- Molecuilder-devel

[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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[SCM] MoleCuilder branch ThreadFixes created. v1.4.7-17-g38074bf
by git＠ins.uni-bonn.de 29 Aug '14

29 Aug '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 created at 38074bf6c963bbf4bc326b7725ba73b8eccd79f4 (commit) - Log ----------------------------------------------------------------- commit 38074bf6c963bbf4bc326b7725ba73b8eccd79f4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 29 11:46:02 2014 +0200 THREADFIX: Fixed ActionQueue with respect to mutex and threads. - run_thread is now last member variable, hence started after all other variables are initialized. - separated accesses to queues and to run_thread_isIdle flag. Also renamed its mutex for easier association with it. commit b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 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 f825283d8fd2fad85e199cb3a32f98980f29ceb5 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. commit 052c10a6e270eaffbd69149bcd5c6bbaadab9752 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 28 10:48:24 2014 +0200 MEMFIX: Tesselation::operator() did not free linkedlist. commit 7ee21dd85ecc96fef7cf8272cb7e5755f57d1e65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 28 09:24:18 2014 +0200 MEMFIX: Many analysis_correlation function allocated return map twice. - outmap was the culprit, probably when empty (but allocated) was returned when no atoms are allocated, two new's appeared. commit 6b3e5eabbfb866e42ce576818aeadd95719a1ac6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 27 22:10:38 2014 +0200 MEMFIX: PartialNucleiChargeFitter lost memory. - operator() and constructMatrix() use heap memory to avoid always allocating memory for charge grids but did not always free'd the memory or allocated onto pointer with allocated memory. commit 96c7d2359255253121a4625cd3a9933834b44391 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 27 21:59:01 2014 +0200 MEMFIX: PotentialRegistry's dstor forgot cleanup(). - also we purge static potential factory and registry instances in cleanup. - dstor of SerializablePotential was not virtual. commit 185e6f9e58b5418b9136e86a172d2cfb6627a2d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 23:35:29 2014 +0200 MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate. commit b0b2d2c9d316c1a252e1177412399808f116a2d9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 23:07:40 2014 +0200 MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory. - serialization always works on fully instantiated RealSpaceMatrix, hence neither createViews nor re-creating content ptr instance is necessary. - MatrixContent newly allocated content but for RealSpaceMatrix it was still present as matrix dimensions have been set. Now it is freed when free_content_on_exit is true. - similar fixes to VectorContent. commit 7f1a1a7e897d84470656f52ade76a74fef5da063 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 17:28:34 2014 +0200 MEMFIX: ActionQueue would loose memory when action failed. - we cleared the queues and forget to delete contained Action instances. commit 3d70e30645becb764684201ccfc596c838a74c3a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 12:48:28 2014 +0200 MEMFIX: Mismatched delete in PdbParser::Save(). commit 09f615ff03d6c900818e07a53ee2c183bbf3bf47 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 10:50:02 2014 +0200 MEMFIX: World's homologies not deleted. - main() now uses int status for storing saveAll() flag. commit 62c378a69a5535affe3a0039648a1cea69f07da3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 19:21:49 2014 +0200 FIX: Made checks in random number engine and distribution regression tests more robust. - with valgrind we see the command line with "lagged_fibbonacci.." and "uniform_smallint", too, resulting in more hits for grep. commit 5200294b51370a326ff7b6b894366ab63dd343f1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 19:12:05 2014 +0200 FIX: regression test add atoms outside boundary had given boundary conditions wrong in arguments. - TESTFIX: test is now marked XFAIL, before it failed because of wrong conditions. commit 25aa5ad00fe2dc8d803d1602be52c8f6e3bc16c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 20:56:38 2014 +0200 FIX: Box::setM() did not use const ref as argument. commit 707a2b0d381b69df9ebf6bc57ce9ffe12636248e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 27 21:58:28 2014 +0200 FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access key_end(). commit 8946a0e70603b6a8930297686e4c9938010b2d9d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 27 20:52:44 2014 +0200 FIX: Process' dstor would always stop() even if not start()ed. - this caused assert failure from Observer cause it had not been signed, but was suddenly signed off. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch stable updated. v1.4.7
