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.TH XPPAUT 1 "Aug  26, 2011" "Version 6.11.1" "XPPAUT Documentation"
.\" Please adjust this date whenever revising the manpage.
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.SH NAME
xppaut \- X Phase plane plus AUTO.  Solves many kinds of equations.
.SH SYNOPSIS
.PD 0
.HP 7
.B xppaut \fR[\fB\-silent\fR] [\fB\-xorfix\fR] [\fB\-convert\fR] 
.IP
\fR[\fB\-newseed\fR] [\fB\-ee\fR] [\fB\-allwin\fR]
.IP
\fR[\fB\-white\fR] [\fB\-setfile\fR \fIfile\fR] \fR[\fB\-runnow\fR]
.IP
\fR[\fB\-bigfont\fR \fIfont\fR] [\fB\-smallfont\fR \fIfont\fR] [\fB\-parfile\fR \fIfile\fR]
.IP
\fR[\fB\-outfile\fR \fIfile\fR] [\fB\-icfile\fR \fIfile\fR] [\fB\-grads \fIboolean\fR] [\fB\-bell \fIboolean\fR]
.IP
\fR[\fB\-forecolor\fR \fIcolor\fR] [\fB\-backcolor\fR \fIcolor\fR] [\fB\-backimage\fR \fIimage\fR]
.IP
\fR[\fB\-quiet \fIboolean\fR] [\fB\-logfile \fIfile\fR] [\fB\-internset \fIboolean\fR] \fR[\fB\-uset\fR \fIsetname\fR]
.IP
\fR[\fB\-rset\fR \fIsetname\fR] [\fB\-include \fIfile\fR]  [\fB\-qics\fR] [\fB\-qpars\fR] [\fB\-qsets\fR]
.IP
\fR[\fB\-anifile \fIfile\fR] [file...]
.PD
.br
.SH DESCRIPTION 
\fBxppaut\fP is a tool for solving:
.PD 0
.HP 
.IP \(bu 4 
differential equations
.IP \(bu 4 
difference equations
.IP \(bu 4 
delay equations
.IP \(bu 4 
functional equations
.IP \(bu 4 
differential-algebraic equation
.IP \(bu 4 
boundary value problems
.IP \(bu 4 
stochastic equations
.PD
.LP
The code brings together a number of useful algorithms and is
written in C. All the graphics and interface are created using 
the X Window System protocol client library Xlib <http://www.xfree86.org>.
.HP 5
\fBxppaut\fP capabilities:
.PD 0
.IP \(bu 4
Handles up to 1950 differential equations.
.IP \(bu 4
There are over a dozen solvers including several for stiff systems, a solver for integral equations and a symplectic solver
.IP \(bu 4
Up to 10 graphics windows can be visible at once and a variety of color combinations is supported
.IP \(bu 4
PostScript output is supported as well as GIF and animated GIF movies
.IP \(bu 4
Post processing is easy and includes the ability to make histograms, FFTs and applying functions to columns of data
.IP \(bu 4
Equilibria and linear stability as well as one-dimensional invariant sets can be computed
.IP \(bu 4
Nullclines and flow fields aid in the qualitative understanding of two-dimensional models
.IP \(bu 4
Poincare maps and equations on cylinders and tori are also supported
.IP \(bu 4
Some useful averaging theory tricks and various methods for dealing with coupled oscillators
.IP \(bu 4
Equations with Dirac delta functions are allowable
.IP \(bu 4
Animations of simulations such as a little pendulum moving back and forth or lamprey swimming
.IP \(bu 4
A curve-fitter based on the Marquardt-Levenberg algorithm which lets you fit dynamical systems to data
.IP \(bu 4
Generate "movies" of three-dimensional views of attractors or parametric changes in the attractor as some parameters vary
.IP \(bu 4
Dynamically link to external subroutines
.IP \(bu 4
From the command line type /dev/stdin as the file and you can write the ODE on the fly
.PD
.SH OPTIONS
.TP
.B \-silent                
Batch run without the interface and dump solutions to a file
.TP
.B \-xorfix                
Work-around for exclusive Or with X on some monitors/graphics setups
.TP
.B \-convert               
Convert old style ODE files (e.g. phaseplane) to new ODE style
.TP
.B \-newseed               
Randomizes the random number generator which will often use the same seed
.TP
.B \-ee	 
.br                               
Emulates shortcuts of Evil Empire style (MS)
.TP
.B \-allwin                
Brings XPP up with all the windows visible
.TP
.B \-white
.br                                
Swaps foreground and background colors 
.TP
.B \-setfile \fIfilename   
Loads the set file before starting up
.TP
.B \-runnow                
Runs ode file immediately upon startup (implied by -silent)
.TP
.B \-bigfont \fIfont        
Use the big font whose filename is given
.TP
.B \-smallfont \fIfont      
Use the small font whose filename is given
.TP
.B \-parfile \fIfilename    
Load parameters from the named file
.TP
.B \-outfile \fIfilename    
Send output to this file (default is output.dat)
.TP
.B \-icfile \fIfilename     
Load initial conditions from the named file
.TP
.B \-forecolor \fIcolor
Hexadecimal color (e.g. 000000) for foreground
.TP
.B \-backcolor \fIcolor  
Hexadecimal color (e.g. EDE9E3) for background
.TP
.B \-mwcolor \fIcolor  
Hexadecimal color (e.g. 808080) for main window
.TP
.B \-dwcolor \fIcolor  
Hexadecimal color (e.g. FFFFFF) for drawing window
.TP
.B \-backimage \fIfilename  
Name of bitmap file (.xbm) to tile in background
.PP
.RS
For example, the following text saved to a file named stipple2.xbm
can be loaded to impart a stippled background.
.PP
.PD 0
.RS
.PP
.PP
#define stipple2_width 2
.PP
#define stipple2_height 2
.PP
static char stipple2_bits[] = {
.PP
 0x02,0x01};
.PP
.PD
.RE
.RE
.TP
.B \-grads \fIB            
Color gradients will (B=1) or will not (B=0) be used
.TP
.B \-width  \fIN              
Minimum width in pixels of main window
.TP
.B \-height \fIN               
Minimum height in pixels of main window
.TP
.B \-bell \fIB            
System bell on events will (B=1) or will not (B=0) be used
.TP
.B \-internset \fIB               
Internal sets will (B=1) or will not (B=0) be run during batch run
.TP
.B \-uset \fIsetname        
Named internal set will be run during batch run
.TP 
.B \-rset \fIsetname 
Named internal set will not be run during batch run
.TP
.B \-include \fIfilename    
Named file will be included (see include directive)
.TP
.B \-qsets
.br
Query internal sets (output saved to OUTFILE)
.TP
.B \-qpars                 
.br
Query parameters (output saved to OUTFILE)
.TP
.B \-qics                  
.br
Query initial conditions (output saved to OUTFILE)
.TP 
.B \-quiet \fIB       
Verbose log messages will (B=0) or will not be (B=1) written
.TP 
.B \-logfile \fIfilename
Verbose log messages are written to named file instead of stdout 
.TP 
.B \-anifile \fIfilename
Load animation (.ani) from the named file
.LP
.SH ENVIRONMENT
 
