README FILE for how to use AUTO to get the horseshoe maps that 
I have produced.

I)

A) First go to:

auto/2000/cmds
Type "source auto.env.csh"

B) For first time AUTO users YOU must do the following: 
go to "auto/2000/src"
then type "configure"
then type "make clean"
then type "make all"

YOU ONLY NEED TO DO STEP B) once

1)
From Matlab get start.dat
(start.dat has your initial solution to FVDP with certain parameters)
Type "mv start.dat root.dat"

(root.dat is your rootname for the problem, you can say for example
fvdpmap.dat)

2)
Then go to root.c file; and edit the parameters;

3)

Go to c.root and edit parameters;


We need to change IRS depending on scenarios:

After converting data for the 1st run; we make IRS = 1;
Later on we can change IRS = 12 (DEPEnding on which pt one is studying)

Then change second line; second element (ICP(I),I=1 NICP) based on if 
changing epsilon, a, omega, y_0 or phi_0
(epsilon = 0, a = 1, omega = 2, y_0 = 3, phi_0 =4)

Change RLO and RL1 depending on situation (for phi example, it needs to go
from 0 to 2*Pi)

For Y we were using -10..10

REST ARE FINE TUNED FOR LATER PURPOSES

4)
Then from Auto:
us('root')

exit Auto;

This creates s.dat

5)

in the file newautoscript; change  s='dat' in the file

6)

In the future, change IRS in the constant files
and change s = root.new' (newautoscript).



7)

Then to run type the following:

"time auto < newautoscript >! outfile &"


8)

To extract the relevant data (y_0, phi_0, y_final and phi_final)
type

"perl stuffextract.pl s.root.new >! out$filename"

9)

Plot in Matlab by opening matlab and then typing:

"run printmap.m"

NOTE: You may need to change the line in printmap.m which is 

A=load('outfile_start3.txt');

to 
A = load('out$filename');