by git＠ins.uni-bonn.de 24 Aug '14

24 Aug '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, stable has been updated via 29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit) via a91710c7feb7eb12c5521615d53366bd9ac68106 (commit) via 0c72e21652645146e2cbb1f6242fc50afb6067c9 (commit) via 07ecc54679bad772b20fd501b5a70c8bbc1d1a43 (commit) via 748fc7c0d1024191307cd0382559ca5a2f64eacb (commit) via 4c9101d28554cfb93912863dd0480b0c485d2c41 (commit) via fc3aff49ca5c026f908b539cde856e13e75c55ba (commit) via ee4f2da6990041aedcb8b339896459f5b4e9b05b (commit) via 2cb77c2ea89ddde7cf8251e67ae8abf0a42baa4c (commit) via 83cc3e89cbdfa13ae454644478d1b5f9ab0a75cb (commit) via 4d6d6a41aa48054402d4325bc285f9594aa74c69 (commit) via d93b4b3101d0910efc6b9f530a4cf26005c926dc (commit) via e9e86f755ec91600316ac1b266d68b3244700842 (commit) via 09806af7c430c059fd0504fee221f5f8ec4ef155 (commit) via fe77dfcd3989b18314077cda402ac1c63695674a (commit) via 0c74aa19d73454589c9ebbe8d61ee3397bca338f (commit) via 3b35e715f8f1469cc9d18d99c6e43aa47954d613 (commit) via 3a33e3e227123ea24a3af9bdd665a5a2c9a43f65 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----------------------------------------------------------------- ----------------------------------------------------------------------- Summary of changes: LinearAlgebra/src/LinearAlgebra/Makefile.am | 7 +- LinearAlgebra/src/LinearAlgebra/Plane.cpp | 7 +- LinearAlgebra/src/LinearAlgebra/Vector.cpp | 35 ++- LinearAlgebra/src/LinearAlgebra/Vector.hpp | 9 +- LinearAlgebra/src/LinearAlgebra/VectorContent.cpp | 3 +- LinearAlgebra/src/unittests/Makefile.am | 7 +- Makefile.am | 8 +- configure.ac | 12 +- m4/boost.m4 | 438 +++++++++++++----- m4/qwt.m4 | 2 +- src/Actions/ActionQueue.cpp | 2 +- src/Actions/ActionRegistry.cpp | 24 +- src/Actions/Action_impl_python.hpp | 24 +- src/Actions/AtomAction/RemoveAction.def | 3 - .../FragmentationAction/FragmentationAction.cpp | 112 +++++- .../FragmentationAutomationAction.cpp | 14 +- .../StoreSaturatedFragmentAction.cpp | 6 +- .../StructuralOptimizationAction.cpp | 117 +++++ .../StructuralOptimizationAction.def | 36 ++ .../StructuralOptimizationAction.hpp | 22 + src/Actions/GlobalListOfActions.hpp | 183 ++++---- .../GraphAction/CorrectBondDegreeAction.cpp | 164 +++++++ .../GraphAction/CorrectBondDegreeAction.def | 37 ++ .../GraphAction/CorrectBondDegreeAction.hpp | 22 + src/Actions/Makefile.am | 15 +- .../MoleculeAction/ForceAnnealingAction.cpp | 166 +++++++ .../MoleculeAction/ForceAnnealingAction.def | 40 ++ .../MoleculeAction/ForceAnnealingAction.hpp | 22 + .../MoleculeAction/VerletIntegrationAction.cpp | 97 ++++- .../MoleculeAction/VerletIntegrationAction.def | 8 +- src/Actions/UndoRedoHelpers.cpp | 72 +++- src/Actions/UndoRedoHelpers.hpp | 60 +++- src/Actions/unittests/Makefile.am | 13 +- src/Analysis/unittests/Makefile.am | 11 +- src/Atom/AtomicInfo.cpp | 3 + src/Atom/AtomicInfo.hpp | 1 + src/Atom/TesselPoint.cpp | 6 + src/Atom/TesselPoint.hpp | 8 + src/Atom/atom.cpp | 9 + src/Atom/atom.hpp | 8 + src/Atom/atom_atominfo.cpp | 12 + src/Atom/atom_atominfo.hpp | 17 + src/Atom/atom_bondedparticleinfo.cpp | 6 + src/Atom/atom_bondedparticleinfo.hpp | 8 +- src/Atom/unittests/Makefile.am | 6 +- src/Descriptors/unittests/Makefile.am | 6 +- src/Dynamics/AtomicForceManipulator.hpp | 144 ++++++ src/Dynamics/ForceAnnealing.hpp | 159 +++++++ src/Dynamics/MinimiseConstrainedPotential.cpp | 2 +- src/Dynamics/MinimiseConstrainedPotential.hpp | 2 +- src/Dynamics/VerletForceIntegration.hpp | 151 +----- src/Element/elements_db.cpp | 24 +- src/Element/unittests/Makefile.am | 9 +- src/Filling/unittests/Makefile.am | 20 +- .../Automation/MPQCCommandFragmentController.cpp | 9 +- .../Automation/MPQCCommandFragmentController.hpp | 11 + .../Automation/MPQCFragmentController.cpp | 5 +- src/Fragmentation/Automation/Makefile.am | 2 +- ...gmentController_ReceiveResultContainer_impl.hpp | 8 +- src/Fragmentation/Exporters/ExportGraph.cpp | 261 ++++++----- src/Fragmentation/Exporters/ExportGraph.hpp | 14 +- .../Exporters/ExportGraph_ToFiles.cpp | 7 +- .../Exporters/ExportGraph_ToFiles.hpp | 3 +- src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp | 5 +- src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp | 5 +- src/Fragmentation/Exporters/SaturatedBond.cpp | 132 ++++++ src/Fragmentation/Exporters/SaturatedBond.hpp | 89 ++++ src/Fragmentation/Exporters/SaturatedFragment.cpp | 258 +++++++++-- src/Fragmentation/Exporters/SaturatedFragment.hpp | 46 ++- .../Exporters/SaturationDistanceMaximizer.cpp | 302 ++++++++++++ .../Exporters/SaturationDistanceMaximizer.hpp | 147 ++++++ src/Fragmentation/Exporters/unittests/Makefile.am | 24 +- .../unittests/SaturatedFragmentUnitTest.cpp | 9 +- .../SaturationDistanceMaximizerUnitTest.cpp | 137 ++++++ .../SaturationDistanceMaximizerUnitTest.hpp | 43 ++ .../unittests/stubs/SaturatedBondStub.cpp | 73 +++ src/Fragmentation/Fragmentation.cpp | 2 +- src/Fragmentation/Homology/unittests/Makefile.am | 10 +- src/Fragmentation/Interfragmenter.cpp | 12 +- src/Fragmentation/Makefile.am | 4 + src/Fragmentation/Summation/Containers/Makefile.am | 2 +- .../Summation/Containers/unittests/Makefile.am | 6 +- .../Summation/Converter/DataConverter.hpp | 8 + src/Fragmentation/Summation/Converter/Makefile.am | 2 +- src/Fragmentation/Summation/Makefile.am | 2 +- src/Fragmentation/Summation/SetValues/Makefile.am | 2 +- .../Summation/SetValues/unittests/Makefile.am | 14 +- src/Fragmentation/Summation/unittests/Makefile.am | 16 +- src/Fragmentation/unittests/Makefile.am | 6 +- src/FunctionApproximation/unittests/Makefile.am | 6 +- src/Graph/BreadthFirstSearchAdd.cpp | 190 -------- src/Graph/BreadthFirstSearchAdd.hpp | 82 ---- src/Graph/CyclicStructureAnalysis.cpp | 253 ++++++----- src/Graph/CyclicStructureAnalysis.hpp | 6 +- src/Graph/Makefile.am | 2 - src/Graph/unittests/Makefile.am | 6 +- src/Jobs/Makefile.am | 2 +- src/Jobs/unittests/Makefile.am | 6 +- src/LinkedCell/unittests/Makefile.am | 24 +- src/Makefile.am | 120 ++--- src/Parameters/Makefile.am | 1 + src/Parameters/unittests/Makefile.am | 12 +- src/Parser/Parameters/unittests/Makefile.am | 34 +- src/Parser/PdbParser.cpp | 9 +- src/Parser/unittests/Makefile.am | 18 +- src/Parser/unittests/ParserPdbUnitTest.cpp | 14 + src/Potentials/Specifics/unittests/Makefile.am | 18 +- src/Potentials/unittests/Makefile.am | 9 +- src/RandomNumbers/Makefile.am | 8 +- src/RandomNumbers/unittests/Makefile.am | 12 +- src/Shapes/Makefile.am | 3 + src/Shapes/unittests/Makefile.am | 49 +-- src/Tesselation/Makefile.am | 74 +++ src/Tesselation/unittests/Makefile.am | 8 +- src/UIElements/CommandLineUI/unittests/Makefile.am | 4 +- src/UIElements/Makefile.am | 4 +- src/UIElements/Menu/unittests/Makefile.am | 10 +- src/UIElements/Views/Qt4/Plotting/Makefile.am | 2 +- src/UIElements/Views/Qt4/QDebugStream.hpp | 7 +- src/UIElements/Views/Qt4/QtTimeLine.cpp | 16 +- src/builder_init.cpp | 27 +- src/documentation/install.dox | 11 +- src/molecule.cpp | 494 ++++++++++---------- src/molecule.hpp | 2 +- src/unittests/Makefile.am | 91 +++- .../testsuite-calculations-1_2-dimethoxyethane.at | 2 +- .../testsuite-calculations-1_2-dimethylbenzene.at | 2 +- ...testsuite-calculations-2-methylcyclohexanone.at | 2 +- ...testsuite-calculations-N_N-dimethylacetamide.at | 2 +- .../testsuite-calculations-anthracene.at | 3 +- .../Calculations/testsuite-calculations-benzene.at | 2 +- .../testsuite-calculations-cholesterol.at | 2 +- .../testsuite-calculations-coronene.at | 3 +- .../testsuite-calculations-cycloheptane.at | 2 +- ...estsuite-calculations-dimethyl_bromomalonate.at | 2 +- .../Calculations/testsuite-calculations-glucose.at | 2 +- .../Calculations/testsuite-calculations-heptan.at | 2 +- .../testsuite-calculations-isoleucine.at | 2 +- .../testsuite-calculations-naphthalene.at | 3 +- .../testsuite-calculations-neohexane.at | 2 +- .../testsuite-calculations-phenanthrene.at | 3 +- .../Calculations/testsuite-calculations-proline.at | 2 +- .../testsuite-calculations-putrescine.at | 2 +- .../testsuite-calculations-tartaric_acid.at | 2 +- tests/CodeChecks/Makefile.am | 3 +- .../CodeChecks/testsuite-testsuite-in-makefile.at | 53 +++ tests/CodeChecks/testsuite.at | 2 + .../testsuite-fragmenting-anthracene-order1.at | 2 +- .../testsuite-fragmenting-anthracene-order2.at | 2 +- .../testsuite-fragmenting-anthracene-order3.at | 2 +- .../testsuite-fragmenting-anthracene-order4.at | 2 +- .../testsuite-fragmenting-anthracene-order5.at | 2 +- .../testsuite-fragmenting-anthracene-order6.at | 2 +- .../testsuite-fragmenting-coronene-order1.at | 2 +- .../testsuite-fragmenting-coronene-order2.at | 2 +- .../testsuite-fragmenting-coronene-order3.at | 2 +- .../testsuite-fragmenting-coronene-order4.at | 2 +- .../testsuite-fragmenting-coronene-order5.at | 2 +- .../testsuite-fragmenting-coronene-order6.at | 2 +- .../testsuite-fragmenting-naphthalene-order1.at | 2 +- .../testsuite-fragmenting-naphthalene-order2.at | 2 +- .../testsuite-fragmenting-naphthalene-order3.at | 2 +- .../testsuite-fragmenting-naphthalene-order4.at | 2 +- .../testsuite-fragmenting-naphthalene-order5.at | 2 +- .../testsuite-fragmenting-naphthalene-order6.at | 2 +- .../testsuite-fragmenting-phenanthrene-order1.at | 2 +- .../testsuite-fragmenting-phenanthrene-order2.at | 2 +- .../testsuite-fragmenting-phenanthrene-order3.at | 2 +- .../testsuite-fragmenting-phenanthrene-order4.at | 2 +- .../testsuite-fragmenting-phenanthrene-order5.at | 2 +- .../testsuite-fragmenting-phenanthrene-order6.at | 2 +- tests/Fragmentations/testsuite.at | 2 +- tests/JobMarket/Makefile.am | 4 +- tests/Makefile.am | 4 +- tests/regression/Makefile.am | 36 +- .../Molecules/ForceAnnealing/post/test-undo.conf | 83 ++++ .../Molecules/ForceAnnealing/post/test.conf | 83 ++++ .../pre/test.conf | 0 .../pre/test.forces | 0 .../testsuite-molecules-force-annealing.at | 56 +++ .../VerletIntegration/post/test-undo.conf | 83 ++++ .../testsuite-molecules-verlet-integration.at | 8 +- tests/regression/Molecules/testsuite-molecules.at | 3 + 183 files changed, 4592 insertions(+), 1627 deletions(-) create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.cpp create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.def create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.hpp create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.cpp create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.def create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.hpp create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.cpp create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.def create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.hpp create mode 100644 src/Dynamics/AtomicForceManipulator.hpp create mode 100644 src/Dynamics/ForceAnnealing.hpp create mode 100644 src/Fragmentation/Exporters/SaturatedBond.cpp create mode 100644 src/Fragmentation/Exporters/SaturatedBond.hpp create mode 100644 src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp create mode 100644 src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp create mode 100644 src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp create mode 100644 src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp create mode 100644 src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp delete mode 100644 src/Graph/BreadthFirstSearchAdd.cpp delete mode 100644 src/Graph/BreadthFirstSearchAdd.hpp create mode 100644 src/Tesselation/Makefile.am create mode 100644 tests/CodeChecks/testsuite-testsuite-in-makefile.at create mode 100644 tests/regression/Molecules/ForceAnnealing/post/test-undo.conf create mode 100644 tests/regression/Molecules/ForceAnnealing/post/test.conf copy tests/regression/Molecules/{VerletIntegration => ForceAnnealing}/pre/test.conf (100%) copy tests/regression/Molecules/{VerletIntegration => ForceAnnealing}/pre/test.forces (100%) create mode 100644 tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at create mode 100644 tests/regression/Molecules/VerletIntegration/post/test-undo.conf hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.7 created. v1.4.7
by git＠ins.uni-bonn.de 24 Aug '14

24 Aug '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 annotated tag, v1.4.7 has been created at f64c759050946a7b3803cc35b4665db46d63f8aa (tag) tagging 29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit) replaces v1.4.6 tagged by Frederik Heber on Thu Aug 21 09:00:02 2014 +0200 - Log ----------------------------------------------------------------- Hydrogen saturation should now work with any atoms, not just up valence of 4. Added action for structure optimization. Enabled compilation of molecuilder with Ubuntu 14.04 (gcc48, boost1.55, autoconf 2.6.8, automake 1.11.3). This version contains the following branches: 29b35ef Candidate_v1.4.7 (distcheck fix, versioning) 0c72e21 Fixes_Ubuntu14_04 (enfored automake option subdir-objects, shared libMolecuilder, INCLUDES in Makefile.am deprecated, boost.m4 updated, boost::thread fixes) 2cb77c2 VariousFixes (qDebug output in GUI case, fixes to CyclicStructureAnalysis)) 3a33e3e StructuralOptimization (added ForceAnnealingAction and MakroAction StructureOptimizationAction, undo/redo of VerletIntegrationAction) 343c5aa EnhancingHydrogenSaturation (SaturatedFragment rewrite, added CorrectBondDegreeAction and SaturationDistanceMaximizer) Frederik Heber (50): TESTFIX: Regression test series Calculations would not run in parallel. FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. FIX: VectorContent::Normalize() did not check for zero factor. FIX: Plane's cstor did not check for linear dependence in a numerical stable way. FIX: elements db uses wrong hbondangle for degree 1. Vector::Is...