AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.
Use DSTEST instead of uninitialized RDS in diagnostics when converged already.
Fix compilation with GCC 10, by making DGEMV calls consistent. This fixes #8.
Use "use mpi" instead of include mpif.h.
This avoids issues with gcc 10 argument mismatches and is still compatible
with many older MPIs.
Don't use STOP for normal termination.
This avoids reporting innocent floating point exceptions.
Fix parallel make for building.
Implement MPI parallel version of RNRM2 (RNRM2P) and RINTG (RINTGP)
The serial ones gave incorrect results.
Add "make install" and "make install-strip" targets
Add "make check" and "make distclean" targets.
Use -g by default, introduce --enable-debug configure flag for extra debugging.
--enable-debug sets extra FP and bound checking flags for GNU Fortran.
Preserve order for complex multipliers when sorting Floquet
multipliers, and do not select a complex multiplier by accident when
the second multiplier should be 1 or -1 (on PD/LP curves). Fixes #15.
Zero initialize Jacobian matrices in HomCont.
Some demos such as "she" don't fill them completely, causing use of
uninitialized variables.
Python
Fix display of labels in interactive plots for Matplotlib 2.2 and
newer. Thanks to Edgardo Villar-Sepúlveda for reporting.
Catch IOError for fcon cleanup. Avoids issues with macOS.
PLAUT04
Update header for current stable Inventor version (2.1.5) (#4) (B Thomas)
Fix failure to set SOXTLIB in configure with Open Inventor. Fixes #4 (B Thomas)
Support Qt5 with SoQt
Flatten autoconf configuration and use pkg-config autoconf macros for Coin and Qt
PLAUT
Replace do termination labels with ENDDO
This fixes warnings such as
Warning: Fortran 2018 deleted feature: DO termination statement
which is not END DO or CONTINUE with label 10 at (1)
Remove tek2ps, use tek2plot from GNU plotutils instead.
tek2ps has a copyright incompatible with the rest of AUTO, prohibiting
commercial redistribution, which is a problem for some Linux distributions.
Although it is rarely used any more, tek2plot from GNU plotutils can be
easily used as an alternative to tek2ps.
Testing
CI: Run GitHub Actions tests on Ubuntu 18.04, 20.04 and macOS 10.15.
Manual
Fix documentation for Jacobian of the boundary conditions.
Thanks to @giuseppetomassetti for spotting this. Fixes #17
Eliminate use of moreverb/subfigure packages, instead use fancyvrb/subfig.
This way a more basic TeX installation is sufficient, e.g.
basictex on a Mac.
Avoid MX in abcb demo, by decreasing NMX to avoid numerical noise
Increase NTST in fnb demo, for better reproducibility
Tighten NBC check in snh and pcl demos.
This avoids MPI workers (where NBC=0) trying to compute the Lin vector.
Check for MPI worker in PVLS for r3b demo
v0.9.2
3 years ago
0.9.2:
Main AUTO
Print eigenvalues in Hopf detection function if following a
BP curve or an Rn/BT has been detected.
Don't write MAX/MIN for IPS==-2, that is, IVPs (request by Sebius).
Replace tabs with spaces in continuation lines (bug reported by Sebius).
Fix warnings reported by newer GCCs.
Update included BLAS from www.netlib.org/blas (LAST UPDATE:
Tuesday Apr 19th 2011)
Use 3-digit exponents for all 19.10 formats (in solution files),
to avoid numbers such as 1.1234567891-100.
Fix constant file output for strings with backslashes, using "'"+str(s)+"'"
instead of repr(s) (report from Sebius Doedel).
Thanks to Felix Becker [email protected]: fix error detected
by -fcheck=bounds in ae.f90 and bvp.f90.
Use TRIM(ATYPE)//'0' instead of ATYPE//'0' to fix a problem detecting
spurious Torus bifurcations. Thanks to Medhi Paak for reporting this bug.
Change sorting algorithm for Floquet multipliers from selection to insertion
sort to keep complex conjugates together correctly. Solves sorting
issue reported by Medhi Paak and Sebius Doedel.
Only compute L2-NORM (or similar) for WRTBV9 if IID>=2, else it is
not used.
Better MPI parallelization:
The code in bvp.f90 has been parallelized so that the solution
vectors are nearly always distributed and only concatenated when
Newton iterations converge (for mesh adaptation, solution
measures, and I/O). This speeds up the code significantly for higher
processor counts.
Some work space arrays used in the linear solver now have the
minimum size required (of length NTST/NP+log2(NTST) instead of
length NTST where NP is the number of processors). This significantly
reduces memory consumption.
