CHANGELOG

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.
0.8.0:
* Main AUTO:
  - Support for codimension-two bifurcations:
    - Add support for detecting Generalized-Hopf/Bautin (GH), Bogdanov-Takens
      (BT), Zero-Hopf (ZH), and Cusp (CP) bifurcations in algebraic systems
      along Hopf (HB) and fold (LP) curves.
    - Add support for detection of 1:1 (R1), 1:2 (R2), 1:3 (R3), and 1:4 (R4)
      resonances for limit cycles and maps along fold (LP), period-doubling (PD)
      and torus (TR) curves.
    - Add support for detection of fold-flip (LPD), fold-torus (LTR), and
      flip-torus (PTR), bifurcations for maps along LP, PD, and TR curves.
  - Improved support for maps:
    - Display PD or TR instead of HB for period-doubling and Neimark-Sacker
      bifurcations.
    - Implement branch switching at period-doubling bifurcations for maps.
      The discrete period is taken from PAR(11). Maps are then iterated n times
      and the derivatives are determined from the basic derivatives using the
      chain rule.
    - PD continuation for maps now uses a smaller system (2n+1 dim), similar to
      folds.
  - Improved support for waves (IPS=11,12):
    - Fix continuation of Hopf bifurcations.
    - Period doublings with ISW=-1 are now possible..
    - Permit continuation of PD/LP/TR/BP, where applicable.
    - Don't change IPS anymore for waves but check explicitly for 11 or 12
      instead.
  - AUTO constants:
    - Use JAC=-1 if you only specify the function derivatives (DFDU) without
      parameter derivatives (DFDP) in equation files.
    - Let IID=0 produce no diagnostic output.
    - Introduce new AUTO constant IIS to optionally add no direction information
      to solution files to save space:
      IIS=0 no directions in s files.
      IIS=1 only directions for LP(BVP),BP,PD,TR
      IIS=2 for all points except RG
      IIS=3 everywhere
    - New: LAB=n starts with label n
    - New: IBR=n starts with branch n
    - New: TY='HB4' redefines type of restart label to be a Hopf bifurcation
      with period in PAR(4).    
    - New: UZSTOP, like UZR but stops, to avoid minus signs in the UZR lists.
    - Change default values of NMX and NPR to 0.
  - Changed the Hopf/Neimark-Sacker bifurcation following algorithm to use a
    reduced standard augmented system. (2n+2 instead of 3n+2, see Kuznetsov,
    3rd ed., (10.80)).
    This makes it possible to detect BT bifurcations on Hopf curves;
    the algorithm is forced to stop there.
    The Hopf phase condition was replaced by a symmetric expression that
    approximates the previously used phase condition.
  - Added support for computing the first Lyapunov coefficient for Hopf
    bifurcations to detect GH bifs and print supercritical/subcritical
    information in diagnostics file.
  - Avoid calculating derivatives numerically when possible for HB, LP, PD, TR,
    and HomCont continuations to improve accuracy and performance.
    Note (esp. for HomCont) that equation files now need parameter derivatives
    with JAC=1; use JAC=-1 if only variable derivatives are present.
    Existing demos were adjusted.
  - Reorganized test function zero detection:
    - Merged individual bifurcation checks into a loop.
    - FNCS is no longer a dummy procedure; the variable ITEST determines the
      test function that is used. This allows for the removal of many unused
      arguments. Also eliminate IAP(26) for IUZR.
    - Do not try to find a special point after non-convergence.
      Adjust ITP while looking for a special point where appropriate.
    - Correct mid-value given to Mueller's method in special point locators:
      RDS can be changed by STEPBV/STEPAE so needs to be added to the right-hand
      value S1 after instead of before calling it.
    - Modified the special point locators to be more accurate:
      * if Newton iterations do not converge, revert to the previous converged
        state and report "possible special point"
      * try all special points: do not report one or disable other types
        as soon as one is found
      * recompute test functions if the locator has changed UPS through
        STEPAE/STEPBV, using STEPPED and ISTEPPED variables.
      * some demos now report new labels (pp3, sib, tfc, tor)
    - Change Mueller's method to avoid loss of significance, by multiplying
      -c+r by (-c-r)/(-c-r) and evaluating the result manually.
    - Completely recover the previous state if a special point is not found.
    - Added some logic to deal with multiple test functions becoming zero at
      a special point. Make explicit that "first come, first served" except for
      a few exceptions.
  - Do not transpose DFDU in inner loop because it destroys the assumed zeros
    that can be skipped in the user's FUNC.
  - Detect overflows for PAR(*) with respect to NPAR after calling PVLS.
    PAR(*) always has at least NPARX elements.
  - Only print and use the basic Floquet multipliers for BP/LP/PD/TR
    continuations of limit cycles. For this, NULLVC needs to return the pivot
    rows, so a set of independent rows can be found for parts of the monodromy
    matrix factors.
