Physics 329 - Intro Computational Physics - UT Austin - Spring 1998

Physics 329: Introduction to Computational Physics: Software Availability and Usage Hints

This document will be updated throughout the course

Index

Maple
ser/vs
libbhutil.a
pp2d
GLUT
libp329f.a
ghostview
gnuplot
sm (Supermongo)
latex and tex
xdvi
dvips
IRIS/NAG Explorer

Maple: One of the two major general-purpose "symbolic manipulation" packages (also general-purpose programming environments), and the one that we will study in this course. On the SGIs type
```
% xmaple
```
for the GUI version (in which case make sure your DISPLAY environment variable is set correctly if running on a remote machine), or
```
% maple
```
for a terminal-based (text) session. In the latter instance you should see something like this.
```
% maple
    |\^/|     Maple V Release 5 (University of Texas at Austin)
._|\|   |/|_. Copyright (c) 1981-1997 by Waterloo Maple Inc. All rights
 \  MAPLE  /  reserved. Maple and Maple V are registered trademarks of
 <____ ____>  Waterloo Maple Inc.
      |       Type ? for help.
> 
```
If there is any sequence of Maple commands that you find yourself typing at the beginning of each session (maple or xmaple) you can put them in a file .mapleinit in your home directory, whereafter they will automatically be executed each time you use Maple.
IRIS Explorer: A powerful scientific visualization system available on the Center SGI machines, including einstein. You need to be logged into einstein via the graphics console to use the software. Complete documentation for the system is available via the Online Books selection of the pull-down Help menu which should appear in the "Toolchest" located in the upper right corner of the screen when you login. To use, simply type
```
      % explorer
```
Here are links to the IRIS Explorer Center and Postscript versions of the User's Guide with graphics and without graphics.

libbbhutil.a: Fortran- and C-callable output utility routines written for the Binary Black Holes Grand Challenge Project. Available on SGIs and HPCF Cray machines. Postscript ``man-style'' documentation for the C routines is available here. Fortran routines have the same names (gft_out_bbox etc.) and can be either called, or invoked as integer functions. For output of 2- and 3-D arrays on uniform finite-difference meshes, the routines

      gft_out_bbox

should suffice. Here is a usage example:

      integer      nx,        ny
      parameter  ( nx = 65,   ny = 33 )

      real*8       gfcn(nx,ny)
      real*8       xmin,      xmax,     ymin,     ymax, 
     &             time

      integer      shape(2),  rank
      real*8       bbox(4)
               .
               .
               .
c------------------------------------------------------
c     'bbox' defines 'bounding box' of coords.
c     associated with the data:
c
c     bbox := ( xmin, xmax, ymin, ymax )
c------------------------------------------------------
      bbox(1) = xmin
      bbox(2) = xmax
      bbox(3) = ymin
      bbox(4) = ymax

      rank = 2
      shape(1) = nx
      shape(2) = ny
 
      do it = 1 , nt
              .
              .
              .
c------------------------------------------------------
c     The first (string) arg. to 'gft_out_bbox'
c     is stripped of non alphanumeric/underscore 
c     characters (including punctuation) if necessary,
c     and then used as the 'stem' for a filename of 
c     the form 'stem.sdf'.  All calls to 'gft_out_bbox'
c     with the same string result in output to the 
c     same file.
c------------------------------------------------------
         time = it * 1.0d0
         call gft_out_bbox('gfcn',time,shape,rank,
     &                      bbox,gfcn)
      end do
              .
              .
              .

