0.9.1:
* Main AUTO:
- Fix makefile dependency problem.
- Create *F variants for FNBL, BCBL, and ICBL to allow toolboxes to follow
folds in general BVPs by supplying their ODEs, boundary, and integral
conditions.
- Make HomCont use those new interfaces in toolboxbv.f90 to be able to follow
LPs for homoclinic orbits in n+1 parameters.
* Python:
- Fix problem about AUTO complaining about a missing solution file when using
old-style constant files.
- Write out complete fort.2 file in case of problems to be able to reproduce
a run quickly.
0.9.0:
* Main AUTO:
- Allow to use the AUTO constant "U" for constant-in-time solutions for BVPs.
- Do not try to compute first Lyapunov coefficient if a Bogdanov-Takens
bifurcation function is already detected, which gave erroneous results.
(Bug reported by Christoph Kirst <ckirst@nld.ds.mpg.de>)
- Turn off detection of PD/TR/Rn bifurcations for 2 dimensional systems.
They should not occur but sometimes the Floquet multipliers are
inaccurate.
- Fix issue with directly reading python/test_data/c.ab from Fortran,
ignoring spaces directly after { or [.
- Reintroduce the AUTO_COMMAND_PREFIX environment variable from AUTO2000
for running with MPI.
- Reading AUTO constants from standard input instead of fort.2:
- Avoid BACKSPACE for reading the old-style ICP list read NICP manually.
- Completely eliminate BACKSPACE for fort.2 reads by manually reading
the first non-blank characters on each line and checking for a number:
in which case it is an old-style constants file.
- If fort.2 does not exist, then read from standard input.
- A special value for the AUTO constant 's', namely s='/' is used by the
Python interface to also pass solution files using standard input,
following the line containing s='/'.
- BP continuation (BPCONT) improvements:
- Use explicit derivatives where possible for algebraic equations,
limit cycles, and BVPs.
- Merge common code for boundary conditions for BVPs.
- Cleanups, so the indices are consistent between fixed/variable period
continuations.
- Match coordinates in start/restart systems for BPCONT for LCs/BVPs to
simplify code.
- Shuffle internal parameters so that unused internal parameters
can be dropped after they are no longer necessary.
- Pass UPOLD from solvebv to FUNI via extra coordinates in UOLD past NDIM.
This eliminates an implementation problem in BPCONT where it is needed to
reevaluate F(UOLD) but it did so for the new parameter values.
- Avoid unnecessary repeat calculations of UPOLD.
- Use UPOLD directly for BP continuation for BVPs.
- Add more comments to BP cont functions and make RLOLD accessible to
toolbox functions.
- Automatically add -m32 to g++ for 64bit Macs with 32bit Coin3D, avoiding
the need to specify this manually.
- Make extending solutions (in STPNT) possible from loci of bifurcations,
including certain old solution files.
- Force recalculation of the direction vector if dimensions have changed.
- Avoid memory allocations where possible in extended systems with expanded
Jacobian matrices.
- Copy UOLD in STUPV to avoid problems.
- Check for infinite Floquet multipliers to avoid floating-point exceptions.
- Centralize ITPST*10+ITP calculations out of toolboxes.
- Replace ITP in toolbox test functions by ASCII ATYPE for clarity.
- Extract type/number from restarts like IRS='LPD1' manually to deal with
three-letter types.
- Internally denote special points without stability changes by for example
'HB0' witha trailing '0'. Allows for special handling in LCSP**,
where these are used in the first detection but ignored after.
* PyPLAUT:
- Fixes and workarounds to get PyPLAUT to work with Matplotlib 1.1:
- To get 2D limits for Matplotlib 1.1, use get_xlim/get_ylim explicitly
from the 2D Axes class.
- Fix 3D graphics problem with Matplotlib 1.1.
- Add comments to default autorc file.
- Reorder autorc commands to move often-used settings at the top.
- Do not plot unplottable 3D curves (when at least one coordinate
is invalid for a particular branch).
- Deal with d0/d1/... autorc options correctly if they use True/False
instead of numbers.
- Add a strategic garbage collect call to avoid memory issues.
- Fix memory leak when using the labelnames setting.
- Use azimuth/elevation settings if one of them is commented out.
* PLAUT04:
- Change order of settings in plaut04.rc in order of importance.
- Fix plotting s files without matching b files.
- Fix crash when plotting bifurcation curves if no solution is present.
- Check for PT 9999 for wraparound in bifurcation diagrams.
- Fix "@r3b" or plaut04 -r3b without other arguments.
* Python:
- Parse blank lines with spaces in constants files correctly (reported
by Jorge Galan-Vioque).
- Make working with branches a little easier:
- Negative indices now work on a branch ([-1] for the last point).
- save(list of branches, 'xxx') now works.
- 'TY' for 'TY name' now works on points in branches.
- Allow s.PAR to be used directly as an argument for the PAR= AUTO constant.
(Based on a suggestion by Jan-Hendrik Schleimer
<jan-hendrik.schleimer@bccn-berlin.de>.)
- Avoid read() on already read & parsed solutions.
- Parse more Fortran-style floating point constants, in the form of 2-3
(which means 2e-3).
- Fixes for Python 3.
- The run command now uses input redirection instead of fort.2/fort.3
to pass constants and solutions to AUTO.
* Shell commands:
- @H, @R, @h, and @r now use input redirection instead of fort.2 to
supply AUTO with constants.
The @ commands automatically add s='xxx' to avoid copying to fort.3.
Together with sv='xxx' this allows running multiple AUTO instances
within the same folder.
* Demos:
- Updated enz, log, hen, lrz, dd2, pp2, ffn, and exp demos.
* Manual:
- Document role of PAR(12).
- Specify location of Mac OS X development tools.
- Updated demos.
