Physics 381C - Spring 1997

Physics 381C: Computational Physics: Software Availability and Usage Hints

This document will be updated throughout the course

libp329f.a: p329f.f: Source code for the p329f library. p329fsa.f: Sample driver for library routines.
libvcyc.a: Black-box routines for solving Poisson equation in 1, 2 and 3-d. Available on SGIs (see instructor for Cray usage). See source code vcyc.f for usage information. Sample driver routine: mg0.f, include file mgprob.inc and Makefile. Sample load statement:
```
      f77 -g -n32 pgm.o \
         -lvcyc -lv3util -lv2util -lvutil -lutilio -lutilmath -o pgm
```
grlat2d: SGI specific graphics utility for plotting 2d spin (binary valued) lattices. Fortran source code tlat2d.f and Makefile illustrating use.
ser (aka vs): SGI specific graphics utility for analyzing time series of 1 dimensional data. Brief overview of usage. Warning: This software is research-quality, not commercial quality, and there is essentially no documentation other than the source code. However, despite its many quirks, ser is a very powerful tool for analyzing the output of finite-difference codes in one spatial dimension and time. Any of the Center for Relativity graduate students or postdocs who are working with me will be happy to give you a quick tutorial, as will I.
FFT routines: libfftpack.a contains Fortran-callable routines for performing single and double precision FFTs. Available on einstein. Documentation for the double precision routines is available here. Sample usage:
```
      f77 -g -n32 pgm.o -lfftpack -o pgm
```
Sample main program, tfft.f and Makefile which uses some of the basic routines.
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 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. Note that the types

      BBH_I,      BBH_D,       BBH_C

are synonymous with

      int,        double,      char

in C, and

      integer,    real*8,      character

in Fortran. Fortran routines have the same names (gft_write_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_write_bbox
      gft_close_all

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_write_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.hdf'.  All calls to 'gft_write_bbox'
c     with the same string result in output to the 
c     same file.
c------------------------------------------------------
         time = it * 1.0d0
         call gft_write_bbox('gfcn',time,shape,rank,
     &                       bbox,gfcn)
      end do
c------------------------------------------------------
c     'gft_close_all' MUST be called after all 'gft_'
c     output is complete.
c------------------------------------------------------
      call gft_close_all()
              .
              .
              .

The gft_ routines use the NCSA HDF format and libraries. HDF is a machine-independent binary format; thus data output using gft_write_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 ReadHDF_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.

Linking to libbbhutil.a on einstein:

   % f77 -g -n32 -L/usr/localn32/lib pgm.o \
         -lbbhutil -lmfhdf -ldf -ljpeg -lz -o pgm

Linking to libbbhutil.a on charon:

   % cf77 -L/hpcf/u0/ph/az/phaz337/lib  pgm.o \
          -lbbhutil -lnetcdf -ldf -o pgm

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