- Molecuilder-devel

[SCM] branch MolecuilderGuiTestSuite deleted. v1.4.10-41-ge67b26d
by git＠ins.uni-bonn.de 18 May '15

18 May '15

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 "". The branch, MolecuilderGuiTestSuite has been deleted was e67b26d9321f460da28ba298696ea5e9997dbadd - Log ----------------------------------------------------------------- e67b26d9321f460da28ba298696ea5e9997dbadd tempcommit: Excluding testsuite.at and Makefile.am modifications in createGuiChecks. Merge with ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] branch MolecuilderGuiTestSuite created. v1.4.10-41-ge67b26d
by git＠ins.uni-bonn.de 17 May '15

17 May '15

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 "". The branch, MolecuilderGuiTestSuite has been created at e67b26d9321f460da28ba298696ea5e9997dbadd (commit) - Log ----------------------------------------------------------------- commit e67b26d9321f460da28ba298696ea5e9997dbadd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 10:58:56 2015 +0200 tempcommit: Excluding testsuite.at and Makefile.am modifications in createGuiChecks. Merge with commit 24ba9d399a30a6f1089ff4f8c708e9ce962954a3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 10:58:43 2015 +0200 tempcommit: Fixes to GuiChecks makefile.am. Merge with ... commit 2f78dedab99635deb633805d1e2dd7828a9b28ce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 10:04:04 2015 +0200 FIX: Regression test set-parameters-mpqc undo compared against wrong file. - functionality is actually working and removed XFAIL_IF. commit d421e99bd1d52763e0e51102806b2cc5078709ac Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:34:31 2015 +0200 Added "--testsingle" switch for line-by-line execution. - QTUIFactory checks for additional "single" and activates then a special mode which uses the newly split executePythonScript. commit c24a03429680d72807b8563f2cc26a701b258bda Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:02:25 2015 +0200 tempcommit: Removed specific queries for RandomNumberDistribution_Parameters. - also removed RandomNumberDistribution_ParametersType from TypeEnumContainer. commit 72048c1f62521e65ca103e27bfdc9edf51834217 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:24:19 2015 +0200 Replaced all std::string by ParameterPair where used as ("key = value;") tuples. - this fixes an issue with vectors of key-value-pairs converted into a single string for use in a python command. commit 1b76bd4e0d0d417f9550df3c3c9ac34e92fbe0ac Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:22:43 2015 +0200 Added ParameterPair (i.e. "key = value;") to allow other string output. - this will solve the problem of vectors of key-value-pairs not properly converted into a single string because of missing semicolon. commit 671a0d7a1dadd57836e3b954891008b14d08c229 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:22:40 2015 +0200 Added all new guichecks regression tests generated from createGuiChecks.sh script. commit 3d3806b3fe80492889e36b078ac020563ddaf65a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:03:03 2015 +0200 Added script file to generate guichecks testsuite from regression tests. commit f57477d40ace4ac4c42ede5e5f1e4fbc4d33549f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 09:12:44 2015 +0200 Added DryRun and NoDryRun actions. - actions (un)set a flag inside ActionQueue to which only those permitted by an advocate pattern have access. - added testsuite tests for both dry-run, no-dry-run, and storing sessions. - explained use of action in userguide. commit 5bbdc51b776ea0a055cf89c5f37a32199f4cd987 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:24:48 2015 +0200 Added GuiCheck "AddAtoms". commit a09f5aa4ca16a5184a1a64fe8504c5576e3af9e4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 21:49:52 2015 +0200 Added testsuite "GuiChecks" with extra target guicheck. - this allows starting the testsuite on the graphical interface. - checks for working testlauncher inside molecuildergui with single and multiple scripts. commit 7162d64647012c6f149ebfc471badf9c128417b9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:20:52 2015 +0200 Command-line arguments are passed to QApplication inside QtUIFactory. commit 31094f82215bdfcd128eb4dd949e06b3042072f8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:17:55 2015 +0200 Added "--test"-mode to UI switch in builder_init. - this will allow to launch molecuildergui with a set of scripts to execute. commit 8cd7dee9ee71edac12983065a29236d80365374b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:33:08 2015 +0200 MOVEME: Split executePythonScript into file and string script option. - as python script is internally a string anyway, this allows more freedom in creating or internally modifying python scripts. commit 06993ecb24e553d7fd2081b4d733f40e007e7c65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:32:01 2015 +0200 FIX: double inclusion protection used already used name. - PythonScripting instead of PythonScripting_impl. commit 645f55e87502d3647d80248b8a8bcc981c2aa934 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 08:44:58 2015 +0200 FIX: VerboseAction would store invalid undostate (just success). - this is due to switch between whether verbosity actually changes or not. However, we always have to return a full undostate (or just success if no undo can be performed) when undo/redo is implemented. commit 22ac22aca3c37906d62a9c98e92163e0784a003b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:25:29 2015 +0200 FIX: Fastparsing regression test contained one broken line. - this occurred in 2700983e. commit f0cf79849c9d80e77e36a5b95dbd51578f8b1ab3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:06:44 2015 +0200 FIX: Setting window title in QtMainWindow. commit b9b49e727d9d3d89c559b4370e78e73dd898f45d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Feb 6 14:22:15 2015 +0100 createMoleculeMesh now checks that minradius is at least the minimum bond length in the molecule. commit 88afc98ce3204073139972574abd21cf592b7f3a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:25:11 2015 +0100 Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. - renamed