  - Reorganized the linear solver so the algorithm works independently
    of the parallellization so results are identical independent of the number
    of processors used.
  - Fix GETP for the step size, that is, GETP('STP',0,U).
  - Sort purely imaginary eigenvalues for conservative systems returned
    by GETP('EIG',...) by imaginary part.
  - Fix stability information for last point on curve.
  - Improve torus bifurcation initialiation by using the correct sin/cos
    functions.
  - Move the torus angle back to PAR(12) so it can be explicitly specified in
    ICP and monitored that way.
  - Use consistent sign for branch direction also when switching branches,
    not just for normal branches.
  - If the parameter direction is close to zero when starting a new
    branch, look at the other parameters and coordinates instead to
    find a positive direction. This should make branch directions
    unique in most cases across architectures.
  - Physically swap columns and rows in Gauss elimination routines.
  - Do not write a space before the header line on standard output.
  - Update lapack routines to v 3.2.2.
    Change DGESVJ to not divide by zero for zero columns.
  - Use a derived type (AUTOPARAMETERS) AP instead of IAP and RAP.
  - To makes the reduction algorithm in the linear solver more elegant,
    replaced part of the role of S1 by A1.
  - Reorganization of source code with toolboxes:
    - Renamed autlib1.f to main.f90, autlib2.f to solvebv.f90, 
      autlib4.f to floquet.f90, and autlib5.f to homcont.f90.
    - Split general bvp interface routines from autlib3.f & bvp.f90 into
      toolboxbv.f90.
    - Split off equilibrium (equilibrium.f90), map (maps.f90), periodic
      solution (periodic.f90), optimization (optimization.f90), and
      parabolic PDE routines (parabolic.f90) from autlib3.f.
    - Do allocation of PAR, THU, THL, IUZ, and VUZ arrays later to reduce the
      number of parameters passed.
    - Moved function dispatchers to toolboxes.
    - Moved "redefinition of constants" to toolboxes.
    - Introduced AP%NTEST, which can be set in the toolboxes, to replace
      AP%NUZR+xx.
    - Renamed UZR to TEST and IUZR to ITEST to clarify that this array is used
      for all test functions and not just user-defined ones.
    - Renamed PVLI to FNCI to provide a generic test function interface.
      Called with ITEST=0 it calls PVLS.
    - Adjusted MPI to work with changed toolbox interface.
      Transferred AP structure directly with MPI.
  - MPI improvements:
    - Only send parts of a1, a2, s1, bb, cc, and faa from workers to master that
      are needed. This speeds up the MPI parallel code significantly.
      Let MPI send and receive matrix parts in a recursive fashion on demand.
      This makes the nested dissection work more in parallel with less
      communication.
      Example: reduction for NTST=8, 4 CPUs.
      CPU  0   1   2   3
      1.  12  34  56  78, CPU1 sends 4 to CPU0, CPU3 sends 8 to CPU2.
      2.  24      68    , CPU2 sends 8 to CPU0
      3.  48
      This sequence is similar to the sequence documented for AUTO94P but
      reversed in this way: AUTO94P used:
      CPU  0   1   2   3
      1.  12  34  56  78, CPU0 sends 2 to CPU1, CPU2 sends 6 to CPU3.
      2.      24      68, CPU1 sends 4 to CPU3
      3.              48
      The new way has the advantage that all non-parallel processing is
      done in the master, CPU0.
    - Make MPI work with HomCont. A few more MPI adjustments to print better
      error messages.
    - Replace STOP by CALL AUTOSTOP, to give MPI a chance to cleanly finish.
* PyPLAUT:
  - Introduced new boolean "letter_symbols" option to use letters for symbols
    (like in plot()) or not (like in @pp).
  - Add "labelnames" plotter option for autorc, so we can do
    labelnames={"U(1)":"$x",PAR(1):"$p"}.
  - Improve handing of margins and font sizes in matplotlib plotter.
  - Allow symbol sizes using "circle5" etc.
  - Changed the bifurcation/solution selector to radiobutton style.
  - Uses Pmw's RadioSelect and MainMenuBar widgets.
* PLAUT04:
  - Add an option to plot by branch ID instead of sequential branch.
    Coloring method -4 now correspond to "CURV" and -7 to "BRAN".
  - New plaut04 option: R3B=Yes to switch on R3B mode. Used by the r3b demo so
    that @pl works.
  - Made r3bplaut04 a run-time option instead of a separate binary,
    ie. "plaut04 -r3b".
  - Removed some arbitrary limits on the number of parameters and labels in
    files that are plotted.
  - When testing PLAUT04, change directories to allow the current directory
    to be deleted on Windows. Get plaut04.rc from the specified directory
    in PLAUT04.
* Python:
  - Drop Python 2.2 compatibility. Python 2.3 is the new minimum.
  - Let writeRaw/writeRawFilename use the coordarray and indepvararray
    structures directly, to be much faster.
  - Fix dlb/klb/deleteLabel with function argument across multiple branches.
  - Added error messages if the length of the produced fort.7 file is 0 or
    you try to run AUTO with an empty solution list or bifurcation diagram.
  - Add more diagnostics for run() with wrong IRS or missing equation file