.B \fBXPPSTART\fP
.RS
File browser will open to the specified path. This may be useful in an instructional setting to point to a mapped drive containing course materials.
.RE
.TP
.B \fBXPPHELP\fP
.RS
Path to the XPPAUT documentation file <xpphelp.html> (e.g. /usr/share/doc/xppaut/html/xpphelp.html)
.RE
.TP
.B \fBXPPBROWSER\fP
Web browser to view documentation (e.g. /usr/bin/firefox)
.RE
.SH FILES
Each user can customize the behavior and appearance of Xppaut via the
file \(lq$HOME/.xpprc\(rq. Where the environment variable $HOME points
to the user's home directory. On most systems $HOME will already be set.
Each option line in .xpprc begins with the \(lq@\(rq symbol followed by a comma-separated list of options. Comment
lines begin with the \(lq#\(rq symbol and are ignored.
  


.PD 0
.RS
# Example .xpprc file
.PP
@ maxstor=50000
.PP
@ meth=qualrk,tol=1e-6,atol=1e-6
.PP
#Set up a customized look
.PP
@ but=quit:fq,bell=1
.PP
@ bigfont=lucidasanstypewriter-bold-14,grads=1
.PP
# thats it
.PD
.RE
.PP

An list of the extensive options are given below. For complete description of
each of these options the reader is referred to the technical documentation for Xppaut.

ATOL,
AUTOEVAL,
AUTOVAR,
AUTOXMAX,
AUTOXMIN,
AUTOYMAX,
AUTOYMIN,
AXES,
BACK,
BACKCOLOR,
BACKIMAGE,
BANDLO,
BANDUP,
BELL,
BIGFONT,
BOUND,
BUT,
COLORMAP,
DELAY,
DLL_FUN,
DLL_LIB,
DS,
DSMAX,
DSMIN,
DT,
DTMAX,
DTMIN,
DWCOLOR,
EPSL,
EPSS,
EPSU,
FOLD,
FORECOLOR,
GRADS,
HEIGHT,
JAC_EPS,
LOGFILE,
LT,
MAXSTOR,
METH,
MWCOLOR,
NCOL,
NEWT_ITER,
NEWT_TOL,
NJMP,
NMAX,
NMESH,
NORMMAX,
NORMMIN,
NPLOT,
NPR,
NTST,
OUT,
OUTPUT,
PARMAX,
PARMIN,
PHI,
POIMAP,
POIPLN,
POISGN,
POISTOP,
POIVAR,
PS_COLOR,
PS_FONT,
PS_FSIZE,
PS_LW,
QUIET,
RANGE,
RANGEHIGH,
RANGELOW,
RANGEOLDIC,
RANGEOVER,
RANGERESET,
RANGESTEP,
RUNNOW,
SEC,
SEED,
SMALLFONT,
SMC,
SPC,
STOCH,
T0,
THETA,
TOL,
TOR_PER,
TOTAL,
TRANS,
UEC,
UMC,
UPC,
VMAXPTS,
WIDTH,
XHI,
XLO,
XMAX,
XMIN,
XNC,
XP#,
YHI,
YLO,
YMAX,
YMIN,
YNC,
YP#,
ZMAX,
ZMIN,
ZP#,


.SH HELP
Note: On typical X Window installations the command \fIxlsfonts\fP lists available fonts. 
For example, the following command lists only the available fixed width fonts:  
.PP
.PD 0
.RS
xlsfonts | grep -i -e "typewriter" \\
.RS
-e "mono" -e "^[0-9]x[0-9]" \\
.PP
-e "fixed" -e "-c-" -e "-m-" | sort
.PD
.PP
.RE
.RE
Note: For a listing of standard hexadecimal colors see <http://en.wikipedia.org/wiki/Web_colors>.

.SH AUTHOR
This manual page was written by Isaac Jones <ijones@syntaxpolice.org>,
for the Debian GNU/Linux system on March  4, 2002. 
This man page was updated by D. P. Dougherty on Jan 4, 2011.
This man page was updated by B. Ermentrout on Feb 26, 2011.