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The branch, stable has been updated via 7e3e41e91a0984ec94e5f979ff3e508719937876 (commit) via 6029a669c919139fdd1b0addd74222bb7f5b554d (commit) via caece420aa82700e7677c24d798be09340eed2bd (commit) via 74459a014f105522f5db261ac058254c9aa7c0c7 (commit) via 415ddd8a44847064389eb3783769c8531725615c (commit) via 975b83561278df8e9f4dc52a379883b4c726b00e (commit) via cc6e5c6fa2abf74b6087c374278e2a20dc23706e (commit) via 0d416866348175de64612b7f88582c36f2167054 (commit) via c09f94cdc954e2f3fdb4fb3874c75bef78adc1f7 (commit) via d9f2b33b806913c901266dd646463bfa637d037e (commit) via 7fc447cf6e5f39763e2d76adfc3ffe01ea36ec89 (commit) via af53848739f011c706c567deb35d90e7f2dab281 (commit) via 36053cf50efb19714f34f33fe6fe7ef9b53476d0 (commit) via ec43a23d0170171eb03b8ba386b9614f17aac7f4 (commit) via 5eaa23bd73ba44a21854e46c30abc8410b66a897 (commit) via d76d652c439e3216a6d56d8fb74dd0b915b8ca4a (commit) via 5c78e3afa08a9e0a73d348dd405a8249cdf7fbdd (commit) via 0b3cf478c9569fcda12e7fa2a23ce41dce06d3a3 (commit) via e3f9b80d5a45922ea986e97533d2de2e0d584f83 (commit) via 6072456df16de51edeb395389b4617d370a9e89b (commit) via 606c24d442402928a4a643fa8f1452585aa85583 (commit) via 5f364e928bcbf3272d4c59007b121e86fd612d79 (commit) via e8fde00b42f0f7fee23203a3df8f0254c65be588 (commit) via 830adfc5dc23b3ce24ece17705ff89ef12744705 (commit) via 4d5dfa6c9840a4a17e5a4e6555d544f50615248e (commit) via ae68b5f76dedc09e012623d28c2fec0b821dda69 (commit) via a2a2f74e1b5173a3e4d4090d8ec2a57e0f765552 (commit) via c9db50416501589af2b7bec9760cc6129d4b6fe3 (commit) via 9bac150dd34b92ce8dd42a103b5790c0ed592303 (commit) via f47e00b9f5f390d99eb3b523faf1a7e16ed49fd6 (commit) via 237f9339687fa2ab9fabd26196828a79d99f1307 (commit) via ec7511a359cc1cad57d684179dda96580726d26d (commit) via 4b10fd259e02818d3e9bbe2f0ba3ab5dfa66f4ae (commit) via 57388c9454d489af0cc8b661fac65879bf5c122c (commit) from 5a2d986e91cb234cc443e56577928ffc34be1b35 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 7e3e41e91a0984ec94e5f979ff3e508719937876 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri May 2 08:41:58 2014 +0200 Set version to 1.4.5. - MoleCuilder library is now 13:3:1. - Codename "Half marathon" (If you train for such an event, try to finish in less than one hour and forty-five minutes). commit 6029a669c919139fdd1b0addd74222bb7f5b554d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Apr 13 14:48:51 2014 +0200 Added largely extended userguide with some images into subfolder of doc folder. - Munched docbook into something workable: - the big problem was out-of-source build in conjunction with the figures in the userguide. - I did not try hard enough with img.src.path but used entityref instead together with a catalog file. - so in all, we have followed: - http://movementarian.org/docs/docbook-autotools/index.html - http://www.sagehill.net/docbookxsl/GraphicsLocations.html - ... this was a long way ... - am_conditioning on both xsltproc and fop. commit caece420aa82700e7677c24d798be09340eed2bd Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Mar 20 18:23:35 2014 +0100 Enhanced documentation significantly. - went through all of the constructs and updated each. - enhanced documentation ofr Fragmentation::FragmentMolecule(). commit 74459a014f105522f5db261ac058254c9aa7c0c7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Feb 19 20:35:28 2014 +0100 Added --disable-action-thread to allow disabling of extra run thread. - this removes all functionality related to having ActionQueue::run() executed in a distinct thread. - the extra thread is currently disabled by default as probably some stuff in QtGUI will be broken (bonds disappearing while being drawn ...) commit 415ddd8a44847064389eb3783769c8531725615c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 00:56:36 2013 +0200 ActionQueue now contains a run thread. - otherwise the progress bar of the QtMainWindow cannot be seen as waitForResults() takes up all of the executing thread. - added mutex for operations modifying the queue. - added ActionQueue::run() and ::stop(), used by friend stopQueue(). - insertAction() now makes use of a tempqueue that is added to true queue during run() instead of calling the actions directly. - new stopQueue() in cleanUp.hpp is used by module_exit in pyMoleCuilder