 55.413 49.908 1.00 2.20 O +ATOM 11 CB TYR 2 37.435 55.181 50.334 1.00 2.20 C +ATOM 12 CG TYR 2 37.114 53.730 49.965 1.00 2.20 C +ATOM 13 CD1 TYR 2 63.941 53.443 48.667 1.00 2.20 C +ATOM 14 CD2 TYR 2 37.335 52.770 50.864 1.00 2.20 C +ATOM 15 CE1 TYR 2 63.307 52.208 48.533 1.00 2.20 C +ATOM 16 CE2 TYR 2 64.099 51.479 50.710 1.00 2.20 C +ATOM 17 CZ TYR 2 63.364 51.227 49.609 1.00 2.20 C +ATOM 18 OH TYR 2 62.707 49.988 49.335 1.00 2.20 O +ATOM 19 H TYR 2 37.354 57.491 51.057 1.00 2.20 H +ATOM 20 HA TYR 2 63.432 56.286 48.885 1.00 2.20 H +ATOM 21 1HB TYR 2 38.231 55.452 49.608 1.00 2.20 H +ATOM 22 2HB TYR 2 37.755 55.323 51.388 1.00 2.20 H +ATOM 23 HD1 TYR 2 63.923 54.237 47.936 1.00 2.20 H +ATOM 24 HD2 TYR 2 37.903 52.927 51.769 1.00 2.20 H +ATOM 25 HE1 TYR 2 62.757 52.046 47.618 1.00 2.20 H +ATOM 26 HE2 TYR 2 36.928 50.659 51.383 1.00 2.20 H +ATOM 27 HH TYR 2 62.698 49.543 50.185 1.00 2.20 H +ATOM 28 N GLY 3 62.348 56.027 51.889 1.00 2.20 N +ATOM 29 CA GLY 3 61.190 55.543 52.630 1.00 2.20 C +ATOM 30 C GLY 3 61.521 54.777 53.785 1.00 2.20 C +ATOM 31 O GLY 3 61.784 55.348 54.815 1.00 2.20 O +ATOM 32 H GLY 3 63.110 56.441 52.381 1.00 2.20 H +ATOM 33 1HA GLY 3 60.484 55.045 51.982 1.00 2.20 H +ATOM 34 2HA GLY 3 60.720 56.396 53.098 1.00 2.20 H +ATOM 35 N GLY 4 61.635 53.486 53.563 1.00 2.20 N +ATOM 36 CA GLY 4 62.106 52.574 54.553 1.00 2.20 C +ATOM 37 C GLY 4 61.776 51.139 54.314 1.00 2.20 C +ATOM 38 O GLY 4 62.160 50.287 55.106 1.00 2.20 O +ATOM 39 H GLY 4 61.371 53.145 52.664 1.00 2.20 H +ATOM 40 1HA GLY 4 61.567 52.864 55.443 1.00 2.20 H +ATOM 41 2HA GLY 4 63.167 52.742 54.667 1.00 2.20 H +ATOM 42 N PHE 5 61.023 50.729 53.228 1.00 2.20 N +ATOM 43 CA PHE 5 60.456 49.373 53.096 1.00 2.20 C +ATOM 44 C PHE 5 61.594 48.516 52.479 1.00 2.20 C +ATOM 45 O PHE 5 62.476 48.976 51.743 1.00 2.20 O +ATOM 46 CB PHE 5 59.184 49.177 52.242 1.00 2.20 C +ATOM 47 CG PHE 5 58.031 49.807 52.960 1.00 2.20 C +ATOM 48 CD1 PHE 5 57.658 51.151 52.876 1.00 2.20 C +ATOM 49 CD2 PHE 5 57.319 49.048 53.912 1.00 2.20 C +ATOM 50 CE1 PHE 5 56.683 51.698 53.683 1.00 2.20 C +ATOM 51 CE2 PHE 5 56.281 49.638 54.717 1.00 2.20 C +ATOM 52 CZ PHE 5 56.015 50.979 54.669 1.00 2.20 C +ATOM 53 H PHE 5 60.615 51.393 52.606 1.00 2.20 H +ATOM 54 HA PHE 5 60.234 49.004 54.087 1.00 2.20 H +ATOM 55 1HB PHE 5 58.898 48.140 51.962 1.00 2.20 H +ATOM 56 2HB PHE 5 59.316 49.589 51.218 1.00 2.20 H +ATOM 57 HD1 PHE 5 58.156 51.754 52.131 1.00 2.20 H +ATOM 58 HD2 PHE 5 57.542 47.992 53.950 1.00 2.20 H +ATOM 59 HE1 PHE 5 56.559 52.771 53.679 1.00 2.20 H +ATOM 60 HE2 PHE 5 55.671 49.049 55.387 1.00 2.20 H +ATOM 61 HZ PHE 5 55.308 51.421 55.357 1.00 2.20 H +ATOM 62 N MET 6 61.612 47.186 52.740 1.00 2.20 N +ATOM 63 CA MET 6 62.631 46.285 52.270 1.00 2.20 C +ATOM 64 C MET 6 62.487 46.185 50.721 1.00 2.20 C +ATOM 65 O MET 6 61.359 46.146 50.185 1.00 2.20 O +ATOM 66 CB MET 6 62.668 44.854 52.918 1.00 2.20 C +ATOM 67 CG MET 6 62.625 44.873 54.439 1.00 2.20 C +ATOM 68 SD MET 6 64.082 45.536 55.267 1.00 2.20 S +ATOM 69 CE MET 6 63.236 45.804 56.877 1.00 2.20 C +ATOM 70 H MET 6 60.799 46.835 53.198 1.00 2.20 H +ATOM 71 HA MET 6 63.559 46.797 52.477 1.00 2.20 H +ATOM 72 1HB MET 6 63.623 44.313 52.747 1.00 2.20 H +ATOM 73 2HB MET 6 61.805 44.212 52.640 1.00 2.20 H +ATOM 74 1HG MET 6 61.759 45.472 54.792 1.00 2.20 H +ATOM 75 2HG MET 6 62.440 43.812 54.711 1.00 2.20 H +ATOM 76 1HE MET 6 62.580 44.936 57.104 1.00 2.20 H +ATOM 77 2HE MET 6 62.523 46.647 56.752 1.00 2.20 H +ATOM 78 3HE MET 6 64.002 46.024 30.280 1.00 2.20 H +ATOM 79 NT NMA 7 63.626 46.088 49.997 1.00 2.20 N +ATOM 80 CAT NMA 7 63.612 45.756 48.604 1.00 2.20 C +ATOM 81 HNT NMA 7 37.117 46.212 50.482 1.00 2.20 H +ATOM 82 1HT NMA 7 62.559 45.550 48.315 1.00 2.20 H +ATOM 83 2HT NMA 7 36.983 44.948 48.431 1.00 2.20 H +ATOM 84 3HT NMA 7 63.902 46.686 48.072 1.00 2.20 H + TER + END diff --git a/examples/files/tmp.py b/examples/files/tmp.py new file mode 100644 index 0000000..63808e2 --- /dev/null +++ b/examples/files/tmp.py @@ -0,0 +1,6 @@ +d = dump("dump.kinase") +r = gl(d) +r.zoom(1.3) +r.q(12) +r.acol([1,4,6,8,9],["white","red","green","blue","purple"]) +r.show(0) diff --git a/examples/files/tmp.r3d b/examples/files/tmp.r3d new file mode 100644 index 0000000..ca7e50b --- /dev/null +++ b/examples/files/tmp.r3d @@ -0,0 +1,10020 @@ +Raster3D header file +51 51 tiles in x,y +10 10 pixels 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0.45 0.501960784314 0.0 0.501960784314 diff --git a/examples/files/vec.txt b/examples/files/vec.txt new file mode 100644 index 0000000..3eabce0 --- /dev/null +++ b/examples/files/vec.txt @@ -0,0 +1,33 @@ +# test file of column data +Step Temperature E_pair E_bond E_total Pressure Volume + 0 1.0019297 0 0 0.68645902 0.47826346 733.92473 + 1000 1 -0.3541344 0 0.3310025 1.471929 788.80874 + 2000 1 -0.40581755 0 0.27931935 1.3444013 815.07966 + 3000 1 -0.53487842 0 0.15025847 1.5881028 838.85908 + 4000 1 -0.56788721 0 0.11724969 1.5870075 867.65296 + 5000 1 -0.49969634 0 0.18544056 1.3461368 897.39498 + 6000 1 -0.46128743 0 0.22384946 1.2535238 916.0006 + 7000 1 -0.44495472 0 0.24018217 1.2604379 923.45772 + 8000 1 -0.43113095 0 0.25400595 1.3020687 922.74025 + +# comment in middle of data + + 9000 1 -0.37283611 0 0.31230079 1.0383053 926.35044 + 10000 1 -0.41317676 0 0.27196014 1.0430468 923.77242 + 11000 1 -0.39163654 0 0.29350036 1.1417985 924.17464 + 12000 1 -0.40243311 0 0.28270378 1.1857218 926.0797 + 13000 1 -0.39552697 0 0.28960993 1.0909948 930.73504 + 14000 1 -0.38651967 0 0.29861723 1.019887 932.46408 + 15000 1 -0.36137982 0 0.32375708 1.0862526 934.52524 + 16000 1 -0.38895837 0 0.29617853 1.0782077 937.54986 + 17000 1 -0.36593408 0 0.31920282 1.0433347 937.86368 + 18000 1 -0.36862138 0 0.31651552 1.0541325 936.44677 + 19000 1 -0.34653171 0 0.33860519 1.0383193 936.06753 + 20000 1 -0.4198566 0 0.26528029 1.1931375 929.06482 + 21000 1 -0.37716741 0 0.30796949 1.0620287 933.67326 + 22000 1 -0.39545011 0 0.28968679 1.0645021 933.58553 + 23000 1 -0.36365319 0 0.3214837 1.049493 933.6992 + 24000 1 -0.35620009 0 0.3289368 1.0211735 935.87224 + 25000 1 -0.39356635 0 0.29157055 0.99663982 935.394 + +end of data diff --git a/examples/group_energy.py b/examples/group_energy.py new file mode 100644 index 0000000..f5e478b --- /dev/null +++ b/examples/group_energy.py @@ -0,0 +1,107 @@ +# compute pairwise energy between 2 groups of atoms + +# Syntax: group_energy.py data.file dump.file1 dump.file2 ... +# Author: Paul Crozier (Sandia) + +# return distance sq between 2 atoms with PBC + +def distance(box,x1,y1,z1,x2,y2,z2): + + delx = x2 - x1 + dely = y2 - y1 + delz = z2 - z1 + + xprd = box[3] - box[0] + yprd = box[4] - box[1] + zprd = box[5] - box[2] + + if abs(delx) > 0.5*xprd: + if delx < 0.0: + delx += xprd + else: + delx -= xprd + if abs(dely) > 0.5*yprd: + if dely < 0.0: + dely += yprd + else: + dely -= yprd + if abs(delz) > 0.5*zprd: + if delz < 0.0: + delz += zprd + else: + delz -= zprd + + distsq = delx*delx + dely*dely + delz*delz + return distsq + +# main script + +if len(argv) < 3: + raise StandardError,"group_energy.py data.file dump.file1 dump.file2 ..." + +dt = data(argv[1]) # data file +q = dt.get("Atoms",4) + +files = ' '.join(argv[2:]) # dump files +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +p = pair("lj/charmm/coul/charmm") +p.coeff(dt) + +cut1 = 8.0 # potential cutoffs +cut2 = 10.0 +cut3 = 8.0 +cut4 = 10.0 +p.init(cut1,cut2,cut3,cut4) + +maxcut = cut1 +if cut2 > maxcut: maxcut = cut2 +if cut3 > maxcut: maxcut = cut3 +if cut4 > maxcut: maxcut = cut4 +maxcut_sq = maxcut*maxcut + +while 1: + time = d.next() + if time < 0: break + d.unscale(time) + + box = (d.snaps[0].xlo,d.snaps[0].ylo,d.snaps[0].zlo, + d.snaps[0].xhi,d.snaps[0].yhi,d.snaps[0].zhi) + d.aselect.all(time) + d.aselect.test("$id >= 14306 and $id <= 14516",time) # 1st group + id1,type1,x1,y1,z1 = d.vecs(time,"id","type","x","y","z") + d.aselect.all(time) # 2nd group + d.aselect.test("$id >= 1 and $id <= 7243 or $id >= 7274 and $id <= 14283", + time) + id2,type2,x2,y2,z2 = d.vecs(time,"id","type","x","y","z") + id1 = map(int,id1) + id2 = map(int,id2) + type1 = map(int,type1) + type2 = map(int,type2) + n1 = len(type1) + n2 = len(type2) + for i in xrange(n1): + id1[i] -= 1 + type1[i] -= 1 + for i in xrange(n2): + id2[i] -= 1 + type2[i] -= 1 + + e_coul_sum = 0.0 + e_vdwl_sum = 0.0 + for i in xrange(n1): + typei = type1[i] + qi = q[id1[i]] + for j in xrange(n2): + rsq = distance(box,x1[i],y1[i],z1[i],x2[j],y2[j],z2[j]) + if rsq < maxcut_sq: + eng_coul,eng_vdwl = p.single(rsq,typei,type2[j],qi,q[id2[j]]) + e_coul_sum += eng_coul + e_vdwl_sum += eng_vdwl + print "eng_coul = %g at timestep %d" % (e_coul_sum,time) + print "eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time) + + d.tselect.none() + d.tselect.one(time) + d.delete() diff --git a/examples/movie_bucky.py b/examples/movie_bucky.py new file mode 100644 index 0000000..112081a --- /dev/null +++ b/examples/movie_bucky.py @@ -0,0 +1,32 @@ +# movie of bucky-ball data + +d = dump("dump.bucky") +d.set("$center = ((int($id)-1)/61+1)*61") +d.owrap("center") + +r = raster(d) +r.file = "bucky" +r.acol([1,2,3],["blue","red","green"]) +r.arad([1,2,3],[0.5,0.5,2.5]) +r.box(1) + +# spin + +d.tselect.test("$t == 0") +r.pan(60,150,1,60,30,1) +r.all(0,25,0) + +# slice + +r.pan() +r.rotate(60,30) +r.select = "$x < -17 + (1-%g) * 34 and $type > 1" +r.all(0,25,25) + +# timestep animation + +d.tselect.all() +d.aselect.test("$type > 1") +r.rotate(60,30) +r.select = "" +r.all(50) diff --git a/examples/movie_flow.py b/examples/movie_flow.py new file mode 100644 index 0000000..833220f --- /dev/null +++ b/examples/movie_flow.py @@ -0,0 +1,16 @@ +# movie of flow around obstacle + +d = dump("dump.flow") +d.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"vx",7,"vy") +d.set("$ke = sqrt($vx*$vx + $vy*$vy)") +d.spread("vx",100,"color") +d.atype = "color" + +r = raster(d) +r.acol(range(100),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"]) +r.arad(range(100),0.5) +r.rotate(0,-90) +r.zoom(1.5) +r.file = "flow" + +r.all() diff --git a/examples/movie_melt.py b/examples/movie_melt.py new file mode 100644 index 0000000..9574c64 --- /dev/null +++ b/examples/movie_melt.py @@ -0,0 +1,20 @@ +# movie of melting LJ solid + +a = dump("dump.melt") +a.tselect.test("$t == 0") +a.scale() +a.set("$ix = int($x * 4)") +a.set("$iy = int($y * 4)") +a.set("$iz = int($z * 4)") +a.set("$type = ($ix + $iy + $iz) % 2 + 1") +a.unscale() +a.tselect.all() +a.clone(0,"type") + +r = raster(a) +r.acol([1,2],["red","green"]) +r.arad([1,2],0.5) +r.file = "melt" +r.pan(130,25,1,60,135,0.6) + +r.all() diff --git a/examples/movie_micelle.py b/examples/movie_micelle.py new file mode 100644 index 0000000..00f60df --- /dev/null +++ b/examples/movie_micelle.py @@ -0,0 +1,12 @@ +# movie of self-assembling micelles + +d = dump("dump.micelle") + +s = svg(d) +s.acol([1,2,3,4],["blue","red","cyan","yellow"]) +s.arad(range(4),0.5) +s.zoom(1.5) + +s.file = "micelle" + +s.all() diff --git a/examples/movie_peptide.py b/examples/movie_peptide.py new file mode 100644 index 0000000..376f4ea --- /dev/null +++ b/examples/movie_peptide.py @@ -0,0 +1,8 @@ +# movie of solvated peptide data + +d = dump("dump.peptide") +d.unwrap() +p = pdb("peptide",d) +r.file = "peptide" +r = rasmol(p) +r.all() diff --git a/examples/movie_tri.py b/examples/movie_tri.py new file mode 100644 index 0000000..9d65a05 --- /dev/null +++ b/examples/movie_tri.py @@ -0,0 +1,32 @@ +# movie of triangular particle data + +d = dump("dump.tri") +d.set("$center = ((int($id)-1)/36+1)*36") +d.owrap("center") + +r = raster(d) +r.bg("white") +r.file = "tri" +r.acol([1,2],["blue","red"]) +r.arad([1,2],0.5) +r.box(1) + +# spin + +d.tselect.test("$t == 0") +r.pan(60,150,1,60,30,1) +r.all(0,25,0) + +# slice + +r.pan() +r.rotate(60,30) +r.select = "$x < -12 + (1-%g) * 24" +r.all(0,25,25) + +# timestep animation + +d.tselect.all() +r.rotate(60,30) +r.select = "" +r.all(50) diff --git a/examples/test_animate.py b/examples/test_animate.py new file mode 100644 index 0000000..6547252 --- /dev/null +++ b/examples/test_animate.py @@ -0,0 +1,14 @@ +# simple test of animate tool +# requires files/bucky*png files + +a = animate("files/bucky*png") +a.play() +a.delay(0.1) +a.back() +a.last() +a.first() +a.next() +a.previous() +a.frame(1) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_bdump.py b/examples/test_bdump.py new file mode 100644 index 0000000..2e25d54 --- /dev/null +++ b/examples/test_bdump.py @@ -0,0 +1,12 @@ +# simple test of dump tool +# requires files/dump.peptide.only and files/dump.bond +# uses gl and vcr tools to visualize peptide molecule with bonds + +dm = dump("files/dump.peptide.only") +b = bdump("files/dump.bond") +b.map(1,"id",2,"type",3,"atom1",4,"atom2") +dm.extra(b) +g = gl(dm) +v = vcr(g) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_cdata.py b/examples/test_cdata.py new file mode 100644 index 0000000..3965f82 --- /dev/null +++ b/examples/test_cdata.py @@ -0,0 +1,34 @@ +# simple test of cdata tool +# creates tmp.cdata + +c = cdata() + +c.box("box",0,0,0,10,5,5) +c.sphere("nucleus",7,2,2,1) +c.cap("organelle",'x',2.5,2.5,1,1.5,3.5) +c.q("nucleus",5) +c.union("interior","nucleus","organelle") + +c.surf("nuc","nucleus") +c.surfselect("nuchalf","nuc","$z < 2.0") + +c.part("A",100,"box","interior") +c.part("B",100,"nucleus") +c.part2d("C",100,"organelle") + +c.write("tmp.cdata","box","nucleus","organelle","A","B","C") + +c.lbox("linebox",0,0,0,10,5,5) +c.unselect() +c.select("A","B","C","linebox","organelle","nuchalf") + +#s = svg(c) +#s.rotate(0,0) +#s.lrad(0,0.1) +#s.lcol(0,"yellow") +#s.show(0) + +g = gl(c) +v = vcr(g) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_cfg.py b/examples/test_cfg.py new file mode 100644 index 0000000..2e55ac0 --- /dev/null +++ b/examples/test_cfg.py @@ -0,0 +1,12 @@ +# simple test of cfg tool +# requires files/dump.peptide.* +# creates tmp*.cfg + +d = dump("files/dump.peptide.*") +d.sort() +x = cfg(d) +x.one() +x.many() +x.single(0,"tmp.single") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_chain.py b/examples/test_chain.py new file mode 100644 index 0000000..17350da --- /dev/null +++ b/examples/test_chain.py @@ -0,0 +1,17 @@ +# simple test of chain tool +# creates tmp.data.chain file + +c = chain(500,0.7,1,1,2) +c.seed = 54321 +c.build(25,10) + +c.mtype = 2 +c.btype = 2 +c.blen = 1.5 +c.dmin = 1.2 +c.id = "end1" +c.build(10,25) + +c.write("tmp.data.chain") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_clog.py b/examples/test_clog.py new file mode 100644 index 0000000..8eeaaa7 --- /dev/null +++ b/examples/test_clog.py @@ -0,0 +1,16 @@ +# simple test of clog tool +# requires files/log.ccell +# creates tmp.clog and tmp.clog.two + +c = log("files/log.ccell") + +print "# of vectors =",c.nvec +print "length of vectors =",c.nlen +print "names of vectors =",c.names + +time,a,b = c.get("Step","prey","predator") +print a,b +c.write("tmp.clog") +c.write("tmp.clog.two","Step","prey") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_data.py b/examples/test_data.py new file mode 100644 index 0000000..b5c4bd8 --- /dev/null +++ b/examples/test_data.py @@ -0,0 +1,30 @@ +# simple test of data tool +# requires files/data.micelle +# creates tmp.data + +d = data("files/data.micelle") +d.map(1,"id",3,"type",4,"x",5,"y",6,"z") +coeffs = d.get("Masses") +print "Masses",coeffs +x = d.get("Atoms",4) +print "X of 1st atom",x[0] + +d.title = "New LAMMPS data file" + +natoms = d.headers["atoms"] +vec = range(1,natoms+1) +vec.reverse() +d.replace("Atoms",1,vec) + +dm = dump("files/dump.micelle") +d.newxyz(dm,1000) + +flag = 0 +while 1: + index,time,flag = d.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines= d.viz(index) + +d.write("tmp.data") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_dump.py b/examples/test_dump.py new file mode 100644 index 0000000..13abb94 --- /dev/null +++ b/examples/test_dump.py @@ -0,0 +1,54 @@ +# simple test of dump tool +# requires files/dump.peptide and files/dump.peptide.* +# creates tmp.* files + +d = dump("files/dump.peptide") + +d.tselect.none() +d.tselect.one(2000) +d.tselect.all() +d.tselect.skip(2) +d.tselect.all() +d.tselect.test("$t >= 4000 and $t <= 6000") +d.delete() + +d.aselect.all() +d.aselect.test("$id <= 10") + +d.write("tmp.dump") +d.scatter("tmp") + +d = dump("files/dump.peptide") +d.scale() +d.unscale() +d.unwrap() +d.wrap() +d.set("$xyz = $x + $y + $z") +d.spread("x",100,"color") +d.clone(0,"color") + +print "Time",d.time() +color = d.atom(1,"color") +print "Color of atom 1",color +d.aselect.test("$id <= 10") +color = d.vecs(1000,"color") +print "Color of 1st 10 atoms in step 1000",color + +d.atype = "color" + +flag = 0 +while 1: + index,time,flag = d.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = d.viz(index) + colors = [atom[1] for atom in atoms] + print time,colors + +d = dump("files/dump.peptide.*",0) +while 1: + time = d.next() + if time < 0: break + +print "Incrementally read snaps =",d.nsnaps + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_ensight.py b/examples/test_ensight.py new file mode 100644 index 0000000..52889da --- /dev/null +++ b/examples/test_ensight.py @@ -0,0 +1,11 @@ +# simple test of xyz tool +# requires files/dump.micelle.* +# creates tmp*.case, etc + +d = dump("files/dump.micelle") +e = ensight(d) +e.one() +e.many() +e.single(0) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_gl.py b/examples/test_gl.py new file mode 100644 index 0000000..2ddd1a9 --- /dev/null +++ b/examples/test_gl.py @@ -0,0 +1,28 @@ +# simple test of gl tool +# requires files/dump.kinase +# creates tmp*.png + +d = dump("files/dump.kinase") +g = gl(d) + +g.bg("white") +g.rotate(60,130) +g.box(1) +g.q(10) +g.file = "tmp" + +g.show(0) +g.all() + +from vizinfo import colors + +g.acol([1,4,6,8,9],["gray","red","blue","green","yellow"]) +g.arad(range(9),0.3) +#g.label(0.2,0.4,'h',15,"red","test label #1") +#g.label(-0.2,-0.4,'h',15,"yellow","test label #2") + +g.show(0) +g.pan(60,130,1,60,30,0.5) +g.all(0,10,0) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_gnu.py b/examples/test_gnu.py new file mode 100644 index 0000000..125205b --- /dev/null +++ b/examples/test_gnu.py @@ -0,0 +1,33 @@ +# simple test of gnu tool +# creates tmp.eps + +g = gnu() + +g("plot sin(x) with lines") + +a = range(10) +b = [3,6,2,5,7,3,6,5,3,1] + +g.plot(a) +g.plot(a,b) +g.plot(a,b,b,a) +g.mplot(0,10,2,"tmp",a,b) + +g.export("tmp.gnu",a,b) + +g.select(2) +g.plot(a,b,b,a) +g.hide(1) + +g.aspect(1.0) +g.title("My title","x-axis","y-axis") +g.xrange(1,8) +g.yrange(2,7) +g.label(5,4,"this is a test label") +g.curve(1,'g') +g.curve(2,'m') +g.ylog() + +g.save("tmp") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_histo.py b/examples/test_histo.py new file mode 100644 index 0000000..b4a9f00 --- /dev/null +++ b/examples/test_histo.py @@ -0,0 +1,13 @@ +# simple test of histo tool +# requires files/dump.kinase + +d = dump("files/dump.kinase") +h = histo(d) +x,y = h.compute('x',25) +g = gnu() +g.xtitle("X position") +g.ytitle("Particle Count") +g.title("Histogram of Particle Density") +g.plot(x,y) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_image.py b/examples/test_image.py new file mode 100644 index 0000000..66a41f5 --- /dev/null +++ b/examples/test_image.py @@ -0,0 +1,9 @@ +# simple test of image tool +# requires files/bucky*.png + +i = image("files/bucky*.png") +i.convert("files/bucky*.png","tmp*.gif") +i.montage("","files/bucky*.png","tmp*.gif","tmpnew*.png") +i.view("") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_ldump.py b/examples/test_ldump.py new file mode 100644 index 0000000..d360b5f --- /dev/null +++ b/examples/test_ldump.py @@ -0,0 +1,15 @@ +# simple test of dump tool +# requires files/dump.lines +# uses gl and vcr tools to visualize line segments + +d = dump("files/dump.lines") +ld = ldump("files/dump.lines") +ld.map(1,"id",2,"type",6,"end1x",7,"end1y",8,"end2x",9,"end2y") +d.extra(ld) +g = gl(d) +g.arad(0,0.2) +g.lrad(1,5) +g.lcol(1,"green") +v = vcr(g) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_log.py b/examples/test_log.py new file mode 100644 index 0000000..40c1d7c --- /dev/null +++ b/examples/test_log.py @@ -0,0 +1,16 @@ +# simple test of log tool +# requires files/log.obstacle +# creates tmp.log and tmp.log.two + +lg = log("files/log.obstacle") + +print "# of vectors =",lg.nvec +print "length of vectors =",lg.nlen +print "names of vectors =",lg.names + +time,temp,press = lg.get("Step","Temp","Press") +print temp,press +lg.write("tmp.log") +lg.write("tmp.log.two","Step","E_pair") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_matlab.py b/examples/test_matlab.py new file mode 100644 index 0000000..73b785a --- /dev/null +++ b/examples/test_matlab.py @@ -0,0 +1,33 @@ +# simple test of matlab tool +# creates tmp.eps + +m = matlab() + +a = range(10) +b = [3,6,2,5,7,3,6,5,3,1] + +m.plot(a) +m.plot(a,b) +m.plot(a,b,b,a) +m.mplot(0,10,2,"tmp",a,b) + +m("3*400 - 50") + +m.export("tmp.gnu",a,b) + +m.select(2) +m.plot(a,b,b,a) +m.hide(1) + +m.aspect(1.0) +m.title("My title","x-axis","y-axis") +m.xrange(1,8) +m.yrange(2,7) +m.label(5,4,"this is a test label") +m.curve(1,'g') +m.curve(2,'m') +m.ylog() + +m.save("tmp") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_mdump.py b/examples/test_mdump.py new file mode 100644 index 0000000..6ba6119 --- /dev/null +++ b/examples/test_mdump.py @@ -0,0 +1,35 @@ +# simple test of mdump tool +# requires files/mesh.grain +# creates tmp.* files + +m = mdump("files/mesh.grain") + +m.tselect.none() +m.tselect.one(200) +m.tselect.all() +m.tselect.skip(2) +m.tselect.all() +m.tselect.test("$t >= 100 and $t <= 200") +m.delete() + +print "Time",m.time() + +m.map(2,"spin") +m.etype = "spin" + +flag = 0 +while 1: + index,time,flag = m.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = m.viz(index) + colors = [tri[1] for tri in tris] + print time,colors + +m = dump("files/mesh.grain",0) +while 1: + time = m.next() + if time < 0: break + +print "Incrementally read snaps =",m.nsnaps + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_pair.py b/examples/test_pair.py new file mode 100644 index 0000000..530a23b --- /dev/null +++ b/examples/test_pair.py @@ -0,0 +1,11 @@ +# simple test of pair tool +# requires files/data.rhodo + +p = pair("lj/charmm/coul/charmm") +d = data("files/data.rhodo") +p.coeff(d) +p.init(8.0,10.0) +ev,ec = p.single(5.0,1,2,0.5,-0.5) +print "Energies",ev,ec + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_patch.py b/examples/test_patch.py new file mode 100644 index 0000000..3df1657 --- /dev/null +++ b/examples/test_patch.py @@ -0,0 +1,10 @@ +# simple test of patch tool +# creates tmp.data.patch file + +p = patch(0.5) +p.seed = 54321 +p.build(100,"hex2",1,2,3) +p.build(50,"tri5",4,5) +p.write("tmp.data.patch") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_pdbfile.py b/examples/test_pdbfile.py new file mode 100644 index 0000000..e28594f --- /dev/null +++ b/examples/test_pdbfile.py @@ -0,0 +1,20 @@ +# simple test of pdbfile tool +# requires files/dump.peptide.* and files/peptide.pdb +# creates tmp*.pdb + +d = dump("files/dump.peptide.*") +p = pdbfile("files/peptide",d) +p.one() +p.many() +p.single(0,"tmp.single") + +n = flag = 0 +while 1: + index,time,flag = p.iterator(flag) + if flag == -1: break + p.single(time,"tmp.single") + n += 1 + +print "Incrementally processed %d PDB files" % n + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_plotview.py b/examples/test_plotview.py new file mode 100644 index 0000000..52d8d68 --- /dev/null +++ b/examples/test_plotview.py @@ -0,0 +1,18 @@ +# simple test of plotview tool +# requires files/log.obstacle +# creates tmp.plotview.eps + +lg = log("files/log.obstacle") +g = gnu() +p = plotview(lg,g) + +p.select(1) +p.select(6) +p.yes(2) +p.yes(5) +p.no(2) + +p.file("tmp.plotview") +p.save() + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_rasmol.py b/examples/test_rasmol.py new file mode 100644 index 0000000..eda4c3a --- /dev/null +++ b/examples/test_rasmol.py @@ -0,0 +1,21 @@ +# simple test of rasmol tool +# requires files/dump.peptide and files/peptide.pdb +# creates tmp*.pdb and tmp*.gif + +d = dump("files/dump.peptide") +d.unwrap() +p = pdbfile("files/peptide",d) +r = rasmol(p) +r.file = "tmp" + +print "kill image window when ready to contine ..." +r.show(0) +r.all() + +# change RasMol settings, run all() with those settings + +print "change RasMol settings as desired, then type 'quit' ..." +r.run(0) +r.all("tmp.rasmol") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_raster.py b/examples/test_raster.py new file mode 100644 index 0000000..08b7882 --- /dev/null +++ b/examples/test_raster.py @@ -0,0 +1,31 @@ +# simple test of raster tool +# requires files/dump.kinase +# creates tmp*.png + +d = dump("files/dump.kinase") +r = raster(d) + +r.bg("white") +r.rotate(60,130) +r.box(1) +r.file = "tmp" + +print "kill image window when ready to contine ..." +r.show(0) +r.all() +a1 = animate("tmp0*png") + +from vizinfo import colors + +r.acol([1,4,6,8,9],["gray","red","blue","green","yellow"]) +r.arad(range(9),0.3) +r.label(0.2,0.4,'h',15,"red","test label #1") +r.label(-0.2,-0.4,'h',15,"yellow","test label #2") + +print "kill image window when ready to contine ..." +r.show(0) +r.pan(60,130,1,60,30,0.5) +r.all(0,10,0) +a2 = animate("tmp0*png") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_svg.py b/examples/test_svg.py new file mode 100644 index 0000000..489ad2a --- /dev/null +++ b/examples/test_svg.py @@ -0,0 +1,29 @@ +# simple test of svg tool +# requires files/dump.kinase +# creates tmp*.png + +d = dump("files/dump.kinase") +s = svg(d) + +s.bg("white") +s.rotate(60,130) +s.box(1) +s.file = "tmp" + +print "kill image window when ready to contine ..." +s.show(0) +s.all() + +from vizinfo import colors + +s.acol([1,4,6,8,9],["gray","red","blue","green","yellow"]) +s.arad(range(9),0.3) +s.label(0.2,0.4,'h',15,"red","test label #1") +s.label(-0.2,-0.4,'h',15,"yellow","test label #2") + +print "kill image window when ready to contine ..." +s.show(0) +s.pan(60,130,1,60,30,0.5) +s.all(0,10,0) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_vcr.py b/examples/test_vcr.py new file mode 100644 index 0000000..4ffa053 --- /dev/null +++ b/examples/test_vcr.py @@ -0,0 +1,17 @@ +# simple test of vcr tool +# requires files/bucky*png files + +d = dump("files/dump.micelle") +dt = data("files/data.micelle") +d.extra(dt) +g = gl(d) +g.rotate(0,270) +v = vcr(g) +v.q(10) +v.box() +v.axis() +v.clipxlo(0.2) +v.clipxhi(0.5) +v.play() + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_vec.py b/examples/test_vec.py new file mode 100644 index 0000000..6773dd0 --- /dev/null +++ b/examples/test_vec.py @@ -0,0 +1,16 @@ +# simple test of vec tool +# requires files/vec.txt +# creates tmp.vec and tmp.vec.two + +v = vec("files/vec.txt") + +print "# of vectors =",v.nvec +print "length of vectors =",v.nlen +print "names of vectors =",v.names + +time,temp,press = v.get(1,"col2",6) +print temp,press +v.write("tmp.vec") +v.write("tmp.vec.two","col1",3) + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_vmd.py b/examples/test_vmd.py new file mode 100644 index 0000000..de9da59 --- /dev/null +++ b/examples/test_vmd.py @@ -0,0 +1,11 @@ +# simple test of vmd tool +# requires files/dump.peptide.only and files/dump.bond +# uses gl and vcr tools to visualize peptide molecule with bonds + +v = vmd() +v('menu main off') +v.rep('VDW') +v.new('files/peptide.pdb','pdb') +v.flush() + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_vtk.py b/examples/test_vtk.py new file mode 100644 index 0000000..61d78d6 --- /dev/null +++ b/examples/test_vtk.py @@ -0,0 +1,11 @@ +# simple test of vtk tool +# requires files/dump.peptide.* +# creates tmp*.vtk + +d = dump("files/dump.peptide.*") +v = vtk(d) +v.one() +v.many() +v.single(0,"tmp.single") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/examples/test_xyz.py b/examples/test_xyz.py new file mode 100644 index 0000000..aa1d68e --- /dev/null +++ b/examples/test_xyz.py @@ -0,0 +1,11 @@ +# simple test of xyz tool +# requires files/dump.peptide.* +# creates tmp*.xyz + +d = dump("files/dump.peptide.*") +x = xyz(d) +x.one() +x.many() +x.single(0,"tmp.single") + +print "all done ... type CTRL-D to exit Pizza.py" diff --git a/scripts/README b/scripts/README new file mode 100644 index 0000000..5e42162 --- /dev/null +++ b/scripts/README @@ -0,0 +1,20 @@ +This directory contains a collection of scripts written by Pizza.py +users that are generically useful; you may wish to use them directly +or modify them for your own purposes. You can add your own scripts to +this directory as well. + +Any script in this directory (or other directories you define, see the +Pizza.py manual), can be run from Pizza.py, by typing a line +appropriate to the script's syntax, e.g. + +% pizza.py -f movie.py svg 0.5 60 135 dump.* from the shell +> @run movie.py svg 0.5 60 135 dump.* from Pizza.py + +The top of each script file describes its purpose and syntax. That +information can be be accessed from within Pizza.py by typing "??" or +"? name.py" or "?? name.py". + +Many of the scripts can also be run directly from Python (without +running Pizza.py), so long as the Pizza.py tools (Python files) it +needs to import (e.g. log.py) can be found by Python. + diff --git a/scripts/angle_distribute.py b/scripts/angle_distribute.py new file mode 100644 index 0000000..1f03398 --- /dev/null +++ b/scripts/angle_distribute.py @@ -0,0 +1,156 @@ +#!/usr/bin/python + +# Script: angle_distribute.py +# Purpose: binned angle distributions by angle type +# Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ... +# datafile = lammps data file +# nbin = # of bins per angle type +# theta_min = min expected angle +# theta_max = max expected angle length +# outfile = file to write stats to +# files = series of dump files +# Example: angle_distribute.py pore.data 1000 110. 120. angles.out pore.dump.1 +# Author: Paul Crozier (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +from math import sqrt,acos,atan +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 7: + raise StandardError, \ + "Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ..." + +dt = data(argv[1]) +nbins = int(argv[2]) +theta_min = float(argv[3]) +theta_max = float(argv[4]) +outfile = argv[5] +files = ' '.join(argv[6:]) + +# get the angles from the data file + +angle = dt.get("Angles") +nangles = len(angle) +atype = nangles * [0] +iatom = nangles * [0] +jatom = nangles * [0] +katom = nangles * [0] +for i in xrange(nangles): + atype[i] = int(angle[i][1] - 1) + iatom[i] = int(angle[i][2] - 1) + jatom[i] = int(angle[i][3] - 1) + katom[i] = int(angle[i][4] - 1) + +ntypes = 0 +for i in xrange(nangles): ntypes = max(angle[i][1],ntypes) +ntypes = int(ntypes) +ncount = ntypes * [0] +bin = nbins * [0] +for i in xrange(nbins): + bin[i] = ntypes * [0] + +# read snapshots one-at-a-time + +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +PI = 4.0*atan(1.0) + +while 1: + time = d.next() + if time == -1: break + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + + xprd = box[3] - box[0] + yprd = box[4] - box[1] + zprd = box[5] - box[2] + + d.unscale() + d.sort() + x,y,z = d.vecs(time,"x","y","z") + + for i in xrange(nangles): + + delx1 = x[iatom[i]] - x[jatom[i]] + dely1 = y[iatom[i]] - y[jatom[i]] + delz1 = z[iatom[i]] - z[jatom[i]] + + if abs(delx1) > 0.5*xprd: + if delx1 < 0.0: + delx1 += xprd + else: + delx1 -= xprd + if abs(dely1) > 0.5*yprd: + if dely1 < 0.0: + dely1 += yprd + else: + dely1 -= yprd + if abs(delz1) > 0.5*zprd: + if delz1 < 0.0: + delz1 += zprd + else: + delz1 -= zprd + + r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1) + + delx2 = x[katom[i]] - x[jatom[i]] + dely2 = y[katom[i]] - y[jatom[i]] + delz2 = z[katom[i]] - z[jatom[i]] + + if abs(delx2) > 0.5*xprd: + if delx2 < 0.0: + delx2 += xprd + else: + delx2 -= xprd + if abs(dely2) > 0.5*yprd: + if dely2 < 0.0: + dely2 += yprd + else: + dely2 -= yprd + if abs(delz2) > 0.5*zprd: + if delz2 < 0.0: + delz2 += zprd + else: + delz2 -= zprd + + r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2) + + c = delx1*delx2 + dely1*dely2 + delz1*delz2 + c /= r1*r2 + + if (c > 1.0): c = 1.0 + if (c < -1.0): c = -1.0 + + theta = 180.0*acos(c)/PI + + ibin = int(nbins*(theta - theta_min)/(theta_max - theta_min) + 0.5) + if ((ibin >= 0) and (ibin <= nbins-1)): + bin[ibin][atype[i]] += nbins + ncount[atype[i]] += 1 + else: + print "Warning: angle outside specified range" + print "angle type:", atype[i]+1 + print "angle number:", i + print time, + +print +print "Printing normalized angle distributions to",outfile + +fp = open(outfile,"w") +theta_range = theta_max - theta_min +for i in xrange(nbins): + print >>fp, theta_min + theta_range*float(i)/float(nbins), + for j in xrange(ntypes): + if (ncount[j] > 0): + print >>fp, float(bin[i][j])/float(ncount[j])/theta_range, + else: + print >>fp, 0.0, + print >>fp +fp.close() diff --git a/scripts/block.py b/scripts/block.py new file mode 100644 index 0000000..2576904 --- /dev/null +++ b/scripts/block.py @@ -0,0 +1,137 @@ +#!/usr/bin/python + +# Script: block.py +# Purpose: thermodynamic block averages from LAMMPS log files +# Syntax: block.py nblocks nskip log.1 log.2 ... +# nblocks = number of blocks for block averages +# nskip = skip first nskip samples in the log file(s) +# files = series of log files (LAMMPS thermo one style only) +# Example: block.py 10 0 log.* +# Author: Paul Crozier (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from log import log +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 4: + raise StandardError, "Syntax: block.py nblocks nskip log.1 log.2 ..." + +nblocks = int(argv[1]) +nskip = int(argv[2]) +files = ' '.join(argv[3:]) + +l = log(files) + +# assumes LAMMPS thermo style one + +e_bond,e_pair,e_total,pressure,step,temperature = \ + l.get("E_bond","E_pair", "E_total", "Pressure", "Step", "Temperature") +if "Volume" in l.names: + vflag = 1 + volume = l.get("Volume") +else: vflag = 0 + +print "Computing %g block averages" % nblocks +print "Skipping first %g samples" % nskip + +n = len(step) +n_per_block = (n-nskip)/nblocks +k = nskip +temperature_ave = [] +e_bond_ave = [] +e_pair_ave = [] +e_total_ave = [] +pressure_ave = [] +volume_ave = [] + +print +print " Block Samples Temperature E_bond E_pair", \ + " E_total Pressure Volume" + +for i in xrange(nblocks): + temperature_sum = 0 + e_bond_sum = 0 + e_pair_sum = 0 + e_total_sum = 0 + pressure_sum = 0 + volume_sum = 0 + samples = 0 + for j in xrange(n_per_block): + temperature_sum += temperature[k] + e_bond_sum += e_bond[k] + e_pair_sum += e_pair[k] + e_total_sum += e_total[k] + pressure_sum += pressure[k] + if vflag: volume_sum += volume[k] + samples += 1 + k += 1 + temperature_ave.append(temperature_sum/samples) + e_bond_ave.append(e_bond_sum/samples) + e_pair_ave.append(e_pair_sum/samples) + e_total_ave.append(e_total_sum/samples) + pressure_ave.append(pressure_sum/samples) + volume_ave.append(volume_sum/samples) + print " %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ + (i+1, samples, temperature_ave[i], e_bond_ave[i], e_pair_ave[i], \ + e_total_ave[i], pressure_ave[i], volume_ave[i]) + +grand_ave_temperature = 0.0 +grand_ave_e_bond = 0.0 +grand_ave_e_pair = 0.0 +grand_ave_e_total = 0.0 +grand_ave_pressure = 0.0 +grand_ave_volume = 0.0 +stdev_temperature = 0.0 +stdev_e_bond = 0.0 +stdev_e_pair = 0.0 +stdev_e_total = 0.0 +stdev_pressure = 0.0 +stdev_volume = 0.0 +for i in xrange(nblocks): + grand_ave_temperature += temperature_ave[i] + grand_ave_e_bond += e_bond_ave[i] + grand_ave_e_pair += e_pair_ave[i] + grand_ave_e_total += e_total_ave[i] + grand_ave_pressure += pressure_ave[i] + grand_ave_volume += volume_ave[i] +grand_ave_temperature /= nblocks +grand_ave_e_bond /= nblocks +grand_ave_e_pair /= nblocks +grand_ave_e_total /= nblocks +grand_ave_pressure /= nblocks +grand_ave_volume /= nblocks +for i in xrange(nblocks): + stdev_temperature += (temperature_ave[i] - grand_ave_temperature)* \ + (temperature_ave[i] - grand_ave_temperature) + stdev_e_bond += (e_bond_ave[i] - grand_ave_e_bond)* \ + (e_bond_ave[i] - grand_ave_e_bond) + stdev_e_pair += (e_pair_ave[i] - grand_ave_e_pair)* \ + (e_pair_ave[i] - grand_ave_e_pair) + stdev_e_total += (e_total_ave[i] - grand_ave_e_total)* \ + (e_total_ave[i] - grand_ave_e_total) + stdev_pressure += (pressure_ave[i] - grand_ave_pressure)* \ + (pressure_ave[i] - grand_ave_pressure) + stdev_volume += (volume_ave[i] - grand_ave_volume)* \ + (volume_ave[i] - grand_ave_volume) +from math import * +stdev_temperature = sqrt(stdev_temperature/(nblocks-1)) +stdev_e_bond = sqrt(stdev_e_bond/(nblocks-1)) +stdev_e_pair = sqrt(stdev_e_pair/(nblocks-1)) +stdev_e_total = sqrt(stdev_e_total/(nblocks-1)) +stdev_pressure = sqrt(stdev_pressure/(nblocks-1)) +stdev_volume = sqrt(stdev_volume/(nblocks-1)) + +print " ====================================================", \ + "===================================" + +print " Ave. %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ + (grand_ave_temperature, grand_ave_e_bond, grand_ave_e_pair, \ + grand_ave_e_total, grand_ave_pressure, grand_ave_volume) + +print " Stdev %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ + (stdev_temperature, stdev_e_bond, stdev_e_pair, \ + stdev_e_total, stdev_pressure, stdev_volume) diff --git a/scripts/bond_distribute.py b/scripts/bond_distribute.py new file mode 100644 index 0000000..de2a600 --- /dev/null +++ b/scripts/bond_distribute.py @@ -0,0 +1,122 @@ +#!/usr/bin/python + +# Script: bond_distribute.py +# Purpose: binned bond length distributions by bond type +# Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ... +# datafile = lammps data file +# nbin = # of bins per bond type +# rmin = min expected bond length +# rmax = max expected bond length +# outfile = file to write stats to +# files = series of dump files +# Example: bond_distribute.py pore.data 1000 1.5 1.85 bonds.out pore.dump.1 +# Author: Paul Crozier (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +from math import sqrt +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 7: + raise StandardError, \ + "Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ..." + +dt = data(argv[1]) +nbins = int(argv[2]) +rmin = float(argv[3]) +rmax = float(argv[4]) +outfile = argv[5] +files = ' '.join(argv[6:]) + +# get the bonds from the data file + +bond = dt.get("Bonds") +nbonds = len(bond) +btype = nbonds * [0] +iatom = nbonds * [0] +jatom = nbonds * [0] +for i in xrange(nbonds): + btype[i] = int(bond[i][1] - 1) + iatom[i] = int(bond[i][2] - 1) + jatom[i] = int(bond[i][3] - 1) + +ntypes = 0 +for i in xrange(nbonds): ntypes = max(bond[i][1],ntypes) +ntypes = int(ntypes) +ncount = ntypes * [0] +bin = nbins * [0] +for i in xrange(nbins): + bin[i] = ntypes * [0] + +# read snapshots one-at-a-time + +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +while 1: + time = d.next() + if time == -1: break + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + + xprd = box[3] - box[0] + yprd = box[4] - box[1] + zprd = box[5] - box[2] + + d.unscale() + d.sort() + x,y,z = d.vecs(time,"x","y","z") + + for i in xrange(nbonds): + + delx = x[jatom[i]] - x[iatom[i]] + dely = y[jatom[i]] - y[iatom[i]] + delz = z[jatom[i]] - z[iatom[i]] + + if abs(delx) > 0.5*xprd: + if delx < 0.0: + delx += xprd + else: + delx -= xprd + if abs(dely) > 0.5*yprd: + if dely < 0.0: + dely += yprd + else: + dely -= yprd + if abs(delz) > 0.5*zprd: + if delz < 0.0: + delz += zprd + else: + delz -= zprd + + r = sqrt(delx*delx + dely*dely + delz*delz) + + ibin = int(nbins*(r - rmin)/(rmax - rmin) + 0.5) + if ((ibin >= 0) and (ibin <= nbins-1)): + bin[ibin][btype[i]] += nbins + ncount[btype[i]] += 1 + else: + print "Warning: bond distance outside specified range" + print "Bond type:", btype[i]+1 + print "Bond number:", i + print time, + +print +print "Printing bond distance normalized distribution to",outfile + +fp = open(outfile,"w") +rrange = rmax - rmin +for i in xrange(nbins): + print >>fp, rmin + rrange*float(i)/float(nbins), + for j in xrange(ntypes): + if (ncount[j] > 0): + print >>fp, float(bin[i][j])/float(ncount[j])/rrange, + else: + print >>fp, 0.0, + print >>fp +fp.close() diff --git a/scripts/clogview.py b/scripts/clogview.py new file mode 100644 index 0000000..fbf80cb --- /dev/null +++ b/scripts/clogview.py @@ -0,0 +1,32 @@ +#!/usr/bin/python + +# Script: clogview.py +# Purpose: plots of ChemCell log-file concentration data +# Syntax: clogview.py gnu/matlab files ... +# gnu/matlab = style of plots to create +# files = one or more log files +# Example: clogview.py gnu log.* +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from clog import clog +from plotview import plotview +from gnu import gnu +from matlab import matlab +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 3: + raise StandardError, "Syntax: clogview.py gnu/matlab files ..." + +style = argv[1] +files = ' '.join(argv[2:]) + +c = clog(files) +exec "plot = %s()" % style +p = plotview(c,plot) +p.x = "Time" + diff --git a/scripts/cluster.py b/scripts/cluster.py new file mode 100644 index 0000000..c932f8a --- /dev/null +++ b/scripts/cluster.py @@ -0,0 +1,123 @@ +#!/usr/bin/python + +# Script: cluster.py +# Purpose: histogram of cluster size of type2 atoms near type1 +# Syntax: cluster.py type1 type2 cutoff nbin dump.1 dump.2 ... +# type1,type2 = atom types (1-N) +# cutoff = only consider atom pairs within distance cutoff +# nbin = # of bins for histogram +# files = series of dump files +# Example: cluster.py 1 5 2.0 10 dump.* +# Author: Steve Plimpton (Sandia) + +# for all snapshots, for each type1 atom, count # of type2 atoms within cutoff +# will be very slow (N^2) if are too many type1 atoms + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +from gnu import gnu +if not globals().has_key("argv"): argv = sys.argv + +# main script + +# function to compute distance sq between 2 atoms with PBC + +def distance(atom1,atom2,box): + x1 = atom1[2] + y1 = atom1[3] + z1 = atom1[4] + x2 = atom2[2] + y2 = atom2[3] + z2 = atom2[4] + + delx = x2 - x1 + dely = y2 - y1 + delz = z2 - z1 + + xprd = box[3] - box[0] + yprd = box[4] - box[1] + zprd = box[5] - box[2] + + if abs(delx) > 0.5*xprd: + if delx < 0.0: + delx += xprd + else: + delx -= xprd + if abs(dely) > 0.5*yprd: + if dely < 0.0: + dely += yprd + else: + dely -= yprd + if abs(delz) > 0.5*zprd: + if delz < 0.0: + delz += zprd + else: + delz -= zprd + + distsq = delx*delx + dely*dely + delz*delz + return distsq + +# main script + +if len(argv) < 6: + raise StandardError,"cluster.py type1 type2 cutoff nbin dump.1 dump.2 ..." + +type1 = int(argv[1]) +type2 = int(argv[2]) +cutoff = float(argv[3]) +nbin = int(argv[4]) +files = ' '.join(argv[5:]) + +# read in dump file(s) and select only type1 or type2 atoms + +d = dump(files) +d.aselect.test("$type == %d or $type == %d" % (type1,type2)) + +# loop over snapshots +# viz returns list of atoms in one snapshot + +cutsq = cutoff*cutoff +cluster = nbin*[0] + +print "Clustering ..." + +flag = 0 +while 1: + which,time,flag = d.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris = d.viz(which) + print time, + sys.stdout.flush() + + # loop over all type1 atoms + + n = len(atoms) + for i in xrange(n): + itype = atoms[i][1] + if itype != type1: continue + ncount = 0 + + # loop over all type2 atoms + # increment cluster count if distance is within cutoff + + for j in xrange(n): + jtype = atoms[j][1] + if jtype != type2 or i == j: continue + distsq = distance(atoms[i],atoms[j],box) + if distsq < cutsq: ncount += 1 + + # increment histogram count + + if ncount >= nbin: cluster[nbin-1] += 1 + else: cluster[ncount] += 1 + +print +print "Cluster size and count:" +for i in range(nbin): print i,cluster[i] + +# comment out if don't want plot + +#g = gnu() +#g.plot(range(nbin),cluster) diff --git a/scripts/density.py b/scripts/density.py new file mode 100644 index 0000000..3ed6724 --- /dev/null +++ b/scripts/density.py @@ -0,0 +1,77 @@ +#!/usr/bin/python + +# Script: density.py +# Purpose: binned atom density by atom type +# Syntax: density.py x/y/z nbin outfile files ... +# x/y/z = get density distribution along this axis +# nbin = # of bins in desired direction +# outfile = file to write flux stats to +# files = series of dump files +# Example: density.py z 100 dens.out dump.* +# Author: Paul Crozier (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 5: + raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..." + +direction = argv[1] +nbins = int(argv[2]) +outfile = argv[3] +files = ' '.join(argv[4:]) + +# read snapshots one-at-a-time + +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +first = 1 +nsnaps = 0 +while 1: + time = d.next() + if time == -1: break + + if first: + tmp,ntypes = d.minmax("type") + ntypes = int(ntypes) + bin = nbins * [0] + for i in xrange(nbins): bin[i] = ntypes * [0] + first = 0 + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + vol = (box[3] - box[0]) * (box[4] - box[1]) * (box[5] - box[2]) + + if direction == "x": type,x = d.vecs(time,"type","x") + elif direction == "y": type,x = d.vecs(time,"type","y") + elif direction == "z": type,x = d.vecs(time,"type","z") + + type = map(int,type) + natoms = len(type) + for i in xrange(natoms): type[i] -= 1 + + for i in xrange(natoms): + ibin = int(nbins*x[i] + 0.5) + if (ibin < 0): ibin += nbins + if (ibin > nbins-1): ibin -= nbins + bin[ibin][type[i]] += nbins/vol + nsnaps += 1 + print time, + +print +print "Printing ", direction, "-directional density distribution in mol/L to",outfile +conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L + +fp = open(outfile,"w") +for i in xrange(nbins): + print >>fp, float(i)/float(nbins), + for j in xrange(ntypes): + print >>fp, conversion*bin[i][j]/nsnaps, + print >>fp +fp.close() diff --git a/scripts/density2d.py b/scripts/density2d.py new file mode 100644 index 0000000..8823e68 --- /dev/null +++ b/scripts/density2d.py @@ -0,0 +1,138 @@ +#!/usr/bin/python + +# Script: density2d.py +# Purpose: binned atom density by atom type +# Syntax: density.py x/y/z nbin vmin vmax outfile files ... +# x/y/z = get density distribution along this (vertical) axis, +# bining along the other two (planar) axes +# nbin = # of bins along each of planar axes +# vmin, vmax = min and max along the vertical axis, +# use 0 for both for the complete box +# outfile = file to write flux stats to +# files = series of dump files +# Example: density2d.py z 100 dens.out dump.* +# Modified from density.py: David Hart (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +import numpy as np +from dump import dump +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 5: + raise StandardError, "Syntax: density.py x/y/z nbin vmin vmax outfile files ..." + +direction = argv[1] +nbins = int(argv[2]) +if nbins < 1: + nbins = 100 +try: + zmin = float(argv[3]) +except ValueError: + zmin = -np.inf +try: + zmax = float(argv[4]) +except ValueError: + zmax = np.inf +if zmax == zmin: + zmin = -np.inf + zmax = np.inf +outfile = argv[5] +files = ' '.join(argv[6:]) + +# read snapshots one-at-a-time + +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") +bidirect = 'x/y' +first = 1 +nsnaps = 0 +dx = 0 +dy = 0 +x0 = 0 +y0 = 0 +vol = 0 + +while 1: + time = d.next() + if time == -1: break + + if first: + tmp,ntypes = d.minmax("type") + ntypes = int(ntypes) + bin = np.zeros(shape=(nbins,nbins,ntypes)) + first = 0 + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + vol = (box[3] - box[0]) * (box[4] - box[1]) * (box[5] - box[2]) + + if direction == "z": + type,x,y,z = d.vecs(time,"type","x","y","z") + bidirect = 'x/y' + dx = box[3] - box[0] + dy = box[4] - box[1] + dz = box[5] - box[2] + x0 = box[0] + float(dx)/float(nbins)/2.0 + y0 = box[1] + float(dy)/float(nbins)/2.0 + zmax = min(zmax,box[5]) + zmin = max(zmin,box[2]) + elif direction == "y": + type,x,y,z = d.vecs(time,"type","x","z","y") + bidirect = 'x/z' + dx = box[3] - box[0] + dy = box[5] - box[2] + dz = box[4] - box[1] + x0 = box[0] + float(dx)/float(nbins)/2.0 + y0 = box[2] + float(dy)/float(nbins)/2.0 + zmax = min(zmax,box[4]) + zmin = max(zmin,box[1]) + elif direction == "x": + type,x,y,z = d.vecs(time,"type","y","z","x") + bidirect = 'y/z' + dx = box[4] - box[1] + dy = box[5] - box[2] + dz = box[3] - box[0] + x0 = box[1] + float(dx)/float(nbins)/2.0 + y0 = box[2] + float(dy)/float(nbins)/2.0 + zmax = min(zmax,box[3]) + zmin = max(zmin,box[0]) + vol = dx * dy * float(zmax - zmin) + + type = map(int,type) + natoms = len(type) + for i in xrange(natoms): type[i] -= 1 + + for i in xrange(natoms): + ibin = int(nbins*x[i]) + jbin = int(nbins*y[i]) + zloc = float(z[i])*float(dz) + if zloc < zmin or zloc > zmax: continue + if (ibin < 0): ibin = 0 + if (ibin > nbins-1): ibin = nbins - 1 + if (jbin < 0): jbin = 0 + if (jbin > nbins-1): jbin = nbins - 1 + bin[jbin][ibin][type[i]] += nbins*nbins/vol + nsnaps += 1 + print time, + +print +print "Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile) +conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L + +fp = open(outfile,"w") +# '''Uncomment for column headers. Commented for consistency with density.py''' +# print >>fp, " %8s %8s " %('ra', 'rb'), +# for k in xrange(ntypes): +# print >>fp, " %8s " %(k), +# print >>fp +for i in xrange(nbins): + for j in xrange(nbins): + print >>fp, " %8.3f %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)), + for k in xrange(ntypes): + print >>fp, " %8.3f " % (conversion*bin[j][i][k]/nsnaps), + print >>fp +fp.close() diff --git a/scripts/density_area.py b/scripts/density_area.py new file mode 100644 index 0000000..fd10d89 --- /dev/null +++ b/scripts/density_area.py @@ -0,0 +1,97 @@ +#!/usr/bin/python + +# Script: density_area.py +# Purpose: binned atom density by atom type and running area under the curve +# Syntax: density.py x/y/z nbin outfile files ... +# x/y/z = get density distribution along this axis +# nbin = # of bins in desired direction +# outfile = file to write flux stats to +# files = series of dump files +# Example: density_area.py z 100 dens.out dump.* +# Author: Paul Crozier (Sandia). +# Modified by Jeff Greathouse (Sandia) to include +# calculation of area under the curve + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 5: + raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..." + +direction = argv[1] +nbins = int(argv[2]) +outfile = argv[3] +files = ' '.join(argv[4:]) + +# read snapshots one-at-a-time + +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +first = 1 +nsnaps = 0 +ntypes = 0 +while 1: + time = d.next() + if time == -1: break + + if first: + tmp,ntypes = d.minmax("type") + ntypes = int(ntypes) + bin = nbins * [0] + for i in xrange(nbins): bin[i] = ntypes * [0] + first = 0 + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + vol = (box[3] - box[0]) * (box[4] - box[1]) * (box[5] - box[2]) + + if direction == "x": type,x = d.vecs(time,"type","x") + elif direction == "y": type,x = d.vecs(time,"type","y") + elif direction == "z": type,x = d.vecs(time,"type","z") + + type = map(int,type) + natoms = len(type) + for i in xrange(natoms): type[i] -= 1 + + for i in xrange(natoms): + ibin = int(nbins*x[i] + 0.5) + if (ibin < 0): ibin += nbins + if (ibin > nbins-1): ibin -= nbins + bin[ibin][type[i]] += nbins/vol + nsnaps += 1 + print time, + +print +print "Printing ",direction,"-directional density distribution in mol/L to", \ + outfile +conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L + +# Output as x, density_1, area_1, ... + +fp = open(outfile,"w") +first = 1 +xden = nbins * [0] +yden = nbins * [0] +for i in xrange(nbins): yden[i] = ntypes * [0] +sum = ntypes * [0] +for i in xrange(nbins): + xden[i] = float(i)/float(nbins) + print >>fp, xden[i], + if first: + for j in xrange(ntypes): + yden[i][j] = conversion*bin[i][j]/nsnaps + print >>fp, yden[i][j], sum[j], + first = 0 + else: + for j in xrange(ntypes): + yden[i][j] = conversion*bin[i][j]/nsnaps + sum[j] += 0.5 * (xden[i] - xden[i-1]) * (yden[i][j] + yden[i-1][j]) + print >>fp, yden[i][j], sum[j], + print >>fp +fp.close() diff --git a/scripts/distance.py b/scripts/distance.py new file mode 100644 index 0000000..255b86e --- /dev/null +++ b/scripts/distance.py @@ -0,0 +1,75 @@ +#!/usr/bin/python + +# Script: distance.py +# Purpose: check if any atom pairs are closer than specified distance +# Syntax: distance.py maxcut dump.file1 dump.file2 ... +# maxcut = flag atoms which are less than this distance apart +# Example: distance.py 0.95 dump.file1 +# Author: Paul Crozier (Sandia) + +# print out 2 atoms less than maxcut apart (with PBC) + +from math import sqrt + +if len(argv) < 3: + raise StandardError,"distance.py maxcut dump.file1 dump.file2 ..." + +maxcut = float(argv[1]) +maxcut_sq = maxcut*maxcut + +files = ' '.join(argv[2:]) # dump files +d = dump(files,0) +d.map(1,"id",2,"type",3,"x",4,"y",5,"z") + +while 1: + time = d.next() + if time < 0: break + d.unscale(time) + + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, + d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) + d.aselect.all(time) + id,type,x,y,z = d.vecs(time,"id","type","x","y","z") + n = len(x) + + xprd = box[3] - box[0] + yprd = box[4] - box[1] + zprd = box[5] - box[2] + + for i in xrange(n): + for j in xrange(i+1,n): + + delx = x[j] - x[i] + if abs(delx) > 0.5*xprd: + if delx < 0.0: + delx += xprd + else: + delx -= xprd + if (delx*delx < maxcut_sq): + + dely = y[j] - y[i] + if abs(dely) > 0.5*yprd: + if dely < 0.0: + dely += yprd + else: + dely -= yprd + if ((dely*dely + delx*delx) < maxcut_sq): + + delz = z[j] - z[i] + if abs(delz) > 0.5*zprd: + if delz < 0.0: + delz += zprd + else: + delz -= zprd + + rsq = delx*delx + dely*dely + delz*delz + + if rsq < maxcut_sq: + print "time = %d, id[i] = %d, id[j] = %d," \ + " type[i] = %d, type[j] = %d, distance = %g" % \ + (time, id[i], id[j], type[i], type[j], sqrt(rsq)) + + d.tselect.none() + d.tselect.one(time) + print "timestep = ", time + d.delete() diff --git a/scripts/dview.py b/scripts/dview.py new file mode 100644 index 0000000..7335847 --- /dev/null +++ b/scripts/dview.py @@ -0,0 +1,19 @@ +#!/usr/bin/python + +# Script: dview.py +# Purpose: launch vcr tool on LAMMPS dump files +# Syntax: dview.py dump.1 dump.2 ... +# files = one or more dump files +# Example: dview.py dump.* +# Author: Steve Plimpton (Sandia) + +# main script + +if len(argv) < 2: + raise StandardError, "Syntax: dview.py dump.1 ..." + +files = ' '.join(argv[1:]) + +d = dump(files) +g = gl(d) +v = vcr(g) diff --git a/scripts/dview_standalone.py b/scripts/dview_standalone.py new file mode 100755 index 0000000..022f2b8 --- /dev/null +++ b/scripts/dview_standalone.py @@ -0,0 +1,33 @@ +#!/usr/bin/python + +# Script: dview.py +# Purpose: launch vcr tool on LAMMPS dump files +# Syntax: dview.py dump.1 dump.2 ... +# files = one or more dump files +# Example: dview.py dump.* +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump + +# w/out Pizza.py these lines need to come before import of gl tool +import Tkinter +tkroot = Tkinter.Tk() +tkroot.withdraw() + +from gl import gl +from vcr import vcr +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 2: + raise StandardError, "Syntax: dview.py dump.1 ..." + +files = ' '.join(argv[1:]) + +d = dump(files) +g = gl(d) +v = vcr(g) diff --git a/scripts/flux.py b/scripts/flux.py new file mode 100644 index 0000000..dec15a8 --- /dev/null +++ b/scripts/flux.py @@ -0,0 +1,87 @@ +#!/usr/bin/python + +# Script: flux.py +# Purpose: flux of atoms through a user-defined plane +# Syntax: flux.py x/y/z plane outfile files ... +# x/y/z = measure flux in x, y, or z direction +# plane = plane where flux is measured, fraction of L from 0 to 1 +# outfile = file to write flux stats to +# files = series of dump files +# Example: flux.py z 0.5 flux.out dump.* +# Author: Paul Crozier (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 5: + raise StandardError, "Syntax: flux.py x/y/z plane outfile files ..." + +direction = argv[1] +scaled_plane = float(argv[2]) +outfile = argv[3] +files = ' '.join(argv[4:]) +d = dump(files) +d.unwrap() +tmp,ntypes = d.minmax("type") +ntypes = int(ntypes) +ntypes += 1 + +# loop over snapshots and compute net flux vs. first snapshot + +f = open(outfile,"w") + +jconfig = crossings = 0 +flag = 0 + +while 1: + which,time,flag = d.iterator(flag) + if flag == -1: break + + if direction == "x": + id,type,x = d.vecs(time,"id","type","x") + lo = d.snaps[which].xlo + hi = d.snaps[which].xhi + elif direction == "y": + id,type,x = d.vecs(time,"id","type","y") + lo = d.snaps[which].ylo + hi = d.snaps[which].yhi + elif direction == "z": + id,type,x = d.vecs(time,"id","type","z") + lo = d.snaps[which].zlo + hi = d.snaps[which].zhi + + prd = hi - lo + plane = lo + scaled_plane*prd + + print time, + sys.stdout.flush() + + natoms = len(x) + if jconfig == 0: x_initial = (natoms+1) * [0] + jconfig += 1 + + typeflux = ntypes * [0] + + for i in xrange(natoms): + id[i] = int(id[i]) + type[i] = int(type[i]) + if jconfig == 1: x_initial[id[i]] = x[i] + if x_initial[id[i]] < plane and x[i] > plane : + crossings = int((x[i] - plane)/prd) + 1 + typeflux[type[i]] += crossings + elif x_initial[id[i]] > plane and x[i] < plane : + crossings = int((plane - x[i])/prd) + 1 + typeflux[type[i]] -= crossings + + print >>f,time, + for j in xrange(ntypes-1): + print >>f,typeflux[j+1], + print >>f +print + +f.close() diff --git a/scripts/iview.py b/scripts/iview.py new file mode 100644 index 0000000..6509f1c --- /dev/null +++ b/scripts/iview.py @@ -0,0 +1,20 @@ +#!/usr/bin/python + +# Script: iview.py +# Purpose: launch animate tool on series of image files +# Syntax: iview.py files ... +# files = one or more image files +# Example: iview.py image*png +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from animate import animate +if not globals().has_key("argv"): argv = sys.argv + +# main script +# this could be done with one-line alias in shell start-up file + +if len(argv) < 2: raise StandardError, "Syntax: iview.py files ..." +a = animate(' '.join(argv[1:])) diff --git a/scripts/logview.py b/scripts/logview.py new file mode 100644 index 0000000..79dad87 --- /dev/null +++ b/scripts/logview.py @@ -0,0 +1,31 @@ +#!/usr/bin/python + +# Script: logview.py +# Purpose: plots of LAMMPS log-file thermodynamic data +# Syntax: logview.py gnu/matlab files ... +# gnu/matlab = style of plots to create +# files = one or more log files +# Example: logview.py gnu log.* +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from log import log +from plotview import plotview +from gnu import gnu +from matlab import matlab +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 3: + raise StandardError, "Syntax: logview.py gnu/matlab files ..." + +style = argv[1] +files = ' '.join(argv[2:]) + +lg = log(files) +exec "plot = %s()" % style +p = plotview(lg,plot) + diff --git a/scripts/movie.py b/scripts/movie.py new file mode 100644 index 0000000..611077c --- /dev/null +++ b/scripts/movie.py @@ -0,0 +1,33 @@ +#!/usr/bin/python + +# Script: movie.py +# Purpose: create images from LAMMPS dump snapshots +# Syntax: movie.py raster/svg theta phi dump.1 dump.2 ... +# raster/svg = style of image to create +# theta/phi = vertical (z) and azimuthal angle to view from +# files = one or more dump files +# Example: movie.py svg 60 130 dump.* +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from dump import dump +from raster import raster +from svg import svg +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) < 5: + raise StandardError, "Syntax: movie.py raster/svg theta phi dump.1 ..." + +style = argv[1] +theta = float(argv[2]) +phi = float(argv[3]) +files = ' '.join(argv[4:]) + +d = dump(files) +exec "viz = %s(d)" % style +viz.rotate(theta,phi) +viz.all() diff --git a/scripts/plot.py b/scripts/plot.py new file mode 100644 index 0000000..4311149 --- /dev/null +++ b/scripts/plot.py @@ -0,0 +1,30 @@ +#!/usr/bin/python + +# Script: plot.py +# Purpose: plots of a file of vectors +# Syntax: plot.py gnu/matlab file +# gnu/matlab = style of plots to create +# file = a file with columns of data +# Example: plot.py gnu file.dat +# Author: Steve Plimpton (Sandia) + +# enable script to run from Python directly w/out Pizza.py + +import sys +from plotview import plotview +from gnu import gnu +from matlab import matlab +if not globals().has_key("argv"): argv = sys.argv + +# main script + +if len(argv) != 3: + raise StandardError, "Syntax: plot.py gnu/matlab file" + +style = argv[1] +file = argv[2] + +v = vec(file) +exec "plot = %s()" % style +p = plotview(v,plot) + diff --git a/src/DEFAULTS.py b/src/DEFAULTS.py new file mode 100644 index 0000000..f13ac12 --- /dev/null +++ b/src/DEFAULTS.py @@ -0,0 +1,106 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# -------------- +# -------------- + +# 3 variables used by Pizza.py +# to use TOOLS or SCRIPTS, edit and uncomment the line +# to use EXCLUDE, add to the existing list + +# TOOLS = list of extra directories that contain Pizza.py tools +# Pizza.py will load all *.py files as tools from TOOLS dirs, then pizza/src +# this ordering means your tool can override a Pizza.py tool of the same name +# SCRIPTS = list of extra directories that contain Pizza.py scripts +# Pizza.py will look in working dir, SCRIPTS dirs, then pizza/scripts +# this ordering means your script can override a Pizza.py script of same name +# EXCLUDE = Python files to NOT load as tools when Pizza.py starts +# typically done for auxiliary Python files that are not tools +# any non-tool Python files from your TOOLS dirs should be added to list + +#PIZZA_TOOLS = ["~/mystuff/new_pizza_tools"] +#PIZZA_SCRIPTS = ["~/mystuff/new_pizza_scripts"] +PIZZA_EXCLUDE = ["pizza", "DEFAULTS", "vizinfo"] + +# -------------- +# -------------- + +# Pathname for programs executed by various Pizza.py tools + +# if you don't use a tool, it's settings can be ignored +# the default values are program names with no path +# to use a default value, the executable must therefore be in your path +# to change a default, uncomment and edit the PIZZA variable line + +# -------------- + +# ImageMagick programs to manipulate image files +# DISPLAY = program to view GIF, PNG, SVG files +# tools that use it: rasmol, raster, svg +# CONVERT = program to convert one image format to another +# MONTAGE = program to stitch 2 images together +# tools that use it: image + +#PIZZA_DISPLAY = "/usr/bin/display" +#PIZZA_CONVERT = "/usr/bin/convert" +#PIZZA_MONTAGE = "/usr/bin/montage" + +# -------------- + +# GNUPLOT = the GnuPlot plotting package +# GNUTERM = terminal setting used by GnuPlot +# tools that use it: gnu + +#PIZZA_GNUPLOT = "gnuplot" +#PIZZA_GNUTERM = "x11" +#PIZZA_GNUTERM = "aqua" # for Macs with Aquaterm installed + +# -------------- + +# GUNZIP = program to uncompress gzipped files +# tools that use it: data dump log + +#PIZZA_GUNZIP = "gunzip" + +# -------------- + +# LABEL3D = program to put a label on a Raster3D image +# RENDER = the Raster3D visualization rendering engine +# tools that use it: raster + +#PIZZA_LABEL3D = "label3d" +#PIZZA_RENDER = "render" + +# -------------- + +# MATLAB = the MatLab numerical analysis and plotting package +# tools that use it: matlab + +#PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm" + +# -------------- + +# RASMOL = the RasMol visualization package +# tools that use it: rasmol + +#PIZZA_RASMOL = "rasmol" + +# -------------- + +# VMD = the VMD visualization package +# tools that use it: vmd + +#PIZZA_VMDNAME = "vmd" # good settings for a Linux box +#PIZZA_VMDDIR = "/usr/local/lib/vmd" +#PIZZA_VMDDEV = "win" +#PIZZA_VMDARCH = "LINUX" + +#PIZZA_VMDNAME = "vmd" # good settings for a Mac +#PIZZA_VMDDIR = "/Applications/VMD\ 1.8.7.app/Contents/vmd" +#PIZZA_VMDDEV = "win" +#PIZZA_VMDARCH = "MACOSXX86" diff --git a/src/DEFAULTS.pyc b/src/DEFAULTS.pyc new file mode 100644 index 0000000..65a486b Binary files /dev/null and b/src/DEFAULTS.pyc differ diff --git a/src/animate.py b/src/animate.py new file mode 100644 index 0000000..0b696db --- /dev/null +++ b/src/animate.py @@ -0,0 +1,212 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# animate tool + +oneline = "Animate a series of image files" + +docstr = """ +a = animate("image*.png") create GUI to animate set of image files + +Actions (same as GUI widgets): + +a.first() go to first frame +a.prev() go to previous frame +a.back() play backwards from current frame to start +a.stop() stop on current frame +a.play() play from current frame to end +a.next() go to next frame +a.last() go to last frame + +a.frame(31) set frame slider +a.delay(0.4) set delay slider +""" + +# History +# 8/05, Matt Jones (BYU): original version + +# ToDo list +# make image window non-resizable while displaying an image +# allow for file conversion, e.g. animate("png","image*jpg") + +# Variables +# tkroot = root of entire Tk +# files = list of file names +# images = list of Tkimage objects +# nframes = number of images +# index = current frame (0 to N-1) +# loop_flag = set to 1 or -1 when play or back pushed +# set to 0 when stop is pushed +# delay_value = delay between frames (secs) +# delay_msec = delay in millisec + +# Imports and external programs + +import sys, os, commands, re, glob +from Tkinter import * +from ImageTk import PhotoImage + +# Class definition + +class animate: + + # -------------------------------------------------------------------- + + def __init__(self,filestr): + self.loop_flag = 0 + self.delay_value = 0.0 + self.delay_msec = 0 + + # convert filestr into full list of files + + list = str.split(filestr) + self.files = [] + for file in list: self.files += glob.glob(file) + self.nframes = len(self.files) + if self.nframes == 0: raise StandardError, "No files to load" + + # load all images + + self.images = [] + for i in xrange(self.nframes): + self.images.append(PhotoImage(file=self.files[i])) + + # grab Tk instance from main + + from __main__ import tkroot + self.tkroot = tkroot + + # GUI control window + + win1 = Toplevel(tkroot) + win1.title("Pizza.py animate tool") + + holder1 = Frame(win1) + button1 = Button(holder1,text="<<",command=self.first).pack(side=LEFT) + button2 = Button(holder1,text="<",command=self.previous).pack(side=LEFT) + button3 = Button(holder1,text="Back",command=self.back).pack(side=LEFT) + button4 = Button(holder1,text="Stop",command=self.stop).pack(side=LEFT) + button5 = Button(holder1,text="Play",command=self.play).pack(side=LEFT) + button6 = Button(holder1,text=">",command=self.next).pack(side=LEFT) + button7 = Button(holder1,text=">>",command=self.last).pack(side=LEFT) + holder1.pack(side=TOP) + + holder2 = Frame(win1) + self.slider_frame = Scale(holder2,from_=0,to=self.nframes-1, + command=self.frame,orient=HORIZONTAL, + label=" Frame") + self.slider_delay = Scale(holder2,from_=0.0,to=1.0,resolution=0.1, + command=self.delay,orient=HORIZONTAL, + label=" Delay") + self.slider_frame.pack(side=LEFT) + self.slider_delay.pack(side=LEFT) + holder2.pack(side=TOP) + + holder3 = Frame(win1) + self.label_frame = Label(holder3) + self.label_frame.pack(side=LEFT) + holder3.pack(side=TOP) + + # image window + + win2 = Toplevel(tkroot) + self.image_pane = Label(win2,image=self.images[0]) + self.image_pane.pack(side=BOTTOM) + tkroot.update_idletasks() # force window to appear + + # display 1st image + + self.index = 0 + self.display(self.index) + + # -------------------------------------------------------------------- + + def first(self): + self.index = 0 + self.display(self.index) + + # -------------------------------------------------------------------- + + def last(self): + self.index = self.nframes - 1 + self.display(self.index) + + # -------------------------------------------------------------------- + + def previous(self): + if self.index > 0: self.index -= 1 + self.display(self.index) + + # -------------------------------------------------------------------- + + def next(self): + if self.index < self.nframes - 1: self.index += 1 + self.display(self.index) + + # -------------------------------------------------------------------- + + def back(self): + if self.loop_flag != 0: return + self.loop_flag = -1 + if self.index == 0: + self.index = self.nframes - 1 + self.display(self.index) + self.loop() + + # -------------------------------------------------------------------- + + def play(self): + if self.loop_flag != 0: return + self.loop_flag = 1 + if self.index == self.nframes - 1: + self.index = 0 + self.display(self.index) + self.loop() + + # -------------------------------------------------------------------- + + def stop(self): + self.loop_flag = 0 + + # -------------------------------------------------------------------- + # loop forward or back until end of animation + + def loop(self): + if self.loop_flag == 1 and self.index == self.nframes - 1: + self.loop_flag = 0 + if self.loop_flag == -1 and self.index == 0: + self.loop_flag = 0 + if self.loop_flag == 0: return + + self.index += self.loop_flag + self.display(self.index) + self.tkroot.update_idletasks() + self.tkroot.after(self.delay_msec,self.loop) + + # -------------------------------------------------------------------- + # display a frame corresponding to iframe + + def display(self,iframe): + self.image_pane.configure(image=self.images[iframe]) + self.slider_frame.set(iframe) + textstr = "Frame: %d File: %s" % (iframe,self.files[iframe]) + self.label_frame.configure(text=textstr) + + # -------------------------------------------------------------------- + + def frame(self,value): + self.index = int(value) + self.display(self.index) + + # -------------------------------------------------------------------- + + def delay(self,value): + self.delay_value = float(value) + self.slider_delay.set(self.delay_value) + self.delay_msec = int(1000*self.delay_value) + diff --git a/src/animate.pyc b/src/animate.pyc new file mode 100644 index 0000000..3ac85df Binary files /dev/null and b/src/animate.pyc differ diff --git a/src/bdump.py b/src/bdump.py new file mode 100644 index 0000000..9e4f4af --- /dev/null +++ b/src/bdump.py @@ -0,0 +1,283 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# bdump tool + +oneline = "Read dump files with bond info" + +docstr = """ +b = bdump("dump.one") read in one or more dump files +b = bdump("dump.1 dump.2.gz") can be gzipped +b = bdump("dump.