[Molecuilder-devel] [SCM] MoleCuilder branch stable created. v1.4.5-44-g2a03b00

14 Jul 2014


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The branch, stable has been created
        at  2a03b00b33c43f417fdf3452727473a2043f2638 (commit)

- Log -----------------------------------------------------------------
commit 2a03b00b33c43f417fdf3452727473a2043f2638
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 29 04:44:41 2014 +0200

    Set version to 1.4.6.
    
    - MoleCuilder library is now 13:4:1.
    - Codename "Robert Scott" (polar explorer, second to reach the south pole, was
      born 146 years ago)

commit d8821e62974799dc0fa0b06ad6a9ec1bc73b57a8
Merge: c73e35f a61dbbe
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 14 13:16:23 2014 +0200

    Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable
    
    Conflicts:
    	src/Actions/ActionQueue.cpp
    	src/Actions/FragmentationAction/FragmentationAction.cpp
    	src/Actions/PotentialAction/FitParticleChargesAction.cpp
    
    - in ActionQueue taking over both changes.
    - FragmentationAction added Status message where we don't complain for not
      having HAVE_JOBMARKET anymore. Removed.
    - FitParticleChargesAction had charge averaging and error message in case of
      no present fragments overlapping.

commit a61dbbe03ddbe4f5f0a22574b63fb4d32e312493
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 13 15:03:31 2014 +0200

    In CommandLineUI actions are skipped after failing action.
    
    - ActionQueue has queryable flag lastActionOk.
    - CommandLineWindow uses flag to check whether to queue further actions.
    - added regression test in the context of fragmentation-automation.

commit abfc95ba5c74e7d73ba21441037391420169955e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 13 09:50:39 2014 +0200

    Added test for mpqc and fragmentation calculations in target extracheck.
    
    - calculations take some time, hence these tests are only executed in
      extracheck.
    - extracheck only does something in case of disable-jobmarket.

commit 99692c9432d0e1c94ff5a06b6e7bc5ac1a6c1e27
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 13 01:17:29 2014 +0200

    FIX: Preparation of temporary filename in SystemCommandJob now working correctly.

commit d6a7b9066f589c9d821d442a8d23585ebd632c24
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 13 01:05:27 2014 +0200

    Specifying executable and suffix in SystemCommandJob with MPQCCommandFragmentController.
    
    - now requiring JobMarket 1.1.5 (if given) for updated SystemCommandJob.
    - SystemCommandJob allows specifying a suffix to the temporary file.
    - this allows adding ".in" to MPQCCommandJob's temporary file name.

commit 18ed8c7a1d88e9db52b1b57a548546f17406a526
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 7 22:43:47 2014 +0200

    All HAVE_VMG also check for HAVE_JOBMARKET.
    
    - right now VMG is not activated when we lack JobMarket anyway, but this is
      actually safer.
    - FramentationLongRangeResults no longer compiled in when lacking VMG.

commit 2e584e7ebd971c6cbd41f1ca6d93bb5fe7887849
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Apr 27 16:36:58 2014 +0200

    Removed (very) old joiner and analyzer programs.
    
    - they are not needed anymore when FragmentationAutomation works also without
      JobMarket now.

commit bf0ff325add9c6c7128a5dc3877f74aa7589da2e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:57:20 2014 +0200

    Using MPQCCommandFragmentController in FragmentationAutomationAction.
    
    - FragmentationAction does not lament missing JobMarket and output-types.

commit 1d17e57c9c64b6781a9d183fcf18872bae9cf9b9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:57:57 2014 +0200

    Added MPQCCommandFragmentController.
    
    - MPQCCommandFragmentController mimicks JobMarket's FragmentController or
      SpecificFragmentController, respectively, without relying on JobMarket.
    - modified FragmentJob to grant MPQCCommandFragmentController access to to
      setId(). In JobMarket access is granted to FragmentController which we do
      not inherit from here.

commit c73e35f66c0f01f80b5db60d4be99c3921abcb85
Merge: 4e5bf51 26b4d62
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Jun 28 22:03:14 2014 +0200

    Merge branch 'StatusToAllActions' into stable

commit 4e5bf51bd8dbec42331f2d499ea6f0df4beabd08
Merge: 1b1fa57 0ef9127
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Jun 28 22:03:02 2014 +0200

    Merge branch 'QtGUI_LogBox' into stable

commit 0ef9127937748a00a4b5acfe70e56c991aed77b0
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 23:30:53 2014 +0200

    QtLogBox catches mousePressEvent and selects atom in log.
    