    argument. Fix online help in a few places.
  - The global runner is now used to always keep the current constants and
    solution data, so that run() always repeats the latest run, run(DS='-')
    reverts, etc.
    load() with a non-keyword argument now always resets the current constants.
    But handle "unames", "parnames", "e", "homcont", "auto_dir"
    as special keys for parseC objects: they are not overwritten when a new
    constants file is read without such keys.
  - Make the global runner local to the current auto environment.
    Mainly this is to let auto('foo.auto') use a clean state.
  - Reset current solution if IRS=0.
  - Remove unused kw argument from parseS' read() and readFilename() methods.
  - Simplified log and err redirection system by having only one interface:
    log and err need to be objects with write() and flush() methods; if None
    (the default), stdout and stderr are used.
    Be able to redirect ls and cat so the tests can see everything on
    sys.stdout.err & log now affect sys.stdout and sys.stderr so we can capture
    print statements from AUTO scripts as well.
  - Use an open file so we only read headers using sl('name'). When writing
    the file, everything is read into memory to avoid overwriting.
  - Reorganize parseS to keep track of when the s-file if fully read so
    it can be closed. Always read the file completely on Windows.
  - Explicitly close auto script files after reading them.
  - Branches in bifurcation diagrams can now deal with solutions using the ()
    notation, and will write solutions and diagnostics.
    Functional notation for deleting labels is generalized to apply to any
    () notation, to select labels for solution lists of bifurcation diagrams.
  - Allow loadbd([list]).
  - Further straightening out of AUTOSolution constructor, also to facilitate
    adding parameters through PAR.
    s=load([1,2,3]); s=load(s,PAR={1:2}) now works.
  - Created an update() method for parseS.AUTOSolution objects.
    Use a few sets and disallow strange "constants" key for parseC.
    parseS.AUTOSolution's c attribute can now be None to indicate that no
    constants are attached.
  - The AUTOSolution constructor no longer allows AUTO constants as keywords.
    These are now handled by load().
  - Fix headers of merged branches to get the header of the forward branch.
  - Don't try to import Numeric on 64-bit systems.
* Shell commands:
  - Eliminated compile-time limits on the maximum number of labels and
    branches in the utilities using a linked list and dynamic allocation.
  - Adjust @zr, @db, @tr, PLAUT04, and @fc to solution files without directions
    generated with IIS<3.
  - In @ll/listlabels/@lb, use as much space for the label number as in normal
    AUTO output.
* Demos:
  - Added test infrastructure in test directory. See README file there.
  - Added LP1/BP1 stopping conditions to BPCONT demos since those branches
    double back in machine-dependent ways.
  - Use UZSTOP where appropriate.
  - abcb: Switch off unreliable BP detection during BP cont.
  - dd2: Improve to perform period-doublings.
  - fhh: Add stopping condition in because inclination flips with complex
    eigenvalues do not make sense. Make IF changes to the correct constant file.
  - fhh: Adjusted tolerances a bit to avoid an MX and further adjustments.
  - fnb: Increase NTST for robustness.
  - fnb: Fix starting label for last run to be the third from below.
  - fnb: Further adjustments to make this demo more robust.
  - log and hen: Added two demos for maps: Logistic and Hénon.
  - phs and tor: make more robust. Do not copy c.xxx.1 to c.xxx if c.xxx
    already exists with copydemo().
  - pla: Update Plant demo to be less sensitive, mostly as suggested by Sebius.
  - python/n-body: Added plaut04.rc file to; solve issues with logged plaut04
    spawning.
  - r3b: Use a numerical tolerance to determine purely imaginary eigenvalues.
  - r3b: Setting ITNW=7 for V1 family gives consistent results.
  - r3b: Made more robust.
  - r3b: Reorganized initial part using TY= constant.
  - snh: Fix typo in equation in the manual for SN-Hopf demo.
  - snh: Truncate nu2 to [-2,2] to avoid floating point exceptions with acos.
  - snh: Adjusted DSMIN to work with new test function algorithms.
  - snh: Put a stopping condition on delta to avoid MX-ing sensitively.
  - tfc: Avoid MX by increasing NTST.
  - tor: set maximum period to avoid MX in last run.
* Manual:
  - Use hyperref in the manual; change to use pdflatex. Update reference for
    Desroches paper.
  - Add acroread to list of viewers.
0.7.3:
* Main AUTO:
  - Fix typo in auto.env.sh
  - Fix compilation with ifort.
* Python:
  - Fix a problem with load(U=...) to change U(*) values with respect to STPNT.
0.7.2:
* Main AUTO:
  - Fix torus bifurcation initialization; a long standing bug was fixed: torus
    continuations did not work from TR labels where the relevant Floquet
    multipliers have negative real part.
  - Fix some intents that are reported as errors by gfortran 4.5 and ifort. 
  - HomCont: initialize ISTART to 5 in DATA block.
  - For plotter: in fort.7 use stability of previous point for bifurcation