*") wildcard expands to multiple files +b = bdump("dump.*",0) two args = store filenames, but don't read + + incomplete and duplicate snapshots are deleted + no column name assignment is performed + +time = b.next() read next snapshot from dump files + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed + +b.map(1,"id",3,"x") assign names to atom columns (1-N) + + must assign id,type,atom1,atom2 + +time,box,atoms,bonds,tris,lines = b.viz(index) return list of viz objects + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = NULL + atoms = NULL + bonds = id,type,atom1,atom2 for each line as 2d array + tris = NULL + lines = NULL +""" + +# History +# 11/10, Steve Plimpton (SNL): original version + +# Variables +# flist = list of dump file names +# increment = 1 if reading snapshots one-at-a-time +# nextfile = which file to read from via next() +# eof = ptr into current file for where to read via next() +# nsnaps = # of snapshots +# snaps = list of snapshots +# names = dictionary of column names: +# key = "id", value = column # (0 to M-1) +# Snap = one snapshot +# time = time stamp +# natoms = # of atoms +# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1 + +# Imports and external programs + +import sys, commands, re, glob, types +from os import popen + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class bdump: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.snaps = [] + self.nsnaps = 0 + self.names = {} + + # flist = list of all dump file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no bdump file specified" + + if len(list) == 1: + self.increment = 0 + self.read_all() + else: + self.increment = 1 + self.nextfile = 0 + self.eof = 0 + + # -------------------------------------------------------------------- + + def read_all(self): + + # read all snapshots from each file + # test for gzipped files + + for file in self.flist: + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + snap = self.read_snapshot(f) + while snap: + self.snaps.append(snap) + print snap.time, + sys.stdout.flush() + snap = self.read_snapshot(f) + + f.close() + print + + # sort entries by timestep, cull duplicates + + self.snaps.sort(self.compare_time) + self.cull() + self.nsnaps = len(self.snaps) + print "read %d snapshots" % self.nsnaps + + # -------------------------------------------------------------------- + # read next snapshot from list of files + + def next(self): + + if not self.increment: raise StandardError,"cannot read incrementally" + + # read next snapshot in current file using eof as pointer + # if fail, try next file + # if new snapshot time stamp already exists, read next snapshot + + while 1: + f = open(self.flist[self.nextfile],'rb') + f.seek(self.eof) + snap = self.read_snapshot(f) + if not snap: + self.nextfile += 1 + if self.nextfile == len(self.flist): return -1 + f.close() + self.eof = 0 + continue + self.eof = f.tell() + f.close() + try: + self.findtime(snap.time) + continue + except: break + + self.snaps.append(snap) + snap = self.snaps[self.nsnaps] + self.nsnaps += 1 + + return snap.time + + # -------------------------------------------------------------------- + # read a single snapshot from file f + # return snapshot or 0 if failed + # assign column names if not already done and file is self-describing + # convert xs,xu to x + + def read_snapshot(self,f): + try: + snap = Snap() + item = f.readline() + snap.time = int(f.readline().split()[0]) # just grab 1st field + item = f.readline() + snap.natoms = int(f.readline()) + item = f.readline() + + if snap.natoms: + words = f.readline().split() + ncol = len(words) + for i in xrange(1,snap.natoms): + words += f.readline().split() + floats = map(float,words) + if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float) + else: atoms = np.zeros((snap.natoms,ncol),np.float) + start = 0 + stop = ncol + for i in xrange(snap.natoms): + atoms[i] = floats[start:stop] + start = stop + stop += ncol + else: atoms = None + snap.atoms = atoms + return snap + except: + return 0 + + # -------------------------------------------------------------------- + # map atom column names + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "bdump map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # -------------------------------------------------------------------- + # return vector of snapshot time stamps + + def time(self): + vec = self.nsnaps * [0] + i = 0 + for snap in self.snaps: + vec[i] = snap.time + i += 1 + return vec + + # -------------------------------------------------------------------- + # sort snapshots on time stamp + + def compare_time(self,a,b): + if a.time < b.time: + return -1 + elif a.time > b.time: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + # delete successive snapshots with duplicate time stamp + + def cull(self): + i = 1 + while i < len(self.snaps): + if self.snaps[i].time == self.snaps[i-1].time: + del self.snaps[i] + else: + i += 1 + + # -------------------------------------------------------------------- + # return list of bonds to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] + + time = snap.time + id = self.names["id"] + type = self.names["type"] + atom1 = self.names["atom1"] + atom2 = self.names["atom2"] + + # create line list from id,type,atom1,atom2 + # abs() of type since could be negative + + bonds = [] + for i in xrange(snap.natoms): + atom = snap.atoms[i] + bonds.append([int(atom[id]),abs(int(atom[type])), + int(atom[atom1]),int(atom[atom2])]) + + return time,None,None,bonds,None,None + +# -------------------------------------------------------------------- +# one snapshot + +class Snap: + pass diff --git a/src/bdump.pyc b/src/bdump.pyc new file mode 100644 index 0000000..218188a Binary files /dev/null and b/src/bdump.pyc differ diff --git a/src/cdata.py b/src/cdata.py new file mode 100644 index 0000000..3020fc5 --- /dev/null +++ b/src/cdata.py @@ -0,0 +1,2312 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# how to specify and print 2d particles + +# cdata tool + +oneline = "Read, create, manipulate ChemCell data files" + +docstr = """ +c = cdata() create a datafile object +c = cdata("mem.surf") read in one or more ChemCell data files +c = cdata("mem.part.gz mem.surf") can be gzipped +c = cdata("mem.*") wildcard expands to multiple files +c.read("mem.surf") read in one or more data files + + read() has same argument options as constructor + files contain the following kinds of entries, each of which becomes an object + particles, triangles, region, facets + particles is a list of particles -> becomes a group + triangles is 3 lists of vertices, triangles, connections -> becomes a surf + region is a ChemCell command defining a region -> becomes a region + facets is a CUBIT format of vertices and triangles -> becomes a surf + each object is assigned an ID = name in file + ID can be any number or string, must be unique + +c.box(ID,xlo,ylo,zlo,xhi,yhi,zhi) create a box region +c.sphere(ID,x,y,z,r) create a sphere region +c.shell(ID,x,y,z,r,rinner) create a shell region +c.cyl(ID,'x',c1,c2,r,lo,hi) create a axis-aligned cylinder region +c.cap(ID,'x',c1,c2,r,lo,hi) create a axis-aligned capped-cylinder region +c.q(ID,q1,q2,...) set region triangulation quality factors + + box() can create an axis-aligned plane, line, or point if lo=hi + cyl() can create an axis-aligned circle if lo=hi + for cyl() and cap(): 'x' c1,c2 = y,z; 'y' c1,c2 = x,z; 'z' c,c2 = x,y + q's are size factors for region triangulation + for box, q1,q2,q3 = # of divisions per xyz of box + for sphere or shell, q1 = # of divisions per face edge of embedded cube + for cyl or cap, q1 = # of divisions per face edge of end cap, must be even + q2 = # of divisions along length of cylinder + +c.line(ID,x1,y1,z1,x2,y2,z2) create a line object with one line +c.lbox(ID,xlo,ylo,zlo,xhi,yhi,zhi) create a line object with 12 box lines + +c.surf(ID,id-region) create a triangulated surf from a region +c.surftri(ID,id-surf,t1,t2,...) create a tri surf from list of id-surf tris +c.surfselect(ID,id-surf,test) create a tri surf from test on id-surf tris +c.bins(ID,nx,ny) set binning parameters for a surf + + triangulation of a shell is just done for the outer sphere + for surftri(), one or more tri indices (1-N) must be listed + for surfselect(), test is string like "$x < 2.0 and $y > 0.0" + bins are used when particles are created inside/outside a surf + +c.part(ID,n,id_in) create N particles inside object id_in +c.part(ID,n,id_in,id_out) particles are also outside object id_out +c.part2d(ID,n,id_on) create 2d particles on object id_on +c.partarray(ID,nx,nz,nz,x,y,z,dx,dy,dz) create 3d grid of particles +c.partring(ID,n,x,y,z,r,'x') create ring of particles +c.partsurf(ID,id_on) change surf of existing 2d particle group +c.seed(43284) set random # seed (def = 12345) + + generate particle positions randomly (unless otherwise noted) + for part(), id_in and id_out must be IDs of a surf, region, or union object + inside a union object means inside any of the lower-level objects + outside a union object means outside all of the lower-level objects + for part2d(), id_on must be ID of a surf, region, or union object + for part2d(), particles will be written as 2d assigned to surf id_on + for partring(), ring axis is in 'x','y', or 'z' direction + partsurf() changes surf id_on for an existing 2d particle group + +x,n = c.random(ID) pick a random pt on surf of object ID +c.project(ID,ID2,dx,dy,dz,eps,fg) project particles in ID to surf of obj ID2 + + random() returns pt = [x,y,z] and normal vec n [nx,ny,nz] + for random(), ID can be surf or region obj + project() remaps particle coords in group ID + moves each particle along dir until they are within eps of surface + if no fg arg, dir = (dx,dy,dz) + if fg arg, dir = line from particle coord to (dx,dy,dz) + ID2 can be surf or region obj + particles are converted to 2d assigned to surf ID2 + +c.center(ID,x,y,z) set center point of object +c.trans(ID,dx,dy,dz) translate an object +c.rotate(ID,'x',1,1,0,'z',-1,1,0) rotate an object +c.scale(ID,sx,sy,sz) scale an object + + objects must be surface or particle group, regions cannot be changed + for center(), default is middle of bounding box (set when obj is created) + for rotate(), set any 2 axes, must be orthogonal, 3rd is inferred + object is rotated so that it's current xyz axes point along new ones + rotation and scaling occur relative to center point + +c.union(ID,id1,id2,...) create a new union object from id1,id2,etc +c.join(ID,id1,id2,...) create a new object by joining id1,id2,etc +c.delete(id1,id2,...) delete one or more objects +c.rename(ID,IDnew) rename an object +c.copy(ID,IDnew) create a new object as copy of old object + + for union, all lower-level objects must be of surface, region, or union style + for join, all joined objects must be of same style: group, surf, line + new object is the same style + +c.select(id1,id2,...) select one or more objects +c.select() select all objects +c.unselect(id1,id2,...) unselect one or more objects +c.unselect() unselect all objects + + selection applies to write() and viz() + +c.write("file") write all selected objs to ChemCell file +c.write("file",id1,id2,...) write only listed & selected objects to file +c.append("file") append all selected objs to ChemCell file +c.append("file",id1,id2,...) append only listed & selected objects + + union objects are skipped, not written to file + +index,time,flag = c.iterator(0/1) loop over single snapshot +time,box,atoms,bonds,tris,lines = c.viz(index) return list of viz objects + + iterator() and viz() are compatible with equivalent dump calls + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = timestep index within dump object (only 0 for data file) + time = timestep value (only 0 for data file) + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected objs for specified timestep index (must be 0) + time = 0 + box = [xlo,ylo,zlo,xhi,yhi,zhi] + atoms = id,type,x,y,z for each atom as 2d array + NULL if atoms do not exist + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + regions are triangulated according to q() settings by viz() + NULL if surfaces do not exist + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + NULL if lines do not exist + types are assigned to each object of same style in ascending order +""" + +# History +# 11/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# nselect = 1 = # of snapshots +# ids = dictionary of IDs that points to object index +# objs = list of objects, style = REGION, SURFACE, GROUP, UNION + +# Imports and external programs + +import sys, glob +from os import popen +from math import sqrt,pi,cos,sin,fabs +from copy import deepcopy + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class cdata: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.nselect = 1 + self.ids = {} + self.objs = [] + self.random = Random(12345) + + if len(list): self.read(*list) + + # -------------------------------------------------------------------- + + def read(self,*list): + + # flist = list of all data file names + + words = list[0].split() + flist = [] + for word in words: flist += glob.glob(word) + if len(flist) == 0 and len(list) == 1: + raise StandardError,"no data file specified" + + for file in flist: + + # test for gzipped file + + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + # read all entries in file + + while 1: + line = f.readline() + if not line: break + line = line.strip() + if not line: continue + elif line.find("triangles") == 0: flag = "triangles" + elif line.find("particles") == 0: flag = "particles" + elif line.find("facets") == 0: flag = "facets" + elif line.find("region") == 0: flag = "region" + else: + print "unknown line:",line + raise StandardError, "unrecognized ChemCell data file" + + # create a surface object from set of triangles or facets + + if flag == "triangles" or flag == "facets": + tmp,id,nvert,ntri = line.split() + nvert = int(nvert) + ntri = int(ntri) + + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + f.readline() + vertices = [] + for i in xrange(nvert): + list = f.readline().split() + vertices.append([float(value) for value in list[1:]]) + f.readline() + triangles = [] + for i in xrange(ntri): + list = f.readline().split() + triangles.append([int(value) for value in list[1:]]) + + if flag == "triangles": + f.readline() + connections = [] + for i in xrange(ntri): + list = f.readline().split() + connections.append([int(value) for value in list[1:]]) + else: + connections = connect(nvert,ntri,triangles) + + obj = Surface() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = SURFACE + obj.nvert = nvert + obj.ntri = ntri + obj.vertices = vertices + obj.triangles = triangles + obj.connections = connections + obj.center() + + print id, + sys.stdout.flush() + + # create a group object from list of particles + + if flag == "particles": + words = line.split() + id = words[1] + npart = int(words[2]) + + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + f.readline() + xyz = [] + for i in xrange(npart): + list = f.readline().split() + xyz.append([float(value) for value in list[1:]]) + + obj = Group() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = GROUP + if len(words) == 3: obj.on_id = "" + else: obj.on_id = words[3] + obj.npart = npart + obj.xyz = xyz + obj.center() + + print id, + sys.stdout.flush() + + # create a region object from ChemCell region command + + if flag == "region": + words = line.split() + id = words[1] + style = words[2] + args = words[3:] + + if style == "box": + obj = Box(*args) + obj.substyle = BOX + elif style == "sphere": + obj = Sphere(*args) + obj.substyle = SPHERE + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + + print id, + sys.stdout.flush() + + f.close() + print + + # -------------------------------------------------------------------- + # create box region + + def box(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Box(*args) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + obj.substyle = BOX + + # -------------------------------------------------------------------- + # create sphere region + + def sphere(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Sphere(*args) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + obj.substyle = SPHERE + + # -------------------------------------------------------------------- + # create shell region + + def shell(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Shell(*args) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + obj.substyle = SHELL + + # -------------------------------------------------------------------- + # create cylinder region + + def cyl(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Cylinder(*args) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + obj.substyle = CYLINDER + + # -------------------------------------------------------------------- + # create a capped-cylinder region + + def cap(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Capped(*args) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = REGION + obj.substyle = CAPPED + + # -------------------------------------------------------------------- + # set quality factors for a region's triangulation routine + + def q(self,id,*args): + obj = self.objs[self.ids[id]] + if obj.style != REGION: + raise StandardError,"Can only use q() on a region object" + n = 1 + for arg in args: + cmd = "obj.q%d = arg" % n + exec cmd + n += 1 + + # -------------------------------------------------------------------- + # create a line object with single line + + def line(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Line() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = LINE + obj.nline = 0 + obj.pairs = [] + + obj.addline(args) + + # -------------------------------------------------------------------- + # create a line object with 12 lines for a box + + def lbox(self,id,*args): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Line() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = LINE + obj.nline = 0 + obj.pairs = [] + + xlo,ylo,zlo,xhi,yhi,zhi = args + obj.addline([xlo,ylo,zlo,xhi,ylo,zlo]) + obj.addline([xlo,yhi,zlo,xhi,yhi,zlo]) + obj.addline([xlo,yhi,zhi,xhi,yhi,zhi]) + obj.addline([xlo,ylo,zhi,xhi,ylo,zhi]) + obj.addline([xlo,ylo,zlo,xlo,yhi,zlo]) + obj.addline([xhi,ylo,zlo,xhi,yhi,zlo]) + obj.addline([xhi,ylo,zhi,xhi,yhi,zhi]) + obj.addline([xlo,ylo,zhi,xlo,yhi,zhi]) + obj.addline([xlo,ylo,zlo,xlo,ylo,zhi]) + obj.addline([xhi,ylo,zlo,xhi,ylo,zhi]) + obj.addline([xhi,yhi,zlo,xhi,yhi,zhi]) + obj.addline([xlo,yhi,zlo,xlo,yhi,zhi]) + + # -------------------------------------------------------------------- + # create a triangulated surface object from a region object + + def surf(self,id,id_region): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + region = self.objs[self.ids[id_region]] + region.triangulate() + + obj = Surface() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = SURFACE + obj.nvert = region.nvert + obj.ntri = region.ntri + obj.vertices = deepcopy(region.vertices) + obj.triangles = deepcopy(region.triangles) + obj.connections = deepcopy(region.connections) + obj.center() + + # -------------------------------------------------------------------- + # create a triangulated surface object + # from list of tri indices (1-N) in id_surf obj + + def surftri(self,id,id_surf,*list): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + o = self.objs[self.ids[id_surf]] + + obj = Surface() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = SURFACE + obj.nvert = 0 + obj.ntri = 0 + obj.vertices = [] + obj.triangles = [] + + # subtract 1 from tri and vert to convert to C indexing from (1-N) + + for i in list: + v1 = o.triangles[i-1][0] + v2 = o.triangles[i-1][1] + v3 = o.triangles[i-1][2] + obj.vertices.append(o.vertices[v1-1][:]) + obj.vertices.append(o.vertices[v2-1][:]) + obj.vertices.append(o.vertices[v3-1][:]) + obj.triangles.append([obj.nvert+1,obj.nvert+2,obj.nvert+3]) + obj.nvert += 3 + obj.ntri += 1 + + # make any connections in new set of triangles + + obj.connections = connect(obj.nvert,obj.ntri,obj.triangles) + obj.center() + + # -------------------------------------------------------------------- + # create a triangulated surface object + # from subset of tris in id_surf obj that meet test string + + def surfselect(self,id,id_surf,teststr): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + o = self.objs[self.ids[id_surf]] + + obj = Surface() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = SURFACE + obj.nvert = 0 + obj.ntri = 0 + obj.vertices = [] + obj.triangles = [] + + # replace $var with o.vertices reference and compile test string + + cmd1 = teststr.replace("$x","o.vertices[v1][0]") + cmd1 = cmd1.replace("$y","o.vertices[v1][1]") + cmd1 = "flag1 = " + cmd1.replace("$z","o.vertices[v1][2]") + ccmd1 = compile(cmd1,'','single') + + cmd2 = teststr.replace("$x","o.vertices[v2][0]") + cmd2 = cmd2.replace("$y","o.vertices[v2][1]") + cmd2 = "flag2 = " + cmd2.replace("$z","o.vertices[v2][2]") + ccmd2 = compile(cmd2,'','single') + + cmd3 = teststr.replace("$x","o.vertices[v3][0]") + cmd3 = cmd3.replace("$y","o.vertices[v3][1]") + cmd3 = "flag3 = " + cmd3.replace("$z","o.vertices[v3][2]") + ccmd3 = compile(cmd3,'','single') + + # loop over triangles in id_surf + # 3 vertices must satisfy all 3 tests for tri's inclusion in new surf obj + + for tri in o.triangles: + v1 = tri[0] - 1 + v2 = tri[1] - 1 + v3 = tri[2] - 1 + exec ccmd1 + exec ccmd2 + exec ccmd3 + if flag1 and flag2 and flag3: + obj.vertices.append(o.vertices[v1][:]) + obj.vertices.append(o.vertices[v2][:]) + obj.vertices.append(o.vertices[v3][:]) + obj.triangles.append([obj.nvert+1,obj.nvert+2,obj.nvert+3]) + obj.nvert += 3 + obj.ntri += 1 + + # make any connections in new set of triangles + + obj.connections = connect(obj.nvert,obj.ntri,obj.triangles) + obj.center() + + # -------------------------------------------------------------------- + # set binning parameters for a surface + + def bins(self,id,nx,ny): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE: + raise StandardError,"Can only set bins for surface" + obj.nbinx = nx + obj.nbiny = ny + + # -------------------------------------------------------------------- + # create a group object with npart particles + # use inside and outside as constraints on particle coords + + def part(self,id,npart,in_id,out_id=None): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + obj = Group() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = GROUP + obj.on_id = "" + obj.npart = npart + obj.xyz = [] + + in_obj = self.objs[self.ids[in_id]] + if out_id: out_obj = self.objs[self.ids[out_id]] + + # pre-process SURFACE objects to bin their triangles for faster searching + + if in_obj.style == SURFACE: in_obj.inside_prep() + if out_id and out_obj.style == SURFACE: out_obj.inside_prep() + + # bounding box for generating points + + xlo,ylo,zlo,xhi,yhi,zhi = in_obj.bbox() + xsize = xhi-xlo + ysize = yhi-ylo + zsize = zhi-zlo + + # generate particles until have enough that satisfy in/out constraints + + count = attempt = 0 + while count < npart: + attempt += 1 + x = xlo + self.random() * xsize + y = ylo + self.random() * ysize + z = zlo + self.random() * zsize + if not in_obj.inside(x,y,z): continue + if out_id and out_obj.inside(x,y,z): continue + obj.xyz.append([x,y,z]) + count += 1 + + obj.center() + print "Created %d particles in %d attempts" % (count,attempt) + + # -------------------------------------------------------------------- + # create a group object with npart 2d particles on surface of on_id object + + def part2d(self,id,npart,on_id): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + obj = Group() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = GROUP + obj.on_id = on_id + obj.npart = npart + obj.xyz = [] + + on_obj = self.objs[self.ids[on_id]] + if on_obj.style != SURFACE and on_obj.style != REGION and \ + on_obj.style != UNION: + raise StandardError,"Illegal ID to place particles on" + totalarea = on_obj.area() + + for count in xrange(npart): + area = self.random() * totalarea + pt,norm = on_obj.loc2d(area,self.random) + obj.xyz.append(pt) + + obj.center() + print "Created %d particles on area of %g" % (npart,totalarea) + + # -------------------------------------------------------------------- + # create a 3d array of particles + # array size = Nx by Ny by Nz + # lower left corner of array = x,y,z + # array spacing = dx,dy,dz + + def partarray(self,id,nx,ny,nz,x,y,z,dx,dy,dz): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + obj = Group() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = GROUP + obj.on_id = "" + obj.npart = nx * ny * nz + obj.xyz = [] + + for k in xrange(nz): + znew = z + k*dz + for j in xrange(ny): + ynew = y + j*dy + for i in xrange(nx): + xnew = x + i*dx + obj.xyz.append([xnew,ynew,znew]) + + obj.center() + print "Created %d particles" % (nx*ny*nz) + + # -------------------------------------------------------------------- + # create a ring of N particles + # ring center and radius = x,y,z,r + # ring axis = 'x' or 'y' or 'z' + + def partring(self,id,n,x,y,z,r,axis): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + + obj = Group() + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = GROUP + obj.on_id = "" + obj.npart = n + obj.xyz = [] + + deltheta = 2.0*pi / n + for i in xrange(n): + if axis == 'x': + xnew = x + ynew = y + r * cos(i*deltheta) + znew = z + r * sin(i*deltheta) + elif axis == 'y': + xnew = x + r * cos(i*deltheta) + ynew = y + znew = z + r * sin(i*deltheta) + elif axis == 'z': + xnew = x + r * cos(i*deltheta) + ynew = y + r * sin(i*deltheta) + znew = z + obj.xyz.append([xnew,ynew,znew]) + + obj.center() + print "Created %d particles" % n + + # -------------------------------------------------------------------- + # change surface assignment for a 2d group of particles + + def partsurf(self,id,on_id): + obj = self.objs[self.ids[id]] + if obj.style != GROUP: + raise StandardError,"Must use particle group with partsurf()" + if obj.on_id == "": + raise StandardError,"Must use partsurf() with 2d particles" + obj.on_id = on_id + + # -------------------------------------------------------------------- + # set random number seed + + def seed(self,new_seed): + self.random.seed = new_seed + + # -------------------------------------------------------------------- + # pick a random pt on surf of object and return pt and normal vec + + def random(self,id): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE and obj.style != REGION: + raise StandardError,"Must use surf or region with random()" + + totalarea = obj.area() + area = self.random() * totalarea + pt,norm = obj.loc2d(area,self.random) + return pt,norm + + # -------------------------------------------------------------------- + # project particles in ID to surface of object ID2 + # direction to project depends on flag + # if no flag, dir = (dx,dy,dz) from every particle + # if yes flag, dir = particle coord to (dx,dy,dz) + + def project(self,id,id2,dx,dy,dz,EPS,flag=None): + obj = self.objs[self.ids[id]] + if obj.style != GROUP: + raise StandardError,"Must use particle group as 1st obj of project()" + obj_on = self.objs[self.ids[id2]] + if obj_on.style != SURFACE and obj_on.style != REGION: + raise StandardError,"Must use surf or region as 2nd obj of project()" + + # pre-process SURFACE to bin its triangles for faster searching + + if obj_on.style == SURFACE: obj_on.inside_prep() + + # for each particle, move it in dir from current location + # move along dir until get within EPS of surf + # factor = multiply bracketing distance by this amount each iteration + # maxscale = max multiple of dir vector to bracket in each direction + + factor = 2 + maxscale = 10.0 + + for i in xrange(obj.npart): + x,y,z = obj.xyz[i] + if flag: dir = [dx-x,dy-y,dz-z] + else: dir = [dx,dy,dz] + normalize(dir) + + # start = in/out at starting pt + # stop = in/out at bracketing pt + + start = obj_on.inside(x,y,z) + if start: stop = 0 + else: stop = 1 + + # iterate to find bracketing point or until scale dist > maxdist + # bracket pt = xyz +/- scale*dir + # multiply scale by factor each iteration + + #print "AAA",i,start,stop,x,y,z,dir + + scale = EPS + bracket = start + while scale < maxscale: + xnew,ynew,znew = x+scale*dir[0], y+scale*dir[1], z+scale*dir[2] + bracket = obj_on.inside(xnew,ynew,znew) + #print "BBB",xnew,ynew,znew,scale,bracket + if bracket == stop: break + xnew,ynew,znew = x-scale*dir[0], y-scale*dir[1], z-scale*dir[2] + bracket = obj_on.inside(xnew,ynew,znew) + #print "CCC",xnew,ynew,znew,scale,bracket + if bracket == stop: break + scale *= factor + + if bracket == start: + raise StandardError,"Could not find bracket point for particle %d" % i + + # bisection search to zoom in to within EPS of surface + # separation = distance between 2 points + + delx = xnew-x; dely = ynew-y; delz = znew-z + separation = sqrt(delx*delx + dely*dely + delz*delz) + while separation > EPS: + xmid = 0.5 * (x + xnew) + ymid = 0.5 * (y + ynew) + zmid = 0.5 * (z + znew) + value = obj_on.inside(xmid,ymid,zmid) + if value == start: + x = xmid; y = ymid; z = zmid + else: + xnew = xmid; ynew = ymid; znew = zmid + delx = xnew-x; dely = ynew-y; delz = znew-z + separation = sqrt(delx*delx + dely*dely + delz*delz) + + obj.xyz[i][0] = x + obj.xyz[i][1] = y + obj.xyz[i][2] = z + + obj.on_id = id2 + obj.center() + + # -------------------------------------------------------------------- + # set center pt of an object + + def center(self,id,x,y,z): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE and obj.style != GROUP: + raise StandardError,"Can only use center() on a surface or group object" + obj.center(x,y,z) + + # -------------------------------------------------------------------- + # translate an object by dx,dy,dz displacement + # add displacement to its vertices and center pt + + def trans(self,id,dx,dy,dz): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE and obj.style != GROUP: + raise StandardError,"Can only use trans() on a surface or group object" + obj.xc += dx + obj.yc += dy + obj.zc += dz + + # apply translation to each vertex or part coord + + if obj.style == SURFACE: + for i in xrange(obj.nvert): + obj.vertices[i][0] += dx + obj.vertices[i][1] += dy + obj.vertices[i][2] += dz + elif obj.style == GROUP: + for i in xrange(obj.npart): + obj.xyz[i][0] += dx + obj.xyz[i][1] += dy + obj.xyz[i][2] += dz + + # -------------------------------------------------------------------- + # rotate an object so current coord xyz axes align with new ones + # rotate around center pt + # old coord axes = 100, 010, 001 + # xyz new = new coord axes, orthonormalized + # transformation: r_new = Lij r_old + # Lij = direction cosine of inew along jold where i,j = x,y,z + # direction cosine for 2 unit vecs is just cos(theta) + + def rotate(self,id,axis1,i1,j1,k1,axis2,i2,j2,k2): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE and obj.style != GROUP: + raise StandardError,"Can only use rotate() on a surface or group object" + + # create xyz old and new + + xnew = ynew = znew = None + if axis1 == 'x': xnew = [i1,j1,k1] + elif axis1 == 'y': ynew = [i1,j1,k1] + elif axis1 == 'z': znew = [i1,j1,k1] + else: raise StandardError,"Illegal rotate arguments" + if axis2 == 'x': xnew = [i2,j2,k2] + elif axis2 == 'y': ynew = [i2,j2,k2] + elif axis2 == 'z': znew = [i2,j2,k2] + else: raise StandardError,"Illegal rotate arguments" + if not xnew: xnew = cross(ynew,znew) + elif not ynew: ynew = cross(znew,xnew) + elif not znew: znew = cross(xnew,ynew) + else: raise StandardError,"Illegal rotate arguments" + normalize(xnew) + normalize(ynew) + normalize(znew) + + # apply rotation matrix of direction cosines to each vertex or part coord + + if obj.style == SURFACE: + for i in xrange(obj.nvert): + x = obj.vertices[i][0] - obj.xc + y = obj.vertices[i][1] - obj.yc + z = obj.vertices[i][2] - obj.zc + xn = xnew[0]*x + xnew[1]*y + xnew[2]*z + yn = ynew[0]*x + ynew[1]*y + ynew[2]*z + zn = znew[0]*x + znew[1]*y + znew[2]*z + obj.vertices[i][0] = xn + obj.xc + obj.vertices[i][1] = yn + obj.yc + obj.vertices[i][2] = zn + obj.zc + elif obj.style == GROUP: + for i in xrange(obj.npart): + x = obj.xyz[i][0] - obj.xc + y = obj.xyz[i][1] - obj.yc + z = obj.xyz[i][2] - obj.zc + xn = xnew[0]*x + ynew[0]*y + znew[0]*z + yn = xnew[1]*x + ynew[1]*y + znew[1]*z + zn = xnew[2]*x + ynew[2]*y + znew[2]*z + obj.xyz[i][0] = xn + obj.xc + obj.xyz[i][1] = yn + obj.yc + obj.xyz[i][2] = zn + obj.zc + + # -------------------------------------------------------------------- + # scale an object by sx,sy,sz factors + # scale its vertices relative to center pt + + def scale(self,id,sx,sy,sz): + obj = self.objs[self.ids[id]] + if obj.style != SURFACE and obj.style != GROUP: + raise StandardError,"Can only use scale() on a surface or group object" + if obj.style == SURFACE: + for i in xrange(obj.nvert): + obj.vertices[i][0] = obj.xc + sx * (obj.vertices[i][0] - obj.xc) + obj.vertices[i][1] = obj.yc + sy * (obj.vertices[i][1] - obj.yc) + obj.vertices[i][2] = obj.zc + sz * (obj.vertices[i][2] - obj.zc) + elif obj.style == GROUP: + for i in xrange(obj.npart): + obj.xyz[i][0] = obj.xc + sx * (obj.xyz[i][0] - obj.xc) + obj.xyz[i][1] = obj.yc + sy * (obj.xyz[i][1] - obj.yc) + obj.xyz[i][2] = obj.zc + sz * (obj.xyz[i][2] - obj.zc) + + # -------------------------------------------------------------------- + # create union object from list of other objects + + def union(self,id,*list): + if self.ids.has_key(id): + raise StandardError,"ID %s is already in use" % id + obj = Union(self.ids,self.objs,*list) + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = UNION + + # -------------------------------------------------------------------- + # join objects in list to form a new object + # only possible for group, surface, line objects + + def join(self,id,*list): + style = self.objs[self.ids[list[0]]].style + if style == GROUP: obj = Group() + elif style == SURFACE: obj = Surface() + elif style == LINE: obj = Line() + else: raise StandardError,"Cannot perform join on these object styles" + obj.select = 1 + self.ids[id] = len(self.objs) + self.objs.append(obj) + obj.id = id + obj.style = style + + if style == GROUP: + obj.on_id = self.objs[self.ids[list[0]]].on_id + obj.npart = 0 + obj.xyz = [] + elif style == SURFACE: + obj.nvert = obj.ntri = 0 + obj.vertices = [] + obj.triangles = [] + obj.connections = [] + elif style == LINE: + obj.nline = 0 + obj.pairs = [] + + for id in list: + o = self.objs[self.ids[id]] + if o.style != style: + raise StandardError,"All joined objects must be of same style" + + # force deep copy of particle coords + + if style == GROUP: + if o.on_id != obj.on_id: + raise StandardError,"Particle group surfaces do not match" + for i in xrange(o.npart): + xyz = o.xyz[i][:] + obj.xyz.append(xyz) + obj.npart += o.npart + obj.center() + + # force deep copy of triangle vertices and indices + # increment vertex and triangle indices b/c now have previous surfaces + + elif style == SURFACE: + for i in xrange(o.nvert): + vert = o.vertices[i][:] + obj.vertices.append(vert) + for i in xrange(o.ntri): + tri = [iv+obj.nvert for iv in o.triangles[i]] + obj.triangles.append(tri) + connect = o.connections[i][:] + if connect[0]: connect[0] += obj.ntri + if connect[2]: connect[2] += obj.ntri + if connect[4]: connect[4] += obj.ntri + obj.connections.append(connect) + obj.nvert += o.nvert + obj.ntri += o.ntri + obj.center() + + # force deep copy of line pt pairs + + elif style == LINE: + pairs = o.pairs[:] + obj.pairs += (pairs) + obj.nline += o.nline + + # -------------------------------------------------------------------- + # delete each object in list + # reset values in ids since some indices are decremented + + def delete(self,*list): + for id in list: + i = self.ids[id] + del self.ids[id] + del self.objs[i] + for key in self.ids.keys(): + j = self.ids[key] + if j > i: self.ids[key] = j-1 + + # -------------------------------------------------------------------- + # rename the ID of an object + # check that new name doesn't already exist + + def rename(self,idold,idnew): + i = self.ids[idold] + if self.ids.has_key(idnew): + raise StandardError,"ID %s is already in use" % id + self.ids[idnew] = i + self.objs[i].id = idnew + del self.ids[idold] + + # -------------------------------------------------------------------- + # create a deep copy of an object and assign it a new ID + # check that new name doesn't already exist + + def copy(self,idold,idnew): + obj = deepcopy(self.objs[self.ids[idold]]) + obj.select = 1 + if self.ids.has_key(idnew): + raise StandardError,"ID %s is already in use" % id + self.ids[idnew] = len(self.objs) + self.objs.append(obj) + obj.id = idnew + + # -------------------------------------------------------------------- + # set selection flag for each object in list + # if list is empty, select all + + def select(self,*list): + if len(list) == 0: list = self.ids.keys() + for id in list: + obj = self.objs[self.ids[id]] + obj.select = 1 + + # -------------------------------------------------------------------- + # unset selection flag for each object in list + # if list is empty, unselect all + + def unselect(self,*list): + if len(list) == 0: list = self.ids.keys() + for id in list: + obj = self.objs[self.ids[id]] + obj.select = 0 + + # -------------------------------------------------------------------- + # write out list of objects to data file via filewrite() + # open a new file + + def write(self,file,*list): + if not len(list): vlist = range(len(self.objs)) + else: + vlist = [] + for id in list: vlist.append(self.ids[id]) + + fp = open(file,'w') + self.filewrite(fp,vlist) + fp.close() + + # -------------------------------------------------------------------- + # append list of objects to data file via filewrite() + # open existing file for appending + + def append(self,file,*list): + if not len(list): vlist = range(len(self.objs)) + else: + vlist = [] + for id in list: vlist.append(self.ids[id]) + + fp = open(file,'a') + self.filewrite(fp,vlist) + fp.close() + + # -------------------------------------------------------------------- + # write out list of objects to previously opened data file + # for particles, write as 3d or 2d depending on on_id + + def filewrite(self,fp,vlist): + for index in vlist: + obj = self.objs[index] + if not obj.select: continue + if obj.style == GROUP: + if not obj.on_id: + print >>fp,"particles %s %d" % (obj.id,obj.npart) + else: + print >>fp,"particles %s %d %s" % (obj.id,obj.npart,obj.on_id) + print >>fp + for i in xrange(obj.npart): + print >>fp,i+1,obj.xyz[i][0],obj.xyz[i][1],obj.xyz[i][2] + print >>fp + if obj.style == SURFACE: + print >>fp,"triangles %s %d %d" % (obj.id,obj.nvert,obj.ntri) + print >>fp + for i in xrange(obj.nvert): + print >>fp,i+1,obj.vertices[i][0],obj.vertices[i][1], \ + obj.vertices[i][2] + print >>fp + for i in xrange(obj.ntri): + print >>fp,i+1,obj.triangles[i][0],obj.triangles[i][1], \ + obj.triangles[i][2] + print >>fp + for i in xrange(obj.ntri): + print >>fp,i+1,obj.connections[i][0],obj.connections[i][1], \ + obj.connections[i][2],obj.connections[i][3], \ + obj.connections[i][4],obj.connections[i][5] + if obj.style == REGION: + print >>fp,"region %s" % obj.command() + + # -------------------------------------------------------------------- + # iterator called from other tools + + def iterator(self,flag): + if flag == 0: return 0,0,1 + return 0,0,-1 + + # -------------------------------------------------------------------- + # return list of atoms and triangles to viz for cdata object + + def viz(self,isnap): + if isnap: + raise StandardError, "cannot call cdata.viz() with isnap != 0" + + # create atom list from sum of all particle groups + # id = running count + # type = running type of particle group + + id = itype = 0 + atoms = [] + for obj in self.objs: + if obj.style != GROUP: continue + if not obj.select: continue + itype += 1 + for xyz in obj.xyz: + id += 1 + atoms.append([id,itype,xyz[0],xyz[1],xyz[2]]) + + # no bonds + + bonds = [] + + # create triangle list from sum of all surfaces and regions + # id = running count + # type = type of set of tris + + id = itype = 0 + tris = [] + for obj in self.objs: + if obj.style != SURFACE and obj.style != REGION: continue + if not obj.select: continue + if obj.style == REGION: obj.triangulate() + itype += 1 + for tri in obj.triangles: + v1 = obj.vertices[tri[0]-1] + v2 = obj.vertices[tri[1]-1] + v3 = obj.vertices[tri[2]-1] + list = v1 + v2 + v3 + n = normal(list[0:3],list[3:6],list[6:9]) + id += 1 + tris.append([id,itype] + list + n) + + # create line list from sum of all line objects + + id = itype = 0 + lines = [] + for obj in self.objs: + if obj.style != LINE: continue + if not obj.select: continue + itype += 1 + for pair in obj.pairs: + id += 1 + lines.append([id,itype] + pair) + + return 0,self.bbox(),atoms,bonds,tris,lines + + # -------------------------------------------------------------------- + # time query from other tools + + def findtime(self,n): + if n == 0: return 0 + raise StandardError, "no step %d exists" % (n) + + # -------------------------------------------------------------------- + # return box size + + def maxbox(self): + return self.bbox() + + # -------------------------------------------------------------------- + # return box that bounds all selected objects + + def bbox(self): + xlo = ylo = zlo = BIG + xhi = yhi = zhi = -BIG + for obj in self.objs: + if not obj.select: continue + xxlo,yylo,zzlo,xxhi,yyhi,zzhi = obj.bbox() + if xxlo < xlo: xlo = xxlo + if yylo < ylo: ylo = yylo + if zzlo < zlo: zlo = zzlo + if xxhi > xhi: xhi = xxhi + if yyhi > yhi: yhi = yyhi + if zzhi > zhi: zhi = zzhi + + return (xlo,ylo,zlo,xhi,yhi,zhi) + +# -------------------------------------------------------------------- +# object styles + +EPSILON = 1.0e-6 +BIG = 1.0e20 + +REGION = 1 +SURFACE = 2 +GROUP = 3 +UNION = 4 + +BOX = 5 +SPHERE = 6 +SHELL = 7 +CYLINDER = 8 +CAPPED = 9 +LINE = 10 + +# -------------------------------------------------------------------- +# random number generator class + +IM = 2147483647 +AM = 1.0/IM +IA = 16807 +IQ = 127773 +IR = 2836 + +class Random: + def __init__(self,seed): + self.seed = seed + + def __call__(self): + k = self.seed/IQ + self.seed = IA*(self.seed-k*IQ) - IR*k + if self.seed < 0: self.seed += IM + return AM*self.seed + +# -------------------------------------------------------------------- +# triangulated surface + +class Surface: + + def __init__(self): + self.nbinx = self.nbiny = 0 + + # bounding box + + def bbox(self): + list = [float(vert[0]) for vert in self.vertices] + xlo = min(list) + xhi = max(list) + list = [float(vert[1]) for vert in self.vertices] + ylo = min(list) + yhi = max(list) + list = [float(vert[2]) for vert in self.vertices] + zlo = min(list) + zhi = max(list) + + return (xlo,ylo,zlo,xhi,yhi,zhi) + + # set center point explicitly or set to middle of bounding box + + def center(self,*xyz): + if len(xyz): + self.xc = xyz[0] + self.yc = xyz[1] + self.zc = xyz[2] + else: + xlo,ylo,zlo,xhi,yhi,zhi = self.bbox() + self.xc = 0.5 * (xlo + xhi) + self.yc = 0.5 * (ylo + yhi) + self.zc = 0.5 * (zlo + zhi) + + # bin 2d-projected triangles into xy plane for nbinx by nbiny bins + # each bin overlayed by triangle's xy bounding box stores the triangle index + # EPSILON insures that bins completely overlay surface bounding box + # self.xlo, self.ylo, self.dxinv, self.dyinv, self.bin are used by inside() + + def inside_prep(self): + self.xlo,self.ylo,self.zlo,self.xhi,self.yhi,self.zhi = self.bbox() + xsize = self.xhi - self.xlo + ysize = self.yhi - self.ylo + if self.nbinx == 0 and self.nbiny == 0: + binsize = sqrt(xsize*ysize / (self.ntri/2)) + self.nbinx = int(xsize/binsize) + self.nbiny = int(ysize/binsize) + if self.nbinx < 2: self.nbinx = 2 + if self.nbiny < 2: self.nbiny = 2 + self.dxinv = 1.0 / (xsize / self.nbinx + EPSILON) + self.dyinv = 1.0 / (ysize / self.nbiny + EPSILON) + + print "Binning %d triangles into %d by %d bins ..." % \ + (self.ntri,self.nbinx,self.nbiny) + + self.bin = [] + for i in xrange(self.nbinx): + self.bin.append(self.nbiny*[0]) + for j in xrange(self.nbiny): + self.bin[i][j] = [] + + for m in xrange(self.ntri): + v1 = self.vertices[self.triangles[m][0]-1] + v2 = self.vertices[self.triangles[m][1]-1] + v3 = self.vertices[self.triangles[m][2]-1] + xmin = min((v1[0],v2[0],v3[0])) + xmax = max((v1[0],v2[0],v3[0])) + ymin = min((v1[1],v2[1],v3[1])) + ymax = max((v1[1],v2[1],v3[1])) + ilo = int((xmin - self.xlo) * self.dxinv) + ihi = int((xmax - self.xlo) * self.dxinv) + jlo = int((ymin - self.ylo) * self.dyinv) + jhi = int((ymax - self.ylo) * self.dyinv) + for i in xrange(ilo,ihi+1): + for j in xrange(jlo,jhi+1): + self.bin[i][j].append(m) + + print "Done with binning" + + # check for inside assumes that surf is a closed set of triangles + # consider a line segment from x,y,z to x,y,INF + # project 3d triangles to xy plane + # only need examine triangles in bin that point is in + # if pt is outside bins, don't need to check + # x,y,z is inside surf if line segment intersects an odd number of triangles + # intersection test: + # is xy pt in bounding rectangle of tri in xy plane ? + # is xy pt inside tri in xy plane (including edges and vertices) ? + # compute ztri = z value of xy pt on plane of 3d tri + # if z of pt is <= ztri, then line segment intersects the tri + + def inside(self,x,y,z): + ix = int((x - self.xlo) * self.dxinv) + iy = int((y - self.ylo) * self.dyinv) + if ix < 0 or ix >= self.nbinx or iy < 0 or iy >= self.nbiny: return 0 + n = len(self.bin[ix][iy]) + + hit = 0 + for m in xrange(n): + itri = self.bin[ix][iy][m] + tri = self.triangles[itri] + + v1 = self.vertices[tri[0]-1] + v2 = self.vertices[tri[1]-1] + v3 = self.vertices[tri[2]-1] + + # is x,y in bounding box of 2d triangle ? + + if x < v1[0] and x < v2[0] and x < v3[0]: continue + if x > v1[0] and x > v2[0] and x > v3[0]: continue + if y < v1[1] and y < v2[1] and y < v3[1]: continue + if y > v1[1] and y > v2[1] and y > v3[1]: continue + + # is x,y inside 2d triangle ? + # cross product of each edge with vertex-to-point must have same sign + # cross product = 0 is OK, means point is on edge or vertex + + c1 = (v2[0]-v1[0])*(y-v1[1]) - (v2[1]-v1[1])*(x-v1[0]) + c2 = (v3[0]-v2[0])*(y-v2[1]) - (v3[1]-v2[1])*(x-v2[0]) + c3 = (v1[0]-v3[0])*(y-v3[1]) - (v1[1]-v3[1])*(x-v3[0]) + if c1 < 0: + if c2 > 0 or c3 > 0: continue + elif c1 > 0: + if c2 < 0 or c3 < 0: continue + else: + if c2 < 0 and c3 > 0: continue + if c2 > 0 and c3 < 0: continue + + # represent x,y point in basis of 2 triangle edge vectors + # p = (x,y) - v1, v = v2 - v1, w = v3 - v2 + # find alpha,beta such that p = alpha v + beta w + # by solving system of 2 linear eqs for their intersection + # denom (vx - vy * wx/xy) cannot be 0 since would imply vx/vy = wx/wy + # and thus e1 would be parallel to e2 + # if wy = 0, vy cannot be 0, since e1 would be parallel to e2 + + px = x - v1[0]; + py = y - v1[1] + vx = v2[0] - v1[0] + vy = v2[1] - v1[1] + wx = v3[0] - v2[0] + wy = v3[1] - v2[1] + if wy: alpha = (px - py * wx/wy) / (vx - vy * wx/wy) + else: alpha = py/vy + if wx: beta = (px - alpha * vx) / wx + else: beta = (py - alpha * vy) / wy + pz = alpha * (v2[2] - v1[2]) + beta * (v3[2] - v2[2]) + if z <= pz + v1[2]: hit += 1 + + return hit % 2 + + # surface area + # areas = cummulative total area of all triangles + # triangle area = 1/2 of magnitude of cross product of 2 edge vectors + + def area(self): + a = 3*[0] + self.areas = [] + sum = 0.0 + for tri in self.triangles: + v1 = self.vertices[tri[0]-1] + v2 = self.vertices[tri[1]-1] + v3 = self.vertices[tri[2]-1] + a[0] = (v2[1]-v1[1])*(v3[2]-v1[2]) - (v2[2]-v1[2])*(v3[1]-v1[1]) + a[1] = (v2[2]-v1[2])*(v3[0]-v1[0]) - (v2[0]-v1[0])*(v3[2]-v1[2]) + a[2] = (v2[0]-v1[0])*(v3[1]-v1[1]) - (v2[1]-v1[1])*(v3[0]-v1[0]) + sum += 0.5 * sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]) + self.areas.append(sum) + return sum + + # return a random location on one of triangles + + def loc2d(self,area,random): + for i in xrange(self.ntri): + if area < self.areas[i]: break + v1 = self.vertices[self.triangles[i][0]-1] + v2 = self.vertices[self.triangles[i][1]-1] + v3 = self.vertices[self.triangles[i][2]-1] + r1 = random() + r2 = random() + if r2 > r1: + tmp = r1 + r1 = r2 + r2 = tmp + x = v1[0] + r1*(v2[0] - v1[0]) + r2*(v3[0] - v2[0]) + y = v1[1] + r1*(v2[1] - v1[1]) + r2*(v3[1] - v2[1]) + z = v1[2] + r1*(v2[2] - v1[2]) + r2*(v3[2] - v2[2]) + list = v1 + v2 + v3 + return [x,y,z],normal(list[0:3],list[3:6],list[6:9]) + +# -------------------------------------------------------------------- +# group of particles + +class Group: + def bbox(self): + list = [xyz[0] for xyz in self.xyz] + xlo = min(list) + xhi = max(list) + list = [xyz[1] for xyz in self.xyz] + ylo = min(list) + yhi = max(list) + list = [xyz[2] for xyz in self.xyz] + zlo = min(list) + zhi = max(list) + + return (xlo,ylo,zlo,xhi,yhi,zhi) + + # set center point explicitly or set to middle of bounding box + + def center(self,*xyz): + if len(xyz): + self.xc = xyz[0] + self.yc = xyz[1] + self.zc = xyz[2] + else: + xlo,ylo,zlo,xhi,yhi,zhi = self.bbox() + self.xc = 0.5 * (xlo + xhi) + self.yc = 0.5 * (ylo + yhi) + self.zc = 0.5 * (zlo + zhi) + +# -------------------------------------------------------------------- +# box region + +class Box: + def __init__(self,*list): + self.xlo = float(list[0]) + self.ylo = float(list[1]) + self.zlo = float(list[2]) + self.xhi = float(list[3]) + self.yhi = float(list[4]) + self.zhi = float(list[5]) + self.q1 = self.q2 = self.q3 = 1 + + # bounding box around region + + def bbox(self): + return (self.xlo,self.ylo,self.zlo,self.xhi,self.yhi,self.zhi) + + # return 1,0 for xyz inside/outside the region + + def inside(self,x,y,z): + if x < self.xlo or x > self.xhi: return 0 + if y < self.ylo or y > self.yhi: return 0 + if z < self.zlo or z > self.zhi: return 0 + return 1 + + # triangulate the region + # set nvert,ntri,vertices,triangles,connections + # convert vertices from unit box to lo/hi box + # convert tuples returned by box_triangluate (used for dict lookup) to lists + + def triangulate(self): + vertices,triangles = box_triangulate(self.q1,self.q2,self.q3) + self.nvert = len(vertices) + self.ntri = len(triangles) + self.vertices = [] + for i in xrange(self.nvert): + v1 = self.xlo + vertices[i][0]*(self.xhi-self.xlo) + v2 = self.ylo + vertices[i][1]*(self.yhi-self.ylo) + v3 = self.zlo + vertices[i][2]*(self.zhi-self.zlo) + self.vertices.append([v1,v2,v3]) + self.triangles = [] + for i in xrange(self.ntri): + self.triangles.append([triangles[i][0],triangles[i][1],triangles[i][2]]) + self.connections = connect(self.nvert,self.ntri,self.triangles) + + # surface area of region + + def area(self): + xsize = self.xhi - self.xlo + ysize = self.yhi - self.ylo + zsize = self.zhi - self.zlo + self.areas = [] + sum = ysize*zsize + self.areas.append(sum) + sum += ysize*zsize + self.areas.append(sum) + sum += xsize*zsize + self.areas.append(sum) + sum += xsize*zsize + self.areas.append(sum) + sum += xsize*ysize + self.areas.append(sum) + sum += xsize*ysize + self.areas.append(sum) + return sum + + # return a random location on surface of region + + def loc2d(self,area,random): + xsize = self.xhi - self.xlo + ysize = self.yhi - self.ylo + zsize = self.zhi - self.zlo + r1 = random() + r2 = random() + if area <= self.areas[0]: + return [self.xlo,self.ylo + r1*ysize,self.zlo + r2*zsize],[-1,0,0] + elif area <= self.areas[1]: + return [self.xhi,self.ylo + r1*ysize,self.zlo + r2*zsize],[1,0,0] + elif area <= self.areas[2]: + return [self.xlo + r1*xsize,self.ylo,self.zlo + r2*zsize],[0,-1,0] + elif area <= self.areas[3]: + return [self.xlo + r1*xsize,self.yhi,self.zlo + r2*zsize],[0,1,0] + elif area <= self.areas[4]: + return [self.xlo + r1*xsize,self.ylo + r2*ysize,self.zlo],[0,0,-1] + else: + return [self.xlo + r1*xsize,self.ylo + r2*ysize,self.zhi],[0,0,1] + + # ChemCell text to create the region + + def command(self): + return "%s box %g %g %g %g %g %g" % (self.id,self.xlo,self.ylo,self.zlo, + self.xhi,self.yhi,self.zhi) + +# -------------------------------------------------------------------- +# sphere region + +class Sphere: + def __init__(self,*list): + self.x = float(list[0]) + self.y = float(list[1]) + self.z = float(list[2]) + self.r = float(list[3]) + self.rsq = self.r*self.r + self.q1 = 2 + + # bounding box around region + + def bbox(self): + return (self.x-self.r,self.y-self.r,self.z-self.r, \ + self.x+self.r,self.y+self.r,self.z+self.r) + + # return 1,0 for xyz inside/outside the region + + def inside(self,x,y,z): + dx = x - self.x + dy = y - self.y + dz = z - self.z + rsq = dx*dx + dy*dy + dz*dz + if rsq > self.rsq: return 0 + return 1 + + # triangulate the region + # set nvert,ntri,vertices,triangles,connections + # convert vertices from unit box to sphere at (x,y,z) with radius r + # normalize() pushes vertices to surface of sphere + # convert tuples returned by box_triangluate (used for dict lookup) to lists + + def triangulate(self): + vertices,triangles = box_triangulate(self.q1,self.q1,self.q1) + self.nvert = len(vertices) + self.ntri = len(triangles) + self.vertices = [] + for i in xrange(self.nvert): + v1 = vertices[i][0] - 0.5 + v2 = vertices[i][1] - 0.5 + v3 = vertices[i][2] - 0.5 + c = [v1,v2,v3] + normalize(c) + c[0] = self.x + self.r*c[0] + c[1] = self.y + self.r*c[1] + c[2] = self.z + self.r*c[2] + self.vertices.append(c) + self.triangles = [] + for i in xrange(self.ntri): + self.triangles.append([triangles[i][0],triangles[i][1],triangles[i][2]]) + self.connections = connect(self.nvert,self.ntri,self.triangles) + + # surface area of region + + def area(self): + value = 4 * pi * self.r*self.r + return value + + # return a random location on surface of region + + def loc2d(self,area,random): + while 1: + x = random() - 0.5 + y = random() - 0.5 + z = random() - 0.5 + if x*x + y*y + z*z <= 0.25: break + c = [x,y,z] + normalize(c) + return [self.x + self.r*c[0], self.y + self.r*c[1], self.z + self.r*c[2]],c + + # ChemCell text to create the region + + def command(self): + return "%s sphere %g %g %g %g" % (self.id,self.x,self.y,self.z,self.r) + +# -------------------------------------------------------------------- +# shell region +# inherits most functionality from Sphere, adds inner radius +# loc2d is only only outer surface, inherited from Sphere + +class Shell(Sphere): + def __init__(self,*list): + self.rinner = float(list[4]) + self.innersq = self.rinner*self.rinner + + def inside(self,x,y,z): + dx = x - self.x + dy = y - self.y + dz = z - self.z + rsq = dx*dx + dy*dy + dz*dz + if rsq > self.rsq or rsq < self.innersq: return 0 + return 1 + + def command(self): + return "%s shell %g %g %g %g %g" % (self.id,self.x,self.y,self.z, + self.r,self.rinner) + +# -------------------------------------------------------------------- +# cylinder region + +class Cylinder: + def __init__(self,*list): + self.axis = list[0] + self.c1 = list[1] + self.c2 = list[2] + self.r = list[3] + self.lo = list[4] + self.hi = list[5] + self.rsq = self.r*self.r + self.q1 = 2 + self.q2 = 1 + + # bounding box around region + + def bbox(self): + if self.axis == 'x': + return (self.lo,self.c1-self.r,self.c2-self.r, \ + self.hi,self.c1+self.r,self.c2+self.r) + elif self.axis == 'y': + return (self.c1-self.r,self.lo,self.c2-self.r, \ + self.c1+self.r,self.hi,self.c2+self.r) + elif self.axis == 'z': + return (self.c1-self.r,self.c2-self.r,self.lo, \ + self.c1+self.r,self.c2+self.r,self.hi) + + # return 1,0 for xyz inside/outside the region + + def inside(self,x,y,z): + if self.axis == 'x': + d1 = y - self.c1 + d2 = z - self.c2 + d3 = x + elif self.axis == 'y': + d1 = x - self.c1 + d2 = z - self.c2 + d3 = y + elif self.axis == 'z': + d1 = x - self.c1 + d2 = y - self.c2 + d3 = z + rsq = d1*d1 + d2*d2 + if rsq > self.rsq: return 0 + if d3 < self.lo or d3 > self.hi: return 0 + return 1 + + # triangulate the region + # set nvert,ntri,vertices,triangles,connections + # convert vertices from unit box to cylinder with correct axis + # x,y have spacings for ends of cylinder, z has spacings for axis of cylinder + # convert tuples returned by box_triangluate (used for dict lookup) to lists + + def triangulate(self): + vertices,triangles = box_triangulate(self.q1,self.q1,self.q2) + self.nvert = len(vertices) + self.ntri = len(triangles) + self.vertices = [] + for i in xrange(self.nvert): + v1 = vertices[i][0] - 0.5 + v2 = vertices[i][1] - 0.5 + v3 = vertices[i][2] + c = [v1,v2,0] + normalize(c) + if fabs(v1) >= fabs(v2): length = 2*fabs(v1) + if fabs(v2) >= fabs(v1): length = 2*fabs(v2) + c[0] *= length + c[1] *= length + p1 = self.c1 + self.r*c[0] + p2 = self.c2 + self.r*c[1] + p3 = self.lo + v3*(self.hi - self.lo) + if self.axis == 'x': self.vertices.append([p3,p1,p2]) + elif self.axis == 'y': self.vertices.append([p1,p3,p2]) + elif self.axis == 'z': self.vertices.append([p1,p2,p3]) + self.triangles = [] + for i in xrange(self.ntri): + self.triangles.append([triangles[i][0],triangles[i][1],triangles[i][2]]) + self.connections = connect(self.nvert,self.ntri,self.triangles) + + # surface area of region + + def area(self): + self.areas = [] + sum = pi * self.rsq + self.areas.append(sum) + sum += pi * self.rsq + self.areas.append(sum) + sum += 2 * pi * self.r * (self.hi - self.lo) + self.areas.append(sum) + return sum + + # return a random location on surface of region + + def loc2d(self,area,random): + if area <= self.areas[0]: + while 1: + r1 = random() - 0.5 + r2 = random() - 0.5 + if r1*r1 + r2*r2 < 0.25: break + if self.axis == 'x': + return [self.lo,self.c1 + 2*r1*self.r,self.c2 + 2*r2*self.r],[-1,0,0] + elif self.axis == 'y': + return [self.c1 + 2*r1*self.r,self.lo,self.c2 + 2*r2*self.r],[0,-1,0] + elif self.axis == 'z': + return [self.c1 + 2*r1*self.r,self.c2 + 2*r2*self.r,self.lo],[0,0,-1] + elif area <= self.areas[1]: + while 1: + r1 = random() - 0.5 + r2 = random() - 0.5 + if r1*r1 + r2*r2 < 0.25: break + if self.axis == 'x': + return [self.hi,self.c1 + 2*r1*self.r,self.c2 + 2*r2*self.r],[1,0,0] + elif self.axis == 'y': + return [self.c1 + 2*r1*self.r,self.hi,self.c2 + 2*r2*self.r],[0,1,0] + elif self.axis == 'z': + return [self.c1 + 2*r1*self.r,self.c2 + 2*r2*self.r,self.hi],[0,0,1] + else: + r1 = 2*pi*random() + r2 = random() + if self.axis == 'x': + n = [0,cos(r1),sin(r1)] + return [self.lo + r2*(self.hi-self.lo), + self.c1 + self.r*cos(r1), + self.c2 + self.r*sin(r1)],n + elif self.axis == 'y': + n = [cos(r1),0,sin(r1)] + return [self.c1 + self.r*cos(r1), + self.lo + r2*(self.hi-self.lo), + self.c2 + self.r*sin(r1)],n + elif self.axis == 'z': + n = [cos(r1),sin(r1),0] + return [self.c1 + self.r*cos(r1), + self.c2 + self.r*sin(r1), + self.lo + r2*(self.hi-self.lo)],n + + # ChemCell text to create the region + + def command(self): + return "%s cylinder %s %g %g %g %g %g" % (self.id,self.axis, + self.c1,self.c2,self.r, + self.lo,self.hi) + +# -------------------------------------------------------------------- +# capped-cylinder region + +class Capped: + def __init__(self,*list): + self.axis = list[0] + self.c1 = list[1] + self.c2 = list[2] + self.r = list[3] + self.lo = list[4] + self.hi = list[5] + self.rsq = self.r*self.r + self.q1 = 2 + self.q2 = 1 + + # bounding box around region + + def bbox(self): + if self.axis == 'x': + return (self.lo-self.r,self.c1-self.r,self.c2-self.r, \ + self.hi+self.r,self.c1+self.r,self.c2+self.r) + elif self.axis == 'y': + return (self.c1-self.r,self.lo-self.r,self.c2-self.r, \ + self.c1+self.r,self.hi+self.r,self.c2+self.r) + elif self.axis == 'z': + return (self.c1-self.r,self.c2-self.r,self.lo-self.r, \ + self.c1+self.r,self.c2+self.r,self.hi+self.r) + + # return 1,0 for xyz inside/outside the region + + def inside(self,x,y,z): + if self.axis == 'x': + d1 = y - self.c1 + d2 = z - self.c2 + d3 = x + elif sef.axis == 'y': + d1 = x - self.c1 + d2 = z - self.c2 + d3 = y + elif self.axis == 'z': + d1 = x - self.c1 + d2 = y - self.c2 + d3 = z + rsq = d1*d1 + d2*d2 + if d3 >= self.lo and d3 <= self.hi: + if rsq > self.rsq: return 0 + elif d3 < self.lo: + if d1*d1 + d2*d2 + (d3-self.lo)*(d3-self.lo) > self.rsq: return 0 + else: + if d1*d1 + d2*d2 + (d3-self.hi)*(d3-self.hi) > self.rsq: return 0 + return 1 + + # triangulate the region + # set nvert,ntri,vertices,triangles,connections + # convert vertices from unit box to cylinder with correct axis + # x,y have spacings for ends of cylinder + # z has spacings for axis of cylinder plus 1/2 of q1 on each end cap + # convert tuples returned by box_triangluate (used for dict lookup) to lists + + def triangulate(self): + if self.q1 % 2: raise StandardError,"Capped cylinder q1 must be even" + vertices,triangles = box_triangulate(self.q1,self.q1,self.q2+self.q1) + self.nvert = len(vertices) + self.ntri = len(triangles) + self.vertices = [] + cutlo = self.q1/2 * 1.0/(self.q2+self.q1) + EPSILON + cuthi = 1.0 - cutlo + for i in xrange(self.nvert): + v1 = vertices[i][0] + v2 = vertices[i][1] + v3 = vertices[i][2] + if v3 < cutlo: + c = [v1-0.5,v2-0.5,(v3-cutlo)*(0.5/cutlo)] + normalize(c) + p1 = self.c1 + self.r*c[0] + p2 = self.c2 + self.r*c[1] + p3 = self.lo + self.r*c[2] + elif v3 > cuthi: + c = [v1-0.5,v2-0.5,(v3-cuthi)*(0.5/cutlo)] + normalize(c) + p1 = self.c1 + self.r*c[0] + p2 = self.c2 + self.r*c[1] + p3 = self.hi + self.r*c[2] + else: + c = [v1-0.5,v2-0.5,0.0] + normalize(c) + p1 = self.c1 + self.r*c[0] + p2 = self.c2 + self.r*c[1] + p3 = self.lo + (v3-cutlo)/(cuthi-cutlo) * (self.hi - self.lo) + if self.axis == 'x': self.vertices.append([p3,p1,p2]) + elif self.axis == 'y': self.vertices.append([p1,p3,p2]) + elif self.axis == 'z': self.vertices.append([p1,p2,p3]) + self.triangles = [] + for i in xrange(self.ntri): + self.triangles.append([triangles[i][0],triangles[i][1],triangles[i][2]]) + self.connections = connect(self.nvert,self.ntri,self.triangles) + + # surface area of region + + def area(self): + self.areas = [] + sum = 2 * pi * self.rsq + self.areas.append(sum) + sum += 2 * pi * self.rsq + self.areas.append(sum) + sum += 2 * pi * self.r * (self.hi - self.lo) + self.areas.append(sum) + return sum + + # return a random location on surface of region + + def loc2d(self,area,random): + if area <= self.areas[0]: + while 1: + r1 = random() - 0.5 + r2 = random() - 0.5 + r3 = random() - 0.5 + if r3 <= 0 and r1*r1 + r2*r2 + r3*r3 < 0.25: break + c = [r1,r2,r3] + normalize(c) + if self.axis == 'x': + return [self.lo + c[2]*self.r, + self.c1 + c[0]*self.r, + self.c2 + c[1]*self.r],[c[2],c[0],c[1]] + elif self.axis == 'y': + return [self.c1 + c[0]*self.r, + self.lo + c[2]*self.r, + self.c2 + c[1]*self.r],[c[0],c[2],c[1]] + elif self.axis == 'z': + return [self.c1 + c[0]*self.r, + self.c2 + c[1]*self.r, + self.lo + c[2]*self.r],[c[0],c[1],c[2]] + elif area <= self.areas[1]: + while 1: + r1 = random() - 0.5 + r2 = random() - 0.5 + r3 = random() - 0.5 + if r3 >= 0 and r1*r1 + r2*r2 + r3*r3 < 0.25: break + c = [r1,r2,r3] + normalize(c) + if self.axis == 'x': + return [self.hi + c[2]*self.r, + self.c1 + c[0]*self.r, + self.c2 + c[1]*self.r],[c[2],c[0],c[1]] + elif self.axis == 'y': + return [self.c1 + c[0]*self.r, + self.hi + c[2]*self.r, + self.c2 + c[1]*self.r],[c[0],c[2],c[1]] + elif self.axis == 'z': + return [self.c1 + c[0]*self.r, + self.c2 + c[1]*self.r, + self.hi + c[2]*self.r],[c[0],c[1],c[2]] + else: + r1 = 2*pi*random() + r2 = random() + if self.axis == 'x': + n = [0,cos(r1),sin(r1)] + return [self.lo + r2*(self.hi-self.lo), + self.c1 + self.r*cos(r1), + self.c2 + self.r*sin(r1)],n + elif self.axis == 'y': + n = [cos(r1),0,sin(r1)] + return [self.c1 + self.r*cos(r1), + self.lo + r2*(self.hi-self.lo), + self.c2 + self.r*sin(r1)],n + elif self.axis == 'z': + n = [cos(r1),sin(r1),0] + return [self.c1 + self.r*cos(r1), + self.c2 + self.r*sin(r1), + self.lo + r2*(self.hi-self.lo)],n + + # ChemCell text to create the region + + def command(self): + return "%s capped %s %g %g %g %g %g" % (self.id,self.axis, + self.c1,self.c2,self.r, + self.lo,self.hi) + +# -------------------------------------------------------------------- +# set of line segments + +class Line: + def bbox(self): + list = [pair[0] for pair in self.pairs] + list += [pair[3] for pair in self.pairs] + xlo = min(list) + xhi = max(list) + list = [pair[1] for pair in self.pairs] + list += [pair[4] for pair in self.pairs] + ylo = min(list) + yhi = max(list) + list = [pair[2] for pair in self.pairs] + list += [pair[5] for pair in self.pairs] + zlo = min(list) + zhi = max(list) + return (xlo,ylo,zlo,xhi,yhi,zhi) + + def addline(self,coords): + self.pairs.append(list(coords)) + +# -------------------------------------------------------------------- +# union object that contains other objects +# pass in parent cdata IDs and object list to constructor +# self.objs = list of child objects + +class Union: + def __init__(self,ids,objs,*list): + self.objs = [] + for id in list: + obj = objs[ids[id]] + if obj.style != SURFACE and obj.style != REGION and obj.style != UNION: + raise StandardError,"Union child object is of invalid style" + self.objs.append(obj) + + # bounding box around all child objects + + def bbox(self): + xlo,ylo,zlo,xhi,yhi,zhi = self.objs[0].bbox() + for obj in self.objs[1:]: + xxlo,yylo,zzlo,xxhi,yyhi,zzhi = obj.bbox() + if xxlo < xlo: xlo = xxlo + if yylo < ylo: ylo = yylo + if zzlo < zlo: zlo = zzlo + if xxhi > xhi: xhi = xxhi + if yyhi > yhi: yhi = yyhi + if zzhi > zhi: zhi = zzhi + return (xlo,ylo,zlo,xhi,yhi,zhi) + + # return 1,0 for xyz inside/outside the union + # inside union if inside any of its child objects + + def inside(self,x,y,z): + for obj in self.objs: + if obj.inside(x,y,z): return 1 + return 0 + + # surface area of union + # areas = cummulative total area for child objects + + def area(self): + self.areas = [] + sum = 0.0 + for obj in self.objs: + sum += obj.area() + self.areas.append(sum) + return sum + + # return a random location on surface of one of child objects + + def loc2d(self,area,random): + for i in xrange(len(self.objs)): + if area < self.areas[i]: break + if i > 0: area -= self.areas[i] + return self.objs[i].loc2d(area,random) + +# -------------------------------------------------------------------- +# return c = a x b + +def cross(a,b): + c = 3*[0] + c[0] = a[1]*b[2] - a[2]*b[1] + c[1] = a[2]*b[0] - a[0]*b[2] + c[2] = a[0]*b[1] - a[1]*b[0] + return c + +# -------------------------------------------------------------------- +# normalize vector a to unit length + +def normalize(a): + length = sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]) + if length == 0.0: return + a[0] /= length + a[1] /= length + a[2] /= length + +# -------------------------------------------------------------------- +# compute normal for a triangle with 3 vertices + +def normal(x,y,z): + v1 = 3*[0] + v1[0] = y[0] - x[0] + v1[1] = y[1] - x[1] + v1[2] = y[2] - x[2] + + v2 = 3*[0] + v2[0] = z[0] - y[0] + v2[1] = z[1] - y[1] + v2[2] = z[2] - y[2] + + n = 3*[0] + n[0] = v1[1]*v2[2] - v1[2]*v2[1] + n[1] = v1[2]*v2[0] - v1[0]*v2[2] + n[2] = v1[0]*v2[1] - v1[1]*v2[0] + + length = sqrt(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]) + n[0] /= length + n[1] /= length + n[2] /= length + + return n + +# -------------------------------------------------------------------- +# create connections between triangles for a triangulated surface + +def connect(nvert,ntri,triangles): + + # triangles have list of 3 vertices + # create inverted v2tri where each vertex has list of triangles it is in + + v2tri = [] + for i in xrange(nvert): v2tri.append([]); + + for i in xrange(ntri): + for vert in triangles[i]: v2tri[vert-1].append(i) + + # loop over triangles to reset connections + + connections = [] + for i in xrange(ntri): + + # zero connections + + connect = 6*[0] + connections.append(connect) + + # tri123 = list of tris attached to each vertex of triangle i + + v = triangles[i] + tri1 = v2tri[v[0]-1] + tri2 = v2tri[v[1]-1] + tri3 = v2tri[v[2]-1] + + # loop over attached tris and look for 2nd vertex in each of 3 edges + # when find it, set connection triangle and edge values + + for itri in tri1: + if itri == i: continue + if v[1] in triangles[itri]: + connect[0] = itri+1 + m = triangles[itri].index(v[0]) + n = triangles[itri].index(v[1]) + if (m == 0 and n == 1) or (m == 1 and n == 0): connect[1] = 1 + elif (m == 1 and n == 2) or (m == 2 and n == 1): connect[1] = 2 + else: connect[1] = 3 + break + + for itri in tri2: + if itri == i: continue + if v[2] in triangles[itri]: + connect[2] = itri+1 + m = triangles[itri].index(v[1]) + n = triangles[itri].index(v[2]) + if (m == 0 and n == 1) or (m == 1 and n == 0): connect[3] = 1 + elif (m == 1 and n == 2) or (m == 2 and n == 1): connect[3] = 2 + else: connect[3] = 3 + break + + for itri in tri3: + if itri == i: continue + if v[0] in triangles[itri]: + connect[4] = itri+1 + m = triangles[itri].index(v[2]) + n = triangles[itri].index(v[0]) + if (m == 0 and n == 1) or (m == 1 and n == 0): connect[5] = 1 + elif (m == 1 and n == 2) or (m == 2 and n == 1): connect[5] = 2 + else: connect[5] = 3 + break + + return connections + +# -------------------------------------------------------------------- +# add a vertex v to vertices list unless already exists in vdict dictionary +# return index of where v is in vertices list + +def vertex(v,vertices,vdict): + if vdict.has_key(v): return vdict[v] + n = len(vertices) + vertices.append(v) + vdict[v] = n + return n + +# -------------------------------------------------------------------- +# triangulate a unit box from (0,0,0) to (1,1,1) with spacings q1,q2,q3 +# return lists of vertices and triangles +# insure right-hand rule for each tri points OUT of the box + +def box_triangulate(q1,q2,q3): + if q1: dx = 1.0 / q1 + if q2: dy = 1.0 / q2 + if q3: dz = 1.0 / q3 + vdict = {} + vertices = [] + triangles = [] + for j in xrange(q2): + for k in xrange(q3): + v1 = (0, j*dy, k*dz) + v2 = (0, (j+1)*dy, k*dz) + v3 = (0, (j+1)*dy, (k+1)*dz) + v4 = (0, j*dy, (k+1)*dz) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv3+1,iv2+1]) + triangles.append([iv1+1,iv4+1,iv3+1]) + v1 = (1, j*dy, k*dz) + v2 = (1, (j+1)*dy, k*dz) + v3 = (1, (j+1)*dy, (k+1)*dz) + v4 = (1, j*dy, (k+1)*dz) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv2+1,iv3+1]) + triangles.append([iv1+1,iv3+1,iv4+1]) + for i in xrange(q1): + for k in xrange(q3): + v1 = (i*dx, 0, k*dz) + v2 = ((i+1)*dx, 0, k*dz) + v3 = ((i+1)*dx, 0, (k+1)*dz) + v4 = (i*dx, 0, (k+1)*dz) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv2+1,iv3+1]) + triangles.append([iv1+1,iv3+1,iv4+1]) + v1 = (i*dx, 1, k*dz) + v2 = ((i+1)*dx, 1, k*dz) + v3 = ((i+1)*dx, 1, (k+1)*dz) + v4 = (i*dx, 1, (k+1)*dz) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv3+1,iv2+1]) + triangles.append([iv1+1,iv4+1,iv3+1]) + for i in xrange(q1): + for j in xrange(q2): + v1 = (i*dx, j*dy, 0) + v2 = ((i+1)*dx, j*dy, 0) + v3 = ((i+1)*dx, (j+1)*dy, 0) + v4 = (i*dx, (j+1)*dy, 0) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv3+1,iv2+1]) + triangles.append([iv1+1,iv4+1,iv3+1]) + v1 = (i*dx, j*dy, 1) + v2 = ((i+1)*dx, j*dy, 1) + v3 = ((i+1)*dx, (j+1)*dy, 1) + v4 = (i*dx, (j+1)*dy, 1) + iv1 = vertex(v1,vertices,vdict) + iv2 = vertex(v2,vertices,vdict) + iv3 = vertex(v3,vertices,vdict) + iv4 = vertex(v4,vertices,vdict) + triangles.append([iv1+1,iv2+1,iv3+1]) + triangles.append([iv1+1,iv3+1,iv4+1]) + return vertices,triangles diff --git a/src/cdata.pyc b/src/cdata.pyc new file mode 100644 index 0000000..1983f90 Binary files /dev/null and b/src/cdata.pyc differ diff --git a/src/cfg.py b/src/cfg.py new file mode 100644 index 0000000..8cefd38 --- /dev/null +++ b/src/cfg.py @@ -0,0 +1,187 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# cfg tool + +oneline = "Convert LAMMPS snapshots to AtomEye CFG format" + +docstr = """ +c = cfg(d) d = object containing atom coords (dump, data) + +c.one() write all snapshots to tmp.cfg +c.one("new") write all snapshots to new.cfg +c.many() write snapshots to tmp0000.cfg, tmp0001.cfg, etc +c.many("new") write snapshots to new0000.cfg, new0001.cfg, etc +c.single(N) write snapshot for timestep N to tmp.cfg +c.single(N,"file") write snapshot for timestep N to file.cfg +""" + +# History +# 11/06, Aidan Thompson (SNL): original version + +# ToDo list +# should decide if dump is scaled or not, since CFG prints in scaled coords +# this creates a simple AtomEye CFG format +# there is more complex format we could write out +# which allows for extra atom info, e.g. to do atom coloring on +# how to dump for a triclinic box, since AtomEye accepts this + +# Variables +# data = data file to read from + +# Imports and external programs + +import sys + +# Class definition + +class cfg: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def one(self,*args): + if len(args) == 0: file = "tmp.cfg" + elif args[0][-4:] == ".cfg": file = args[0] + else: file = args[0] + ".cfg" + + f = open(file,"w") + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + xlen = box[3]-box[0] + ylen = box[4]-box[1] + zlen = box[5]-box[2] + + print >>f,"Number of particles = %d " % len(atoms) + print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time + print >>f,"H0(1,1) = %20.10f A " % xlen + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(2,2) = %20.10f A " % ylen + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(3,3) = %20.10f A " % zlen + print >>f,"#" + + for atom in atoms: + itype = int(atom[1]) + xfrac = (atom[2]-box[0])/xlen + yfrac = (atom[3]-box[1])/ylen + zfrac = (atom[4]-box[2])/zlen +# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) + print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) + + print time, + sys.stdout.flush() + n += 1 + + f.close() + print "\nwrote %d snapshots to %s in CFG format" % (n,file) + + # -------------------------------------------------------------------- + + def many(self,*args): + if len(args) == 0: root = "tmp" + else: root = args[0] + + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + if n < 10: + file = root + "000" + str(n) + elif n < 100: + file = root + "00" + str(n) + elif n < 1000: + file = root + "0" + str(n) + else: + file = root + str(n) + file += ".cfg" + f = open(file,"w") + + xlen = box[3]-box[0] + ylen = box[4]-box[1] + zlen = box[5]-box[2] + + print >>f,"Number of particles = %d " % len(atoms) + print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time + print >>f,"H0(1,1) = %20.10f A " % xlen + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(2,2) = %20.10f A " % ylen + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(3,3) = %20.10f A " % zlen + print >>f,"#" + + for atom in atoms: + itype = int(atom[1]) + xfrac = (atom[2]-box[0])/xlen + yfrac = (atom[3]-box[1])/ylen + zfrac = (atom[4]-box[2])/zlen +# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) + print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) + + print time, + sys.stdout.flush() + f.close() + n += 1 + + print "\nwrote %s snapshots in CFG format" % n + + # -------------------------------------------------------------------- + + def single(self,time,*args): + if len(args) == 0: file = "tmp.cfg" + elif args[0][-4:] == ".cfg": file = args[0] + else: file = args[0] + ".cfg" + + which = self.data.findtime(time) + time,box,atoms,bonds,tris,lines = self.data.viz(which) + f = open(file,"w") + + xlen = box[3]-box[0] + ylen = box[4]-box[1] + zlen = box[5]-box[2] + + print >>f,"Number of particles = %d " % len(atoms) + print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time + print >>f,"H0(1,1) = %20.10f A " % xlen + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(2,2) = %20.10f A " % ylen + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(3,3) = %20.10f A " % zlen + print >>f,"#" + + for atom in atoms: + itype = int(atom[1]) + xfrac = (atom[2]-box[0])/xlen + yfrac = (atom[3]-box[1])/ylen + zfrac = (atom[4]-box[2])/zlen +# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) + print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) + + f.close() diff --git a/src/cfg.pyc b/src/cfg.pyc new file mode 100644 index 0000000..ec8545b Binary files /dev/null and b/src/cfg.pyc differ diff --git a/src/chain.py b/src/chain.py new file mode 100644 index 0000000..cc6a1c2 --- /dev/null +++ b/src/chain.py @@ -0,0 +1,245 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# chain tool + +oneline = "Create bead-spring chains for LAMMPS input" + +docstr = """ +c = chain(N,rho) setup box with N monomers at reduced density rho +c = chain(N,rho,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1) + +c.seed = 48379 set random # seed (def = 12345) +c.mtype = 2 set type of monomers (def = 1) +c.btype = 1 set type of bonds (def = 1) +c.blen = 0.97 set length of bonds (def = 0.97) +c.dmin = 1.02 set min dist from i-1 to i+1 site (def = 1.02) + +c.id = "chain" set molecule ID to chain # (default) +c.id = "end1" set molecule ID to count from one end of chain +c.id = "end2" set molecule ID to count from either end of chain + +c.build(100,10) create 100 chains, each of length 10 + + can be invoked multiple times interleaved with different settings + must fill box with total of N monomers + +c.write("data.file") write out all built chains to LAMMPS data file +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# n = number of monomers +# rhostar = reduced density +# seed = 12345 +# mtype = type of monomers +# btype = type of bonds +# blen = length of bonds +# dmin = minimum distance from i-1 to i+1 +# id = "chain","end1",or "end2" +# atoms = list of atoms +# bonds = list of bonds +# xprd,yprd,zprd = x,y,z box size +# xlo,ylo,zlo = -xyz prd / 2 +# xhi,yhi,zhi = x,y,zprd /2 + +# Imports and external programs + +import math +from data import data + +# Class definition + +class chain: + + # -------------------------------------------------------------------- + + def __init__(self,n,rhostar,*list): + self.n = n + self.rhostar = rhostar + xaspect = yaspect = zaspect = 1.0 + if len(list): + xaspect = list[0] + yaspect = list[1] + zaspect = list[2] + self.seed = 12345 + self.mtype = 1 + self.btype = 1 + self.blen = 0.97 + self.dmin = 1.02 + self.id = "chain" + self.atoms = [] + self.bonds = [] + + volume = n/rhostar + prd = pow(volume/xaspect/yaspect/zaspect,1.0/3.0) + self.xprd = xaspect * prd + self.xlo = -self.xprd/2.0 + self.xhi = self.xprd/2.0 + self.yprd = yaspect * prd + self.ylo = -self.yprd/2.0 + self.yhi = self.yprd/2.0 + self.zprd = zaspect * prd + self.zlo = -self.zprd/2.0 + self.zhi = self.zprd/2.0 + + print "Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd) + + # -------------------------------------------------------------------- + + def build(self,n,nper): + for ichain in xrange(n): + atoms = [] + bonds = [] + id_atom_prev = id_mol_prev = id_bond_prev = 0 + if len(self.atoms): + id_atom_prev = self.atoms[-1][0] + id_mol_prev = self.atoms[-1][1] + if len(self.bonds): + id_bond_prev = self.bonds[-1][0] + + for imonomer in xrange(nper): + if imonomer == 0: + x = self.xlo + self.random()*self.xprd + y = self.ylo + self.random()*self.yprd + z = self.zlo + self.random()*self.zprd + ix = iy = iz = 0 + else: + restriction = True + while restriction: + rsq = 2.0 + while rsq > 1.0: + dx = 2.0*self.random() - 1.0 + dy = 2.0*self.random() - 1.0 + dz = 2.0*self.random() - 1.0 + rsq = dx*dx + dy*dy + dz*dz + r = math.sqrt(rsq) + dx,dy,dz = dx/r,dy/r,dz/r + x = atoms[-1][3] + dx*self.blen + y = atoms[-1][4] + dy*self.blen + z = atoms[-1][5] + dz*self.blen + restriction = False + if imonomer >= 2: + dx = x - atoms[-2][3] + dy = y - atoms[-2][4] + dz = z - atoms[-2][5] + if math.sqrt(dx*dx + dy*dy + dz*dz) <= self.dmin: + restriction = True + + x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz) + idatom = id_atom_prev + imonomer + 1 + if self.id == "chain": + idmol = id_mol_prev + 1 + elif self.id == "end1": + idmol = imonomer + 1 + elif self.id == "end2": + idmol = imonomer + 1 + if idmol > nper/2: + idmol = nper - imonomer + else: + raise StandardError,"chain ID is not a valid value" + + atoms.append([idatom,idmol,self.mtype,x,y,z,ix,iy,iz]) + if imonomer: + bondid = id_bond_prev + imonomer + bonds.append([bondid,self.btype,idatom-1,idatom]) + + self.atoms += atoms + self.bonds += bonds + + # -------------------------------------------------------------------- + + def write(self,file): + if len(self.atoms) != self.n: + raise StandardError,"%d monomers instead of requested %d" % \ + (len(self.atoms),self.n) + + list = [atom[2] for atom in self.atoms] + atypes = max(list) + + btypes = 0 + if len(self.bonds): + list = [bond[1] for bond in self.bonds] + btypes = max(list) + + # create the data file + + d = data() + d.title = "LAMMPS FENE chain data file" + d.headers["atoms"] = len(self.atoms) + d.headers["bonds"] = len(self.bonds) + d.headers["atom types"] = atypes + d.headers["bond types"] = btypes + d.headers["xlo xhi"] = (self.xlo,self.xhi) + d.headers["ylo yhi"] = (self.ylo,self.yhi) + d.headers["zlo zhi"] = (self.zlo,self.zhi) + + lines = [] + for i in range(atypes): lines.append("%d 1.0\n" % (i+1)) + d.sections["Masses"] = lines + + lines = [] + for atom in self.atoms: + line = "%d %d %d %g %g %g %d %d %d\n" % \ + (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], + atom[6], atom[7], atom[8]) + lines.append(line) + d.sections["Atoms"] = lines + + lines = [] + for bond in self.bonds: + line = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3]) + lines.append(line) + d.sections["Bonds"] = lines + + d.write(file) + + # -------------------------------------------------------------------- + + def pbc(self,x,y,z,ix,iy,iz): + if x < self.xlo: + x += self.xprd + ix -= 1 + elif x >= self.xhi: + x -= self.xprd + ix += 1 + if y < self.ylo: + y += self.yprd + iy -= 1 + elif y >= self.yhi: + y -= self.yprd + iy += 1 + if z < self.zlo: + z += self.zprd + iz -= 1 + elif z >= self.zhi: + z -= self.zprd + iz += 1 + return x,y,z,ix,iy,iz + + # -------------------------------------------------------------------- + + def random(self): + k = self.seed/IQ + self.seed = IA*(self.seed-k*IQ) - IR*k + if self.seed < 0: + self.seed += IM + return AM*self.seed + +# -------------------------------------------------------------------- +# random # generator constants + +IM = 2147483647 +AM = 1.0/IM +IA = 16807 +IQ = 127773 +IR = 2836 diff --git a/src/chain.pyc b/src/chain.pyc new file mode 100644 index 0000000..37aa614 Binary files /dev/null and b/src/chain.pyc differ diff --git a/src/clog.py b/src/clog.py new file mode 100644 index 0000000..2137b84 --- /dev/null +++ b/src/clog.py @@ -0,0 +1,301 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# clog tool + +oneline = "Read ChemCell and SPPARKS log files and extract time-series data" + +docstr = """ +c = clog("file1") read in one or more log files +c = clog("log1 log2.gz") can be gzipped +c = clog("file*") wildcard expands to multiple files +c = clog("log.cell","Time") 2nd arg = start string for time section +c = clog("log.cell","",0) 3rd arg = average all runs + + incomplete and duplicate thermo entries are deleted + if specify 2nd arg, it delimits a time section + no 2nd arg or empty string, use default which is ChemCell specific + if specify any 3rd arg, average all runs, assume all start at time 0 + +nvec = c.nvec # of vectors of thermo info +nlen = c.nlen length of each vectors +names = c.names list of vector names +a,b,... = c.get("A","B",...) return one or more vectors of values +c.write("file.txt") write all vectors to a file +c.write("file.txt","A","B",...) write listed vectors to a file + + get and write allow abbreviated (uniquely) vector names +""" + +# History +# 1/06, Steve Plimpton (SNL): original version +# 2/09, modified to allow different firststr for different log files + +# ToDo list + +# Variables +# nvec = # of vectors +# nlen = length of each vector +# names = list of vector names +# ptr = dictionary, key = name, value = index into data for which column +# data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1 +# firststr = string that begins a time-series section in log file + +# Imports and external programs + +import sys, re, glob +from os import popen + +try: tmp = PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class clog: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.nvec = 0 + self.names = [] + self.ptr = {} + self.data = [] + self.firststr = "Step Time" + self.ave = 0 + + # flist = list of all log file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no log file specified" + + if len(list) > 1 and len(list[1]): self.firststr = list[1] + if len(list) == 3: self.ave = 1 + + self.read_all() + + # -------------------------------------------------------------------- + # read all log data from all files + + def read_all(self): + self.read_header(self.flist[0]) + if self.nvec == 0: raise StandardError,"log file has no values" + + # read all files + + for file in self.flist: self.read_one(file) + print + + # if no average, sort entries by timestep, cull duplicates + # if average, call self.average() + + if self.ave == 0: + self.data.sort(self.compare) + self.cull() + else: self.average() + + self.nlen = len(self.data) + print "read %d log entries" % self.nlen + + # -------------------------------------------------------------------- + + def get(self,*keys): + if len(keys) == 0: + raise StandardError, "no log vectors specified" + + map = [] + for key in keys: + if self.ptr.has_key(key): + map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique log vector %s not found" % key + + vecs = [] + for i in range(len(keys)): + vecs.append(self.nlen * [0]) + for j in xrange(self.nlen): + vecs[i][j] = self.data[j][map[i]] + + if len(keys) == 1: return vecs[0] + else: return vecs + + # -------------------------------------------------------------------- + + def write(self,filename,*keys): + if len(keys): + map = [] + for key in keys: + if self.ptr.has_key(key): + map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique log vector %s not found" % key + else: + map = range(self.nvec) + + f = open(filename,"w") + for i in xrange(self.nlen): + for j in xrange(len(map)): + print >>f,self.data[i][map[j]], + print >>f + f.close() + + # -------------------------------------------------------------------- + + def compare(self,a,b): + if a[0] < b[0]: + return -1 + elif a[0] > b[0]: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + + def cull(self): + i = 1 + while i < len(self.data): + if self.data[i][0] == self.data[i-1][0]: del self.data[i] + else: i += 1 + + # -------------------------------------------------------------------- + + def average(self): + counts = [] + data = [] + nlen = 0 + + i = j = 0 + while i < len(self.data): + if self.data[i][0] == 0: j = 0 + if j >= nlen: + counts.append(0) + data.append(self.nvec*[0]) + nlen += 1 + counts[j] += 1 + for m in xrange(self.nvec): data[j][m] += self.data[i][m] + j += 1 + i += 1 + + for i in xrange(nlen): + for j in xrange(self.nvec): + data[i][j] /= counts[j] + + self.nlen = nlen + self.data = data + + # -------------------------------------------------------------------- + + def read_header(self,file): + if file[-3:] == ".gz": + txt = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r').read() + else: + txt = open(file).read() + + s1 = txt.find(self.firststr) + s2 = txt.find("\n",s1) + line = txt[s1:s2] + words = line.split() + for i in range(len(words)): + self.names.append(words[i]) + self.ptr[words[i]] = i + + self.nvec = len(self.names) + + # -------------------------------------------------------------------- + + def read_one(self,*list): + + # if 2nd arg exists set file ptr to that value + # read entire (rest of) file into txt + + file = list[0] + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb') + else: + f = open(file,'rb') + + if len(list) == 2: f.seek(list[1]) + txt = f.read() + if file[-3:] == ".gz": eof = 0 + else: eof = f.tell() + f.close() + + start = last = 0 + while not last: + + # chunk = contiguous set of concentration entries + # s1 = 1st char on 1st line of chunk + # s2 = 1st char on line after chunk + # set last = 1 if this is last chunk in file, leave 0 otherwise + # set start = position in file to start looking for next chunk + # rewind eof if final entry is incomplete + + s1 = txt.find(self.firststr,start) + s2 = txt.find("Loop time of",start+1) + + if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2 + s1 = txt.find("\n",s1) + 1 + elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1 + s1 = 0 + elif s1 == -1 and s2 >= 0: # found s2, but no s1 + last = 1 + s1 = 0 + elif s1 >= 0 and s2 == -1: # found s1, but no s2 + last = 1 + s1 = txt.find("\n",s1) + 1 + s2 = txt.rfind("\n",s1) + 1 + eof -= len(txt) - s2 + elif s1 == -1 and s2 == -1: # found neither + # could be end-of-file section + # or entire read was one chunk + + if txt.find("Loop time of",start) == start: # end of file, so exit + eof -= len(txt) - start # reset eof to "Loop" + break + + last = 1 # entire read is a chunk + s1 = 0 + s2 = txt.rfind("\n",s1) + 1 + eof -= len(txt) - s2 + if s1 == s2: break + + chunk = txt[s1:s2-1] + start = s2 + + # split chunk into entries + # parse each entry for numeric fields, append to data + + lines = chunk.split("\n") + for line in lines: + words = line.split() + self.data.append(map(float,words)) + + # print last timestep of chunk + + print int(self.data[len(self.data)-1][0]), + sys.stdout.flush() + + return eof diff --git a/src/clog.pyc b/src/clog.pyc new file mode 100644 index 0000000..35bab67 Binary files /dev/null and b/src/clog.pyc differ diff --git a/src/data.py b/src/data.py new file mode 100644 index 0000000..b2c9344 --- /dev/null +++ b/src/data.py @@ -0,0 +1,379 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# data tool + +oneline = "Read, write, manipulate LAMMPS data files" + +docstr = """ +d = data("data.poly") read a LAMMPS data file, can be gzipped +d = data() create an empty data file + +d.map(1,"id",3,"x") assign names to atom columns (1-N) + +coeffs = d.get("Pair Coeffs") extract info from data file section +q = d.get("Atoms",4) + + 1 arg = all columns returned as 2d array of floats + 2 args = Nth column returned as vector of floats + +d.reorder("Atoms",1,3,2,4,5) reorder columns (1-N) in a data file section + + 1,3,2,4,5 = new order of previous columns, can delete columns this way + +d.title = "My LAMMPS data file" set title of the data file +d.headers["atoms"] = 1500 set a header value +d.sections["Bonds"] = lines set a section to list of lines (with newlines) +d.delete("bonds") delete a keyword or section of data file +d.delete("Bonds") +d.replace("Atoms",5,vec) replace Nth column of section with vector +d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N + + newxyz assumes id,x,y,z are defined in both data and dump files + also replaces ix,iy,iz if they are defined + +index,time,flag = d.iterator(0/1) loop over single data file snapshot +time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects + + iterator() and viz() are compatible with equivalent dump calls + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = timestep index within dump object (only 0 for data file) + time = timestep value (only 0 for data file) + flag = -1 when iteration is done, 1 otherwise + viz() returns info for specified timestep index (must be 0) + time = 0 + box = [xlo,ylo,zlo,xhi,yhi,zhi] + atoms = id,type,x,y,z for each atom as 2d array + bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array + NULL if bonds do not exist + tris = NULL + lines = NULL + +d.write("data.new") write a LAMMPS data file +""" + +# History +# 8/05, Steve Plimpton (SNL): original version +# 11/07, added triclinic box support + +# ToDo list + +# Variables +# title = 1st line of data file +# names = dictionary with atom attributes as keys, col #s as values +# headers = dictionary with header name as key, value or tuple as values +# sections = dictionary with section name as key, array of lines as values +# nselect = 1 = # of snapshots + +# Imports and external programs + +from os import popen + +try: tmp = PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class data: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.nselect = 1 + + if len(list) == 0: + self.title = "LAMMPS data file" + self.names = {} + self.headers = {} + self.sections = {} + return + + file = list[0] + if file[-3:] == ".gz": f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + self.title = f.readline() + self.names = {} + + headers = {} + while 1: + line = f.readline() + line = line.strip() + if len(line) == 0: + continue + found = 0 + for keyword in hkeywords: + if line.find(keyword) >= 0: + found = 1 + words = line.split() + if keyword == "xlo xhi" or keyword == "ylo yhi" or \ + keyword == "zlo zhi": + headers[keyword] = (float(words[0]),float(words[1])) + elif keyword == "xy xz yz": + headers[keyword] = \ + (float(words[0]),float(words[1]),float(words[2])) + else: + headers[keyword] = int(words[0]) + if not found: + break + + sections = {} + while 1: + found = 0 + for pair in skeywords: + keyword,length = pair[0],pair[1] + if keyword == line: + found = 1 + if not headers.has_key(length): + raise StandardError, \ + "data section %s has no matching header value" % line + f.readline() + list = [] + for i in xrange(headers[length]): list.append(f.readline()) + sections[keyword] = list + if not found: + raise StandardError,"invalid section %s in data file" % line + f.readline() + line = f.readline() + if not line: + break + line = line.strip() + + f.close() + self.headers = headers + self.sections = sections + + # -------------------------------------------------------------------- + # assign names to atom columns + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "data map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # -------------------------------------------------------------------- + # extract info from data file fields + + def get(self,*list): + if len(list) == 1: + field = list[0] + array = [] + lines = self.sections[field] + for line in lines: + words = line.split() + values = map(float,words) + array.append(values) + return array + elif len(list) == 2: + field = list[0] + n = list[1] - 1 + vec = [] + lines = self.sections[field] + for line in lines: + words = line.split() + vec.append(float(words[n])) + return vec + else: + raise StandardError, "invalid arguments for data.get()" + + # -------------------------------------------------------------------- + # reorder columns in a data file field + + def reorder(self,name,*order): + n = len(order) + natoms = len(self.sections[name]) + oldlines = self.sections[name] + newlines = natoms*[""] + for index in order: + for i in xrange(len(newlines)): + words = oldlines[i].split() + newlines[i] += words[index-1] + " " + for i in xrange(len(newlines)): + newlines[i] += "\n" + self.sections[name] = newlines + + # -------------------------------------------------------------------- + # replace a column of named section with vector of values + + def replace(self,name,icol,vector): + lines = self.sections[name] + newlines = [] + j = icol - 1 + for i in xrange(len(lines)): + line = lines[i] + words = line.split() + words[j] = str(vector[i]) + newline = ' '.join(words) + '\n' + newlines.append(newline) + self.sections[name] = newlines + + # -------------------------------------------------------------------- + # replace x,y,z in Atoms with x,y,z values from snapshot ntime of dump object + # assumes id,x,y,z are defined in both data and dump files + # also replaces ix,iy,iz if they are defined + + def newxyz(self,dm,ntime): + nsnap = dm.findtime(ntime) + + if dm.scaled(nsnap): scaleflag = 1 + else: scaleflag = 0 + dm.sort(ntime) + + if scaleflag: dm.unscale(ntime) + x,y,z = dm.vecs(ntime,"x","y","z") + if scaleflag: dm.scale(ntime) + + self.replace("Atoms",self.names['x']+1,x) + self.replace("Atoms",self.names['y']+1,y) + self.replace("Atoms",self.names['z']+1,z) + + if dm.names.has_key("ix") and self.names.has_key("ix"): + ix,iy,iz = dm.vecs(ntime,"ix","iy","iz") + self.replace("Atoms",self.names['ix']+1,ix) + self.replace("Atoms",self.names['iy']+1,iy) + self.replace("Atoms",self.names['iz']+1,iz) + + # -------------------------------------------------------------------- + # delete header value or section from data file + + def delete(self,keyword): + + if self.headers.has_key(keyword): del self.headers[keyword] + elif self.sections.has_key(keyword): del self.sections[keyword] + else: raise StandardError, "keyword not found in data object" + + # -------------------------------------------------------------------- + # write out a LAMMPS data file + + def write(self,file): + f = open(file,"w") + print >>f,self.title + for keyword in hkeywords: + if self.headers.has_key(keyword): + if keyword == "xlo xhi" or keyword == "ylo yhi" or \ + keyword == "zlo zhi": + pair = self.headers[keyword] + print >>f,pair[0],pair[1],keyword + elif keyword == "xy xz yz": + triple = self.headers[keyword] + print >>f,triple[0],triple[1],triple[2],keyword + else: + print >>f,self.headers[keyword],keyword + for pair in skeywords: + keyword = pair[0] + if self.sections.has_key(keyword): + print >>f,"\n%s\n" % keyword + for line in self.sections[keyword]: + print >>f,line, + f.close() + + # -------------------------------------------------------------------- + # iterator called from other tools + + def iterator(self,flag): + if flag == 0: return 0,0,1 + return 0,0,-1 + + # -------------------------------------------------------------------- + # time query from other tools + + def findtime(self,n): + if n == 0: return 0 + raise StandardError, "no step %d exists" % (n) + + # -------------------------------------------------------------------- + # return list of atoms and bonds to viz for data object + + def viz(self,isnap): + if isnap: raise StandardError, "cannot call data.viz() with isnap != 0" + + id = self.names["id"] + type = self.names["type"] + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + + xlohi = self.headers["xlo xhi"] + ylohi = self.headers["ylo yhi"] + zlohi = self.headers["zlo zhi"] + box = [xlohi[0],ylohi[0],zlohi[0],xlohi[1],ylohi[1],zlohi[1]] + + # create atom list needed by viz from id,type,x,y,z + + atoms = [] + atomlines = self.sections["Atoms"] + for line in atomlines: + words = line.split() + atoms.append([int(words[id]),int(words[type]), + float(words[x]),float(words[y]),float(words[z])]) + + # create list of current bond coords from list of bonds + # assumes atoms are sorted so can lookup up the 2 atoms in each bond + + bonds = [] + if self.sections.has_key("Bonds"): + bondlines = self.sections["Bonds"] + for line in bondlines: + words = line.split() + bid,btype = int(words[0]),int(words[1]) + atom1,atom2 = int(words[2]),int(words[3]) + atom1words = atomlines[atom1-1].split() + atom2words = atomlines[atom2-1].split() + bonds.append([bid,btype, + float(atom1words[x]),float(atom1words[y]), + float(atom1words[z]), + float(atom2words[x]),float(atom2words[y]), + float(atom2words[z]), + float(atom1words[type]),float(atom2words[type])]) + + tris = [] + lines = [] + return 0,box,atoms,bonds,tris,lines + + # -------------------------------------------------------------------- + # return box size + + def maxbox(self): + xlohi = self.headers["xlo xhi"] + ylohi = self.headers["ylo yhi"] + zlohi = self.headers["zlo zhi"] + return [xlohi[0],ylohi[0],zlohi[0],xlohi[1],ylohi[1],zlohi[1]] + + # -------------------------------------------------------------------- + # return number of atom types + + def maxtype(self): + return self.headers["atom types"] + +# -------------------------------------------------------------------- +# data file keywords, both header and main sections + +hkeywords = ["atoms","lines","tris", + "bonds","angles","dihedrals","impropers", + "atom types","bond types","angle types","dihedral types", + "improper types","xlo xhi","ylo yhi","zlo zhi","xy xz yz"] + +skeywords = [["Masses","atom types"], + ["Atoms","atoms"],["Lines","lines"],["Triangles","tris"], + ["Bonds","bonds"], + ["Angles","angles"],["Dihedrals","dihedrals"], + ["Impropers","impropers"],["Velocities","atoms"], + ["Pair Coeffs","atom types"], + ["Bond Coeffs","bond types"],["Angle Coeffs","angle types"], + ["Dihedral Coeffs","dihedral types"], + ["Improper Coeffs","improper types"], + ["BondBond Coeffs","angle types"], + ["BondAngle Coeffs","angle types"], + ["MiddleBondTorsion Coeffs","dihedral types"], + ["EndBondTorsion Coeffs","dihedral types"], + ["AngleTorsion Coeffs","dihedral types"], + ["AngleAngleTorsion Coeffs","dihedral types"], + ["BondBond13 Coeffs","dihedral types"], + ["AngleAngle Coeffs","improper types"]] diff --git a/src/data.pyc b/src/data.pyc new file mode 100644 index 0000000..f257b3c Binary files /dev/null and b/src/data.pyc differ diff --git a/src/dump.py b/src/dump.py new file mode 100644 index 0000000..1a8884e --- /dev/null +++ b/src/dump.py @@ -0,0 +1,1264 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# dump tool + +oneline = "Read, write, manipulate dump files and particle attributes" + +docstr = """ +d = dump("dump.one") read in one or more dump files +d = dump("dump.1 dump.2.gz") can be gzipped +d = dump("dump.*") wildcard expands to multiple files +d = dump("dump.*",0) two args = store filenames, but don't read + + incomplete and duplicate snapshots are deleted + if atoms have 5 or 8 columns, assign id,type,x,y,z (ix,iy,iz) + atoms will be unscaled if stored in files as scaled + +time = d.next() read next snapshot from dump files + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment or unscaling is performed + +d.map(1,"id",3,"x") assign names to atom columns (1-N) + + not needed if dump file is self-describing + +d.tselect.all() select all timesteps +d.tselect.one(N) select only timestep N +d.tselect.none() deselect all timesteps +d.tselect.skip(M) select every Mth step +d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps +d.delete() delete non-selected timesteps + + selecting a timestep also selects all atoms in the timestep + skip() and test() only select from currently selected timesteps + test() uses a Python Boolean expression with $t for timestep value + Python comparison syntax: == != < > <= >= and or + +d.aselect.all() select all atoms in all steps +d.aselect.all(N) select all atoms in one step +d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps +d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step + + all() with no args selects atoms from currently selected timesteps + test() with one arg selects atoms from currently selected timesteps + test() sub-selects from currently selected atoms + test() uses a Python Boolean expression with $ for atom attributes + Python comparison syntax: == != < > <= >= and or + $name must end with a space + +d.write("file") write selected steps/atoms to dump file +d.write("file",head,app) write selected steps/atoms to dump file +d.scatter("tmp") write selected steps/atoms to multiple files + + write() can be specified with 2 additional flags + headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append + scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc + +d.scale() scale x,y,z to 0-1 for all timesteps +d.scale(100) scale atom coords for timestep N +d.unscale() unscale x,y,z to box size to all timesteps +d.unscale(1000) unscale atom coords for timestep N +d.wrap() wrap x,y,z into periodic box via ix,iy,iz +d.unwrap() unwrap x,y,z out of box via ix,iy,iz +d.owrap("other") wrap x,y,z to same image as another atom +d.sort() sort atoms by atom ID in all selected steps +d.sort("x") sort atoms by column value in all steps +d.sort(1000) sort atoms in timestep N + + scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms + wrap(), unwrap(), owrap() require ix,iy,iz be defined + owrap() requires a column be defined which contains an atom ID + name of that column is the argument to owrap() + x,y,z for each atom is wrapped to same image as the associated atom ID + useful for wrapping all molecule's atoms the same so it is contiguous + +m1,m2 = d.minmax("type") find min/max values for a column +d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value +d.setv("type",vector) set a column to a vector of values +d.spread("ke",N,"color") 2nd col = N ints spread over 1st col +d.clone(1000,"color") clone timestep N values to other steps + + minmax() operates on selected timesteps and atoms + set() operates on selected timesteps and atoms + left hand side column is created if necessary + left-hand side column is unset or unchanged for non-selected atoms + equation is in Python syntax + use $ for column names, $name must end with a space + setv() operates on selected timesteps and atoms + if column label does not exist, column is created + values in vector are assigned sequentially to atoms, so may want to sort() + length of vector must match # of selected atoms + spread() operates on selected timesteps and atoms + min and max are found for 1st specified column across all selected atoms + atom's value is linear mapping (1-N) between min and max + that is stored in 2nd column (created if needed) + useful for creating a color map + clone() operates on selected timesteps and atoms + values at every timestep are set to value at timestep N for that atom ID + useful for propagating a color map + +t = d.time() return vector of selected timestep values +fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N +fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N + + atom() returns vectors with one value for each selected timestep + vecs() returns vectors with one value for each selected atom in the timestep + +index,time,flag = d.iterator(0/1) loop over dump snapshots +time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects +d.atype = "color" set column returned as "type" by viz +d.extra(obj) extract bond/tri/line info from obj + + iterator() loops over selected timesteps + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = index within dump object (0 to # of snapshots) + time = timestep value + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected atoms for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = id,type,x,y,z for each atom as 2d array + bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array + if extra() used to define bonds, else NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + if extra() used to define tris, else NULL + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + if extra() used to define lines, else NULL + atype is column name viz() will return as atom type (def = "type") + extra() extracts bonds/tris/lines from obj each time viz() is called + obj can be data object for bonds, cdata object for tris and lines, + bdump object for bonds, mdump object for tris, ldump object for lines +""" + +# History +# 8/05, Steve Plimpton (SNL): original version +# 12/09, David Hart (SNL): allow use of NumPy or Numeric + +# ToDo list +# try to optimize this line in read_snap: words += f.readline().split() +# allow $name in aselect.test() and set() to end with non-space +# should next() snapshot be auto-unscaled ? + +# Variables +# flist = list of dump file names +# increment = 1 if reading snapshots one-at-a-time +# nextfile = which file to read from via next() +# eof = ptr into current file for where to read via next() +# scale_original = 0/1/-1 if coords were read in as unscaled/scaled/unknown +# nsnaps = # of snapshots +# nselect = # of selected snapshots +# snaps = list of snapshots +# names = dictionary of column names: +# key = "id", value = column # (0 to M-1) +# tselect = class for time selection +# aselect = class for atom selection +# atype = name of vector used as atom type by viz extract +# bondflag = 0 if no bonds, 1 if they are defined statically, 2 if dynamic +# bondlist = static list of bonds to return w/ viz() for all snapshots +# triflag = 0 if no tris, 1 if they are defined statically, 2 if dynamic +# trilist = static list of tris to return w/ viz() for all snapshots +# lineflag = 0 if no lines, 1 if they are defined statically, 2 if dynamic +# linelist = static list of lines to return w/ viz() for all snapshots +# objextra = object to get bonds,tris,lines from dynamically +# Snap = one snapshot +# time = time stamp +# tselect = 0/1 if this snapshot selected +# natoms = # of atoms +# nselect = # of selected atoms in this snapshot +# aselect[i] = 0/1 for each atom +# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float) +# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1 + +# Imports and external programs + +import sys, commands, re, glob, types +from os import popen +from math import * # any function could be used by set() +import os + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class dump: + + # -------------------------------------------------------------------- + + def __init__(self,*input,**kwargs): + + self.snaps = [] + self.nsnaps = self.nselect = 0 + self.names = {} + self.tselect = tselect(self) + self.aselect = aselect(self) + self.atype = "type" + self.bondflag = 0 + self.bondlist = [] + self.triflag = 0 + self.trilist = [] + self.lineflag = 0 + self.linelist = [] + self.multiprocflag = 0 + self.fileNums = [] + self.objextra = None + + outputfl = True + if isinstance(input[0],dict): # multiprocessing code (the [0] comes from the asteriks in the argumentlist) + dictionary = input[0] + + # check whether to output or not + if "debugMode" in dictionary: outputfl = dictionary["debugMode"] + + if outputfl: print "number of subprocess:", os.getpid() + + self.flist = dictionary["filelist"] + self.multiprocflag = 1 + self.increment = 0 + self.read_all(output=outputfl) + else: # serial code + # flist = list of all dump file names + words = input[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(input) == 1: + raise StandardError,"no dump file specified" + + if len(input) == 1: + self.increment = 0 + self.read_all(output=outputfl) + else: + self.increment = 1 + self.nextfile = 0 + self.eof = 0 + + # -------------------------------------------------------------------- + + def read_all(self, **kwargs): + + # read all snapshots from each file + # test for gzipped files + + # check whether to output or not + outputfl = True + if "output" in kwargs: outputfl = kwargs["output"] + + if outputfl: print "reading dump file..." + + for i, file in enumerate(self.flist): + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + snap = self.read_snapshot(f) + while snap: + self.snaps.append(snap) + if outputfl: print snap.time, + self.fileNums.append(snap.time) + sys.stdout.flush() + snap = self.read_snapshot(f) + + f.close() + if outputfl: print + + # sort entries by timestep, cull duplicates + + self.snaps.sort(self.compare_time) + self.fileNums.sort() + self.cull() + self.nsnaps = len(self.snaps) + #print "read %d snapshots" % self.nsnaps + + # select all timesteps and atoms + + self.tselect.all(output=outputfl) + + # set default names for atom columns if file wasn't self-describing + + if len(self.snaps) == 0: + if outputfl: print "no column assignments made" + elif len(self.names): + if outputfl: print "assigned columns:",self.names2str() + else: + if outputfl: print "no column assignments made" + pass + + # if snapshots are scaled, unscale them + + if (not self.names.has_key("x")) or \ + (not self.names.has_key("y")) or \ + (not self.names.has_key("z")): + print "dump scaling status is unknown" + elif self.nsnaps > 0: + if self.scale_original == 1: self.unscale() + elif self.scale_original == 0: print "dump is already unscaled" + else: print "dump scaling status is unknown" + + # -------------------------------------------------------------------- + # read next snapshot from list of files + + def next(self): + + if not self.increment: raise StandardError,"cannot read incrementally" + + # read next snapshot in current file using eof as pointer + # if fail, try next file + # if new snapshot time stamp already exists, read next snapshot + + while 1: + f = open(self.flist[self.nextfile],'rb') + f.seek(self.eof) + snap = self.read_snapshot(f) + if not snap: + self.nextfile += 1 + if self.nextfile == len(self.flist): return -1 + f.close() + self.eof = 0 + continue + self.eof = f.tell() + f.close() + try: + self.findtime(snap.time) + continue + except: break + + # select the new snapshot with all its atoms + + self.snaps.append(snap) + snap = self.snaps[self.nsnaps] + snap.tselect = 1 + snap.nselect = snap.natoms + for i in xrange(snap.natoms): snap.aselect[i] = 1 + self.nsnaps += 1 + self.nselect += 1 + + return snap.time + + # -------------------------------------------------------------------- + # read a single snapshot from file f + # return snapshot or 0 if failed + # assign column names if not already done and file is self-describing + # set scale_original to 0/1/-1 for unscaled/scaled/unknown + # convert xs,xu to x + + def read_snapshot(self,f): + try: + snap = Snap() + item = f.readline() + snap.time = int(f.readline().split()[0]) # just grab 1st field + item = f.readline() + snap.natoms = int(f.readline()) + + snap.aselect = np.zeros(snap.natoms) + + item = f.readline() + words = f.readline().split() + snap.xlo,snap.xhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.ylo,snap.yhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.zlo,snap.zhi = float(words[0]),float(words[1]) + + item = f.readline() + if len(self.names) == 0: + self.scale_original = -1 + xflag = yflag = zflag = -1 + words = item.split()[2:] + if len(words): + for i in range(len(words)): + if words[i] == "x" or words[i] == "xu": + xflag = 0 + self.names["x"] = i + elif words[i] == "xs" or words[i] == "xsu": + xflag = 1 + self.names["x"] = i + elif words[i] == "y" or words[i] == "yu": + yflag = 0 + self.names["y"] = i + elif words[i] == "ys" or words[i] == "ysu": + yflag = 1 + self.names["y"] = i + elif words[i] == "z" or words[i] == "zu": + zflag = 0 + self.names["z"] = i + elif words[i] == "zs" or words[i] == "zsu": + zflag = 1 + self.names["z"] = i + else: self.names[words[i]] = i + if xflag == 0 and yflag == 0 and zflag == 0: self.scale_original = 0 + if xflag == 1 and yflag == 1 and zflag == 1: self.scale_original = 1 + + if snap.natoms: + words = f.readline().split() + ncol = len(words) + for i in xrange(1,snap.natoms): + words += f.readline().split() + floats = map(float,words) + if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float) + else: atoms = np.zeros((snap.natoms,ncol),np.float) + start = 0 + stop = ncol + for i in xrange(snap.natoms): + atoms[i] = floats[start:stop] + start = stop + stop += ncol + else: atoms = None + snap.atoms = atoms + return snap + except: + return 0 + + # -------------------------------------------------------------------- + # map atom column names + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "dump map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # -------------------------------------------------------------------- + # delete unselected snapshots + + def delete(self): + ndel = i = 0 + while i < self.nsnaps: + if not self.snaps[i].tselect: + del self.snaps[i] + self.nsnaps -= 1 + ndel += 1 + else: i += 1 + print "%d snapshots deleted" % ndel + print "%d snapshots remaining" % self.nsnaps + + # -------------------------------------------------------------------- + # scale coords to 0-1 for all snapshots or just one + + def scale(self,*list): + if len(list) == 0: + print "Scaling dump ..." + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + for snap in self.snaps: self.scale_one(snap,x,y,z) + else: + i = self.findtime(list[0]) + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + self.scale_one(self.snaps[i],x,y,z) + + # -------------------------------------------------------------------- + + def scale_one(self,snap,x,y,z): + xprdinv = 1.0 / (snap.xhi - snap.xlo) + yprdinv = 1.0 / (snap.yhi - snap.ylo) + zprdinv = 1.0 / (snap.zhi - snap.zlo) + atoms = snap.atoms + atoms[:,x] = (atoms[:,x] - snap.xlo) * xprdinv + atoms[:,y] = (atoms[:,y] - snap.ylo) * yprdinv + atoms[:,z] = (atoms[:,z] - snap.zlo) * zprdinv + + # -------------------------------------------------------------------- + # unscale coords from 0-1 to box size for all snapshots or just one + + def unscale(self,*list): + if len(list) == 0: + print "Unscaling dump ..." + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + for snap in self.snaps: self.unscale_one(snap,x,y,z) + else: + i = self.findtime(list[0]) + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + self.unscale_one(self.snaps[i],x,y,z) + + # -------------------------------------------------------------------- + + def unscale_one(self,snap,x,y,z): + xprd = snap.xhi - snap.xlo + yprd = snap.yhi - snap.ylo + zprd = snap.zhi - snap.zlo + atoms = snap.atoms + atoms[:,x] = snap.xlo + atoms[:,x]*xprd + atoms[:,y] = snap.ylo + atoms[:,y]*yprd + atoms[:,z] = snap.zlo + atoms[:,z]*zprd + + # -------------------------------------------------------------------- + # wrap coords from outside box to inside + + def wrap(self): + print "Wrapping dump ..." + + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + ix = self.names["ix"] + iy = self.names["iy"] + iz = self.names["iz"] + + for snap in self.snaps: + xprd = snap.xhi - snap.xlo + yprd = snap.yhi - snap.ylo + zprd = snap.zhi - snap.zlo + atoms = snap.atoms + atoms[:,x] -= atoms[:,ix]*xprd + atoms[:,y] -= atoms[:,iy]*yprd + atoms[:,z] -= atoms[:,iz]*zprd + + # -------------------------------------------------------------------- + # unwrap coords from inside box to outside + + def unwrap(self): + print "Unwrapping dump ..." + + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + ix = self.names["ix"] + iy = self.names["iy"] + iz = self.names["iz"] + + for snap in self.snaps: + xprd = snap.xhi - snap.xlo + yprd = snap.yhi - snap.ylo + zprd = snap.zhi - snap.zlo + atoms = snap.atoms + atoms[:,x] += atoms[:,ix]*xprd + atoms[:,y] += atoms[:,iy]*yprd + atoms[:,z] += atoms[:,iz]*zprd + + # -------------------------------------------------------------------- + # wrap coords to same image as atom ID stored in "other" column + # if dynamic extra lines or triangles defined, owrap them as well + + def owrap(self,other): + print "Wrapping to other ..." + + id = self.names["id"] + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + ix = self.names["ix"] + iy = self.names["iy"] + iz = self.names["iz"] + iother = self.names[other] + + for snap in self.snaps: + xprd = snap.xhi - snap.xlo + yprd = snap.yhi - snap.ylo + zprd = snap.zhi - snap.zlo + atoms = snap.atoms + ids = {} + for i in xrange(snap.natoms): + ids[atoms[i][id]] = i + for i in xrange(snap.natoms): + j = ids[atoms[i][iother]] + atoms[i][x] += (atoms[i][ix]-atoms[j][ix])*xprd + atoms[i][y] += (atoms[i][iy]-atoms[j][iy])*yprd + atoms[i][z] += (atoms[i][iz]-atoms[j][iz])*zprd + # should bonds also be owrapped ? + if self.lineflag == 2 or self.triflag == 2: + self.objextra.owrap(snap.time,xprd,yprd,zprd,ids,atoms,iother,ix,iy,iz) + + # -------------------------------------------------------------------- + # convert column names assignment to a string, in column order + + def names2str(self): + ncol = max(self.names.values()) #len(self.snaps[0].atoms[0]) + pairs = self.names.items() + values = self.names.values() + str = "" + for i in xrange(ncol): + if i in values: str += pairs[values.index(i)][0] + ' ' + return str + + # -------------------------------------------------------------------- + # sort atoms by atom ID in all selected timesteps by default + # if arg = string, sort all steps by that column + # if arg = numeric, sort atoms in single step + + def sort(self,*list, **kwargs): + + # check whether to output or not + outputfl = True + if "output" in kwargs: outputfl = kwargs["output"] + + if len(list) == 0: + if outputfl: print "Sorting selected snapshots ..." + id = self.names["id"] + for snap in self.snaps: + if snap.tselect: self.sort_one(snap,id) + elif type(list[0]) is types.StringType: + if outputfl: print "Sorting selected snapshots by %s ..." % list[0] + id = self.names[list[0]] + for snap in self.snaps: + if snap.tselect: self.sort_one(snap,id) + else: + i = self.findtime(list[0]) + id = self.names["id"] + self.sort_one(self.snaps[i],id) + + # -------------------------------------------------------------------- + # sort a single snapshot by ID column + + def sort_one(self,snap,id): + atoms = snap.atoms + ids = atoms[:,id] + ordering = np.argsort(ids) + for i in xrange(len(atoms[0])): + atoms[:,i] = np.take(atoms[:,i],ordering) + + # -------------------------------------------------------------------- + # write a single dump file from current selection + + def write(self,file,header=1,append=0): + if len(self.snaps): namestr = self.names2str() + if not append: f = open(file,"w") + else: f = open(file,"a") + for snap in self.snaps: + if not snap.tselect: continue + print snap.time, + sys.stdout.flush() + + if header: + print >>f,"ITEM: TIMESTEP" + print >>f,snap.time + print >>f,"ITEM: NUMBER OF ATOMS" + print >>f,snap.nselect + print >>f,"ITEM: BOX BOUNDS" + print >>f,snap.xlo,snap.xhi + print >>f,snap.ylo,snap.yhi + print >>f,snap.zlo,snap.zhi + print >>f,"ITEM: ATOMS",namestr + + atoms = snap.atoms + nvalues = len(atoms[0]) + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + line = "" + for j in xrange(nvalues): + if (j < 2): + line += str(int(atoms[i][j])) + " " + else: + line += str(atoms[i][j]) + " " + print >>f,line + f.close() + print "\n%d snapshots" % self.nselect + + # -------------------------------------------------------------------- + # write one dump file per snapshot from current selection + + def scatter(self,root): + if len(self.snaps): namestr = self.names2str() + for snap in self.snaps: + if not snap.tselect: continue + print snap.time, + sys.stdout.flush() + + file = root + "." + str(snap.time) + f = open(file,"w") + print >>f,"ITEM: TIMESTEP" + print >>f,snap.time + print >>f,"ITEM: NUMBER OF ATOMS" + print >>f,snap.nselect + print >>f,"ITEM: BOX BOUNDS" + print >>f,snap.xlo,snap.xhi + print >>f,snap.ylo,snap.yhi + print >>f,snap.zlo,snap.zhi + print >>f,"ITEM: ATOMS",namestr + + atoms = snap.atoms + nvalues = len(atoms[0]) + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + line = "" + for j in xrange(nvalues): + if (j < 2): + line += str(int(atoms[i][j])) + " " + else: + line += str(atoms[i][j]) + " " + print >>f,line + f.close() + print "\n%d snapshots" % self.nselect + + # -------------------------------------------------------------------- + # find min/max across all selected snapshots/atoms for a particular column + + def minmax(self,colname): + icol = self.names[colname] + min = 1.0e20 + max = -min + for snap in self.snaps: + if not snap.tselect: continue + atoms = snap.atoms + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + if atoms[i][icol] < min: min = atoms[i][icol] + if atoms[i][icol] > max: max = atoms[i][icol] + return (min,max) + + # -------------------------------------------------------------------- + # set a column value via an equation for all selected snapshots + + def set(self,eq): + print "Setting ..." + pattern = "\$\w*" + list = re.findall(pattern,eq) + + lhs = list[0][1:] + if not self.names.has_key(lhs): + self.newcolumn(lhs) + + for item in list: + name = item[1:] + column = self.names[name] + insert = "snap.atoms[i][%d]" % (column) + eq = eq.replace(item,insert) + ceq = compile(eq,'','single') + + for snap in self.snaps: + if not snap.tselect: continue + for i in xrange(snap.natoms): + if snap.aselect[i]: exec ceq + + # -------------------------------------------------------------------- + # set a column value via an input vec for all selected snapshots/atoms + + def setv(self,colname,vec): + print "Setting ..." + if not self.names.has_key(colname): + self.newcolumn(colname) + icol = self.names[colname] + + for snap in self.snaps: + if not snap.tselect: continue + if snap.nselect != len(vec): + raise StandardError,"vec length does not match # of selected atoms" + atoms = snap.atoms + m = 0 + for i in xrange(snap.natoms): + if snap.aselect[i]: + atoms[i][icol] = vec[m] + m += 1 + + # -------------------------------------------------------------------- + # clone value in col across selected timesteps for atoms with same ID + + def clone(self,nstep,col): + istep = self.findtime(nstep) + icol = self.names[col] + id = self.names["id"] + ids = {} + for i in xrange(self.snaps[istep].natoms): + ids[self.snaps[istep].atoms[i][id]] = i + for snap in self.snaps: + if not snap.tselect: continue + atoms = snap.atoms + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + j = ids[atoms[i][id]] + atoms[i][icol] = self.snaps[istep].atoms[j][icol] + + # -------------------------------------------------------------------- + # values in old column are spread as ints from 1-N and assigned to new column + + def spread(self,old,n,new): + iold = self.names[old] + if not self.names.has_key(new): self.newcolumn(new) + inew = self.names[new] + + min,max = self.minmax(old) + print "min/max = ",min,max + + gap = max - min + invdelta = n/gap + for snap in self.snaps: + if not snap.tselect: continue + atoms = snap.atoms + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + ivalue = int((atoms[i][iold] - min) * invdelta) + 1 + if ivalue > n: ivalue = n + if ivalue < 1: ivalue = 1 + atoms[i][inew] = ivalue + + # -------------------------------------------------------------------- + # return vector of selected snapshot time stamps + + def time(self): + vec = self.nselect * [0] + i = 0 + for snap in self.snaps: + if not snap.tselect: continue + vec[i] = snap.time + i += 1 + return vec + + # -------------------------------------------------------------------- + # extract vector(s) of values for atom ID n at each selected timestep + + def atom(self,n,*list): + if len(list) == 0: + raise StandardError, "no columns specified" + columns = [] + values = [] + for name in list: + columns.append(self.names[name]) + values.append(self.nselect * [0]) + ncol = len(columns) + + id = self.names["id"] + m = 0 + for snap in self.snaps: + if not snap.tselect: continue + atoms = snap.atoms + for i in xrange(snap.natoms): + if atoms[i][id] == n: break + if atoms[i][id] != n: + raise StandardError, "could not find atom ID in snapshot" + for j in xrange(ncol): + values[j][m] = atoms[i][columns[j]] + m += 1 + + if len(list) == 1: return values[0] + else: return values + + # -------------------------------------------------------------------- + # extract vector(s) of values for selected atoms at chosen timestep + + def vecs(self,n,*list): + snap = self.snaps[self.findtime(n)] + + if len(list) == 0: + raise StandardError, "no columns specified" + columns = [] + values = [] + for name in list: + columns.append(self.names[name]) + values.append(snap.nselect * [0]) + ncol = len(columns) + + m = 0 + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + for j in xrange(ncol): + values[j][m] = snap.atoms[i][columns[j]] + m += 1 + + if len(list) == 1: return values[0] + else: return values + + # -------------------------------------------------------------------- + # add a new column to every snapshot and set value to 0 + # set the name of the column to str + + def newcolumn(self,str): + ncol = len(self.snaps[0].atoms[0]) + self.map(ncol+1,str) + for snap in self.snaps: + atoms = snap.atoms + if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float) + else: newatoms = np.zeros((snap.natoms,ncol+1),np.float) + newatoms[:,0:ncol] = snap.atoms + snap.atoms = newatoms + + # -------------------------------------------------------------------- + # sort snapshots on time stamp + + def compare_time(self,a,b): + if a.time < b.time: + return -1 + elif a.time > b.time: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + # delete successive snapshots with duplicate time stamp + + def cull(self): + i = 1 + while i < len(self.snaps): + if self.snaps[i].time == self.snaps[i-1].time: + del self.snaps[i] + else: + i += 1 + + # -------------------------------------------------------------------- + # iterate over selected snapshots + + def iterator(self,flag): + start = 0 + if flag: start = self.iterate + 1 + for i in xrange(start,self.nsnaps): + if self.snaps[i].tselect: + self.iterate = i + return i,self.snaps[i].time,1 + return 0,0,-1 + + # -------------------------------------------------------------------- + # return list of atoms to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + # augment with bonds, tris, lines if extra() was invoked + + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + + snap = self.snaps[isnap] + + time = snap.time + box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi] + id = self.names["id"] + type = self.names[self.atype] + x = self.names["x"] + y = self.names["y"] + z = self.names["z"] + + # create atom list needed by viz from id,type,x,y,z + # need Numeric/Numpy mode here + + atoms = [] + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + atom = snap.atoms[i] + atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]]) + + # create list of bonds from static or dynamic bond list + # then generate bond coords from bondlist + # alist = dictionary of atom IDs for atoms list + # lookup bond atom IDs in alist and grab their coords + # try is used since some atoms may be unselected + # any bond with unselected atom is not added to bonds + # need Numeric/Numpy mode here + + bonds = [] + if self.bondflag: + if self.bondflag == 1: bondlist = self.bondlist + elif self.bondflag == 2: + tmp1,tmp2,tmp3,bondlist,tmp4,tmp5 = self.objextra.viz(time,1) + alist = {} + for i in xrange(len(atoms)): alist[int(atoms[i][0])] = i + for bond in bondlist: + try: + i = alist[bond[2]] + j = alist[bond[3]] + atom1 = atoms[i] + atom2 = atoms[j] + bonds.append([bond[0],bond[1],atom1[2],atom1[3],atom1[4], + atom2[2],atom2[3],atom2[4],atom1[1],atom2[1]]) + except: continue + + # create list of tris from static or dynamic tri list + # if dynamic, could eliminate tris for unselected atoms + + tris = [] + if self.triflag: + if self.triflag == 1: tris = self.trilist + elif self.triflag == 2: + tmp1,tmp2,tmp3,tmp4,tris,tmp5 = self.objextra.viz(time,1) + + # create list of lines from static or dynamic tri list + # if dynamic, could eliminate lines for unselected atoms + + lines = [] + if self.lineflag: + if self.lineflag == 1: lines = self.linelist + elif self.lineflag == 2: + tmp1,tmp2,tmp3,tmp4,tmp5,lines = self.objextra.viz(time,1) + + return time,box,atoms,bonds,tris,lines + + # -------------------------------------------------------------------- + + def findtime(self,n): + for i in xrange(self.nsnaps): + if self.snaps[i].time == n: return i + raise StandardError, "no step %d exists" % n + + # -------------------------------------------------------------------- + # return maximum box size across all selected snapshots + + def maxbox(self): + xlo = ylo = zlo = None + xhi = yhi = zhi = None + for snap in self.snaps: + if not snap.tselect: continue + if xlo == None or snap.xlo < xlo: xlo = snap.xlo + if xhi == None or snap.xhi > xhi: xhi = snap.xhi + if ylo == None or snap.ylo < ylo: ylo = snap.ylo + if yhi == None or snap.yhi > yhi: yhi = snap.yhi + if zlo == None or snap.zlo < zlo: zlo = snap.zlo + if zhi == None or snap.zhi > zhi: zhi = snap.zhi + return [xlo,ylo,zlo,xhi,yhi,zhi] + + # -------------------------------------------------------------------- + # return maximum atom type across all selected snapshots and atoms + + def maxtype(self): + icol = self.names["type"] + max = 0 + for snap in self.snaps: + if not snap.tselect: continue + atoms = snap.atoms + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + if atoms[i][icol] > max: max = atoms[i][icol] + return int(max) + + # -------------------------------------------------------------------- + # grab bonds/tris/lines from another object + # if static, grab once, else store obj to grab dynamically + + def extra(self,arg): + + # data object, grab bonds statically + + if type(arg) is types.InstanceType and ".data" in str(arg.