source: debian/changelog

molecuilder (1.7.0-1) UNRELEASED; urgency=low

  Major
  * saturate (fixes to polyhedra and scaling) and bondify (new)
  * potentials are first class citizens
  * proper path from molecule, to automated fragmentation, computation, homologies and finally potential training (and visualizing in the UI).
  * convenience changes in the UI: bigger icons, context menu in gl view, potential tab with plotting
  * enhancements to python scripting: numpy compatibility, wait returns status, python3
  * works inside jupyter notebooks.
  * can be deployed to k8s for large-scale computations.
  * graph6 strings, evaluating stability and chemical space evaluation
  * more selection actions

  Minor
  * switch to simpler kubernetes-aimed worker-server setup (health probes, workers don't register but accessed through load balancer)
  * potential list shown in UI, new actions to add and remove, also potential curves are plotted in UI
  * general fixes to potential setup to make them work as compound potentials
  * undomark action
  * Undo is again without dialog, undo mark is an extra action now.
  * context menu (right-click) in gl view to manipulate atoms directly
  * docker file contained in repo
  * bondify has undo/redo
  * switched all python to python3
  * graph6 fixes and writing strings
  * generatePotentialAction generates all combinations
  * full numpy getter and setter to atom position, velocities, and forces.
  * saturate action allows for just using outer shell (unocc and occ orbitals, only unocc used for adding hydrogens) 
  * stretch bond falls back to tabled distances for element pairs on zero length
  * select atom's bond neighbors
  * select atoms randomly
  * calculate pair correlation between element and selected atoms.

  Fixes
  * corrected units and computation in SaveEnergies, renamed from SaveTemperatures
  * InputAction will also save that file on exit

 -- Frederik Heber <heber@molecuilder.com>  Wed, 22 Oct 2025 19:13:00 +0100

molecuilder (1.6.1-1) UNRELEASED; urgency=low

  * Added ChemicalSpaceEvaluator Action to assess stability of all possible
    molecules that match a given Graph6 string using fragmentation method
    principles.
  * Python Interface supports (and recommends using) named parameters.
    Moreover, save-session will write scripts with named parameters.
  * GUI displays forces and velocities as additional vectors per atom.
  * AutomationFragmentationAction checks whether workers are still busy and
    aborts when all workers have crashed.
  * JobMarket: is now robust when worker or server is killed by signal.
  * JobMarket: Added GetNumbersOfWorkerOperation.
  * ForceAnnealing/StructreOptimization Action can now take the bond graph
    information into account and significantly speed up optimization up to a 
    factor of 3.
  * added molecular dynamics and structure optimization integration tests.
  * FIX: recreated and fixed guicheck tests.
  * StretchBondAction now takes the bond graph into account.
  * Added examples test case with many ways of translation atoms, see blog 
    post.
  * enhanced precision of tremolo format making it the recommended file format
    to use!
  * Tremolo file format now supports multiple time steps.
  * DOCU: Updated userguide on empirical potential using HomologyGraph.
  * Added SelectAtomByName action.
  * DOCU: several fixes to userguide.
  * FIX: GUI again reacts to WorldTime changes, i.e. time slider.
  * changed email address to sent bug reports to.
  * Added AtomRandomPerturbation to randomly displace atoms.
  * DOCU: explained wait() necessity in python scripts.
  * StepWorldTime now uses a single argument.
  * FIX: Status messages are now always pushed to log, even when logging is
    captured in GUI.
  * RotateToPAS has working undo/redo.
  * Added RotateAroundBond action for rotating molecule around specific bond.
  * Added very powerful GeometryObjects to use as any vector object or for 
    simply measuring distances and angles in the GUI.
  * CodePatterns, fix: Chronos is thread-safe, and protecting Verbosity.
  * fixes: regression tests ports between 11024 and 19999.
  * builds on Ubuntu 16.04
  * MemDebug is now disabled by default.

 -- Frederik Heber <heber@molecuilder.com>  Fri, 02 Mar 2017 23:45:24 +0100

molecuilder (1.6.0-1) UNRELEASED; urgency=low

  * Dependent packages CodePatterns, JobMarket, levmar, MPQC(_open), and vmg
    are now contained in the distribution under ThirdParty packages.
  * Debian package can be easily created.

 -- Frederik Heber <heber@molecuilder.com>  Fri, 02 Mar 2017 23:45:24 +0100

molecuilder (1.5.4-1) UNRELEASED; urgency=low

  * initial code for allowing charge grids for long-range calculations to work
    independently for fragments.
  * fixes to SaturateBond, now properly working by using full
    SphericalPointDistribution and combinatorial matching to present bonds.
  * fragment results can now be parsed and save in extra action, not bound to
    fragmentationautomation oder analysefragmentresults.
  * fixed fragmentation on subset of atoms.
  * QtFragmentList now supports proper sorting.
  * logview in GUI may be disabled by configure-switch.
  * fitted partial charges are now stored using save/parse-particle-parameters.
  * introduced implicit charges.
  * fragmentation-automation fails when server is not/no longer accessible.
  * fit-partial-charges fits to currently selected atoms and creates unique
    particles.
  * removed parse-tremolo-potentials as is superceded by
    parse-particle-parameters.

 -- Frederik Heber <heber@molecuilder.com>  Fri, 30 Sep 2016 17:45:24 +0200

molecuilder (1.5.3-1) UNRELEASED; urgency=low
  
  * QtGui now crashes only in 1-2% of all regression tests (new record).
  * we copy all information regarding visual entities and regaring the 
    displayed lists via QtObserved... instances or via central ..Observer
    entities.
  
 -- Frederik Heber <heber@molecuilder.com>  Sun, 25 Apr 2016 09:11:24 +0200

molecuilder (1.5.2-1) UNRELEASED; urgency=low
  
  * Introduced QtObservedInstanceBoard as clean interface between World and QtGui.
  * Bugfix to FillRegularGrid.
  * FitParticleCharge -> FitPartialCharge.
  
 -- Frederik Heber <heber@molecuilder.com>  Sun, 03 Mar 2016 13:48:57 +0100

molecuilder (1.5.1-1) UNRELEASED; urgency=low
 
  * Incorporated libcodepatterns rename and other fixes for debian packaging.
  * More efficient bounding box in molecule, effectively O(log N).
  * Enhanced hbond distances with more values and consolidated from
    optimization calculations.
  * VMG forces now are also working for the long-range part.
  * Interdistance now combines couples of fragments till a given order.
  * Smearing of electronic charge distributions greatly improves electronic
    long-range component.
  
 -- Frederik Heber <heber@molecuilder.com>  Sun, 06 Feb 2016 23:16:00 +0100

molecuilder (1.5.0-1) UNRELEASED; urgency=low
  
  * Initial Release.
  * This is my first Debian package.
  
 -- Frederik Heber <heber@molecuilder.com>  Sun, 09 Aug 2015 21:37:00 +0100