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, Fix_QtGui_Testmode_not_showing_atoms has been created at 65a73184853e7894f8c1ba485eb4be5aeadc8673 (commit) - Log ----------------------------------------------------------------- commit 65a73184853e7894f8c1ba485eb4be5aeadc8673 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 19:56:03 2015 +0100 Revert "Added mutex to QtObservedInstanceBoard." This reverts commit d6047811a42782cb37d49830bc6e17d3b3344f68. commit 9f3f9e56a581dc70fb89d4d5c805a1b9133fa9b1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 19:55:42 2015 +0100 Revert "tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811" This reverts commit 039eb1d53b41317c75d39a6563658582140d83d2. commit 039eb1d53b41317c75d39a6563658582140d83d2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 18:43:21 2015 +0100 tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811 commit 08f75432db31263ed75f1e0313881f79ad1d3669 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:41:51 2015 +0100 tempcommit: Merge with e228f3 commit 1832dcfa09ffeb5afd0995ea16cd9f9184e55c80 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:26:57 2015 +0100 tempcommit: Merge with 5aa1f2b7 commit 8d7fd984e57ad3b7f731ae516575b5d5d6c07f11 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:18:41 2015 +0100 tempcommit: Merge with e228f3 commit d6047811a42782cb37d49830bc6e17d3b3344f68 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:17:46 2015 +0100 Added mutex to QtObservedInstanceBoard. commit e228f3ba9206ecc217c85ae73ee38e5d4c708fc5 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:15:30 2015 +0100 TODO: QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback. - due to Qt's signal/slot destruction, which follows no proper order, we need to invalidate callback when their owners are destroyed. Each has a note-function() that flips the boolean to show the callbacks invalidity. - TODO: So far this is not nice, especially w.r.t to ObservedValue_wCallback because of templatization. We cannot place them in a loop and this makes this very error-prone once more Values are added ... commit d96f9a55c651a1c31a14cdd2b670739c244a4ef2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:14:57 2015 +0100 tempcommit: Need to split signedOn maps for atoms and molecule due to different number of channels. Merge with ...? commit dc05d81bfe40be3c1ebfc4fec8f0305adce08217 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:13:33 2015 +0100 tempcommit: merge with eda203c3 commit b47afb72fab6df9dcd5f84cae5ac3d29800413bf Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 17:07:39 2015 +0100 FIX: Qt's parent properly set from QtMainWindow's point of view. commit 73fcc4d0eb85a7339453cb79a5421a0bd595b392 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 16:58:50 2015 +0100 Revert "DROPME: Removed logging into QtLogBox for debugging." This reverts commit 57b9cd365da71ff1d62c3ce6c112e331b086289f. commit 6e03cac48ca5729cfedfe279432bada76497baf6 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 15:14:07 2015 +0100 tempcommit: merge with a8c9551b commit eda203c3214c9cbf233c4820cd727a0f39a8d658 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 15:07:55 2015 +0100 tempcommit: Equipped QtInfoBox with mutex and split clearTabs(). - this avoids a memory corruption with signal/slots as the first atomRemoved() signal also removes the molecule and hence the QtObservedMolecule ptr who is the recipient of the subsequent moleculeRemoved() signal. commit e54456aae6e9d661d577a0d9c7f05cef7b339b51 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 15:07:41 2015 +0100 tempcommit: merge with 70c61bd4+ commit 571fcbfee2a325e073fcd5a0547bb3ade866c384 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 12:54:29 2015 +0100 FIX: All ObservedValue getters now return const references. - this should avoid some unnecessary copying. commit 271060fcd1c1de868a06b88d8f1e34baece52521 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 12:36:21 2015 +0100 FIX: molecuilder.py is now loaded after GUI is done initializing. - otherwise consequences of loaded session (atoms, ...) are not displayed. - originally, this was done on purpose as it is quicker to just load stuff into the world and then tell the GUI to show what's there. However, now, due to constraints with different threads, this is no longer possible. commit 95a757bd9e1a5660ed590dc64a0503195ee32596 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 12:35:53 2015 +0100 tempcommit: Merge with 7a8832d4 commit 12ecc9a464e868e2095278c8287986ee5b0f9b4d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 12:06:30 2015 +0100 QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues. commit 785fde32fe13558ebf6870591ef8b9152f0a93bf Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 12:06:14 2015 +0100 tempcommit: merge with 7a8832d4 commit 5aa1f2b7ccecfee7e1238002ab0885590c9d3791 