__class__): + self.bondflag = 0 + try: + bondlist = [] + bondlines = arg.sections["Bonds"] + for line in bondlines: + words = line.split() + bondlist.append([int(words[0]),int(words[1]), + int(words[2]),int(words[3])]) + if bondlist: + self.bondflag = 1 + self.bondlist = bondlist + except: + raise StandardError,"could not extract bonds from data object" + + # cdata object, grab tris and lines statically + + elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__): + self.triflag = self.lineflag = 0 + try: + tmp,tmp,tmp,tmp,tris,lines = arg.viz(0) + if tris: + self.triflag = 1 + self.trilist = tris + if lines: + self.lineflag = 1 + self.linelist = lines + except: + raise StandardError,"could not extract tris/lines from cdata object" + + # mdump object, grab tris dynamically + + elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__): + self.triflag = 2 + self.objextra = arg + + # bdump object, grab bonds dynamically + + elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__): + self.bondflag = 2 + self.objextra = arg + + # ldump object, grab tris dynamically + + elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__): + self.lineflag = 2 + self.objextra = arg + + # tdump object, grab tris dynamically + + elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__): + self.triflag = 2 + self.objextra = arg + + else: + raise StandardError,"unrecognized argument to dump.extra()" + + # -------------------------------------------------------------------- + + def compare_atom(self,a,b): + if a[0] < b[0]: + return -1 + elif a[0] > b[0]: + return 1 + else: + return 0 + +# -------------------------------------------------------------------- +# one snapshot + +class Snap: + pass + +# -------------------------------------------------------------------- +# time selection class + +class tselect: + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def all(self,**kwargs): + + # check whether to output or not + outputfl = True + if "output" in kwargs: outputfl = kwargs["output"] + + data = self.data + for snap in data.snaps: + snap.tselect = 1 + data.nselect = len(data.snaps) + data.aselect.all() + if outputfl: print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def one(self,n): + data = self.data + for snap in data.snaps: + snap.tselect = 0 + i = data.findtime(n) + data.snaps[i].tselect = 1 + data.nselect = 1 + data.aselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def none(self): + data = self.data + for snap in data.snaps: + snap.tselect = 0 + data.nselect = 0 + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def skip(self,n): + data = self.data + count = n-1 + for snap in data.snaps: + if not snap.tselect: continue + count += 1 + if count == n: + count = 0 + continue + snap.tselect = 0 + data.nselect -= 1 + data.aselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def test(self,teststr): + data = self.data + snaps = data.snaps + cmd = "flag = " + teststr.replace("$t","snaps[i].time") + ccmd = compile(cmd,'','single') + for i in xrange(data.nsnaps): + if not snaps[i].tselect: continue + exec ccmd + if not flag: + snaps[i].tselect = 0 + data.nselect -= 1 + data.aselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + +# -------------------------------------------------------------------- +# atom selection class + +class aselect: + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def all(self,*args): + data = self.data + if len(args) == 0: # all selected timesteps + for snap in data.snaps: + if not snap.tselect: continue + for i in xrange(snap.natoms): snap.aselect[i] = 1 + snap.nselect = snap.natoms + else: # one timestep + n = data.findtime(args[0]) + snap = data.snaps[n] + for i in xrange(snap.natoms): snap.aselect[i] = 1 + snap.nselect = snap.natoms + + # -------------------------------------------------------------------- + + def test(self,teststr,*args): + data = self.data + + # replace all $var with snap.atoms references and compile test string + + pattern = "\$\w*" + list = re.findall(pattern,teststr) + for item in list: + name = item[1:] + column = data.names[name] + insert = "snap.atoms[i][%d]" % column + teststr = teststr.replace(item,insert) + cmd = "flag = " + teststr + ccmd = compile(cmd,'','single') + + if len(args) == 0: # all selected timesteps + for snap in data.snaps: + if not snap.tselect: continue + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + exec ccmd + if not flag: + snap.aselect[i] = 0 + snap.nselect -= 1 + for i in xrange(data.nsnaps): + if data.snaps[i].tselect: + print "%d atoms of %d selected in first step %d" % \ + (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time) + break + for i in xrange(data.nsnaps-1,-1,-1): + if data.snaps[i].tselect: + print "%d atoms of %d selected in last step %d" % \ + (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time) + break + + else: # one timestep + n = data.findtime(args[0]) + snap = data.snaps[n] + for i in xrange(snap.natoms): + if not snap.aselect[i]: continue + exec ccmd + if not flag: + snap.aselect[i] = 0 + snap.nselect -= 1 diff --git a/src/dump.pyc b/src/dump.pyc new file mode 100644 index 0000000..3c32593 Binary files /dev/null and b/src/dump.pyc differ diff --git a/src/dump2force.py b/src/dump2force.py new file mode 100644 index 0000000..8bbcc0e --- /dev/null +++ b/src/dump2force.py @@ -0,0 +1,246 @@ +#!/usr/bin/python +""" +A simple routine to load in a LIGGGHTS hybrid dump file containing +contact and contact force data and convert into a .vtk unstructured +grid which can be used to visualise the force network. + +Contributing author: Mark Bentley, Space Research Institute, +Austrian Academy of Sciences, mark.bentley@oeaw.ac.at + +evtk is used to write binary VTK files: +https://bitbucket.org/pauloh/pyevtk + +The pizza.py bdump command is used to handle LIGGGHTS dump files and +therefore PYTHONPATH must include the pizza/src location. + +""" + +try: from evtk.vtk import VtkFile, VtkGroup, VtkUnstructuredGrid +except: print "Need package evtk for dump2force, https://bitbucket.org/pauloh/pyevtk" + +try: from bdump import bdump +except: print "Need bdump moldule for dump2force" + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +import sys, os + + +# TODO: use a try/except here to check for missing modules, and report +# TODO: ask for timestep or timestep range as input +# TODO make it a class.... +# TODO: check for periodic boundaries and avoid connecting points that map across them + + +# Check for command line arguments +if len(sys.argv) != 2: + sys.exit('Usage: dump2forcenetwork.py , where filename is typically dump.') + +elif len(sys.argv) == 2: # we have one input param, that should be parsed as a filename + filename = str(sys.argv[1]) + if not os.path.isfile(filename): + sys.exit('File ' + filename + ' does not exist!') + +splitname = filename.split('.') + +if len(splitname) == 2 and splitname[0].lower() == 'dump': + fileprefix = splitname[1] +else: + fileprefix = splitname[0] + +inputpath = os.path.abspath(filename) +inputdir = os.path.split(inputpath)[0] + +# create a sub-directory for the output .vtu files +outputdir = os.path.join(inputdir,fileprefix) +try: + os.mkdir(outputdir) +except: + pass + +# Read in the dump file - since we can have many contacts (i.e. >> nparticles) +# and many timesteps I will deal with one timestep at a time in memory, +# write to the appropriate .vtu file for a single timestep, then move on. + +forcedata = bdump(filename,0) + +groupfile = fileprefix +groupfile = os.path.join(inputdir,groupfile) +groupfile = VtkGroup(groupfile) + +fileindex = 0 +timestep = forcedata.next() + +# check that we have the right number of colums (11) +if forcedata.snaps[fileindex].natoms !=0 and len(forcedata.snaps[0].atoms[0]) != 11: + print "Error - dump file requires all parameters from a compute pair/gran/local id pos force (11 in total)" + sys.exit + +# loop through available timesteps +# +while timestep >= 0: + + # data are stored as pos1 (3) pos2 (3) id1 id2 force (3) for 11 columns + # assign names to atom columns (1-N) + forcedata.map(1,"x1",2,"y1",3,"z1",4,"x2",5,"y2",6,"z2",7,"id1",8,"id2",9,"fx",10,"fy",11,"fz") + + # check for contact data (some timesteps may have no particles in contact) + # + # NB. if one loads two datasets into ParaView with defined timesteps, but in which + # one datasets has some missing, data for the previous timestep are still displayed - + # this means that it is better here to generate "empty" files for these timesteps. + + if forcedata.snaps[fileindex].natoms == 0: + vtufile = fileprefix+'_'+str(timestep)+'.vtu' + vtufile = os.path.join(outputdir,vtufile) + vtuwrite = file(vtufile,'w') + vtuwrite.write(""" + + + + + + + + + + + +""") + + else: + + # number of cells = number of interactions (i.e. entries in the dump file) + ncells = len(forcedata.snaps[fileindex].atoms) + + # extract the IDs as an array of integers + id1 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id1"]],dtype=long) + id2 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id2"]],dtype=long) + + # and convert to lists + id1 = id1.tolist() + id2 = id2.tolist() + + # concatenate into a single list + ids = [] + ids = id1[:] + ids.extend(id2) + + # convert to a set and back to remove duplicates, then sort + ids = list(set(ids)) + ids.sort() + + # number of points = number of unique IDs (particles) + npoints = len(ids) + + # create empty arrays to hold x,y,z data + x = np.zeros( npoints, dtype=np.float64) + y = np.zeros( npoints, dtype=np.float64) + z = np.zeros( npoints, dtype=np.float64) + + print 'Timestep:',str(timestep),'npoints=',str(npoints),'ncells=',str(ncells) + + # Point data = location of each unique particle + # + # The order of this data is important since we use the position of each particle + # in this list to reference particle connectivity! We will use the order of the + # sorted ids array to determine this. + + counter = 0 + for id in ids: + if id in id1: + index = id1.index(id) + xtemp,ytemp,ztemp = forcedata.snaps[fileindex].atoms[index,forcedata.names["x1"]], \ + forcedata.snaps[fileindex].atoms[index,forcedata.names["y1"]], \ + forcedata.snaps[fileindex].atoms[index,forcedata.names["z1"]] + else: + index = id2.index(id) + xtemp,ytemp,ztemp = forcedata.snaps[fileindex].atoms[index,forcedata.names["x2"]], \ + forcedata.snaps[fileindex].atoms[index,forcedata.names["y2"]], \ + forcedata.snaps[fileindex].atoms[index,forcedata.names["z2"]] + + x[counter]=xtemp + y[counter]=ytemp + z[counter]=ztemp + counter += 1 + + # Now create the connectivity list - this corresponds to pairs of IDs, but referencing + # the order of the ids array, so now we loop through 0..ncells and have to connect + # id1 and id2, so I need to see where in ids these correspond to + + # create an empty array to hold particle pairs + connections = np.zeros( 2*ncells, dtype=int ) + + for pair in range(ncells): + connections[2*pair],connections[2*pair+1] = ids.index(id1[pair]),ids.index(id2[pair]) + + # The offset array is simply generated from 2*(1..ncells) + offset=(np.arange(ncells,dtype=int)+1)*2 + + # The type array is simply ncells x 3 (i.e. a VTKLine type) + celltype = np.ones(ncells,dtype=int)*3 + + # Finally we need force data for each cell + force = np.sqrt( np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["fx"]],dtype=np.float64)**2 + \ + np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["fy"]],dtype=np.float64)**2 + \ + np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["fz"]],dtype=np.float64)**2 ) + + # Now we have enough data to create the file: + # Points - (x,y,z) (npoints) + # Cells + # Connectivity - connections (ncells,2) + # Offset - offset (ncells) + # type - celltype (ncells) + # Celldata - force (ncells) + + # create a VTK unstructured grid (.vtu) file + vtufile = fileprefix+'_'+str(timestep) + vtufile = os.path.join(outputdir,vtufile) + w = VtkFile(vtufile, VtkUnstructuredGrid) + vtufile += '.vtu' + + w.openGrid() + w.openPiece(npoints=npoints, ncells=ncells) + + # Set up Points data + w.openElement("Points") + w.addData("points", (x,y,z) ) + w.closeElement("Points") + + # Set up Cell data + w.openElement("Cells") + w.addData("connectivity", connections ) + + w.addData("offsets", offset) + w.addData("types", celltype) + w.closeElement("Cells") + + # Set up force data + w.openData("Cell", scalars = "force") + w.addData("force", force) + w.closeData("Cell") + + # Wrap up + w.closePiece() + w.closeGrid() + + # Append binary data + w.appendData( (x,y,z) ) + w.appendData(connections).appendData(offset).appendData(celltype) + w.appendData(data = force) + w.save() + + # Add this file to the group of all timesteps + groupfile.addFile(filepath = os.path.relpath(vtufile,inputdir), sim_time = timestep) + + fileindex += 1 + timestep = forcedata.next() + +# end of main loop - close group file +groupfile.save() + diff --git a/src/dump2force.pyc b/src/dump2force.pyc new file mode 100644 index 0000000..fb9b8e9 Binary files /dev/null and b/src/dump2force.pyc differ diff --git a/src/ensight.py b/src/ensight.py new file mode 100644 index 0000000..7c68ef1 --- /dev/null +++ b/src/ensight.py @@ -0,0 +1,510 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# ensight tool + +oneline = "Convert LAMMPS snapshots or meshes to Ensight format" + +docstr = """ +e = ensight(d) d = object with atoms or elements (dump,data,mdump) +e.change = 1 set to 1 if element nodal xyz change with time (def = 0) +e.maxtype = 10 max particle type, set if query to data will be bad + +e.one() +e.one("new") +e.one("cns","Centro","eng","Energy") +e.one("new","cns","Centro","eng","Energy") + write all snapshots as an Ensight data set + Ensight header file = tmp.case (no 1st arg) or new.case + Ensight coord file = tmp.xyz or new.xyz + additional pairs of args create auxiliary files: + tmp.cns, tmp.eng or new.cns, new.eng + cns,eng = column name in dump file and file name suffix + Centro,Energy = Ensight name for the variable + +e.increment() same args as one(), but process dump out-of-core + +e.many() same args as one(), but create multiple Ensight files + tmp0000.xyz, tmp0001.xyz, etc + new0000.cns, new0001.cns, etc + new0000.eng, new0001.eng, etc + +e.single(N) same args as one() prepended by N, but write a single snap +""" + +# History +# 10/06, Steve Plimpton (SNL): original version + +# ToDo list +# binary files +# create vector or tensor variable files, not just scalar +# via pair of args like ["vx","vy","vz"],"vel" + +# Variables +# data = data file to read from +# which = 0 for particles, 1 for elements +# change = 0 for unchanging mesh coords, 1 for changing mesh coords (def = 0) + +# Imports and external programs + +import sys, types + +# Class definition + +class ensight: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.change = 0 + self.maxtype = 0 + self.data = data + if type(data) is types.InstanceType and ".dump" in str(data.__class__): + self.which = 0 + elif type(data) is types.InstanceType and ".data" in str(data.__class__): + self.which = 0 + elif type(data) is types.InstanceType and ".mdump" in str(data.__class__): + self.which = 1 + elif type(data) is types.InstanceType and ".cdata" in str(data.__class__): + self.which = 1 + else: + raise StandardError,"unrecognized object passed to ensight" + + # -------------------------------------------------------------------- + + def one(self,*args): + if len(args) % 2 == 0: root = "tmp" + else: + root = args[0] + args = args[1:] + + pairs = [] + for i in range(0,len(args),2): pairs.append([args[i],args[i+1]]) + + # max # of types for all steps in Ensight files + + if self.which == 0 and self.maxtype == 0: + self.maxtype = self.data.maxtype() + + # write Ensight *.case header file + + f = open("%s.case" % root,"w") + times = self.data.time() + self.case_file(f,root,pairs,0,len(times),times) + f.close() + + # open additional files + + f = open(root + ".xyz","w") + vfiles = [] + for pair in pairs: vfiles.append(open(root + "." + pair[0],"w")) + + # loop over snapshots + # write coords into xyz file, variables into their files + + first = 1 + n = flag = etype = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + + if self.which == 0: + print >>f,"BEGIN TIME STEP" + time,box,atoms,bonds,tris,lines = self.data.viz(which) + self.coord_file_atoms(f,box,atoms) + print >>f,"END TIME STEP" + elif self.change == 0 and first: + print >>f,"BEGIN TIME STEP" + time,box,nodes,elements,nvalues,evalues = self.data.mviz(which) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + first = 0 + print >>f,"END TIME STEP" + elif self.change: + print >>f,"BEGIN TIME STEP" + time,box,nodes,elements,nvalues,evalues = self.data.mviz(which) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + print >>f,"END TIME STEP" + + for i in range(len(pairs)): + print >>vfiles[i],"BEGIN TIME STEP" + values = self.data.vecs(time,pairs[i][0]) + if self.which == 0: + self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values) + else: + self.variable_file_elements(vfiles[i],pairs[i][1],etype,values) + print >>vfiles[i],"END TIME STEP" + + print time, + sys.stdout.flush() + n += 1 + + # close additional files + + f.close() + for f in vfiles: f.close() + + print "\nwrote %s snapshots in Ensight format" % n + + # -------------------------------------------------------------------- + + def increment(self,*args): + if len(args) % 2 == 0: root = "tmp" + else: + root = args[0] + args = args[1:] + + pairs = [] + for i in range(0,len(args),2): pairs.append([args[i],args[i+1]]) + + # max # of types for all steps in Ensight files + + if self.which == 0 and self.maxtype == 0: + self.maxtype = self.data.maxtype() + + # open additional files + + f = open(root + ".xyz","w") + vfiles = [] + for pair in pairs: vfiles.append(open(root + "." + pair[0],"w")) + + # loop over snapshots + # write coords into xyz file, variables into their files + + times = [] + first = 1 + n = etype = 0 + while 1: + time = self.data.next() + if time == -1: break + times.append(time) + self.data.tselect.one(time) + self.data.delete() + + if self.which == 0: + print >>f,"BEGIN TIME STEP" + time,box,atoms,bonds,tris,lines = self.data.viz(0) + self.coord_file_atoms(f,box,atoms) + print >>f,"END TIME STEP" + elif self.change == 0 and first: + print >>f,"BEGIN TIME STEP" + time,box,nodes,elements,nvalues,evalues = self.data.mviz(0) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + first = 0 + print >>f,"END TIME STEP" + elif self.change: + print >>f,"BEGIN TIME STEP" + time,box,nodes,elements,nvalues,evalues = self.data.mviz(0) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + print >>f,"END TIME STEP" + + for i in range(len(pairs)): + print >>vfiles[i],"BEGIN TIME STEP" + values = self.data.vecs(time,pairs[i][0]) + if self.which == 0: + self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values) + else: + self.variable_file_elements(vfiles[i],pairs[i][1],etype,values) + print >>vfiles[i],"END TIME STEP" + + print time, + sys.stdout.flush() + n += 1 + + # close additional files + + f.close() + for f in vfiles: f.close() + + # write Ensight *.case header file now that know all timesteps + + f = open("%s.case" % root,"w") + self.case_file(f,root,pairs,0,len(times),times) + f.close() + + print "\nwrote %s snapshots in Ensight format" % n + + # -------------------------------------------------------------------- + + def many(self,*args): + if len(args) % 2 == 0: root = "tmp" + else: + root = args[0] + args = args[1:] + + pairs = [] + for i in range(0,len(args),2): pairs.append([args[i],args[i+1]]) + + # max # of types for all steps in Ensight files + + if self.which == 0 and self.maxtype == 0: + self.maxtype = self.data.maxtype() + + # write Ensight *.case header file + + f = open("%s.case" % root,"w") + times = self.data.time() + self.case_file(f,root,pairs,1,len(times),times) + f.close() + + # loop over snapshots + # generate unique filenames + # write coords into one xyz file per snapshot, variables into their files + + first = 1 + n = flag = etype = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + + files = [] + if n < 10: + file = root + "000" + str(n) + ".xyz" + for pair in pairs: + files.append(root + "000" + str(n) + "." + pair[0]) + elif n < 100: + file = root + "00" + str(n) + ".xyz" + for pair in pairs: + files.append(root + "00" + str(n) + "." + pair[0]) + elif n < 1000: + file = root + "0" + str(n) + ".xyz" + for pair in pairs: + files.append(root + "0" + str(n) + "." + pair[0]) + else: + file = root + str(n) + ".xyz" + for pair in pairs: + files.append(root + str(n) + "." + pair[0]) + + if self.which == 0: + f = open(file,"w") + time,box,atoms,bonds,tris,lines = self.data.viz(which) + self.coord_file_atoms(f,box,atoms) + f.close() + elif self.change == 0 and first: + f = open(root + ".xyz","w") + time,box,nodes,elements,nvalues,evalues = self.data.mviz(which) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + first = 0 + f.close() + elif self.change: + f = open(file,"w") + time,box,nodes,elements,nvalues,evalues = self.data.mviz(which) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + f.close() + + for i in range(len(pairs)): + values = self.data.vecs(time,pairs[i][0]) + f = open(files[i],"w") + if self.which == 0: + self.variable_file_atoms(f,pairs[i][1],atoms,values) + else: + self.variable_file_elements(f,pairs[i][1],etype,values) + f.close() + + print time, + sys.stdout.flush() + n += 1 + + print "\nwrote %s snapshots in Ensight format" % n + + # -------------------------------------------------------------------- + + def single(self,time,*args): + if len(args) % 2 == 0: root = "tmp" + else: + root = args[0] + args = args[1:] + + pairs = [] + for i in range(0,len(args),2): pairs.append([args[i],args[i+1]]) + + # max # of types for all steps in Ensight files + + if self.which == 0 and self.maxtype == 0: + self.maxtype = self.data.maxtype() + + # write Ensight *.case header file + + f = open("%s.case" % root,"w") + self.case_file(f,root,pairs,0,1,[time]) + f.close() + + # write coords into xyz file, variables into their files + + which = self.data.findtime(time) + etype = 0 + + f = open(root + ".xyz","w") + if self.which == 0: + time,box,atoms,bonds,tris,lines = self.data.viz(which) + self.coord_file_atoms(f,box,atoms) + else: + time,box,nodes,elements,nvalues,evalues = self.data.mviz(which) + self.coord_file_elements(f,box,nodes,elements) + etype = len(elements[0]) + f.close() + + for i in range(len(pairs)): + values = self.data.vecs(time,pairs[i][0]) + f = open(root + "." + pairs[i][0],"w") + if self.which == 0: + self.variable_file_atoms(f,pairs[i][1],atoms,values) + else: + self.variable_file_elements(f,pairs[i][1],etype,values) + f.close() + + # -------------------------------------------------------------------- + # write Ensight case file + + def case_file(self,f,root,pairs,multifile,nsnaps,times): + print >>f,"# Ensight case file\n" + print >>f,"FORMAT\ntype: ensight gold\n" + + if self.which == 0: + if multifile: +# print >>f,"GEOMETRY\nmodel: %s****.xyz change_coords_only\n" % root + print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root + else: +# print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz change_coords_only\n" % root + print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root + else: + if self.change == 0: + print >>f,"GEOMETRY\nmodel: %s.xyz\n" % root + elif multifile: + print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root + else: + print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root + + if len(pairs): + print >>f,"VARIABLE" + for pair in pairs: + if self.which == 0: + if multifile: + print >>f,"scalar per node: %s %s****.%s" % (pair[1],root,pair[0]) + else: + print >>f,"scalar per node: 1 1 %s %s.%s" % (pair[1],root,pair[0]) + else: + if multifile: + print >>f,"scalar per element: %s %s****.%s" % (pair[1],root,pair[0]) + else: + print >>f,"scalar per element: 1 1 %s %s.%s" % (pair[1],root,pair[0]) + print >>f + + print >>f,"TIME" + print >>f,"time set: 1" + print >>f,"number of steps:",nsnaps + print >>f,"filename start number: 0" + print >>f,"filename increment: 1" + print >>f,"time values:" + for i in range(nsnaps): + print >>f,times[i], + if i % 10 == 9: print >>f + print >>f + print >>f + + if not multifile: + print >>f,"FILE" + print >>f,"file set: 1" + print >>f,"number of steps:",nsnaps + + # -------------------------------------------------------------------- + # write Ensight coordinates for atoms + # partition into "parts" + # one part = coords for all atoms of a single type + + def coord_file_atoms(self,f,box,atoms): + print >>f,"Particle geometry\nfor a collection of atoms" + print >>f,"node id given" + print >>f,"element id off" + print >>f,"extents" + print >>f,"%12.5e%12.5e" % (box[0],box[3]) + print >>f,"%12.5e%12.5e" % (box[1],box[4]) + print >>f,"%12.5e%12.5e" % (box[2],box[5]) + + for type in xrange(1,self.maxtype+1): + print >>f,"part" + print >>f,"%10d" % type + print >>f,"type",type + print >>f,"coordinates" + group = [atom for atom in atoms if int(atom[1]) == type] + print >>f,"%10d" % len(group) + for atom in group: print >>f,"%10d" % int(atom[0]) + for atom in group: print >>f,"%12.5e" % atom[2] + for atom in group: print >>f,"%12.5e" % atom[3] + for atom in group: print >>f,"%12.5e" % atom[4] + print >>f,"point" + print >>f,"%10d" % len(group) + for i in xrange(1,len(group)+1): print >>f,"%10d" % i + + # -------------------------------------------------------------------- + # write Ensight coordinates for elements + + def coord_file_elements(self,f,box,nodes,elements): + print >>f,"Element geometry\nfor a collection of elements" + print >>f,"node id given" + print >>f,"element id given" + print >>f,"extents" + print >>f,"%12.5e%12.5e" % (box[0],box[3]) + print >>f,"%12.5e%12.5e" % (box[1],box[4]) + print >>f,"%12.5e%12.5e" % (box[2],box[5]) + + print >>f,"part" + print >>f,"%10d" % 1 + print >>f,"all elements" + print >>f,"coordinates" + print >>f,"%10d" % len(nodes) + for node in nodes: print >>f,"%10d" % int(node[0]) + for node in nodes: print >>f,"%12.5e" % node[2] + for node in nodes: print >>f,"%12.5e" % node[3] + for node in nodes: print >>f,"%12.5e" % node[4] + + if len(elements[0]) == 5: print >>f,"tria3" + elif len(elements[0]) == 6: print >>f,"tetra4" + else: raise StandardError,"unrecognized element type" + print >>f,"%10d" % len(elements) + + for element in elements: print >>f,"%10d" % int(element[0]) + if len(elements[0]) == 5: + for element in elements: + print >>f,"%10d%10d%10d" % \ + (int(element[2]),int(element[3]),int(element[4])) + elif len(elements[0]) == 6: + for element in elements: + print >>f,"%10d%10d%10d%10d" % \ + (int(element[2]),int(element[3]),int(element[4]),int(element[5])) + + # -------------------------------------------------------------------- + # write Ensight variable values for atoms + # partition into "parts" + # one part = values for all atoms of a single type + + def variable_file_atoms(self,f,name,atoms,values): + print >>f,"Particle %s" % name + for type in xrange(1,self.maxtype+1): + print >>f,"part" + print >>f,"%10d" % type + print >>f,"coordinates" + group = [values[i] for i in xrange(len(atoms)) + if int(atoms[i][1]) == type] + for value in group: print >>f,"%12.5e" % value + + # -------------------------------------------------------------------- + # write Ensight variable values for elements + + def variable_file_elements(self,f,name,etype,values): + print >>f,"Element %s" % name + print >>f,"part" + print >>f,"%10d" % 1 + if etype == 5: print >>f,"tria3" + elif etype == 6: print >>f,"tetra4" + for value in values: print >>f,"%12.5e" % value diff --git a/src/ensight.pyc b/src/ensight.pyc new file mode 100644 index 0000000..1784de5 Binary files /dev/null and b/src/ensight.pyc differ diff --git a/src/gl.py b/src/gl.py new file mode 100644 index 0000000..b0312cf --- /dev/null +++ b/src/gl.py @@ -0,0 +1,1330 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# gl tool + +oneline = "3d interactive visualization via OpenGL" + +docstr = """ +g = gl(d) create OpenGL display for data in d + + d = atom snapshot object (dump, data) + +g.bg("black") set background color (def = "black") +g.size(N) set image size to NxN +g.size(N,M) set image size to NxM +g.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +g.shift(x,y) translate by x,y pixels in view window (def = 0,0) +g.zoom(0.5) scale image by factor (def = 1) +g.box(0/1/2) 0/1/2 = none/variable/fixed box +g.box(0/1/2,"green") set box color +g.box(0/1/2,"red",4) set box edge thickness +g.file = "image" file prefix for created images (def = "image") + +g.show(N) show image of snapshot at timestep N + +g.all() make images of all selected snapshots +g.all(P) images of all, start file label at P +g.all(N,M,P) make M images of snapshot N, start label at P + +g.pan(60,135,1.0,40,135,1.5) pan during all() operation +g.pan() no pan during all() (default) + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values + +g.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +g.select = "" no extra aselect (default) + + %g varies from 0.0 to 1.0 from beginning to end of all() + +g.acol(2,"green") set atom colors by atom type (1-N) +g.acol([2,4],["red","blue"]) 1st arg = one type or list of types +g.acol(0,"blue") 2nd arg = one color or list of colors +g.acol(range(20),["red","blue"]) if list lengths unequal, interpolate +g.acol(range(10),"loop") assign colors in loop, randomly ordered + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next + +g.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol() + +g.bcol() set bond color, same args as acol() +g.brad() set bond thickness, same args as arad() + +g.tcol() set triangle color, same args as acol() +g.tfill() set triangle fill, 0 fill, 1 line, 2 both + +g.lcol() set line color, same args as acol() +g.lrad() set line thickness, same args as arad() + +g.adef() set atom/bond/tri/line properties to default +g.bdef() default = "loop" for colors, 0.45 for radii +g.tdef() default = 0.25 for bond/line thickness +g.ldef() default = 0 fill + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors["nickname"] = [R,G,B] set new RGB values from 0 to 255 + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc + +Settings specific to gl tool: + +g.q(10) set quality of image (def = 5) +g.axis(0/1) turn xyz axes off/on +g.ortho(0/1) perspective (0) vs orthographic (1) view +g.clip('xlo',0.25) clip in xyz from lo/hi at box fraction (0-1) +g.reload() force all data to be reloaded +g.cache = 0/1 turn off/on GL cache lists (def = on) +theta,phi,x,y,scale,up = g.gview() grab all current view parameters +g.sview(theta,phi,x,y,scale,up) set all view parameters + + data reload is necessary if dump selection is used to change the data + cache lists usually improve graphics performance + gview returns values to use in other commands: + theta,phi are args to rotate() + x,y are args to shift() + scale is arg to zoom() + up is a 3-vector arg to sview() +""" + +# History +# 9/05, Steve Plimpton (SNL): original version + +# ToDo list +# when do aselect with select str while looping N times on same timestep +# would not let you grow # of atoms selected + +# Variables +# ztheta = vertical angle from z-azis of viewpoint +# azphi = azimuthal angle of viewpoint +# xshift,yshift = xy translation of scene (in pixels) +# distance = size of simulation box (largest dim) +# eye = viewpoint distance from center of scene +# file = filename prefix to use for images produced +# boxflag = 0/1/2 for drawing simulation box: none/variable/fixed +# bxcol = color of box +# bxthick = thickness of box lines +# bgcol = color of background +# vizinfo = scene attributes +# center[3] = center point of simulation box +# view[3] = direction towards eye in simulation box (unit vector) +# up[3] = screen up direction in simulation box (unit vector) +# right[3] = screen right direction in simulation box (unit vector) + +# Imports and external programs + +from math import sin,cos,sqrt,pi,acos +from OpenGL.Tk import * +from OpenGL.GLUT import * +import Image +from vizinfo import vizinfo + +# Class definition + +class gl: + +# -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + self.root = None + self.xpixels = 512 + self.ypixels = 512 + self.ztheta = 60 + self.azphi = 30 + self.scale = 1.0 + self.xshift = self.yshift = 0 + + self.file = "image" + self.boxflag = 0 + self.bxcol = [1,1,0] + self.bxthick = 0.3 + self.bgcol = [0,0,0] + self.labels = [] + self.panflag = 0 + self.select = "" + + self.axisflag = 0 + self.orthoflag = 1 + self.nslices = 5 + self.nstacks = 5 + self.nsides = 10 + self.theta_amplify = 2 + self.shiny = 2 + + self.clipflag = 0 + self.clipxlo = self.clipylo = self.clipzlo = 0.0 + self.clipxhi = self.clipyhi = self.clipzhi = 1.0 + + self.nclist = 0 + self.calllist = [0] # indexed by 1-Ntype, so start with 0 index + self.cache = 1 + self.cachelist = 0 + + self.boxdraw = [] + self.atomdraw = [] + self.bonddraw = [] + self.tridraw = [] + self.linedraw = [] + + self.ready = 0 + glutInit() # some versions of freeglut require this before any GLUT call + self.create_window() + + self.vizinfo = vizinfo() + self.adef() + self.bdef() + self.tdef() + self.ldef() + + self.center = 3*[0] + self.view = 3*[0] + self.up = 3*[0] + self.right = 3*[0] + self.viewupright() + + # -------------------------------------------------------------------- + + def bg(self,color): + from vizinfo import colors + self.bgcol = [colors[color][0]/255.0,colors[color][1]/255.0, + colors[color][2]/255.0] + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def size(self,xnew,ynew=None): + self.xpixels = xnew + if not ynew: self.ypixels = self.xpixels + else: self.ypixels = ynew + self.create_window() + + # -------------------------------------------------------------------- + + def axis(self,value): + self.axisflag = value + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def create_window(self): + if self.root: self.root.destroy() + + from __main__ import tkroot + self.root = Toplevel(tkroot) + self.root.title('Pizza.py gl tool') + + self.w = MyOpengl(self.root,width=self.xpixels,height=self.ypixels, + double=1,depth=1) + self.w.pack(expand=YES) +# self.w.pack(expand=YES,fill=BOTH) + + glViewport(0,0,self.xpixels,self.ypixels) + glEnable(GL_LIGHTING); + glEnable(GL_LIGHT0); + glEnable(GL_DEPTH_TEST); + glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,GL_TRUE); + glPolygonMode(GL_FRONT_AND_BACK,GL_FILL) + + self.rtrack = self.xpixels + if self.ypixels > self.xpixels: self.rtrack = self.ypixels + + self.w.redraw = self.redraw + self.w.parent = self + self.w.tkRedraw() + tkroot.update_idletasks() # force window to appear + + # -------------------------------------------------------------------- + + def clip(self,which,value): + if which == "xlo": + self.clipxlo = value + if value > self.clipxhi: self.clipxlo = self.clipxhi + elif which == "xhi": + self.clipxhi = value + if value < self.clipxlo: self.clipxhi = self.clipxlo + elif which == "ylo": + self.clipylo = value + if value > self.clipyhi: self.clipylo = self.clipyhi + elif which == "yhi": + self.clipyhi = value + if value < self.clipylo: self.clipyhi = self.clipylo + elif which == "zlo": + self.clipzlo = value + if value > self.clipzhi: self.clipzlo = self.clipzhi + elif which == "zhi": + self.clipzhi = value + if value < self.clipzlo: self.clipzhi = self.clipzlo + + oldflag = self.clipflag + if self.clipxlo > 0 or self.clipylo > 0 or self.clipzlo > 0 or \ + self.clipxhi < 1 or self.clipyhi < 1 or self.clipzhi < 1: + self.clipflag = 1 + else: self.clipflag = 0 + + if oldflag == 0 and self.clipflag == 0: return + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def q(self,value): + self.nslices = value + self.nstacks = value + self.make_atom_calllist() + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def ortho(self,value): + self.orthoflag = value + self.w.tkRedraw() + + # -------------------------------------------------------------------- + # set unit vectors for view,up,right from ztheta,azphi + # assume +z in scene should be up on screen (unless looking down z-axis) + # right = up x view + + def viewupright(self): + self.view[0] = cos(pi*self.azphi/180) * sin(pi*self.ztheta/180) + self.view[1] = sin(pi*self.azphi/180) * sin(pi*self.ztheta/180) + self.view[2] = cos(pi*self.ztheta/180) + + if self.ztheta == 0.0: + self.up[0] = cos(pi*self.azphi/180) + self.up[1] = -sin(pi*self.azphi/180) + self.up[2] = 0.0 + elif self.ztheta == 180.0: + self.up[0] = cos(pi*self.azphi/180) + self.up[1] = sin(pi*self.azphi/180) + self.up[2] = 0.0 + else: + dot = self.view[2] # dot = (0,0,1) . view + self.up[0] = -dot*self.view[0] # up projected onto v = dot * v + self.up[1] = -dot*self.view[1] # up perp to v = up - dot * v + self.up[2] = 1.0 - dot*self.view[2] + + self.up = vecnorm(self.up) + self.right = veccross(self.up,self.view) + + # -------------------------------------------------------------------- + # reset ztheta,azphi and thus view,up.right + # called as function from Pizza.py + + def rotate(self,ztheta,azphi): + self.ztheta = ztheta + self.azphi = azphi + self.viewupright() + self.setview() + self.w.tkRedraw() + + # -------------------------------------------------------------------- + # return all view params to reproduce current display via sview() + + def gview(self): + return self.ztheta,self.azphi,self.xshift,self.yshift,self.scale,self.up + + # -------------------------------------------------------------------- + # set current view, called by user with full set of view params + # up is not settable via any other call, all other params are + + def sview(self,ztheta,azphi,xshift,yshift,scale,up): + self.ztheta = ztheta + self.azphi = azphi + self.xshift = xshift + self.yshift = yshift + self.scale = scale + self.up[0] = up[0] + self.up[1] = up[1] + self.up[2] = up[2] + self.up = vecnorm(self.up) + self.view[0] = cos(pi*self.azphi/180) * sin(pi*self.ztheta/180) + self.view[1] = sin(pi*self.azphi/180) * sin(pi*self.ztheta/180) + self.view[2] = cos(pi*self.ztheta/180) + self.right = veccross(self.up,self.view) + self.setview() + self.w.tkRedraw() + + # -------------------------------------------------------------------- + # rotation triggered by mouse trackball + # project old,new onto unit trackball surf + # rotate view,up around axis of rotation = old x new + # right = up x view + # reset ztheta,azphi from view + + def mouse_rotate(self,xnew,ynew,xold,yold): + + # change y pixels to measure from bottom of window instead of top + + yold = self.ypixels - yold + ynew = self.ypixels - ynew + + # vold = unit vector to (xold,yold) projected onto trackball + # vnew = unit vector to (xnew,ynew) projected onto trackball + # return (no rotation) if either projection point is outside rtrack + + vold = [0,0,0] + vold[0] = xold - (0.5*self.xpixels + self.xshift) + vold[1] = yold - (0.5*self.ypixels + self.yshift) + vold[2] = self.rtrack*self.rtrack - vold[0]*vold[0] - vold[1]*vold[1] + if vold[2] < 0: return + vold[2] = sqrt(vold[2]) + vold = vecnorm(vold) + + vnew = [0,0,0] + vnew[0] = xnew - (0.5*self.xpixels + self.xshift) + vnew[1] = ynew - (0.5*self.ypixels + self.yshift) + vnew[2] = self.rtrack*self.rtrack - vnew[0]*vnew[0] - vnew[1]*vnew[1] + if vnew[2] < 0: return + vnew[2] = sqrt(vnew[2]) + vnew = vecnorm(vnew) + + # rot = trackball rotation axis in screen ref frame = vold x vnew + # theta = angle of rotation = sin(theta) for small theta + # axis = rotation axis in body ref frame described by right,up,view + + rot = veccross(vold,vnew) + theta = sqrt(rot[0]*rot[0] + rot[1]*rot[1] + rot[2]*rot[2]) + theta *= self.theta_amplify + + axis = [0,0,0] + axis[0] = rot[0]*self.right[0] + rot[1]*self.up[0] + rot[2]*self.view[0] + axis[1] = rot[0]*self.right[1] + rot[1]*self.up[1] + rot[2]*self.view[1] + axis[2] = rot[0]*self.right[2] + rot[1]*self.up[2] + rot[2]*self.view[2] + axis = vecnorm(axis) + + # view is changed by (axis x view) scaled by theta + # up is changed by (axis x up) scaled by theta + # force up to be perp to view via up_perp = up - (up . view) view + # right = up x view + + delta = veccross(axis,self.view) + self.view[0] -= theta*delta[0] + self.view[1] -= theta*delta[1] + self.view[2] -= theta*delta[2] + self.view = vecnorm(self.view) + + delta = veccross(axis,self.up) + self.up[0] -= theta*delta[0] + self.up[1] -= theta*delta[1] + self.up[2] -= theta*delta[2] + + dot = vecdot(self.up,self.view) + self.up[0] -= dot*self.view[0] + self.up[1] -= dot*self.view[1] + self.up[2] -= dot*self.view[2] + self.up = vecnorm(self.up) + + self.right = veccross(self.up,self.view) + + # convert new view to ztheta,azphi + + self.ztheta = acos(self.view[2])/pi * 180.0 + if (self.ztheta == 0.0): self.azphi = 0.0 + else: self.azphi = acos(self.view[0]/sin(pi*self.ztheta/180.0))/pi * 180.0 + if self.view[1] < 0: self.azphi = 360.0 - self.azphi + self.setview() + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def shift(self,x,y): + self.xshift = x; + self.yshift = y; + self.setview() + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def zoom(self,scale): + self.scale = scale + self.setview() + self.w.tkRedraw() + + # -------------------------------------------------------------------- + # set view params needed by redraw + # input: center = center of box + # distance = size of scene (longest box length) + # scale = zoom factor (1.0 = no zoom) + # xshift,yshift = translation factor in pixels + # view = unit vector from center to viewpoint + # up = unit vector in up direction in scene + # right = unit vector in right direction in scene + # output: eye = distance to view scene from + # xto,yto,zto = point to look to + # xfrom,yfrom,zfrom = point to look from + + def setview(self): + if not self.ready: return # no distance since no scene yet + + self.eye = 3 * self.distance / self.scale + xfactor = 0.5*self.eye*self.xshift/self.xpixels + yfactor = 0.5*self.eye*self.yshift/self.ypixels + + self.xto = self.center[0] - xfactor*self.right[0] - yfactor*self.up[0] + self.yto = self.center[1] - xfactor*self.right[1] - yfactor*self.up[1] + self.zto = self.center[2] - xfactor*self.right[2] - yfactor*self.up[2] + + self.xfrom = self.xto + self.eye*self.view[0] + self.yfrom = self.yto + self.eye*self.view[1] + self.zfrom = self.zto + self.eye*self.view[2] + + # -------------------------------------------------------------------- + # box attributes, also used for triangle lines + + def box(self,*args): + self.boxflag = args[0] + if len(args) > 1: + from vizinfo import colors + self.bxcol = [colors[args[1]][0]/255.0,colors[args[1]][1]/255.0, + colors[args[1]][2]/255.0] + if len(args) > 2: self.bxthick = args[2] + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + # grab all selected snapshots from data object + # add GL-specific info to each bond + + def reload(self): + print "Loading data into gl tool ..." + data = self.data + + self.timeframes = [] + self.boxframes = [] + self.atomframes = [] + self.bondframes = [] + self.triframes = [] + self.lineframes = [] + + box = [] + if self.boxflag == 2: box = data.maxbox() + + flag = 0 + while 1: + which,time,flag = data.iterator(flag) + if flag == -1: break + time,boxone,atoms,bonds,tris,lines = data.viz(which) + if self.boxflag < 2: box = boxone + if bonds: self.bonds_augment(bonds) + + self.timeframes.append(time) + self.boxframes.append(box) + self.atomframes.append(atoms) + self.bondframes.append(bonds) + self.triframes.append(tris) + self.lineframes.append(lines) + + print time, + sys.stdout.flush() + print + + self.nframes = len(self.timeframes) + self.distance = compute_distance(self.boxframes[0]) + self.center = compute_center(self.boxframes[0]) + self.ready = 1 + self.setview() + + # -------------------------------------------------------------------- + + def nolabel(self): + self.cachelist = -self.cachelist + self.labels = [] + + # -------------------------------------------------------------------- + # show a single snapshot + # distance from snapshot box or max box for all selected steps + + def show(self,ntime): + data = self.data + which = data.findtime(ntime) + time,box,atoms,bonds,tris,lines = data.viz(which) + if self.boxflag == 2: box = data.maxbox() + self.distance = compute_distance(box) + self.center = compute_center(box) + + if bonds: self.bonds_augment(bonds) + + self.boxdraw = box + self.atomdraw = atoms + self.bonddraw = bonds + self.tridraw = tris + self.linedraw = lines + + self.ready = 1 + self.setview() + self.cachelist = -self.cachelist + self.w.tkRedraw() + self.save() + + # -------------------------------------------------------------------- + + def pan(self,*list): + if len(list) == 0: self.panflag = 0 + else: + self.panflag = 1 + self.ztheta_start = list[0] + self.azphi_start = list[1] + self.scale_start = list[2] + self.ztheta_stop = list[3] + self.azphi_stop = list[4] + self.scale_stop = list[5] + + # -------------------------------------------------------------------- + + def all(self,*list): + data = self.data + if len(list) == 0: + nstart = 0 + ncount = data.nselect + elif len(list) == 1: + nstart = list[0] + ncount = data.nselect + else: + ntime = list[0] + nstart = list[2] + ncount = list[1] + + if self.boxflag == 2: box = data.maxbox() + + # loop over all selected steps + # distance from 1st snapshot box or max box for all selected steps + # recompute box center on 1st step or if panning + + if len(list) <= 1: + + n = nstart + i = flag = 0 + while 1: + which,time,flag = data.iterator(flag) + if flag == -1: break + + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,time) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + self.viewupright() + + if n == nstart or self.panflag: self.center = compute_center(box) + + if bonds: self.bonds_augment(bonds) + + self.boxdraw = box + self.atomdraw = atoms + self.bonddraw = bonds + self.tridraw = tris + self.linedraw = lines + + self.ready = 1 + self.setview() + self.cachelist = -self.cachelist + self.w.tkRedraw() + self.save(file) + + print time, + sys.stdout.flush() + i += 1 + n += 1 + + # loop ncount times on same step + # distance from 1st snapshot box or max box for all selected steps + # recompute box center on 1st step or if panning + + else: + + which = data.findtime(ntime) + + n = nstart + for i in range(ncount): + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,ntime) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + self.viewupright() + + if n == nstart or self.panflag: self.center = compute_center(box) + + if bonds: self.bonds_augment(bonds) + + self.boxdraw = box + self.atomdraw = atoms + self.bonddraw = bonds + self.tridraw = tris + self.linedraw = lines + + self.ready = 1 + self.setview() + self.cachelist = -self.cachelist + self.w.tkRedraw() + self.save(file) + + print n, + sys.stdout.flush() + n += 1 + + print "\n%d images" % ncount + + # -------------------------------------------------------------------- + + def display(self,index): + self.boxdraw = self.boxframes[index] + self.atomdraw = self.atomframes[index] + self.bonddraw = self.bondframes[index] + self.tridraw = self.triframes[index] + self.linedraw = self.lineframes[index] + + self.ready = 1 + self.cachelist = -self.cachelist + self.w.tkRedraw() + return (self.timeframes[index],len(self.atomdraw)) + + # -------------------------------------------------------------------- + # draw the GL scene + + def redraw(self,o): + # clear window to background color + + glClearColor(self.bgcol[0],self.bgcol[1],self.bgcol[2],0) + glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT) + + # not ready if no scene yet + + if not self.ready: return + + # set view from eye, distance, 3 lookat vectors (from,to,up) + + glMatrixMode(GL_PROJECTION) + glLoadIdentity() + if self.orthoflag: + glOrtho(-0.25*self.eye,0.25*self.eye,-0.25*self.eye,0.25*self.eye, + self.eye-2*self.distance,self.eye+2*self.distance) + else: + gluPerspective(30.0,1.0,0.01,10000.0) + + glMatrixMode(GL_MODELVIEW) + glLoadIdentity() + gluLookAt(self.xfrom,self.yfrom,self.zfrom,self.xto,self.yto,self.zto, + self.up[0],self.up[1],self.up[2]) + + # draw scene from display list if caching allowed and list hasn't changed + # else redraw and store as new display list if caching allowed + + if self.cache and self.cachelist > 0: glCallList(self.cachelist); + else: + if self.cache: + if self.cachelist < 0: glDeleteLists(-self.cachelist,1) + self.cachelist = glGenLists(1) + glNewList(self.cachelist,GL_COMPILE_AND_EXECUTE) + + # draw box, clip-box, xyz axes, lines + + glDisable(GL_LIGHTING) + + if self.boxflag: + self.draw_box(0) + if self.clipflag: self.draw_box(1) + if self.axisflag: self.draw_axes() + + ncolor = self.vizinfo.nlcolor + for line in self.linedraw: + itype = int(line[1]) + if itype > ncolor: raise StandardError,"line type too big" + red,green,blue = self.vizinfo.lcolor[itype] + glColor3f(red,green,blue) + thick = self.vizinfo.lrad[itype] + glLineWidth(thick) + glBegin(GL_LINES) + glVertex3f(line[2],line[3],line[4]) + glVertex3f(line[5],line[6],line[7]) + glEnd() + + glEnable(GL_LIGHTING) + + # draw non-clipped scene = atoms, bonds, triangles + +# draw atoms as collection of points +# cannot put PointSize inside glBegin +# so probably need to group atoms by type for best performance +# or just allow one radius +# need to scale radius appropriately with box size +# or could leave it at absolute value +# use POINT_SMOOTH to enable anti-aliasing and round points +# multiple timesteps via vcr::play() is still not fast +# caching makes it fast for single frame, but multiple frames is slow +# need to enable clipping + +# if not self.clipflag: +# glDisable(GL_LIGHTING) +# glEnable(GL_POINT_SMOOTH) +# glPointSize(self.vizinfo.arad[int(self.atomdraw[0][1])]) +# glBegin(GL_POINTS) +# for atom in self.atomdraw: +# red,green,blue = self.vizinfo.acolor[int(atom[1])] +# glColor(red,green,blue) +# glVertex3d(atom[2],atom[3],atom[4]) +# glEnd() +# glEnable(GL_LIGHTING) + + if not self.clipflag: + for atom in self.atomdraw: + glTranslatef(atom[2],atom[3],atom[4]); + glCallList(self.calllist[int(atom[1])]); + glTranslatef(-atom[2],-atom[3],-atom[4]); + + if self.bonddraw: + bound = 0.25 * self.distance + ncolor = self.vizinfo.nbcolor + for bond in self.bonddraw: + if bond[10] > bound: continue + itype = int(bond[1]) + if itype > ncolor: raise StandardError,"bond type too big" + red,green,blue = self.vizinfo.bcolor[itype] + rad = self.vizinfo.brad[itype] + glPushMatrix() + glTranslatef(bond[2],bond[3],bond[4]) + glRotatef(bond[11],bond[12],bond[13],0.0) + glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]); + glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny); + obj = gluNewQuadric() + gluCylinder(obj,rad,rad,bond[10],self.nsides,self.nsides) + glPopMatrix() + + if self.tridraw: + fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])] + + if fillflag != 1: + if fillflag: + glEnable(GL_POLYGON_OFFSET_FILL) + glPolygonOffset(1.0,1.0) + glBegin(GL_TRIANGLES) + ncolor = self.vizinfo.ntcolor + for tri in self.tridraw: + itype = int(tri[1]) + if itype > ncolor: raise StandardError,"tri type too big" + red,green,blue = self.vizinfo.tcolor[itype] + glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]); + glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny); + glNormal3f(tri[11],tri[12],tri[13]) + glVertex3f(tri[2],tri[3],tri[4]) + glVertex3f(tri[5],tri[6],tri[7]) + glVertex3f(tri[8],tri[9],tri[10]) + glEnd() + if fillflag: glDisable(GL_POLYGON_OFFSET_FILL) + + if fillflag: + glDisable(GL_LIGHTING) + glPolygonMode(GL_FRONT_AND_BACK,GL_LINE) + glLineWidth(self.bxthick) + glColor3f(self.bxcol[0],self.bxcol[1],self.bxcol[2]) + glBegin(GL_TRIANGLES) + for tri in self.tridraw: + glVertex3f(tri[2],tri[3],tri[4]) + glVertex3f(tri[5],tri[6],tri[7]) + glVertex3f(tri[8],tri[9],tri[10]) + glEnd() + glEnable(GL_LIGHTING) + glPolygonMode(GL_FRONT_AND_BACK,GL_FILL) + + # draw clipped scene = atoms, bonds, triangles + + else: + box = self.boxdraw + xlo = box[0] + self.clipxlo*(box[3] - box[0]) + xhi = box[0] + self.clipxhi*(box[3] - box[0]) + ylo = box[1] + self.clipylo*(box[4] - box[1]) + yhi = box[1] + self.clipyhi*(box[4] - box[1]) + zlo = box[2] + self.clipzlo*(box[5] - box[2]) + zhi = box[2] + self.clipzhi*(box[5] - box[2]) + + for atom in self.atomdraw: + x,y,z = atom[2],atom[3],atom[4] + if x >= xlo and x <= xhi and y >= ylo and y <= yhi and \ + z >= zlo and z <= zhi: + glTranslatef(x,y,z); + glCallList(self.calllist[int(atom[1])]); + glTranslatef(-x,-y,-z); + + if self.bonddraw: + bound = 0.25 * self.distance + ncolor = self.vizinfo.nbcolor + for bond in self.bonddraw: + xmin = min2(bond[2],bond[5]) + xmax = max2(bond[2],bond[5]) + ymin = min2(bond[3],bond[6]) + ymax = max2(bond[3],bond[6]) + zmin = min2(bond[4],bond[7]) + zmax = max2(bond[4],bond[7]) + if xmin >= xlo and xmax <= xhi and \ + ymin >= ylo and ymax <= yhi and zmin >= zlo and zmax <= zhi: + if bond[10] > bound: continue + itype = int(bond[1]) + if itype > ncolor: raise StandardError,"bond type too big" + red,green,blue = self.vizinfo.bcolor[itype] + rad = self.vizinfo.brad[itype] + glPushMatrix() + glTranslatef(bond[2],bond[3],bond[4]) + glRotatef(bond[11],bond[12],bond[13],0.0) + glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]); + glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny); + obj = gluNewQuadric() + gluCylinder(obj,rad,rad,bond[10],self.nsides,self.nsides) + glPopMatrix() + + if self.tridraw: + fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])] + + if fillflag != 1: + if fillflag: + glEnable(GL_POLYGON_OFFSET_FILL) + glPolygonOffset(1.0,1.0) + glBegin(GL_TRIANGLES) + ncolor = self.vizinfo.ntcolor + for tri in self.tridraw: + xmin = min3(tri[2],tri[5],tri[8]) + xmax = max3(tri[2],tri[5],tri[8]) + ymin = min3(tri[3],tri[6],tri[9]) + ymax = max3(tri[3],tri[6],tri[9]) + zmin = min3(tri[4],tri[7],tri[10]) + zmax = max3(tri[4],tri[7],tri[10]) + if xmin >= xlo and xmax <= xhi and \ + ymin >= ylo and ymax <= yhi and \ + zmin >= zlo and zmax <= zhi: + itype = int(tri[1]) + if itype > ncolor: raise StandardError,"tri type too big" + red,green,blue = self.vizinfo.tcolor[itype] + glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION, + [red,green,blue,1.0]); + glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny); + glNormal3f(tri[11],tri[12],tri[13]) + glVertex3f(tri[2],tri[3],tri[4]) + glVertex3f(tri[5],tri[6],tri[7]) + glVertex3f(tri[8],tri[9],tri[10]) + glEnd() + if fillflag: glDisable(GL_POLYGON_OFFSET_FILL) + + if fillflag: + glDisable(GL_LIGHTING) + glPolygonMode(GL_FRONT_AND_BACK,GL_LINE) + glLineWidth(self.bxthick) + glColor3f(self.bxcol[0],self.bxcol[1],self.bxcol[2]) + glBegin(GL_TRIANGLES) + for tri in self.tridraw: + xmin = min3(tri[2],tri[5],tri[8]) + xmax = max3(tri[2],tri[5],tri[8]) + ymin = min3(tri[3],tri[6],tri[9]) + ymax = max3(tri[3],tri[6],tri[9]) + zmin = min3(tri[4],tri[7],tri[10]) + zmax = max3(tri[4],tri[7],tri[10]) + if xmin >= xlo and xmax <= xhi and \ + ymin >= ylo and ymax <= yhi and \ + zmin >= zlo and zmax <= zhi: + glVertex3f(tri[2],tri[3],tri[4]) + glVertex3f(tri[5],tri[6],tri[7]) + glVertex3f(tri[8],tri[9],tri[10]) + glEnd() + glEnable(GL_LIGHTING) + glPolygonMode(GL_FRONT_AND_BACK,GL_FILL) + + if self.cache: glEndList() + + glFlush() + + # -------------------------------------------------------------------- + # make new call list for each atom type + # called when atom color/rad/quality is changed + + def make_atom_calllist(self): + # extend calllist array if necessary + + if self.vizinfo.nacolor > self.nclist: + for i in range(self.vizinfo.nacolor-self.nclist): self.calllist.append(0) + self.nclist = self.vizinfo.nacolor + + # create new calllist for each atom type + + for itype in xrange(1,self.vizinfo.nacolor+1): + if self.calllist[itype]: glDeleteLists(self.calllist[itype],1) + ilist = glGenLists(1) + self.calllist[itype] = ilist + glNewList(ilist,GL_COMPILE) + red,green,blue = self.vizinfo.acolor[itype] + rad = self.vizinfo.arad[itype] + glColor3f(red,green,blue); + +# glPointSize(10.0*rad) +# glBegin(GL_POINTS) +# glVertex3f(0.0,0.0,0.0) +# glEnd() + + glMaterialfv(GL_FRONT,GL_EMISSION,[red,green,blue,1.0]); + glMaterialf(GL_FRONT,GL_SHININESS,self.shiny); + glutSolidSphere(rad,self.nslices,self.nstacks) + glEndList() + + # -------------------------------------------------------------------- + # augment bond info returned by viz() with info needed for GL draw + # info = length, theta, -dy, dx for bond orientation + + def bonds_augment(self,bonds): + for bond in bonds: + dx = bond[5] - bond[2] + dy = bond[6] - bond[3] + dz = bond[7] - bond[4] + length = sqrt(dx*dx + dy*dy + dz*dz) + dx /= length + dy /= length + dz /= length + theta = acos(dz)*180.0/pi + bond += [length,theta,-dy,dx] + + # -------------------------------------------------------------------- + + def draw_box(self,flag): + xlo,ylo,zlo,xhi,yhi,zhi = self.boxdraw + + if flag: + tmp = xlo + self.clipxlo*(xhi - xlo) + xhi = xlo + self.clipxhi*(xhi - xlo) + xlo = tmp + tmp = ylo + self.clipylo*(yhi - ylo) + yhi = ylo + self.clipyhi*(yhi - ylo) + ylo = tmp + tmp = zlo + self.clipzlo*(zhi - zlo) + zhi = zlo + self.clipzhi*(zhi - zlo) + zlo = tmp + + glLineWidth(self.bxthick) + glColor3f(self.bxcol[0],self.bxcol[1],self.bxcol[2]) + + glBegin(GL_LINE_LOOP) + glVertex3f(xlo,ylo,zlo) + glVertex3f(xhi,ylo,zlo) + glVertex3f(xhi,yhi,zlo) + glVertex3f(xlo,yhi,zlo) + glEnd() + + glBegin(GL_LINE_LOOP) + glVertex3f(xlo,ylo,zhi) + glVertex3f(xhi,ylo,zhi) + glVertex3f(xhi,yhi,zhi) + glVertex3f(xlo,yhi,zhi) + glEnd() + + glBegin(GL_LINES) + glVertex3f(xlo,ylo,zlo) + glVertex3f(xlo,ylo,zhi) + glVertex3f(xhi,ylo,zlo) + glVertex3f(xhi,ylo,zhi) + glVertex3f(xhi,yhi,zlo) + glVertex3f(xhi,yhi,zhi) + glVertex3f(xlo,yhi,zlo) + glVertex3f(xlo,yhi,zhi) + glEnd() + + # -------------------------------------------------------------------- + + def draw_axes(self): + xlo,ylo,zlo,xhi,yhi,zhi = self.boxdraw + + delta = xhi-xlo + if yhi-ylo > delta: delta = yhi-ylo + if zhi-zlo > delta: delta = zhi-zlo + delta *= 0.1 + + glLineWidth(self.bxthick) + + glBegin(GL_LINES) + glColor3f(1,0,0) + glVertex3f(xlo-delta,ylo-delta,zlo-delta) + glVertex3f(xhi-delta,ylo-delta,zlo-delta) + glColor3f(0,1,0) + glVertex3f(xlo-delta,ylo-delta,zlo-delta) + glVertex3f(xlo-delta,yhi-delta,zlo-delta) + glColor3f(0,0,1) + glVertex3f(xlo-delta,ylo-delta,zlo-delta) + glVertex3f(xlo-delta,ylo-delta,zhi-delta) + glEnd() + + # -------------------------------------------------------------------- + + def save(self,file=None): + self.w.update() # force image on screen to be current before saving it + + pstring = glReadPixels(0,0,self.xpixels,self.ypixels, + GL_RGBA,GL_UNSIGNED_BYTE) + snapshot = Image.fromstring("RGBA",(self.xpixels,self.ypixels),pstring) + snapshot = snapshot.transpose(Image.FLIP_TOP_BOTTOM) + + if not file: file = self.file + snapshot.save(file + ".png") + + # -------------------------------------------------------------------- + + def adef(self): + self.vizinfo.setcolors("atom",range(100),"loop") + self.vizinfo.setradii("atom",range(100),0.45) + self.make_atom_calllist() + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def bdef(self): + self.vizinfo.setcolors("bond",range(100),"loop") + self.vizinfo.setradii("bond",range(100),0.25) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def tdef(self): + self.vizinfo.setcolors("tri",range(100),"loop") + self.vizinfo.setfills("tri",range(100),0) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def ldef(self): + self.vizinfo.setcolors("line",range(100),"loop") + self.vizinfo.setradii("line",range(100),0.25) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def acol(self,atypes,colors): + self.vizinfo.setcolors("atom",atypes,colors) + self.make_atom_calllist() + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def arad(self,atypes,radii): + self.vizinfo.setradii("atom",atypes,radii) + self.make_atom_calllist() + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def bcol(self,btypes,colors): + self.vizinfo.setcolors("bond",btypes,colors) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def brad(self,btypes,radii): + self.vizinfo.setradii("bond",btypes,radii) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def tcol(self,ttypes,colors): + self.vizinfo.setcolors("tri",ttypes,colors) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def tfill(self,ttypes,flags): + self.vizinfo.setfills("tri",ttypes,flags) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def lcol(self,ltypes,colors): + self.vizinfo.setcolors("line",ltypes,colors) + self.cachelist = -self.cachelist + self.w.tkRedraw() + + # -------------------------------------------------------------------- + + def lrad(self,ltypes,radii): + self.vizinfo.setradii("line",ltypes,radii) + self.cachelist = -self.cachelist + self.w.tkRedraw() + +# -------------------------------------------------------------------- +# derived class from Togl's Opengl +# overwrite redraw, translate, rotate, scale methods +# latter 3 are mouse-motion methods + +class MyOpengl(Opengl): + def __init__(self, master, cnf={}, **kw): + args = (self,master,cnf) + Opengl.