add/remove-bond -> add/remove-bond(s) to emphasize this. - added regression test on three selected atoms. - modified userguide entry for both actions. commit 2fcef36f8dcba275ab6b2280c2ac65fea1f5322a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 22:28:27 2015 +0100 Added SaturateAction that uses SphericalPointDistribution. - added saturate-atoms to userguide. - added regression test fpr saturate-atoms. commit 0241c59e7f10c73f87336715af0aadac2b2d4db1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Trimmed down SphericalPointDistribution to what is needed at the moment. commit f54930fdd572cf1e5e916da920bdad10f75cd695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 041b77534fcad37539d2dc51316181ca20789d92 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit e895f78dbdbe38b130210c4366e7fed23c4fe47a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit f47efd4ebdb376bfe1356fa44faf9dfb3aadcee1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 12:07:22 2015 +0100 FIX: Bond cylinders were wrongly scaled and too long with degree larger than one. - we have to first translate, then rotate, then scale. The last two were interchanged before. This is fixed. commit 605b920d2069e10cd6251ac3594f694e3a77a4aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 16:33:42 2015 +0100 TESTFIX: Output for target "extracheck" in logs is not helpful if just the log is sent back. - now the resulting energy is stated in the log as well. commit 6a62766a98501b3d23237fd55ecf9e408d515b6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 26 21:26:48 2015 +0100 FIX: MPQCData::DoValenceOnly was wrongly initialized. commit 52dfccf25b899535cbc0c015b9e1f78b9091a02f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 22:19:53 2015 +0100 FIX: QDebugStream is now protected against multiple writes to log window. - writes bracketed with bool. - we had multiple, seemingly random segfaults in QDebugStream when inserting new text. commit b569b869983a53f9cfd8504c35519a4e5d5816ae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 18:37:49 2015 +0100 FIX: MPQCCommandFragmentController failed to add jobs due to false return value type. - bool is now an unsigned int. - kudos to Ralph Thesen und Sambasiva Rao Chinnamsetty for stumbling over the bug. commit ca09be78bbfa6e8031a56eeddb3ea077f2898239 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:51:25 2015 +0100 FIX: FragmentationAutomationAction checks FragmentControllers' exitflags. - this way we can tell when the connection to the server fails and we need to interrupt the Action and return failure. commit c17aa82e3ef91ee1d287c21853069780b7d77509 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:50:27 2015 +0100 FIX: ActionSequence now checks whether an Action in the sequence fails. - otherwise if we are to repeat the sequence for 200 steps and one of the Actions fails on the first step, we still go through all of the remaining steps. commit 0763cebcd4404462360473dcb6a67eb7d3459907 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:31:53 2015 +0100 Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect. - this fixes the bug where the molecular dynamics actions would flip the double bonds in an aromatic ring during the simulation steps because the bond degrees are reset even though the bond graph is present and should be re-used. commit cd5aa0e9ee7d7b9d60b2e207fefdcbdff931dba3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:30:48 2015 +0100 Added correct-bonddegree to MolDyn and StructOpt Actions. - this is not really necessary as FragmentationAction will correct bond degrees but it is nonetheless cleaner this way. commit 329cf3be784f771a68fd139004a418721050fa4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:57:10 2015 +0100 FIX: All MakroActions now have prototype_actions and copy from that. - this fixes the segfault when calling a MakroAction such as MolecularDynamics and unchecking output-every-step, causing the OutputAction to be removed from the sequence, and when re-performing Action with again unchecked option, the action cannot be removed any longer. - prototype_actions is prepared in ActionRegistry on program start and all cloned MakroActions copy their specific actions set and MakroAction accesses it via a ref in callAll(). commit c1d8370d3b839d18339477ec374e2e99aa98c3b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 13:18:33 2015 +0100 FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ids. - this is potentially risky as popping a selection may occur at a later stage where the ptrs has been deallocated. Hence, we now store only ids and these get reselected on popping. - also fixed some faulty message with respect to associated Actions. commit c2661740e680214aedbfd198a49ab05ae0eedc43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:37:44 2015 +0100 Undoing atom/molecule removal will also recreate bonds. - TESTFIX: Molecule/Remove Undo had wrong check file (bonds were still missing) commit e23fecd7d546524c9be983551b4b3a1efbdea050 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:34:57 2015 +0100 Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId(). - I just stumbled over this, trying to recreate bonds from removed atoms and Contains looks for the Nr not the Id ... commit 91730001a1c217b3fd68de844f85cfef323e7c5c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 10:23:51 2015 +0100 FIX: UndoRedoHelpers' AddBondsFromBondInfo would add bonds doubly. - also, if adding goes wrong, added bonds are now removed again. commit b56114adf8691cb8640747de16866a6c1d22f7da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 20:43:55 2015 +0100 FIX: Action..::outputAsPython now accesses parameters via getUnvalidated(). - added Value::getUnvalidated() and Parameter::getUnvalidated() for access at store-session. - this fixes a bug when OutputAsAction had been used whose filename would no longer be valid as the file now exists. This would cause an assertion and the whole OutputAsAction would fail. ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] branch MolecuilderGuiTestSuite deleted. v1.4.10-27-g0142f85
by git＠ins.uni-bonn.de 17 May '15