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 11:49:06 2015 +0100 xtended QtObservedMolecule by Center, NonHydrogenCount, and BondCount. - added Cacheable MoleculeCenter to molecule which is cleverly updated. commit 7a8832d4d20ecc2d2ff1aed5d2ca5f66be24695a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 11:48:16 2015 +0100 Extended QtObservedAtom by Name and Molecule. - added extra signal MoleculeChaned to AtomObservable. commit 834ff2cd2cd7749afa723eb22f681f2722b342ff Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 30 00:11:39 2015 +0100 tempcommit: Merge with 087563d29 commit abc9ea4cdbe2032f5fe794618b80a6a7d9513b91 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 23:52:15 2015 +0100 tempcommit: merge with 74d1bd0 commit 087563d292ebfaff5e237b4898d8a1fce4023cdb Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 23:22:53 2015 +0100 QtMoleculeList takes InstanceBoard and listens to its molecule signals. commit 74d1bd00b1401eb63c10b46a6a2b67f7132db9f4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 23:21:30 2015 +0100 All QtMoleculeItem now heed QtObservedMolecule. - QtMoleculeItems no longer use Observer/Observable but get updates via signal/slot from QtObservedMolecule. commit 6356a6059f318b7bd416858a363d7a283b456aa1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 22:55:51 2015 +0100 Added AtomCount and FormulaChanged to QtObservedMolecule. commit 3b881145335c6ff16050bf12b91a96fe28d29684 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 19:45:46 2015 +0100 tempcommit: merge with 1c293cec commit 672945f5568c3592c37bee33145d3a62a7d0e091 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 19:45:22 2015 +0100 tempcommit: merge with 0fb2d3c3 commit 7d8b8b43517de6849f3bb430ad05db0059e990c6 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 19:38:02 2015 +0100 FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff(). commit 0fb2d3c39f1eab131b6ee8cfcc9fca9f9f7ced38 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 19:31:07 2015 +0100 Revert "QtObserved..::AllSignedOnChannels is needed statically." This reverts commit 080cc49c388944e7782fa8e00e79b58a16b75974. commit 8bc85f6767371493ec33741f717bb09f9d89fbde Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 19:30:33 2015 +0100 tempcommit: Merge with 70c61bd4 commit a345227a313fe74b7e6b9f511ca909664fe97b2a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 17:22:46 2015 +0100 tempcommit: Merge with a8c9551b commit 9e007daf870bfbcf45ef770c4621e818439e3585 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 17:20:24 2015 +0100 tempcommit: Fixing signals of QtObservedMolecule. Check and merge with 92a780a commit 6c6d3c2df81a2c98c86f7475b5131dc955d5187c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 17:17:34 2015 +0100 tempcommit: activateObserver needs to be called after insertion into ObservedValuesContainer. Merge with c0943f48 commit 9881c3b93ce026abf818cdb1eb54905ac2bd65f2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 17:16:49 2015 +0100 tempcommit: Added again check on lastremoved.. to InstanceBoard. commit 080cc49c388944e7782fa8e00e79b58a16b75974 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 17:15:40 2015 +0100 QtObserved..::AllSignedOnChannels is needed statically. - this is used to check whether all ObservedValues already had their subjectKilled() called. commit b775b7ab9e68e656ce1078acbca5bd80429d9829 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:26:13 2015 +0100 tempcommit: Merge with ad571e28 commit f50b98a0d968216c12648ab5b3d71845dc55df6c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:26:02 2015 +0100 tempcommit: Merge with 5a7b4a23 commit 8b16324d3cf9be7dbdf92a601c4c3a67c3297b0d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:24:15 2015 +0100 tempcommit: Merge with c0943f48 commit ad571e284a59bf54e939d7a4a3025466f30381f5 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:23:18 2015 +0100 tempcommit: Merge with a8c9551b commit 5a7b4a23d77105c2b2ad6d3cf83663c33cd8834a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:22:44 2015 +0100 tempcommit: Merge with 92a780aa commit 70c61bd41e1e139d3f3e552ed794aa741c736325 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 16:12:34 2015 +0100 No more ObservedValues_t from QtObservedInstanceBoard. - we now work with QtObserved..::ptr directly everywhere. commit 89a166473561b51e254c1cb815611d71c4726d11 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 15:46:17 2015 +0100 tempcommit: merge with e6d34be3 commit c0943f48129c534587407d263d59cb56aa9a836d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 15:41:13 2015 +0100 ObservedValuesContainer now stores QtObserved.. instances directly. - we need this as QtObservedAtom and ..Molecule must signOn() to World's instance right away. If later requests to ObservedValuesContainer::get() cause new signOn()s, then these might