September 2014 - Molecuilder-devel

[SCM] MoleCuilder branch ThreadFixes deleted. v1.4.7-17-g38074bf
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, ThreadFixes has been deleted was 38074bf6c963bbf4bc326b7725ba73b8eccd79f4 ----------------------------------------------------------------------- 38074bf6c963bbf4bc326b7725ba73b8eccd79f4 THREADFIX: Fixed ActionQueue with respect to mutex and threads. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch MemFixes created. v1.4.7-17-g5524ae9
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, MemFixes has been created at 5524ae96797a4fa7244c906512ec2bde76c952b3 (commit) - Log ----------------------------------------------------------------- commit 5524ae96797a4fa7244c906512ec2bde76c952b3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 29 11:43:10 2014 +0200 DOCU: Update on test policy with respect to now working valgrind tests. commit 8d4eaa3c9914c99397ccf2583e276838c176a082 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 30 15:25:53 2014 +0200 MEMFIX: ElementDbAction would loose memory when parsing command-line arguments failed. - UndoState was allocated too early. commit 11d433d190a134a3015b4de85d3738c20a307688 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 29 11:44:20 2014 +0200 MEMFIX: ActionQueue was not stopped() when argument parsing failed. - this just caused an exception and the ActionQueue thread would be aborted uncleanly. This is only affected --enable-action-thread. - CommandLineParser calls ActionQueue::stop() on catching exception. - CommandLineParser also rethrows std::exception when parsing of command-line arguments went wrong (not faulty but completely missing values). - ActionQueue uses exitflag of 134 on std::exception. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch MemFixes deleted. v1.4.7-16-gb4d77c0
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, MemFixes has been deleted was b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 ----------------------------------------------------------------------- b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 DOCU: Update on test policy with respect to now working valgrind tests. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch MemFixes created. v1.4.7-16-gb4d77c0
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, MemFixes has been created at b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Cleanup_old_code created. v1.4.7-13-g5a9f4c1
by git＠ins.uni-bonn.de 10 Sep '14

10 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Cleanup_old_code has been created at 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b (commit) - Log ----------------------------------------------------------------- commit 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 20:27:04 2014 +0200 Removed lots of commented-out code from GLWorldView. commit 2b7375290eb8729da103864ee7aab10467ed3346 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 18:50:10 2014 +0200 Removed PrepareClustersInWater(). commit aa55d00dbcc8c34ecf6c22c2d29232d84d0cc262 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 5 20:31:09 2014 +0200 Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction. - copied code from PrepareClustersInWater() and FillRegularGridAction as a start, not working yet. - TESTFIX: Removed -u from regression tests InvalidCommands as new SuspendInMoleculeAction no longer has any values without default values. commit 2528d8462c54c9cdfb2d41b92bd6e34d9fd0c364 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:57:23 2014 +0200 Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions. - these are no longer needed as Actions have been removed. commit 16c7dd3fc6c66022b4b13c912de169a1f812196c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:54:30 2014 +0200 Removed FillVoidWithMolecule and FillWithMolecule actions. - these can be replaced by FillRegularGrid/FillVolume and FillSurface. - TESTFIX: DipoleCorrelation used fill-void, replaced by fill-regular-grid. commit df9f200764a5636d8eb51224f34c27dbd7463b9a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 21:11:14 2014 +0200 Refactored FillSurfaceAction to also use FillerPreparators. - added ShapeSurfaceFillerPreparator for preparing the filler. - added new SurfaceRandomInserter for randomly translating filled-in molecule on shape's surface (no rotational randomness as RandomInserter cannot be forced to the alignment axis). - TESTFIX: renamed Filling regression folder SphericalSurface -> FillSurface. - TESTS: added FillSurface filling regression tests for every present shape, we let everywhere and nowhere fail hard in performCall(), as this works also with disable-debug. commit 6801f4f3b7ed127fa9a9c8afe64f82d34df963d2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 20:00:26 2014 +0200 Added FillVolumeAction for filling a Shape's volume. - added ShapeFillerPreparator for preparing the volume filler. - FIX: MeshAdaptor should include Mesh.hpp. - added regression tests for FillVolume for all present shapes. - all but cylinder fail because of missing implementation, are marked as XFAIL for the moment, except everywhere and nowhere of FillVolume which say they fail explicitly. (this is not an implementation problem, for these shapes filling makes no sense.) We explicitly check for the currently failing shape types and let the Action fail (cause this works also in disable-debug). commit 36f45c7566bcbd1eab7647b44689588ab0fb839c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 4 17:30:59 2014 +0200 FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/. commit cae61447a8c102b09ec82b970c3991c54f311fb5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 2 17:06:31 2014 +0200 Extracted filler preparing functionality from FillRegularGridAction. - initialization functions placed into BaseFillerPreparator and derived BoxFillerPreparator. - slimmed down FillRegularGridAction. - DOCU: Extended documentation on new FillerPreparators. commit a090e3bbbb29271069f6efbe5ae41f0b9d0dcd57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 14:46:54 2014 +0200 FIX: FillRegularGridAction requires filler molecule at origin. - FillRegularGridAction uses CenterEdge as does FillRegularSurface. - TESTFIX: coordinates shifted by z=0.504 because filler water molecule was not centered at origin before (and not fully inside positive octant either). commit 833b155e089160225200039831a7742be7bb1a16 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:54:02 2014 +0200 FIX: Changes to function signatures in molecule_geometry. - no more returning allocated pointer (Vector *) - no more Pointers as parameters. - removed functions that are only convenience and have nothing to do with the molecule. - changes elsewhere due to signature changes. commit 2d701e7056fe4b1af51c7f20e51cc77ee82ff91b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:36:11 2014 +0200 FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector(). commit 40bb9e2215e41bb1d3b215cb9b5ae55b04153352 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 12:10:53 2014 +0200 FIX: molecule::Translate() uses AtomSet directly. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Cleanup_old_code deleted. v1.4.7-13-g9d37d49
by git＠ins.uni-bonn.de 10 Sep '14

