README

Quick Install:

In Linux do the following:

1. Download the .tgz file into a temporary directory

2. Uncompress it

3. Type make

4. Test the binary xppaut 4b. copy xppaut where you want it or

5. Type make install (probably need to be root)

6. Note that xppaut will be installed in /usr/X11R6/bin - so you might want to move it.

7. make uninstall removes the program from your system

Please read this before asking me about compilation. If you have never compiled a big program before, then perhaps you should ask someone to help you, like your sysadmin who gets paid to answer these kinds of questions.

		Notes on the Makefile.  

Copy the distributed Makefile to Makefile.old. Then edit the Makefile according to the comments within it. You may also have to alter the Makefile in libI77

The main reason that compilation fails is that the required X libraries cannot be found. You should thus alter the Makefile to tell the compiler where to find the libraries.

Add

-I

to the CFLAGS line and add

-L

to the LFLAGS line. This should do the trick. Ask your sysop for the correct pathnames.

Notes on the RS6000: (thanks to Artie Sherman)

1. For those without gcc, they can run the standard IBM C-compiler, xlc, with a set of definitions that fake a Sun compiler. I just added the following stanza to the file /etc/xlc.cfg:

bsdcc: use = DEFLT crt = /lib/crt0.o mcrt = /lib/mcrt0.o gcrt = /lib/gcrt0.o libraries = -lbsd, -lc proflibs = -L/lib/profiled,-L/usr/lib/profiled options = -H512,-T512, -qlanglvl=extended, -qnoro,-D_BSD, -D_NON STD_TYPES, -D_NO_PROTO,-bnodelcsect, -U__STR__, -U__MATH__

(The options must be on a single, wrapped line)

and did: "ln /bin/cc /bin/xlc"

2. In the makefile, I used CC=bsdcc

*** RECENT SIMPLIFICATIONS FOR RS6000 USERS: *** Artie Sherman says the following seems to work!

CC= cc CFLAGS= -O -DAUTO -DCVODE_YES LIBS= -lX11 -lm $(CC) -DAUTO -o xppaut $(OBJECTS) $(AUTOOBJ) $(LDFLAGS)
libcvode. libf2cm.a $(LIBS)

Notes on SOLARIS

On some machines GCC is bad. Thus, you should use the SunPro compiler, cc. Change CC from gcc to cc in the main Makefile and in the makefiles in the cvodesrc/ and libI77/ directories.

    Notes on SUN

I have been told that it may be necessaty to add the line -lsocket to the compile line to make versions > 3.85 on the SUN under gcc.

Notes on the DEC alpha

What a pain in the ass this machine was. But, thanks to the DEC I am now ready for any other 64 bit machines. I compiled and ran the test program for XPPAUT on the DEC alpha using the DEC compiler cc. I have not succeeded in getting it to work under gcc. You should definitely use the included libf2cm.a for this. I tried a precompiled version of libf2c.a and it crashed. This is because f2c uses lots of "long" declarations which on the DEC are 64 bits while I treated them as 32 bits (the old standard). My version of the f2c stuff in the subdirectory libI77 works.

MORE NOTES ON DEC/OSF!! The cc compiler that comes with DEC has problems with my new parser since I use some (possibly illegal) pointer arithmetic which doesn't seem to bother GCC (or WATCOM for Win95!) Thus I have included the old version of the parser in the distribution. To use this, just change a few lines in the Makefile. In the section called SOURCES change parser.c
to parserslow.c

and in the section called OBJECTS change parser.o to parserslow.o

Then remake and hopefully it will work

Notes on the SGI with gcc

1. In the Makefile in cvodesrc/ and libI77/ delete the commands for ranlib as this is not necessary for the SGIs.

2. In libI77/endfile.c libI77/open.c remove the following from the two extern declarations: char *mkstemp() These are near the top of the file

3. Compile without dynamic linking

MACOSX

Yup, this works fine! I've compiled it on an IMac, a big G4 PPC, IBook, and Titanium.