fail. commit e6d34be30f840209719f7a0075f29dfbbca6529c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 15:02:35 2015 +0100 Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer. - this avoids some more duplicated code. commit a8c9551b45087863cb04b87bdf54ffd64ded6f08 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 13:52:29 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_molecule. - see previous commit for explanations. commit 92a780aa795996a1d3bd79a2083b2794115b3782 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 11:46:45 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_atom. - i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via Qt signals. These signals are connected to a QtObservedAtom which in turn now contains all the ObservedValue functionality. - this is preparatory for having a single (Observed)Atom as representer of its associated World's atom in the QtGui part of the code. commit 2f158c56623234be6ebfbc278761bd440773f715 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 29 10:52:10 2015 +0100 Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer. - this avoids a lot of code duplication. commit 76d18f39134465d8a544751f9e36f6cc11e3cbed Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 14:57:10 2015 +0100 Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard. commit 6a50bb20ea7ea1b24f4ffac1990bc37d9078d426 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 14:24:10 2015 +0100 Added QtObservedAtom and ..Molecule() instances. commit 1c293cecf80bebccd7bd90664c05f0aae700e3c9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 14:23:09 2015 +0100 Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard. - this is preparatory for adding ObservedAtom and ObservedMolecule classes that combine all observed information on either type. commit 066f19447803d0bf7000ac80c17ecbfe55c290e0 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 13:09:43 2015 +0100 AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..(). commit a869e049c07be3cf8a6950d3b1bf73b71c6cdf7a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 13:08:04 2015 +0100 Added recreateAtom() and recreateMolecule() to World. - in order to overcome problems with Qt signals being delayed so much that in between sending and receiving the id of a newly instantiated atom has changed, we need to set the right id (after undo/redo commands) right away. For this, these two new functions are well-suited. commit e8cb76a185c93938c78d43387229180d20fe6e07 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 10:20:53 2015 +0100 GLMoleculeObject_molecule does not listen directly to molecule::AtomInserted/Removed. - this is done by QtInstanceInformationBoard instead. commit 0e8af80722e2f47e6b65e77c8cb0ad1abc12b91d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 10:20:09 2015 +0100 QtInstanceInformationBoard has now unique maps for either set of ObservedValues. commit 97bb26d4907d865970184db65245b6070b7da9d7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 28 10:13:15 2015 +0100 FIX: GLMoleculeObject_atom and .._molecule need to account for multiple subjectKilled(), one per channel. commit 338e3a86a7595d963f667cbaef3c44f38063e4e1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 20:51:05 2015 +0200 Revert "tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule." This reverts commit 61b8538c5cad80c1af7db190009b1406dcb696f9. Conflicts: src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp - readded MissedStateMap in GLWorldScene. commit 9d7f587da43870b91b2e6990586cb2c461b42126 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 20:28:45 2015 +0200 tempcommit: QtInstanceInformationBoard informs about AtomRemoved, AtomInserted via molecule. commit 7547a3be8fd2121c65b2ddeb5df6d377924c8cfa Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 20:28:23 2015 +0200 tempcommit: Selection uses direct connection. commit 4445f7735e8e685a8e8b404e73ce91f85bda383f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 20:27:50 2015 +0200 tempcommit: Removed resetAtoms() and PresentAtoms from GLMoleculeObject_molecule. - this information must come from instanceboard. commit 4c6952672301696fa7fc10a169afa9a97e67fc2c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 19:20:40 2015 +0200 QtInstanceInformationBoard also informs about index changes. commit 2b65b4846cdb14011409001d8870719c72973a77 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 19:20:13 2015 +0200 tempcommit: GLMoleculeObject_atom uses resetBonds() to add initial bonds. commit e962bf24ac918adb591a550e600008d9efa4ccfa Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 18:48:19 2015 +0200 tempcommit: .._atom and .._molecule now return ObservedValue to QtInstanceInformationBoard. - this way we can transfer these from one GLMoleculeObject_atom to another. commit 61b8538c5cad80c1af7db190009b1406dcb696f9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 