17 May '15

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 "". The branch, MolecuilderGuiTestSuite has been deleted was 0142f851d6a501dd30409718b5f7f3289064586d - Log ----------------------------------------------------------------- 0142f851d6a501dd30409718b5f7f3289064586d Added GuiCheck "AddAtoms". ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] branch MolecuilderGuiTestSuite created. v1.4.10-27-g0142f85
by git＠ins.uni-bonn.de 13 May '15

13 May '15

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 "". The branch, MolecuilderGuiTestSuite has been created at 0142f851d6a501dd30409718b5f7f3289064586d (commit) - Log ----------------------------------------------------------------- commit 0142f851d6a501dd30409718b5f7f3289064586d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:24:48 2015 +0200 Added GuiCheck "AddAtoms". commit dadfc2736f073c2cf40480b03f0d4795f9c2208a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 21:49:52 2015 +0200 Added testsuite "GuiChecks" with extra target guicheck. - this allows starting the testsuite on the graphical interface. - checks for working testlauncher inside molecuildergui with single and multiple scripts. commit cc796287601af4eadd66fddaaaa7126ad060caa0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:20:52 2015 +0200 Command-line arguments are passed to QApplication inside QtUIFactory. commit 8ea41d1d2614f7b65303812884abed59891384fb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:17:55 2015 +0200 Added "--test"-mode to UI switch in builder_init. - this will allow to launch molecuildergui with a set of scripts to execute. commit f0cf79849c9d80e77e36a5b95dbd51578f8b1ab3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:06:44 2015 +0200 FIX: Setting window title in QtMainWindow. commit b9b49e727d9d3d89c559b4370e78e73dd898f45d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Feb 6 14:22:15 2015 +0100 createMoleculeMesh now checks that minradius is at least the minimum bond length in the molecule. commit 88afc98ce3204073139972574abd21cf592b7f3a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:25:11 2015 +0100 Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. - renamed add/remove-bond -> add/remove-bond(s) to emphasize this. - added regression test on three selected atoms. - modified userguide entry for both actions. commit 2fcef36f8dcba275ab6b2280c2ac65fea1f5322a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 22:28:27 2015 +0100 Added SaturateAction that uses SphericalPointDistribution. - added saturate-atoms to userguide. - added regression test fpr saturate-atoms. commit 0241c59e7f10c73f87336715af0aadac2b2d4db1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Trimmed down SphericalPointDistribution to what is needed at the moment. commit f54930fdd572cf1e5e916da920bdad10f75cd695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 041b77534fcad37539d2dc51316181ca20789d92 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit e895f78dbdbe38b130210c4366e7fed23c4fe47a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit f47efd4ebdb376bfe1356fa44faf9dfb3aadcee1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 12:07:22 2015 +0100 FIX: Bond cylinders were wrongly scaled and too long with degree larger than one. - we have to first translate, then rotate, then scale. The last two were interchanged before. This is fixed. commit 605b920d2069e10cd6251ac3594f694e3a77a4aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 16:33:42 2015 +0100 TESTFIX: Output for target "extracheck" in logs is not helpful if just the log is sent back. - now the resulting energy is stated in the log as well. commit 6a62766a98501b3d23237fd55ecf9e408d515b6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 26 21:26:48 2015 +0100 FIX: MPQCData::DoValenceOnly was wrongly initialized. commit 52dfccf25b899535cbc0c015b9e1f78b9091a02f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 22:19:53 2015 +0100 FIX: QDebugStream is now protected against multiple writes to log window. - writes bracketed with bool. - we had multiple, seemingly random segfaults in QDebugStream when inserting new text. commit b569b869983a53f9cfd8504c35519a4e5d5816ae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 18:37:49 2015 +0100 FIX: MPQCCommandFragmentController failed to add jobs due to false return value type. - bool is now an unsigned int. - kudos to Ralph Thesen und Sambasiva Rao Chinnamsetty for stumbling over the bug. commit ca09be78bbfa6e8031a56eeddb3ea077f2898239 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:51:25 2015 +0100 FIX: FragmentationAutomationAction checks FragmentControllers' exitflags. - this way we can tell when the connection to the server fails and we need to interrupt the Action and return failure. commit c17aa82e3ef91ee1d287c21853069780b7d77509 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:50:27 2015 +0100 FIX: ActionSequence now checks whether an Action in the sequence fails. - otherwise if we are to repeat the sequence for 200 steps and one of the Actions fails on the first step, we still go through all of the remaining steps. commit 0763cebcd4404462360473dcb6a67eb7d3459907 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:31:53 2015 +0100 Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect. - this fixes the bug where the molecular dynamics actions would flip the double bonds in an aromatic ring during the simulation steps because the bond degrees are reset even though the bond graph is present and should be re-used. commit cd5aa0e9ee7d7b9d60b2e207fefdcbdff931dba3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:30:48 2015 +0100 Added correct-bonddegree to MolDyn and StructOpt Actions. - this is not really necessary as FragmentationAction will correct bond degrees but it is nonetheless cleaner this way. commit 329cf3be784f771a68fd139004a418721050fa4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:57:10 2015 +0100 FIX: All MakroActions now have prototype_actions and copy from that. - this fixes the segfault when calling a MakroAction such as MolecularDynamics and unchecking output-every-step, causing the OutputAction to be removed from the sequence, and when re-performing Action with again unchecked option, the action cannot be removed any longer. - prototype_actions is prepared in ActionRegistry on program start and all cloned MakroActions copy their specific actions set and MakroAction accesses it via a ref in callAll(). commit c1d8370d3b839d18339477ec374e2e99aa98c3b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 13:18:33 2015 +0100 FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ids. - this is potentially risky as popping a selection may occur at a later stage where the ptrs has been deallocated. Hence, we now store only ids and these get reselected on popping. - also fixed some faulty message with respect to associated Actions. commit c2661740e680214aedbfd198a49ab05ae0eedc43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:37:44 2015 +0100 Undoing atom/molecule removal will also recreate bonds. - TESTFIX: Molecule/Remove Undo had wrong check file (bonds were still missing) commit e23fecd7d546524c9be983551b4b3a1efbdea050 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:34:57 2015 +0100 Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId(). - I just stumbled over this, trying to recreate bonds from removed atoms and Contains looks for the Nr not the Id ... commit 91730001a1c217b3fd68de844f85cfef323e7c5c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 10:23:51 2015 +0100 FIX: UndoRedoHelpers' AddBondsFromBondInfo would add bonds doubly. - also, if adding goes wrong, added bonds are now removed again. commit b56114adf8691cb8640747de16866a6c1d22f7da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 20:43:55 2015 +0100 FIX: Action..::outputAsPython now accesses parameters via getUnvalidated(). - added Value::getUnvalidated() and Parameter::getUnvalidated() for access at store-session. - this fixes a bug when OutputAsAction had been used whose filename would no longer be valid as the file now exists. This would cause an assertion and the whole OutputAsAction would fail. ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] MoleCuilder branch Fix_VMGForces deleted. v1.4.9-15-g30bff67
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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, Fix_VMGForces has been deleted was 30bff67aa3428b5502ae8a9a116a176be12a5572 ----------------------------------------------------------------------- 30bff67aa3428b5502ae8a9a116a176be12a5572 tempcommit: Some changes to InterfaceVMGJob on force summation. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel deleted. v1.4.9-40-g2050b29
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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, Refactoring_QtMoleculeList_as_QModel has been deleted was 2050b29519e754ad0beb183c35ca29f6a1821f0d ----------------------------------------------------------------------- 2050b29519e754ad0beb183c35ca29f6a1821f0d Commented-out all debugging messages in QtMoleculeList rewrite. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.10 deleted. v1.4.10
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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_v1.4.10 has been deleted was 2e7afe95e7fc92ca90ef771dbb8089a436d2189a ----------------------------------------------------------------------- 2e7afe95e7fc92ca90ef771dbb8089a436d2189a Set version to 1.4.10. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_smallchanges deleted. v1.4.9-2-g7305d52
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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_smallchanges has been deleted was 7305d5268402221ff02978b5f2ec39cb12bbd238 ----------------------------------------------------------------------- 7305d5268402221ff02978b5f2ec39cb12bbd238 Removed extra option actionname from HelpAction. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules deleted. v1.4.9-25-g4f2895f
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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_TesselatedLargeMolecules has been deleted was 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 ----------------------------------------------------------------------- 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 FIX: World::SetTime() erased molecules twice. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.10 created. v1.4.10
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