1. Download the system developers kit (has gcc and the other compilation tools)
2. Download the XFree86 package - with all the X libraries
3. Optional - grab the free Orobos X server - much better than the one in XDarwin. It uses X Darwin however, so you still need it.
4. In the Makefile, uncomment the CFLAGS which have -DMACOSX
5. Delete the dynamic libs from the linkage

HP ITANIUM under redhat

Ok, this was sort of a bitch, but it seems to work.

Use -DNOERRNO -DWCTYPE in the Makefiles in libI77 and main source

---

Version history

VERSION 7.0 November 2012 So much new stuff......

lots in between :)

VERSION 5.85 July 2003

• added crosscorrelation
• fixed some bugs
• added clone which sort of works
• added postscript options like font size, font type, line width

VERSION 5.6 Sept 2002

• added POISSON(t) function
• nullclines in the animator

VERSION 5.54 July 2002

• fixed a global flag error finally
• Makefile is reorganized and easier read
• added "#include" construction to ODE files

VERSION 5.53 June 2002

• minor bug fixes
• fixes to Makefile
• more info on different architectures

VERSION 5.5 Mar 2002

• Integrate over 1800 equations
• new command line -setfile lets you load up the setfile (good mainly for batch)
• added "only" statement to ODE files. Lets you save only the listed variables during a batch integration.
• Fixed some more bugs

VERSION 5.4 Sept 2001

• added extensive help which is callable from XPP- File Help
• mostly internal changes on how menus and popups work
• only the main window pops up. Remaining windows can be pulled up at the top frame and close at your leisure.
• some support for user defined buttons in ODE file scripts.
• new command line option: xppaut -allwin brings up all the windows like before

VERSION 5.0 Jan 2001

• improved text rendering with sub/super scripts and mixed symbols
• added a widget for viewing the ODE file and also for creating "active" tutorials within the ODE file. This is really cool - see the example lecar.ode
• made it possible to extend the dimension of AUTO problems - see AUTLIM.H You can change it to bigger than 50
• added some capabilities for finding homoclinics in AUTO by using the projection boundary method described by Sandstede et al in HOMCONT
• added two new integrators: a Rosenbrock stiff integrator and a symplectic integrator for systems of the form x'' = F(x) x \in R^n
• various bugs fixed

VERSION 4.75 Sept 2000

Cleaned up some bugs and compilation warnings Can now save Kinescope frames to disk Changed the way that range integrate works under the silent mode Added "comets" to the animator Added range for Liapunov exponents Added GIF encoder and animated GIF creator for making animations

VERSION 4.55 Aug 2000 Added banded version for CVODE. Huge speedups can be gained! Added "array blocks" for PDEs Added dynamic linking to external definitions of right-hand sides (see tstdll.ode and funexample.c) Fixed some bugs in the function editor Added a few more initialization options "@ commands" Allow user to specify colors of Nullclines and Invariant manifolds Fixed a MAJOR bug in the computation of stable and unstable manifolds Changed the delay stability analyzer - it is better now. Fixed bugs in the implementation of AUTO's boundary value solver Added ability to print colorcoded trajectories in postscript Added higher order interpolation option to tables

VERSION 4.3 January 2000 a. Fixed some bugs, added the ability to have up to 400 parameters b. Added a Liapunov exponent calculation c. Added the ability to save the nullclines to a file d. Added colormap features. 6 different colormaps allowed now. e. Changed the delay handle to use a cubic interpolation. f. Added a new operator del_shft to combine the shift and the delay together. g. Extended the maximum length of expressions to 1000 characters h. Changed the command line from -noicon to -iconify. The default is to not iconify the windows. I also switched the meaning of XORFIX so that the default works on LINUX and WINDOWS. Sorry if this screws everyone up i. Added ability to make portrait postscript files j. Added two new integrators - Dormand-Prince 5 and 8(3). k. Fixed a bug in the STIFF/GEAR integrators that arose when the number of equations exceeded 300 l. Rewrote "Kinescope" so that it works much faster and doesnt crash the X server

VERSION 4.01 Minor fixes here and there. Added a little file lister etc so that if you just type XPP from the command line you can navigate through files before loading one up. I have (alas) eliminated the "(c)reate" option since it uses the old impenetrable syntax. If any users really miss it, I will put it back in reluctantly.