18:47:31 2015 +0200 tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule. - basically all replaced by QtInstanceInformationBoard connections. commit 58737c96ffae94195696088c0a78976c1aaa8451 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 18:46:36 2015 +0200 tempcommit: Removed countSubjectKilled() and deprecator cstors from .._molecule. commit dc5c8f72db61ba5a149ede2a997a1a3c40528e63 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 18:45:21 2015 +0200 tempcommit: Removed countSubjectKilled() and deprecated cstors from .._atom. commit 8fd310cf6a723b7458fb7aa2e46c971fb3cefb7a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 18:03:53 2015 +0200 tempcommit: QtInstanceInformationBoard signOn maps need to store ref, not id. Merge with ... - we cannot access atom's id as only AtomObservable is left. commit 664d3ee7336ae4219f5826083bc628b676796504 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:21:37 2015 +0200 tempcommit: not using const ref in binding updateBoundingBox() for molecule. commit 57b9cd365da71ff1d62c3ce6c112e331b086289f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:21:16 2015 +0200 DROPME: Removed logging into QtLogBox for debugging. commit 9e0a33ac8bdd6947c0a04fd73187cea4b68a2722 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:20:56 2015 +0200 tempcommit: Additions to DROPME: debugging output. Merge with ... commit ca20d7b996c43666281013354bd200c6451dea86 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:20:34 2015 +0200 tempcommit: Fixes to QtInstanceInformationBoard. Merge with ... commit 2a1fa1f4859c41480232bbf66ef1af0a0031927b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:19:46 2015 +0200 tempcommit: Merge with e84e2c80 commit d77744bf3b3c4edca89a7d4346166d0e9fcd01e4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:18:13 2015 +0200 DROPME: Added debugging output to QtInstanceInformationBoard. commit 72cd6215eed6def5c3c4d89e5df800e7684d088f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:17:43 2015 +0200 FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet). commit e0ff31fa724d04612bcaa4b652b1bfbb80ba9ad1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:17:19 2015 +0200 tempcommit: resetTesselationHull() only called when owner still present. commit 44d90cfbf4c0582186c8158941c0d02978b92f08 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:16:53 2015 +0200 Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule. commit ce326e15d9e99bbab30b4772cb336a3c5d2fa7a7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:16:30 2015 +0200 GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene. commit a7a81684ba0cf49e1bd43c0272a542de73424dce Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:13:14 2015 +0200 FIX: QtMoleculeItem not signing off after subjectKilled(). commit 36f72a26eff131507efec4b9d4668ab086fd7d8a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 23 17:12:42 2015 +0200 tempcommit: QtInstanceBoard lifetime managed by parent QtMainWindow. Merge with ... commit 1c50baf9829a26f204938f7c6f0db62ccf17c719 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 21:46:52 2015 +0200 tempcommit: Replaced connections GLWorldView with QtInstanceInformationBoard. commit bf1de432c42165753bd9c996bd2b5e4b5cfb6205 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 21:08:44 2015 +0200 tempcommit: Enhanced ObservedValue_wCallback to take a bound getIndex function(). - additionally, we route internally to ObservedValue::get() and this gets us out of the painful situation where we need to supply an index getter to the ObservedValue that monitors the index (and hence must be present already to bind to its get function). commit e84e2c80597cedd0d64825fb5cef8b951359c789 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 19:03:48 2015 +0200 tempcommit: Final version of QtInstanceInformationBoard. commit cc861e0f1fcce8aaf29d231e672495d718a48949 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 19:01:09 2015 +0200 Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter. - this is a precursor for when the ObservedValues reside with QtInstanceInformationBoard. commit 57d3ae2e8eb2070b76bae18e2b6c05b89b6cf2c4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 18:59:19 2015 +0200 tempcommit: Merge with f6e0c328 commit 0a0cbe536dd01a4864f68d9b4cb39942f20c4ff1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 18:58:32 2015 +0200 tempcommit: Merge with 96d38bf commit 33bdeff78e8289331e8eea760bb818e6fd13ab17 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 18:57:48 2015 +0200 tempcommit: Merge with af7a33c5 commit 59c1c6f8b33a2deceab5c6d8263f5e9fd8744c9f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 18:47:35 2015 +0200 temcommit: Merge with f6e0c328 commit 2683c18da13ba37c11a576121ca65c72bfa4944a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 17:42:17 2015 +0200 Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface. - this is meant as a instantiator of all ObservedValue's needed by QtGui for representing information from the World. The ObservedValue's are instantiated separately w.r.t. to the instance for the visual representation. This is light-weight and can be performed in the same thread, while the visual representation's instantiation can be done elsewhere and there we just need to access the ready ObservedValue's that exist as long as they are needed by the QtGui. commit 085a87610d66db8fb9e578b0a11501791051478c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 17:41:24 2015 +0200 tempcommit: Merge with f6e0c328 commit ed08e1426da5dcaaf57c69953f8349e21fe4999f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 17:41:01 2015 +0200 tempcommit: Merge with af7a33c5f commit 96d38bfd524a4e0eaa1d48ca99c0bb32673fcf61 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 15:28:19 2015 +0200 GLMoleculeObject_bond's ObservedValues is now all static. - again, the same change as with .._molecule and .._atom. commit af7a33c5f26d7efcc83ad69bd3f59333751ca04e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 14:55:30 2015 +0200 GLMoleculeObject_atom's ObservedValues is now all static. - this is equivalent to the changes to GLMoleculeObject_molecule. commit e9c2370056ed4e15d17f470f44487b1b4300be62 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 14:42:13 2015 +0200 FIX: World needs to first destroy the molecule, then release its ids. - this is similar to the change for the atom. commit f6e0c32812b93f7790837a0e033ab7be689ede42 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 14:40:14 2015 +0200 GLMoleculeObject_molecule's ObservedValues is now all static. - this is preparatory for extracting their instantation to an external class InstanceInformationBoard that keeps track of the lives of instances in the World that are needed inside QtGui (e.g. for visual representation). commit 190990ab5eb8412c3ce3d49cbdde37d18de10e19 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 14:18:30 2015 +0200 FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly. - we need an old and a new set, i.e. the difference needs to be discernable between updates. However, so far we updated the old set directly, too. commit c6f7d851f7c828041d233968209abd07c53b0eb2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 17 11:09:07 2015 +0200 DROPME: Switching to log tab in worldTab for test-single. commit cfcbd701acc2c2d72b56189edae70c870bce4819 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 16 21:48:20 2015 +0200 FIX: World::destroy..() did not emit SelectionChanged signal. commit 01ee257b96b3aa8d62e48dfae817ae0ab653c9c7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 16 13:51:16 2015 +0200 FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector. - the idea is that a GLMoleculeObject may only remove itself _after_ each and every contained Observer has gotten the subjectKilled() signal from the Observables. Only then will destroying the Object and its members thereby not cause any signOff() which try to access Observables or their channels which are no longer present. This can be imagined as a graph where we have to start destroying object at the very bottom. - This is the avoid the following conflict: A superior object gets note of a molecule to be removed. It sends the visual representation a signal to remove itself, which causes it to use signOff(). On a parallel track (in another thread) we have the observed object calling subjectKilled() to inform any Observer about its immediate destruction. These two tracks collide. Now, we let first pass all subjectKilled() and when the last Observable has gotten its signal, we begin destroying the visual rep. - rerouted signal/slots accordingly. commit d0225f4933595168bf533fabce90f7d419db754a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 16 10:59:22 2015 +0200 FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver(). - we just take note that we are signedOff. commit 568a2ce22f8ef6124b26c0e1d410ebc7af6cff91 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 16 10:58:31 2015 +0200 FIX: GLWorldScene has additional moleculePrepared... slots and signals. - i.e. we first insert into MoleculesInMap via direct connection and then signal is emitted (queued) to construct the actual GLMoleculeObject_molecule. commit 5e96c742ba17709d74218898f5f708dbbf5228bb Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 16 10:56:48 2015 +0200 FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box. - we don't longer need the hack as we have the molecule cleverly updating the box and an ObservedValue. commit d9ca9621d208e1af1fdaf75e5e2c1b5022e8e459 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 15 11:08:37 2015 +0200 QtFavoriteActions uses ObservedValue for checking last queued action's name. commit 