    - this should ease graphical debugging a lot.

commit e0b5f07b569ad48c9e5c6ed53968f1e215c43d1b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 23:00:14 2014 +0200

    Added QtLogBox to QtMainWindow, using QDebugStream to display log.

commit 7f8c9ad6477b6f1c9412bc613327680267c2d70f
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Apr 26 19:19:09 2014 +0200

    FIX: Need to purge FragmentationResultContainer.
    
    - otherwise molecuilder stalls on quit.
    - requires JobMarket includes for pyMoleCuilder.

commit 786d28e4533ffcfc1d63d95f08f65c92dd946946
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:24:32 2014 +0200

    Lib..FragmentationAutomation and lib..Jobs now also compiled without JobMarket.
    
    - FragmentationAutomationAction, MolecularDynamics.., and ParseFragmentJobs..
       are also compiled, makes sense with upcoming MPQCCommandFragmentController.
    - must not compile SpecificFragmentController or MPQCFragmentController
      without JobMarket.
    - now requires libboost_iostreams.
    - this is due to MPQCCommandJob fiddling with streams to convert results.

commit 2cc7faa758cecbb1c378dc72c67f25dfd7cbd323
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:25:58 2014 +0200

    LibJobMarket only compiled in if CONDJOBMARKET.

commit 1dfe00d53becf9875c49a1c974659affcd083a2b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:43:17 2014 +0200

    Added inclusion switch on HAVE_JOBMARKET for files depending on JobMarket.
    
    - this is preparatory for using MPQCCommandJob without JobMarket.
    - this is possible with several basic files taken over from JobMarket project.
    - changes to ExportGraph_ToJobs, needs to export MPQCCommandJob when no
      HAVE_JOBMARKET is given.

commit c3de511c88d74c7dd3ee27b035ff60e0ecf0b720
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 23 13:19:14 2014 +0200

    Added FragmentJob, ..Result, JobId, SystemCommandJob, and types from JobMarket.
    
    - taken over from version v1.1.4 with disclaimer adapted.
    - changed include paths to JobMarket -> Jobs/JobMarket.
    - these files are only used when no HAVE_JOBMARKET is defined.
    - SystemCommandJob had Info, causing extra Chronos entry.

commit a498c1b15125817769fd9b27a366acd471b6b413
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 22 18:11:59 2014 +0200

    Extracted ResultContainer from ReceiveResultContainer.

commit d4eaf11f136baa85a4bdfa982418399b22a44110
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 22 17:59:51 2014 +0200

    Renamed ResultContainer -> ReceivedResultContainer.
    
    - this belongs to SpecificFragmentController.
    - renamed _ResultContainer_impl -> _ReceiveResultContainer_impl.
    - FIX: also renamed inclusion guard.

commit a42feea2484491fdb28f92c73043956e00a2d922
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 24 23:56:03 2014 +0200

    FIX: lib...FragmentationAutomation was linked in outside CONDJOBMARKET.

commit 37ef6d9c81dd05d5433115e175bac28b62275986
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Mar 20 18:29:00 2014 +0100

    Changed element class and periodentafel to have and use functions from ion.
    
    - If ionization is zero, fall back to other function.

commit 31bd9c87bb06e45f77fe0e6e5b0d8ca6a9751ae7
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Mar 20 18:28:44 2014 +0100

    Added ion class, derived from element.

commit 9b68fc02f36ed091c9bb88104aedd4c88c66f0dd
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 5 23:12:01 2014 +0100

    FitParticleChargesAction now averages over all fitted partial charges.
    
    - i.e. we iterate over all fragments and not just fit the first.

commit 550f2a98ea5244ef1fc747f6debbc4635e941f7c
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 5 22:36:44 2014 +0100

    Enhanced error messages in FitParticleChargesAction.

commit e1fe7e9e5ab6e5acab3403d31d4139a02a1c1754
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Feb 27 21:15:41 2014 +0100

    FunctionModel now uses list_of_arguments to split sequence of subsets of distances.
    
    - this fixes ambiguities with the set of distances:
      Imagine the distances within a water molecule as OH (A) and HH (B).
      We then may have a sequence of argument_t as AABAAB. And with the current
      implementation of CompoundPotential::splitUpArgumentsByModels() we would
      always choose the latter (and more complex) model. Hence, we make two calls
      to TriplePotential_Angle, instead of calls twice to PairPotential_Harmonic
      for A, one to PairPotential_Harmonic for B, and once to TriplePotential_Angle
      for AAB.
    - now, we new list looks like A,A,B,AAB where each tuple of distances can be
      uniquely associated with a specific potential.
    - changed signatures of EmpiricalPotential::operator(), ::derivative(),
      ::parameter_derivative(). This involved changing all of the current specific
      potentials and CompoundPotential.
    - TrainingData must discern between the InputVector_t (just all distances) and
      the FilteredInputVector_t (tuples of subsets of distances).
    - FunctionApproximation now has list_of_arguments_t as parameter to evaluate()
      and evaluate_derivative().
    - DOCU: docu change in TrainingData.

commit 16227a32089e461901d97290d3e2fb626919cf26
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Feb 27 22:44:28 2014 +0100

    Removed FunctionModel::getSpecificExtractor() that is not needed anymore.
    