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, v1.4.10 has been created at cea2621f22f0473fd56d7e402fb7a500d1946fc8 (tag) tagging 2e7afe95e7fc92ca90ef771dbb8089a436d2189a (commit) replaces v1.4.9 tagged by Frederik Heber on Wed Feb 4 19:58:25 2015 +0100 - Log ----------------------------------------------------------------- Molecules (with many atoms) can now be shown as tesselated surface. Complete rewrite of the GUI's list of molecules tab. No need to add "--actionname" anymore, just supply help with the desired action name. This version contains the following branches: 2e7afe9 Candidate_v1.4.10 (Memfixes, Qt-boost clash fix, and some followup fixes) 55feff5 GUI_smallchanges (no more extra actionname, default value adding) 27e4646 Refactoring_QtMoleculeList_as_QModel (complete and extensive rewrite of thr shown molecule list such that adds and removals are lightweight) 0ac85c3 GUI_TesselatedLargeMolecules (with working tesselation one may switch between molecules shown by their atoms or shown by the tesselated surface) Frederik Heber (49): GLMoleculeObject_atoms and .._bonds are now children of .._molecule. GLMoleculeObject have m_visible, settable in QtMoleculeList. GLMoleculeObject_molecule display tesselated surface in m_visible case. Molecule relays atom's PositionChanged as AtomMoved signal. GLMoleculeObject_molecule listens to AtomMoved signal to update hull only when necessary. Hovering over molecules is working including update of QtInfoBox. Molecules can be (un)selected by clicking on the tesselation hull. Molecule's Visibility can be changed "group-wise". Added MeshFreeType to GLMoleculeObject. World removes empty molecules. For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw(). GLWorldView's view may be changed via keyboard (especially zoom). Extended selection action for Molecule ids to multiple ids. Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. Added new RemoveAction for molecules. Undo/Redobuttons are grayed out when respective Action not possible. FIX: Bonds from new molecules are instantiated, too. FIX: Failing Actions do not clear ActionQueue/History anymore. FIX: ActionQueue is no longer cleared when Action fails. FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was given. Added push/pop[Atoms|Molecules]Selection to World. Added Push/PopAtom selection actions. Added Push/PopMolecules selection action. Added TranslateMolecule action. FIX: World::SetTime() erased molecules twice. FIX: On defined LOG_OBSERVER we also enableLogging() in main(). atom::father is now accessible through getter and setter only. FIX: Atom is notified when its father dies and resets father to itself then. Added AboutToBeRemoved channel to molecule. MEMFIX: removeAtomsinMolecule() worked directly with molecule::iterator which accesses invalid memory. Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. First change to convert QtMoleculeList into QStandardItemModel. Header row is correct again in QtMoleculeList. Moved QtMoleculeList files into own subfolder. Added basic QtMoleculeItem and ...Factory. Added a slew of specific QtMoleculeItem for each of the COLUMNs. Modified QtMoleculeList to use QtMoleculeItemFactory. Moved rowsSelected() over to QtMoleculeListView. Visibility checkstate is working for molecule and group item. Commented-out all debugging messages in QtMoleculeList rewrite. Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10 Merge branch 'Refactoring_QtMoleculeList_as_QModel' into Candidate_v1.4.10 CommandLineParser adds Action's default values as implicit. Removed extra option actionname from HelpAction. MEMFIX: Mismatched delete[] in SuspendInMoleculeAction. MEMFIX: LoadAction undo must not use molecule::iterator for atom removal. FIX: Qt and boost crash together in boost::Q_FOREACH. FIX: We must use --help directly instead of --actionname in checking whether Action is present. Set version to 1.4.10. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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