35ccc012ef350e6eb15b273b40f361af989bc6ae Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Oct 15 11:08:09 2015 +0200 tempcommit: FIX: ActionQueue was setting lastchangedaction twice. Put into Fix_ActionQueue... branch commit f7a37da6c306abfadb52abc833485cdeedf65874 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 14 11:18:05 2015 +0200 FIX: Fitting domain to window on QtMainWindow's init. commit 405dc5ea68d53a7ed220e143bb0dfe7082866028 Merge: 14a618b 62d092e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 22:14:45 2015 +0200 Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.2 commit 62d092e08dbdb67e4f00547587c38322bf8bb828 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Sep 9 00:12:20 2015 +0200 Rewrote ChargeSmearer to use visitor pattern. - this is used for going over the bspline domain. - we need it when the support does not fit onto grid and when we need to recalculate the normalization. commit 17e4fde191dda907bf7bd206803886c13e02d440 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 7 21:03:37 2015 +0200 Added new option DoSmearElectronicCharges to FragmentationAutomationAction. - this uses ChargeSmearer: is prepared in InterfaceVMGJob and used in WindowGrid_converter. - VMGJob and VMGFragmentController need to pass along the DoSmearCharges option from the command-line. commit 445ce6d3846182eaf130a6a73ea863d0a443e6f0 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 7 08:25:28 2015 +0200 Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then write values. - this is required for smearing electronic charge distributions as we then write also neighboring values. commit cceb8cfe148cf346613694b5f15bde9f95e63393 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Sep 2 11:16:58 2015 +0200 Added ChargeSmearer that is only compiled for CONDVMG. - we store the spline values in a singleton such that they are calculated only once. commit 92232f71902106c7de16c1208aa802471f88fbb1 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Sep 11 16:14:00 2015 +0200 Adding warning when inter-distance is given less then minimum required rcut. commit cee9e8b8d814bc0aaefacaf9bdc81d5ca2f2876b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 1 15:47:28 2015 +0200 Added Interfragmenter::findLargestCutoff() to find largest Rcut not causing additional inter-fragments. - so far, the function is only used in FragmentationAction by merely printing the distance. commit b1c5f46c2e8356c3a5cb7319f77fe3e21793f787 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 1 15:46:05 2015 +0200 Interfragmenter now combines two fragments up to (in sum) till MaxOrder. - before only fragments of each MaxOrder were allowed, now the sum of their bond order must not exceed maxOrder, i.e. MaxOrder of 4 means 1+1, 1+2, 1+3, 2+2, 3+1, 2+1, 1+1 (with order of left and right fragment that are joined). commit 0d90534c2cfcca7121d5161e6f235225bdb4c0df Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 1 10:31:54 2015 +0200 Exracted several functions out of Interfragmenter::operator(). - extracted Interfragmenter::getAtomKeysetMap(), ::getNeighborsOutsideMolecule(), ::getAtomSpecificKeySetMap(), ::combineFragments(). - this is preparatory for enhancing the Interfragmenter to automatically ascertaining a certain "distance" between fragments for long-range interactions. That is, we may afterwards smear out nuclear and electronic charge distributions up to said distance without them overlapping outside of a present fragments (i.e. without capturing their short-range interactions elsewhere). commit 7537d191a569f0b72f4ef6db9b9ae70d575a463f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Mar 16 17:05:28 2015 +0100 Removing setting net force to zero and setting hasForce to true. commit 00d815ca595052983db7c34a5f62e31c775c680e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 14 12:58:32 2015 +0100 FIX: Need to divide by global number of particles, when summing later, in ExportSolution. commit 6e73f5af95ffb4eb1a979d776df10f17828e74f9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Oct 26 00:01:51 2014 +0200 Added debugging changes to InterfaceVMGJob on force summation. commit ff347fc31ed5cd23e7ad30c79dd005ca9145acb2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 7 12:21:09 2015 +0100 Added gathering of full and longrange forces into extra file. - added new structs to VMGDataFusedMap for summation. - tempcommit: we do not have the full index set available, hence it just accumulated all indices from all fragments into a sorted set and use this in lieu of the full index set. We need to check how the full solution is constructed and how indices to the particles and their force vectors can be assigned. - extended printFullSolution() by another table with short- and long-range forces. commit 20bb3b83b5704876159d8aeede5c88f78cb27559 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Oct 26 