10 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Cleanup_old_code has been deleted was 9d37d49fb97beb7b4a04dad48e185202bd075fc9 ----------------------------------------------------------------------- 9d37d49fb97beb7b4a04dad48e185202bd075fc9 Removed lots of commented-out code from GLWorldView. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Cleanup_old_code created. v1.4.7-13-g9d37d49
by git＠ins.uni-bonn.de 10 Sep '14

10 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Cleanup_old_code has been created at 9d37d49fb97beb7b4a04dad48e185202bd075fc9 (commit) - Log ----------------------------------------------------------------- commit 9d37d49fb97beb7b4a04dad48e185202bd075fc9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 20:27:04 2014 +0200 Removed lots of commented-out code from GLWorldView. commit 6e12f56f8b65e5db654b2770b1225cd26839ab8f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 18:50:10 2014 +0200 Removed PrepareClustersInWater(). commit a0da4fd1c122d8bc14eb9fb84be8446707bdea34 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 5 20:31:09 2014 +0200 Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction. - copied code from PrepareClustersInWater() and FillRegularGridAction as a start, not working yet. - TESTFIX: Removed -u from regression tests InvalidCommands as new SuspendInMoleculeAction no longer has any values without default values. commit 54387c654375bc1ac220eb5077a0cd18314705b2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:57:23 2014 +0200 Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions. - these are no longer needed as Actions have been removed. commit cf2271f0f76b3b3923aa0fd41ab5b90569628694 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:54:30 2014 +0200 Removed FillVoidWithMolecule and FillWithMolecule actions. - these can be replaced by FillRegularGrid/FillVolume and FillSurface. - TESTFIX: DipoleCorrelation used fill-void, replaced by fill-regular-grid. commit 1c1a2d3a425370045c2e51ad34a8e120a5eecd1b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 21:11:14 2014 +0200 Refactored FillSurfaceAction to also use FillerPreparators. - added ShapeSurfaceFillerPreparator for preparing the filler. - added new SurfaceRandomInserter for randomly translating filled-in molecule on shape's surface (no rotational randomness as RandomInserter cannot be forced to the alignment axis). - TESTFIX: renamed Filling regression folder SphericalSurface -> FillSurface. - TESTS: added FillSurface filling regression tests for every present shape. commit d1ea5d6f228dd21f95414ad1fe8c5c9af52e361c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 20:00:26 2014 +0200 Added FillVolumeAction for filling a Shape's volume. - added ShapeFillerPreparator for preparing the volume filler. - FIX: MeshAdaptor should include Mesh.hpp. - added regression tests for FillVolume for all present shapes. - all but cylinder fail because of missing implementation, are marked as XFAIL for the moment, except everywhere and nowhere of FillVolume which say they fail explicitly. (this is not an implementation problem, for these shapes filling makes no sense.) commit 36f45c7566bcbd1eab7647b44689588ab0fb839c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 4 17:30:59 2014 +0200 FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/. commit cae61447a8c102b09ec82b970c3991c54f311fb5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 2 17:06:31 2014 +0200 Extracted filler preparing functionality from FillRegularGridAction. - initialization functions placed into BaseFillerPreparator and derived BoxFillerPreparator. - slimmed down FillRegularGridAction. - DOCU: Extended documentation on new FillerPreparators. commit a090e3bbbb29271069f6efbe5ae41f0b9d0dcd57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 14:46:54 2014 +0200 FIX: FillRegularGridAction requires filler molecule at origin. - FillRegularGridAction uses CenterEdge as does FillRegularSurface. - TESTFIX: coordinates shifted by z=0.504 because filler water molecule was not centered at origin before (and not fully inside positive octant either). commit 833b155e089160225200039831a7742be7bb1a16 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 1 17:54:02 2014 +0200 FIX: Changes to function signatures in molecule_geometry. - no more returning allocated pointer (Vector *) - no more Pointers as parameters. - removed functions that are only convenience and have nothing to do with the molecule. - changes elsewhere due to signature changes. commit 2d701e7056fe4b1af51c7f20e51cc77ee82ff91b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:36:11 2014 +0200 FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector(). commit 40bb9e2215e41bb1d3b215cb9b5ae55b04153352 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 12:10:53 2014 +0200 FIX: molecule::Translate() uses AtomSet directly. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_Fixes created. v1.4.7-13-g0741f4d
by git＠ins.uni-bonn.de 10 Sep '14