    - it was only used in FitPotentialAction generating WorstFragmentMap.
    - strangely required to change the order of some libraries
      (libMolecuilderFragmentation_Summation needed further down).

commit f4496dfa7f4fdd324a537113b0d2419c2bc7496f
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Feb 27 22:26:39 2014 +0100

    Extracted associating each configuration with its L2 error into TrainingData.

commit 4e009d7565cb91ce80fa628407fbf1936e23d12c
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Feb 27 18:46:49 2014 +0100

    Extracted function from PotentialFitPotentialAction::performCall().
    
    - new function getNumbersFromElements().
    - also added warning when take-best-of and set-threshold have both been used.

commit 1ba8a154f0c3a28438bcfafdbb90182004c65f55
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Feb 27 20:07:56 2014 +0100

    DOCU: Extended documentation on FunctionApproximation and potential fitting.

commit 26b4d62081a948abd7e73ffa88b6aec3eb1e5234
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 15:56:27 2014 +0200

    All Actions now give correct failure status via STATUS() macro.

commit 0b6b770c3a01e40e913e85102527423a7acc09e0
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 15:55:01 2014 +0200

    ActionQueue gives caught failure of Action and success via pushStatus().

commit 378f2d5ba8914489acde58f6de2d54c2e0ae84ba
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 13:02:54 2014 +0200

    Updated all UI's StatusIndicator classes to use ActionStatusList.
    
    - CommandLineStatusIndicator and TextStatusIndicator just print the message.
    - QtStatusBar has a QTimer that updates the status message in second
      intervals.

commit 26b4eb453c6d8c6ccdb34e5b8a56f055e76a561b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 11:17:06 2014 +0200

    Added observable ActionStatusList to ActionQueue.
    
    - this allows to fetch Status messages from Actions at a central place.
    - Action::pushStatus() as befriended proxy to ActionQueue::pushStatus() added.
    - equipped ActionStatusList with a thread lock to protect access.

commit 3ded2b779a607bf609e8dbfd11734a0b924f6597
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 19 14:28:15 2014 +0200

    FIX: TxMenu and CommandLineWindow lacked waitQueue() in the wait-for-key loop.
    
    - this has occured due to queueAction() introduction.
    - otherwise the UI is destroyed before even the first Action has started.

commit 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jun 25 00:16:55 2014 +0200

    TESTFIX: Reduced size of loaded file for regression test InvertMolecules to speed up.

commit 89604a46c1db5a85643b922ce06b5f4b5f0c5345
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jun 25 00:14:38 2014 +0200

    TESTFIX: Changed size of loaded file for unselection AllMolecules regression test.

commit f678fc41737d988593634f12c8a2a6dbb76c282f
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jun 25 00:06:02 2014 +0200

    TESTFIX: Reduced box size in FillRegularGrid to speed up regression test.

commit e4157b9b9699796a9b05157d81e33042b7670e3b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jun 25 00:02:45 2014 +0200

    TESTFIX: Reduced box size in DipoleCorrelation-DiscreteAngle regression test to speed up.
    
    - the histogram files have not yet been changed.

commit 6d3cb81a37b7c7089163a6bbf61f4c8e6874cc81
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jun 24 23:57:37 2014 +0200

    TESTFIX: reduced dbond file size in regression test Molecules/BondFile.

commit 2cc1cbe98dd0605266ded20ff583bfaf6b64fb77
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jun 24 23:29:38 2014 +0200

    TESTFIX: FillSphericalSurface regression now with just 20 instead of 200 fill points.

commit 1dbbebbd0643e4b6a024acbe95232cacda8a7a10
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jun 24 23:41:19 2014 +0200

    TESTFIX: reduced required threshold for fit-potential regression tests to speed up.

commit 0932c2cf081d696ef9cc91e7a5183c13064994e0
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jun 26 09:41:59 2014 +0200

    FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype.
    
    - this caused all engines to always start with default seed of 1, irrespective
      of the set parameter. The engine is always cloned from prototypes in the
      factory that can be manipulated to change their parameters. Hence, clone
      needs to set the seed (the engine's only parameter).
    - EmpiricalPotentials now use RandomNumberGenerator to obtain random starting
      values.
    - TESTFIX: fit-potential regression tests now use fixed seed in order to always
      take the same amount of time (some test runs in debug mode take very long
      because of ill-chosen random values).

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