00:00:30 2014 +0200 MPQCData now also uses FragmentForces (instead of typedef forcevector). - required small changes to MPQCCommandJob due to changed typedef. - we need to maintain the old code which used vector of forces. Therefore, the serialization version of MPQCData is increased and a simple conversion routine added. commit 94db134a7b8bcdb17a2134fe1c6ca1aed4aded49 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 25 23:56:32 2014 +0200 Again changes to obtain correct longrange forces, also forces are optional. - renamed particle_forces -> forces to make it consistent with MPQCData_Fused. - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the latter cannot serve as template arguments. - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t. - changed ConvertMPQCDataToForceMap() into template function ConvertDataToForceMap(), working also on VMGDataForceMap_t. - this required changes in FragmentationShortRangeResults. - FragmentationLongRangeResults now also converts the longrange forces correctly. - AnalyseFragmentResults now prints also a ..VMGForces.dat file. - VMGData's forces are now optional to some degree and analysis chain can deal with it. - introducing forces we must still maintain working code when results without forces are calculated (e.g. as in the regression tests). Hence, a boolean im VMGData and FragmentationLongRangeResults states whether forces have been found or not and whether these should be summed up or not subsequently. commit 14a618bda4c5471ea8d26d9429a8c964bd366dff Merge: b19f280 b61bd5e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 22:10:12 2015 +0200 Merge branch 'Fix_debianpackage' into Candidate_v1.5.2 commit b19f2801b7152275a338f8cc95c051ccd1679bb7 Merge: 18f47f8 24f4251 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 22:10:00 2015 +0200 Merge branch 'Fix_ActionQueue_lastchangedaction' into Candidate_v1.5.2 commit 18f47f88da033fc8b97a339b874684f5aba29199 Merge: 0a3449a dace6c7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 22:09:38 2015 +0200 Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.2 commit 0a3449a7a998a2d08cf2b499e980ab657da627b8 Merge: dcff593 2f429ef Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 22:09:22 2015 +0200 Merge branch 'Better_HBondDistances' into Candidate_v1.5.2 commit dcff593de06c56b6b49d074d77955a90c552aaa2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Aug 31 14:38:50 2015 +0200 Implemented more efficient per-molecule bounding box information. - molecule now has internal bimaps to know the extent of itself in a cheap way, right map needs to be multiset_of to allow for non-unique values. - moved BoundingBoxInfo from GLMolObject to molecule. - is itself a Cacheable and is requested from GLMoleculeObject_molecule on new channel BoundingBoxChanged. - Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved. - in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry. commit a06378771ff430b3ce4652d680ae761a08426668 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Aug 31 14:38:30 2015 +0200 FIX: Removed double coding in molecule::erase(). commit 59e799680d2829d1437a7c22cb6820332ca100a5 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Oct 13 16:33:52 2015 +0200 FIX: World needs to first destroy the atom, then release its ids. commit ceaab1dbd47046505deba359f3a96512689de872 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 29 09:40:52 2015 +0200 AddAtom now adds a molecule (atom always associated with a molecule). - also by default, constructs a new molecule if none has been selected. - we missed changing the atom id on redo (new ones have different ids) and especially now telling the associated molecule about it. This is changed with a new molecule::changeAtomId(). commit b61bd5e8f51d73a916f0e0a2fcd4dcadcf84dfd8 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 2 23:10:12 2015 +0200 Fixed levmar m4 to use pkgconfig and locate. - we don't need to give with-levmar which allows debuild to make use of the installed package. commit 6227207a85bc7078c5be7985f12def5bac3f8287 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 2 23:09:53 2015 +0200 Added all required libboost.. to Build-depends. commit 3c6b4067162cb45d4e7ac87de102c3c8683d0a5b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 28 12:41:00 2015 +0200 Changed debian files to heber@molecuilder.com and changed boost dep. - we now just depend on libboost-dev (i.e. on all). commit 2f429ef69adf29a1bf0267338e9cecd1fb5b238c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 22 20:02:47 2015 +0200 Elements are now parsed as string (and tried for being int). - this allows to parse both "He" and "2", i.e. both symbol and atomic number. - this works for both command-line and Python. commit 3b1c369fabf5039957cb70e0059346c668d0eebf Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Sep 11 08:40:03 2015 +0200 Entered