10 Sep '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_Fixes has been created at 0741f4d175456b6ffd128ea624a7a20273533b6c (commit) - Log ----------------------------------------------------------------- commit 0741f4d175456b6ffd128ea624a7a20273533b6c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:38:24 2014 +0200 FIX: new item is just to some default values in QtMoleculeList, filled later anway. commit 86c0133532eb8e9d465ff746bcea0aecae8de1e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 8 23:20:12 2014 +0200 QMenu extended for tooltips, but not working yet. - somehow no QHelpEvents are triggered that would cause display of tooltips for QActions as menuitems. commit 1631101c583989217756e201430f3b6f4e8c6e90 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 8 23:15:11 2014 +0200 In QTUI Dialog window now has a meaningful title. - Dialog cstor now requires a title. - UIFactory::makeDialog() needs to be provided with this title. - Menu::populateActions() uses addAction with twice just the token. - Action::createDialog() provides title from its Traits. commit 152e5c638ad572ebf3bef92b902419d5c7ca5504 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 8 21:33:39 2014 +0200 FIX: Querys now have own description as tooltip, not Action's. commit 0fe13544341ccb9e5f81e1da9701139c95742ec6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 20:22:02 2014 +0200 In QTUI empty dialogs no longer have to be confirmed. - this was already present but hasQueries() did always end up true as it also counted all EmptyQuery. - TESTFIX: Removed grep of description for regression test WarrantyAction as EmptyQuery is no longer handle()d. commit 95cfacdff536aaf7fb3937c5b0656feb10da531c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 20:21:38 2014 +0200 Added FileSuffixValidator to all Actions where missing but appropriate. - also clean up some unnecessary includes. commit dae15830575cff1e67648579393887f666f06f35 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 7 19:44:06 2014 +0200 FileQtQuery retrieves valid suffixes from validators. - added getFlatListFromHierarchyOfValidators() that steps through the hierarchy of validators and generates a flat vector with all matching types. - Or_Validatorm Not_Validator::getA(), ::getB() added. (present for And_... already). - FileSuffixValidator::getSuffix(), ParserFileValidator::getSuffixes() added. commit ce4126dccd4487e1bb02f6582b75fc09fdf73408 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 30 17:16:38 2014 +0200 FIX: Added update mechanism to GLWorldScene when WorldTime changes. - bonds were not updated when WorldTime changed, atoms only change because each was subscribed to WorldTime. - Now, just GLWorldView is subscribed to WorldTime::TimeChanged, emitting TimeChanged and activating GLWorldScene::updated() signal. - GLWorldScene has access to private reset..() functions of GLMoleculeObject_atom and GLMoleculeObject_bond. - added GLWorldScene::update(), enhancing (also modified) ::init() function. It does not use molecules anymore, but directly the World's atoms. These are iterated over, checked whether already present and updated or added. Similarly with bonds. update() is activated on signal updated(). commit 8592c990d61a1b6a469219b569e217550fa13b6b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 09:40:55 2014 +0200 FIX: GLMoleculeObject_shape might use empty point list for tesselation. - this causes segfault if a "nowhere" shape was created. Signal ShapedAdded causes tesselation of this shape and storing the mesh but the tesselation routine does not work if less than three points are given. - added check to Tesselation::operator() for at least three points. - MEMFIX: Tesselation object never deleted. commit 42ffb581447753ba079ae9d6bec125084a90b079 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 15:27:55 2014 +0200 FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps before. - we use WorldTime's current time step only now. commit dc798d46df2d2028d2fe5f96f29aac56230c6797 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 13:19:34 2014 +0200 FIX: Removed some misleading output of CorrectBondDegreeAction. commit 388dddec6195c09047052f2aef28f5ad6c39ce20 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 02:00:21 2014 +0200 World::setTime() now only copies bond graph, does not re-create it. - this gives us more flexibility when doing MD/Opt because we may decice for ourselves whether we want to remain (within the fragmentation scheme) in the structure governed by the same bond graph ... or seek even for a different structure (although that's not so easy due to charge neutrality). commit 553c546a9212dd6cedc74651403cde0e33e0c47f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 15 01:59:33 2014 +0200 Added option keep-bondgraph to MolecularDynamicsAction and StructuralOptimizationAction. - this removes the actions to re-create the bond graph per MD/OPT step from the sequence of actions. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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