__init__(*args,**kw) + Opengl.autospin_allowed = 0 + + # redraw Opengl scene + # call parent redraw() method + + def tkRedraw(self,*dummy): + if not self.initialised: return + self.tk.call(self._w,'makecurrent') + self.redraw(self) + self.tk.call(self._w,'swapbuffers') + + # left button translate + # access parent xshift/yshift and call parent trans() method + + def tkTranslate(self,event): + dx = event.x - self.xmouse + dy = event.y - self.ymouse + x = self.parent.xshift + dx + y = self.parent.yshift - dy + self.parent.shift(x,y) + self.tkRedraw() + self.tkRecordMouse(event) + + # middle button trackball + # call parent mouse_rotate() method + + def tkRotate(self,event): + self.parent.mouse_rotate(event.x,event.y,self.xmouse,self.ymouse) + self.tkRedraw() + self.tkRecordMouse(event) + + # right button zoom + # access parent scale and call parent zoom() method + + def tkScale(self,event): + scale = 1 - 0.01 * (event.y - self.ymouse) + if scale < 0.001: scale = 0.001 + elif scale > 1000: scale = 1000 + scale *= self.parent.scale + self.parent.zoom(scale) + self.tkRedraw() + self.tkRecordMouse(event) + +# -------------------------------------------------------------------- +# draw a line segment + +def segment(p1,p2): + glVertex3f(p1[0],p1[1],p1[2]) + glVertex3f(p2[0],p2[1],p2[2]) + +# -------------------------------------------------------------------- +# normalize a 3-vector to unit length + +def vecnorm(v): + length = sqrt(v[0]*v[0] + v[1]*v[1] + v[2]*v[2]) + return [v[0]/length,v[1]/length,v[2]/length] + +# -------------------------------------------------------------------- +# dot product of two 3-vectors + +def vecdot(v1,v2): + return v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2] + +# -------------------------------------------------------------------- +# cross product of two 3-vectors + +def veccross(v1,v2): + v = [0,0,0] + v[0] = v1[1]*v2[2] - v1[2]*v2[1] + v[1] = v1[2]*v2[0] - v1[0]*v2[2] + v[2] = v1[0]*v2[1] - v1[1]*v2[0] + return v + +# -------------------------------------------------------------------- +# return characteristic distance of simulation domain = max dimension + +def compute_distance(box): + distance = box[3]-box[0] + if box[4]-box[1] > distance: distance = box[4]-box[1] + if box[5]-box[2] > distance: distance = box[5]-box[2] + return distance + +# -------------------------------------------------------------------- +# return center of box as 3 vector + +def compute_center(box): + c = [0,0,0] + c[0] = 0.5 * (box[0] + box[3]) + c[1] = 0.5 * (box[1] + box[4]) + c[2] = 0.5 * (box[2] + box[5]) + return c + +# -------------------------------------------------------------------- +# return min of 2 values + +def min2(a,b): + if b < a: a = b + return a + +# -------------------------------------------------------------------- +# return max of 2 values + +def max2(a,b): + if b > a: a = b + return a + +# -------------------------------------------------------------------- +# return min of 3 values + +def min3(a,b,c): + if b < a: a = b + if c < a: a = c + return a + +# -------------------------------------------------------------------- +# return max of 3 values + +def max3(a,b,c): + if b > a: a = b + if c > a: a = c + return a diff --git a/src/gnu.py b/src/gnu.py new file mode 100644 index 0000000..f6f0167 --- /dev/null +++ b/src/gnu.py @@ -0,0 +1,383 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# gnu tool + +oneline = "Create plots via GnuPlot plotting program" + +docstr = """ +g = gnu() start up GnuPlot +g.stop() shut down GnuPlot process + +g.plot(a) plot vector A against linear index +g.plot(a,b) plot B against A +g.plot(a,b,c,d,...) plot B against A, D against C, etc +g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc + + each plot argument can be a tuple, list, or Numeric/NumPy vector + mplot loops over range(M,N,S) and create one plot per iteration + last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors + each plot is made from a portion of the vectors, depending on loop index i + Ith plot is of b[0:i] vs a[0:i], etc + series of plots saved as file0000.eps, file0001.eps, etc + if use xrange(),yrange() then plot axes will be same for all plots + +g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot + +g.enter() enter GnuPlot shell +gnuplot> plot sin(x) with lines type commands directly to GnuPlot +gnuplot> exit, quit exit GnuPlot shell + +g.export("data",range(100),a,...) create file with columns of numbers + + all vectors must be of equal length + could plot from file with GnuPlot command: plot 'data' using 1:2 with lines + +g.select(N) figure N becomes the current plot + + subsequent commands apply to this plot + +g.hide(N) delete window for figure N +g.save("file") save current plot as file.eps + +Set attributes for current plot: + +g.erase() reset all attributes to default values +g.aspect(1.3) aspect ratio +g.xtitle("Time") x axis text +g.ytitle("Energy") y axis text +g.title("My Plot") title text +g.title("title","x","y") title, x axis, y axis text +g.xrange(xmin,xmax) x axis range +g.xrange() default x axis range +g.yrange(ymin,ymax) y axis range +g.yrange() default y axis range +g.xlog() toggle x axis between linear and log +g.ylog() toggle y axis between linear and log +g.label(x,y,"text") place label at x,y coords +g.curve(N,'r') set color of curve N + + colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue + 'm' = magenta, 'c' = cyan, 'y' = yellow +""" + +# History +# 8/05, Matt Jones (BYU): original version +# 9/05, Steve Plimpton: added mplot() method + +# ToDo list +# allow choice of JPG or PNG or GIF when saving ? +# can this be done from GnuPlot or have to do via ImageMagick convert ? +# way to trim EPS plot that is created ? +# hide does not work on Mac aqua +# select does not pop window to front on Mac aqua + +# Variables +# current = index of current figure (1-N) +# figures = list of figure objects with each plot's attributes +# so they aren't lost between replots + +# Imports and external programs + +import types, os + +try: from DEFAULTS import PIZZA_GNUPLOT +except: PIZZA_GNUPLOT = "gnuplot" +try: from DEFAULTS import PIZZA_GNUTERM +except: PIZZA_GNUTERM = "x11" + +# Class definition + +class gnu: + + # -------------------------------------------------------------------- + + def __init__(self): + self.GNUPLOT = os.popen(PIZZA_GNUPLOT,'w') + self.file = "tmp.gnu" + self.figures = [] + self.select(1) + + # -------------------------------------------------------------------- + + def stop(self): + self.__call__("quit") + del self.GNUPLOT + + # -------------------------------------------------------------------- + + def __call__(self,command): + self.GNUPLOT.write(command + '\n') + self.GNUPLOT.flush() + + # -------------------------------------------------------------------- + + def enter(self): + while 1: + command = raw_input("gnuplot> ") + if command == "quit" or command == "exit": return + self.__call__(command) + + # -------------------------------------------------------------------- + # write plot vectors to files and plot them + + def plot(self,*vectors): + if len(vectors) == 1: + file = self.file + ".%d.1" % self.current + linear = range(len(vectors[0])) + self.export(file,linear,vectors[0]) + self.figures[self.current-1].ncurves = 1 + else: + if len(vectors) % 2: raise StandardError,"vectors must come in pairs" + for i in range(0,len(vectors),2): + file = self.file + ".%d.%d" % (self.current,i/2+1) + self.export(file,vectors[i],vectors[i+1]) + self.figures[self.current-1].ncurves = len(vectors)/2 + self.draw() + + # -------------------------------------------------------------------- + # create multiple plots from growing vectors, save to numbered files + # don't plot empty vector, create a [0] instead + + def mplot(self,start,stop,skip,file,*vectors): + n = 0 + for i in range(start,stop,skip): + partial_vecs = [] + for vec in vectors: + if i: partial_vecs.append(vec[:i]) + else: partial_vecs.append([0]) + self.plot(*partial_vecs) + + if n < 10: newfile = file + "000" + str(n) + elif n < 100: newfile = file + "00" + str(n) + elif n < 1000: newfile = file + "0" + str(n) + else: newfile = file + str(n) + + self.save(newfile) + n += 1 + + # -------------------------------------------------------------------- + # write list of equal-length vectors to filename + + def export(self,filename,*vectors): + n = len(vectors[0]) + for vector in vectors: + if len(vector) != n: raise StandardError,"vectors must be same length" + f = open(filename,'w') + nvec = len(vectors) + for i in xrange(n): + for j in xrange(nvec): + print >>f,vectors[j][i], + print >>f + f.close() + + # -------------------------------------------------------------------- + # select plot N as current plot + + def select(self,n): + self.current = n + if len(self.figures) < n: + for i in range(n - len(self.figures)): + self.figures.append(figure()) + cmd = "set term " + PIZZA_GNUTERM + ' ' + str(n) + self.__call__(cmd) + if self.figures[n-1].ncurves: self.draw() + + # -------------------------------------------------------------------- + # delete window for plot N + + def hide(self,n): + cmd = "set term %s close %d" % (PIZZA_GNUTERM,n) + self.__call__(cmd) + + # -------------------------------------------------------------------- + # save plot to file.eps + # final re-select will reset terminal + # do not continue until plot file is written out + # else script could go forward and change data file + # use tmp.done as semaphore to indicate plot is finished + + def save(self,file): + self.__call__("set terminal postscript enhanced solid lw 2 color portrait") + cmd = "set output '%s.eps'" % file + self.__call__(cmd) + if os.path.exists("tmp.done"): os.remove("tmp.done") + self.draw() + self.__call__("!touch tmp.done") + while not os.path.exists("tmp.done"): continue + self.__call__("set output") + self.select(self.current) + + # -------------------------------------------------------------------- + # restore default attributes by creating a new fig object + + def erase(self): + fig = figure() + fig.ncurves = self.figures[self.current-1].ncurves + self.figures[self.current-1] = fig + self.draw() + + # -------------------------------------------------------------------- + + def aspect(self,value): + self.figures[self.current-1].aspect = value + self.draw() + + # -------------------------------------------------------------------- + + def xrange(self,*values): + if len(values) == 0: + self.figures[self.current-1].xlimit = 0 + else: + self.figures[self.current-1].xlimit = (values[0],values[1]) + self.draw() + + # -------------------------------------------------------------------- + + def yrange(self,*values): + if len(values) == 0: + self.figures[self.current-1].ylimit = 0 + else: + self.figures[self.current-1].ylimit = (values[0],values[1]) + self.draw() + + # -------------------------------------------------------------------- + + def label(self,x,y,text): + self.figures[self.current-1].labels.append((x,y,text)) + self.figures[self.current-1].nlabels += 1 + self.draw() + + # -------------------------------------------------------------------- + + def nolabels(self): + self.figures[self.current-1].nlabel = 0 + self.figures[self.current-1].labels = [] + self.draw() + + # -------------------------------------------------------------------- + + def title(self,*strings): + if len(strings) == 1: + self.figures[self.current-1].title = strings[0] + else: + self.figures[self.current-1].title = strings[0] + self.figures[self.current-1].xtitle = strings[1] + self.figures[self.current-1].ytitle = strings[2] + self.draw() + + # -------------------------------------------------------------------- + + def xtitle(self,label): + self.figures[self.current-1].xtitle = label + self.draw() + + # -------------------------------------------------------------------- + + def ytitle(self,label): + self.figures[self.current-1].ytitle = label + self.draw() + + # -------------------------------------------------------------------- + + def xlog(self): + if self.figures[self.current-1].xlog: + self.figures[self.current-1].xlog = 0 + else: + self.figures[self.current-1].xlog = 1 + self.draw() + + # -------------------------------------------------------------------- + + def ylog(self): + if self.figures[self.current-1].ylog: + self.figures[self.current-1].ylog = 0 + else: + self.figures[self.current-1].ylog = 1 + self.draw() + + # -------------------------------------------------------------------- + + def curve(self,num,color): + fig = self.figures[self.current-1] + while len(fig.colors) < num: fig.colors.append(0) + fig.colors[num-1] = colormap[color] + self.draw() + + # -------------------------------------------------------------------- + # draw a plot with all its settings + # just return if no files of vectors defined yet + + def draw(self): + fig = self.figures[self.current-1] + if not fig.ncurves: return + + cmd = 'set size ratio ' + str(1.0/float(fig.aspect)) + self.__call__(cmd) + + cmd = 'set title ' + '"' + fig.title + '"' + self.__call__(cmd) + cmd = 'set xlabel ' + '"' + fig.xtitle + '"' + self.__call__(cmd) + cmd = 'set ylabel ' + '"' + fig.ytitle + '"' + self.__call__(cmd) + + if fig.xlog: self.__call__("set logscale x") + else: self.__call__("unset logscale x") + if fig.ylog: self.__call__("set logscale y") + else: self.__call__("unset logscale y") + if fig.xlimit: + cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']' + self.__call__(cmd) + else: self.__call__("set xr [*:*]") + if fig.ylimit: + cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']' + self.__call__(cmd) + else: self.__call__("set yr [*:*]") + + self.__call__("set nolabel") + for i in range(fig.nlabels): + x = fig.labels[i][0] + y = fig.labels[i][1] + text = fig.labels[i][2] + cmd = 'set label ' + '\"' + text + '\" at ' + str(x) + ',' + str(y) + self.__call__(cmd) + + self.__call__("set key off") + cmd = 'plot ' + for i in range(fig.ncurves): + file = self.file + ".%d.%d" % (self.current,i+1) + if len(fig.colors) > i and fig.colors[i]: + cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i] + else: + cmd += "'" + file + "' using 1:2 with lines, " + self.__call__(cmd[:-2]) + +# -------------------------------------------------------------------- +# class to store settings for a single plot + +class figure: + + def __init__(self): + self.ncurves = 0 + self.colors = [] + self.title = "" + self.xtitle = "" + self.ytitle = "" + self.aspect = 1.3 + self.xlimit = 0 + self.ylimit = 0 + self.xlog = 0 + self.ylog = 0 + self.nlabels = 0 + self.labels = [] + +# -------------------------------------------------------------------- +# line color settings + +colormap = {'k':-1, 'r':1, 'g':2, 'b':3, 'm':4, 'c':5, 'y':7} diff --git a/src/gnu.pyc b/src/gnu.pyc new file mode 100644 index 0000000..0e9ec3f Binary files /dev/null and b/src/gnu.pyc differ diff --git a/src/histo.py b/src/histo.py new file mode 100644 index 0000000..f1bd621 --- /dev/null +++ b/src/histo.py @@ -0,0 +1,86 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# histo tool + +oneline = "Particle density histogram from a dump" + +docstr = """ +h = histo(d) d = dump/cdump object + +x,y = h.compute('x',N,lo,hi) compute histogram in dim with N bins + + lo/hi are optional, if not used histo will be over entire box +""" + +# History +# 12/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# data = dump object + +# Imports and external programs + +# Class definition + +class histo: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def compute(self,dim,nbins,lo=None,hi=None): + if dim == 'x': idim = 2 + elif dim == 'y': idim = 3 + elif dim == 'z': idim = 4 + else: raise StandardError,"illegal dim value" + + y = nbins*[0] + + count = 0 + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + if not lo: + if dim == 'x': + lo = box[0] + hi = box[3] + elif dim == 'y': + lo = box[1] + hi = box[4] + elif dim == 'z': + lo = box[2] + hi = box[5] + + delta = (hi-lo) / nbins; + invdelta = 1.0/delta + + for atom in atoms: + coord = atom[idim] + ibin = int((coord-lo) * invdelta) + if ibin < 0 or ibin >= nbins: continue + y[ibin] += 1 + count += 1 + + n += 1 + + x = nbins*[0] + for i in xrange(nbins): x[i] = (i+0.5)*delta + + print "histogram snapshots = ",n + print "histogram counts (per snap) = %d (%g)" % (count,float(count)/n) + print "histogram bounds = ",lo,hi + return x,y diff --git a/src/histo.pyc b/src/histo.pyc new file mode 100644 index 0000000..9692190 Binary files /dev/null and b/src/histo.pyc differ diff --git a/src/image.py b/src/image.py new file mode 100644 index 0000000..f8611b5 --- /dev/null +++ b/src/image.py @@ -0,0 +1,233 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# image tool + +oneline = "View and manipulate images" + +docstr = """ +i = image("my1.gif my2.gif") display thumbnails of matching images +i = image("*.png *.gif") wildcards allowed +i = image("") blank string matches all image suffixes +i = image() no display window opened if no arg + + image suffixes for blank string = *.png, *.bmp, *.gif, *.tiff, *.tif + click on a thumbnail to view it full-size + click on thumbnail again to remove full-sized version + +i.view("*.png *.gif") display thumbnails of matching images + + view arg is same as constructor arg + +i.convert("image*.svg","new*.png") each SVG file to PNG +i.convert("image*.svg","new*.jpg","-quality 50") 3rd arg is switch +i.convert("image*.png","movie.mpg") all PNGs to MPG movie +i.convert("image*.png","movie.mpg","-resize 128x128") 3rd arg is switch +i.montage("","image*.png","plot*.png","two*.png") image + plot = two +i.montage("-geometry 512x512","i*.png","new.png") 1st arg is switch + + convert with 2 wildcard args loops over 1st set of files to make 2nd set + convert with not all wildcard args will issue single convert command + montage with all wildcard args loops over 1st set of files, + combines with one file from other sets, to make last set of files + montage with not all wildcard args will issue single montage command +""" + +# History +# 8/05, Matt Jones (BYU): original version +# 9/05, Steve Plimpton: added convert() and montage() methods + +# ToDo list + +# Variables + +# Imports and external programs + +import sys, os, commands, re, glob +from math import * +from Tkinter import * +import Pmw +import Image,ImageTk + +try: from DEFAULTS import PIZZA_CONVERT +except: PIZZA_CONVERT = "convert" +try: from DEFAULTS import PIZZA_MONTAGE +except: PIZZA_MONTAGE = "montage" + +# Class definition + +class image: + + # -------------------------------------------------------------------- + + def __init__(self,filestr=None): + if filestr == None: return + self.view(filestr) + + def view(self,filestr): + + # convert filestr into full list of files + + if filestr == "": filestr = ' '.join(extensions) + list = str.split(filestr) + files = [] + for file in list: files += glob.glob(file) + if len(files) == 0: raise StandardError, "no image files to load" + + # grab Tk instance from main + + from __main__ import tkroot + + # GUI control window + + gui = Toplevel(tkroot) + gui.title('Pizza.py image tool') + + scroll = \ + Pmw.ScrolledFrame(gui,usehullsize=1,hull_width=420,hull_height=500) + pane = scroll.interior() + + ncolumns = 4 + for i in xrange(len(files)): + + # create new row frame if 1st in column + + if i % ncolumns == 0: rowframe = Frame(pane) + oneframe = Frame(rowframe) + + # create a thumbnail of image + + im = Image.open(files[i]) + imt = im.copy() + imt.thumbnail((60,60),Image.ANTIALIAS) + basename = os.path.basename(files[i]) + imt.save("tmp." + basename) + thumbnail = ImageTk.PhotoImage(file = "tmp." + basename) + os.remove("tmp." + basename) + + # read in full size image + # create a thumbnail object that links to it + # create button that calls the thumbnail, label with filename + # buttton needs to store thumbnail else it is garbage collected + + big = ImageTk.PhotoImage(file=files[i]) + obj = thumbnails(gui,files[i],big,thumbnail) + Button(oneframe,image=thumbnail,command=obj.display).pack(side=TOP) + Label(oneframe,text=basename).pack(side=BOTTOM) + + # pack into row frame + + oneframe.pack(side=LEFT) + if (i+1) % ncolumns == 0: rowframe.pack(side=TOP) + + if len(files) % ncolumns != 0: rowframe.pack(side=TOP) + scroll.pack(side=LEFT) + + # -------------------------------------------------------------------- + # wrapper on ImageMagick convert command + + def convert(self,file1,file2,switch=""): + if file1.find('*') < 0 or file2.find('*') < 0: + cmd = "%s %s %s %s" % (PIZZA_CONVERT,switch,file1,file2) + commands.getoutput(cmd) + return + + index = file1.index('*') + pre1 = file1[:index] + post1 = file1[index+1:] + index = file2.index('*') + pre2 = file2[:index] + post2 = file2[index+1:] + expr = "%s(.*)%s" % (pre1,post1) + + filelist = glob.glob(file1) + for file1 in filelist: + middle = re.search(expr,file1).group(1) + file2 = "%s%s%s" % (pre2,middle,post2) + cmd = "%s %s %s %s" % (PIZZA_CONVERT,switch,file1,file2) + print middle, + sys.stdout.flush() + commands.getoutput(cmd) + print + + # -------------------------------------------------------------------- + # wrapper on ImageMagick montage command + + def montage(self,switch,*fileargs): + nsets = len(fileargs) + if nsets < 2: raise StandardError,"montage requires 2 or more file args" + + for i in range(nsets): + if fileargs[i].find('*') < 0: + cmd = "%s %s" % (PIZZA_MONTAGE,switch) + for j in range(nsets): cmd += " %s" % fileargs[j] + commands.getoutput(cmd) + return + + nfiles = len(glob.glob(fileargs[0])) + filesets = [] + for i in range(nsets-1): + filesets.append(glob.glob(fileargs[i])) + if len(filesets[-1]) != nfiles: + raise StandardError,"each montage arg must represent equal # of files" + + index = fileargs[0].index('*') + pre1 = fileargs[0][:index] + post1 = fileargs[0][index+1:] + index = fileargs[-1].index('*') + preN = fileargs[-1][:index] + postN = fileargs[-1][index+1:] + expr = "%s(.*)%s" % (pre1,post1) + + for i in range(nfiles): + cmd = "%s %s" % (PIZZA_MONTAGE,switch) + for j in range(nsets-1): cmd += " %s" % filesets[j][i] + middle = re.search(expr,filesets[0][i]).group(1) + fileN = "%s%s%s" % (preN,middle,postN) + cmd += " %s" % fileN + commands.getoutput(cmd) + print middle, + sys.stdout.flush() + print + +# -------------------------------------------------------------------- +# thumbnail class + +class thumbnails: + + def __init__(self,root,name,bigimage,thumbimage): + self.root = root + self.big = bigimage + self.thumb = thumbimage + self.name = name + self.bigexist = 0 + self.window = None + + def display(self): + + # destroy the big image window + + if self.bigexist: + self.bigexist = 0 + if self.window: + self.window.destroy() + self.window = None + + # create a new window with the big image + + else: + self.bigexist = 1 + self.window = Toplevel(self.root) + Label(self.window,text=self.name).pack(side=TOP) + Label(self.window,image=self.big).pack(side=BOTTOM) + +# -------------------------------------------------------------------- +# list of file extensions to test for +# could add any extensions that PIL recognizes + +extensions = ["*.png", "*.bmp", "*.gif", "*.tiff", "*.tif"] diff --git a/src/image.pyc b/src/image.pyc new file mode 100644 index 0000000..223061b Binary files /dev/null and b/src/image.pyc differ diff --git a/src/ldump.py b/src/ldump.py new file mode 100644 index 0000000..30bf1bf --- /dev/null +++ b/src/ldump.py @@ -0,0 +1,341 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# ldump tool + +oneline = "Read dump files with line segment info" + +docstr = """ +l = ldump("dump.one") read in one or more dump files +l = ldump("dump.1 dump.2.gz") can be gzipped +l = ldump("dump.*") wildcard expands to multiple files +l = ldump("dump.*",0) two args = store filenames, but don't read + + incomplete and duplicate snapshots are deleted + no column name assignment is performed + +time = l.next() read next snapshot from dump files + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed + +l.map(1,"id",3,"x") assign names to atom columns (1-N) + + must assign id,type,end1x,end1y,end2x,end2y + +time,box,atoms,bonds,tris,lines = l.viz(index) return list of viz objects + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = NULL + bonds = NULL + tris = NULL + lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array + id,type are from associated atom + +l.owrap(...) wrap lines to same image as their atoms + + owrap() is called by dump tool's owrap() + useful for wrapping all molecule's atoms/lines the same so it is contiguous +""" + +# History +# 11/10, Steve Plimpton (SNL): original version + +# Variables +# flist = list of dump file names +# increment = 1 if reading snapshots one-at-a-time +# nextfile = which file to read from via next() +# eof = ptr into current file for where to read via next() +# nsnaps = # of snapshots +# snaps = list of snapshots +# names = dictionary of column names: +# key = "id", value = column # (0 to M-1) +# Snap = one snapshot +# time = time stamp +# natoms = # of atoms +# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float) +# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1 + +# Imports and external programs + +import sys, commands, re, glob, types +from os import popen + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class ldump: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.snaps = [] + self.nsnaps = 0 + self.names = {} + + # flist = list of all dump file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no ldump file specified" + + if len(list) == 1: + self.increment = 0 + self.read_all() + else: + self.increment = 1 + self.nextfile = 0 + self.eof = 0 + + # -------------------------------------------------------------------- + + def read_all(self): + + # read all snapshots from each file + # test for gzipped files + + for file in self.flist: + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + snap = self.read_snapshot(f) + while snap: + self.snaps.append(snap) + print snap.time, + sys.stdout.flush() + snap = self.read_snapshot(f) + + f.close() + print + + # sort entries by timestep, cull duplicates + + self.snaps.sort(self.compare_time) + self.cull() + self.nsnaps = len(self.snaps) + print "read %d snapshots" % self.nsnaps + + # -------------------------------------------------------------------- + # read next snapshot from list of files + + def next(self): + + if not self.increment: raise StandardError,"cannot read incrementally" + + # read next snapshot in current file using eof as pointer + # if fail, try next file + # if new snapshot time stamp already exists, read next snapshot + + while 1: + f = open(self.flist[self.nextfile],'rb') + f.seek(self.eof) + snap = self.read_snapshot(f) + if not snap: + self.nextfile += 1 + if self.nextfile == len(self.flist): return -1 + f.close() + self.eof = 0 + continue + self.eof = f.tell() + f.close() + try: + self.findtime(snap.time) + continue + except: break + + self.snaps.append(snap) + snap = self.snaps[self.nsnaps] + self.nsnaps += 1 + + return snap.time + + # -------------------------------------------------------------------- + # read a single snapshot from file f + # return snapshot or 0 if failed + + def read_snapshot(self,f): + try: + snap = Snap() + item = f.readline() + snap.time = int(f.readline().split()[0]) # just grab 1st field + item = f.readline() + snap.natoms = int(f.readline()) + + item = f.readline() + words = f.readline().split() + snap.xlo,snap.xhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.ylo,snap.yhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.zlo,snap.zhi = float(words[0]),float(words[1]) + + item = f.readline() + + if snap.natoms: + words = f.readline().split() + ncol = len(words) + for i in xrange(1,snap.natoms): + words += f.readline().split() + floats = map(float,words) + if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float) + else: atoms = np.zeros((snap.natoms,ncol),np.float) + start = 0 + stop = ncol + for i in xrange(snap.natoms): + atoms[i] = floats[start:stop] + start = stop + stop += ncol + else: atoms = None + snap.atoms = atoms + return snap + except: + return 0 + + # -------------------------------------------------------------------- + # map atom column names + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "ldump map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # -------------------------------------------------------------------- + # return vector of snapshot time stamps + + def time(self): + vec = self.nsnaps * [0] + i = 0 + for snap in self.snaps: + vec[i] = snap.time + i += 1 + return vec + + # -------------------------------------------------------------------- + # sort snapshots on time stamp + + def compare_time(self,a,b): + if a.time < b.time: + return -1 + elif a.time > b.time: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + + def findtime(self,n): + for i in xrange(self.nsnaps): + if self.snaps[i].time == n: return i + raise StandardError, "no step %d exists" % n + + # -------------------------------------------------------------------- + # delete successive snapshots with duplicate time stamp + + def cull(self): + i = 1 + while i < len(self.snaps): + if self.snaps[i].time == self.snaps[i-1].time: + del self.snaps[i] + else: + i += 1 + + # -------------------------------------------------------------------- + # return list of lines to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] + + time = snap.time + box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi] + id = self.names["id"] + type = self.names["type"] + end1x = self.names["end1x"] + end1y = self.names["end1y"] + end2x = self.names["end2x"] + end2y = self.names["end2y"] + + # create line list from id,type,end1x,end1y,end2x,end2y + # don't add line if all 4 values are 0 since not a line + + lines = [] + for i in xrange(snap.natoms): + atom = snap.atoms[i] + e1x = atom[end1x] + e1y = atom[end1y] + e2x = atom[end2x] + e2y = atom[end2y] + if e1x == 0.0 and e1y == 0.0 and e2x == 0.0 and e2y == 0.0: continue + lines.append([atom[id],atom[type],e1x,e1y,0.0,e2x,e2y,0.0]) + + return time,box,None,None,None,lines + + # -------------------------------------------------------------------- + # wrap line end points associated with atoms thru periodic boundaries + # invoked by dump() when it does an owrap() on its atoms + + def owrap(self,time,xprd,yprd,zprd,idsdump,atomsdump,iother,ix,iy,iz): + id = self.names["id"] + end1x = self.names["end1x"] + end1y = self.names["end1y"] + end2x = self.names["end2x"] + end2y = self.names["end2y"] + + isnap = self.findtime(time) + snap = self.snaps[isnap] + atoms = snap.atoms + + # idump = index of my line I in dump's atoms + # jdump = atom J in dump's atoms that atom I was owrapped on + # delx,dely = offset applied to atom I and thus to line I + + for i in xrange(snap.natoms): + tag = atoms[i][id] + idump = idsdump[tag] + jdump = idsdump[atomsdump[idump][iother]] + delx = (atomsdump[idump][ix]-atomsdump[jdump][ix])*xprd + dely = (atomsdump[idump][iy]-atomsdump[jdump][iy])*yprd + atoms[i][end1x] += delx + atoms[i][end1y] += dely + atoms[i][end2x] += delx + atoms[i][end2y] += dely + +# -------------------------------------------------------------------- +# one snapshot + +class Snap: + pass diff --git a/src/ldump.pyc b/src/ldump.pyc new file mode 100644 index 0000000..e9dd207 Binary files /dev/null and b/src/ldump.pyc differ diff --git a/src/log.py b/src/log.py new file mode 100644 index 0000000..7020c21 --- /dev/null +++ b/src/log.py @@ -0,0 +1,334 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# log tool + +oneline = "Read LAMMPS log files and extract thermodynamic data" + +docstr = """ +l = log("file1") read in one or more log files +l = log("log1 log2.gz") can be gzipped +l = log("file*") wildcard expands to multiple files +l = log("log.lammps",0) two args = store filename, but don't read + + incomplete and duplicate thermo entries are deleted + +time = l.next() read new thermo info from file + + used with 2-argument constructor to allow reading thermo incrementally + return time stamp of last thermo read + return -1 if no new thermo since last read + +nvec = l.nvec # of vectors of thermo info +nlen = l.nlen length of each vectors +names = l.names list of vector names +t,pe,... = l.get("Time","KE",...) return one or more vectors of values +l.write("file.txt") write all vectors to a file +l.write("file.txt","Time","PE",...) write listed vectors to a file + + get and write allow abbreviated (uniquely) vector names +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# nvec = # of vectors +# nlen = length of each vector +# names = list of vector names +# ptr = dictionary, key = name, value = index into data for which column +# data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1 +# style = style of LAMMPS log file, 1 = multi, 2 = one, 3 = gran +# firststr = string that begins a thermo section in log file +# increment = 1 if log file being read incrementally +# eof = ptr into incremental file for where to start next read + +# Imports and external programs + +import sys, re, glob +from os import popen + +try: tmp = PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class log: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.nvec = 0 + self.names = [] + self.ptr = {} + self.data = [] + + # flist = list of all log file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no log file specified" + + if len(list) == 1: + self.increment = 0 + self.read_all() + else: + if len(self.flist) > 1: + raise StandardError,"can only incrementally read one log file" + self.increment = 1 + self.eof = 0 + + # -------------------------------------------------------------------- + # read all thermo from all files + + def read_all(self): + self.read_header(self.flist[0]) + if self.nvec == 0: raise StandardError,"log file has no values" + + # read all files + + for file in self.flist: self.read_one(file) + print + + # sort entries by timestep, cull duplicates + + self.data.sort(self.compare) + self.cull() + self.nlen = len(self.data) + print "read %d log entries" % self.nlen + + # -------------------------------------------------------------------- + + def next(self): + if not self.increment: raise StandardError,"cannot read incrementally" + + if self.nvec == 0: + try: open(self.flist[0],'r') + except: return -1 + self.read_header(self.flist[0]) + if self.nvec == 0: return -1 + + self.eof = self.read_one(self.flist[0],self.eof) + return int(self.data[-1][0]) + + # -------------------------------------------------------------------- + + def get(self,*keys): + if len(keys) == 0: + raise StandardError, "no log vectors specified" + + map = [] + for key in keys: + if self.ptr.has_key(key): + map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique log vector %s not found" % key + + vecs = [] + for i in range(len(keys)): + vecs.append(self.nlen * [0]) + for j in xrange(self.nlen): + vecs[i][j] = self.data[j][map[i]] + + if len(keys) == 1: return vecs[0] + else: return vecs + + # -------------------------------------------------------------------- + + def write(self,filename,*keys): + if len(keys): + map = [] + for key in keys: + if self.ptr.has_key(key): + map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique log vector %s not found" % key + else: + map = range(self.nvec) + + f = open(filename,"w") + for i in xrange(self.nlen): + for j in xrange(len(map)): + print >>f,self.data[i][map[j]], + print >>f + f.close() + + # -------------------------------------------------------------------- + + def compare(self,a,b): + if a[0] < b[0]: + return -1 + elif a[0] > b[0]: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + + def cull(self): + i = 1 + while i < len(self.data): + if self.data[i][0] == self.data[i-1][0]: del self.data[i] + else: i += 1 + + # -------------------------------------------------------------------- + + def read_header(self,file): + str_multi = "----- Step" + str_one = "Step " + + if file[-3:] == ".gz": + txt = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r').read() + else: + txt = open(file).read() + + if txt.find(str_multi) >= 0: + self.firststr = str_multi + self.style = 1 + elif txt.find(str_one) >= 0: + self.firststr = str_one + self.style = 2 + else: + return + + if self.style == 1: + s1 = txt.find(self.firststr) + s2 = txt.find("\n--",s1) + pattern = "\s(\S*)\s*=" + keywords = re.findall(pattern,txt[s1:s2]) + keywords.insert(0,"Step") + i = 0 + for keyword in keywords: + self.names.append(keyword) + self.ptr[keyword] = i + i += 1 + + else: + s1 = txt.find(self.firststr) + s2 = txt.find("\n",s1) + line = txt[s1:s2] + words = line.split() + for i in range(len(words)): + self.names.append(words[i]) + self.ptr[words[i]] = i + + self.nvec = len(self.names) + + # -------------------------------------------------------------------- + + def read_one(self,*list): + + # if 2nd arg exists set file ptr to that value + # read entire (rest of) file into txt + + file = list[0] + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb') + else: + f = open(file,'rb') + + if len(list) == 2: f.seek(list[1]) + txt = f.read() + if file[-3:] == ".gz": eof = 0 + else: eof = f.tell() + f.close() + + start = last = 0 + while not last: + + # chunk = contiguous set of thermo entries (line or multi-line) + # s1 = 1st char on 1st line of chunk + # s2 = 1st char on line after chunk + # set last = 1 if this is last chunk in file, leave 0 otherwise + # set start = position in file to start looking for next chunk + # rewind eof if final entry is incomplete + + s1 = txt.find(self.firststr,start) + s2 = txt.find("Loop time of",start+1) + + if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2 + if self.style == 2: + s1 = txt.find("\n",s1) + 1 + elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1 + s1 = 0 + elif s1 == -1 and s2 >= 0: # found s2, but no s1 + last = 1 + s1 = 0 + elif s1 >= 0 and s2 == -1: # found s1, but no s2 + last = 1 + if self.style == 1: + s2 = txt.rfind("\n--",s1) + 1 + else: + s1 = txt.find("\n",s1) + 1 + s2 = txt.rfind("\n",s1) + 1 + eof -= len(txt) - s2 + elif s1 == -1 and s2 == -1: # found neither + # could be end-of-file section + # or entire read was one chunk + + if txt.find("Loop time of",start) == start: # end of file, so exit + eof -= len(txt) - start # reset eof to "Loop" + break + + last = 1 # entire read is a chunk + s1 = 0 + if self.style == 1: + s2 = txt.rfind("\n--",s1) + 1 + else: + s2 = txt.rfind("\n",s1) + 1 + eof -= len(txt) - s2 + if s1 == s2: break + + chunk = txt[s1:s2-1] + start = s2 + + # split chunk into entries + # parse each entry for numeric fields, append to data + + if self.style == 1: + sections = chunk.split("\n--") + pat1 = re.compile("Step\s*(\S*)\s") + pat2 = re.compile("=\s*(\S*)") + for section in sections: + word1 = [re.search(pat1,section).group(1)] + word2 = re.findall(pat2,section) + words = word1 + word2 + self.data.append(map(float,words)) + + else: + lines = chunk.split("\n") + for line in lines: + words = line.split() + self.data.append(map(float,words)) + + # print last timestep of chunk + + print int(self.data[len(self.data)-1][0]), + sys.stdout.flush() + + return eof diff --git a/src/log.pyc b/src/log.pyc new file mode 100644 index 0000000..d454f4b Binary files /dev/null and b/src/log.pyc differ diff --git a/src/lpp.py b/src/lpp.py new file mode 100644 index 0000000..3665e49 --- /dev/null +++ b/src/lpp.py @@ -0,0 +1,183 @@ +oneline = "writing pp-data in vtk format automatically, saving memory" + +docstr = """this is the docstr of LIGGGHTSPostProcessing""" + +from dump import dump +from math import floor +from math import ceil +from vtk import vtk +import glob +import multiprocessing +import sys +import time +import os +import exceptions +# changes py p.s. - include a few command line options +import getopt + +class lpp: + + #============================================================================= + # creates a filelist, seperates it to sublists + # creates multiple processes + # calls lppWorker for each sublist + # lppWorker + # calls dump, vtk and manyGran for the given list of files + # returns 0 + #============================================================================= + + def __init__(self, *list, **kwargs): + # do argument parsing, raise errors if non-integers were given + # this can be changed if one wants less overhead but use more memory: + # make this figure higher but if possible a multiple of 8 + self.cpunum = multiprocessing.cpu_count() + self.chunksize = 8 + + if "--chunksize" in kwargs: + try: + if int(kwargs["--chunksize"]) > 0: + self.chunksize = int(kwargs["--chunksize"]) + else: raise ValueError + except ValueError: + raise ValueError, "Invalid or no argument given for chunksize" + + if "--cpunum" in kwargs: + try: + if int(kwargs["--cpunum"]) > 0 and int(kwargs["--cpunum"]) <= self.cpunum: + self.cpunum = int(kwargs["--cpunum"]) + else: raise ValueError + except ValueError: + raise ValueError, "Invalid or no argument given for cpunum" + + + # suppress output with 'False' + if "--debug" in kwargs: self.debugMode = True + else: self.debugMode = False + + if "--quiet" in kwargs: + self.output = False + self.debugMode = False + else: self.output = True + + if self.output: + print "starting LIGGGHTS memory optimized parallel post processing" + print "chunksize:", self.chunksize, "-->",self.chunksize,\ + "files are processed per chunk. If you run out of memory reduce chunksize." + starttime = time.time() + + if self.debugMode: print "number of process:", os.getpid() + + # check whether file-list is nonempty + self.flist = list[0] + if len(self.flist) == 0 and len(list) == 1: + raise StandardError, "no dump file specified" + + if self.output: + print "Working with", self.cpunum, "processes..." + + # seperate list in pieces of 96+rest + listlen = len(self.flist) + self.slices = [] + + residualPresent = int(bool(listlen-floor(listlen/self.chunksize)*self.chunksize)) + + for i in xrange(int(floor(listlen/self.chunksize))+residualPresent): + slice = self.flist[i*self.chunksize:(i+1)*self.chunksize] + self.slices.append(slice) + self.flist = [] + + output = "" + if "-o" in kwargs: output = kwargs["-o"] + # generate input for lppWorker + dumpInput = [{"filelist":self.slices[i],\ + "debugMode":self.debugMode,"output":output} for i in xrange(len(self.slices))] + + numberOfRuns = len(dumpInput) + i = 0 + while i < len(dumpInput): + + if self.output: + print "calculating chunks",i+1,"-",min(i+self.cpunum,numberOfRuns),"of",numberOfRuns + + if self.debugMode: print "input of this \"map\": ",dumpInput[i:i+self.cpunum] + + # create job_server + job_server = multiprocessing.Pool(processes = self.cpunum) + + # map lppWorker on all inputs via job_server (parallelly) + job_server.map(lppWorker,dumpInput[i:i+self.cpunum]) + + # close jobserver + job_server.close() + i += self.cpunum + + endtime = time.time() + if self.output: + print "wrote", listlen,"granular snapshots in VTK format" + print "time needed:",endtime-starttime,"sec" + +def lppWorker(input): + flist = input["filelist"] + debugMode = input["debugMode"] + outfileName = input["output"] + #print "number of subprocess:", os.getpid() + #print flist,"\n\n" + + flistlen = len(flist) + splitfname = flist[0].rsplit(".") + if outfileName == "": + # generate name of manyGran + granName = splitfname[len(splitfname)-1] + elif outfileName.endswith("/"): + granName = outfileName + splitfname[len(splitfname)-1] + else: + granName = outfileName + + # call dump, vtk, manyGran + try: + d = dump({"filelist":flist, "debugMode":debugMode}) + v = vtk(d) + if debugMode: print "\nfileNums: ",d.fileNums,"\n" + v.manyGran(granName,fileNos=d.fileNums,output=debugMode) + except KeyboardInterrupt: + raise + + return 0 + +def printHelp(): + print "usage: pizza [options] dump.example\n where dump.example is a filename",\ + "or regular expression passing all relevant dump files to pizza." + print "Important command line options:" + print "-o fname : define output file name (default is liggghts + timestep number)" + print "--chunksize : sets the chunksize, default: 8" + print "--cpunum : sets the number of processes to start, default (and maximum)",\ + "is the amout of cpu cores avaliable at your system" + print "--help : writes this help message and exits" + print "For details, read README_GRANULAR.txt" + +if __name__ == "__main__": + if len(sys.argv) > 1: + # parse options + optlist, args = getopt.gnu_getopt(sys.argv[1:],'o:',['chunksize=','cpunum=','debug','help','quiet']) + optdict = dict(optlist) + if "--help" in optdict: + printHelp() + else: + try: + lpp(args,**optdict) + except KeyboardInterrupt: + print "aborted by user" + except BaseException, e: + print "aborting due to errors:", e + + #=========================================================================== + # except: + # if sys.exc_type == exceptions.SystemExit: + # pass + # else: + # print sys.exc_info() + #=========================================================================== + else: + printHelp() + + diff --git a/src/lpp.pyc b/src/lpp.pyc new file mode 100644 index 0000000..7775407 Binary files /dev/null and b/src/lpp.pyc differ diff --git a/src/matlab.py b/src/matlab.py new file mode 100644 index 0000000..9cde9b0 --- /dev/null +++ b/src/matlab.py @@ -0,0 +1,379 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# matlab tool + +oneline = "Create plots via MatLab numerical analysis program" + +docstr = """ +m = matlab() start up MatLab +m.stop() shut down MatLab process + +m.plot(a) plot vector A against linear index +m.plot(a,b) plot B against A +m.plot(a,b,c,d,...) plot B against A, D against C, etc +m.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc + + each plot argument can be a tuple, list, or Numeric/NumPy vector + mplot loops over range(M,N,S) and create one plot per iteration + last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors + each plot is made from a portion of the vectors, depending on loop index i + Ith plot is of b[0:i] vs a[0:i], etc + series of plots saved as file0000.eps, file0001.eps, etc + if use xrange(),yrange() then plot axes will be same for all plots + +m("c = a + b") execute string in MatLab + +m.enter() enter MatLab shell +matlab> c = a + b type commands directly to MatLab +matlab> exit, quit exit MatLab shell + +m.export("data",range(100),a,...) create file with columns of numbers + + all vectors must be of equal length + could plot from file with MatLab commands: + cols = importdata('data') + plot(cols(:,1),cols(:,2)) + +m.select(N) figure N becomes the current plot + + subsequent commands apply to this plot + +m.hide(N) delete window for figure N +m.save("file") save current plot as file.eps + +Set attributes for current plot: + +m.erase() reset all attributes to default values +m.aspect(1.3) aspect ratio +m.xtitle("Time") x axis text +m.ytitle("Energy") y axis text +m.title("My Plot") title text +m.title("title","x","y") title, x axis, y axis text +m.xrange(xmin,xmax) x axis range +m.xrange() default x axis range +m.yrange(ymin,ymax) y axis range +m.yrange() default y axis range +m.xlog() toggle x axis between linear and log +m.ylog() toggle y axis between linear and log +m.label(x,y,"text") place label at x,y coords +m.curve(N,'r') set color of curve N +m.curve(N,'g','--') set color and line style of curve N +m.curve(N,'b','-','v') set color, line style, symbol of curve N + + colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue + 'm' = magenta, 'c' = cyan, 'y' = yellow + styles: '-' = solid, '--' = dashed, ':' = dotted, '-.' = dash-dot + symbols: '+' = plus, 'o' = circle, '*' = asterik, 'x' = X, + 's' = square, 'd' = diamond, '^' = up triangle, + 'v' = down triangle, '>' = right triangle, + '<' = left triangle, 'p' = pentagram, 'h' = hexagram +""" + +# History +# 8/05, Matt Jones (BYU): original version + +# ToDo list +# allow choice of JPG or PNG or GIF when saving via "saveas" command +# have vec/array import/export functions to pass variables between +# Pizza.py and MatLab and have them named in MatLab + +# Variables +# current = index of current figure (1-N) +# figures = list of figure objects with each plot's attributes +# so they aren't lost between replots +# import command to yank MatLab variables back to Python +# allow for alternate export command to name the variables from Python +# in MatLab and vice versa + +# Imports and external programs + +import types, os + +try: from DEFAULTS import PIZZA_MATLAB +except: PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm" + +# Class definition + +class matlab: + + # -------------------------------------------------------------------- + + def __init__(self): + self.MATLAB = os.popen(PIZZA_MATLAB,'w') + self.file = "tmp.matlab" + self.figures = [] + self.select(1) + + # -------------------------------------------------------------------- + + def stop(self): + self.__call__("quit") + del self.MATLAB + + # -------------------------------------------------------------------- + + def __call__(self,command): + self.MATLAB.write(command + '\n') + self.MATLAB.flush() + + # -------------------------------------------------------------------- + + def enter(self): + while 1: + command = raw_input("matlab> ") + if command == "quit" or command == "exit": return + self.__call__(command) + + # -------------------------------------------------------------------- + # write plot vectors to files and plot them + + def plot(self,*vectors): + if len(vectors) == 1: + file = self.file + ".%d.1" % self.current + linear = range(len(vectors[0])) + self.export(file,linear,vectors[0]) + self.figures[self.current-1].ncurves = 1 + else: + if len(vectors) % 2: raise StandardError,"vectors must come in pairs" + for i in range(0,len(vectors),2): + file = self.file + ".%d.%d" % (self.current,i/2+1) + self.export(file,vectors[i],vectors[i+1]) + self.figures[self.current-1].ncurves = len(vectors)/2 + self.draw() + + # -------------------------------------------------------------------- + # create multiple plots from growing vectors, save to numbered files + # don't plot empty vector, create a [0] instead + + def mplot(self,start,stop,skip,file,*vectors): + n = 0 + for i in range(start,stop,skip): + partial_vecs = [] + for vec in vectors: + if i: partial_vecs.append(vec[:i]) + else: partial_vecs.append([0]) + self.plot(*partial_vecs) + + if n < 10: newfile = file + "000" + str(n) + elif n < 100: newfile = file + "00" + str(n) + elif n < 1000: newfile = file + "0" + str(n) + else: newfile = file + str(n) + + self.save(newfile) + n += 1 + + # -------------------------------------------------------------------- + # write list of equal-length vectors to filename + + def export(self,filename,*vectors): + n = len(vectors[0]) + for vector in vectors: + if len(vector) != n: raise StandardError,"vectors must be same length" + f = open(filename,'w') + nvec = len(vectors) + for i in xrange(n): + for j in xrange(nvec): + print >>f,vectors[j][i], + print >>f + f.close() + + # -------------------------------------------------------------------- + # select plot N as current plot + + def select(self,n): + self.current = n + if len(self.figures) < n: + for i in range(n - len(self.figures)): + self.figures.append(figure()) + self.draw() + + # -------------------------------------------------------------------- + # delete window for plot N + + def hide(self,n): + cmd = "set(figure(%d),'Visible','off')" % n + self.__call__(cmd) + + # -------------------------------------------------------------------- + # save plot to file.eps + # do not continue until plot file is written out + # else script could go forward and change data file + # use tmp.done as semaphore to indicate plot is finished + + def save(self,file): + if os.path.exists("tmp.done"): os.remove("tmp.done") + cmd = "saveas(gcf,'%s.eps','psc2')" % file + self.__call__(cmd) + self.__call__("!touch tmp.done") + while not os.path.exists("tmp.done"): continue + + # -------------------------------------------------------------------- + # restore default attributes by creating a new fig object + + def erase(self): + fig = figure() + fig.ncurves = self.figures[self.current-1].ncurves + self.figures[self.current-1] = fig + self.draw() + + # -------------------------------------------------------------------- + + def aspect(self,value): + self.figures[self.current-1].aspect = value + self.draw() + + # -------------------------------------------------------------------- + + def xrange(self,*values): + if len(values) == 0: + self.figures[self.current-1].xlimit = 0 + else: + self.figures[self.current-1].xlimit = (values[0],values[1]) + self.draw() + + # -------------------------------------------------------------------- + + def yrange(self,*values): + if len(values) == 0: + self.figures[self.current-1].ylimit = 0 + else: + self.figures[self.current-1].ylimit = (values[0],values[1]) + self.draw() + + # -------------------------------------------------------------------- + + def label(self,x,y,text): + self.figures[self.current-1].labels.append((x,y,text)) + self.figures[self.current-1].nlabels += 1 + self.draw() + + # -------------------------------------------------------------------- + + def nolabels(self): + self.figures[self.current-1].nlabel = 0 + self.figures[self.current-1].labels = [] + self.draw() + + # -------------------------------------------------------------------- + + def title(self,*strings): + if len(strings) == 1: + self.figures[self.current-1].title = strings[0] + else: + self.figures[self.current-1].title = strings[0] + self.figures[self.current-1].xtitle = strings[1] + self.figures[self.current-1].ytitle = strings[2] + self.draw() + + # -------------------------------------------------------------------- + + def xtitle(self,label): + self.figures[self.current-1].xtitle = label + self.draw() + + # -------------------------------------------------------------------- + + def ytitle(self,label): + self.figures[self.current-1].ytitle = label + self.draw() + + # -------------------------------------------------------------------- + + def xlog(self): + if self.figures[self.current-1].xlog: + self.figures[self.current-1].xlog = 0 + else: + self.figures[self.current-1].xlog = 1 + self.draw() + + # -------------------------------------------------------------------- + + def ylog(self): + if self.figures[self.current-1].ylog: + self.figures[self.current-1].ylog = 0 + else: + self.figures[self.current-1].ylog = 1 + self.draw() + + # -------------------------------------------------------------------- + + def curve(self,num,*settings): + fig = self.figures[self.current-1] + while len(fig.curves) < num: fig.curves.append('') + value = settings[0] + if len(settings) >= 2: value += settings[1] + if len(settings) >= 3: value += settings[2] + fig.curves[num-1] = value + self.draw() + + # -------------------------------------------------------------------- + # draw a plot with all its settings + # just return if no files of vectors defined yet + + def draw(self): + fig = self.figures[self.current-1] + if not fig.ncurves: return + self.__call__("figure(%d)" % self.current) + + if not fig.xlog and not fig.ylog: cmd = "plot" + elif fig.xlog and not fig.ylog: cmd = "semilogx" + elif not fig.xlog and fig.ylog: cmd = "semilogy" + elif fig.xlog and fig.ylog: cmd = "loglog" + + cmd += '(' + for i in range(fig.ncurves): + file = self.file + ".%d.%d" % (self.current,i+1) + readcmd = "pizza%d = importdata('%s');" % (i+1,file) + self.__call__(readcmd) + if len(fig.curves) > i: + cmd += "pizza%d(:,1),pizza%d(:,2),'%s'," % (i+1,i+1,fig.curves[i]) + else: + cmd += "pizza%d(:,1),pizza%d(:,2),''," % (i+1,i+1) + cmd = cmd[:-1] + ",'LineWidth',1.5)" # kludge on line width for now + # problem is it applies to all curves + self.__call__(cmd) # should allow other attributes set + + cmd = "set(gca,'PlotBoxAspectRatio',[%g,1,1])" % float(fig.aspect) + self.__call__(cmd) + + # kludge to set title sizes + self.__call__("title('%s','FontSize',16)" % fig.title) + self.__call__("xlabel('%s','FontSize',16)" % fig.xtitle) + self.__call__("ylabel('%s','FontSize',16)" % fig.ytitle) + + if fig.xlimit == 0 or fig.ylimit == 0: self.__call__("axis auto") + if fig.xlimit: + self.__call__("xlim([%g,%g])" % (fig.xlimit[0],fig.xlimit[1])) + if fig.ylimit: + self.__call__("ylim([%g,%g])" % (fig.ylimit[0],fig.ylimit[1])) + + for i in range(fig.nlabels): + x = fig.labels[i][0] + y = fig.labels[i][1] + text = fig.labels[i][2] # kludge to set label font size + self.__call__("text(%g,%g,'%s','FontSize',16)" % (x,y,text)) + +# -------------------------------------------------------------------- +# class to store settings for a single plot + +class figure: + + def __init__(self): + self.ncurves = 0 + self.curves = [] + self.title = "" + self.xtitle = "" + self.ytitle = "" + self.aspect = 1.3 + self.xlimit = 0 + self.ylimit = 0 + self.xlog = 0 + self.ylog = 0 + self.nlabels = 0 + self.labels = [] diff --git a/src/matlab.pyc b/src/matlab.pyc new file mode 100644 index 0000000..ccf7ee6 Binary files /dev/null and b/src/matlab.pyc differ diff --git a/src/mdump.py b/src/mdump.py new file mode 100644 index 0000000..82c5dc6 --- /dev/null +++ b/src/mdump.py @@ -0,0 +1,903 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# mdump tool + +oneline = "Read, write, manipulate mesh dump files" + +docstr = """ +m = mdump("mesh.one") read in one or more mesh dump files +m = mdump("mesh.1 mesh.2.gz") can be gzipped +m = mdump("mesh.*") wildcard expands to multiple files +m = mdump("mesh.*",0) two args = store filenames, but don't read + + incomplete and duplicate snapshots are deleted + +time = m.next() read next snapshot from dump files + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment or unscaling is performed + +m.map(2,"temperature") assign names to element value columns (1-N) + +m.tselect.all() select all timesteps +m.tselect.one(N) select only timestep N +m.tselect.none() deselect all timesteps +m.tselect.skip(M) select every Mth step +m.tselect.test("$t >= 100 and $t < 10000") select matching timesteps +m.delete() delete non-selected timesteps + + selecting a timestep also selects all elements in the timestep + skip() and test() only select from currently selected timesteps + test() uses a Python Boolean expression with $t for timestep value + Python comparison syntax: == != < > <= >= and or + +m.eselect.all() select all elems in all steps +m.eselect.all(N) select all elems in one step +m.eselect.test("$id > 100 and $type == 2") select match elems in all steps +m.eselect.test("$id > 100 and $type == 2",N) select matching elems in one step + + all() with no args selects atoms from currently selected timesteps + test() with one arg selects atoms from currently selected timesteps + test() sub-selects from currently selected elements + test() uses a Python Boolean expression with $ for atom attributes + Python comparison syntax: == != < > <= >= and or + $name must end with a space + +t = m.time() return vector of selected timestep values +fx,fy,... = m.vecs(1000,"fx","fy",...) return vector(s) for timestep N + + vecs() returns vectors with one value for each selected elem in the timestep + +index,time,flag = m.iterator(0/1) loop over mesh dump snapshots +time,box,atoms,bonds,tris,lines = m.viz(index) return list of viz objects +nodes,elements,nvalues,evalues = m.mviz(index) return list of mesh viz objects +m.etype = "color" set column returned as "type" by viz + + iterator() loops over selected timesteps + iterator() called with arg = 0 first time, with arg = 1 on subsequent calls + index = index within dump object (0 to # of snapshots) + time = timestep value + flag = -1 when iteration is done, 1 otherwise + viz() returns info for selected elements for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = NULL + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array + each element is decomposed into tris + lines = NULL + mviz() returns info for all elements for specified timestep index + can also call as mviz(time,1) and will find index of preceding snapshot + time = timestep value + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + nodes = list of nodes = id,type,x,y,z + elements = list of elements = id,type,node1,node2,... + nvalues = list of node values = id,type,value1,value2,... + evalues = list of element values = id,type,value1,value2,... + etype is column name viz() will return as element type (def = "" = elem type) +""" + +# History +# 11/06, Steve Plimpton (SNL): original version +# 12/09, David Hart (SNL): allow use of NumPy or Numeric + +# Variables +# flist = list of dump file names +# increment = 1 if reading snapshots one-at-a-time +# nextfile = which file to read from via next() +# eof = ptr into current file for where to read via next() +# nsnaps = # of snapshots +# nselect = # of selected snapshots +# snaps = list of snapshots +# names = dictionary of column names: +# key = "id", value = column # (0 to M-1) +# tselect = class for time selection +# eselect = class for element selection +# etype = name of vector used as element type by viz extract (def = "") +# Snap = one snapshot +# time = time stamp +# tselect = 0/1 if this snapshot selected +# nflag = 0/1 if this snapshot has nodal coords (may be copies) +# eflag = 0/n if this snapshot has elements (may be copies) +# 1 = tri, 2 = tet, 3 = square, 4 = cube +# nvalueflag = 0/1 if this snapshot has nodal values +# evalueflag = 0/1 if this snapshot has element values +# nselect = # of selected elements in this snapshot +# eselect[i] = 0/1 for each element +# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float) +# nnodes = # of nodes +# nodes[i][j] = 2d array of floats, i = 0 to Nnod-1, j = 0 to Ncol +# nelements = # of elements +# elements[i][j] = 2d array of floats, i = 0 to Nel-1, j = 0 to Ncol +# nnvalues = # of node values +# nvalues[i][j] = 2d array of floats, i = 0 to Nnod-1, j = 0 to Ncol +# nevalues = # of node values +# evalues[i][j] = 2d array of floats, i = 0 to Nel-1, j = 0 to Ncol + +# Imports and external programs + +import sys, commands, re, glob, types +from os import popen +from math import * # any function could be used by set() + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class mdump: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.snaps = [] + self.nsnaps = self.nselect = 0 + self.names = {} + self.tselect = tselect(self) + self.eselect = eselect(self) + self.etype = "" + + # flist = list of all dump file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no dump file specified" + + if len(list) == 1: + self.increment = 0 + self.read_all() + else: + self.increment = 1 + self.nextfile = 0 + self.eof = 0 + + # -------------------------------------------------------------------- + + def read_all(self): + + # read all snapshots from each file + # test for gzipped files + + for file in self.flist: + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + snap = self.read_snapshot(f) + while snap: + self.snaps.append(snap) + print snap.time, + sys.stdout.flush() + snap = self.read_snapshot(f) + + f.close() + print + + # sort entries by timestep, cull and combine duplicates + + self.snaps.sort(self.compare_time) + self.cull() + + # sort all node, element, nvalue, evalue arrays by ID + + for snap in self.snaps: + if snap.nflag: + array = snap.nodes + ids = array[:,0] + ordering = np.argsort(ids) + for i in xrange(len(array[0])): + array[:,i] = np.take(array[:,i],ordering) + if snap.eflag: + array = snap.elements + ids = array[:,0] + ordering = np.argsort(ids) + for i in xrange(len(array[0])): + array[:,i] = np.take(array[:,i],ordering) + if snap.nvalueflag: + array = snap.nvalues + ids = array[:,0] + ordering = np.argsort(ids) + for i in xrange(len(array[0])): + array[:,i] = np.take(array[:,i],ordering) + if snap.evalueflag: + array = snap.evalues + ids = array[:,0] + ordering = np.argsort(ids) + for i in xrange(len(array[0])): + array[:,i] = np.take(array[:,i],ordering) + + # reference definitions of nodes and elements in previous timesteps + + self.reference() + + self.nsnaps = len(self.snaps) + print "read %d snapshots" % self.nsnaps + + # select all timesteps and elements + + self.tselect.all() + + # -------------------------------------------------------------------- + # read next snapshot from list of files + + def next(self): + + if not self.increment: raise StandardError,"cannot read incrementally" + + # read next snapshot in current file using eof as pointer + # if fail, try next file + # if new snapshot time stamp already exists, read next snapshot + + while 1: + f = open(self.flist[self.nextfile],'rb') + f.seek(self.eof) + snap = self.read_snapshot(f) + if not snap: + self.nextfile += 1 + if self.nextfile == len(self.flist): return -1 + f.close() + self.eof = 0 + continue + self.eof = f.tell() + f.close() + try: + self.findtime(snap.time) + continue + except: break + + # select the new snapshot with all its elements + + self.snaps.append(snap) + snap = self.snaps[self.nsnaps] + snap.tselect = 1 + snap.nselect = snap.nelements + if snap.eflag: + for i in xrange(snap.nelements): snap.eselect[i] = 1 + self.nsnaps += 1 + self.nselect += 1 + + return snap.time + + # -------------------------------------------------------------------- + # read a single snapshot from file f + # return snapshot or 0 if failed + + def read_snapshot(self,f): + try: + snap = Snap() + item = f.readline() + snap.time = int(f.readline()) + snap.nflag = snap.eflag = snap.nvalueflag = snap.evalueflag = 0 + str = f.readline() + if "NUMBER OF NODES" in str: snap.nflag = 1 + elif "NUMBER OF TRIANGLES" in str: snap.eflag = 1 + elif "NUMBER OF TETS" in str: snap.eflag = 2 + elif "NUMBER OF SQUARES" in str: snap.eflag = 3 + elif "NUMBER OF CUBES" in str: snap.eflag = 4 + elif "NUMBER OF NODE VALUES" in str: snap.nvalueflag = 1 + elif "NUMBER OF ELEMENT VALUES" in str: snap.evalueflag = 1 + else: raise StandardError,"unrecognized snapshot in dump file" + n = int(f.readline()) + + if snap.eflag: snap.eselect = np.zeros(n) + + if snap.nflag: + item = f.readline() + words = f.readline().split() + snap.xlo,snap.xhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.ylo,snap.yhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.zlo,snap.zhi = float(words[0]),float(words[1]) + + item = f.readline() + if n: + words = f.readline().split() + ncol = len(words) + for i in xrange(1,n): + words += f.readline().split() + floats = map(float,words) + if oldnumeric: values = np.zeros((n,ncol),np.Float) + else: values = np.zeros((n,ncol),np.float) + start = 0 + stop = ncol + for i in xrange(n): + values[i] = floats[start:stop] + start = stop + stop += ncol + else: values = None + + if snap.nflag: + snap.nodes = values; snap.nnodes = n + elif snap.eflag: + snap.elements = values; snap.nelements = n + elif snap.nvalueflag: + snap.nvalues = values; snap.nnvalues = n + elif snap.evalueflag: + snap.evalues = values; snap.nevalues = n + return snap + except: + return 0 + + # -------------------------------------------------------------------- + # map atom column names + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "mdump map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # delete unselected snapshots + + # -------------------------------------------------------------------- + + def delete(self): + ndel = i = 0 + while i < self.nsnaps: + if not self.snaps[i].tselect: + del self.snaps[i] + self.nsnaps -= 1 + ndel += 1 + else: i += 1 + print "%d snapshots deleted" % ndel + print "%d snapshots remaining" % self.nsnaps + + # -------------------------------------------------------------------- + # sort elements by ID in all selected timesteps or one timestep + + def sort(self,*list): + if len(list) == 0: + print "Sorting selected snapshots ..." + id = self.names["id"] + for snap in self.snaps: + if snap.tselect: self.sort_one(snap,id) + else: + i = self.findtime(list[0]) + id = self.names["id"] + self.sort_one(self.snaps[i],id) + + + # -------------------------------------------------------------------- + # sort a single snapshot by ID column + + def sort_one(self,snap,id): + atoms = snap.atoms + ids = atoms[:,id] + ordering = np.argsort(ids) + for i in xrange(len(atoms[0])): + atoms[:,i] = np.take(atoms[:,i],ordering) + + # -------------------------------------------------------------------- + # return vector of selected snapshot time stamps + + def time(self): + vec = self.nselect * [0] + i = 0 + for snap in self.snaps: + if not snap.tselect: continue + vec[i] = snap.time + i += 1 + return vec + + # -------------------------------------------------------------------- + # extract vector(s) of values for selected elements at chosen timestep + + def vecs(self,n,*list): + snap = self.snaps[self.findtime(n)] + if not snap.evalues: + raise StandardError, "snapshot has no element values" + + if len(list) == 0: + raise StandardError, "no columns specified" + columns = [] + values = [] + for name in list: + columns.append(self.names[name]) + values.append(snap.nselect * [0]) + ncol = len(columns) + + m = 0 + for i in xrange(len(snap.evalues)): + if not snap.eselect[i]: continue + for j in xrange(ncol): + values[j][m] = snap.evalues[i][columns[j]] + m += 1 + + if len(list) == 1: return values[0] + else: return values + + # -------------------------------------------------------------------- + # sort snapshots on time stamp + + def compare_time(self,a,b): + if a.time < b.time: + return -1 + elif a.time > b.time: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + # delete successive snapshots with duplicate time stamp + # if have same timestamp, combine them if internal flags are different + + def cull(self): + i = 1 + while i < len(self.snaps): + if self.snaps[i].time == self.snaps[i-1].time: + if self.snaps[i].nflag: + if not self.snaps[i-1].nflag: + self.snaps[i-1].nflag = 1 + self.snaps[i-1].nnodes = self.snaps[i].nnodes + self.snaps[i-1].nodes = self.snaps[i].nodes + self.snaps[i-1].xlo = self.snaps[i].xlo + self.snaps[i-1].xhi = self.snaps[i].xhi + self.snaps[i-1].ylo = self.snaps[i].ylo + self.snaps[i-1].yhi = self.snaps[i].yhi + self.snaps[i-1].zlo = self.snaps[i].zlo + self.snaps[i-1].zhi = self.snaps[i].zhi + elif self.snaps[i].eflag: + if not self.snaps[i-1].eflag: + self.snaps[i-1].eflag = self.snaps[i].eflag + self.snaps[i-1].nelements = self.snaps[i].nelements + self.snaps[i-1].elements = self.snaps[i].elements + self.snaps[i-1].eselect = self.snaps[i].eselect + elif self.snaps[i].nvalueflag: + if not self.snaps[i-1].nvalueflag: + self.snaps[i-1].nvalueflag = 1 + self.snaps[i-1].nnvalues = self.snaps[i].nnvalues + self.snaps[i-1].nvalues = self.snaps[i].nvalues + elif self.snaps[i].evalueflag: + if not self.snaps[i-1].evalueflag: + self.snaps[i-1].evalueflag = 1 + self.snaps[i-1].nevalues = self.snaps[i].nevalues + self.snaps[i-1].evalues = self.snaps[i].evalues + del self.snaps[i] + else: + i += 1 + + # -------------------------------------------------------------------- + # insure every snapshot has node and element connectivity info + # if not, point it at most recent shapshot that does + + def reference(self): + for i in xrange(len(self.snaps)): + if not self.snaps[i].nflag: + for j in xrange(i,-1,-1): + if self.snaps[j].nflag: + self.snaps[i].nflag = self.snaps[j].nflag + self.snaps[i].nnodes = self.snaps[j].nnodes + self.snaps[i].nodes = self.snaps[j].nodes + self.snaps[i].xlo = self.snaps[j].xlo + self.snaps[i].xhi = self.snaps[j].xhi + self.snaps[i].ylo = self.snaps[j].ylo + self.snaps[i].yhi = self.snaps[j].yhi + self.snaps[i].zlo = self.snaps[j].zlo + self.snaps[i].zhi = self.snaps[j].zhi + break + if not self.snaps[i].nflag: + raise StandardError,"no nodal coords found in previous snapshots" + if not self.snaps[i].eflag: + for j in xrange(i,-1,-1): + if self.snaps[j].eflag: + self.snaps[i].eflag = self.snaps[j].eflag + self.snaps[i].nelements = self.snaps[j].nelements + self.snaps[i].elements = self.snaps[j].elements + self.snaps[i].eselect = self.snaps[j].eselect + break + if not self.snaps[i].eflag: + raise StandardError,"no elem connections found in previous snapshots" + + # -------------------------------------------------------------------- + # iterate over selected snapshots + + def iterator(self,flag): + start = 0 + if flag: start = self.iterate + 1 + for i in xrange(start,self.nsnaps): + if self.snaps[i].tselect: + self.iterate = i + return i,self.snaps[i].time,1 + return 0,0,-1 + + # -------------------------------------------------------------------- + # return list of triangles to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] + + time = snap.time + box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi] + if self.etype == "": type = -1 + else: type = self.names[self.etype] + + atoms = [] + bonds = [] + + # create triangle list from all elements + # for type, either use element type (-1) or user-defined column in evalues + + tris = [] + nodes = snap.nodes + for i in xrange(snap.nelements): + if not snap.eselect[i]: continue + element = snap.elements[i] + if snap.evalueflag: evalue = snap.evalues[i] + else: evalues = [] + + # single tri, normal = up + + if snap.eflag == 1: + v1 = nodes[int(element[2])-1][2:5].tolist() + v2 = nodes[int(element[3])-1][2:5].tolist() + v3 = nodes[int(element[4])-1][2:5].tolist() + list = v1 + v2 + v3 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + + # single tet, convert to 4 tris, normals = out + + elif snap.eflag == 2: + v1 = nodes[int(element[2])-1][2:5].tolist() + v2 = nodes[int(element[3])-1][2:5].tolist() + v3 = nodes[int(element[4])-1][2:5].tolist() + v4 = nodes[int(element[5])-1][2:5].tolist() + list = v1 + v2 + v4 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v2 + v3 + v4 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v4 + v3 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v3 + v2 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + + # single square, convert to 2 tris, normals = up + + elif snap.eflag == 3: + v1 = nodes[int(element[2])-1][2:5].tolist() + v2 = nodes[int(element[3])-1][2:5].tolist() + v3 = nodes[int(element[4])-1][2:5].tolist() + v4 = nodes[int(element[5])-1][2:5].tolist() + list = v1 + v2 + v3 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v3 + v4 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + + # single cube, convert to 12 tris, normals = out + + elif snap.eflag == 4: + v1 = nodes[int(element[2])-1][2:5].tolist() + v2 = nodes[int(element[3])-1][2:5].tolist() + v3 = nodes[int(element[4])-1][2:5].tolist() + v4 = nodes[int(element[5])-1][2:5].tolist() + v5 = nodes[int(element[6])-1][2:5].tolist() + v6 = nodes[int(element[7])-1][2:5].tolist() + v7 = nodes[int(element[8])-1][2:5].tolist() + v8 = nodes[int(element[9])-1][2:5].tolist() + list = v1 + v3 + v2 # lower z face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v4 + v3 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v5 + v6 + v7 # upper z face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v5 + v7 + v8 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v2 + v6 # lower y face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v6 + v5 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v4 + v7 + v3 # upper y face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v4 + v8 + v7 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v8 + v4 # lower x face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v1 + v5 + v8 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v2 + v3 + v7 # upper x face + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + list = v2 + v7 + v6 + n = normal(list[0:3],list[3:6],list[6:9]) + if type == -1: tris.append([element[0],element[1]] + list + n) + else: tris.append([element[0],evalue[type]] + list + n) + + lines = [] + + return time,box,atoms,bonds,tris,lines + + # -------------------------------------------------------------------- + # return lists of node/element info for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + + def mviz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] + + time = snap.time + box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi] + nvalues = [] + if snap.nvalueflag: nvalues = snap.nvalues + evalues = [] + if snap.nvalueflag: evalues = snap.evalues + + return time,box,snap.nodes,snap.elements,nvalues,evalues + + # -------------------------------------------------------------------- + + def findtime(self,n): + for i in xrange(self.nsnaps): + if self.snaps[i].time == n: return i + raise StandardError, "no step %d exists" % n + + # -------------------------------------------------------------------- + # return maximum box size across all selected snapshots + + def maxbox(self): + xlo = ylo = zlo = None + xhi = yhi = zhi = None + for snap in self.snaps: + if not snap.tselect: continue + if xlo == None or snap.xlo < xlo: xlo = snap.xlo + if xhi == None or snap.xhi > xhi: xhi = snap.xhi + if ylo == None or snap.ylo < ylo: ylo = snap.ylo + if yhi == None or snap.yhi > yhi: yhi = snap.yhi + if zlo == None or snap.zlo < zlo: zlo = snap.zlo + if zhi == None or snap.zhi > zhi: zhi = snap.zhi + return [xlo,ylo,zlo,xhi,yhi,zhi] + + # -------------------------------------------------------------------- + + def compare_atom(self,a,b): + if a[0] < b[0]: + return -1 + elif a[0] > b[0]: + return 1 + else: + return 0 + +# -------------------------------------------------------------------- +# one snapshot + +class Snap: + pass + +# -------------------------------------------------------------------- +# time selection class + +class tselect: + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def all(self): + data = self.data + for snap in data.snaps: + snap.tselect = 1 + data.nselect = len(data.snaps) + data.eselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def one(self,n): + data = self.data + for snap in data.snaps: + snap.tselect = 0 + i = data.findtime(n) + data.snaps[i].tselect = 1 + data.nselect = 1 + data.eselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def none(self): + data = self.data + for snap in data.snaps: + snap.tselect = 0 + data.nselect = 0 + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def skip(self,n): + data = self.data + count = n-1 + for snap in data.snaps: + if not snap.tselect: continue + count += 1 + if count == n: + count = 0 + continue + snap.tselect = 0 + data.nselect -= 1 + data.eselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + + # -------------------------------------------------------------------- + + def test(self,teststr): + data = self.data + snaps = data.snaps + cmd = "flag = " + teststr.replace("$t","snaps[i].time") + ccmd = compile(cmd,'','single') + for i in xrange(data.nsnaps): + if not snaps[i].tselect: continue + exec ccmd + if not flag: + snaps[i].tselect = 0 + data.nselect -= 1 + data.eselect.all() + print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) + +# -------------------------------------------------------------------- +# element selection class + +class eselect: + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def all(self,*args): + data = self.data + if len(args) == 0: # all selected timesteps + for snap in data.snaps: + if not snap.tselect: continue + for i in xrange(snap.nelements): snap.eselect[i] = 1 + snap.nselect = snap.nelements + else: # one timestep + n = data.findtime(args[0]) + snap = data.snaps[n] + for i in xrange(snap.nelements): snap.eselect[i] = 1 + snap.nselect = snap.nelements + + # -------------------------------------------------------------------- + + def test(self,teststr,*args): + data = self.data + + # replace all $var with snap.atoms references and compile test string + + pattern = "\$\w*" + list = re.findall(pattern,teststr) + for item in list: + name = item[1:] + column = data.names[name] + insert = "snap.atoms[i][%d]" % column + teststr = teststr.replace(item,insert) + cmd = "flag = " + teststr + ccmd = compile(cmd,'','single') + + if len(args) == 0: # all selected timesteps + for snap in data.snaps: + if not snap.tselect: continue + for i in xrange(snap.nelements): + if not snap.eselect[i]: continue + exec ccmd + if not flag: + snap.eselect[i] = 0 + snap.nselect -= 1 + for i in xrange(data.nsnaps): + if data.snaps[i].tselect: + print "%d atoms of %d selected in first step %d" % \ + (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time) + break + for i in xrange(data.nsnaps-1,-1,-1): + if data.snaps[i].tselect: + print "%d atoms of %d selected in last step %d" % \ + (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time) + break + + else: # one timestep + n = data.findtime(args[0]) + snap = data.snaps[n] + for i in xrange(snap.nelements): + if not snap.eselect[i]: continue + exec ccmd + if not flag: + snap.eselect[i] = 0 + snap.nselect -= 1 + +# -------------------------------------------------------------------- +# compute normal for a triangle with 3 vertices + +def normal(x,y,z): + v1 = 3*[0] + v1[0] = y[0] - x[0] + v1[1] = y[1] - x[1] + v1[2] = y[2] - x[2] + + v2 = 3*[0] + v2[0] = z[0] - y[0] + v2[1] = z[1] - y[1] + v2[2] = z[2] - y[2] + + n = 3*[0] + n[0] = v1[1]*v2[2] - v1[2]*v2[1] + n[1] = v1[2]*v2[0] - v1[0]*v2[2] + n[2] = v1[0]*v2[1] - v1[1]*v2[0] + + length = sqrt(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]) + n[0] /= length + n[1] /= length + n[2] /= length + + return n diff --git a/src/mdump.pyc b/src/mdump.pyc new file mode 100644 index 0000000..afa73d1 Binary files /dev/null and b/src/mdump.pyc differ diff --git a/src/pair.py b/src/pair.py new file mode 100644 index 0000000..ad64d4b --- /dev/null +++ b/src/pair.py @@ -0,0 +1,267 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# pair tool + +oneline = "Compute LAMMPS pairwise energies" + +docstr = """ +p = pair("lj/charmm/coul/charmm") create pair object for specific pair style + + available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm + +p.coeff(d) extract pairwise coeffs from data object +p.init(cut1,cut2,...) setup based on coeffs and cutoffs + + init args are specific to pair style: + lj/cut = cutlj + lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional) + lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul + (last 2 optional) + +e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy + + pairwise energy between 2 atoms at distance rsq with their attributes + args are specific to pair style: + lj/cut = rsq,itype,jtype + lj/cut/coul/cut = rsq,itype,jtype,q1,q2 + lj/charmm/coul/charmm = rsq,itype,jtype,q1,q2 +""" + +# History +# 8/05, Steve Plimpton and Paul Crozier (SNL): original version +# 9/05, Paul Crozier (SNL): added lj/cut and lj/cut/coul/cut + +# ToDo list + +# Variables + +# Imports and external programs + +from math import sqrt + +# Class definition + +class pair: + + # -------------------------------------------------------------------- + + def __init__(self,style): + + # map generic methods to style-specific methods + + if style == "lj/cut": + self.coeff_func = self.coeff_lj_cut + self.init_func = self.init_lj_cut + self.single_func = self.single_lj_cut + elif style == "lj/cut/coul/cut": + self.coeff_func = self.coeff_lj_cut_coul_cut + self.init_func = self.init_lj_cut_coul_cut + self.single_func = self.single_lj_cut_coul_cut + elif style == "lj/charmm/coul/charmm": + self.coeff_func = self.coeff_lj_charmm_coul_charmm + self.init_func = self.init_lj_charmm_coul_charmm + self.single_func = self.single_lj_charmm_coul_charmm + else: + raise StandardError, "this pair style not yet supported" + + # -------------------------------------------------------------------- + # generic coeff method + + def coeff(self,data): + self.coeff_func(data) + + # -------------------------------------------------------------------- + # generic init method, as many args as needed + + def init(self,*list): + self.init_func(list) + + # -------------------------------------------------------------------- + # generic single method, as many args as needed + + def single(self,*list): + return self.single_func(list) + + # -------------------------------------------------------------------- + # -------------------------------------------------------------------- + # lj/cut methods + + def coeff_lj_cut(self,data): + epsilon = data.get("Pair Coeffs",2) + sigma = data.get("Pair Coeffs",3) + ntypes = len(epsilon) + + self.lj3 = [] + self.lj4 = [] + for i in xrange(ntypes): + self.lj3.append(ntypes * [0]) + self.lj4.append(ntypes * [0]) + for j in xrange(ntypes): + epsilon_ij = sqrt(epsilon[i]*epsilon[j]) + sigma_ij = sqrt(sigma[i]*sigma[j]) + self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0); + self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0); + + # -------------------------------------------------------------------- + # args = cutlj + + def init_lj_cut(self,list): + cut_lj = list[0] + self.cut_ljsq = cut_lj*cut_lj + + # -------------------------------------------------------------------- + # args = rsq,itype,jtype + + def single_lj_cut(self,list): + rsq = list[0] + itype = list[1] + jtype = list[2] + + r2inv = 1.0/rsq + + if rsq < self.cut_ljsq: + r6inv = r2inv*r2inv*r2inv + eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype]) + else: eng_vdwl = 0.0 + + return eng_vdwl + + # -------------------------------------------------------------------- + # -------------------------------------------------------------------- + # lj/cut/coul/cut methods + + def coeff_lj_cut_coul_cut(self,data): + epsilon = data.get("Pair Coeffs",2) + sigma = data.get("Pair Coeffs",3) + ntypes = len(epsilon) + + self.lj3 = [] + self.lj4 = [] + for i in xrange(ntypes): + self.lj3.append(ntypes * [0]) + self.lj4.append(ntypes * [0]) + for j in xrange(ntypes): + epsilon_ij = sqrt(epsilon[i]*epsilon[j]) + sigma_ij = sqrt(sigma[i]*sigma[j]) + self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0); + self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0); + + # -------------------------------------------------------------------- + # args = cutlj, cut_coul (cut_coul optional) + + def init_lj_cut_coul_cut(self,list): + self.qqr2e = 332.0636 # convert energy to kcal/mol + cut_lj = list[0] + self.cut_ljsq = cut_lj*cut_lj + + if len(list) == 1: cut_coul = cut_lj + else: cut_coul = list[1] + self.cut_coulsq = cut_coul*cut_coul + + # -------------------------------------------------------------------- + # args = rsq,itype,jtype,q1,q2 + + def single_lj_cut_coul_cut(self,list): + rsq = list[0] + itype = list[1] + jtype = list[2] + q1 = list[3] + q2 = list[4] + + r2inv = 1.0/rsq + + if rsq < self.cut_coulsq: eng_coul = self.qqr2e * q1*q2*sqrt(r2inv) + else: eng_coul = 0.0 + + if rsq < self.cut_ljsq: + r6inv = r2inv*r2inv*r2inv + eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype]) + else: eng_vdwl = 0.0 + + return eng_coul,eng_vdwl + + # -------------------------------------------------------------------- + # -------------------------------------------------------------------- + # lj/charmm/coul/charmm methods + + def coeff_lj_charmm_coul_charmm(self,data): + epsilon = data.get("Pair Coeffs",2) + sigma = data.get("Pair Coeffs",3) + ntypes = len(epsilon) + + self.lj3 = [] + self.lj4 = [] + for i in xrange(ntypes): + self.lj3.append(ntypes * [0]) + self.lj4.append(ntypes * [0]) + for j in xrange(ntypes): + epsilon_ij = sqrt(epsilon[i]*epsilon[j]) + sigma_ij = 0.5 * (sigma[i] + sigma[j]) + self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0); + self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0); + + # -------------------------------------------------------------------- + # args = cutlj_inner,cutlj,cutcoul_inner,cut_coul (last 2 optional) + + def init_lj_charmm_coul_charmm(self,list): + self.qqr2e = 332.0636 # convert energy to kcal/mol + cut_lj_inner = list[0] + cut_lj = list[1] + + self.cut_lj_innersq = cut_lj_inner*cut_lj_inner + self.cut_ljsq = cut_lj*cut_lj + + if len(list) == 2: + cut_coul_inner = cut_lj_inner + cut_coul = cut_lj + else: + cut_coul_inner = list[2] + cut_coul = list[3] + self.cut_coul_innersq = cut_coul_inner*cut_coul_inner + self.cut_coulsq = cut_coul*cut_coul + + self.denom_lj = (self.cut_ljsq-self.cut_lj_innersq) * \ + (self.cut_ljsq-self.cut_lj_innersq) * \ + (self.cut_ljsq-self.cut_lj_innersq); + self.denom_coul = (self.cut_coulsq-self.cut_coul_innersq) * \ + (self.cut_coulsq-self.cut_coul_innersq) * \ + (self.cut_coulsq-self.cut_coul_innersq); + + # -------------------------------------------------------------------- + # args = rsq,itype,jtype,q1,q2 + + def single_lj_charmm_coul_charmm(self,list): + rsq = list[0] + itype = list[1] + jtype = list[2] + q1 = list[3] + q2 = list[4] + + r2inv = 1.0/rsq + + if rsq < self.cut_coulsq: + eng_coul = self.qqr2e * q1*q2*sqrt(r2inv) + if rsq > self.cut_coul_innersq: + switch1 = (self.cut_coulsq-rsq) * (self.cut_coulsq-rsq) * \ + (self.cut_coulsq + 2.0*rsq - 3.0*self.cut_coul_innersq) / \ + self.denom_coul + eng_coul *= switch1 + else: eng_coul = 0.0 + + if rsq < self.cut_ljsq: + r6inv = r2inv*r2inv*r2inv + eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype]) + if rsq > self.cut_lj_innersq: + switch1 = (self.cut_ljsq-rsq) * (self.cut_ljsq-rsq) * \ + (self.cut_ljsq + 2.0*rsq - 3.0*self.cut_lj_innersq) / \ + self.denom_lj + eng_vdwl *= switch1 + else: eng_vdwl = 0.0 + + return eng_coul,eng_vdwl diff --git a/src/pair.pyc b/src/pair.pyc new file mode 100644 index 0000000..12e1709 Binary files /dev/null and b/src/pair.pyc differ diff --git a/src/patch.py b/src/patch.py new file mode 100644 index 0000000..2bf0cd6 --- /dev/null +++ b/src/patch.py @@ -0,0 +1,1360 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# patch tool + +oneline = "Create patchy Lennard-Jones particles for LAMMPS input" + +docstr = """ +p = patch(vfrac) setup box with a specified volume fraction +p = patch(vfrac,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1) + +p.seed = 48379 set random # seed (def = 12345) +p.randomized = 0 1 = choose next particle randomly, 0 = as generated +p.dim = 2 set dimension of created box (def = 3) +p.blen = 0.97 set length of tether bonds (def = 0.97) +p.dmin = 1.02 set min r from i-1 to i+1 tether site (def = 1.02) +p.lattice = [Nx,Ny,Nz] generate Nx by Ny by Nz lattice of particles + + if lattice is set, Nx*Ny*Nz must equal N for build + lattice = [0,0,0] = generate N particles randomly, default + +p.build(100,"hex2",1,2,3) create 100 "hex2" particles with types 1,2,3 + + can be invoked multiple times + keywords: + c60hex2: diam,1,2,3 = C-60 with 2 hex patches and ctr part, types 1,2,3 + hex2: diam,1,2 = one large particle with 2 7-mer hex patches, types 1,2 + hex4: diam,1,2 = one large particle with 4 7-mer hex patches, types 1,2 + ring: diam,N,1,2 = one large part with equatorial ring of N, types 1,2 + ball: diam,m1,m2,1,2,3 = large ball with m12-len tethers, types 1,2,3 + tri5: 1,2 = 3-layer 5-size hollow tri, types 1,2 + rod: N,m1,m2,1,2,3 = N-length rod with m12-len tethers, types 1,2,3 + tri: N,m1,m2,m3,1,2,3,4 = N-size tri with m123-len tethers, types 1-4 + hex: m1,m2,m3,m4,m5,m6,1,2,3,4,5,6,7 = 7-atom hex with m-len tethers, t 1-7 + dimer: r,1 = two particles r apart, type 1, no bond + star2d: N,r,1 = 2d star of length N (odd), beads r apart, type 1, no bonds + box2d: N,M,r,1 = 2d NxM box, beads r apart, type 1, no bonds + tritet: A,m = 4-tri tet with edge length A, tri type m + tribox: Alo,Ahi,Blo,Bhi,Clo,Chi,m = 12-tri box with side lengths A,B,C & m + linebox: Alo,Ahi,Blo,Bhi,m = 4-line 2d rectangle with random side lengths + from Alo to Ahi and Blo to Bhi, line type m + linetri: Alo,Ahi,Blo,Bhi,m = 3-line 2d triangle with random base + from Alo to Ahi and height Blo to Bhi, type m + +p.write("data.patch") write out system to LAMMPS data file +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# vfrac = desired volume fraction +# x,y,z = aspect ratio of box (def = 1,1,1) +# seed = random seed +# molecules = list of atoms, grouped by molecule + +# Imports and external programs + +from math import sqrt,pi,cos,sin +from data import data + +# Class definition + +class patch: + + # -------------------------------------------------------------------- + + def __init__(self,vfrac,*list): + self.vfrac = vfrac + self.xaspect = self.yaspect = self.zaspect = 1.0 + if len(list): + self.xaspect = list[0] + self.yaspect = list[1] + self.zaspect = list[2] + self.seed = 12345 + self.randomized = 1 + self.dim = 3 + self.molecules = [] + self.volume = 0 + self.blen = 0.97 + self.dmin = 1.02 + self.lattice = [0,0,0] + self.style = "molecular" + + # -------------------------------------------------------------------- + # call style method with extra args + # adds to volume and atom list + # reset self.style for lines and triangles + + def build(self,n,style,*types): + if style == "linebox" or style == "linetri": self.style = "line" + if style == "tritet" or style == "tribox": self.style = "tri" + cmd = "atoms,bonds,tris,segments,volume = self.%s(*types)" % style + for i in xrange(n): + exec cmd + self.molecules.append([atoms,bonds,tris,segments]) + self.volume += volume + + # -------------------------------------------------------------------- + # create the atom coords in a scaled-size box of correct dimension + # write them to LAMMPS data file + + def write(self,file): + if self.dim == 3: self.write3d(file) + else: self.write2d(file) + + # -------------------------------------------------------------------- + # write a 3d simulation to data file + + def write3d(self,file): + volume = self.volume/self.vfrac + prd = pow(volume/self.xaspect/self.yaspect/self.zaspect,1.0/3.0) + self.xprd = self.xaspect * prd + self.xlo = -self.xprd/2.0 + self.xhi = self.xprd/2.0 + self.yprd = self.yaspect * prd + self.ylo = -self.yprd/2.0 + self.yhi = self.yprd/2.0 + self.zprd = self.zaspect * prd + self.zlo = -self.zprd/2.0 + self.zhi = self.zprd/2.0 + + if self.lattice[0] or self.lattice[1] or self.lattice[2]: + latflag = 1 + if self.lattice[0]*self.lattice[1]*self.lattice[2] != \ + len(self.molecules): + raise StandardError,"lattice inconsistent with # of molecules" + else: latflag = 0 + + idatom = idbond = idtri = idmol = 0 + atoms = [] + bonds = [] + tris = [] + xp = 3*[0] + yp = 3*[0] + zp = 3*[0] + + while self.molecules: + if self.randomized: i = int(self.random()*len(self.molecules)) + else: i = 0 + molecule = self.molecules.pop(i) + + idmol += 1 + triples = [] + + # xp[3],yp[3],zp[3] = randomly oriented, normalized basis vectors + # xp is in random direction + # yp is random dir crossed into xp + # zp is xp crossed into yp + + xp[0] = self.random() - 0.5 + xp[1] = self.random() - 0.5 + xp[2] = self.random() - 0.5 + r = sqrt(xp[0]*xp[0] + xp[1]*xp[1] + xp[2]*xp[2]) + xp[0],xp[1],xp[2] = xp[0]/r,xp[1]/r,xp[2]/r + + r0 = self.random() - 0.5 + r1 = self.random() - 0.5 + r2 = self.random() - 0.5 + yp[0] = r1*xp[2] - r2*xp[1] + yp[1] = r2*xp[0] - r0*xp[2] + yp[2] = r0*xp[1] - r1*xp[0] + r = sqrt(yp[0]*yp[0] + yp[1]*yp[1] + yp[2]*yp[2]) + yp[0],yp[1],yp[2] = yp[0]/r,yp[1]/r,yp[2]/r + + zp[0] = xp[1]*yp[2] - xp[2]*yp[1] + zp[1] = xp[2]*yp[0] - xp[0]*yp[2] + zp[2] = xp[0]*yp[1] - xp[1]*yp[0] + r = sqrt(zp[0]*zp[0] + zp[1]*zp[1] + zp[2]*zp[2]) + zp[0],zp[1],zp[2] = zp[0]/r,zp[1]/r,zp[2]/r + + #xp[0] = 1; xp[1] = 0; xp[2] = 0 + #yp[0] = 0; yp[1] = 1; yp[2] = 0 + #zp[0] = 0; zp[1] = 0; zp[2] = 1 + + # random origin or lattice site for new particle + + if latflag == 0: + xorig = self.xlo + self.random()*self.xprd + yorig = self.ylo + self.random()*self.yprd + zorig = self.zlo + self.random()*self.zprd + else: + ix = (idmol-1) % self.lattice[0] + iy = (idmol-1)/self.lattice[0] % self.lattice[1] + iz = (idmol-1) / (self.lattice[0]*self.lattice[1]) + xorig = self.xlo + ix*self.xprd/self.lattice[0] + yorig = self.ylo + iy*self.yprd/self.lattice[1] + zorig = self.zlo + iz*self.zprd/self.lattice[2] + + #xorig = 0; yorig = 0; zorig = 0 + + # unpack bonds in molecule before atoms so idatom = all previous atoms + + for bond in molecule[1]: + idbond += 1 + bonds.append([idbond,bond[0],bond[1]+idatom+1,bond[2]+idatom+1]) + + # unpack triples in molecule as displacements from associated atom + + for triple in molecule[2]: triples.append(triple) + + # unpack atoms in molecule + # xnew,ynew,xnew = coeffs in new rotated basis vectors + # x,y,z = coeffs in original xyz axes + # format data file for moleular or tri atom style + + if self.style == "molecular": + for atom in molecule[0]: + idatom += 1 + xnew = atom[1] + ynew = atom[2] + znew = atom[3] + x = xorig + xnew*xp[0] + ynew*yp[0] + znew*zp[0] + y = yorig + xnew*xp[1] + ynew*yp[1] + znew*zp[1] + z = zorig + xnew*xp[2] + ynew*yp[2] + znew*zp[2] + ix = iy = iz = 0 + x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz) + atoms.append([idatom,idmol,atom[0],x,y,z,ix,iy,iz]) + + elif self.style == "tri": + for i,atom in enumerate(molecule[0]): + idatom += 1 + xnew = atom[1] + ynew = atom[2] + znew = atom[3] + x = xorig + xnew*xp[0] + ynew*yp[0] + znew*zp[0] + y = yorig + xnew*xp[1] + ynew*yp[1] + znew*zp[1] + z = zorig + xnew*xp[2] + ynew*yp[2] + znew*zp[2] + mass = 1.0 + ix = iy = iz = 0 + x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz) + if not triples: triflag = 0 + else: triflag = 1 + atoms.append([idatom,idmol,atom[0],triflag,mass,x,y,z,ix,iy,iz]) + + if triflag: + triple = triples[i] + xtri = triple[0] + ytri = triple[1] + ztri = triple[2] + triple[0] = xorig + xtri*xp[0] + ytri*yp[0] + ztri*zp[0] + triple[1] = yorig + xtri*xp[1] + ytri*yp[1] + ztri*zp[1] + triple[2] = zorig + xtri*xp[2] + ytri*yp[2] + ztri*zp[2] + triple[0],triple[1],triple[2] = \ + self.pbc_near(triple[0],triple[1],triple[2],x,y,z) + xtri = triple[3] + ytri = triple[4] + ztri = triple[5] + triple[3] = xorig + xtri*xp[0] + ytri*yp[0] + ztri*zp[0] + triple[4] = yorig + xtri*xp[1] + ytri*yp[1] + ztri*zp[1] + triple[5] = zorig + xtri*xp[2] + ytri*yp[2] + ztri*zp[2] + triple[3],triple[4],triple[5] = \ + self.pbc_near(triple[3],triple[4],triple[5],x,y,z) + xtri = triple[6] + ytri = triple[7] + ztri = triple[8] + triple[6] = xorig + xtri*xp[0] + ytri*yp[0] + ztri*zp[0] + triple[7] = yorig + xtri*xp[1] + ytri*yp[1] + ztri*zp[1] + triple[8] = zorig + xtri*xp[2] + ytri*yp[2] + ztri*zp[2] + triple[6],triple[7],triple[8] = \ + self.pbc_near(triple[6],triple[7],triple[8],x,y,z) + tris.append([idatom] + triple) + + # create the data file + + list = [atom[2] for atom in atoms] + atypes = max(list) + + d = data() + d.title = "LAMMPS data file for Nanoparticles" + d.headers["atoms"] = len(atoms) + d.headers["atom types"] = atypes + if bonds: + d.headers["bonds"] = len(bonds) + d.headers["bond types"] = 1 + if tris: d.headers["tris"] = len(tris) + d.headers["xlo xhi"] = (self.xlo,self.xhi) + d.headers["ylo yhi"] = (self.ylo,self.yhi) + d.headers["zlo zhi"] = (self.zlo,self.zhi) + + # atoms section of data file + + records = [] + if self.style == "molecular": + for atom in atoms: + one = "%d %d %d %g %g %g %d %d %d\n" % \ + (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], + atom[6], atom[7], atom[8]) + records.append(one) + elif self.style == "tri": + for atom in atoms: + one = "%d %d %d %d %g %g %g %g %d %d %d\n" % \ + (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], + atom[6], atom[7], atom[8], atom[9], atom[10]) + records.append(one) + d.sections["Atoms"] = records + + # bonds section of data file + + if bonds: + lines = [] + for bond in bonds: + line = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3]) + lines.append(line) + d.sections["Bonds"] = lines + + # triangles section of data file + + if tris: + records = [] + for tri in tris: + one = "%d %g %g %g %g %g %g %g %g %g\n" % \ + (tri[0],tri[1],tri[2],tri[3],tri[4],tri[5], + tri[6],tri[7],tri[8],tri[9]) + records.append(one) + d.sections["Triangles"] = records + + d.write(file) + + # -------------------------------------------------------------------- + # write a 2d simulation to data file + + def write2d(self,file): + volume = self.volume/self.vfrac + prd = pow(volume/self.xaspect/self.yaspect,1.0/2.0) + self.xprd = self.xaspect * prd + self.xlo = -self.xprd/2.0 + self.xhi = self.xprd/2.0 + self.yprd = self.yaspect * prd + self.ylo = -self.yprd/2.0 + self.yhi = self.yprd/2.0 + self.zprd = 1.0 + self.zlo = -0.5 + self.zhi = 0.5 + + if self.lattice[0] or self.lattice[1]: + latflag = 1 + if self.lattice[0]*self.lattice[1] != len(self.molecules): + raise StandardError,"lattice inconsistent with # of molecules" + else: latflag = 0 + + idatom = idbond = idmol = 0 + atoms = [] + bonds = [] + lines = [] + xp = 3*[0] + yp = 3*[0] + + while self.molecules: + if self.randomized: i = int(self.random()*len(self.molecules)) + else: i = 0 + molecule = self.molecules.pop(i) + + idmol += 1 + segments = [] + + # xp[2],yp[2] = randomly oriented, normalized basis vectors + # xp is in random direction + # yp is (0,0,1) crossed into xp + + xp[0] = self.random() - 0.5 + xp[1] = self.random() - 0.5 + r = sqrt(xp[0]*xp[0] + xp[1]*xp[1]) + xp[0],xp[1] = xp[0]/r,xp[1]/r + + yp[0] = -xp[1] + yp[1] = xp[0] + r = sqrt(yp[0]*yp[0] + yp[1]*yp[1]) + yp[0],yp[1] = yp[0]/r,yp[1]/r + + # random origin or lattice site for new particle + + if latflag == 0: + xorig = self.xlo + self.random()*self.xprd + yorig = self.ylo + self.random()*self.yprd + zorig = 0.0 + else: + ix = (idmol-1) % self.lattice[0] + iy = (idmol-1) / self.lattice[0] + xorig = self.xlo + ix*self.xprd/self.lattice[0] + yorig = self.ylo + iy*self.yprd/self.lattice[1] + zorig = 0.0 + + # unpack bonds in molecule before atoms so idatom = all previous atoms + + for bond in molecule[1]: + idbond += 1 + bonds.append([idbond,bond[0],bond[1]+idatom+1,bond[2]+idatom+1]) + + # unpack segments in molecule as displacements from associated atom + + for segment in molecule[3]: segments.append(segment) + + # unpack atoms in molecule + # xnew,ynew,xnew = coeffs in new rotated basis vectors + # x,y,z = coeffs in original xyz axes + # format data file for moleular or line atom style + + if self.style == "molecular": + for i,atom in enumerate(molecule[0]): + idatom += 1 + xnew = atom[1] + ynew = atom[2] + x = xorig + xnew*xp[0] + ynew*yp[0] + y = yorig + xnew*xp[1] + ynew*yp[1] + z = atom[3] + ix = iy = iz = 0 + x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz) + atoms.append([idatom,idmol,atom[0],x,y,z,ix,iy,iz]) + + elif self.style == "line": + for i,atom in enumerate(molecule[0]): + idatom += 1 + xnew = atom[1] + ynew = atom[2] + x = xorig + xnew*xp[0] + ynew*yp[0] + y = yorig + xnew*xp[1] + ynew*yp[1] + z = atom[3] + mass = 1.0 + ix = iy = iz = 0 + x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz) + if not segments: lineflag = 0 + else: lineflag = 1 + atoms.append([idatom,idmol,atom[0],lineflag,mass,x,y,z,ix,iy,iz]) + + if lineflag: + segment = segments[i] + xseg = xnew + segment[0] + yseg = ynew + segment[1] + segment[0] = xorig + xseg*xp[0] + yseg*yp[0] + segment[1] = yorig + xseg*xp[1] + yseg*yp[1] + segment[0],segment[1],tmp = \ + self.pbc_near(segment[0],segment[1],0,x,y,z) + xseg = xnew + segment[2] + yseg = ynew + segment[3] + segment[2] = xorig + xseg*xp[0] + yseg*yp[0] + segment[3] = yorig + xseg*xp[1] + yseg*yp[1] + segment[2],segment[3],tmp = \ + self.pbc_near(segment[2],segment[3],0,x,y,z) + lines.append([idatom] + segment) + + # create the data file + + list = [atom[2] for atom in atoms] + atypes = max(list) + + d = data() + d.title = "LAMMPS data file for Nanoparticles" + d.headers["atoms"] = len(atoms) + d.headers["atom types"] = atypes + if bonds: + d.headers["bonds"] = len(bonds) + d.headers["bond types"] = 1 + if lines: d.headers["lines"] = len(lines) + d.headers["xlo xhi"] = (self.xlo,self.xhi) + d.headers["ylo yhi"] = (self.ylo,self.yhi) + d.headers["zlo zhi"] = (self.zlo,self.zhi) + + # atoms section of data file + + records = [] + if self.style == "molecular": + for atom in atoms: + one = "%d %d %d %g %g %g %d %d %d\n" % \ + (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], + atom[6], atom[7], atom[8]) + records.append(one) + elif self.style == "line": + for atom in atoms: + one = "%d %d %d %d %g %g %g %g %d %d %d\n" % \ + (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], + atom[6], atom[7], atom[8], atom[9], atom[10]) + records.append(one) + d.sections["Atoms"] = records + + # bonds section of data file + + if bonds: + records = [] + for bond in bonds: + one = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3]) + records.append(one) + d.sections["Bonds"] = records + + # lines section of data file + + if lines: + records = [] + for line in lines: + one = "%d %g %g %g %g\n" % (line[0],line[1],line[2],line[3],line[4]) + records.append(one) + d.sections["Lines"] = records + + d.write(file) + + # -------------------------------------------------------------------- + # adjust x,y,z to be inside periodic box + + def pbc(self,x,y,z,ix,iy,iz): + if x < self.xlo: + x += self.xprd + ix -= 1 + elif x >= self.xhi: + x -= self.xprd + ix += 1 + if y < self.ylo: + y += self.yprd + iy -= 1 + elif y >= self.yhi: + y -= self.yprd + iy += 1 + if z < self.zlo: + z += self.zprd + iz -= 1 + elif z >= self.zhi: + z -= self.zprd + iz += 1 + return x,y,z,ix,iy,iz + + # -------------------------------------------------------------------- + # adjust xnew,ynew,znew to be near x,y,z in periodic sense + + def pbc_near(self,xnew,ynew,znew,x,y,z): + if x-xnew > 0.5*self.xprd: xnew += self.xprd + elif xnew-x > 0.5*self.xprd: xnew -= self.xprd + if y-ynew > 0.5*self.yprd: ynew += self.yprd + elif ynew-y > 0.5*self.yprd: ynew -= self.yprd + if z-znew > 0.5*self.zprd: znew += self.zprd + elif znew-z > 0.5*self.zprd: znew -= self.zprd + return xnew,ynew,znew + + # -------------------------------------------------------------------- + # params = diam,type1,type2,type3 + # type1 = type of non-patch atoms, type2 = type of patch atoms + # type3 = type of center-of-sphere atom + + def c60hex2(self,*params): + template = BUCKY_60 + diam = params[0] + patches = [[params[2],[1,2,3,4,5,6,34,35,46,47,48,60]], + [params[3],[61]]] + atoms = make_sphere(template,diam,params[1],patches) + volume = 4.0/3.0 * pi * diam*diam*diam/8 + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = diam,type1,type2 + # type1 = type of large center atom, type2 = type of hex patch atoms + + def hex2(self,*params): + diam = params[0] + type1 = params[1] + type2 = params[2] + + atoms = [] + atoms.append([type1,0.0,0.0,0.0]) + + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.5,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-0.5,-sqrt(3.0)/2)) + + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.5,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-0.5,-sqrt(3.0)/2)) + + volume = 4.0/3.0 * pi * diam*diam*diam/8 + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = diam,type1,type2 + # type1 = type of large center atom, type2 = type of hex patch atoms + + def hex4(self,*params): + diam = params[0] + type1 = params[1] + type2 = params[2] + + atoms = [] + atoms.append([type1,0.0,0.0,0.0]) + + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.5,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5*diam,-0.5,-sqrt(3.0)/2)) + + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-1.0,0.0)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-0.5,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,0.5,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5*diam,-0.5,-sqrt(3.0)/2)) + + atoms.append(atom_on_sphere(diam,type2,0.0,0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,1.0,0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,-1.0,0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5,0.5*diam,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5,0.5*diam,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5,0.5*diam,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5,0.5*diam,-sqrt(3.0)/2)) + + atoms.append(atom_on_sphere(diam,type2,0.0,-0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,1.0,-0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,-1.0,-0.5*diam,0.0)) + atoms.append(atom_on_sphere(diam,type2,0.5,-0.5*diam,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5,-0.5*diam,sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,0.5,-0.5*diam,-sqrt(3.0)/2)) + atoms.append(atom_on_sphere(diam,type2,-0.5,-0.5*diam,-sqrt(3.0)/2)) + + volume = 4.0/3.0 * pi * diam*diam*diam/8 + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = diam,nring,type1,type2 + # nring = # of particles in ring + # type1 = type of large center atom, type2 = type of ring atoms + + def ring(self,*params): + diam = params[0] + nring = params[1] + type1 = params[2] + type2 = params[3] + + atoms = [] + atoms.append([type1,0.0,0.0,0.0]) + + for i in range(nring): + atoms.append([type2,0.5*diam*cos(i * 2*pi/nring), + 0.5*diam*sin(i * 2*pi/nring),0.0]) + + volume = 4.0/3.0 * pi * diam*diam*diam/8 + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = diam,m1,m2,ntype,m1type,m2type + # ntype = type of big central ball + # m12,m12type = length of tethers on each side of ball (m12 = 0 = no tether) + # set three types of bonds: + # 1 = big to small, 2 = small to small, 3 = across two tethers + + def ball(self,*params): + diam = params[0] + m1 = params[1] + m2 = params[2] + ntype = params[3] + m1type = params[4] + m2type = params[5] + + atoms = [] + atoms.append([ntype,0.0,0.0,0.0]) + + if m1: + atoms.append([m1type,0.5*diam+0.5,0.0,0.0]) + atoms += tether(m1-1,m1type,self.blen,self.dmin, + [ntype,0.5*diam-0.5,0.0,0.0],atoms[1],self.random) + if m2: + atoms.append([m2type,-0.5*diam-0.5,0.0,0.0]) + atoms += tether(m2-1,m2type,self.blen,self.dmin, + [ntype,-0.5*diam+0.5,0.0,0.0],atoms[1+m1],self.random) + + bonds = [] + for i in range(m1): + if i == 0: bonds.append([1,0,1]) + else: bonds.append([2,1+i-1,1+i]) + for i in range(m2): + if i == 0: bonds.append([1,0,1+m1]) + else: bonds.append([2,1+m1+i-1,1+m1+i]) + if m1 and m2: bonds.append([3,1,m1+1]) + + volume = 4.0/3.0 * pi * diam*diam*diam/8 + (m1+m2)*pi/6.0 + return atoms,bonds,[],[],volume + + # -------------------------------------------------------------------- + # params = type1,type2 + # type1 = type of 1/3 layers, type2 = type of middle layer + + def tri5(self,*params): + template = TRI5_HOLLOW + nlayer = 3 + patches = [[params[1],[13,14,15,16,17,18,19,20,21,22,23,24]]] + + atoms = [] + n = 0 + for iz in range(nlayer): + for atom in template: + n += 1 + type = params[0] + for pair in patches: + patch = pair[1] + if n in patch: type = pair[0] + x,y,z = atom[0],atom[1],atom[2] + iz + atoms.append([type,x,y,z]) + + volume = nlayer * 0.5 * 5.0 * 5.0*sqrt(3)/2 + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = n,m1,m2,ntype,m1type,m2type + # n,ntype = length/type of rod + # m12,m12type = length of tethers on each end (m12 = 0 = no tether) + + def rod(self,*params): + n = params[0] + m1 = params[1] + m2 = params[2] + ntype = params[3] + m1type = params[4] + m2type = params[5] + + atoms = [] + for i in range(n): + x,y,z = i*self.blen,0.0,0.0 + atoms.append([ntype,x,y,z]) + + if m1: atoms += tether(m1,m1type,self.blen,self.dmin, + atoms[n-2],atoms[n-1],self.random) + if m2: atoms += tether(m2,m2type,self.blen,self.dmin, + atoms[1],atoms[0],self.random) + + bonds = [] + for i in range(m1): + if i == 0: bonds.append([1,n-1,n]) + else: bonds.append([1,n+i-1,n+i]) + for i in range(m2): + if i == 0: bonds.append([1,0,n+m1]) + else: bonds.append([1,n+m1+i-1,n+m1+i]) + + volume = (n+m1+m2) * pi / 6.0 + return atoms,bonds,[],[],volume + + # -------------------------------------------------------------------- + # params = nsize,m1,m2,m3,ntype,m1type,m2type,m3type + # nsize,ntype = size,type of triangle center + # m123,m123type = length of tethers on each corner (m123 = 0 = no tether) + + def tri(self,*params): + nsize = params[0] + m1 = params[1] + m2 = params[2] + m3 = params[3] + ntype = params[4] + m1type = params[5] + m2type = params[6] + m3type = params[7] + + atoms = [] + for i in range(nsize): + n = nsize - i + for j in range(n): + x,y,z = 0.5*i*self.blen + j*self.blen, i*self.blen*sqrt(3.0)/2.0, 0.0 + atoms.append([ntype,x,y,z]) + + n = len(atoms) + if m1: atoms += tether(m1,m1type,self.blen,self.dmin, + atoms[1],atoms[0],self.random) + if m2: atoms += tether(m2,m2type,self.blen,self.dmin, + atoms[nsize-2],atoms[nsize-1],self.random) + if m3: atoms += tether(m3,m3type,self.blen,self.dmin, + atoms[n-2],atoms[n-1],self.random) + + bonds = [] + for i in range(m1): + if i == 0: bonds.append([1,0,n]) + else: bonds.append([1,n+i-1,n+i]) + for i in range(m2): + if i == 0: bonds.append([1,nsize-1,n+m1]) + else: bonds.append([1,n+m1+i-1,n+m1+i]) + for i in range(m3): + if i == 0: bonds.append([1,n-1,n+m1+m2]) + else: bonds.append([1,n+m1+m2+i-1,n+m1+m2+i]) + + volume = (nsize*(nsize+1)/2 + m1+m2+m3) * pi / 6.0 + return atoms,bonds,[],[],volume + + # -------------------------------------------------------------------- + # params = m1,m2,m3,m4,m5,m6,ntype,m1type,m2type,m3type,m4type,m5type,m6type + # ntype = type of hex center + # m123456,m123456type = length of tethers on each corner (m = 0 = no tether) + + def hex(self,*params): + m1 = params[0] + m2 = params[1] + m3 = params[2] + m4 = params[3] + m5 = params[4] + m6 = params[5] + ntype = params[6] + m1type = params[7] + m2type = params[8] + m3type = params[9] + m4type = params[10] + m5type = params[11] + m6type = params[12] + + atoms = [] + atoms.append([ntype,0.0,0.0,0.0]) + atoms.append([ntype,self.blen,0.0,0.0]) + atoms.append([ntype,-self.blen,0.0,0.0]) + atoms.append([ntype,self.blen/2.0,self.blen*sqrt(3.0)/2.0,0.0]) + atoms.append([ntype,-self.blen/2.0,self.blen*sqrt(3.0)/2.0,0.0]) + atoms.append([ntype,self.blen/2.0,-self.blen*sqrt(3.0)/2.0,0.0]) + atoms.append([ntype,-self.blen/2.0,-self.blen*sqrt(3.0)/2.0,0.0]) + + n = len(atoms) + if m1: atoms += tether(m1,m1type,self.blen,self.dmin, + atoms[0],atoms[1],self.random) + if m2: atoms += tether(m2,m2type,self.blen,self.dmin, + atoms[0],atoms[2],self.random) + if m3: atoms += tether(m3,m3type,self.blen,self.dmin, + atoms[0],atoms[3],self.random) + if m4: atoms += tether(m4,m4type,self.blen,self.dmin, + atoms[0],atoms[4],self.random) + if m5: atoms += tether(m5,m5type,self.blen,self.dmin, + atoms[0],atoms[5],self.random) + if m6: atoms += tether(m6,m6type,self.blen,self.dmin, + atoms[0],atoms[6],self.random) + + bonds = [] + for i in range(m1): + if i == 0: bonds.append([1,1,n]) + else: bonds.append([1,n+i-1,n+i]) + for i in range(m2): + if i == 0: bonds.append([1,2,n+m1]) + else: bonds.append([1,n+m1+i-1,n+m1+i]) + for i in range(m3): + if i == 0: bonds.append([1,3,n+m1+m2]) + else: bonds.append([1,n+m1+m2+i-1,n+m1+m2+i]) + for i in range(m4): + if i == 0: bonds.append([1,4,n+m1+m2+m3]) + else: bonds.append([1,n+m1+m2+m3+i-1,n+m1+m2+m3+i]) + for i in range(m5): + if i == 0: bonds.append([1,5,n+m1+m2+m3+m4]) + else: bonds.append([1,n+m1+m2+m3+m4+i-1,n+m1+m2+m3+m4+i]) + for i in range(m6): + if i == 0: bonds.append([1,6,n+m1+m2+m3+m4+m5]) + else: bonds.append([1,n+m1+m2+m3+m4+m5+i-1,n+m1+m2+m3+m4+m5+i]) + + volume = (7 + m1+m2+m3+m4+m5+m6) * pi / 6.0 + return atoms,bonds,[],[],volume + + # -------------------------------------------------------------------- + # params = sep,type + # sep = separation distance of two particles + # type = type of 2 particles + + def dimer(self,*params): + sep = params[0] + type = params[1] + + atoms = [] + x,y,z = 0.0,0.0,0.0 + atoms.append([type,x,y,z]) + x,y,z = sep,0.0,0.0 + atoms.append([type,x,y,z]) + + volume = 2 * pi / 6.0 # need to account for overlap and 2d/3d + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = N,sep,type + # N = lengths of each arm of star (must be odd) + # sep = separation distance of consecutive particles + # type = type of all particles + + def star2d(self,*params): + n = params[0] + sep = params[1] + type = params[2] + if n % 2 == 0: + raise StandardError, "N in patch::star2d is not odd" + middle = n/2 + + atoms = [] + x,y,z = 0.0,0.0,0.0 + atoms.append([type,x,y,z]) + for i in range(n): + i -= middle + if i == 0: continue + x,y,z = i*sep,0.0,0.0 + atoms.append([type,x,y,z]) + for i in range(n): + i -= middle + if i == 0: continue + x,y,z = 0.0,i*sep,0.0 + atoms.append([type,x,y,z]) + + volume = (2*n-1) * pi / 6.0 # need to account for overlap and 2d/3d + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = N,M,sep,type + # N,M = lengths of each side of box + # sep = separation distance of consecutive particles + # type = type of all particles + + def box2d(self,*params): + n = params[0] + m = params[1] + sep = params[2] + type = params[3] + + height = (m-1) * sep + width = (n-1) * sep + + atoms = [] + for i in range(n): + x,y,z = i*sep,0.0,0.0 + atoms.append([type,x,y,z]) + for i in range(n): + x,y,z = i*sep,height,0.0 + atoms.append([type,x,y,z]) + for i in range(1,m-1,1): + x,y,z = 0.0,i*sep,0.0 + atoms.append([type,x,y,z]) + for i in range(1,m-1,1): + x,y,z = width,i*sep,0.0 + atoms.append([type,x,y,z]) + + volume = (2*(n+m-2)) * pi / 6.0 # need to account for overlap and 2d/3d + return atoms,[],[],[],volume + + # -------------------------------------------------------------------- + # params = a,type + # a = edge length of tet + # type = type of each vertex in tet + + def tritet(self,*params): + a = params[0] + type = params[1] + cubeside = a/sqrt(2) + v = 0.5*cubeside + + atoms = [] + tris = [] + + # 4 corner pts of tet + + c1 = [+v/2,+v/2,+v/2] + c2 = [-v/2,-v/2,+v/2] + c3 = [-v/2,+v/2,-v/2] + c4 = [+v/2,-v/2,-v/2] + + # 4 triangles on faces of tet, outward normals via rh rule + + tris.append(c1+c3+c2) + tris.append(c1+c2+c4) + tris.append(c1+c3+c4) + tris.append(c2+c3+c4) + + # 4 atoms at centroids of 4 triangles + + atoms.append([type,(c1[0]+c3[0]+c2[0])/3.0,(c1[1]+c3[1]+c2[1])/3.0, + (c1[2]+c3[2]+c2[2])/3.0]) + atoms.append([type,(c1[0]+c2[0]+c4[0])/3.0,(c1[1]+c2[1]+c4[1])/3.0, + (c1[2]+c2[2]+c4[2])/3.0]) + atoms.append([type,(c1[0]+c3[0]+c4[0])/3.0,(c1[1]+c3[1]+c4[1])/3.0, + (c1[2]+c3[2]+c4[2])/3.0]) + atoms.append([type,(c2[0]+c3[0]+c4[0])/3.0,(c2[1]+c3[1]+c4[1])/3.0, + (c2[2]+c3[2]+c4[2])/3.0]) + + volume = sqrt(2)/12 * a*a*a + return atoms,[],tris,[],volume + + # -------------------------------------------------------------------- + # params = Alo,Ahi,Blo,Bhi,Clo,Chi,type + # Alo to Ahi = bounds of edge length in x of box + # Blo to Bhi = bounds of edge length in y of box + # Clo to Chi = bounds of edge length in y of box + # type = type of each vertex in rectangular box + + def tribox(self,*params): + alo = params[0] + ahi = params[1] + blo = params[2] + bhi = params[3] + clo = params[4] + chi = params[5] + type = params[6] + + a = alo + self.random()*(ahi-alo) + b = blo + self.random()*(bhi-blo) + c = clo + self.random()*(chi-clo) + + atoms = [] + tris = [] + + # 8 corner pts of rectangular box + + c1 = [-a/2,-b/2,-c/2] + c2 = [+a/2,-b/2,-c/2] + c3 = [-a/2,+b/2,-c/2] + c4 = [+a/2,+b/2,-c/2] + c5 = [-a/2,-b/2,+c/2] + c6 = [+a/2,-b/2,+c/2] + c7 = [-a/2,+b/2,+c/2] + c8 = [+a/2,+b/2,+c/2] + + # 12 triangles on faces of cube, outward normals via rh rule + + tris.append(c1+c7+c3) + tris.append(c1+c5+c7) + tris.append(c2+c4+c8) + tris.append(c2+c8+c6) + tris.append(c1+c2+c6) + tris.append(c1+c6+c5) + tris.append(c3+c8+c4) + tris.append(c3+c7+c8) + tris.append(c1+c4+c2) + tris.append(c1+c3+c4) + tris.append(c5+c6+c8) + tris.append(c5+c8+c7) + + # 12 atoms at centroids of 12 triangles + + atoms.append([type,(c1[0]+c7[0]+c3[0])/3.0,(c1[1]+c7[1]+c3[1])/3.0, + (c1[2]+c7[2]+c3[2])/3.0]) + atoms.append([type,(c1[0]+c5[0]+c7[0])/3.0,(c1[1]+c5[1]+c7[1])/3.0, + (c1[2]+c5[2]+c7[2])/3.0]) + atoms.append([type,(c2[0]+c4[0]+c8[0])/3.0,(c2[1]+c4[1]+c8[1])/3.0, + (c2[2]+c4[2]+c8[2])/3.0]) + atoms.append([type,(c2[0]+c8[0]+c6[0])/3.0,(c2[1]+c8[1]+c6[1])/3.0, + (c2[2]+c8[2]+c6[2])/3.0]) + atoms.append([type,(c1[0]+c2[0]+c6[0])/3.0,(c1[1]+c2[1]+c6[1])/3.0, + (c1[2]+c2[2]+c6[2])/3.0]) + atoms.append([type,(c1[0]+c6[0]+c5[0])/3.0,(c1[1]+c6[1]+c5[1])/3.0, + (c1[2]+c6[2]+c5[2])/3.0]) + atoms.append([type,(c3[0]+c8[0]+c4[0])/3.0,(c3[1]+c8[1]+c4[1])/3.0, + (c3[2]+c8[2]+c4[2])/3.0]) + atoms.append([type,(c3[0]+c7[0]+c8[0])/3.0,(c3[1]+c7[1]+c8[1])/3.0, + (c3[2]+c7[2]+c8[2])/3.0]) + atoms.append([type,(c1[0]+c4[0]+c2[0])/3.0,(c1[1]+c4[1]+c2[1])/3.0, + (c1[2]+c4[2]+c2[2])/3.0]) + atoms.append([type,(c1[0]+c3[0]+c4[0])/3.0,(c1[1]+c3[1]+c4[1])/3.0, + (c1[2]+c3[2]+c4[2])/3.0]) + atoms.append([type,(c5[0]+c6[0]+c8[0])/3.0,(c5[1]+c6[1]+c8[1])/3.0, + (c5[2]+c6[2]+c8[2])/3.0]) + atoms.append([type,(c5[0]+c8[0]+c7[0])/3.0,(c5[1]+c8[1]+c7[1])/3.0, + (c5[2]+c8[2]+c7[2])/3.0]) + + volume = a*b*c + return atoms,[],tris,[],volume + + # -------------------------------------------------------------------- + # params = Alo,Ahi,Blo,Bhi,type + # Alo to Ahi = bounds of edge length in x of rectangle + # Blo to Bhi = bounds of edge length in y of rectangle + # type = type of each line segment in rectangle + + def linebox(self,*params): + alo = float(params[0]) + ahi = float(params[1]) + blo = float(params[2]) + bhi = float(params[3]) + type = params[4] + + a = alo + self.random()*(ahi-alo) + b = blo + self.random()*(bhi-blo) + + atoms = [] + segments = [] + + # 4 atoms at center points of line segments in 2d + + atoms.append([type,0,-b/2,0]) + atoms.append([type,a/2,0,0]) + atoms.append([type,0,b/2,0]) + atoms.append([type,-a/2,0,0]) + + # 4 line segments as displacements from atom + + segments.append([-a/2,0,a/2,0]) + segments.append([0,-b/2,0,b/2]) + segments.append([a/2,0,-a/2,0]) + segments.append([0,b/2,0,-b/2]) + + volume = a*b + return atoms,[],[],segments,volume + + # -------------------------------------------------------------------- + # params = Alo,Ahi,Blo,Bhi,type + # Alo to Ahi = bounds of base length in x of triangle + # Blo to Bhi = bounds of heigth in y of isosceles triangle + # type = type of each line segment in triangle + + def linetri(self,*params): + alo = float(params[0]) + ahi = float(params[1]) + blo = float(params[2]) + bhi = float(params[3]) + type = params[4] + + base = alo + self.random()*(ahi-alo) + ht = blo + self.random()*(bhi-blo) + + atoms = [] + segments = [] + + # 3 atoms at center points of line segments in 2d + + atoms.append([type,0,-ht/2,0]) + atoms.append([type,base/4,0,0]) + atoms.append([type,-base/4,0,0]) + + # 3 line segments as displacements from atom + + segments.append([-base/2,0,base/2,0]) + segments.append([base/4,-ht/2,-base/4,ht/2]) + segments.append([base/4,ht/2,-base/4,-ht/2]) + + volume = 0.5*base*ht + return atoms,[],[],segments,volume + + # -------------------------------------------------------------------- + + def random(self): + k = self.seed/IQ + self.seed = IA*(self.seed-k*IQ) - IR*k + if self.seed < 0: + self.seed += IM + return AM*self.seed + +# -------------------------------------------------------------------- +# random number generator class + +IM = 2147483647 +AM = 1.0/IM +IA = 16807 +IQ = 127773 +IR = 2836 + +# -------------------------------------------------------------------- +# push atom onto sphere surface of diam and return [type,x,y,z] + +def atom_on_sphere(diam,type,x,y,z): + if x == 0.0 and y == 0.0 and z == 0.0: scale = 0.0 + else: scale = 0.5*diam / sqrt(x*x + y*y + z*z) + return [type,scale*x,scale*y,scale*z] + +# -------------------------------------------------------------------- +# make a sphere from a template with some atoms in patches w/ different types + +def make_sphere(template,diam,type0,patches): + atoms = [] + n = 0 + for atom in template: + n += 1 + type = type0 + for pair in patches: + patch = pair[1] + if n in patch: + type = pair[0] + atoms.append(atom_on_sphere(diam,type,atom[0],atom[1],atom[2])) + return atoms + +# -------------------------------------------------------------------- +# build a tether of length M of mtype, connected to atom1 with prev atom0 +# blen = bond length between successive tether atoms +# dmin = length restriction between atoms i-1,i+1 + +def tether(m,mtype,blen,dmin,atom0,atom1,random): + atoms = [atom0,atom1] + for i in range(m): + imonomer = len(atoms) + restriction = True + while restriction: + rsq = 2.0 + while rsq > 1.0: + dx = 2.0*random() - 1.0 + dy = 2.0*random() - 1.0 + dz = 2.0*random() - 1.0 + rsq = dx*dx + dy*dy + dz*dz + r = sqrt(rsq) + dx,dy,dz = dx/r,dy/r,dz/r + x = atoms[imonomer-1][1] + dx*blen + y = atoms[imonomer-1][2] + dy*blen + z = atoms[imonomer-1][3] + dz*blen + dx = x - atoms[imonomer-2][1] + dy = y - atoms[imonomer-2][2] + dz = z - atoms[imonomer-2][3] + restriction = False + if sqrt(dx*dx + dy*dy + dz*dz) <= dmin: restriction = True + if not restriction: atoms.append([mtype,x,y,z]) + return atoms[2:] + +# -------------------------------------------------------------------- +# templates + +TRI5_HOLLOW = ((0,0,0),(1,0,0),(2,0,0),(3,0,0),(4,0,0), + (0.5,sqrt(3)/2,0),(3.5,sqrt(3)/2,0), + (1.0,2*sqrt(3)/2,0),(3.0,2*sqrt(3)/2,0), + (1.5,3*sqrt(3)/2,0),(2.5,3*sqrt(3)/2,0), + (2.0,4*sqrt(3)/2,0)) + +SIMPLE_7 = ((0,0,0),(1,0,0),(-1,0,0),(0,1,0),(0,-1,0),(0,0,1),(0,0,-1)) + +# C60 with added center point at end + +BUCKY_60 = ((0.014416695, 1.232517, -3.260650), + (1.236417, 1.719517, -2.768650), + (2.292417, 0.8265171, -2.492650), + (2.122416, -0.5504832, -2.709650), + (0.8954167, -1.040483, -3.204650), + (-0.1565833, -0.1504831, -3.479650), + (-1.018583, 1.984517, -2.678650), + (-0.4355836, 2.936517, -1.826650), + (0.9584165, 2.773517, -1.881650), + (1.734416, 2.937517, -0.7156501), + (3.065417, 0.9905167, -1.331650), + (2.790417, -1.238483, -1.682650), + (2.234416, -2.418483, -1.146650), + (1.012417, -2.905483, -1.638650), + (0.3414168, -2.215483, -2.669650), + (-1.052583, -2.051483, -2.614650), + (-1.360583, -0.7754831, -3.114650), + (-2.397583, -0.020483017, -2.529650), + (-2.227583, 1.356517, -2.312650), + (-1.059583, 3.265517, -0.6046500), + (-2.262583, 2.640517, -0.2406499), + (-2.848583, 1.684517, -1.095650), + (-3.402583, 0.5095167, -0.5616500), + (-3.124583, -0.5444832, -1.447650), + (-2.815583, -1.825483, -0.9456501), + (-1.781583, -2.577483, -1.527650), + (-1.113584, -3.265483, -0.5006499), + (0.2864165, -3.429483, -0.5566499), + (3.373417, -0.2854834, -0.8306501), + (1.018416, -1.984483, 2.678350), + (2.227417, -1.356483, 2.312350), + (2.398417, 0.020516872, 2.530350), + (1.360417, 0.7755170, 3.114350), + (0.1564164, 0.1505170, 3.479350), + (-1.236583, -1.719483, 2.768350), + (-0.9585834, -2.773483, 1.882350), + (0.4354167, -2.936483, 1.826350), + (1.059417, -3.265483, 0.6053500), + (2.263417, -2.640483, 0.2403500), + (2.848417, -1.684483, 1.096350), + (3.124417, 0.5445170, 1.447350), + (2.815417, 1.825517, 0.9453500), + (1.781417, 2.577517, 1.527350), + (1.052417, 2.051517, 2.614350), + (-0.3415833, 2.215517, 2.669350), + (-0.8955836, 1.040517, 3.204350), + (-2.122583, 0.5505171, 2.710350), + (-2.292583, -0.8264832, 2.492350), + (-1.734583, -2.937483, 0.7163500), + (-2.786583, -2.048483, 0.4413500), + (-3.065583, -0.9904833, 1.331350), + (-3.373584, 0.2855167, 0.8313500), + (-2.790584, 1.238517, 1.683350), + (-2.233583, 2.418517, 1.146350), + (-1.011583, 2.905517, 1.638350), + (-0.2855835, 3.429517, 0.5563500), + (1.113417, 3.265517, 0.5003500), + (3.402417, -0.5094833, 0.5613500), + (2.786417, 2.047517, -0.4416499), + (-0.014583588, -1.232483, 3.261350), + (0.0, 0.0, 0.0)) + +# -------------------------------------------------------------------- +# C80 + +BUCKY_80 = ((-1.243762, -0.7016125, 3.734700), + (-1.248762, 0.6973875, 3.749700), + (-0.054762483, 1.429388, 3.749700), + (1.189238, 0.7893875, 3.735700), + (1.194237, -0.6086125, 3.783700), + (0.00023752451, -1.340613, 3.782700), + (-2.204762, 1.428387, 3.034700), + (-3.191762, 0.7883875, 2.276700), + (-3.223763, -0.6096125, 2.311700), + (-2.267762, -1.340613, 3.027700), + (0.2282375, -2.540613, 3.098700), + (-0.7787625, -3.147613, 2.340700), + (-2.039762, -2.541613, 2.343700), + (2.160238, -1.356613, 3.098700), + (1.563237, -2.550612, 2.675700), + (-0.2727625, 2.612388, 3.034700), + (-1.601763, 2.612388, 2.591700), + (-3.586762, -1.357612, 1.184700), + (-2.854763, -2.551612, 1.204700), + (2.223238, 1.412387, 3.028700), + (2.006238, 2.595387, 2.312700), + (0.7452375, 3.202387, 2.276700), + (0.3742375, 3.844388, 1.090700), + (-0.9547625, 3.844388, 0.6487002), + (-1.962763, 3.201387, 1.374700), + (-2.992763, 2.595387, 0.6477003), + (-3.595763, 1.411387, 1.090700), + (-3.958763, 0.6633875, -0.036299706), + (-3.930763, -0.7356125, -0.020299911), + (-3.568762, -1.385612, -1.205300), + (-2.837763, -2.579613, -1.186300), + (-2.439763, -3.168612, 0.019700050), + (-1.205762, -3.828612, 0.035700321), + (-0.3907624, -3.817612, 1.174700), + (0.9442375, -3.827612, 0.7516999), + (1.941237, -3.168612, 1.478700), + (3.190238, 0.6643875, 2.343700), + (3.158237, -0.7346125, 2.340700), + (3.579237, -1.384613, 1.175700), + (2.982238, -2.578612, 0.7527003), + (1.244238, 0.7023875, -3.735300), + (1.249238, -0.6976125, -3.750300), + (0.055237532, -1.428612, -3.750300), + (-1.189762, -0.7896125, -3.735300), + (-1.193763, 0.6093875, -3.783300), + (0.00023752451, 1.340387, -3.783300), + (2.205238, -1.428612, -3.034300), + (3.192237, -0.7886125, -2.276300), + (3.224237, 0.6093875, -2.312300), + (2.268238, 1.341388, -3.027300), + (-0.2277625, 2.541388, -3.098300), + (0.7792375, 3.147388, -2.340300), + (2.040237, 2.541388, -2.343300), + (-2.159763, 1.356387, -3.098300), + (-1.562762, 2.550387, -2.675300), + (0.2732375, -2.612613, -3.034300), + (1.601238, -2.612613, -2.592300), + (3.586237, 1.357388, -1.185300), + (2.854238, 2.551387, -1.204300), + (-2.223763, -1.411613, -3.028300), + (-2.005763, -2.595613, -2.312300), + (-0.7457625, -3.201612, -2.277300), + (-0.3747625, -3.844613, -1.090300), + (0.9542375, -3.844613, -0.6482999), + (1.962238, -3.201612, -1.375300), + (2.992238, -2.595613, -0.6482999), + (3.596237, -1.411613, -1.090300), + (3.958237, -0.6636125, 0.036700249), + (3.931237, 0.7353874, 0.019700050), + (3.569237, 1.385387, 1.205700), + (2.837237, 2.579388, 1.185700), + (2.439238, 3.168387, -0.019299984), + (1.205238, 3.828387, -0.036299706), + (0.3902375, 3.818388, -1.175300), + (-0.9447625, 3.828387, -0.7522998), + (-1.941762, 3.168387, -1.478300), + (-3.189763, -0.6646125, -2.344300), + (-3.157763, 0.7343875, -2.340300), + (-3.579762, 1.384387, -1.175300), + (-2.982763, 2.578387, -0.7522998)) diff --git a/src/patch.pyc b/src/patch.pyc new file mode 100644 index 0000000..98bde9c Binary files /dev/null and b/src/patch.pyc differ diff --git a/src/pdbfile.py b/src/pdbfile.py new file mode 100644 index 0000000..1713ada --- /dev/null +++ b/src/pdbfile.py @@ -0,0 +1,289 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# pdb tool + +oneline = "Read, write PDB files in combo with LAMMPS snapshots" + +docstr = """ +p = pdbfile("3CRO") create pdb object from PDB file or WWW +p = pdbfile("pep1 pep2") read in multiple PDB files +p = pdbfile("pep*") can use wildcards +p = pdbfile(d) read in snapshot data with no PDB file +p = pdbfile("3CRO",d) read in single PDB file with snapshot data + + string arg contains one or more PDB files + don't need .pdb suffix except wildcard must expand to file.pdb + if only one 4-char file specified and it is not found, + it will be downloaded from http://www.rcsb.org as 3CRO.pdb + d arg is object with atom coordinates (dump, data) + +p.one() write all output as one big PDB file to tmp.pdb +p.one("mine") write to mine.pdb +p.many() write one PDB file per snapshot: tmp0000.pdb, ... +p.many("mine") write as mine0000.pdb, mine0001.pdb, ... +p.single(N) write timestamp N as tmp.pdb +p.single(N,"new") write as new.pdb + + how new PDB files are created depends on constructor inputs: + if no d: one new PDB file for each file in string arg (just a copy) + if only d specified: one new PDB file per snapshot in generic format + if one file in str arg and d: one new PDB file per snapshot + using input PDB file as template + multiple input PDB files with a d is not allowed + +index,time,flag = p.iterator(0) +index,time,flag = p.iterator(1) + + iterator = loop over number of PDB files + call first time with arg = 0, thereafter with arg = 1 + N = length = # of snapshots or # of input PDB files + index = index of snapshot or input PDB file (0 to N-1) + time = timestep value (time stamp for snapshot, index for multiple PDB) + flag = -1 when iteration is done, 1 otherwise + typically call p.single(time) in iterated loop to write out one PDB file +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list +# for generic PDB file (no template) from a LJ unit system, +# the atoms in PDB file are too close together + +# Variables +# files = list of input PDB files +# data = data object (ccell,data,dump) to read snapshots from +# atomlines = dict of ATOM lines in original PDB file +# key = atom id, value = tuple of (beginning,end) of line + +# Imports and external programs + +import sys, types, glob, urllib + +# Class definition + +class pdbfile: + + # -------------------------------------------------------------------- + + def __init__(self,*args): + if len(args) == 1: + if type(args[0]) is types.StringType: + filestr = args[0] + self.data = None + else: + filestr = None + self.data = args[0] + elif len(args) == 2: + filestr = args[0] + self.data = args[1] + else: raise StandardError, "invalid args for pdb()" + + # flist = full list of all PDB input file names + # append .pdb if needed + + if filestr: + list = filestr.split() + flist = [] + for file in list: + if '*' in file: flist += glob.glob(file) + else: flist.append(file) + for i in xrange(len(flist)): + if flist[i][-4:] != ".pdb": flist[i] += ".pdb" + if len(flist) == 0: + raise StandardError,"no PDB file specified" + self.files = flist + else: self.files = [] + + if len(self.files) > 1 and self.data: + raise StandardError, "cannot use multiple PDB files with data object" + if len(self.files) == 0 and not self.data: + raise StandardError, "no input PDB file(s)" + + # grab PDB file from http://rcsb.org if not a local file + + if len(self.files) == 1 and len(self.files[0]) == 8: + try: + open(self.files[0],'r').close() + except: + print "downloading %s from http://rcsb.org" % self.files[0] + fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0] + urllib.urlretrieve(fetchstr,self.files[0]) + + if self.data and len(self.files): self.read_template(self.files[0]) + + # -------------------------------------------------------------------- + # write a single large PDB file for concatenating all input data or files + # if data exists: + # only selected atoms returned by extract + # atoms written in order they appear in snapshot + # atom only written if its tag is in PDB template file + # if no data: + # concatenate all input files to one output file + + def one(self,*args): + if len(args) == 0: file = "tmp.pdb" + elif args[0][-4:] == ".pdb": file = args[0] + else: file = args[0] + ".pdb" + + f = open(file,'w') + + # use template PDB file with each snapshot + + if self.data: + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + self.convert(f,which) + print >>f,"END" + print time, + sys.stdout.flush() + n += 1 + + else: + for file in self.files: + f.write(open(file,'r').read()) + print >>f,"END" + print file, + sys.stdout.flush() + + f.close() + print "\nwrote %d datasets to %s in PDB format" % (n,file) + + # -------------------------------------------------------------------- + # write series of numbered PDB files + # if data exists: + # only selected atoms returned by extract + # atoms written in order they appear in snapshot + # atom only written if its tag is in PDB template file + # if no data: + # just copy all input files to output files + + def many(self,*args): + if len(args) == 0: root = "tmp" + else: root = args[0] + + if self.data: + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + + if n < 10: + file = root + "000" + str(n) + elif n < 100: + file = root + "00" + str(n) + elif n < 1000: + file = root + "0" + str(n) + else: + file = root + str(n) + file += ".pdb" + + f = open(file,'w') + self.convert(f,which) + f.close() + + print time, + sys.stdout.flush() + n += 1 + + else: + n = 0 + for infile in self.files: + if n < 10: + file = root + "000" + str(n) + elif n < 100: + file = root + "00" + str(n) + elif n < 1000: + file = root + "0" + str(n) + else: + file = root + str(n) + file += ".pdb" + + f = open(file,'w') + f.write(open(infile,'r').read()) + f.close() + print file, + sys.stdout.flush() + + n += 1 + + print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root) + + # -------------------------------------------------------------------- + # write a single PDB file + # if data exists: + # time is timestamp in snapshot + # only selected atoms returned by extract + # atoms written in order they appear in snapshot + # atom only written if its tag is in PDB template file + # if no data: + # time is index into list of input PDB files + # just copy one input file to output file + + def single(self,time,*args): + if len(args) == 0: file = "tmp.pdb" + elif args[0][-4:] == ".pdb": file = args[0] + else: file = args[0] + ".pdb" + f = open(file,'w') + + if self.data: + which = self.data.findtime(time) + self.convert(f,which) + else: + f.write(open(self.files[time],'r').read()) + + f.close() + + # -------------------------------------------------------------------- + # iterate over list of input files or selected snapshots + # latter is done via data objects iterator + + def iterator(self,flag): + if not self.data: + if not flag: self.iterate = 0 + else: + self.iterate += 1 + if self.iterate > len(self.files): return 0,0,-1 + return self.iterate,self.iterate,1 + + return self.data.iterator(flag) + + # -------------------------------------------------------------------- + # read a PDB file and store ATOM lines + + def read_template(self,file): + lines = open(file,'r').readlines() + self.atomlines = {} + for line in lines: + if line.find("ATOM") == 0: + tag = int(line[4:11]) + begin = line[:30] + end = line[54:] + self.atomlines[tag] = (begin,end) + + # -------------------------------------------------------------------- + # convert one set of atoms to PDB format and write to f + + def convert(self,f,which): + time,box,atoms,bonds,tris,lines = self.data.viz(which) + if len(self.files): + for atom in atoms: + id = atom[0] + if self.atomlines.has_key(id): + (begin,end) = self.atomlines[id] + line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end) + print >>f,line, + else: + for atom in atoms: + begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1]) + middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4]) + end = " 1.00 0.00 NONE" + print >>f,begin+middle+end diff --git a/src/pdbfile.pyc b/src/pdbfile.pyc new file mode 100644 index 0000000..1fbf13a Binary files /dev/null and b/src/pdbfile.pyc differ diff --git a/src/pizza.py b/src/pizza.py new file mode 100755 index 0000000..ec88f13 --- /dev/null +++ b/src/pizza.py @@ -0,0 +1,441 @@ +#!