() functions extended for numeric threshold. Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. Refactored SaturatedFragment::saturate() using list of cut bonds. FIX: BondedParticleInfo::BondList is now a typedef. Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. Added new convenience library libMolecuilderTesselation. TESTFIX: extracheck threshold is _relative_ 1e-5. FIX: VectorContent::Normalize() had int, not double. SaturatedFragment can deal with a global saturation position map. Added new Vector::IsParallelTo(). Added SaturatedBond as container for a "dangling bond" and its saturation hydrogens. Added SaturationDistanceMaximizer to determine best alphas for SaturatedBonds. FragmentationAction now compiles global saturation positions information. Added CorrectBondDegreeAction and fixed Calculation tests. Extracted common functions from VerletForceIntegration into AtomicForceManipulator. Sorted GlobalListOfActions. Extended UndoRedoHelpers. Extended VerletIntegrationAction wirth Undo/Redo. Added CodeCheck for ensuring testsuite..at's appear in tests/regression/Makefile.am. Added ForceAnnealingAction. FIX: MolecularDynamicsAction works also without JobMarket. Added MakroAction StructureOptimizationAction. FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount. Giving the maximum components over all force vectors in ForceAnnealing. FIX: PdbParser would write coordinates 4.1000 instead of 5.000. MPQCCommandFragmentController supports FragmentationAutomationAction being a Process. FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver. Fixes due to update to Ubuntu 14.04. FIX: Fixes to Action_impl_python, lacked boost preprocessor includes. FIX: ReceiveResultContainer could not find functions from base class. FIX: Interfragmenter had iter collision. FIX: UnitTestMain placed into convenience libUnitTest. FIX: ActionQueue::run() did not use boost::thread::sleep_for() correctly. QtGUI prints log to console (qDebug) as well. FIX: CyclicStructureAnalysis did not robustly detect all cycles. FIX: Fragmentations tests used -I and not --correct-bonddegree in case of pdb files. Merge branch 'EnhancingHydrogenSaturation' into stable Merge branch 'StructuralOptimization' into stable Merge branch 'VariousFixes' into stable libMolecuilder is now a shared library. FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. DOCU: Updated documentation on Ubuntu 14.04. Merge branch 'Fixes_Ubuntu14_04' into stable Set version to 1.4.7. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.7 created. v1.4.6-50-g29b35ef
by git＠ins.uni-bonn.de 22 Aug '14

22 Aug '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, Candidate_v1.4.7 has been created at 29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit) - Log ----------------------------------------------------------------- commit 29b35efc972c36f104ccae2ad8b50ce095b475e8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 15:23:07 2014 +0200 Set version to 1.4.7. - MoleCuilder library is now 14:0:0. - Codename "Capitalism" (According to a 2011 research article on system theory, 147 companies control the major part of global capitalism) commit a91710c7feb7eb12c5521615d53366bd9ac68106 Merge: 4c9101d 0c72e21 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 21 08:59:33 2014 +0200 Merge branch 'Fixes_Ubuntu14_04' into stable commit 0c72e21652645146e2cbb1f6242fc50afb6067c9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 21 08:59:06 2014 +0200 DOCU: Updated documentation on Ubuntu 14.04. commit 07ecc54679bad772b20fd501b5a70c8bbc1d1a43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 19 15:05:10 2014 +0200 FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. - an assert fails in JobMarket when ids are requested after conneciton to Server was refused and received illegalids are used in jobs and added. - this did not occur so far, as we test only against release JobMarket in version checks. commit 748fc7c0d1024191307cd0382559ca5a2f64eacb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 19 13:17:27 