HBondDistance results from VSpeShape into elements_db. - we now have single bond distances for all elements from 1 to 37. They are mostly consistent with the old values (but some are not, e.g. for element no 20, but they look like copied). commit c85c2e7c1a8f696987bf232998d8eef09d386b99 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Sep 11 03:33:54 2015 +0200 FIX: Element's HBondDistance and HBondAngle were not initialized as -1. - this causes faulty behavior with saturate-atoms (e.g. Li) which showed the bug. - TESTFIX: ElementUnitTest adapted to new default behavior. commit 4f8079f804337514271581f8a67c750b656f2fbb Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Sep 10 17:16:57 2015 +0200 Added Hbonddistance and -angle for sodium (Na). commit e3c4c532b457c1d83d8ac94e74300e037b757ace Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Sep 10 16:41:24 2015 +0200 MpqcParser additionally allows to save optimization jobs. - this is enabled via a new flag "jobtype" that can be either Default or Optimization. - also storing "checkpoint = no" per default for all mpqc input files. This is a safety measures such that no old checkpoint files are used that reside in the same folder accidentally. This is especially important for fragment files. - TESTFIX: changed all regression tests comparing against .in files, added new checkpoint statement. - TESTFIX: changed unit test ParserMpqcUnitTest in the same manner. commit 6c30ab3e28b74461e5739b1fae84da32b57c8642 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Sep 10 16:19:41 2015 +0200 Assertion in SaturateBond now states element. commit d79ca1b812618b68d1781fb9ef48651c790f66f0 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Sep 30 19:54:29 2015 +0200 FIX: SaturateAction would use double instead of single hydrogen bond length. commit 2a7dbe1527726bfd2bc8d6793a86c59deefc3fdf Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 8 10:17:13 2015 +0200 FIX: Help on SetBoundaryConditionsAction did not have capitalized condition name. commit 83a425eb7c3e26118a81096a43c79ffe877b2113 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 25 12:49:02 2014 +0200 Split off sampled_potential im VMGDataMap_t into separate fusion container. - this should correct the output in ..._VMGEnergy.dat commit ce98747dfef7546f47996405283750bc34c9ad5d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Mar 20 18:30:19 2014 +0100 Added extraction of long-range forces from VMGData's array f. commit d200ae2e4a4f8002d6ef527fd7bfa418be477b9c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Mar 20 18:31:42 2014 +0100 Added new SetValues FragmentForces. - struct is particle_forces used in fusion maps and vectors. commit 057c8a49f208862ececbcb5c1adeaf0566d89313 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 7 12:18:59 2015 +0100 FIX: When there's just a single fragment, don't remove the fullsolution. - this usually causes some assert to hit when we test the long-range calculation on a single water molecule where there's only a single fragment and it conincides with the full molecule. Hence, the full solution calculation does not cause an extra fragment job. commit 9593d16ae241f82c256733f785601e2e0cfb9b29 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 17 19:29:19 2014 +0200 FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. - note that so far domains needs to be cubic. commit c20839bcb1af30decfbda10a56579a6b43c683be Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Oct 25 09:54:37 2014 +0200 FIX: Shared libraries's Makefile.am rules are now consistent. - pkgconfig is just given once (in src/Makefile.am). - all have version information, including now pyMoleCuilder.so. commit 24f425178ef9717a191dfb42f15da6fc45bbc899 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit dace6c77620134a6d8c643e895a7d94794d97f13 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 4 14:26:53 2015 +0200 FIX: tests/GuiChecks/atlocal lacked valgrind variable. - note that running molecuilder through valgrind currently produces loads of error messages all connected to the Qt and/or python parts and have in the vast majority nothing to do with molecuilder. We will use our own memory debugger until suitable suppression files can be found. Until that not sensible debugging of memory leaks is possible in the GUI part of the code. commit 08d9df7e636ea0df65e73df162455c8f47deb448 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Oct 2 11:59:44 2015 +0200 FIX: Rename codepatterns -> libcodepatterns. - updated makeDebianPackage.sh to compile with multiple cores. commit ba353982fb33936c0b6e4c92a14dba221dc08c56 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 29 13:47:45 2015 +0200 Package CodePatterns is now called libcodepatterns. - updated m4 file. - also updated .pc files. ----------------------------------------------------------------------- hooks/post-receive --