    points.
* Python:
  - Fix a problem with numpy fromstring and the last element in Fortran
    exponential notation.
  - Fix logical "or" which should be "and" in parseS efficiency header length
    check.
  - Fix plot3() with bifurcation diagram argument.
  - Fix UZR handling with old-style constant files.
  - Fix message for save().
  - Only complain but do not crash if files are missing for append().
  - Fix error_symbol handling for plotter.
* Demos:
  p2c: Remove superfluous and wrong ISP=-2.
  snh: use PAR(4) to store the intended integer codimension instead of using
       mu < 0 which fails when reaching the end of the codim 0 tangencies at
       the Hopf bifurcations.
* Shell commands:
  - Fix bifurcation file write bug in @kuz, @klp, etc.
* PLAUT04:
  - Change SoQt init statement to avoid a crash in Fedora 12.
  - Change HardCopy include path for PLAUT04 for Mac OS X compatibility.
0.7.1:
* Python:
  - Fix solution plotting for plot()/@pp without arguments.
    (reported by Thomas Wagenknecht)
0.7:
* Main AUTO:
  - Allow three parameter continuations for torus bifurcations, fixing
    the angle (Sebius Doedel). See the demo 'tor' for an example.
  - IRS now support strings like IRS='UZ1' in constant files and Python.
  - The new "STOP" constant as an alternative to "SP" allows to clearly
    specify stopping conditions such as STOP=['HB2',UZ2'] which stops at the
    second Hopf or second user defined point, whichever comes first.
    This setting does not switch special points off or on, unlike SP.
  - HomCont now has a new default setting "ISTART=5" which performs a phase
    shift only if the restart solution is not already a homoclinic orbit
    that was continued by HomCont.
  - A problem where extremely flat starts of curves, which sometimes occur
    with heteroclinic and homoclinic orbits, caused the mesh to be wrongly
    calculated was fixed (problem reported by Thomas Wagenknecht).
  - Automatic rotation detection (angular variables) is now switched off
    for heteroclinic orbits in HomCont. This fixes another problem reported
    by Thomas Wagenknecht.
  - Fix crashes with the phase shift algorithm and mesh problems for
    homoclinic branch switching with HomCont, which occurred in a problem
    by Daniele Linaro.
  - Fix crash for BPCONT (algebraic problems) with ISW=2 (reported by
    David Barton).
  - Fix problems with the Intel Fortran compiler ifort (reported by
    Patrick McNeil).
  - Rotations no longer use PAR(19) internally, so this parameter is free to
    use.
  - The following types of continuations now use parameters above NPAR, instead
    of PAR(12), PAR(13), PAR(14), etc. as internal parameters:
    + fold continuations for periodic orbits and general BVPs.
    + branch point continuations for periodic orbits and general BVPs.
    + torus continuations for periodic orbits.
    + period-doubling continuations for periodic orbits.
    Only PAR(11) is reserved for periodic orbits; for general BVPs (IPS=4)
    all parameter indices can be freely used in the equations file.
    For homoclinic branch switching, the internal parameters for the Lin
    vector and the point where the gap is located were moved beyond NPAR
    as well.
  - Solution file headers now have 4 extra fields on the same line:
    NPARI, NDM, IPS, IPRIV which mean: number of internal parameters,
    user dimension, problem type, and a per-problem private field, respectively.
  - Bifurcation diagram files now only print user-specified constants that are
    visually different from the ones used internally, under the heading
    "User-specified constants, where different from above:".
  - Made sure PVLS is always called first, before FUNC, to be able to initialize
    state in user equation files.
  - If pivots are 0 or smaller in absolute value than 1d-308*||A||_max, then
    AUTO will not converge instead of continuing with NaNs
  - Portability problems with some versions of GFortran were fixed, for instance
    avoiding the use of BACKSPACE at EOF for reading constant files.
* PyPLAUT:
  - The plotter PyPLAUT can now plot in three dimensions, if used with a
    suitable version of matplotlib (not 0.98.x). Related new settings for
    autorc and the Python plot() command are:
      minz, maxz, zlabel, zlabel_fontsize, zticks, azimuth, elevation,
      bifurcation_z, solution_z
    @pp, like @p, now accepts some basic 3D commands too (B3D and 3D).
  - A new plot() argument, hide=True, hides the graphics, to be used for
    just printing to a file with matplotlib.
  - The savefig() method of an object returned by plot() saves the file.
  - The new settings:
      coloring_method = "branch"
    or
      coloring_method = "type"
    let the color of the curve depend on the branch number (BR)
    or type number (TY)
  - label="all" (or label = ["all"]) now plots all labels.
  - The plotter now primarily plots by label name, which is useful for appended
    branches of bifurcation diagrams that change the column header name for
    numbered columns.
    Here, for example, "U(1)" denotes just point continuations;
    "MAX U(1)" applies to both "U(1)" and "MAX U(1)" (points and BVPs)