The gft_ routines use a machine-independent binary format; thus data output using gft_out_bbox on a Cray, for example, can be processed on an SGI. On the SGIs, 2- and 3-D data is best visualized using IRIS Explorer. A locally developed module, called ReadSDF_GFT0, is available for Explorer input of data written using the gft_ routines. Here's an image of an Explorer map which uses this module.

pp2d: OpenGL/X Graphics program for animating two dimensional particle motion. May be of use for Homework 3. Currently available only on Center for Relativity SGI machines, but should display on any workstation running X (and X-terms).
Typical usage (second form is for monochrome displays):
```
   % nbody 2.0 0.01 < nbody_input | pp2d 
   % nbody 2.0 0.01 < nbody_input | pp2d -m
```
Help is available via
```
   % pp2d -h
```
The source code, pp2d.c and pp2d.h, may be of interest to those of you interested in using OpenGL for graphics programming. Makefile for pp2d.
GLUT: OpenGL Utility Toolkit Programming Interface. Facilitates construction of OpenGL programs which manipulate windows, handle user-initiated events etc. Available PS documentation: Overview and Specification/Programmer's Guide.
Typical usage (not all Mesa and X libraries will be required for all applications):
```
   % cc -n32 -I/usr/local/include pp2d.c -L/usr/localn32/lib -lglut \
         -lMesaaux -lMesatk -lMesaGLU -lMesaGL -lXmu -lXi -lXext -lX11 \
         -lm -o pp2d
```
libp329fa: Utility library for Fortran 77 programs. Available on SGIs and Crays. Sample driver for utility routines: p329fsa.f. See source code and course notes for further information.
Typical usage:
```
   % f77 pgm.f -L/usr/localn32/lib -lp329 -o pgm
```
ghostview: Available on SGIs and Linux machines. Use for viewing Postscript documents. This is an X-application. As with any X-application, if you are running ghostview on a remote machine, be sure to set your DISPLAY environment variable so that your local display is used.
Typical usage (assuming a remote login to einstein from one the Physics Linux machines):
```
   einstein% set DISPLAY linux1.ph.utexas.edu:0
   einstein% ghostview somefile.ps
```
Note: Not all Postscript files will have .ps extensions, but many do by convention.
gnuplot: X-application available on SGIs and Linux machines. Use for generating X-Y (2D) and some surface plots. Has extensive on-line documentation: type help at the gnuplot prompt for help.
Typical usage:
```
   einstein% gnuplot
             .
             .
             .
   Terminal type set to 'x11'
   gnuplot> help
             .
             .
             .
   gnuplot> quit
```
sm: Supermongo plotting package. Available on SGIs. An alternative to gnuplot which is somewhat quirkier but generally produces more professional-looking (i.e. publication-quality) plots. See on-line postscript documentation and on-line help (type help at the the sm command prompt) for further details. Supermongo runs as an X-application provided the device is set to x11. Ignore the "Can't find entry for iris-ansi-net ..." message at start-up.
Typical usage:
```
   einstein% sm
   Can't find entry for iris-ansi-net in /usr/local/lib/sm/termcap
   Hello Matt, please give me a command
   : device x11
   : help
             .
             .
             .
   : quit
```

latex and tex: Available on SGIs. Scientific typesetting software. Converts .tex source files to .dvi files which can then be previewed using xdvi, or converted to postscript using dvips.
Typical usage:

   % ls 
   document.tex

   % latex document.tex
   This is TeX, Version 3.14159 (C version 6.1)
   (document.tex
   LaTeX2e <1996/06/01>
   Hyphenation patterns for english, german, loaded.
             .
             .
             .
   No file document.aux.
   [1] (document.aux) )
   Output written on document.dvi (1 page, 696 bytes).
   Transcript written on document.log.

   % ls
   document.aux   document.dvi   document.log   document.tex

xdvi: X-application for previewing .dvi files (output from Latex-ing or tex-ing of .tex files). You don't have to explicitly specify the .dvi extension.
Typical usage:
```
   % ls
   document.aux   document.dvi   document.log   document.tex

   % xdvi document
```

dvips: Utility for converting .dvi files to postscript.
Typical usage:

   % ls
   document.aux   document.dvi   document.log   document.tex

   % dvips document
   Got a new papersize
   This is dvips 5.58 Copyright 1986, 1994 Radical Eye Software
   ' TeX output 1997.01.22:1442' -> document.ps
   . [1] 

   % ls 
   document.aux   document.dvi   document.log   document.ps    document.tex