HomCont works with MPI.
BPCont works with MPI.
MPI is properly ignored for algebraic problems so it can be
easily used in scripts and automatic testing, by setting e.g.
AUTO_COMMAND_PREFIX="mpirun -n 4"
AUTO now calls MPI_Init_thread instead of MPI_Init for hybrid
MPI/OpenMP configurations
Better OpenMP parallelization:
Call STUPBV (time derivatives) in parallel for OpenMP.
Parallellize part of fort.8 I/O (FP to string conversion) using OpenMP.
Store UOLD vector into U past NDIM. This allows equation files to
access UOLD in FUNC.
Meshing improvements:
Let INTERP work on two solutions in one loop, to save on recomputing weights.
Simplify INTWTS interface/implementation to remove the need for the array X
and with less potential loss of precision.
Store "E" (deqf/dt) from EQDF into DEQF and use it directly in NEWMSH
This avoids an addition followed by a subtraction which resulted in
rounding errors.
Move to git repository, add .gitignore file (with Andreas Amann)
Adapt configure script, makefiles and shell scripts to newer Mac OS and
Windows (using MSYS2).
Python:
Python 3 support
Adapt for Python3 compatibility (Andreas Amann)
All tests now run for Python3 and Python2
Python3: only use binary mode for solutions, not constants.
Solution files use binary mode for speed since they only contain
numbers and no strings, unlike constants files, but a text mode
workaround is there now just in case the stdin pipe has no binary
buffer.
Python packaging support
Add setup.py/setup.cfg and move Python code to auto subdirectory
(Rike-Benjamin Schuppner)
Add init.py and use relative imports (Rike-Benjamin Schuppner)
Add main.py to simplify testing, and allow "python /path/to/auto"
Python: Change relative to absolute imports and adjust commands.
Absolute imports work more nicely with existing scripts, and are
recommended by PEP8 anyway.
Prompts need to be defined differently with IPython >= 5.
Use numpy.ndim instead of the deprecated numpy.rank.
Remove support for long (~10 years) obsolete Numeric and numarray.
Avoid identifying np.nonzero and np.flatnonzero (Andreas Amann)
Monkey patching np.nonzero to be np.flatnonzero had bad effects on
matplotlib, which depends on the correct np.nonzero to be available.
Avoid plain python in shebangs.
"python" may not exist, but "python3" may exist. The auto and autox shell
scripts now take care of this.
PyPLAUT
For Python 3: fix handling of dashes and parser for autorc files.
If Tk cannot be initialized, hide the plot if possible.
This allows to run the automated test without DISPLAY set.
Use NavigationToolbar2Tk for matplotlib 2.2+
Use get/set_facecolor if available instead of deprecated functions.
Fix problem when updating small plotting window
PLAUT
Fix compilation with newer versions of gfortran:
ANGLE needs 4 elements, otherwise it cannot call ARROWL with it.
PLAUT04
Eliminate use of QT3_SUPPORT methods for pulldown menus.
Eliminate QT3_SUPPORT define.
Qt4 compat for file dialog windows.
Replace insertItem with addItem for lists for Qt4 compatibility.
Use toLocal8Bit() instead of implicit QString->const char * conversions.
Call constructors for QComboBox, QSpinBox, QDialog, etc. in Qt4 style.
Create a seperate method for every pulldown menu entry for better
QT4 compatibility.
Workaround for the menu bar in newer Mac OS X versions (Mavericks+)
Fix set but not used warnings for PLAUT04.
Testing
Setup automated testing (Continuous Integration) using Github
Actions (on Ubuntu)
Compile AUTO and manual
Test with both python2 and python3.
Enabled test with MPI enabled
Properly exit with error code in test scripts.
Upload test artifacts (logfile and verification html).
Adjust r3b demo test reference.
The eighth run of the fhh demo converges (since 703607e for NEWMSH)
Fix two more results for ab demo in test reference.
Manual
Fix documentation illustrating Python data access for lrz demo. Closes #3.
Latex compile fix (Andreas Amann)
the unknown m placement specifier for figures was ignored by older
latex versions but is now an error.
Demos
Make tfc demo more robust.
Tweak EPS* in fhh demo to properly detect UZ in eighth run
Adjust EPSS in fhh demo to still detect the test point.
Increase NTST in ab demo to make it more robust in the last run.
Increase NTST in c.ab.3 to 70 so it does not MX unreliably.
c2c demo: increase NTST a little to make it work correctly with GCC8
Increase NTST in c.fhn.5 to match c.fhn.6 (elimates spurious UZ)