  - @pp now accepts both ',' and ' ' to separate input lists, similar to PLAUT.
* PLAUT04:
  - Print support is added to the File menu if Coin3D is used.
  - With new versions of SoQt, libsimage is no longer necessary. To accomplish
    this, the images of the Sun, the Earth and the stars were converted to JPEG
    format.
  - New settings:
    Object Animation Speed, Sat Animation Speed, Orbit Animation Speed,
    which set default values for the speeds.
  - A new "Draw Coord" menu option, "At Origin" causes the coordinate axes
    to be drawn at the system origin. This corresponds to Coordinate Type = 4
    in (r3b)plaut04.rc.
  - Draw reference planes and spheres, if specified in (r3b)plaut04.rc, via
    the new settings:
    Draw Reference Plane, Draw Reference Sphere, Disk Rotation, Disk Position,
    Disk Radius, Disk Height, Disk Transparency, Disk From File, 
    Sphere Position, Sphere Radius, Sphere Transparency, Sphere From File
* Python:
  - The run command no longer redirects output by default: AUTO writes directly
    to the terminal.
  - When AUTO crashes, stop immediately with an AUTO Runtime Error.
  - Skip entries with a 0 label number in @ls and "print" for bifurcation
    diagrams, and if there are no entries left under a header, don't print the
    header.
  - Default command aliases are now set in AUTOCommands.py instead of .autorc.
  - Before every run(), the Python CLUI explicitly performs memory garbage
    collection, to avoid memory problems.
  - Initially, do not read solution files into memory, but just the headers,
    except for fort.8, because that file is often overwritten.
  - Solution objects now contains keys for corresponding entries in the
    bifurcation diagram file such as "L2-NORM".
  - Add s.b to a solution object, where b is the corresponding point on its
    branch.
  - Branch objects now contain "BR", "TY", and "TY number" keys which you
    can change similar to those of solutions.
  - The dlb, dsp, klb, and ksp functions can now take functions as arguments.
    These functions return a boolean value based on a solution causing it to
    be deleted or kept. A function with two arguments compare the two solutions
    for every combination and if satisfied the second one is deleted or kept.
    This allows for the deletion of "close" solutions.
  - The dlb, dsp, klb, and ksp functions can now be given two file suffix
    arguments, such as dlb("old", "new", f).
  - Improve error reporting: complain about missing files in a clear way,
    not exposing internals.
  - Allow the U keyword for load() to update a solution just like PAR does.
  - Changed writeRaw and toArray to output in table form.
  - Allow mv() and cp() to be used; without () it'll use the shell command.
  - Fixed parsing of headerless bifurcation diagram files.
    The coordinates are then called COLUMN(1), COLUMN(2), etc.
  - Extend @cp/@mv/copy()/move() to accept up to 4 arguments and directories.
  - The Python code no longer tries to be compatible with Python 1.5.2; at
    least Python 2.2 is assumed.
  - The Python code is mostly compatible with Python 3.x.
* Configure checks:
  - Improved Coin3D detection for Mac OS X.
  - Fixed Coin detection to include cppflags from coin-config.
  - Added check for C++ compiler existence (not included by default in
    Ubuntu).
  - Fix C equation files when using AUTO with g95.
* Shell commands:
  - @cp and @mv now accept up to 4 arguments and directories.
  - @rl, @lb, @kuz, @klp, @kbp, and @dlp are more flexible with bifurcation
    diagram files, and can work with older versions of those.
  - @fc and us() always generate the .o file for the equation file,
    in order not to confuse Sun f95.
  - Added lb, db, and rb commands to @lb (autlab), so it can list, relabel
    and delete branches.
* Demos:
  - Converted all demo Fortran files to free-form format.
  - Use IMPLICIT NONE in all demos.
  - Modularized the "brf" and "brc" demos.
    Use dynamic arrays in the "brc" and "brf" demo so NDIM determines the
    number of collocation points.
  - Added a 3-parameter continuation fixing the angle to the "tor" demo.
  - New demo "pcl" that uses Lin's method to connect point-to-cycle connections
    in the Lorenz equations. Thanks to Thorsten Riess and Bernd Krauskopf.
  - New demo "snh": bifurcations of global reinjection orbits near a saddle-node
    Hopf bifurcation: cycle-to-point connections. Also thanks to Thorsten Riess
    and Bernd Krauskopf.
  - New demo "fnc": computation of attracting and repelling slow manifolds
    and the continuation of canard orbits in parameter space in the FitzHugh-
    Nagumo equations. Thanks to Mathieu Desroches and Bernd Krauskopf.
  - Use STOP and NPAR in all demos where applicable.
  - Replaced RL0 and RL1, where used, by conditions in UZR or STOP.
  - Removed A0, A1 except where they are really used.
  - Fixed the 'mtn' HomCont demo: we must explicitly specify NSTAB for
    saddle-node homoclinics.
  - Added autorc files to the demos ab and tor.
* GUI94:
  - The old GUI can now work with .f90 equation files (but not with new-style
    constants files!).