/usr/local/bin/python -i + +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# Change log: +# 8/05, Steve Plimpton (SNL): original version +# 12/09, David Hart (SNL): except hook for Tkinter no-display error +# 5/11, David Hart (SNL): began list of excludes for no-display machines + +# ToDo list: + +# Help strings: + +version = "LPP 1.0 based on pizza - 7 Oct 2011" + +intro = """ +Pizza.py (%s), a toolkit written in Python +type ? for help, CTRL-D to quit +""" + +help = """ +pizza.py switch arg(s) switch arg(s) ... + -s silent (else print start-up help) + -t log dump raster load only these tools + -x raster rasmol load all tools except these + -f mine.py arg1 arg2 run script file with args + -c "vec = range(100)" run Python command + -q quit (else interactive) + +Everything typed at the ">" prompt is a Python command + +Additional commands available at ">" prompt: + ? print help message + ?? one-line for each tool and script + ? raster list tool commands or script syntax + ?? energy.py full documentation of tool or script + !ls -l shell command + @cd .. cd to a new directory + @log tmp.log log all commands typed so far to file + @run block.py arg1 arg2 run script file with args + @time d = dump("*.dump") time a command + +Tools: +""" + +# ------------------------------------------------------------------------- +# modules needed by pizza.py + +import sys, commands, os, string, exceptions, glob, re +from time import clock + +# readline not available in all Pythons + +try: + import readline + readline_flag = 1 +except ImportError, exception: + print "readline option not available" + readline_flag = 0 + +# create global Tk root if Tkinter is loaded +# used by all tools that do GUIs via Tkinter + +nodisplay = False +try: + import Tkinter + tkroot = Tkinter.Tk() + tkroot.withdraw() +except ImportError, exception: + nodisplay = True + pass +except Exception, exception: + nodisplay = True + pass + +# ------------------------------------------------------------------------- +# error trap that enables special commands at interactive prompt + +def trap(type,value,tback): + global argv + + # only check SyntaxErrors + + if not isinstance(value,exceptions.SyntaxError): + sys.__excepthook__(type,value,tback) + return + + # special commands at top level only, not in indented text entry + + if value.text[0].isspace(): + sys.__excepthook__(type,value,tback) + return + + # ? = top-level help + # ?? = one-line description of each tool and script + # ? name = one-line for each tool command or script purpose/syntax + # ?? name = entire documentation for tool or script + # name with no .py suffix is tool, name with .py suffix is script + + if value.text[0] == "?": + words = value.text.split() + + if len(words) == 1 and words[0] == "?": + print intro[1:] % version + print help[1:]," ", + for tool in tools: print tool, + print + + elif len(words) == 1 and words[0] == "??": + for tool in tools: + exec "oneline = oneline_%s" % tool + print "%-11s%s" % (tool,oneline) + print + + scripts = [] + for dir in PIZZA_SCRIPTS[1:]: + list = glob.glob("%s/*.py" % dir) + list.sort() + scripts += list + for script in scripts: + filename = os.path.basename(script) + lines = open(script,'r').readlines() + flag = 0 + for line in lines: + if line.find("Purpose:") >= 0: + flag = 1 + break + if flag: doc = line[line.find("Purpose:")+8:] + else: doc = " not available\n" + print "%-20s%s" % (filename,doc), + + elif len(words) == 2 and words[0] == "?": + if words[1][-3:] == ".py": + fileflag = 0 + for dir in PIZZA_SCRIPTS: + filename = "%s/%s" % (dir,words[1]) + if os.path.isfile(filename): + fileflag = 1 + lineflag = 0 + lines = open(filename,'r').readlines() + for line in lines: + if line.find("# Purpose:") >= 0: print line[2:], + if line.find("# Syntax:") >= 0: + lineflag = 1 + break + if not lineflag: print "%s has no Syntax line" % words[1] + else: print line[2:], + break + if not fileflag: + print "%s is not a recognized script" % words[1] + + else: + if words[1] in tools: + exec "txt = docstr_%s" % words[1] + txt = re.sub("\n\s*\n","\n",txt) + txt = re.sub("\n .*","",txt) + exec "print oneline_%s" % words[1] + print txt + else: + print "%s is not a recognized tool" % words[1] + + elif len(words) == 2 and words[0] == "??": + if words[1][-3:] == ".py": + fileflag = 0 + for dir in PIZZA_SCRIPTS: + filename = "%s/%s" % (dir,words[1]) + if os.path.isfile(filename): + fileflag = 1 + lines = open(filename,'r').readlines() + for line in lines: + if len(line.strip()) == 0: continue + if line[0] == '#': print line, + else: break + break + if not fileflag: + print "%s is not a recognized script" % words[1] + + else: + if words[1] in tools: + exec "print oneline_%s" % words[1] + exec "print docstr_%s" % words[1] + else: + print "%s is not a recognized class" % words[1] + + return + + # shell command like !ls, !ls -l + + if value.text[0] == "!": + os.system(value.text[1:]) + return + + # @ commands = @cd, @log, @run, @time + # for run and time, use namespace in execfile and exec commands + # else variables defined in script/command + # won't be set in top-level Pizza.py + + if value.text[0] == "@": + words = value.text.split() + if words[0][1:] == "cd": + os.chdir(words[1]) + return + elif words[0][1:] == "log": + if readline_flag == 0: + print "cannot use @log without readline module" + return + f = open(words[1],"w") + print >>f,"# pizza.py log file\n" + nlines = readline.get_current_history_length() + for i in xrange(1,nlines): + print >>f,readline.get_history_item(i) + f.close() + return + elif words[0][1:] == "run": + argv = words[1:] + file = argv[0] + flag = 0 + for dir in PIZZA_SCRIPTS: + fullfile = dir + '/' + file + if os.path.exists(fullfile): + flag = 1 + print "Executing file:",fullfile + execfile(fullfile,namespace) + break + if not flag: print "Could not find file",file + return + elif words[0][1:] == "time": + cmd = string.join(words[1:]) + t1 = clock() + exec cmd in namespace + t2 = clock() + print "CPU time = ",t2-t1 + return + + # unrecognized command, let system handle error + + sys.__excepthook__(type,value,tback) + +# ------------------------------------------------------------------------- +# process command-line switches +# store scripts and commands in tasks list + +silent = 0 +yes_tools = [] +no_tools = [] +tasks = [] +quitflag = 0 + +iarg = 1 +while (iarg < len(sys.argv)): + if (sys.argv[iarg][0] != '-'): + print "ERROR: arg is not a switch: %s" % (sys.argv[iarg]) + sys.exit() + if (sys.argv[iarg] == "-s"): + silent = 1 + iarg += 1 + elif (sys.argv[iarg] == "-t"): + jarg = iarg + 1 + while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'): + yes_tools.append(sys.argv[jarg]) + jarg += 1 + iarg = jarg + elif (sys.argv[iarg] == "-x"): + jarg = iarg + 1 + while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'): + no_tools.append(sys.argv[jarg]) + jarg += 1 + iarg = jarg + elif (sys.argv[iarg] == "-f"): + jarg = iarg + 1 + list = [] + while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'): + list.append(sys.argv[jarg]) + jarg += 1 + task = ("script",list) + tasks.append(task) + iarg = jarg + elif (sys.argv[iarg] == "-c"): + jarg = iarg + 1 + list = [] + while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'): + list.append(sys.argv[jarg]) + jarg += 1 + task = ("command",list) + tasks.append(task) + iarg = jarg + elif (sys.argv[iarg] == "-q"): + quitflag = 1 + iarg += 1 + else: + print "ERROR: unknown switch: %s" % (sys.argv[iarg]) + sys.exit() + +# print intro message + +if not silent: print intro[1:] % version, + +# error test on m,x command-line switches + +if len(yes_tools) > 0 and len(no_tools) > 0: + print "ERROR: cannot use -t and -x switches together" + sys.exit() + +# ------------------------------------------------------------------------- +# tools = list of tool names to import +# if -t switch was used, tools = just those files +# else scan for *.py files in all dirs in PIZZA_TOOLS list +# and then Pizza.py src dir (sys.path[0]) + +if not silent: print "Loading tools ..." +if not silent and nodisplay: print "Display not available ... no GUIs" + +try: from DEFAULTS import PIZZA_TOOLS +except: PIZZA_TOOLS = [] +PIZZA_TOOLS = map(os.path.expanduser,PIZZA_TOOLS) +PIZZA_TOOLS.append(sys.path[0]) + +if len(yes_tools) > 0: tools = yes_tools +else: + tools = [] + for dir in PIZZA_TOOLS: + tools += glob.glob(dir + "/*.py") + for i in range(len(tools)): + tools[i] = os.path.basename(tools[i]) + tools[i] = tools[i][:-3] + +# remove duplicate entries, reverse enables removing all but first entry + +tools.reverse() +for tool in tools: + while tools.count(tool) > 1: tools.remove(tool) +tools.reverse() + +# remove tools in EXCLUDE list and command-line -x list + +try: from DEFAULTS import PIZZA_EXCLUDE +except: PIZZA_EXCLUDE = [] +for tool in PIZZA_EXCLUDE: + if tool in tools: tools.remove(tool) +for tool in no_tools: + if tool in tools: tools.remove(tool) + +# add PIZZA_TOOLS dirs to front of module search path (sys.path) +# import each tool as a Python module and its documentation strings +# restore sys.path + +sys.path = PIZZA_TOOLS + sys.path + +failed = [] +for tool in tools: + #print "loading tool '%s'"%tool + if nodisplay and tool in ['gl']: + failed.append(tool) + continue + try: + exec "from %s import %s" % (tool,tool) + exec "from %s import oneline as oneline_%s" % (tool,tool) + exec "from %s import docstr as docstr_%s" % (tool,tool) + except Exception, exception: + print "%s tool did not load:" % tool + print " ",exception + failed.append(tool) + +for dir in PIZZA_TOOLS: sys.path = sys.path[1:] + +# final list of tools: remove tools where import failed, sort them + +for tool in failed: tools.remove(tool) +tools.sort() + +# add current working dir to sys.path so user can import own modules +# cwd isn't in sys.path when Pizza.py is launched + +sys.path.insert(0,'') + +# ------------------------------------------------------------------------- +# PIZZA_SCRIPTS = list of dirs to look in to find scripts + +try: from DEFAULTS import PIZZA_SCRIPTS +except: PIZZA_SCRIPTS = [] +PIZZA_SCRIPTS = map(os.path.expanduser,PIZZA_SCRIPTS) +PIZZA_SCRIPTS.insert(0,'.') +PIZZA_SCRIPTS.append(sys.path[1][:-3] + "scripts") # path for pizza.py + +# run specified script files and commands in order specified +# put arguments in argv so script can access them +# check list of PIZZA_SCRIPTS dirs to find script file +# catch errors so pizza.py will continue even if script is bad +# traceback logic prints where in the script the error occurred + +for task in tasks: + if task[0] == "script": + argv = task[1] + file = argv[0] + try: + flag = 0 + for dir in PIZZA_SCRIPTS: + fullfile = dir + '/' + file + if os.path.exists(fullfile): + print "Executing file:",fullfile + execfile(fullfile) + flag = 1 + break + if not flag: print "Could not find file",file + except StandardError, exception: + (type,value,tback) = sys.exc_info() + print type,value,tback + type = str(type) + type = type[type.find(".")+1:] + print "%s with value: %s" % (type,value) + tback = tback.tb_next + while tback: + print "error on line %d of file %s" % \ + (tback.tb_lineno,tback.tb_frame.f_code.co_filename) + tback = tback.tb_next + elif task[0] == "command": + argv = task[1] + cmd = "" + for arg in argv: cmd += arg + " " + exec cmd + +# ------------------------------------------------------------------------- +# store global namespace +# swap in a new exception handler +# change interactive prompts + +namespace = sys.modules['__main__'].__dict__ +sys.excepthook = trap +sys.ps1 = "> " +sys.ps2 = ". " + +# should now go interactive if launched with "python -i" +# unless -q switch used + +if quitflag > 0: sys.exit() diff --git a/src/plotview.py b/src/plotview.py new file mode 100644 index 0000000..05abc3d --- /dev/null +++ b/src/plotview.py @@ -0,0 +1,190 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# plotview tool + +oneline = "Plot multiple vectors from a data set" + +docstr = """ +p = plotview(d,pl) create GUI for viewing plots + + d = Pizza.py object that contains vectors (log, vec) + pl = Pizza.py plotting object (gnu, matlab) + +p.select(2) select one plot as current (1-N) +p.yes(3) toggle one plot's visibility +p.no(3) + + only one plot is selected at a time + multiple plots can be visible at same time + select is same as clicking on left-side radio-button + yes/no is same as clicking on right-side checkbox + +p.x = "Time" which vector is X vector (1st vec by default) +p.file("pressure") filename prefix for saving a plot +p.save() save currently selected plot to file.eps +""" + +# History +# 8/05, Matt Jones (BYU): original version + +# ToDo list +# option to plot all N vectors against linear index? + +# Variables +# source = source of vector data +# plot = plotting object +# nplots = # of plots (not including 1st vector) +# names = names of plots (from vector source) +# radiovar = index of clicked radio button (0 = none, 1-N) +# checkbuttons = list of check button objects +# checkvars = list of status of check buttons +# checkold = list of status of check buttons before click + +# Imports and external programs + +import sys, re, glob, time +from Tkinter import * + +# Class definition + +class plotview: + + # -------------------------------------------------------------------- + + def __init__(self,source,plot): + self.source = source + self.plot = plot + + # create GUI + + from __main__ import tkroot + root = Toplevel(tkroot) + root.title('Pizza.py plotview tool') + + self.frame1 = Frame(root) + self.frame2 = Frame(root) + self.frame3 = Frame(root) + + Button(self.frame1,text="Print As:",command=self.save).pack(side=TOP) + self.entry = Entry(self.frame1,width=16) + self.entry.insert(0,"tmp") + self.entry.pack(side=TOP) + + Label(self.frame2,text="Select").pack(side=LEFT) + Label(self.frame2,text = "Display").pack(side=RIGHT) + + self.nplots = source.nvec + self.names = source.names + self.x = self.names[0] + + self.radiovar = IntVar() + self.checkbuttons = [] + self.checkvars = [] + self.checkold = [] + + # for each vector (not including 1st) + # create a plot and title it + # create a line in GUI with selection and check button + + for i in range(self.nplots): + self.plot.select(i+1) + self.plot.xtitle(self.x) + self.plot.ytitle(self.names[i]) + self.plot.title(self.names[i]) + + b = BooleanVar() + b.set(0) + self.checkvars.append(b) + self.checkold.append(0) + + line = Frame(self.frame3) + rtitle = "%d %s" % (i+1,self.names[i]) + Radiobutton(line, text=rtitle, value=i+1, variable=self.radiovar, + command=self.radioselect).pack(side=LEFT) + cbutton = Checkbutton(line, variable=b, command=self.check) + cbutton.pack(side=RIGHT) + self.checkbuttons.append(cbutton) + line.pack(side=TOP,fill=X) + + self.radiovar.set(0) + self.frame1.pack(side=TOP) + self.frame2.pack(side=TOP,fill=X) + self.frame3.pack(side=TOP,fill=X) + + # -------------------------------------------------------------------- + # set radio button and checkbox + + def select(self,n): + self.plot.select(n) + self.radiovar.set(n) + self.yes(n) + + # -------------------------------------------------------------------- + # only invoke if currently unset + + def yes(self,n): + if not self.checkvars[n-1].get(): self.checkbuttons[n-1].invoke() + + # -------------------------------------------------------------------- + # only invoke if currently set + + def no(self,n): + if self.checkvars[n-1].get(): self.checkbuttons[n-1].invoke() + + # -------------------------------------------------------------------- + + def file(self,newtext): + oldtext = self.entry.get() + self.entry.delete(0,len(oldtext)) + self.entry.insert(0,newtext) + + # -------------------------------------------------------------------- + + def save(self): + n = self.radiovar.get() + if n == 0: raise StandardError,"no plot selected" + name = self.entry.get() + self.plot.save(name) + + # -------------------------------------------------------------------- + # called when any radio selection button is clicked + + def radioselect(self): + self.select(self.radiovar.get()) + + # -------------------------------------------------------------------- + # called when any checkbox is clicked + # draws or hides plot + # loop is to find which checkbox changed status + # grab x,y data to plot out of source object + + def check(self): + for i in range(self.nplots): + if int(self.checkvars[i].get()) != self.checkold[i]: + if self.checkvars[i].get(): + self.radiovar.set(i+1) + self.plot.select(i+1) + self.plot.xtitle(self.x) + x,y = self.source.get(self.x,self.names[i]) + self.plot.plot(x,y) + else: + if self.radiovar.get() == i+1: self.radiovar.set(0) + self.plot.hide(i+1) + self.checkold[i] = int(self.checkvars[i].get()) + + # -------------------------------------------------------------------- + # called by lammps() tool to update all visible plots with new data + + def refresh(self): + for i in range(self.nplots): + if self.checkvars[i].get(): + self.plot.select(i+1) + self.plot.xtitle(self.x) + x,y = self.source.get(self.x,self.names[i]) + self.plot.plot(x,y) diff --git a/src/plotview.pyc b/src/plotview.pyc new file mode 100644 index 0000000..acdda5a Binary files /dev/null and b/src/plotview.pyc differ diff --git a/src/rasmol.py b/src/rasmol.py new file mode 100644 index 0000000..513eae3 --- /dev/null +++ b/src/rasmol.py @@ -0,0 +1,287 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# rasmol tool + +oneline = "3d visualization via RasMol program" + +docstr = """ +r = rasmol(p) create RasMol wrapper for pdb object p + +r.file = "image" file prefix for created images (def = "image") + +r.show(N) show snapshot at timestep N with default script +r.show(N,"my.rasmol") use file as RasMol script + +r.all() make images of all selected snapshots with def script +r.all("my.rasmol") use file as RasMol script + +r.run(N) run RasMol interactivly on snapshot N +r.run(N,"new.rasmol") adjust via mouse or RasMol commands +r.run(N,"new.rasmol","old.rasmol") type quit to save RasMol script file + + if 2 args, 2nd arg is new script file, else save to "tmp.rasmol" + if 3 args, 3rd arg is initial script file, else use default script +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list +# allow zoom, view, movie, pan settings like other viz tools +# so can specify rock & make fly-by movies of an image + +# Variables + +# Imports and external programs + +import sys, os, commands, re, types +from pdbfile import pdbfile + +try: from DEFAULTS import PIZZA_RASMOL +except: PIZZA_RASMOL = "rasmol" +try: from DEFAULTS import PIZZA_DISPLAY +except: PIZZA_DISPLAY = "display" + +# Class definition + +class rasmol: + + # -------------------------------------------------------------------- + + def __init__(self,pdb): + self.pdb = pdb + self.file = "image" + + # -------------------------------------------------------------------- + + def start(self): + self.RASMOL = os.popen(PIZZA_RASMOL,'w') + + # -------------------------------------------------------------------- + + def enter(self): + while 1: + command = raw_input("rasmol> ") + if command == "quit" or command == "exit": return + self.__call__(command) + + # -------------------------------------------------------------------- + + def __call__(self,command): + self.RASMOL.write(command + '\n') + self.RASMOL.flush() + + # -------------------------------------------------------------------- + + def stop(self): + self.__call__("quit") + del self.RASMOL + + # -------------------------------------------------------------------- + + def show(self,*list): + + # create tmp.pdb with atom data + + n = list[0] + self.pdb.single(n,"tmp.pdb") + + # if RasMol input script specified, read it + # replace load pdb "file" with load pdb "%s" + # if no RasMol input script specified, use rasmol_template + + if len(list) == 2: + rasmol_text = open(list[1],"r").read() + rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text) + else: + rasmol_text = rasmol_template + + # write rasmol_text to tmp.rasmol, substituting tmp.pdb for filename + + f = open("tmp.rasmol","w") + text = rasmol_text % "tmp.pdb" + print >>f,text + f.close() + + # run RasMol to create image in tmp.gif + + self.start() + self.__call__("source tmp.rasmol") + self.__call__("write tmp.gif") + self.stop() + + # display the image + + cmd = "%s tmp.gif" % (PIZZA_DISPLAY) + commands.getoutput(cmd) + + # -------------------------------------------------------------------- + + def all(self,*list): + + # if RasMol script specified, read it + # replace load pdb "file" with load pdb "%s" + # if no RasMol script specified, just use rasmol_template + + if len(list) == 1: + rasmol_text = open(list[0],"r").read() + rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text) + else: + rasmol_text = rasmol_template + + # iterate over all timesteps + # write snapshot to tmpN.pdb + # write RasMol input script to tmpN.rasmol + + n = flag = 0 + while 1: + which,time,flag = self.pdb.iterator(flag) + + if flag == -1: break + + if n < 10: + ncount = "000" + str(n) + elif n < 100: + ncount = "00" + str(n) + elif n < 1000: + ncount = "0" + str(n) + else: + ncount = str(n) + + file_pdb = "tmp%s.pdb" % ncount + self.pdb.single(time,file_pdb) + + text = rasmol_text % file_pdb + file_rasmol = "tmp%s.rasmol" % ncount + f = open(file_rasmol,"w") + print >>f,text + f.close() + + print time, + sys.stdout.flush() + n += 1 + + # run RasMol on each pair of RasMol scripts and PDB files + + self.start() + + loop = n + for n in xrange(loop): + if n < 10: + ncount = "000" + str(n) + elif n < 100: + ncount = "00" + str(n) + elif n < 1000: + ncount = "0" + str(n) + else: + ncount = str(n) + + source_str = "source tmp%s.rasmol" % ncount + self.__call__(source_str) + write_str = "write %s%s.gif" % (self.file,ncount) + self.__call__(write_str) + + self.stop() + + # clean up + + commands.getoutput("rm tmp*.pdb") + commands.getoutput("rm tmp*.rasmol") + + # -------------------------------------------------------------------- + + def run(self,*list): + + # create tmp.pdb with atom data + + n = list[0] + self.pdb.single(n,"tmp.pdb") + + # if RasMol script specified, read it + # replace load pdb "file" with load pdb "%s" + # if no RasMol script specified, just use rasmol_template + + if len(list) == 3: + rasmol_text = open(list[2],"r").read() + rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text) + else: + rasmol_text = rasmol_template + + # write rasmol_text to tmp.rasmol + + f = open("tmp.rasmol","w") + text = rasmol_template % "tmp.pdb" + print >>f,text + f.close() + + # run RasMol to create image in tmp.gif + + self.start() + self.__call__("source tmp.rasmol") + self.enter() + + if len(list) > 1: newfile = list[1] + else: newfile = "tmp.rasmol" + self.__call__("write script %s" % newfile) + self.stop() + +# -------------------------------------------------------------------- +# generic Rasmol script with spacefill option +# PDB filename must be filled in for load command + +rasmol_template = """ +# Creator: RasMol Version 2.7.1 + +zap +load pdb "%s" +background [0,0,0] +set ambient 40 +set specular off + +reset +slab off + +set axes off +set boundingbox off +set unitcell off +set bondmode and +dots off + +# Avoid Colour Problems! +select all +colour bonds none +colour backbone none +colour hbonds none +colour ssbonds none +colour ribbons none +colour white + +# Atoms +colour atoms cpk +spacefill on +set shadow off + +# Bonds +wireframe off + +# Ribbons +ribbons off + +# Backbone +backbone off + +# Labels +labels off + +# Monitors +monitors off + +ssbonds off +hbonds off +""" diff --git a/src/rasmol.pyc b/src/rasmol.pyc new file mode 100644 index 0000000..55645ed Binary files /dev/null and b/src/rasmol.pyc differ diff --git a/src/raster.py b/src/raster.py new file mode 100644 index 0000000..8d6d03d --- /dev/null +++ b/src/raster.py @@ -0,0 +1,669 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# raster tool + +oneline = "3d visualization via Raster3d program" + +docstr = """ +r = raster(d) create Raster3d wrapper for data in d + + d = atom snapshot object (dump, data) + +r.bg("black") set background color (def = "black") +r.size(N) set image size to NxN +r.size(N,M) set image size to NxM +r.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +r.shift(x,y) translate by x,y pixels in view window (def = 0,0) +r.zoom(0.5) scale image by factor (def = 1) +r.box(0/1/2) 0/1/2 = none/variable/fixed box +r.box(0/1/2,"green") set box color +r.box(0/1/2,"red",4) set box edge thickness +r.file = "image" file prefix for created images (def = "image") + +r.show(N) show image of snapshot at timestep N + +r.all() make images of all selected snapshots +r.all(P) images of all, start file label at P +r.all(N,M,P) make M images of snapshot N, start label at P + +r.pan(60,135,1.0,40,135,1.5) pan during all() operation +r.pan() no pan during all() (default) + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values + +r.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +r.select = "" no extra aselect (default) + + %g varies from 0.0 to 1.0 from beginning to end of all() + +r.label(x,y,"h",size,"red","This is a label") add label to each image +r.nolabel() delete all labels + + x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font + size = fontsize (e.g. 10), "red" = color of text + +r.acol(2,"green") set atom colors by atom type (1-N) +r.acol([2,4],["red","blue"]) 1st arg = one type or list of types +r.acol(0,"blue") 2nd arg = one color or list of colors +r.acol(range(20),["red","blue"]) if list lengths unequal, interpolate +r.acol(range(10),"loop") assign colors in loop, randomly ordered + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next + +r.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol() + +r.bcol() set bond color, same args as acol() +r.brad() set bond thickness, same args as arad() + +r.tcol() set triangle color, same args as acol() +r.tfill() set triangle fill, 0 fill, 1 line, 2 both + +r.lcol() set line color, same args as acol() +r.lrad() set line thickness, same args as arad() + +r.adef() set atom/bond/tri/line properties to default +r.bdef() default = "loop" for colors, 0.45 for radii +r.tdef() default = 0.25 for bond/line thickness +r.ldef() default = 0 fill + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors["nickname"] = [R,G,B] set new RGB values from 0 to 255 + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc +""" + +# History +# 8/05, Steve Plimpton (SNL): original version +# 9/05, Steve Plimpton (SNL): adjusted box and label attributes + +# ToDo list +# when do aselect with select str while looping N times on same timestep +# would not let you grow # of atoms selected +# triangles are not drawn with fill type + +# Variables +# ztheta = vertical angle from z-azis to view from +# azphi = azimuthal angle to view from +# xshift,yshift = xy translation of scene (in pixels) +# distance = size of simulation box (largest dim) +# eye = viewpoint distance from center of scene +# file = filename prefix to use for images produced +# boxflag = 0/1/2 for drawing simulation box: none/variable/fixed +# bxcol = color of box +# bxthick = thickness of box +# bgcol = color of background +# vizinfo = scene attributes +# xtrans,ytrans,ztrans = translation factors computed by Raster3d + +# Imports and external programs + +import sys, os, commands, re +from vizinfo import vizinfo +from math import fabs,atan,cos,sin + +try: from DEFAULTS import PIZZA_RENDER +except: PIZZA_RENDER = "render" +try: from DEFAULTS import PIZZA_LABEL3D +except: PIZZA_LABEL3D = "label3d" +try: from DEFAULTS import PIZZA_DISPLAY +except: PIZZA_DISPLAY = "display" + +# Class definition + +class raster: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + self.xpixels = 512 + self.ypixels = 512 + self.ztheta = 60 + self.azphi = 30 + self.scale = 1.0 + self.xshift = self.yshift = 0 + self.eye = 50.0 + + self.file = "image" + self.boxflag = 0 + self.bxcol = [1,1,0] + self.bxthick = 0.3 + self.bgcol = [0,0,0] + self.labels = [] + self.panflag = 0 + self.select = "" + + self.vizinfo = vizinfo() + self.adef() + self.bdef() + self.tdef() + self.ldef() + + # -------------------------------------------------------------------- + + def bg(self,color): + from vizinfo import colors + self.bgcol = [colors[color][0]/255.0,colors[color][1]/255.0, + colors[color][2]/255.0] + + # -------------------------------------------------------------------- + + def size(self,xnew,ynew=None): + self.xpixels = xnew + if not ynew: self.ypixels = self.xpixels + else: self.ypixels = ynew + + # -------------------------------------------------------------------- + + def rotate(self,ztheta,azphi): + self.ztheta = ztheta; + self.azphi = azphi; + + # -------------------------------------------------------------------- + + def shift(self,x,y): + self.xshift = x; + self.yshift = y; + + # -------------------------------------------------------------------- + + def zoom(self,scale): + self.scale = scale; + + # -------------------------------------------------------------------- + + def box(self,*args): + self.boxflag = args[0] + if len(args) > 1: + from vizinfo import colors + self.bxcol = [colors[args[1]][0]/255.0,colors[args[1]][1]/255.0, + colors[args[1]][2]/255.0] + if len(args) > 2: self.bxthick = args[2] + + # -------------------------------------------------------------------- + # scale down point-size by 3x + + def label(self,x,y,font,point,color,text): + from vizinfo import colors + scaledcolor = [colors[color][0]/255.0,colors[color][1]/255.0, + colors[color][2]/255.0] + list = [x,y,fontlist[font],point/3.0,"Left",scaledcolor,text] + self.labels.append(list) + + # -------------------------------------------------------------------- + + def nolabel(self): + self.labels = [] + + # -------------------------------------------------------------------- + # show a single snapshot + # distance from snapshot box or max box for all selected steps + # always pre-call single() to re-center simulation data + + def show(self,ntime): + data = self.data + which = data.findtime(ntime) + time,box,atoms,bonds,tris,lines = data.viz(which) + if self.boxflag == 2: box = data.maxbox() + self.distance = compute_distance(box) + + self.xtrans = self.ytrans = self.ztrans = 0.0 + output = self.single(1,self.file,box,atoms,bonds,tris,lines) + print output + nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output) + self.xtrans = float(nums[0][0]) + self.ytrans = float(nums[0][1]) + self.ztrans = float(nums[0][2]) + + self.single(0,self.file,box,atoms,bonds,tris,lines) + cmd = "%s %s.png" % (PIZZA_DISPLAY,self.file) + commands.getoutput(cmd) + + # -------------------------------------------------------------------- + + def pan(self,*list): + if len(list) == 0: self.panflag = 0 + else: + self.panflag = 1 + self.ztheta_start = list[0] + self.azphi_start = list[1] + self.scale_start = list[2] + self.ztheta_stop = list[3] + self.azphi_stop = list[4] + self.scale_stop = list[5] + + # -------------------------------------------------------------------- + + def all(self,*list): + data = self.data + if len(list) == 0: + nstart = 0 + ncount = data.nselect + elif len(list) == 1: + nstart = list[0] + ncount = data.nselect + else: + ntime = list[0] + nstart = list[2] + ncount = list[1] + + if self.boxflag == 2: box = data.maxbox() + + # loop over all selected steps + # distance from 1st snapshot box or max box for all selected steps + # pre-call single() to re-center simulation data on 1st step or if panning + + if len(list) <= 1: + + n = nstart + i = flag = 0 + while 1: + which,time,flag = data.iterator(flag) + if flag == -1: break + + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,time) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + + if n == nstart or self.panflag: + self.xtrans = self.ytrans = self.ztrans = 0.0 + output = self.single(1,file,box,atoms,bonds,tris,lines) + nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output) + self.xtrans = float(nums[0][0]) + self.ytrans = float(nums[0][1]) + self.ztrans = float(nums[0][2]) + + self.single(0,file,box,atoms,bonds,tris,lines) + print time, + sys.stdout.flush() + i += 1 + n += 1 + + # loop ncount times on same step + # distance from 1st snapshot box or max box for all selected steps + # pre-call single() to re-center simulation data on 1st step or if panning + + else: + + which = data.findtime(ntime) + + n = nstart + for i in range(ncount): + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,ntime) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + + if n == nstart or self.panflag: + self.xtrans = self.ytrans = self.ztrans = 0.0 + output = self.single(1,file,box,atoms,bonds,tris,lines) + nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output) + self.xtrans = float(nums[0][0]) + self.ytrans = float(nums[0][1]) + self.ztrans = float(nums[0][2]) + + self.single(0,file,box,atoms,bonds,tris,lines) + print n, + sys.stdout.flush() + n += 1 + + print "\n%d images" % ncount + + # -------------------------------------------------------------------- + + def single(self,flag,file,box,atoms,bonds,tris,lines): + + matrix = rotation_matrix('x',-self.ztheta,'z',270.0-self.azphi) + + f = open("tmp.r3d","w") + + color = self.bgcol + xshift = 1.6*self.distance/self.scale * self.xshift/self.xpixels + yshift = 1.6*self.distance/self.scale * self.yshift/self.xpixels + header = template[1:] % \ + (self.xpixels,self.ypixels,color[0],color[1],color[2], + self.eye,matrix,self.xtrans+xshift,self.ytrans+yshift, + self.ztrans,1.6*self.distance/self.scale) + print >>f,header, + + # draw box if boxflag or flag is set + # flag = 1 is a pre-call of single to set frame size correctly + # this keeps the view fixed even if atoms move around + + if self.boxflag or flag: box_write(f,box,self.bxcol,self.bxthick) + + ncolor = self.vizinfo.nacolor + for atom in atoms: + itype = int(atom[1]) + if itype > ncolor: raise StandardError,"atom type too big" + color = self.vizinfo.acolor[itype] + rad = self.vizinfo.arad[itype] + print >>f,2 + print >>f,atom[2],atom[3],atom[4],rad,color[0],color[1],color[2] + + # need to include vizinfo.tfill options + + ncolor = self.vizinfo.ntcolor + for tri in tris: + itype = int(tri[1]) + if itype > ncolor: raise StandardError,"tri type too big" + color = self.vizinfo.tcolor[itype] + print >>f,1 + print >>f,tri[2],tri[3],tri[4],tri[5],tri[6],tri[7], \ + tri[8],tri[9],tri[10],color[0],color[1],color[2] + + bound = 0.25 * self.distance + ncolor = self.vizinfo.nbcolor + for bond in bonds: + itype = int(bond[1]) + if itype > ncolor: raise StandardError,"bond type too big" + color = self.vizinfo.bcolor[itype] + rad = self.vizinfo.brad[itype] + if fabs(bond[2]-bond[5]) > bound or fabs(bond[3]-bond[6]) > bound: + continue + print >>f,5 + print >>f,bond[2],bond[3],bond[4],rad, \ + bond[5],bond[6],bond[7],0.0,color[0],color[1],color[2] + + ncolor = self.vizinfo.nlcolor + for line in lines: + itype = int(line[1]) + if itype > ncolor: raise StandardError,"line type too big" + color = self.vizinfo.lcolor[itype] + thick = self.vizinfo.lrad[itype] + print >>f,3 + print >>f,line[2],line[3],line[4],thick, \ + line[5],line[6],line[7],thick,color[0],color[1],color[2] + + for label in self.labels: + print >>f,15 + print >>f,10 + print >>f,label[2],label[3],label[4] + print >>f,11 + print >>f,label[0],label[1],0.0,label[5][0],label[5][1],label[5][2] + print >>f,label[6] + + f.close() + + if len(self.labels) == 0: + cmd = "cat tmp.r3d | %s -png %s.png" % (PIZZA_RENDER,file) + else: + cmd = "cat tmp.r3d | %s -png %s.png" % (PIZZA_LABEL3D,file) + + output = commands.getoutput(cmd) + return output + + # -------------------------------------------------------------------- + + def adef(self): + self.vizinfo.setcolors("atom",range(100),"loop") + self.vizinfo.setradii("atom",range(100),0.45) + + # -------------------------------------------------------------------- + + def bdef(self): + self.vizinfo.setcolors("bond",range(100),"loop") + self.vizinfo.setradii("bond",range(100),0.25) + + # -------------------------------------------------------------------- + + def tdef(self): + self.vizinfo.setcolors("tri",range(100),"loop") + self.vizinfo.setfills("tri",range(100),0) + + # -------------------------------------------------------------------- + + def ldef(self): + self.vizinfo.setcolors("line",range(100),"loop") + self.vizinfo.setradii("line",range(100),0.25) + + # -------------------------------------------------------------------- + + def acol(self,atypes,colors): + self.vizinfo.setcolors("atom",atypes,colors) + + # -------------------------------------------------------------------- + + def arad(self,atypes,radii): + self.vizinfo.setradii("atom",atypes,radii) + + # -------------------------------------------------------------------- + + def bcol(self,btypes,colors): + self.vizinfo.setcolors("bond",btypes,colors) + + # -------------------------------------------------------------------- + + def brad(self,btypes,radii): + self.vizinfo.setradii("bond",btypes,radii) + + # -------------------------------------------------------------------- + + def tcol(self,ttypes,colors): + self.vizinfo.setcolors("tri",ttypes,colors) + + # -------------------------------------------------------------------- + + def tfill(self,ttypes,flags): + self.vizinfo.setfills("tri",ttypes,flags) + + # -------------------------------------------------------------------- + + def lcol(self,ltypes,colors): + self.vizinfo.setcolors("line",ltypes,colors) + + # -------------------------------------------------------------------- + + def lrad(self,ltypes,radii): + self.vizinfo.setradii("line",ltypes,radii) + +# -------------------------------------------------------------------- +# return characteristic distance of simulation domain = max dimension + +def compute_distance(box): + distance = box[3]-box[0] + if box[4]-box[1] > distance: distance = box[4]-box[1] + if box[5]-box[2] > distance: distance = box[5]-box[2] + return distance + +# -------------------------------------------------------------------- +# draw a 12-edge box around simulation domain + +def box_write(f,box,color,thick): + xlo,ylo,zlo = box[0],box[1],box[2] + xhi,yhi,zhi = box[3],box[4],box[5] + red = color[0] + green = color[1] + blue = color[2] + + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,ylo,zlo,thick,xhi,ylo,zlo,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,yhi,zlo,thick,xhi,yhi,zlo,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,ylo,zhi,thick,xhi,ylo,zhi,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,yhi,zhi,thick,xhi,yhi,zhi,thick,red,green,blue) + + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,ylo,zlo,thick,xlo,yhi,zlo,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xhi,ylo,zlo,thick,xhi,yhi,zlo,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,ylo,zhi,thick,xlo,yhi,zhi,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xhi,ylo,zhi,thick,xhi,yhi,zhi,thick,red,green,blue) + + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,ylo,zlo,thick,xlo,ylo,zhi,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xhi,ylo,zlo,thick,xhi,ylo,zhi,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xlo,yhi,zlo,thick,xlo,yhi,zhi,thick,red,green,blue) + print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \ + (xhi,yhi,zlo,thick,xhi,yhi,zhi,thick,red,green,blue) + +# -------------------------------------------------------------------- +# compute 3x3 rotation matrix for viewing angle + +# initially the scene is viewed: +# (1) along the z-axis, looking towards the origin from (0,0,1) +# (2) seeing xy plane, with +y up and +x to the right +# 1st rotation angle rotates the body +# 2nd rotation angle rotates the new body around the new rotated axis +# sign of rotation angles follow right-hand rule + +# rotation_matrix(x/y/z,angle1,x/y/z,angle2) +# x/y/z = 1st axis to rotate around +# angle1 = 1st angle to rotate by +# x/y/z = 2nd axis to rotate around +# angle2 = 2nd angle to rotate by + +def rotation_matrix(coord1,angle1,coord2,angle2): + + # convert rotation angles to radians + + pi = 4.0*atan(1.0) + angle1 = angle1/180.0 * pi + angle2 = angle2/180.0 * pi + + # sines/cosines of 2 angles + + c1 = cos(angle1) + s1 = sin(angle1) + c2 = cos(angle2) + s2 = sin(angle2) + + # 1st rotation matrix + + a11 = a12 = a13 = a21 = a22 = a23 = a31 = a32 = a33 = 0.0 + if coord1 == 'x': + a11 = 1.0 + a22 = a33 = c1 + a23 = s1; a32 = -s1 + elif coord1 == 'y': + a22 = 1.0 + a11 = a33 = c1 + a13 = s1; a31 = -s1 + elif coord1 == 'z': + a33 = 1.0 + a12 = a22 = c1 + a12 = s1; a21 = -s1 + + # 2nd rotation matrix + + b11 = b12 = b13 = b21 = b22 = b23 = b31 = b32 = b33 = 0.0 + if coord2 == 'x': + b11 = 1.0 + b22 = b33 = c2 + b23 = s2; b32 = -s2 + elif coord2 == 'y': + b22 = 1.0 + b11 = b33 = c2 + b13 = s2; b31 = -s2 + elif coord2 == 'z': + b33 = 1.0 + b11 = b22 = c2 + b12 = s2; b21 = -s2 + + # full matrix c = b*a + + c11 = b11*a11 + b12*a21 + b13*a31 + c12 = b11*a12 + b12*a22 + b13*a32 + c13 = b11*a13 + b12*a23 + b13*a33 + + c21 = b21*a11 + b22*a21 + b23*a31 + c22 = b21*a12 + b22*a22 + b23*a32 + c23 = b21*a13 + b22*a23 + b23*a33 + + c31 = b31*a11 + b32*a21 + b33*a31 + c32 = b31*a12 + b32*a22 + b33*a32 + c33 = b31*a13 + b32*a23 + b33*a33 + + # form rotation matrix + # each line padded with 0.0 for 4x4 raster3d matrix + + matrix = "%g %g %g 0.0\n%g %g %g 0.0\n%g %g %g 0.0" % \ + (c11,c12,c13,c21,c22,c23,c31,c32,c33) + return matrix + +# -------------------------------------------------------------------- +# template file for Raster3d + +template = """ +Raster3D header file +%g %g tiles in x,y +0 0 pixels (x,y) per tile +4 anti-aliasing +%g %g %g background color +F no, shadowed rods look funny +25 Phong power +0.15 secondary light contribution +0.05 ambient light contribution +0.25 specular reflection component +%g eye position +1 1 1 main light source postion +%s +%g %g %g %g +3 mixed object types +* +* +* +""" + +# -------------------------------------------------------------------- +# fontlist + +fontlist = {} +fontlist["t"] = "Times-Roman" +fontlist["h"] = "Helvetica" diff --git a/src/raster.pyc b/src/raster.pyc new file mode 100644 index 0000000..0d1aaf9 Binary files /dev/null and b/src/raster.pyc differ diff --git a/src/svg.py b/src/svg.py new file mode 100644 index 0000000..747db72 --- /dev/null +++ b/src/svg.py @@ -0,0 +1,740 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# svg tool + +oneline = "3d visualization via SVG files" + +docstr = """ +s = svg(d) create SVG object for data in d + + d = atom snapshot object (dump, data) + +s.bg("black") set background color (def = "black") +s.size(N) set image size to NxN +s.size(N,M) set image size to NxM +s.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) +s.shift(x,y) translate by x,y pixels in view window (def = 0,0) +s.zoom(0.5) scale image by factor (def = 1) +s.box(0/1/2) 0/1/2 = none/variable/fixed box +s.box(0/1/2,"green") set box color +s.box(0/1/2,"red",4) set box edge thickness +s.file = "image" file prefix for created images (def = "image") + +s.show(N) show image of snapshot at timestep N + +s.all() make images of all selected snapshots +s.all(P) images of all, start file label at P +s.all(N,M,P) make M images of snapshot N, start label at P + +s.pan(60,135,1.0,40,135,1.5) pan during all() operation +s.pan() no pan during all() (default) + + args = z theta, azimuthal phi, zoom factor at beginning and end + values at each step are interpolated between beginning and end values + +s.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() +s.select = "" no extra aselect (default) + + %g varies from 0.0 to 1.0 from beginning to end of all() + +s.label(x,y,"h",size,"red","This is a label") add label to each image +s.nolabel() delete all labels + + x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font + size = fontsize (e.g. 10), "red" = color of text + +s.acol(2,"green") set atom colors by atom type (1-N) +s.acol([2,4],["red","blue"]) 1st arg = one type or list of types +s.acol(0,"blue") 2nd arg = one color or list of colors +s.acol(range(20),["red","blue"]) if list lengths unequal, interpolate +s.acol(range(10),"loop") assign colors in loop, randomly ordered + + if 1st arg is 0, set all types to 2nd arg + if list of types has a 0 (e.g. range(10)), +1 is added to each value + interpolate means colors blend smoothly from one value to the next + +s.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol() + +s.bcol() set bond color, same args as acol() +s.brad() set bond thickness, same args as arad() + +s.tcol() set triangle color, same args as acol() +s.tfill() set triangle fill, 0 fill, 1 line, 2 both + +s.lcol() set line color, same args as acol() +s.lrad() set line thickness, same args as arad() + +s.adef() set atom/bond/tri/line properties to default +s.bdef() default = "loop" for colors, 0.45 for radii +s.tdef() default = 0.25 for bond/line thickness +s.ldef() default = 0 fill + + by default 100 types are assigned + if atom/bond/tri/line has type > # defined properties, is an error + +from vizinfo import colors access color list +print colors list defined color names and RGB values +colors["nickname"] = [R,G,B] set new RGB values from 0 to 255 + + 140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc + +Settings specific to svg tool: + +s.thick = 2.0 pixel thickness of black atom border +""" + +# History +# 8/05, Matt Jones (BYU): original version +# 9/05, Steve Plimpton: adjusted box and label attributes + +# ToDo list +# when do aselect with select str while looping N times on same timestep +# would not let you grow # of atoms selected +# triangles are not drawn with fill type + +# Variables +# ztheta = vertical angle from z-azis to view from +# azphi = azimuthal angle to view from +# xshift,yshift = xy translation of scene (in pixels) +# distance = size of simulation box (largest dim) +# file = filename prefix to use for images produced +# boxflag = 0/1/2 for drawing simulation box: none/variable/fixed +# bxcol = color of box +# bxthick = thickness of box +# bgcol = color of background +# vizinfo = scene attributes + +# Imports and external programs + +import sys, os, commands, re +from vizinfo import vizinfo +from math import sqrt,atan,cos,sin,fabs + +try: from DEFAULTS import PIZZA_DISPLAY +except: PIZZA_DISPLAY = "display" + +# Class definition + +class svg: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + self.xpixels = 512 + self.ypixels = 512 + self.ztheta = 60 + self.azphi = 30 + self.scale = 1.0 + self.xshift = self.yshift = 0 + + self.file = "image" + self.boxflag = 0 + self.bxcol = [1,1,0] + self.bxthick = 0.3 + self.bgcol = [0,0,0] + self.labels = [] + self.panflag = 0 + self.select = "" + self.thick = 1.0 + + self.vizinfo = vizinfo() + self.adef() + self.bdef() + self.tdef() + self.ldef() + + # -------------------------------------------------------------------- + + def bg(self,color): + from vizinfo import colors + self.bgcol = [colors[color][0]/255.0,colors[color][1]/255.0, + colors[color][2]/255.0] + + # -------------------------------------------------------------------- + + def size(self,newx,newy=None): + self.xpixels = xnew + if not ynew: self.ypixels = self.xpixels + else: self.ypixels = ynew + + # -------------------------------------------------------------------- + + def rotate(self,ztheta,azphi): + self.ztheta = ztheta; + self.azphi = azphi; + + # -------------------------------------------------------------------- + + def shift(self,x,y): + self.xshift = x; + self.yshift = y; + + # -------------------------------------------------------------------- + + def box(self,*args): + self.boxflag = args[0] + if len(args) > 1: + from vizinfo import colors + self.bxcol = [colors[args[1]][0]/255.0,colors[args[1]][1]/255.0, + colors[args[1]][2]/255.0] + if len(args) > 2: self.bxthick = args[2] + + # -------------------------------------------------------------------- + + def zoom(self,factor): + self.scale = factor + + # -------------------------------------------------------------------- + + def show(self,ntime): + data = self.data + which = data.findtime(ntime) + time,box,atoms,bonds,tris,lines = data.viz(which) + if self.boxflag == 2: box = data.maxbox() + self.distance = compute_distance(box) + + self.single(self.file,box,atoms,bonds,tris,lines,1) + cmd = "%s %s.svg" % (PIZZA_DISPLAY,self.file) + commands.getoutput(cmd) + + # -------------------------------------------------------------------- + + def pan(self,*list): + if len(list) == 0: self.panflag = 0 + else: + self.panflag = 1 + self.ztheta_start = list[0] + self.azphi_start = list[1] + self.scale_start = list[2] + self.ztheta_stop = list[3] + self.azphi_stop = list[4] + self.scale_stop = list[5] + + # -------------------------------------------------------------------- + + def all(self,*list): + data = self.data + if len(list) == 0: + nstart = 0 + ncount = data.nselect + elif len(list) == 1: + nstart = list[0] + ncount = data.nselect + else: + ntime = list[0] + nstart = list[2] + ncount = list[1] + + if self.boxflag == 2: box = data.maxbox() + + # loop over all selected steps + # distance from 1st snapshot box or max box for all selected steps + # call single() w/ scaling on 1st step or if panning + + if len(list) <= 1: + + n = nstart + i = flag = 0 + while 1: + which,time,flag = data.iterator(flag) + if flag == -1: break + + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,time) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + + scaleflag = 0 + if n == nstart or self.panflag: scaleflag = 1 + + self.single(file,box,atoms,bonds,tris,lines,scaleflag) + print time, + sys.stdout.flush() + i += 1 + n += 1 + + # loop ncount times on same step + # distance from 1st snapshot box or max box for all selected steps + # call single() w/ scaling on 1st step or if panning + + else: + + which = data.findtime(ntime) + + n = nstart + for i in range(ncount): + fraction = float(i) / (ncount-1) + + if self.select != "": + newstr = self.select % fraction + data.aselect.test(newstr,ntime) + time,boxone,atoms,bonds,tris,lines = data.viz(which) + + if self.boxflag < 2: box = boxone + if n == nstart: self.distance = compute_distance(box) + + if n < 10: file = self.file + "000" + str(n) + elif n < 100: file = self.file + "00" + str(n) + elif n < 1000: file = self.file + "0" + str(n) + else: file = self.file + str(n) + + if self.panflag: + self.ztheta = self.ztheta_start + \ + fraction*(self.ztheta_stop - self.ztheta_start) + self.azphi = self.azphi_start + \ + fraction*(self.azphi_stop - self.azphi_start) + self.scale = self.scale_start + \ + fraction*(self.scale_stop - self.scale_start) + + scaleflag = 0 + if n == nstart or self.panflag: scaleflag = 1 + + self.single(file,box,atoms,bonds,tris,lines,scaleflag) + print n, + sys.stdout.flush() + n += 1 + + print "\n%d images" % ncount + + # -------------------------------------------------------------------- + + def label(self,x,y,font,point,color,text): + from vizinfo import colors + scaledcolor = [colors[color][0]/255.0,colors[color][1]/255.0, + colors[color][2]/255.0] + list = [x,y,fontlist[font],point,scaledcolor,text] + self.labels.append(list) + + # -------------------------------------------------------------------- + + def nolabel(self): + self.labels = [] + + # -------------------------------------------------------------------- + + def single(self,file,box,atoms,bonds,tris,lines,scaleflag): + + matrix = rotation_matrix('x',-self.ztheta,'z',270.0-self.azphi) + if scaleflag: + self.factor = self.xpixels*self.scale / (1.6*self.distance) + xctr = 0.5 * (box[0]+box[3]) + yctr = 0.5 * (box[1]+box[4]) + zctr = 0.5 * (box[2]+box[5]) + self.offsetx = matrix[0]*xctr + matrix[3]*yctr + matrix[6]*zctr + self.offsety = matrix[1]*xctr + matrix[4]*yctr + matrix[7]*zctr + + olist = [] + + for atom in atoms: + atom[0] = 0 + newatom = self.transform(atom,matrix) + olist.append(newatom) + + for tri in tris: + tri[0] = 1 + newtri = self.transform(tri,matrix) + olist.append(newtri) + + bound = 0.25 * self.distance + for bond in bonds: + newbond = [2,bond[1]] + dx = bond[5] - bond[2] + dy = bond[6] - bond[3] + dz = bond[7] - bond[4] + r = sqrt(dx*dx+dy*dy+dz*dz) + if not r: r = 1 + rad = self.vizinfo.arad[int(bond[9])] + newbond.append(bond[2] + (r/r - rad/r) * dx) + newbond.append(bond[3] + (r/r - rad/r) * dy) + newbond.append(bond[4] + (r/r - rad/r) * dz) + + # cut off second side of bond + + dx = bond[2] - bond[5] + dy = bond[3] - bond[6] + dz = bond[4] - bond[7] + r = sqrt(dx*dx+dy*dy+dz*dz) + if not r: r = 1 + rad = self.vizinfo.arad[int(bond[8])] + newbond.append(bond[5] + (r/r - rad/r) * dx) + newbond.append(bond[6] + (r/r - rad/r) * dy) + newbond.append(bond[7] + (r/r - rad/r) * dz) + + if fabs(newbond[2]-newbond[5]) > bound or \ + fabs(newbond[3]-newbond[6]) > bound: continue + + newbond = self.transform(newbond,matrix) + if newbond[4] < newbond[7]: newbond[4] = newbond[7] + olist.append(newbond) + + for line in lines: + line[0] = 3 + newline = self.transform(line,matrix) + olist.append(newline) + + if self.boxflag: + x1,y1,z1 = box[0],box[1],box[2] + x2,y2,z2 = box[3],box[4],box[5] + blines = [] + blines.append([4,0,x1,y1,z1,x1,y1,z2]) + blines.append([4,0,x2,y1,z1,x2,y1,z2]) + blines.append([4,0,x2,y2,z1,x2,y2,z2]) + blines.append([4,0,x1,y2,z1,x1,y2,z2]) + blines.append([4,0,x1,y1,z1,x2,y1,z1]) + blines.append([4,0,x1,y2,z1,x2,y2,z1]) + blines.append([4,0,x1,y2,z2,x2,y2,z2]) + blines.append([4,0,x1,y1,z2,x2,y1,z2]) + blines.append([4,0,x1,y1,z1,x1,y2,z1]) + blines.append([4,0,x2,y1,z1,x2,y2,z1]) + blines.append([4,0,x2,y1,z2,x2,y2,z2]) + blines.append([4,0,x1,y1,z2,x1,y2,z2]) + for line in blines: + newline = self.transform(line,matrix) + olist.append(newline) + + # convert objects by factor/offset and sort by z-depth + + self.convert(olist) + olist.sort(cmprz) + + # write SVG file + + file += ".svg" + f = open(file,"w") + + header = ' ' % \ + (self.ypixels,self.xpixels) + header += '' + print >>f,header + + color = '>f,color + + for element in olist: self.write(f,0,element) + for label in self.labels: self.write(f,1,label) + + footer = "" + print >> f,footer + + f.close() + + # -------------------------------------------------------------------- + # rotate with matrix + + def transform(self,obj,matrix): + + onew = obj[0:2] + + if obj[0] == 0: # transform atom + onew.append(matrix[0]*obj[2] + matrix[3]*obj[3] + matrix[6]*obj[4]) + onew.append(matrix[1]*obj[2] + matrix[4]*obj[3] + matrix[7]*obj[4]) + onew.append(matrix[2]*obj[2] + matrix[5]*obj[3] + matrix[8]*obj[4]) + + elif obj[0] == 1: # transform triangle + onew.append(matrix[0]*obj[2] + matrix[3]*obj[3] + matrix[6]*obj[4]) + onew.append(matrix[1]*obj[2] + matrix[4]*obj[3] + matrix[7]*obj[4]) + onew.append(matrix[2]*obj[2] + matrix[5]*obj[3] + matrix[8]*obj[4]) + onew.append(matrix[0]*obj[5] + matrix[3]*obj[6] + matrix[6]*obj[7]) + onew.append(matrix[1]*obj[5] + matrix[4]*obj[6] + matrix[7]*obj[7]) + onew.append(matrix[2]*obj[5] + matrix[5]*obj[6] + matrix[8]*obj[7]) + onew.append(matrix[0]*obj[8] + matrix[3]*obj[9] + matrix[6]*obj[10]) + onew.append(matrix[1]*obj[8] + matrix[4]*obj[9] + matrix[7]*obj[10]) + onew.append(matrix[2]*obj[8] + matrix[5]*obj[9] + matrix[8]*obj[10]) + + else: # transform bond or line + onew.append(matrix[0]*obj[2] + matrix[3]*obj[3] + matrix[6]*obj[4]) + onew.append(matrix[1]*obj[2] + matrix[4]*obj[3] + matrix[7]*obj[4]) + onew.append(matrix[2]*obj[2] + matrix[5]*obj[3] + matrix[8]*obj[4]) + onew.append(matrix[0]*obj[5] + matrix[3]*obj[6] + matrix[6]*obj[7]) + onew.append(matrix[1]*obj[5] + matrix[4]*obj[6] + matrix[7]*obj[7]) + onew.append(matrix[2]*obj[5] + matrix[5]*obj[6] + matrix[8]*obj[7]) + + return onew + + # -------------------------------------------------------------------- + + def convert(self,objlist): + factor = self.factor + offsetx = self.offsetx + offsety = self.offsety + xctr = 0.5 * self.xpixels + self.xshift + yctr = 0.5 * self.ypixels - self.yshift + + for obj in objlist: + if obj[0] == 0: # convert atom + obj[2] = factor*(obj[2] - offsetx) + xctr + obj[3] = yctr - factor*(obj[3] - offsety) + elif obj[0] == 1: # convert triangle + obj[2] = factor*(obj[2] - offsetx) + xctr + obj[3] = yctr - factor*(obj[3] - offsety) + obj[5] = factor*(obj[5] - offsetx) + xctr + obj[6] = yctr - factor*(obj[6] - offsety) + obj[8] = factor*(obj[8] - offsetx) + xctr + obj[9] = yctr - factor*(obj[9] - offsety) + else: # convert bond or line + obj[2] = factor*(obj[2] - offsetx) + xctr + obj[3] = yctr - factor*(obj[3] - offsety) + obj[5] = factor*(obj[5] - offsetx) + xctr + obj[6] = yctr - factor*(obj[6] - offsety) + + # -------------------------------------------------------------------- + + def write(self,f,flag,*args): + if len(args): obj = args[0] + + if flag == 0: + if obj[0] == 0: # atom with its color and radius + itype = int(obj[1]) + if itype > self.vizinfo.nacolor: + raise StandardError,"atom type too big" + color = self.vizinfo.acolor[itype] + rad = self.vizinfo.arad[itype] + print >>f,'' % \ + (obj[2],obj[3],rad*self.factor, + color[0]*255,color[1]*255,color[2]*255,self.thick) + + elif obj[0] == 1: # tri with its color (need to add fill type) + itype = int(obj[1]) + if itype > self.vizinfo.ntcolor: + raise StandardError,"tri type too big" + color = self.vizinfo.tcolor[itype] + print >>f,'' % \ + (obj[2],obj[3],obj[5],obj[6],obj[8],obj[9], + color[0]*255,color[1]*255,color[2]*255) + + elif obj[0] == 2: # bond with its color and thickness + itype = int(obj[1]) + if itype > self.vizinfo.nbcolor: + raise StandardError,"bond type too big" + color = self.vizinfo.bcolor[itype] + thick = self.vizinfo.brad[itype] + print >>f,'' % \ + (obj[2],obj[3],obj[5],obj[6], + color[0]*255,color[1]*255,color[2]*255,thick*self.factor) + + elif obj[0] == 3: # line with its color and thickness + itype = int(obj[1]) + if itype > self.vizinfo.nlcolor: + raise StandardError,"line type too big" + color = self.vizinfo.lcolor[itype] + thick = self.vizinfo.lrad[itype] + print >>f,'' % \ + (obj[2],obj[3],obj[5],obj[6], + color[0]*255,color[1]*255,color[2]*255,thick*self.factor) + + elif obj[0] == 4: # box line with built-in color and thickness + color = self.bxcol + thick = self.bxthick + print >>f,'' % \ + (obj[2],obj[3],obj[5],obj[6], + color[0]*255,color[1]*255,color[2]*255,thick*self.factor) + + elif flag == 1: + x = (obj[0]*self.xpixels) + (self.xpixels/2.0) + y = (self.ypixels/2.0) - (obj[1]*self.ypixels) + color = obj[4] + print >>f,' %s ' % \ + (x,y,obj[3],obj[2],color[0]*255,color[1]*255,color[2]*255, + color[0]*255,color[1]*255,color[2]*255,obj[5]) + + # -------------------------------------------------------------------- + + def adef(self): + self.vizinfo.setcolors("atom",range(100),"loop") + self.vizinfo.setradii("atom",range(100),0.45) + + # -------------------------------------------------------------------- + + def bdef(self): + self.vizinfo.setcolors("bond",range(100),"loop") + self.vizinfo.setradii("bond",range(100),0.25) + + # -------------------------------------------------------------------- + + def tdef(self): + self.vizinfo.setcolors("tri",range(100),"loop") + self.vizinfo.setfills("tri",range(100),0) + + # -------------------------------------------------------------------- + + def ldef(self): + self.vizinfo.setcolors("line",range(100),"loop") + self.vizinfo.setradii("line",range(100),0.25) + + # -------------------------------------------------------------------- + + def acol(self,atypes,colors): + self.vizinfo.setcolors("atom",atypes,colors) + + # -------------------------------------------------------------------- + + def arad(self,atypes,radii): + self.vizinfo.setradii("atom",atypes,radii) + + # -------------------------------------------------------------------- + + def bcol(self,btypes,colors): + self.vizinfo.setcolors("bond",btypes,colors) + + # -------------------------------------------------------------------- + + def brad(self,btypes,radii): + self.vizinfo.setradii("bond",btypes,radii) + + # -------------------------------------------------------------------- + + def tcol(self,ttypes,colors): + self.vizinfo.setcolors("tri",ttypes,colors) + + # -------------------------------------------------------------------- + + def tfill(self,ttypes,flags): + self.vizinfo.setfills("tri",ttypes,flags) + + # -------------------------------------------------------------------- + + def lcol(self,ltypes,colors): + self.vizinfo.setcolors("line",ltypes,colors) + + # -------------------------------------------------------------------- + + def lrad(self,ltypes,radii): + self.vizinfo.setradii("line",ltypes,radii) + +# -------------------------------------------------------------------- +# compare function for the sort method, orders according to z coordinate + +def cmprz(a,b): + if a[4] > b[4]: + return 1 + elif a[4] < b[4]: + return -1 + elif a[4] == b[4]: + return 0 + +# -------------------------------------------------------------------- +# return characteristic distance of simulation domain = max dimension + +def compute_distance(box): + distance = box[3]-box[0] + if box[4]-box[1] > distance: distance = box[4]-box[1] + if box[5]-box[2] > distance: distance = box[5]-box[2] + return distance + +# -------------------------------------------------------------------- +# compute 3x3 rotation matrix for viewing angle + +# initially the scene is viewed: +# (1) along the z-axis, looking towards the origin from (0,0,1) +# (2) seeing xy plane, with +y up and +x to the right +# 1st rotation angle rotates the body +# 2nd rotation angle rotates the new body around the new rotated axis +# sign of rotation angles follow right-hand rule + +# rotation_matrix(x/y/z,angle1,x/y/z,angle2) +# x/y/z = 1st axis to rotate around +# angle1 = 1st angle to rotate by +# x/y/z = 2nd axis to rotate around +# angle2 = 2nd angle to rotate by +# returns the rotation matrix as a string for now + +def rotation_matrix(coord1,angle1,coord2,angle2): + + # convert rotation angles to radians + + pi = 4.0*atan(1.0) + angle1 = angle1/180.0 * pi + angle2 = angle2/180.0 * pi + + # sines/cosines of 2 angles + + c1 = cos(angle1) + s1 = sin(angle1) + c2 = cos(angle2) + s2 = sin(angle2) + + # 1st rotation matrix + + a11 = a12 = a13 = a21 = a22 = a23 = a31 = a32 = a33 = 0.0 + if coord1 == 'x': + a11 = 1.0 + a22 = a33 = c1 + a23 = s1; a32 = -s1 + elif coord1 == 'y': + a22 = 1.0 + a11 = a33 = c1 + a13 = s1; a31 = -s1 + elif coord1 == 'z': + a33 = 1.0 + a12 = a22 = c1 + a12 = s1; a21 = -s1 + + # 2nd rotation matrix + + b11 = b12 = b13 = b21 = b22 = b23 = b31 = b32 = b33 = 0.0 + if coord2 == 'x': + b11 = 1.0 + b22 = b33 = c2 + b23 = s2; b32 = -s2 + elif coord2 == 'y': + b22 = 1.0 + b11 = b33 = c2 + b13 = s2; b31 = -s2 + elif coord2 == 'z': + b33 = 1.0 + b11 = b22 = c2 + b12 = s2; b21 = -s2 + + # full matrix c = b*a + + c11 = b11*a11 + b12*a21 + b13*a31 + c12 = b11*a12 + b12*a22 + b13*a32 + c13 = b11*a13 + b12*a23 + b13*a33 + + c21 = b21*a11 + b22*a21 + b23*a31 + c22 = b21*a12 + b22*a22 + b23*a32 + c23 = b21*a13 + b22*a23 + b23*a33 + + c31 = b31*a11 + b32*a21 + b33*a31 + c32 = b31*a12 + b32*a22 + b33*a32 + c33 = b31*a13 + b32*a23 + b33*a33 + + # form rotation matrix + + matrix = (c11,c12,c13,c21,c22,c23,c31,c32,c33) + return matrix + +# -------------------------------------------------------------------- +# fontlist + +fontlist = {} +fontlist["t"] = "Times" +fontlist["h"] = "Helvetica" diff --git a/src/svg.pyc b/src/svg.pyc new file mode 100644 index 0000000..44bb7e9 Binary files /dev/null and b/src/svg.pyc differ diff --git a/src/tdump.py b/src/tdump.py new file mode 100644 index 0000000..bcfd904 --- /dev/null +++ b/src/tdump.py @@ -0,0 +1,385 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# tdump tool + +oneline = "Read dump files with triangle info" + +docstr = """ +t = tdump("dump.one") read in one or more dump files +t = tdump("dump.1 dump.2.gz") can be gzipped +t = tdump("dump.