and in main() before saveAll(). - cleanup: printTiming() requires now list of action tokens and added new stopAndPurgeQueue() to place waiting for Actions to end into extra function. - added ActionQueue::wait() which allows for synchronization in python scripts, is ignored in session python scripts. Otherwise we wait for ActionQueue's queue to empty during execution of load-session which hangs. - DOCU: added note to python documentation. - added waitQueue() also to purgeStaticInstances(). - static UIFactory::isFactoryPresent() added that allows checking whether we have a UI or are executed within a python script (i.e. pyMoleCuilder). - DOCU: Extended docu on threads and who this affects python scripts. - TESTFIX: changed regression tests on storing python sessions. commit 975b83561278df8e9f4dc52a379883b4c726b00e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Feb 20 21:23:42 2014 +0100 Added ActionQueue::insertAction(). - this is preparatory for allowing Actions to be executed inside an Action's performCall() body. Once ActionQueue::run() is executed in its own thread these command calls would just append an Action to the queue and not run the command. commit cc6e5c6fa2abf74b6087c374278e2a20dc23706e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Sep 28 02:59:47 2013 +0200 Replaced Reactions by simple function exported to pyMoleCuilder. - Reactions are a bad idea from the start, calculations do not need to be undone. Hence, why make them into an Action that is specifically undoable? - removed all Reaction..-related files. - removed ActinQueue::getLastAction(). - removed CalculateBoundingBoxAction, CalculateCellVolumeAction, and CalculateMolarMassAction, replaced by small function in Python folder. - TESTFIX: removed associated regression tests in Analysis. - modified boxmaker.py.in as names of functions changed. - removed Actions/pyMoleCuilder.cpp, is redunant with PythonScripting_impl.hpp. commit 0d416866348175de64612b7f88582c36f2167054 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Aug 29 01:05:38 2013 +0200 Allow setting of invalid values in Value class, Action::performCall() catches ParameterExceptions. Value changes: - Values are now checked with get(). - having the Actions fill their parameters on instantiation may lead to invalid values because actions that, e.g. add an atom and thereby make a so far invalid atomic id now valid, still have to get executed. - hence, we allow setting of invalid values. Validity is check/enforced on get(), i.e. when the Action is actually performed and not before. This is also the very moment where the parameters are first required to be valid. - Parameter::clone() and copy cstor must not use get() as invalid values are there still allowed. - TESTFIX: Value behavior changed. - TESTFIX: regression test add atom outside boundary is working again. - TESTFIX: regression tests load/store-session would be skipped as loading non-present file fails now. We use --help --actionname instead. Action changes: - are turned into Action::failure. - ActionQueue calling an Action wrapped in try/catch-block for ActionFailure. - removed try/catch in doUI(). - as exception (will) occur in ActionQueue's queue_thread, we need to catch it there. As the only thing we do is set the exit flag of the World. We can do this in ActionQueue as well. commit c09f94cdc954e2f3fdb4fb3874c75bef78adc1f7 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 00:19:31 2013 +0200 Transformed FragmentationAutomationAction into a Process. - Removed MaxSteps parameter in Process' cstor (MaxSteps is not a const member anyway). - Action preprocessor magic knows new token BASECLASS by which derivation may be switche from Action to Process (defaults to Action). - FragmentationAutomationAction::performCall() uses start(), stop(), and setMaxSteps(). commit d9f2b33b806913c901266dd646463bfa637d037e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Sep 26 01:02:43 2013 +0200 SpecificFragmentController has a ref to an updatehandler to call in case of new results. - SpecificFragmentController::ResultsContainer::waitForResults() will regularly call the update handler which informs via Process::setCurrSteps(). commit 7fc447cf6e5f39763e2d76adfc3ffe01ea36ec89 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Aug 29 00:08:39 2013 +0200 Renamed