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NEWS
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Version 1.16 2023/08/09
- the 'ttnnp04' rhs module now accepts parameter 'variant' which can take values 'epi', 'endo' or 'mcell';
- new predefined "advance" global k_variable which has nonzero value before the main loop starts;
- an obsolete "window" feature eliminated; this was universal for every device and now is only where needed; should not affect the user interface;
- a few minor errors corrected and inconsistencies removed.
Version 1.15 (2022/02/24)
- parameters pbx, pby, pbz addded to ezstep device to allow periodic boundary conditions;
- devices torx, tory, torz added, to allow periodic boundary conditions in box geometries (to be documented);
- an error in diff and diffstep devices corrected, which affected accuracy of calculations in anisotropic cases with variable diffusivity tensor;
- a few minor errors corrected and inconsistencies removed.
Version 1.14 (2021/05/30)
- In absence of X11 and/or OpenGL graphics, Beatbox now automatically configures so as to not depend on those libraries:
-- In devices that have graphics as facultative functions, these are disabled;
-- Devices that totally depend on those are replaced with dummies.
- Length of the "version" field in the ctlpoint files is increased to 16 (was 12). This means that ctlpoint files written by pre-1.14 versions of Beatbox will not be correctly read by version 1.14 or later.
Version 1.13
- New devices: byteout, pw_mult (to be documented)
- Improved checking of input syntax (diagnosing cases when the name of the defined k-variable is missed).
- The manual doc/beatbox.html revised to describe available cell models a bit better.
- A few minor errors corrected and inconsistencies removed.
Version 1.12.xxxx
- Compatibility with the current version of MPI standard achieved and with legacy versions of it retained.
- record device revised: it now is sequential-only (the parallel version was not working anyway), and can produce automatically numbered output files as well as a single file at the user's coice.
- ezpaint device revised: can draw markers (this is not documented yet)
- The manual doc/beatbox.html revised to correct inaccuracies, fill gaps, and reflect recent changes.
- A few minor errors corrected and inconsistencies removed.
Version 1.11.1052
- Parameters now may be dynamically linked to k-variables or k-expressions (currently applies to ezview parameters)
- Padding of geometries may be controlled
- A few minor errors corrected
Version 1.10.1044
- New devices: matout, ezpaint, ezview.
- k_func knows geom0, geom1.. read/write variables and has advance=1 option.
- Consequently, now one can work with geometry and anisotropy defined within script, without a BBG file.
- ezstep can now do 0D (i.e. reaction without diffusion)
- Bug fixed in ctlpoint (checks when restarting job with different domain partitioning).
- Multiple minor errors and inaccuracies corrected.
- Documentation completed and edited accordingly.
Version 1.9.1012
- New devices: ezstep and ezview
- Option "bythred=1" in ctlpoint device
- Parameter names in rhs b02 corrected
Version 1.8.998
- Points with short fibre vectors in geometries intepreted isotropic.
- Added k-function geom() access geometry data.
- Various improvements and bug fixes, in particular for working with very large grids.
Version 1.7.982
- "configure" is included in distribution so autotools not needed for installation, if only compilation is required
- k_paintgl device added, which paints 2D fields using OpenGL extension of X11
Version 1.6.953
- "ionic" cell model format extended to include Markov Chain (MC) channel descriptions;
rushlarsen device now can do Matrix Rush-Larsen (MRL) timestepping for MCs.
This involved also inclusion of an extract of GNU Scientific Library (GSL).
- New ionic models illustrating handling of MC and work of MRL.
- rk4 device added for Runge-Kutta 4th order solver.
- MPI version now does not create separate "log" file and instead
prints full messages to standard output.
- A bug in singz.c fixed: it was not properly parallelized. The
previous more accurate tip orientation finding alg still available
for sequential runs. Also, it now saves information about found tips
into k-variables.
- Multiple minor errors and inaccuracies corrected.
- Documentation completed and edited accordingly.
Version 1.5.830
- Major change: new device 'rushlarsen', the associated model format
'ionic' and two ionic models in this format, br77 (Beeler-Reuter
1977) and crn98 (Courtemanche Ramirez Nattel 1998). The ionic crn98
is quicker than Courtemanche's original code, mostly due to
tabulation of Vm-dependent functions.
- New device 'diffstep' added
- A typo in diff.c fixed which would have caused wrong result if
diffusion nonuniform in y direction.
- Several smaller changes, mostly of technical nature not concerning
the front-side.
Version 1.4.818
- Major changes: new devices 'adi3d' and 'elliptic' for implicit
diffusion timestepping and bidomain respectively.
- Several bugs fixed, format of stdout and log file improved,
documentation updated.
Version 1.3.567
- Major change: now it is possible to not allocate processes to empty
subdomains (essential when treating 'thin' geometries with high
degree of parallelization.
- The method of domain decomposition can be now chosen from command
line, including explicit decomposition formula.
- New cell models added (mouse, mousevent, crnach)
- Improvements were made in reporting information to standard output
and to the log file, particularly concerning domain partitioning
and domain/process allocation.
- Improvements were made in the manual example scripts, including
change of directory structure (they are now classified by cell
models).
- A few bugs fixed, including a major bug when 'euler' device was
incorrectly filling its space with standard initial conditions when
in parallel mode.
Subversion 1.2.490
- New device added (pause)
- New cell model added (b02)
- Improvements were made in the documenation, logging/error reporting
and example scripts
- Several bug fixes
- The standard output and log file now report the revision
("subversion") number in addition to the main version number.
Version 1.2
- A few new devices (k_imgout, activation, vtkout2, ecg) were added.
- A few new cell models (FKMOD, TNNP, TTNNP04, TTP06) were included.
- Documentation was improved.
- Several minor improvements were made in functionality in a number
of modules and bug fixes.
Version 1.1
- Installation instructions were checked and corrected.
- Existing documentation was updated and corrected, some more
documentation was written.
- A number of unused source files were removed.
- Profiling of devices improved.
- Minor improvements in functionality in a number of modules.
Version 1.0.313
- Initial public release.