2014 +0200 libMolecuilder is now a shared library. - linking error Vector::IsZero(double) with molecuilder(gui), related to libMolecuilderShapes was the root cause for this change. Again, it was not deducible why this error occured: - probably (me tired of these obfuscated linker errors ...) faulted because libMolecuilder is convenience lib while libMolecuilderUI and ..QtUI are shared and deps did not get passed along properly (by libtool) (e.g. ldd showed libMolecuilderShapes prior to libLinearAlgebra, containing said function Vector::IsZero(double), but I cannot influence this ordering and it should not even matter (dynamic linking).) - some cleanup in builder_init.cpp (no more loading of BondGraph from file named "\n". - TESTFIX: libMolecuilder.so added to all unittests, required for e.g. World::purgeInstance() ... and sometimes added libMolecuilderUI.so because libMolecuilder pulled them in due to static entities ... sigh. - removed all src object files from unittest .._SOURCES. This caused distclean faults "thanks" to new subdir-objects (automake). commit 4c9101d28554cfb93912863dd0480b0c485d2c41 Merge: fc3aff4 2cb77c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 15:10:38 2014 +0200 Merge branch 'VariousFixes' into stable commit fc3aff49ca5c026f908b539cde856e13e75c55ba Merge: ee4f2da 3a33e3e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 15:10:07 2014 +0200 Merge branch 'StructuralOptimization' into stable commit ee4f2da6990041aedcb8b339896459f5b4e9b05b Merge: 2a03b00 343c5aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 15:09:40 2014 +0200 Merge branch 'EnhancingHydrogenSaturation' into stable commit 2cb77c2ea89ddde7cf8251e67ae8abf0a42baa4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:01:24 2014 +0200 FIX: Fragmentations tests used -I and not --correct-bonddegree in case of pdb files. - this bond graph was always recalculated and not taken from the parsed file. commit 83cc3e89cbdfa13ae454644478d1b5f9ab0a75cb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 13:47:12 2014 +0200 FIX: CyclicStructureAnalysis did not robustly detect all cycles. - it depended on the sequence of the back edges. In Coronene most back edges lead to two cycles but at least one back edge is attached to only one cycle. - The change is that we now continue after having found a cycle - regardless of whether it is already present or not. This ensures that we find all cycles present. - finding a cycle sets however the size of the BFS horizon (we just look for the minimal cycles). This prevents the BFS from stepping through the whole graph. - rename CycleBFStoRoot() -> findAllCyclesforBackEdge(), calls RetrieveCycleMembers() on each found cycle (not in operator() anymore). - Modified RetrieveCycleMembers() to check whether cycle is present, using IsCyclic checking as a faster mean. - operator() dropped NumCycles, is redundantly contained in allcycles.size(). commit 4d6d6a41aa48054402d4325bc285f9594aa74c69 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 13:46:03 2014 +0200 QtGUI prints log to console (qDebug) as well. - removed in --disable-debug builds. commit d93b4b3101d0910efc6b9f530a4cf26005c926dc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 18 20:22:07 2014 +0200 FIX: ActionQueue::run() did not use boost::thread::sleep_for() correctly. commit e9e86f755ec91600316ac1b266d68b3244700842 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 23:31:27 2014 +0200 FIX: UnitTestMain placed into convenience libUnitTest. - removed UnitTestMain.cpp from all .._SOURCES (except LinearAlgebra). - this is due to subdir-objects: we cannot use absolute paths anymore. automake tries to place .deps folder in the respective source path. Wrapping it up in a library removes this. commit 09806af7c430c059fd0504fee221f5f8ec4ef155 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 22:54:27 2014 +0200 FIX: Interfragmenter had iter collision. commit fe77dfcd3989b18314077cda402ac1c63695674a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 22:53:55 2014 +0200 FIX: ReceiveResultContainer could not find functions from base class. commit 0c74aa19d73454589c9ebbe8d61ee3397bca338f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 22:53:28 2014 +0200 FIX: Fixes to Action_impl_python, lacked boost preprocessor includes. commit 3b35e715f8f1469cc9d18d99c6e43aa47954d613 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 21:07:34 2014 +0200 Fixes due to update to Ubuntu 14.04. - subdir-objects is default behavior for automake. - INCLUDES is deprecated (in favor of AM_CPPFLAGS), made sure that every .._CPPFLAGS includes AM_CPPFLAGS. - updated boost.m4 (serial 22), re-added missing macros. - qwt.m4 does not use QString in constructor, as it pulls in QtCore dependency. - VectorUnitTest lacked libboost_system dep. commit 3a33e3e227123ea24a3af9bdd665a5a2c9a43f65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 14 11:05:32 2014 +0200 FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver. - publisher is always the atom, not the relay. - that's why the time line did not get updated when a molecule with more than one timestep was loaded. commit 45cdce6c6da7af45f28e4182d6539fe1c678f87a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 13 17:08:14 2014 +0200 MPQCCommandFragmentController supports FragmentationAutomationAction being a Process. - i.e. it also calls an update handler when more results have been received. commit 4e65af7c5036d532974d84f76366a623f2c42571 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 13 15:59:54 2014 +0200 FIX: PdbParser would write coordinates 4.1000 instead of 5.000. - we did round in printCoordinates(), without checking for overflow, resulting in 1000 for 999.9 instead of 999. - extended ParserPdbUnitTest to test these cases. commit 7f833c8983a8e1024fff641289db472c6d79c3c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 11 19:56:03 2014 +0200 Giving the maximum components over all force vectors in ForceAnnealing. commit f149722846dcf0a89078f551cedb518a9bef5686 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 10 14:47:43 2014 +0200 FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount. commit e5f61ba098def1991ab9372e13b7d6740dedddc6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 18:22:46 2014 +0200 Added MakroAction StructureOptimizationAction. - performs similarly as MolecularDynamicsAction only using ForceAnnealing. commit ff3edf390edf783afaf6240fd0ef8e87e4412b91 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 16 17:40:44 2014 +0200 FIX: MolecularDynamicsAction works also without JobMarket. - since FragmentationAutomation works without. commit 1a48d2c8c2b6ea08ac53c8fc5998d19145e4eeb8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:49:32 2014 +0200 Added ForceAnnealingAction. - also added regression test. - performs a single optimization step. - added output-every-step for debugging. commit d5f7b82f4661b07c35988437ed7f4a1719b312b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 12:01:05 2014 +0200 Added CodeCheck for ensuring testsuite..at's appear in tests/regression/Makefile.am. - brought files in tests/regression/Makefile.am in alphabetical order. - FIX: testsuite-potential.at was missing. commit 1e45f1fb84ae30e44c393f19156012e19f962ac3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 11:43:22 2014 +0200 Extended VerletIntegrationAction wirth Undo/Redo. - using new UndoRedoHelpers for this. - VerletForceIntegration::operator() does not return bool anymore, check for empty atom set is done in Action. - TESTFIX: Removed XFAIl from regression tests verlet-integration. commit 7e51e12e82c5637d2660d794f1e024fda52a5aa6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 10:00:14 2014 +0200 Extended UndoRedoHelpers. - added removeLastStep(), addNewStep(). - FIX: some UndoRedoHelper functions did not have const arguments as they should. - FIX: AtomicInfo did not set/store force vector of atom. - added AtomInfo::removeTrajectoryStep() and BondedParticleInfo::...() to allow for removal of a time step in the course of undoing. Enhanced AtomInfo, atom, and TesselPoint by removeSteps(), similar to UpdateSteps(). commit 4424959d82789202040886c380e14457ae068293 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 08:54:30 2014 +0200 Sorted GlobalListOfActions. - note that Redo must remain at the front due to technical reasons. commit 51cdfdda92308eff94ae477deb3170f9bd1b79a1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 20 14:50:41 2014 +0200 Extracted common functions from VerletForceIntegration into AtomicForceManipulator. - AtomicForceManipulator contains e.g. parsing forces from file. - removed performConstraintMinimization from VerletForceIntegration. - this is preparatory for ForceAnnealing, also derived from AtomicForceManipulator. - FIX: MoleculeVerletIntegrationAction checks whether atoms are selected and increments WorldTime only in success case. commit 343c5aa67b8af4355dabe12bc32e94678574ee19 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 06:51:13 2014 +0200 Added CorrectBondDegreeAction and fixed