0.6:
* The 2D plotter PyPLAUT can now use matplotlib, be called via the @pp command,
  and operated like the old PLAUT plotter.
  New settings were added to .autorc/autorc for more effective control:
  xlabel, ylabel, xlabel_fontsize, ylabel_fontsize, top_title, top_title_fontsize,
  dashes, solution_coordnames, solution_indepvarname, bifurcation_coordnames,
  stability, default_option, d0, d1, d2, d3, d4.
  PyPLAUT can now also show the stability of branches via dashed curves.
  The coordinate input boxes are more permissive: no need to type quotes or ['t','t','t']:
  just type t. The input boxes now, by default, show the column names from bifurcation
  diagram files.

* A new free-form constants file format is introduced with the following
  new constants: sv, e, s, dat, unames, parnames, SP, U, PAR, NPAR.
  The "dat" constant obsoletes the @fc/us() commands by reading directly from the ASCII
  data file.
  HomCont constants can also be added.
  Strings, set via unames and parnames, can be used in ICP, THU, THL, and UZR.
* Add new setting ISP=4 which detects PDs and TRs but not BPs.
* Implemented SP AUTO constant: SP=["HB1","LP2"] stops at the first HB or
  second LP. SP=["HB","LP"] selects which special points to detect.
* Support new, more compact, dictionary notation for the AUTO constants THL, THU, UZR,
  PAR, and U.
* If IRS is set to -1, then just get the first solution from the solution file.
  Use IRS<-I for the Ith label in the solution file.
* HomCont can automatically detect NSTAB and NUNSTAB, the number of stable and
  unstable eigenvalues in most cases.