*") wildcard expands to multiple files +t = tdump("dump.*",0) two args = store filenames, but don't read + + incomplete and duplicate snapshots are deleted + no column name assignment is performed + +time = t.next() read next snapshot from dump files + + used with 2-argument constructor to allow reading snapshots one-at-a-time + snapshot will be skipped only if another snapshot has same time stamp + return time stamp of snapshot read + return -1 if no snapshots left or last snapshot is incomplete + no column name assignment is performed + +t.map(1,"id",3,"x") assign names to atom columns (1-N) + + must assign id,type,corner1x,corner1y,corner1z,corner2x,corner2y,corner2z,corner3x,corner3y,corner3z + +time,box,atoms,bonds,tris,lines = t.viz(index) return list of viz objects + + viz() returns line info for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot + time = timestep value + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] + atoms = NULL + bonds = NULL + tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3 for each tri as 2d array + id,type are from associated atom + lines = NULL + +t.owrap(...) wrap tris to same image as their atoms + + owrap() is called by dump tool's owrap() + useful for wrapping all molecule's atoms/tris the same so it is contiguous +""" + +# History +# 4/11, Steve Plimpton (SNL): original version + +# Variables +# flist = list of dump file names +# increment = 1 if reading snapshots one-at-a-time +# nextfile = which file to read from via next() +# eof = ptr into current file for where to read via next() +# nsnaps = # of snapshots +# snaps = list of snapshots +# names = dictionary of column names: +# key = "id", value = column # (0 to M-1) +# Snap = one snapshot +# time = time stamp +# natoms = # of atoms +# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float) +# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1 + +# Imports and external programs + +import sys, commands, re, glob, types +from math import sqrt +from os import popen + +try: + import numpy as np + oldnumeric = False +except: + import Numeric as np + oldnumeric = True + +try: from DEFAULTS import PIZZA_GUNZIP +except: PIZZA_GUNZIP = "gunzip" + +# Class definition + +class tdump: + + # -------------------------------------------------------------------- + + def __init__(self,*list): + self.snaps = [] + self.nsnaps = 0 + self.names = {} + + # flist = list of all dump file names + + words = list[0].split() + self.flist = [] + for word in words: self.flist += glob.glob(word) + if len(self.flist) == 0 and len(list) == 1: + raise StandardError,"no ldump file specified" + + if len(list) == 1: + self.increment = 0 + self.read_all() + else: + self.increment = 1 + self.nextfile = 0 + self.eof = 0 + + # -------------------------------------------------------------------- + + def read_all(self): + + # read all snapshots from each file + # test for gzipped files + + for file in self.flist: + if file[-3:] == ".gz": + f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r') + else: f = open(file) + + snap = self.read_snapshot(f) + while snap: + self.snaps.append(snap) + print snap.time, + sys.stdout.flush() + snap = self.read_snapshot(f) + + f.close() + print + + # sort entries by timestep, cull duplicates + + self.snaps.sort(self.compare_time) + self.cull() + self.nsnaps = len(self.snaps) + print "read %d snapshots" % self.nsnaps + + # -------------------------------------------------------------------- + # read next snapshot from list of files + + def next(self): + + if not self.increment: raise StandardError,"cannot read incrementally" + + # read next snapshot in current file using eof as pointer + # if fail, try next file + # if new snapshot time stamp already exists, read next snapshot + + while 1: + f = open(self.flist[self.nextfile],'rb') + f.seek(self.eof) + snap = self.read_snapshot(f) + if not snap: + self.nextfile += 1 + if self.nextfile == len(self.flist): return -1 + f.close() + self.eof = 0 + continue + self.eof = f.tell() + f.close() + try: + self.findtime(snap.time) + continue + except: break + + self.snaps.append(snap) + snap = self.snaps[self.nsnaps] + self.nsnaps += 1 + + return snap.time + + # -------------------------------------------------------------------- + # read a single snapshot from file f + # return snapshot or 0 if failed + + def read_snapshot(self,f): + try: + snap = Snap() + item = f.readline() + snap.time = int(f.readline().split()[0]) # just grab 1st field + item = f.readline() + snap.natoms = int(f.readline()) + + item = f.readline() + words = f.readline().split() + snap.xlo,snap.xhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.ylo,snap.yhi = float(words[0]),float(words[1]) + words = f.readline().split() + snap.zlo,snap.zhi = float(words[0]),float(words[1]) + + item = f.readline() + + if snap.natoms: + words = f.readline().split() + ncol = len(words) + for i in xrange(1,snap.natoms): + words += f.readline().split() + floats = map(float,words) + if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float) + else: atoms = np.zeros((snap.natoms,ncol),np.float) + start = 0 + stop = ncol + for i in xrange(snap.natoms): + atoms[i] = floats[start:stop] + start = stop + stop += ncol + else: atoms = None + snap.atoms = atoms + return snap + except: + return 0 + + # -------------------------------------------------------------------- + # map atom column names + + def map(self,*pairs): + if len(pairs) % 2 != 0: + raise StandardError, "tdump map() requires pairs of mappings" + for i in range(0,len(pairs),2): + j = i + 1 + self.names[pairs[j]] = pairs[i]-1 + + # -------------------------------------------------------------------- + # return vector of snapshot time stamps + + def time(self): + vec = self.nsnaps * [0] + i = 0 + for snap in self.snaps: + vec[i] = snap.time + i += 1 + return vec + + # -------------------------------------------------------------------- + # sort snapshots on time stamp + + def compare_time(self,a,b): + if a.time < b.time: + return -1 + elif a.time > b.time: + return 1 + else: + return 0 + + # -------------------------------------------------------------------- + + def findtime(self,n): + for i in xrange(self.nsnaps): + if self.snaps[i].time == n: return i + raise StandardError, "no step %d exists" % n + + # -------------------------------------------------------------------- + # delete successive snapshots with duplicate time stamp + + def cull(self): + i = 1 + while i < len(self.snaps): + if self.snaps[i].time == self.snaps[i-1].time: + del self.snaps[i] + else: + i += 1 + + # -------------------------------------------------------------------- + # return list of lines to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index + + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] + + time = snap.time + box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi] + id = self.names["id"] + type = self.names["type"] + corner1x = self.names["corner1x"] + corner1y = self.names["corner1y"] + corner1z = self.names["corner1z"] + corner2x = self.names["corner2x"] + corner2y = self.names["corner2y"] + corner2z = self.names["corner2z"] + corner3x = self.names["corner3x"] + corner3y = self.names["corner3y"] + corner3z = self.names["corner3z"] + + # create line list from id,type,corner1x,...corner3z + # don't add line if all 4 values are 0 since not a line + + tris = [] + for i in xrange(snap.natoms): + atom = snap.atoms[i] + c1 = [atom[corner1x],atom[corner1y],atom[corner1z]] + c2 = [atom[corner2x],atom[corner2y],atom[corner2z]] + c3 = [atom[corner3x],atom[corner3y],atom[corner3z]] + n = normal(c1,c2,c3) + if c1[0] == 0.0 and c1[1] == 0.0 and c1[2] == 0.0 and \ + c2[0] == 0.0 and c2[1] == 0.0 and c2[2] == 0.0: continue + tris.append([atom[id],atom[type]] + c1 + c2 + c3 + n) + + return time,box,None,None,tris,None + + # -------------------------------------------------------------------- + # wrap tri corner points associated with atoms thru periodic boundaries + # invoked by dump() when it does an owrap() on its atoms + + def owrap(self,time,xprd,yprd,zprd,idsdump,atomsdump,iother,ix,iy,iz): + id = self.names["id"] + corner1x = self.names["corner1x"] + corner1y = self.names["corner1y"] + corner1z = self.names["corner1z"] + corner2x = self.names["corner2x"] + corner2y = self.names["corner2y"] + corner2z = self.names["corner2z"] + corner3x = self.names["corner3x"] + corner3y = self.names["corner3y"] + corner3z = self.names["corner3z"] + + isnap = self.findtime(time) + snap = self.snaps[isnap] + atoms = snap.atoms + + # idump = index of my line I in dump's atoms + # jdump = atom J in dump's atoms that atom I was owrapped on + # delx,dely = offset applied to atom I and thus to line I + + for i in xrange(snap.natoms): + tag = atoms[i][id] + idump = idsdump[tag] + jdump = idsdump[atomsdump[idump][iother]] + delx = (atomsdump[idump][ix]-atomsdump[jdump][ix])*xprd + dely = (atomsdump[idump][iy]-atomsdump[jdump][iy])*yprd + delz = (atomsdump[idump][iz]-atomsdump[jdump][iz])*zprd + atoms[i][corner1x] += delx + atoms[i][corner1y] += dely + atoms[i][corner1z] += delz + atoms[i][corner2x] += delx + atoms[i][corner2y] += dely + atoms[i][corner2z] += delz + atoms[i][corner3x] += delx + atoms[i][corner3y] += dely + atoms[i][corner3z] += delz + +# -------------------------------------------------------------------- +# one snapshot + +class Snap: + pass + +# -------------------------------------------------------------------- +# compute normal for a triangle with 3 vertices + +def normal(x,y,z): + v1 = 3*[0] + v1[0] = y[0] - x[0] + v1[1] = y[1] - x[1] + v1[2] = y[2] - x[2] + + v2 = 3*[0] + v2[0] = z[0] - y[0] + v2[1] = z[1] - y[1] + v2[2] = z[2] - y[2] + + n = 3*[0] + n[0] = v1[1]*v2[2] - v1[2]*v2[1] + n[1] = v1[2]*v2[0] - v1[0]*v2[2] + n[2] = v1[0]*v2[1] - v1[1]*v2[0] + + length = sqrt(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]) + n[0] /= length + n[1] /= length + n[2] /= length + + return n diff --git a/src/tdump.pyc b/src/tdump.pyc new file mode 100644 index 0000000..e9d528a Binary files /dev/null and b/src/tdump.pyc differ diff --git a/src/vcr.py b/src/vcr.py new file mode 100644 index 0000000..31ba42a --- /dev/null +++ b/src/vcr.py @@ -0,0 +1,510 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# vcr tool + +oneline = "VCR-style GUI for 3d interactive OpenGL visualization" + +docstr = """ +v = vcr(gl1,gl2,...) start vcr GUI with one or more gl windows +v.add(gl) add a gl window to vcr GUI + +Actions (same as GUI widgets): + +v.first() go to first frame +v.prev() go to previous frame +v.back() play backwards from current frame to start +v.stop() stop on current frame +v.play() play from current frame to end +v.next() go to next frame +v.last() go to last frame + +v.frame(31) set frame slider +v.delay(0.4) set delay slider +v.q(5) set quality slider + +v.xaxis() view scene from x axis +v.yaxis() view scene from y axis +v.zaxis() view scene from z axis +v.box() toggle bounding box +v.axis() toggle display of xyz axes +v.norm() recenter and resize the view +v.ortho() toggle ortho/perspective button +v.reload() reload all frames from gl viewer data files + +v.clipxlo(0.2) clip scene at x lo fraction of box +v.clipxhi(1.0) clip at x hi +v.clipylo(0.2) clip in y +v.clipyhi(1.0) +v.clipzlo(0.2) clip in z +v.clipzhi(1.0) + +v.save() save current scene to file.png +v.file("image") set filename +v.saveall() toggle save-all checkbox +""" + +# History +# 8/05, Matt Jones (BYU): original version +# 9/05, Steve Plimpton: modified for GL viewer + +# ToDo list + +# Variables +# tkroot = root of entire Tk +# index = current frame (0 to N-1) +# nframes = number of frames in data +# loop_flag = set to 1 or -1 when play or back pushed +# set to 0 when stop is pushed +# delay_value = delay between frames (secs) +# delay_msec = delay in millisec + +# Imports and external programs + +from Tkinter import * +import types + +# Class definition + +class vcr: + + # -------------------------------------------------------------------- + + def __init__(self,*views): + self.boxflag = 0 + self.axisflag = 0 + self.orthoflag = 1 + self.saveflag = 0 + + self.loop_flag = 0 + self.delay_value = 0.0 + self.delay_msec = 0 + + # load data for each viewer + # if each viewer has different data set, nframes is for 1st viewer + + if len(views) == 0: raise StandardError,"must have at least one GL viewer" + self.viewlist = [] + for view in views: self.viewlist.append(view) + for view in self.viewlist: view.reload() + self.nframes = self.viewlist[0].nframes + + from __main__ import tkroot + self.tkroot = tkroot + root = Toplevel(tkroot) + root.title('Pizza.py vcr tool') + + frame1 = Frame(root) + Button(frame1,text="<<",command=self.first).pack(side=LEFT) + Button(frame1,text="<",command=self.previous).pack(side=LEFT) + Button(frame1,text="Back",command=self.back).pack(side=LEFT) + Button(frame1,text="Stop",command=self.stop).pack(side=LEFT) + Button(frame1,text="Play",command=self.play).pack(side=LEFT) + Button(frame1,text=">",command=self.next).pack(side=LEFT) + Button(frame1,text=">>",command=self.last).pack(side=LEFT) + frame1.pack() + + frame2 = Frame(root) + self.slider_frame = Scale(frame2,from_=0,to=self.nframes-1, + command=self.frame,orient=HORIZONTAL, + label=" Frame") + self.slider_quality = Scale(frame2,from_=3,to=12,orient=HORIZONTAL, + label=" Quality") + self.slider_quality.bind('',self.q) + self.slider_quality.set(5) + self.slider_delay = Scale(frame2,from_=0.0,to=1.0,resolution=0.1, + command=self.delay,orient=HORIZONTAL, + label=" Delay") + self.slider_frame.pack(side=LEFT) + self.slider_quality.pack(side=LEFT) + self.slider_delay.pack(side=LEFT) + frame2.pack() + + frame3 = Frame(root) + self.slider_xlo = Scale(frame3,from_=0.0,to=1.0,resolution=0.01, + command=self.clipxlo,orient=HORIZONTAL, + showvalue=0,label=" xclip") + self.slider_ylo = Scale(frame3,from_=0.0,to=1.0,resolution=0.01, + command=self.clipylo,orient=HORIZONTAL, + showvalue=0,label=" yclip") + self.slider_zlo = Scale(frame3,from_=0.0,to=1.0,resolution=0.01, + command=self.clipzlo,orient=HORIZONTAL, + showvalue=0,label=" zclip") + self.slider_xlo.set(0.0) + self.slider_ylo.set(0.0) + self.slider_zlo.set(0.0) + self.slider_xlo.pack(side=LEFT) + self.slider_ylo.pack(side=LEFT) + self.slider_zlo.pack(side=LEFT) + frame3.pack() + + frame4 = Frame(root) + self.slider_xhi = Scale(frame4,from_=0.0,to=1.0,resolution=0.01, + command=self.clipxhi,orient=HORIZONTAL, + showvalue=0) + self.slider_yhi = Scale(frame4,from_=0.0,to=1.0,resolution=0.01, + command=self.clipyhi,orient=HORIZONTAL, + showvalue=0) + self.slider_zhi = Scale(frame4,from_=0.0,to=1.0,resolution=0.01, + command=self.clipzhi,orient=HORIZONTAL, + showvalue=0) + self.slider_xhi.set(1.0) + self.slider_yhi.set(1.0) + self.slider_zhi.set(1.0) + self.slider_xhi.pack(side=LEFT) + self.slider_yhi.pack(side=LEFT) + self.slider_zhi.pack(side=LEFT) + frame4.pack() + + frame5 = Frame(root) + Button(frame5,text="X",command=self.xaxis).pack(side=LEFT) + Button(frame5,text="Y",command=self.yaxis).pack(side=LEFT) + Button(frame5,text="Z",command=self.zaxis).pack(side=LEFT) + Button(frame5,text="Box",command=self.box).pack(side=LEFT) + Button(frame5,text="Axes",command=self.axis).pack(side=LEFT) + Button(frame5,text="Recenter",command=self.recenter).pack(side=LEFT) + self.button_ortho = Button(frame5,text="Persp",command=self.ortho) + self.button_ortho.pack(side=LEFT) + Button(frame5,text="Reload",command=self.reload).pack(side=LEFT) + frame5.pack() + + frame6 = Frame(root) + Button(frame6,text="Save As:",command=self.save).pack(side=LEFT) + self.entry_file = Entry(frame6,width = 16) + self.entry_file.insert(0,"image") + self.entry_file.pack(side=LEFT) + self.button_save = Checkbutton(frame6,text="SaveAll",command=self.saveall) + self.button_save.pack(side=LEFT) + frame6.pack() + + frame7 = Frame(root) + Label(frame7,text="Mouse LMR = Shift/Rotate/Zoom").pack(padx=5,side=LEFT) + Label(frame7,text="Axes XYZ = Red/Green/Blue").pack(padx=5,side=LEFT) + frame7.pack() + + frame8 = Frame(root) + self.label_frame = Label(frame8,text="Frame 0") + self.label_frame.pack(padx=5,side=LEFT) + self.label_time = Label(frame8,text="Time 0") + self.label_time.pack(padx=5,side=LEFT) + self.label_atoms = Label(frame8,text="Atoms 0") + self.label_atoms.pack(padx=5,side=LEFT) + frame8.pack() + + # display 1st image + + self.index = 0 + self.display() + + # -------------------------------------------------------------------- + + def add(self,view): + self.viewlist.append(view) + view.reload() + view.display(self.index) + + # -------------------------------------------------------------------- + + def first(self): + self.index = 0 + self.slider_frame.set(self.index) + + # -------------------------------------------------------------------- + + def last(self): + self.index = self.nframes - 1 + self.slider_frame.set(self.index) + + # -------------------------------------------------------------------- + + def next(self): + if self.index < self.nframes - 1: + self.index += 1 + self.slider_frame.set(self.index) + + # -------------------------------------------------------------------- + + def previous(self): + if self.index > 0: + self.index -= 1 + self.slider_frame.set(self.index) + + # -------------------------------------------------------------------- + # play backward loop + # disable GL caching while animating + + def back(self): + if self.loop_flag != 0: return + self.loop_flag = -1 + for view in self.viewlist: view.cache = 0 + if self.index == 0: + self.index = self.nframes - 1 + self.slider_frame.set(self.index) + self.tkroot.update() + if self.saveflag: self.saveloop(0) + self.tkroot.after(self.delay_msec,self.loop) + + # -------------------------------------------------------------------- + # play forward loop + # disable GL caching while animating + + def play(self): + if self.loop_flag != 0: return + self.loop_flag = 1 + for view in self.viewlist: view.cache = 0 + if self.index == self.nframes - 1: + self.index = 0 + self.slider_frame.set(self.index) + self.tkroot.update() + if self.saveflag: self.saveloop(0) + self.tkroot.after(self.delay_msec,self.loop) + + # -------------------------------------------------------------------- + # stop looping + # re-enable GL caching when not animating + + def stop(self): + self.loop_flag = 0 + for view in self.viewlist: view.cache = 1 + + # -------------------------------------------------------------------- + # loop forward or back until end of animation + # if save flag is set, change file name and save snapshots + + def loop(self): + if self.loop_flag == 1 and self.index == self.nframes - 1: + self.loop_flag = 0 + if self.loop_flag == -1 and self.index == 0: + self.loop_flag = 0 + if self.loop_flag == 0: + if self.saveflag: self.saveloop(-1) + return + + self.index += self.loop_flag + self.slider_frame.set(self.index) + + # call to view.display() should not be necessary + # since slider_frame already called it + # but seems to be necessary before GL save() saves window to file + # else get previous image saved into file at each frame + + if self.saveflag: + for view in self.viewlist: time,natoms = view.display(self.index) + self.saveloop(1) + + self.tkroot.update_idletasks() + self.tkroot.after(self.delay_msec,self.loop) + + # -------------------------------------------------------------------- + # display a new frame, called in one of 3 ways: + # when frame slider is set by user in GUI + # when user calls v.frame(N) + # when other vcr method calls slider_frame.set(N) + + def frame(self,value): + self.index = int(value) + self.display() + + # -------------------------------------------------------------------- + + def delay(self,value): + self.delay_value = float(value) + self.slider_delay.set(self.delay_value) + self.delay_msec = int(1000*self.delay_value) + + # -------------------------------------------------------------------- + + def q(self,value): + if type(value) is not types.IntType: value = self.slider_quality.get() + self.slider_quality.set(value) + for view in self.viewlist: view.q(value) + + # -------------------------------------------------------------------- + + def xaxis(self): + for view in self.viewlist: + view.zoom(1) + view.shift(0,0) + view.rotate(90,0) + + # -------------------------------------------------------------------- + + def yaxis(self): + for view in self.viewlist: + view.zoom(1) + view.shift(0,0) + view.rotate(90,270) + + # -------------------------------------------------------------------- + + def zaxis(self): + for view in self.viewlist: + view.zoom(1) + view.shift(0,0) + view.rotate(0,270) + + # -------------------------------------------------------------------- + + def box(self): + if self.boxflag: + self.boxflag = 0 + for view in self.viewlist: view.box(0) + else: + self.boxflag = 1 + for view in self.viewlist: view.box(1) + + # -------------------------------------------------------------------- + + def axis(self): + if self.axisflag: + self.axisflag = 0 + for view in self.viewlist: view.axis(0) + else: + self.axisflag = 1 + for view in self.viewlist: view.axis(1) + + # -------------------------------------------------------------------- + + def recenter(self): + for view in self.viewlist: + view.shift(0,0) + view.zoom(1) + + # -------------------------------------------------------------------- + + def ortho(self): + if self.orthoflag: + self.orthoflag = 0 + self.button_ortho.config(text="Ortho") + for view in self.viewlist: view.ortho(0) + else: + self.orthoflag = 1 + self.button_ortho.config(text="Persp") + for view in self.viewlist: view.ortho(1) + + # -------------------------------------------------------------------- + + def reload(self): + for view in self.viewlist: view.reload() + self.display() + + # -------------------------------------------------------------------- + + def clipxlo(self,value): + value = float(value) + hi = float(self.slider_xhi.get()) + if value > hi: value = hi + self.slider_xlo.set(value) + for view in self.viewlist: view.clip('xlo',value) + + # -------------------------------------------------------------------- + + def clipxhi(self,value): + value = float(value) + lo = float(self.slider_xlo.get()) + if value < lo: value = lo + self.slider_xhi.set(value) + for view in self.viewlist: view.clip('xhi',value) + + # -------------------------------------------------------------------- + + def clipylo(self,value): + value = float(value) + hi = float(self.slider_yhi.get()) + if value > hi: value = hi + self.slider_ylo.set(value) + for view in self.viewlist: view.clip('ylo',value) + + # -------------------------------------------------------------------- + + def clipyhi(self,value): + value = float(value) + lo = float(self.slider_ylo.get()) + if value < lo: value = lo + self.slider_yhi.set(value) + for view in self.viewlist: view.clip('yhi',value) + + # -------------------------------------------------------------------- + + def clipzlo(self,value): + value = float(value) + hi = float(self.slider_zhi.get()) + if value > hi: value = hi + self.slider_zlo.set(value) + for view in self.viewlist: view.clip('zlo',value) + + # -------------------------------------------------------------------- + + def clipzhi(self,value): + value = float(value) + lo = float(self.slider_zlo.get()) + if value < lo: value = lo + self.slider_zhi.set(value) + for view in self.viewlist: view.clip('zhi',value) + + # -------------------------------------------------------------------- + # set filename for saving + + def file(self,newtext): + oldtext = self.entry_file.get() + self.entry_file.delete(0,len(oldtext)) + self.entry_file.insert(0,newtext) + + # -------------------------------------------------------------------- + # toggle save all checkbox + + def saveall(self): + if self.saveflag: + self.saveflag = 0 + self.button_save.deselect() + else: + self.saveflag = 1 + self.button_save.select() + + # -------------------------------------------------------------------- + # save current image to file + # if multiple windows change filenames to file.0.png, file.1.png, etc + + def save(self): + file = self.entry_file.get() + if len(self.viewlist) == 1: + self.viewlist[0].file = file + self.viewlist[0].save() + else: + n = 0 + for view in self.viewlist: + view.file = "%s.%d" % (file,n) + view.save() + n += 1 + + # -------------------------------------------------------------------- + # save images when in a play/back loop + # flag 0 = first save, flag 1 = continuing save, flag -1 = stop + + def saveloop(self,flag): + if flag == -1: + self.file(self.fileroot) + return + if flag == 0: self.fileroot = self.entry_file.get() + + if self.index < 10: file = self.fileroot + "000" + str(self.index) + elif self.index < 100: file = self.fileroot + "00" + str(self.index) + elif self.index < 1000: file = self.fileroot + "0" + str(self.index) + else: file = self.fileroot + str(self.index) + + self.file(file) + self.save() + + # -------------------------------------------------------------------- + # display index frame and set status strings + + def display(self): + for view in self.viewlist: time,natoms = view.display(self.index) + self.label_frame.config(text="Frame: %d" % self.index) + self.label_time.config(text="Time: %d" % time) + self.label_atoms.config(text="Atoms: %d" % natoms) diff --git a/src/vcr.pyc b/src/vcr.pyc new file mode 100644 index 0000000..6dcc923 Binary files /dev/null and b/src/vcr.pyc differ diff --git a/src/vec.py b/src/vec.py new file mode 100644 index 0000000..d9e1639 --- /dev/null +++ b/src/vec.py @@ -0,0 +1,145 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# vec tool + +oneline = "Create numeric vectors from columns in file or list of vecs" + +docstr = """ +v = vec("file1") read in numeric vectors from a file +v = vec(array) array = list of numeric vectors + + skip blank lines and lines that start with non-numeric characters + example array with 2 vecs = [[1,2,3,4,5], [10,20,30,40,50]] + assigns names = "col1", "col2", etc + +nvec = v.nvec # of vectors +nlen = v.nlen lengths of vectors +names = v.names list of vector names +x,y,... = l.get(1,"col2",...) return one or more vectors of values +l.write("file.txt") write all vectors to a file +l.write("file.txt","col1",7,...) write listed vectors to a file + + get and write allow abbreviated (uniquely) vector names or digits (1-Nvec) +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# n = length of each vector +# nvec = # of vectors +# names = list of vector names +# ptr = dictionary, key = name, value = index into data for which column +# data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1 + +# Imports and external programs + +import types + +# Class definition + +class vec: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = [] + + if type(data) == types.StringType: + lines = open(data,'r').readlines() + for line in lines: + words = line.split() + if len(words) and words[0][0] in "0123456789.-": + self.data.append(map(float,words)) + elif type(data) == types.ListType: + nlen = len(data[0]) + for list in data[1:]: + if len(list) != nlen: + raise StandardError,"lists are not all same length" + for i in xrange(nlen): + values = [list[i] for list in data] + self.data.append(map(float,values)) + else: + raise StandardError,"invalid argument to vec" + + if len(self.data) == 0: + self.nlen = self.nvec = 0 + else: + self.nlen = len(self.data) + self.nvec = len(self.data[0]) + + self.names = [] + for i in xrange(self.nvec): + self.names.append(str("col%d" % (i+1))) + + self.ptr = {} + for i in xrange(self.nvec): + self.ptr[self.names[i]] = i + + print "read %d vectors of length %d" % (self.nvec,self.nlen) + + # -------------------------------------------------------------------- + + def get(self,*keys): + if len(keys) == 0: + raise StandardError, "no vectors specified" + + map = [] + for key in keys: + if type(key) == types.IntType: map.append(key-1) + elif self.ptr.has_key(key): map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique vector %s not found" % key + + vecs = [] + for i in range(len(keys)): + vecs.append(self.nlen * [0]) + for j in xrange(self.nlen): + vecs[i][j] = self.data[j][map[i]] + + if len(keys) == 1: return vecs[0] + else: return vecs + + # -------------------------------------------------------------------- + + def write(self,filename,*keys): + if len(keys): + map = [] + for key in keys: + if type(key) == types.IntType: map.append(key-1) + elif self.ptr.has_key(key): map.append(self.ptr[key]) + else: + count = 0 + for i in range(self.nvec): + if self.names[i].find(key) == 0: + count += 1 + index = i + if count == 1: + map.append(index) + else: + raise StandardError, "unique vector %s not found" % key + else: + map = range(self.nvec) + + f = open(filename,"w") + for i in xrange(self.nlen): + for j in xrange(len(map)): + print >>f,self.data[i][map[j]], + print >>f + f.close() diff --git a/src/vec.pyc b/src/vec.pyc new file mode 100644 index 0000000..f24c208 Binary files /dev/null and b/src/vec.pyc differ diff --git a/src/vizinfo.py b/src/vizinfo.py new file mode 100644 index 0000000..acc421a --- /dev/null +++ b/src/vizinfo.py @@ -0,0 +1,391 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# vizinfo class, not a top-level Pizza.py tool + +# History +# 8/05, Matt Jones (BYU): original version +# 9/05, Steve Plimpton: added 140-color table + +# ToDo list + +# Variables + +# Imports and external programs + +import types + +# Class definition + +class vizinfo: + """ + Information holder for Pizza.py visualization tools + + acolor,bcolor,tcolor,lcolor = RGB values for each atom/bond/tri/line type + arad = radius of each atom type + brad,lrad = thickness of each bond/line type + tfill = fill flag for each triangle type + + all of these arrays are indexed by object type which runs 1-Ntype + nacolor,nbcolor,ntcolor,nlcolor,narad,nbrad,nlrad,ntfill + are # of types each array holds + actual length is nacolor+1 so that array can be indexed by 1-Ntype + + setcolors() = set atom/bond/tri/line colors + setradii() = set atom/bond/line radii/thickness + setfill() = set triangle fill factor + extend() = grow an array + """ + + # -------------------------------------------------------------------- + + def __init__(self): + self.acolor = [] + self.arad = [] + self.bcolor = [] + self.brad = [] + self.tcolor = [] + self.tfill = [] + self.lcolor = [] + self.lrad = [] + self.nacolor = self.narad = 0 + self.nbcolor = self.nbrad = 0 + self.ntcolor = self.ntfill = 0 + self.nlcolor = self.nlrad = 0 + + # -------------------------------------------------------------------- + # set color RGB for which = atoms, bonds, triangles + + def setcolors(self,which,ids,rgbs): + + # convert args into lists if single values + # if arg = 0, convert to full-range list + + if type(ids) is types.IntType and ids == 0: + if which == "atom": ids = range(self.nacolor) + if which == "bond": ids = range(self.nbcolor) + if which == "tri": ids = range(self.ntcolor) + if which == "line": ids = range(self.nlcolor) + if type(ids) is not types.ListType and type(ids) is not types.TupleType: + ids = [ids] + if type(rgbs) is not types.ListType and type(rgbs) is not types.TupleType: + rgbs = [rgbs] + + # if list of types has a 0, increment each type value + + if 0 in ids: + for i in xrange(len(ids)): ids[i] += 1 + + # extend storage list if necessary + # extend other arrays for same "which" so that gl::make_atom_calllist + # has valid arrays to work with + + if which == "atom": + if max(ids) > self.nacolor: + self.nacolor = self.extend(self.acolor,max(ids)) + self.nacolor = self.extend(self.arad,max(ids)) + if which == "bond": + if max(ids) > self.nbcolor: + self.nbcolor = self.extend(self.bcolor,max(ids)) + self.nbcolor = self.extend(self.brad,max(ids)) + if which == "tri": + if max(ids) > self.ntcolor: + self.ntcolor = self.extend(self.tcolor,max(ids)) + self.ntcolor = self.extend(self.tfill,max(ids)) + if which == "line": + if max(ids) > self.nlcolor: + self.nlcolor = self.extend(self.lcolor,max(ids)) + self.nlcolor = self.extend(self.lrad,max(ids)) + + # set color for each type + # if list lengths match, set directly, else interpolate + # convert final color from 0-255 to 0.0-1.0 + + ntypes = len(ids) + nrgbs = len(rgbs) + + for i in xrange(ntypes): + id = ids[i] + + if rgbs[0] == "loop": + list = colors.keys() + red,green,blue = colors[list[i % len(colors)]] + elif ntypes == nrgbs: + red,green,blue = colors[rgbs[i]] + else: + r = i/float(ntypes-1) * float(nrgbs-1) + jlo = int(r) + jhi = jlo + 1 + if jhi == nrgbs: jhi = nrgbs - 1 + clo = colors[rgbs[jlo]] + chi = colors[rgbs[jhi]] + delta = r - jlo + red = clo[0] + delta*(chi[0]-clo[0]) + green = clo[1] + delta*(chi[1]-clo[1]) + blue = clo[2] + delta*(chi[2]-clo[2]) + + color = [red/255.0,green/255.0,blue/255.0] + + if which == "atom": self.acolor[id] = color + if which == "bond": self.bcolor[id] = color + if which == "tri": self.tcolor[id] = color + if which == "line": self.lcolor[id] = color + + # -------------------------------------------------------------------- + # set radii for which = atoms, bonds, lines + + def setradii(self,which,ids,radii): + + # convert args into lists if single values + # if arg = 0, convert to full-range list + + if type(ids) is types.IntType and ids == 0: + if which == "atom": ids = range(self.narad) + if which == "bond": ids = range(self.nbrad) + if which == "line": ids = range(self.nlrad) + if type(ids) is not types.ListType and type(ids) is not types.TupleType: + ids = [ids] + if type(radii) is not types.ListType and \ + type(radii) is not types.TupleType: + radii = [radii] + + # if list of types has a 0, increment each type value + + if 0 in ids: + for i in xrange(len(ids)): ids[i] += 1 + + # extend storage list if necessary + # extend other arrays for same "which" so that gl::make_atom_calllist + # has valid arrays to work with + + if which == "atom": + if max(ids) > self.narad: + self.narad = self.extend(self.arad,max(ids)) + self.narad = self.extend(self.acolor,max(ids)) + if which == "bond": + if max(ids) > self.nbrad: + self.nbrad = self.extend(self.brad,max(ids)) + self.nbrad = self.extend(self.bcolor,max(ids)) + if which == "line": + if max(ids) > self.nlrad: + self.nlrad = self.extend(self.lrad,max(ids)) + self.nlrad = self.extend(self.lcolor,max(ids)) + + # set radius for each type + # if list lengths match, set directly, else interpolate + + ntypes = len(ids) + nradii = len(radii) + + for i in range(ntypes): + id = ids[i] + + if ntypes == nradii: rad = radii[i] + else: + r = i/float(ntypes-1) * float(nradii-1) + jlo = int(r) + jhi = jlo + 1 + if jhi == nradii: jhi = nradii - 1 + rlo = radii[jlo] + rhi = radii[jhi] + delta = r - jlo + rad = rlo + delta*(rhi-rlo) + + if which == "atom": self.arad[id] = rad + if which == "bond": self.brad[id] = rad + if which == "line": self.lrad[id] = rad + + # -------------------------------------------------------------------- + # set triangle fill style + # 0 = fill only, 1 = line only, 2 = fill and line + + def setfills(self,which,ids,fills): + + # convert args into lists if single values + # if arg = 0, convert to full-range list + + if type(ids) is types.IntType and ids == 0: + ids = range(self.ntfill) + if type(ids) is not types.ListType and type(ids) is not types.TupleType: + ids = [ids] + if type(fills) is not types.ListType and \ + type(fills) is not types.TupleType: + fills = [fills] + + # if list of types has a 0, increment each type value + + if 0 in ids: + for i in xrange(len(ids)): ids[i] += 1 + + # extend storage list if necessary + # extend other arrays for same "which" so that gl::make_atom_calllist + # has valid arrays to work with + + if max(ids) > self.ntfill: + self.ntfill = self.extend(self.tfill,max(ids)) + self.ntfill = self.extend(self.tcolor,max(ids)) + + # set fill flag for each type + # if list lengths match, set directly, else set types to 1st fill value + + if len(fills) == len(ids): + for i in xrange(len(ids)): self.tfill[ids[i]] = int(fills[i]) + else: + for id in ids: self.tfill[id] = int(fills[0]) + + # -------------------------------------------------------------------- + + def extend(self,array,n): + for i in range(n-len(array)+1): array.append(0) + return n + +# -------------------------------------------------------------------- +# dictionary of 140 color names and associated RGB values + +colors = {} + +colors["aliceblue"] = [240, 248, 255] +colors["antiquewhite"] = [250, 235, 215] +colors["aqua"] = [0, 255, 255] +colors["aquamarine"] = [127, 255, 212] +colors["azure"] = [240, 255, 255] +colors["beige"] = [245, 245, 220] +colors["bisque"] = [255, 228, 196] +colors["black"] = [0, 0, 0] +colors["blanchedalmond"] = [255, 255, 205] +colors["blue"] = [0, 0, 255] +colors["blueviolet"] = [138, 43, 226] +colors["brown"] = [165, 42, 42] +colors["burlywood"] = [222, 184, 135] +colors["cadetblue"] = [95, 158, 160] +colors["chartreuse"] = [127, 255, 0] +colors["chocolate"] = [210, 105, 30] +colors["coral"] = [255, 127, 80] +colors["cornflowerblue"] = [100, 149, 237] +colors["cornsilk"] = [255, 248, 220] +colors["crimson"] = [220, 20, 60] +colors["cyan"] = [0, 255, 255] +colors["darkblue"] = [0, 0, 139] +colors["darkcyan"] = [0, 139, 139] +colors["darkgoldenrod"] = [184, 134, 11] +colors["darkgray"] = [169, 169, 169] +colors["darkgreen"] = [0, 100, 0] +colors["darkkhaki"] = [189, 183, 107] +colors["darkmagenta"] = [139, 0, 139] +colors["darkolivegreen"] = [85, 107, 47] +colors["darkorange"] = [255, 140, 0] +colors["darkorchid"] = [153, 50, 204] +colors["darkred"] = [139, 0, 0] +colors["darksalmon"] = [233, 150, 122] +colors["darkseagreen"] = [143, 188, 143] +colors["darkslateblue"] = [72, 61, 139] +colors["darkslategray"] = [47, 79, 79] +colors["darkturquoise"] = [0, 206, 209] +colors["darkviolet"] = [148, 0, 211] +colors["deeppink"] = [255, 20, 147] +colors["deepskyblue"] = [0, 191, 255] +colors["dimgray"] = [105, 105, 105] +colors["dodgerblue"] = [30, 144, 255] +colors["firebrick"] = [178, 34, 34] +colors["floralwhite"] = [255, 250, 240] +colors["forestgreen"] = [34, 139, 34] +colors["fuchsia"] = [255, 0, 255] +colors["gainsboro"] = [220, 220, 220] +colors["ghostwhite"] = [248, 248, 255] +colors["gold"] = [255, 215, 0] +colors["goldenrod"] = [218, 165, 32] +colors["gray"] = [128, 128, 128] +colors["green"] = [0, 128, 0] +colors["greenyellow"] = [173, 255, 47] +colors["honeydew"] = [240, 255, 240] +colors["hotpink"] = [255, 105, 180] +colors["indianred"] = [205, 92, 92] +colors["indigo"] = [75, 0, 130] +colors["ivory"] = [255, 240, 240] +colors["khaki"] = [240, 230, 140] +colors["lavender"] = [230, 230, 250] +colors["lavenderblush"] = [255, 240, 245] +colors["lawngreen"] = [124, 252, 0] +colors["lemonchiffon"] = [255, 250, 205] +colors["lightblue"] = [173, 216, 230] +colors["lightcoral"] = [240, 128, 128] +colors["lightcyan"] = [224, 255, 255] +colors["lightgoldenrodyellow"] = [250, 250, 210] +colors["lightgreen"] = [144, 238, 144] +colors["lightgrey"] = [211, 211, 211] +colors["lightpink"] = [255, 182, 193] +colors["lightsalmon"] = [255, 160, 122] +colors["lightseagreen"] = [32, 178, 170] +colors["lightskyblue"] = [135, 206, 250] +colors["lightslategray"] = [119, 136, 153] +colors["lightsteelblue"] = [176, 196, 222] +colors["lightyellow"] = [255, 255, 224] +colors["lime"] = [0, 255, 0] +colors["limegreen"] = [50, 205, 50] +colors["linen"] = [250, 240, 230] +colors["magenta"] = [255, 0, 255] +colors["maroon"] = [128, 0, 0] +colors["mediumaquamarine"] = [102, 205, 170] +colors["mediumblue"] = [0, 0, 205] +colors["mediumorchid"] = [186, 85, 211] +colors["mediumpurple"] = [147, 112, 219] +colors["mediumseagreen"] = [60, 179, 113] +colors["mediumslateblue"] = [123, 104, 238] +colors["mediumspringgreen"] = [0, 250, 154] +colors["mediumturquoise"] = [72, 209, 204] +colors["mediumvioletred"] = [199, 21, 133] +colors["midnightblue"] = [25, 25, 112] +colors["mintcream"] = [245, 255, 250] +colors["mistyrose"] = [255, 228, 225] +colors["moccasin"] = [255, 228, 181] +colors["navajowhite"] = [255, 222, 173] +colors["navy"] = [0, 0, 128] +colors["oldlace"] = [253, 245, 230] +colors["olive"] = [128, 128, 0] +colors["olivedrab"] = [107, 142, 35] +colors["orange"] = [255, 165, 0] +colors["orangered"] = [255, 69, 0] +colors["orchid"] = [218, 112, 214] +colors["palegoldenrod"] = [238, 232, 170] +colors["palegreen"] = [152, 251, 152] +colors["paleturquoise"] = [175, 238, 238] +colors["palevioletred"] = [219, 112, 147] +colors["papayawhip"] = [255, 239, 213] +colors["peachpuff"] = [255, 239, 213] +colors["peru"] = [205, 133, 63] +colors["pink"] = [255, 192, 203] +colors["plum"] = [221, 160, 221] +colors["powderblue"] = [176, 224, 230] +colors["purple"] = [128, 0, 128] +colors["red"] = [255, 0, 0] +colors["rosybrown"] = [188, 143, 143] +colors["royalblue"] = [65, 105, 225] +colors["saddlebrown"] = [139, 69, 19] +colors["salmon"] = [250, 128, 114] +colors["sandybrown"] = [244, 164, 96] +colors["seagreen"] = [46, 139, 87] +colors["seashell"] = [255, 245, 238] +colors["sienna"] = [160, 82, 45] +colors["silver"] = [192, 192, 192] +colors["skyblue"] = [135, 206, 235] +colors["slateblue"] = [106, 90, 205] +colors["slategray"] = [112, 128, 144] +colors["snow"] = [255, 250, 250] +colors["springgreen"] = [0, 255, 127] +colors["steelblue"] = [70, 130, 180] +colors["tan"] = [210, 180, 140] +colors["teal"] = [0, 128, 128] +colors["thistle"] = [216, 191, 216] +colors["tomato"] = [253, 99, 71] +colors["turquoise"] = [64, 224, 208] +colors["violet"] = [238, 130, 238] +colors["wheat"] = [245, 222, 179] +colors["white"] = [255, 255, 255] +colors["whitesmoke"] = [245, 245, 245] +colors["yellow"] = [255, 255, 0] +colors["yellowgreen"] = [154, 205, 50] diff --git a/src/vizinfo.pyc b/src/vizinfo.pyc new file mode 100644 index 0000000..2fac64f Binary files /dev/null and b/src/vizinfo.pyc differ diff --git a/src/vmd.py b/src/vmd.py new file mode 100644 index 0000000..8b61ee2 --- /dev/null +++ b/src/vmd.py @@ -0,0 +1,217 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# vmd tool + +# Minimalistic VMD embedding for Pizza.py +# (c) 2010 Axel Kohlmeyer +# This class will replace the VMD startup script, +# open a pipe to the executable, +# and feed it Tcl command lines one at a time + +oneline = "Control VMD from python" + +docstr = """ +v = vmd() start up VMD +v.stop() shut down VMD instance +v.clear() delete all visualizations + +v.rep(style) set default representation style. One of + (Lines|VDW|Licorice|DynamicBonds|Points|CPK) +v.new(file[,type]) load new file (default file type 'lammpstrj') +v.data(file[,atomstyle]) load new data file (default atom style 'full') +v.replace(file[,type]) replace current frames with new file +v.append(file[,type]) append file to current frame(s) +v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame + +v.frame(frame) set current frame +v.flush() flush pending input to VMD and update GUI +v.read(file) read Tcl script file (e.g. saved state) + +v.enter() enter interactive shell +v.debug([True|False]) display generated VMD script commands? +""" + +# History +# 11/10, Axel Kohlmeyer (Temple U): original version + +# Imports and external programs + +import types, os +import numpy + +try: from DEFAULTS import PIZZA_VMDNAME +except: PIZZA_VMDNAME = "vmd" +try: from DEFAULTS import PIZZA_VMDDIR +except: PIZZA_VMDDIR = "/usr/local/lib/vmd" +try: from DEFAULTS import PIZZA_VMDDEV +except: PIZZA_VMDDEV = "win" +try: from DEFAULTS import PIZZA_VMDARCH +except: PIZZA_VMDARCH = "LINUX" + +try: import pexpect +except: + print "pexpect from http://pypi.python.org/pypi/pexpect", \ + "is required for vmd tool" + raise + +# Class definition + +class vmd: + + # -------------------------------------------------------------------- + + def __init__(self): + self.vmddir = PIZZA_VMDDIR + self.vmdexe = PIZZA_VMDDIR + '/' + PIZZA_VMDNAME + '_' + PIZZA_VMDARCH + # these are all defaults copied from the vmd launch script + os.environ['VMDDIR'] = PIZZA_VMDDIR + os.environ['VMDDISPLAYDEVICE'] = PIZZA_VMDDEV + os.environ['VMDSCRPOS'] = "596 190" + os.environ['VMDSCRSIZE'] = "669 834" + os.environ['VMDSCRHEIGHT'] = "6.0" + os.environ['VMDSCRDIST'] = "-2.0" + os.environ['VMDTITLE'] = "on" + os.environ['TCL_LIBRARY'] = PIZZA_VMDDIR + "/scripts/tcl" + os.environ['STRIDE_BIN'] = PIZZA_VMDDIR + "/stride_" + PIZZA_VMDARCH + os.environ['SURF_BIN'] = PIZZA_VMDDIR + "/surf_" + PIZZA_VMDARCH + os.environ['TACHYON_BIN'] = PIZZA_VMDDIR + "/tachyon_" + PIZZA_VMDARCH + ldpath = os.environ.get('LD_LIBRARY_PATH','') + if ldpath == '': + os.environ['LD_LIBRARY_PATH'] = PIZZA_VMDDIR + else: + os.environ['LD_LIBRARY_PATH'] = ldpath + ':' + PIZZA_VMDDIR + ldpath = os.environ.get('LD_LIBRARY_PATH','') + if ldpath == '': + os.environ['PYTHONPATH'] = PIZZA_VMDDIR + else: + os.environ['PYTHONPATH'] = PIZZA_VMDDIR + "/scripts/python" + self.debugme = False + # open pipe to vmd and wait until we have a prompt + self.VMD = pexpect.spawn(self.vmdexe) + self.VMD.expect('vmd >') + + # -------------------------------------------------------------------- + # post command to vmd and wait until the prompt returns. + def __call__(self,command): + if self.VMD.isalive(): + self.VMD.sendline(command) + self.VMD.expect('vmd >') + if self.debugme: + print "call+result:"+self.VMD.before + return + + # -------------------------------------------------------------------- + # exit VMD + def stop(self): + self.__call__("quit") + del self.VMD + + # -------------------------------------------------------------------- + # force VMD display and GUI update. + def flush(self): + self.__call__('display update ui') + + # -------------------------------------------------------------------- + # turn on debugging info + def debug(self,status=True): + if status and not self.debugme: + print 'Turning vmd.py debugging ON.' + if not status and self.debugme: + print 'Turning vmd.py debugging OFF.' + self.debugme = status + + # -------------------------------------------------------------------- + # emulate a regular tcl command prompt + def enter(self,mode='tcl'): + self.__call__('menu main off') + self.__call__('menu main on') + while 1: + try: + command = raw_input("vmd > ") + except EOFError: + print "(EOF)" + self.__call__('menu main off') + return + if command == "quit" or command == "exit": + self.__call__('menu main off') + return + if command == "gopython": + print "gopython not supported here" + continue + self.__call__(command) + + # -------------------------------------------------------------------- + # read and execute tcl script file (e.g. a saved state) + def read(self,filename): + self.__call__('play ' + filename) + self.flush() + + # -------------------------------------------------------------------- + # remove all molecules, data and visualizations + def clear(self): + self.__call__("mol delete all") + + # -------------------------------------------------------------------- + # navigate to a given frame + def rep(self,style='Lines'): + if style == 'Lines' or style == 'VDW' or style == 'Licorice' \ + or style == 'DynamicBonds' or style == 'Points' or style == 'CPK': + self.__call__('mol default style ' + style) + # -------------------------------------------------------------------- + # navigate to a given frame + def frame(self,framespec): + self.__call__('animate goto ' + str(framespec)) + + # -------------------------------------------------------------------- + # load a new molecule from a file supported by a molfile plugin + def new(self,filename,filetype='lammpstrj'): + self.__call__('mol new ' + filename + ' type ' + filetype + ' waitfor all') + self.flush() + + # -------------------------------------------------------------------- + # load a new molecule from a data file via the topotools plugin + def data(self,filename,atomstyle='full'): + self.__call__('package require topotools 1.0') + self.__call__('topo readlammpsdata ' + filename + ' ' + atomstyle) + self.flush() + + # -------------------------------------------------------------------- + # append all frames from a given file to the current molecule + def append(self,filename,filetype='lammpstrj'): + self.__call__('set tmol [molinfo top]') + self.__call__('array set viewpoints {}') + self.__call__('foreach mol [molinfo list] { set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}') + self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all') + self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}') + self.flush() + + # -------------------------------------------------------------------- + # replace all frames of a molecule with those from a given file + def update(self,filename,filetype='lammpstrj'): + self.__call__('set tmol [molinfo top]') + self.__call__('array set viewpoints {}') + self.__call__('foreach mol [molinfo list] {set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}') + self.__call__('animate delete all $tmol') + self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all') + self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}') + self.flush() + + # -------------------------------------------------------------------- + # add or overwrite coordinates with coordinates in a snapshot + def set(self,snap,x,y,z,append=True): + self.__call__('set vmdsel [atomselect top all]') + if append: + self.__call__('animate dup [molinfo top]') + cmd = '$vmdsel set {x y z} {' + for idx in range(0,snap.natoms): + cmd += ' {'+str(snap[idx,x])+' '+str(snap[idx,y])+' '+str(snap[idx,z])+'}' + cmd += '}' + self.__call__(cmd) + self.__call__('$vmdsel delete ; unset vmdsel') + self.flush() diff --git a/src/vmd.pyc b/src/vmd.pyc new file mode 100644 index 0000000..88d4d4c Binary files /dev/null and b/src/vmd.pyc differ diff --git a/src/vtk.py b/src/vtk.py new file mode 100644 index 0000000..1b7d9ce --- /dev/null +++ b/src/vtk.py @@ -0,0 +1,435 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# vtk tool + +oneline = "Convert LAMMPS snapshots to VTK format" + +docstr = """ +v = vtk(d) d = object containing atom coords (dump, data) + +v.one() write all snapshots to tmp.vtk +v.one("new") write all snapshots to new.vtk +v.many() write snapshots to tmp0000.vtk, tmp0001.vtk, etc +v.many("new") write snapshots to new0000.vtk, new0001.vtk, etc +v.single(N) write snapshot for timestep N to tmp.vtk +v.single(N,"file") write snapshot for timestep N to file.vtk + + surfaces in snapshot will be written to SURF1.vtk, SURF2.vtk, etc + where each surface (triangle type) is in a different file +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# data = data file to read from + +# Imports and external programs + +import sys, re + +# Class definition + +class vtk: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def one(self,*args): + if len(args) == 0: file = "tmp.vtk" + elif args[0][-4:] == ".vtk": file = args[0] + else: file = args[0] + ".vtk" + + n = flag = 0 + which,time,flag = self.data.iterator(flag) + time,box,atoms,bonds,tris,lines = self.data.viz(which) + print time, + sys.stdout.flush() + + if len(tris): surface(tris) + + allatoms = [] + for atom in atoms: + allatoms.append(atom) + + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + for atom in atoms: allatoms.append(atom) + print time, + sys.stdout.flush() + n += 1 + + particle(file,allatoms) + print "\nwrote %d snapshots to %s in VTK format" % (n,file) + + # -------------------------------------------------------------------- + + def many(self,*args): + if len(args) == 0: root = "tmp" + else: root = args[0] + + surfflag = 0 + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + if surfflag == 0 and len(tris): + surfflag = 1 + surface(tris) + + if n < 10: + file = root + "000" + str(n) + ".vtk" + elif n < 100: + file = root + "00" + str(n) + ".vtk" + elif n < 1000: + file = root + "0" + str(n) + ".vtk" + else: + file = root + str(n) + ".vtk" + + particle(file,atoms) + + print time, + sys.stdout.flush() + n += 1 + + print "\nwrote %s snapshots in VTK format" % n + # -------------------------------------------------------------------- + def manyGran(self,*args,**kwargs): + + # check whether to output or not + outputfl = True + if "output" in kwargs: outputfl = kwargs["output"] + + # read startIndex (offset for filename due to parallel processing) + startIndex = 0 + fileNos = [] + if "fileNos" in kwargs: + fileNos = kwargs["fileNos"] + else: + fileNos = range(len(self.data.snaps)) + + # output name + if len(args) == 0: root = "tmp" + else: root = args[0] + + surfflag = 0 + n = flag = 0 + + # iterate over snaps + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + xlo=self.data.snaps[n].xlo + xhi=self.data.snaps[n].xhi + ylo=self.data.snaps[n].ylo + yhi=self.data.snaps[n].yhi + zlo=self.data.snaps[n].zlo + zhi=self.data.snaps[n].zhi + + atoms=self.data.snaps[n].atoms + names=self.data.names + + if surfflag == 0 and len(tris): + surfflag = 1 + surface(tris) + + if fileNos[n] < 10: + file = root + "000" + str(fileNos[n]) + ".vtk" + file_bb= root + "000" + str(fileNos[n]) + "_boundingBox.vtk" + file_walls= root + "000" + str(fileNos[n]) + "_walls.vtk" + elif fileNos[n] < 100: + file = root + "00" + str(fileNos[n]) + ".vtk" + file_bb= root + "00" + str(fileNos[n]) + "_boundingBox.vtk" + file_walls= root + "00" + str(fileNos[n]) + "_walls.vtk" + elif fileNos[n] < 1000: + file = root + "0" + str(fileNos[n]) + ".vtk" + file_bb= root + "0" + str(fileNos[n]) + "_boundingBox.vtk" + file_walls= root + "0" + str(fileNos[n]) + "_walls.vtk" + else: + file = root + str(fileNos[n]) + ".vtk" + file_bb= root + str(fileNos[n]) + "_boundingBox.vtk" + file_walls= root + str(fileNos[n]) + "_walls.vtk" + + boundingBox(file_bb,xlo,xhi,ylo,yhi,zlo,zhi) + nvalues = 0 + try: nvalues = len(self.data.snaps[0].atoms[0]) + except: nvalues = 0 + particleGran(file,atoms,names,nvalues) + + if outputfl: print time, + if outputfl: sys.stdout.flush() + n += 1 + + if outputfl: print "\nwrote %s granular snapshots in VTK format" % n + # -------------------------------------------------------------------- + + def single(self,time,*args): + if len(args) == 0: file = "tmp.vtk" + elif args[0][-4:] == ".vtk": file = args[0] + else: file = args[0] + ".vtk" + + which = self.data.findtime(time) + time,box,atoms,bonds,tris,lines = self.data.viz(which) + if len(tris): surface(tris) + particle(file,atoms) + +# -------------------------------------------------------------------- +# write list of triangles into VTK surface files: SURF1.vtk, SURF2.vtk, ... +# all triangles of one type constitute 1 surface = 1 file +# create list of unique vertices (via dictionary) from triangle list + +def surface(tris): + ntypes = tris[-1][1] + + for i in xrange(ntypes): + itype = i+1 + v = {} + nvert = ntri = 0 + for tri in tris: + if tri[1] == itype: + ntri += 1 + vert = (tri[2],tri[3],tri[4]) + if not v.has_key(vert): + v[vert] = nvert + nvert += 1 + vert = (tri[5],tri[6],tri[7]) + if not v.has_key(vert): + v[vert] = nvert + nvert += 1 + vert = (tri[8],tri[9],tri[10]) + if not v.has_key(vert): + v[vert] = nvert + nvert += 1 + + keys = v.keys() + vinverse = {} + for key in keys: + vinverse[v[key]] = key + + filename = "SURF" + str(itype) + ".vtk" + f = open(filename,"w") + + print >>f,"# vtk DataFile Version 3.0" + print >>f,"Generated by pizza.py" + print >>f,"ASCII" + print >>f,"DATASET POLYDATA" + print >>f,"POINTS %d float" % nvert + for i in xrange(nvert): + tuple = vinverse[i] + print >>f,tuple[0],tuple[1],tuple[2] + print >>f,"POLYGONS",ntri,4*ntri + for tri in tris: + if tri[1] == itype: + vert = (tri[2],tri[3],tri[4]) + ivert1 = v[vert] + vert = (tri[5],tri[6],tri[7]) + ivert2 = v[vert] + vert = (tri[8],tri[9],tri[10]) + ivert3 = v[vert] + print >>f,3,ivert1,ivert2,ivert3 + print >>f + print >>f,"CELL_DATA",ntri + print >>f,"POINT_DATA",nvert + + f.close() + +# -------------------------------------------------------------------- +# write atoms from one snapshot into file in VTK format + +def particle(file,atoms): + f = open(file,"w") + + print >>f,"# vtk DataFile Version 2.0" + print >>f,"Generated by pizza.py" + print >>f,"ASCII" + print >>f,"DATASET POLYDATA" + print >>f,"POINTS %d float" % len(atoms) + for atom in atoms: + print >>f,atom[2],atom[3],atom[4] + print >>f,"VERTICES",len(atoms),2*len(atoms) + for i in xrange(len(atoms)): + print >>f,1,i + print >>f,"POINT_DATA",len(atoms) + print >>f,"SCALARS atom_type int 1" + print >>f,"LOOKUP_TABLE default" + for atom in atoms: + itype = int(atom[1]) + print >>f,itype, + print >>f + + f.close() + + +def boundingBox(file,xlo,xhi,ylo,yhi,zlo,zhi): + f = open(file,"w") + + print >>f,"# vtk DataFile Version 2.0" + print >>f,"Generated by pizza.py" + print >>f,"ASCII" + print >>f,"DATASET RECTILINEAR_GRID" + print >>f,"DIMENSIONS 2 2 2" + print >>f,"X_COORDINATES 2 float" + print >>f,xlo,xhi + print >>f,"Y_COORDINATES 2 float" + print >>f,ylo,yhi + print >>f,"Z_COORDINATES 2 float" + print >>f,zlo,zhi + +def typestr(o): + string = str(type(o)) + sp = string.split('\'') + return sp[1] + +def particleGran(file,atoms,names,n_values): + f = open(file,"w") + + # if no atoms are present + if atoms == None: + atoms = [] + + # find indices of scalars and vectors + scalars, vectors = findScalarsAndVectors(names) + + # print head + print >>f,"# vtk DataFile Version 2.0" + print >>f,"Generated by lpp.py" + print >>f,"ASCII" + print >>f,"DATASET POLYDATA" + print >>f,"POINTS %d float" % len(atoms) + for atom in atoms: + print >>f, atom[vectors['x']], atom[vectors['x']+1], atom[vectors['x']+2] #atom[3],atom[4],atom[5] #write x,y,z [atom[0]=id, atom[1]=type] + print >>f,"VERTICES",len(atoms),2*len(atoms) + for i in xrange(len(atoms)): + print >>f,1,i + print >>f,"POINT_DATA",len(atoms) + + # print VECTORS + for key in vectors.keys(): + + # don't print coodinates again + if key == 'x': + continue + + vectortype = 'float' + if atoms != []: + vectortype = typestr(atoms[0][vectors[key]]) + if 'float' in vectortype: vectortype = 'float' + elif 'int' in vectortype: vectortype = 'int' + else: vectortype = 'float' + else: # if no atoms are present + pass + + print >>f,"VECTORS",key,vectortype + for atom in atoms: + print >>f, atom[vectors[key]], atom[vectors[key]+1], atom[vectors[key]+2] + + # print SCALARS + for key in scalars.keys(): + scalartype ='' + if atoms != []: + scalartype = typestr(atoms[0][scalars[key]]) + if 'float' in scalartype: scalartype = 'float' + elif 'int' in scalartype: scalartype = 'int' + else: scalartype = 'int' + else: # if no atoms are present + pass + + print >>f,"SCALARS",key,scalartype,1 + print >>f,"LOOKUP_TABLE default" + for atom in atoms: + print >>f, atom[scalars[key]] + + print >>f + + f.close() + +def findScalarsAndVectors(names): + + vectors={} + scalars={} + + # create reversed dictionary {position:name} + indices = {} + for name in names: + indices[names[name]]=name + + # fill missing indices (occurrs e.g. if output is like vx vy vz fx fy fz vx vy vz) + for i in xrange(max(indices)): + if i not in indices: + indices[i]="" + + # compile regexes to find vectors + regvx = re.compile(".*x") + regvy = re.compile(".*y") + regvz = re.compile(".*z") + regf = re.compile("f_.*\[[0-9]+\]") + regc = re.compile("c_.*\[[0-9]+\]") + regv = re.compile("v_.*\[[0-9]+\]") + + # loop over all indices and look if their names represent a vector (if not: it's a scalar) + i = 0 + while i<= max(indices): + + if i+2 <= max(indices) and regvx.match(indices[i]) != None and regvy.match(indices[i+1]) != None and regvz.match(indices[i+2]) != None: + + newname='' + if len(indices[i]) == 1: + newname=indices[i] + else: + newname=indices[i][:-1] + + vectors[newname]=i + i+=3 + continue + + if regf.match(indices[i]) != None or regc.match(indices[i]) != None or regv.match(indices[i]) != None: + + name = indices[i] + number = int( name.split('[')[1].split(']')[0] ) + nextName = name.split('[')[0]+'['+str(number+1)+']' + nextButOneName = name.split('[')[0]+'['+str(number+2)+']' + + newname = name[2:-(len(name.split('[')[1])+1)] + + if i+2 <= max(indices) and indices[i+1] == nextName and indices[i+2] == nextButOneName: + vectors[newname]=i + i+=3 + continue + + else: + scalars[newname]=i + i+=1 + continue + + # program only here if not a vector + if indices[i] != '': + newname = indices[i] + scalars[newname]=i + i+=1 + + if 'x' not in vectors.keys(): + print "vector x y z has to be contained in dump file. please change liggghts input script accordingly." + exit() + + return scalars, vectors + + + diff --git a/src/vtk.pyc b/src/vtk.pyc new file mode 100644 index 0000000..b8012b9 Binary files /dev/null and b/src/vtk.pyc differ diff --git a/src/xyz.py b/src/xyz.py new file mode 100644 index 0000000..66699ab --- /dev/null +++ b/src/xyz.py @@ -0,0 +1,121 @@ +# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html +# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# +# Copyright (2005) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. + +# xyz tool + +oneline = "Convert LAMMPS snapshots to XYZ format" + +docstr = """ +x = xyz(d) d = object containing atom coords (dump, data) + +x.one() write all snapshots to tmp.xyz +x.one("new") write all snapshots to new.xyz +x.many() write snapshots to tmp0000.xyz, tmp0001.xyz, etc +x.many("new") write snapshots to new0000.xyz, new0001.xyz, etc +x.single(N) write snapshot for timestep N to tmp.xyz +x.single(N,"file") write snapshot for timestep N to file.xyz +""" + +# History +# 8/05, Steve Plimpton (SNL): original version + +# ToDo list + +# Variables +# data = data file to read from + +# Imports and external programs + +import sys + +# Class definition + +class xyz: + + # -------------------------------------------------------------------- + + def __init__(self,data): + self.data = data + + # -------------------------------------------------------------------- + + def one(self,*args): + if len(args) == 0: file = "tmp.xyz" + elif args[0][-4:] == ".xyz": file = args[0] + else: file = args[0] + ".xyz" + + f = open(file,"w") + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + print >>f,len(atoms) + print >>f,"Atoms" + for atom in atoms: + itype = int(atom[1]) + print >>f,itype,atom[2],atom[3],atom[4] + + print time, + sys.stdout.flush() + n += 1 + + f.close() + print "\nwrote %d snapshots to %s in XYZ format" % (n,file) + + # -------------------------------------------------------------------- + + def many(self,*args): + if len(args) == 0: root = "tmp" + else: root = args[0] + + n = flag = 0 + while 1: + which,time,flag = self.data.iterator(flag) + if flag == -1: break + time,box,atoms,bonds,tris,lines = self.data.viz(which) + + if n < 10: + file = root + "000" + str(n) + elif n < 100: + file = root + "00" + str(n) + elif n < 1000: + file = root + "0" + str(n) + else: + file = root + str(n) + file += ".xyz" + f = open(file,"w") + print >>f,len(atoms) + print >>f,"Atoms" + for atom in atoms: + itype = int(atom[1]) + print >>f,itype,atom[2],atom[3],atom[4] + print time, + sys.stdout.flush() + f.close() + n += 1 + + print "\nwrote %s snapshots in XYZ format" % n + + # -------------------------------------------------------------------- + + def single(self,time,*args): + if len(args) == 0: file = "tmp.xyz" + elif args[0][-4:] == ".xyz": file = args[0] + else: file = args[0] + ".xyz" + + which = self.data.findtime(time) + time,box,atoms,bonds,tris,lines = self.data.viz(which) + f = open(file,"w") + print >>f,len(atoms) + print >>f,"Atoms" + for atom in atoms: + itype = int(atom[1]) + print >>f,itype,atom[2],atom[3],atom[4] + f.close() diff --git a/src/xyz.pyc b/src/xyz.pyc new file mode 100644 index 0000000..67ea636 Binary files /dev/null and b/src/xyz.pyc differ