File smoldyn.changes of Package smoldyn

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File smoldyn.changes of Package smoldyn

-------------------------------------------------------------------
Tue Mar 17 11:39:04 UTC 2020 - Dilawar Singh <dilawar.s.rajput@gmail.com>

- Update to version 2.61

* Minor bug fixes: improved radialdistfunction and surface detection near system boundaries.

-------------------------------------------------------------------
Fri Apr 19 04:31:03 UTC 2019 - Dilawar Singh <dilawar.s.rajput@gmail.com>

- Removed unnecessary dependency and fixes for debug package.
- Removed packages for other distrbution. Use of %cmake, %cmake_build etc.
  breaks build on Fedora, CentOS etc.

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Tue Apr 16 06:44:40 UTC 2019 - dilawar.s.rajput@gmail.com

- Update to version 2.58

* Support for lambda-rho reaction algorithm
        - Reactions can vary between diffusion- and activation-limited. Smoldyn
          now reports fraction diffusion-influenced although some minor errors
          still remain.
    * Improved single-particle tracking
        - Molecule serial numbers are retained during association and
          dissociation
    * Expanded support for math in input files
        - Command probabilities can depend on molecule position
        - Improved precision in math calculations

- Previous versions:

* 2.57 (3/21/19) - Math supports scientific notation, allowed species change with surface actions, improved single-molecule tracking. Smoldyn is now on github.
    * 2.56 (9/18/18) - Got MinGW compiling to work again for Windows. Fixed minor bugs. Largely completed lambda-rho reaction algorithm support, although some minor calculation errors remain.
    * 2.55 (7/16/18) - Several minor bug fixes. This version was not compiled for Windows due to compiler problems.
    * 2.54 (8/27/17) - Fixed minor bug that affected drift of surface-bound molecules.
    * 2.53 (5/25/17) - Fixed minor bugs that arose when counting molecules during hybrid simulations and fixed errors that arose with certain compilers.
    * 2.52 (5/16/17) - Fixed very minor bug that arose when counting molecules during hybrid simulations.
    * 2.51 (3/15/17) - Fixed trivial bug that caused compiling errors and bug that affected surface-interactions of surface-bound molecules.
    * 2.50 (2/28/17) - Improved support for moving surfaces and developed infrastructure for state-observation functions.
    * 2.49 (2/17/17) - Added partial support for moving surfaces and for the use of basic math functions in input files.
    * 2.48 (11/16/16) - Fixed a few minor bugs which caused crashes in unusual situations.
    * 2.47 (8/30/16) - Improved rule-based modeling with wildcards with fixed bugs, rules for molecular properties, and properties for reaction rules.
    * 2.46 (7/30/16) - Rule-based modeling with wildcards is now true on-the-fly, expanding only as needed.
    * 2.45 (7/15/16) - Fixed several minor bugs, including in equilmol command, math parsing, and hybrid simulations.
    * 2.44 (6/27/16) - Simplified input of reverse reactions and returned freeglut.dll to the windows download.
    * 2.43 (5/18/16) - Improved Libsmoldyn compiling and linking, renamed documentation, and added some commands.
    * 2.42 (4/29/16) - Fixed minor bugs. Excluded volume reactions now work well and added overlapping space hybrid simulation.
    * 2.41 (4/8/16) - Fixed several bugs that arose in v. 2.40, added tutorial section to User's Manual, and improved algorithm for excluded volume reactions.
    * 2.40 (3/22/16) - Lots of new features: rule-based modeling with BioNetGen, rule-based modeling with wildcards, variables and arithmetic in input files, fixed several more bugs in surface diffusion, several new commands.
    * 2.39 (1/15/16) - Fixed another important bug in surface diffusion. Quantitatively validated results. Accelerated virtual box assignment, which especially helps when molecules are unevenly distributed.
    * 2.38 (10/22/15) - Lots of minor bug fixes and feature additions. New features: fixmolcountrange commands, quit_at_end statement, reaction_intersurface statement, more versatile bounce and confspread reactions, works on older Mac systems.
    * 2.37 (10/7/15) - Fixed a major bug that affected diffusion of surface-bound molecules. In the process, sped up surface-bound diffusion. Also added support for single molecule tracking with serial number control and reaction logging.
    * 2.36 (6/9/15) - Fixed a minor bug that affected some bounce type reactions.

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