* Introduce new @ksp, @dsp, @klb, and @dlb commands:
   @dsp -lp abc         removes all 'LP' labels from b.abc and s.abc
   @dsp -bp             removes all 'BP' labels from fort.7 and fort.8
   @dsp -uz abc abc2    removes all 'UZ' labels from b.abc and s.abc;
   			writes to b.abc2 and s.abc2
   @dsp abc             removes all special labels (anything that is not either every NPR
   			steps or an 'UZ' label) from b.abc and s.abc.
   @ksp does the opposite, e.g.:
   @ksp -lp abc	        keeps all 'LP' labels, and removes all other labels in b.abc and
                        s.abc	
  @dlb and @klb retain type numbers in b. files so they can be plotted.
  The new ksp, dsp, klb, and dlb commands in the Python interface work similarly.
* New merge/@mb commands merge branches in bifurcation diagram files.
* New subtract/@sb commands subtract branches using interpolation
  in bifurcation diagram files.
* The relabel (@rl) command is much faster.
* Removed obsolete @ commands.
* Avoid problems on case-insensitive filesystems by using @@R etc. instead of @R;
  make creates @R from @@R and so on, on case-sensitive filesystems.

* Allow manual branch switching for algebraic problems with ISW=-1. Derivatives are
  now stored in solution files to allow this to work reliably.
* The GETP function that can be called via PVLS supports new arguments:
  * 'EIG' obtains eigenvalues and Floquet multipliers:
     index 1, 3, 5,... obtain the real parts of ev's 1, 2, 3,... and 2, 4, 6,... the
     imaginary parts.
     Eigenvalues are ordered by real part.
     Floquet multipliers are ordered by distance from |z|=1.
  * 'NBC' gets the active NBC
  * 'NINT' gets the active NINT
  * 'NTST' gets NTST
  * 'NCOL' gets NCOL
  * 'NDIM' and 'NDX' get the dimension of the extended system
  * 'MXT' gets t value for maximum of component
  * 'MNT' gets t value for minumum of component
  * 'WINT' gets weight for integral; 0<=I<=NCOL
  * 'DTM' gets value for delta t array 1<=I<=NTST
  Some of these together allow for direct access of the solution array in 
* If the last point of a branch has type UZ, PD, HB, LP, etc. then that type is printed
  instead of EP.
* AUTO computes and prints Floquet multipliers, eigenvalues and stability also
  for the first and last points on a branch.
* NBIFX is eliminated from auto.h. Only NPARX is relevant. It now just designates a
  default maximum; it can be changed at runtime by the NPAR auto constant.
* Bifurcation diagram files (fort.7/b.xxx) now have complete headers showing all
  AUTO constants.
* DFDU, DFDP, DBC, and DICD are zero-initialized so it is not necessary to initialize
  those entries in equation files.
* It is now possible to extend a system via STPNT.
* Allow restarting from a point that is not a Hopf bifurcation in a BVP:
  it will be seen as a constant solution on the interval [0,1].
* Use LAPACK instead of EISPACK throughout.
  Eigenvectors might be different than before but are normalized to have the largest
  component positive.
* Better diagnostics for errors in fort.2/c.xxx and fort.12/h.xxx input files.
* Better performance and accuracy for fold continuations through smarter computation of
  the Jacobian matrix.
* The performance of input/output routines and commands has improved, for instance
  by avoiding re-reads.
* Some parallellization and cache use performance improvements.
* Fix issue not detecting Hopf bifurcations and stability changes:
  a tolerance is only set if the trace of the Jacobian is zero and the dimension is
  even so the system is probably conservative.
* Fix numerous bugs, thanks also to Thomas Wagenknecht, Hinke Osinga, Phil Naylor.

* Many Python syntax changes, all backwards-compatible:
  The run command returns a bifurcation diagram object that represents all output,
  and can work in a bd=run(solution,options) fashion.
  The load command returns a solutions + constants to start from.
  The loadbd command returns a bifurcation diagram object from files.
  It is straightforward to obtain all bifurcation points, branches, or a selection
  from bifurcation diagram objects; these objects can be concatenated like standard
  Python lists.
* "load" now supports changing LAB/PT/TY/BR/PAR in a solution.
* In Python allow starting AUTO via "run" directly from a Python solution array.
* Solutions and bifurcation diagrams in Python now use PyDSTool Pointsets and
  can use numpy/numarray/Numeric for efficiency.
* Elimination of internal use of shell commands by the Python CLUI, so it works
  especially faster in Windows and does not depend on a shell.
* Improved ctrl-c handling running Python scripts.
* You can now plot and read gzipped files directly in PyPLAUT and Python commands.
* Introduce "-c" for the auto command (works like python's -c), and preserve already
  set PYTHONPATH.
* Add an r3b boolean parameter to plot3 in the Python CLUI.
* The Python CLUI can now read .auto files with DOS line endings on Unix systems.
* The lp Python CLUI alias now finds limit points instead of Hopf points,
  and cp is no longer aliased to commandCopyDataFiles (conflicts with cp as
  Unix copy).
* Python2.6 compatibility.