Calculation tests. - pdb files do have bond graph but not the right degrees. - there also lies some ambiguity in here as double bonds depend on the chosen matching. commit 5d555048c6955ac3bda0b2cb4b3e6b20ab49880e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 18 19:45:45 2014 +0200 FragmentationAction now compiles global saturation positions information. commit a1d1dd8b043f6987e14d6d37973e71bd8ccad587 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:50:13 2014 +0200 Added SaturationDistanceMaximizer to determine best alphas for SaturatedBonds. - also added simple unit tests that ascertains that with just degree 1 bonds nothing happens. commit bac32f93be11686cd34925f6b8ddc570e886dce7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:45:14 2014 +0200 Added SaturatedBond as container for a "dangling bond" and its saturation hydrogens. - most member variables are private, this prints them for debugging. commit a8f1d258e9e7fda6f62cbc12bf57a09cb5102256 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 23 23:50:08 2014 +0200 Added new Vector::IsParallelTo(). commit 98a293b9263c73baadd2152296722d9dd0d401e9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 18 19:08:09 2014 +0200 SaturatedFragment can deal with a global saturation position map. - so far, we create an empty one in FragmentationAction such that nothing's changed for the moment. - similarly in StoreSaturatedFragmentAction. However, there this is intended as only local information is required (it's only a single fragment). commit bdd5a84d9caf9791ea18d3a07979dee75f9bc54e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 23 11:26:42 2014 +0200 FIX: VectorContent::Normalize() had int, not double. commit 3834b60a172eb5fc5a8f0c36a9bc18ca164bb189 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 17 23:52:05 2014 +0200 TESTFIX: extracheck threshold is _relative_ 1e-5. commit fec597f5b80c0f86e5d9e73637b0ffff32750b57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit de2cbfe9e898e38b885f3727e766bc34f57f9c60 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 9e3fca9793f8283b21549888452621aad9772a63 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 9d32646c6dd4acfd9baa5f5b17e41207adee8b18 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 3fbdca6228d7cb54dd1ec647f23636bf048cea6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit 06804b923c9b82a6dd4f7d932a21781d6e4eae6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 9fd44f7f53b271add9c0ff9fe035e67c63361f09 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 74d179f0dff39a6c2ff23bdd8c5bae931bc4bd12 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:48:11 2014 +0200 FIX: elements db uses wrong hbondangle for degree 1. - angle is cone's opening angle and needs to be zero for degree 1 because the cone is just a line. commit 3567e21ff36698dd519060d6ddaa4ba24e65685f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit c77d36e7ff07e14a81c2f181349203f9d7fd8a50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 72eada0a916425172fc2053704f4ca36992494be Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. commit 8e2779350975a8ced8c8e2d73ad3c4b62c79ab34 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:46:56 2014 +0200 TESTFIX: Regression test series Calculations would not run in parallel. - we have to use $(MAKE), otherwise jobobserver cannot deduce whether it calls a make and does not pass "-j4" option. - regression tests Fragmentations now give status in color. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Generalize_AddHydrogenSaturation deleted. v1.4.5-25-ge82bbb7
by git＠ins.uni-bonn.de 21 Aug '14

21 Aug '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, Generalize_AddHydrogenSaturation has been deleted was e82bbb7fc6750560a3c172437d0a90fb697ff754 ----------------------------------------------------------------------- e82bbb7fc6750560a3c172437d0a90fb697ff754 Triangle case is now done properly. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Add_SaturateAtomsAction deleted. v1.4.5-30-g6de8af2
by git＠ins.uni-bonn.de 21 Aug '14

21 Aug '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, Add_SaturateAtomsAction has been deleted was 6de8af2811afb747a88e9e9fd96f40baa71e43b8 ----------------------------------------------------------------------- 6de8af2811afb747a88e9e9fd96f40baa71e43b8 tempcommit: Marking some fragmentation expression tests again as working. Merge with ... ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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