VERSION 4.00 Fixed a bug in the production of ppm files to make mpeg movies. Up to 600 equations can be integrated. Initial conditions ,parameter, etc windows have scrolling so that they are a more manageable size. A file browser has been added that lets you select files easily. *NEW SET FILES I have drastically altered the way to save simulations so that there is much more saves and it is all commented so that a human can read it. The new SET file command is compatible with the old format so that it can read the old format set files. However, the new set files are not compatible with the old.

VERSION 3.99 (updated) I have added the ability to save into a file just what is plotted on the screen for XMGR compatibility, e.g.

VERSION 3.99

Added "reverse integration " command added PHI=#,THETA=# to @ commands

VERSION 3.98 Oct 1998

Bug fixes here and there and added the ability to continue periodic points of maps.

VERSION 3.95 Aug 1998 Some bug fixes. Added the ability to set delayed initial data in the ODE file.

VERSION 3.91 June 1998

1. Added differential-algebraic capabilities to XPP and WinPP

VERSION 3.90 June 3 1998

1. Minor fixes that make it more compatible with some compilers.
2. Can now integrate up to 400 ODEs (was 300 before)
3. Fixed some problems with global flags
4. Added "derived parameters" which allow you to define parameters in terms of other parameters and which are updated only when the parameters are changed.

VERSION 3.85 Feb 2 1998

1. Include and update the old version of the parser since some compilers complain about the funky pointer arithmetic that I used.
   VERSION 3.8 Dec 23 1997
2. Fixed some stuff
3. Added AUTO stuff for the @ commands
4. Added some cool networky stuff for doing discrete convolutions and operations with sparsely connected neural networks.
5. Doubled the speed of the calculation engine by rewriting the parser.
6. Ported to Windows 95 see xpp4w95.zip

VERSION 3.6 Oct 24 1997

1. Added new command line option to prevent dead iconified windows in fvwm and some other window managers. Call xppaut -noicon
2. Added interspike interval calculation to Poincare maps

VERSION 3.5 Sept 1 1997

1. Frozen nullclines
2. Fixed more bugs in table stuff and array printing
3. Fixed up the shift operator to work on parameters
4. Changed data format in browser to give more decimal places

VERSION 3.0 Mar 3 1997

1. Fixed more bugs
2. Added new version for initial conditions with arrays 3 !!! ANIMATION PACKAGE FOR MAKING CARTOONS WITH SIMULATIONS !!!

Make this from scratch

VERSION 2.71 Nov 18 1996

1. Changed flow field to integrate both forward and backward in time
2. Added m(I)ce option to initial data so that you can click on many initial conditions in a row
3. Added fancy space-time plot to go along with array capabilities
4. Fixed miscellaneous bugs :)

SOON -- version with LOCBIF another bifurcation package will be available SUMMER 1997 Windows 95 version maybe

VERSION 2.6 Oct 3 1996

NOTE: !! Please make this version from scratch ( rm *.o ) !!

1. Main new feature is the addition of the industrial strength stiff solver CVODE, a C language version of LSODE. This is a big piece of code and I only implement a small portion of it. It is optional for now but if you don't want it you must change the Makefile. See below.
2. Added AUTOFREEZE option. Every curve that is integrate is automatically saved. This way you dont have to freeze after every integration. Up to 26 curves can be frozen.
3. Fixed array options for markov processes
4. Fixed arrow head bug
5. Added some new options for @ directives

VERSION 2.52 July 29 1996 New Features:

1. Parameter sliders -- move sliders to change parameters
2. Edit the initial conditions, parameter, BC,etc windows directly
3. Tips on all the menus
4. "Array" handling. The following is valid: x[1..10]'= -x[j]
5. Silent mode -- supports computation without X windows and produces a space delimited ascii file for output
6. Transposition of data arrays.
7. Click and move to get x-y values in any window

VERSION 2.00 of XPP/XPPAUT New features:

1. Added two new integrators:
   i) a quality step Runge-Kutta algorithm that is good for nonstiff problems ii) An alternate stiff integrator based on a Rosenbrock method
2. AUTO interface supports discrete problems

VERSION 1.80 of XPP/XPPAUT New Features:

1. -convert command line argument converts old-style to new style
2. Symbol font and Times fonts in 5 sizes. All Text is editable
3. Add arrows and pointers to plots
4. Import bifurcation diagrams into main window
5. Include information about the graphics, numerics, storage, and X fonts in the ODE files
6. Make 3D movies and movies of trajectories as a parameter varies
7. Stability for delay equations

Detailed INSTALLATION is found by reading install.pdf A user manual is included: xpp_doc.pdf,ps A quick summary of things: xpp_sum.pdf,ps Most of what you want can be found in the documentation. There is also an XPPBOOK coming out soon which gives lots of tricks and examples.

-- Bard Ermentrout [email protected]

PS -- Keep in mind this is sort of a hobby of mine and is not supported by any external funds. I use the program in my research and as such it is skewed in that direction. If anyone out there wants write a slick interface, by all means do it! If you want other features just ask me and if I think that they don't really suck I may include them.

************** NOTE ************************************ I have tried to provide some pointers for creating the binary on most UNIX machines. I have direct access to LINUX, SUN OS, SOLARIS, and HP. I have compiled it on all of these successfully. Please read the notes below. If you are still unable to compile it, then let me know. In the past, it has also been compiled successfully on SGI, DEC Alphas, MAC OSX, Mach Unix for Macintosh, Cygwin for Windows NT Note in the latter two, you will have to define drand48(), srand48() as this is not in their libraries

---

**************** NOTE ***************************************** If you install the new version of XPP over existing versions it is best to start from a clean set of files. Type make clean first.

---

NOTE: New versions have a simplified compilation. Just untar it and type make in the main xpp directory. If errors occur, then you will still have to fix the make files.

	Installation of XPP and XPPAUT

Create a directory and change to it. (I suggest the name xpp) FTP the program (xpp*.tar.gz) to the directory in which you want to install it. I have included as part of this distribution a modified version of the f2c libraries but they do not seem to work on every machine. If you find that they do not work then you will need to ftp f2clib.tar.Z also in the same directory. I have also included sources for the CVODE library. Note that my reduced f2c seems to work on everything these days.

1. The program is a compressed tar file and must be uncompressed with the command:

   gunzip xppaut*.tar.gz

2. Then you should untar the file with the command;

   tar vxf xppaut*.tar

3. Edit the Makefile in the root directory. You mak have to also edit the Makefile in the cvodesrc/ and libI77/ directories.

4. In the main directory, type make

5. Things should go smoothly from here. If there are errors, then, you will probably have to change the Makefiles. There are some hints below. Once you have the binary - called xppaut - test it by going into the directory odes/ and typing

         ../xppaut pend.ode
   

   The file should load up and you can begin to explore it. If it does not then it is probably because the X Server is not responding. Make sure your X environment is set up correctly. Once it has fired up, click on Window and select Zoom In. Then click the mouse inside the main window and holding down the button, drag it on the screen. You should see a rectangle that stretches as you move the mouse. If you do not see this then you should run the program with the -xorfix command line:

../xppaut -xorfix lecar.ode

Repeat the above and you should see the box.

I generally rename xppaut to xpp and if I need the -xorfix flag, I write a small script file called xpp that has one line:

xppaut -xorfix $1 $2

This means I dont have to add -xorfix every time.

Once you are satisfied that it works, move it to a directory in your path. (/usr/local/bin is standard).

There is a document xpp_doc.ps that gives the full documentation for the program and a WWW tutorial.

6. Using the online help: You have to tell your system what your browser is called and where the help files are. This depends on the shell and OS you use. On my Linux box running bash, I type:

   export BROWSER=netscape export XPPHELP=/home/bard/xppnew/help

You should set BROWSER to your web-browser and XPPHELP to the /help subdirectory of your XPP root directory.