* PLAUT04 uses less memory and parses solution, bifurcation diagram and diagnostics
  files more efficiently.
* You can set PLAUT04's axis colours in plaut04.rc.

* All demos were updated to use Python, also thanks to Fabio Dercole.
  Special HomCont (h.xxx) were eliminated from all demos.
* New demos: um2, um3, ph1 (Eusebius Doedel), c2c and p2c (based on work by
  Doedel, Kooi, van Voorn, and Kuznetsov).

* Improved configure script for use with MacOS X.

* Many updates to the manual, also thanks to Fabio Dercole.

0.5:
* PLAUT04 can now also use the SoQt and Qt libraries. That
  makes it easier to compile on various Linux distributions,
  and makes it portable to native Windows and MacOS X without
  an X server. Using SoQt also avoids some issues with LessTif,
  in particular on 64-bit systems where LessTif is unstable.
* PLAUT04 can now show label numbers in bifurcation diagrams.
  plaut04.rc option: "Show Label Numbers"
* The coloring method options in plaut04.rc can now be set
  seperately for solution displays and bifurcation diagrams:
  "Coloring Method Solution" and "Coloring Method Bifurcation".
* You can also set the "Label Sphere Radius" in plaut04.rc.
* The r3b (now with extensive manifold calculations), pp2, pp3,
  lor and bvp demos were updated.
* Some issues with g95 and Sun's Fortran compiler were solved.
* Likewise for the configure script.
* Repaired MPI regression in 0.4.
* Add support for ipython (auto -i) and also auto-quotes
  and auto-parentheses in the normal auto Python CLUI.
* Added some often used shell commands to the Python CLUI:
  "clear","less","mkdir","rmdir","cp","mv","rm".
* Added ex and dmf aliases for execfile and demofile to the
  Python CLUI.
* Added a GETMDMX(NDIM,P0,P1,NMM) routine to obtain the monodromy
  matrix factorization in PVLS (adapted from Kazuyuki Yagasaki).
* Corrected integral conditions for torus bifurcation continuations
  (bug well-spotted by Huguette Croisier).
* Added BPCont: code for BP continuation of periodic solutions and BVPs
  (Fabio Dercole).
* Added BPCont demos: sspg, lcnf, tfc, and abcb.
* Added @lbf, @ls commands, and the writeShort() and writeScreen() Python
  methods for displaying the bifurcation diagram file in a compact way.

0.4:
* AUTO-07p can now continue branch points in two parameters
  (Fabio Dercole)
* Includes all demos that are documented in the manual.
* The manual documents a new tutorial demo ('cusp').
* The run() and load() commands in the Python CLUI have
  been extended to directly specify AUTO constants, save
  and append files as parameters.
* A new splabs() Python CLUI function directly obtains
  special labels from a solution file (e.g., all Hopf
  bifurcation labels).
* You can now run the @ command (@dm, @R, etc.) directly in
  the Python CLUI without having to escape them with a !.
* The number of parameters printed in the bifurcation
  diagram files is now given by NICP; the parameters beyond
  the 7th are displayed as well.
* A higher precision for numbers is used in the bifurcation
  diagram files. This helps when plotting small sections
  of bifurcation diagrams.
* AUTO now allows free-form Fortran for equation files
  (.f90 extension).
* Parallelisation has improved.

0.3:
* The configure script is fixed for certain GNU Fortran
  configurations on Windows and has improved detection
  for the Coin and SoXt libraries for PLAUT04.
* Some PLAUT04 crashes were fixed.
* The MPI parallellization was improved so that most of
  the big data arrays that form the Jacobian matrix are
  split between machines.
  The distribution of memory enables AUTO to work with
  much larger systems.
* Both OpenMP and MPI parallellizations were improved
  so that the setting up the RHS, copying to a smaller
  system and inflation of parameter routines are done
  in parallel.
* An OpenMP parallellization issue with integral conditions,
  and several other small bugs were fixed.
* A few new demos and helper utilities were added.
* The 'total time' reported by AUTO is now the total wall
  clock time for both OpenMP and MPI.

0.2:
* The configure script is fixed if PLAUT04 dependencies
  are not available and is more robust.
* MPI support is ported from AUTO2000.
* A bug is fixed involving the continuation of folds with
  more than two parameters.
* Automake is no longer used for PLAUT04, using just autoconf
  and Makefile.in files for the whole project instead.
* Various performance improvements have been made.

0.1:
* This is a preliminary version of AUTO-07p.