ActionsQueue's queue -> actionqueue. commit af53848739f011c706c567deb35d90e7f2dab281 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 03:58:34 2013 +0200 Actions can now clone() and split off prepare() from call(). - ActionQueue now separates call phase into clone(), prepare(), and call(). - ActionQueue's dstor releases Actions in deque. - CurrentAction is an index as push_back always invalidates iterator. - ActionQueue_t is now a simple vector of ptrs. - call() is now non-interactive, (maybe) interactive part is placed in prepare() where dialogs are used to fill parameters. - only fully prepared Actions are placed in ActionQueue. - ActionQueue obtains action instances from Registry, copies, prepares them, and places them in the queue. - Action::clone() gets QueryOptions as param. This lets us either clone without params or really copy the instance. - If action is called as COMMAND, params have been filled already. - Reactions require a ActionQueue::getLastAction() to actually obtain result of (cloned) Action. - FIX: Calculation now has const has...() and getResult(). commit 36053cf50efb19714f34f33fe6fe7ef9b53476d0 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 02:08:29 2013 +0200 OptionRegistry is now filled by ActionRegistry() not by Action's cstors. - otherwise we cannot instantiate new actions as they re-register options. commit ec43a23d0170171eb03b8ba386b9614f17aac7f4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 15:19:58 2013 +0200 FIX: Process's getters are now const member functions. commit 5eaa23bd73ba44a21854e46c30abc8410b66a897 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Feb 27 18:45:12 2014 +0100 Added sensible default values to MolecularDynamics sequence of Actions. commit d76d652c439e3216a6d56d8fb74dd0b915b8ca4a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Aug 30 23:07:00 2013 +0200 FIX: MPQCDataFragmentMap_t can be summed up in FragmentationShortRangeResults already. - removed from FragmentationLongRangeResults and FragmentationChargeDensity. - this allows to store also short-range only homologies (and calculate potentials without long-range info). commit 5c78e3afa08a9e0a73d348dd405a8249cdf7fbdd Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Aug 29 00:14:02 2013 +0200 FIX: Implemented VersionAction. - yes, it never printed the actual version. commit 0b3cf478c9569fcda12e7fa2a23ce41dce06d3a3 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Feb 20 21:01:25 2014 +0100 FIX: CommandLineWindow::display() did not use present ActionQueue ref. commit e3f9b80d5a45922ea986e97533d2de2e0d584f83 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Feb 20 21:01:11 2014 +0100 FIX: WorldTime's dstor is now virtual. commit 6072456df16de51edeb395389b4617d370a9e89b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Feb 19 01:07:23 2014 +0100 TESTFIX: regression test load-session uses python scripts in pre. - before we used those from post but this invalidates the clear split between what's before and what's after the test. commit 606c24d442402928a4a643fa8f1452585aa85583 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Aug 29 09:49:21 2013 +0200 FIX: Newly created default atom has element hydrogen. - also when instantiated by VectorInterface. - FIX: for cstor with VectorInterface AtomicPosition was not correctly sized. commit 5f364e928bcbf3272d4c59007b121e86fd612d79 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Aug 29 01:07:56 2013 +0200 FIX: Fix typo in error msg of FillRegularGridAction. commit e8fde00b42f0f7fee23203a3df8f0254c65be588 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Mar 30 00:23:43 2014 +0100 FIX: python regression test BoxMaker did not check for 'units'. commit 830adfc5dc23b3ce24ece17705ff89ef12744705 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 22 23:16:48 2014 +0100 FIX: Added/corrected levmar and jobmarket messages in configure. commit 4d5dfa6c9840a4a17e5a4e6555d544f50615248e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Mar 29 23:24:44 2014 +0100 FIX: disabled levmar no longer pulls in fortran compiler requirement. commit ae68b5f76dedc09e012623d28c2fec0b821dda69 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 1 17:26:02 2014 +0100 Fixed some boost serialization static warnings. commit a2a2f74e1b5173a3e4d4090d8ec2a57e0f765552 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 1 16:42:09 2014 +0100 Huge warning fix. - fixed unused variables. - fixed set but unused variables. - fixed signed vs. unsigned int comparison. - fixed static_warning_test<false, 98> (commented out _IMPLEMENT). commit c9db50416501589af2b7bec9760cc6129d4b6fe3 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Nov 11 10:49:57 2013 +0100 FIX: Removed doubly occuring disclaimer in testsuite files in fragmentation. commit 9bac150dd34b92ce8dd42a103b5790c0ed592303 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Jan 11 22:58:31 2014 +0100 FIX: MolecularDynamicsAction needs to clear fragment results after integration. commit f47e00b9f5f390d99eb3b523faf1a7e16ed49fd6 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Jan 11 21:57:55 2014 +0100 FIX: SubgraphDissectionAction is now a MakroAction, fixed store-session. - store-session would skip the select-atoms part. - hence, now we just write SubgraphDissection() command to python script. commit 237f9339687fa2ab9fabd26196828a79d99f1307 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Feb 4 21:32:08 2014 +0100 FIX: MolecularDynamicsAction now prepares normally not inside performCall(). - added protected ActionSequence::removeAction() and pass-thru in MakroAction. - added MakroAction::fillOwnDialog(): We did not cleanly implement the MakroAction's dialogs before. We need to populate queries from the sequeence of Actions and from the MakroAction itself (e.g. for loop count). For the latter, we need another new function for this. - MolecularDynamicsAction removes output action from sequence if not desired. - removed (another) fillAllDialog from MakroAction::performCall(). This has been the source of doubly occuring dialogs (and dialog becoming ever larger on multiple calls). - MolecularDynamicsAction::prepare() also just uses ActionRegistry whose ref is passed as parameter and does not (directly) access ActionQueue. commit ec7511a359cc1cad57d684179dda96580726d26d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Nov 11 10:49:19 2013 +0100 FIX: CyclicStructureAnalysis falsely used DFS, skipped some cycles. - FIX: CyclicStructureAnalysis did use DFS instead of BFS for finding cycles. Note that CyclicStructureAnalysis with coronene would find supercycles and not the smaller interconnected ones. - FIX: Cycles were skipped when all bonds marked cyclic, not enough. In interconnected aromatic rings, bonds may very well be marked as cyclic from earlier extraction of cycles and yet the specific cycle might not have been found yet (e.g. coronene). In this case we now check whether this particular cycle has already been extracted and only skip if so. - TESTFIX: added new fragmentation regression tests on some metallic systems. - this is mainly for regression on bond graph detection and cycle analysis. commit 4b10fd259e02818d3e9bbe2f0ba3ab5dfa66f4ae Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Oct 23 23:57:07 2013 +0200 XmlParser::load() now gives each different charge a different element. - this allows search&replace to the correct element afterwards. commit 57388c9454d489af0cc8b661fac65879bf5c122c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Feb 1 17:26:17 2014 +0100 FIX: Test on skipping load/store session from python script was wrong way round. - FIX: executePythonScript() did not return values, hence was always false. ----------------------------------------------------------------------- Summary of changes: configure.ac | 45 +- doc/Makefile.am | 56 +- doc/userguide.xml | 230 --- doc/userguide/Makefile.am | 4 + doc/userguide/catalog.xml.in | 23 + doc/userguide/createguide.sh | 4 + doc/userguide/css/html.css | 325 ++++ doc/userguide/pictures/dialog_add-atom_tooltip.png | Bin 0 -> 27388 bytes doc/userguide/pictures/dialog_box.png | Bin 0 -> 21176 bytes doc/userguide/pictures/dialog_complex.png | Bin 0 -> 41676 bytes doc/userguide/pictures/dialog_exit.png | Bin 0 -> 22179 bytes doc/userguide/pictures/example_basic_view.png | Bin 0 -> 84818 bytes doc/{ => userguide/pictures}/molecuilder_logo.png | Bin 26634 -> 26634 bytes doc/userguide/userguide.xml | 2043 ++++++++++++++++++++ m4/ax_check_docbook.m4 | 56 + src/Actions/Action.cpp | 99 +- src/Actions/Action.hpp | 21 +- src/Actions/ActionQueue.cpp | 160 ++- src/Actions/ActionQueue.hpp | 88 +- src/Actions/ActionRegistry.cpp | 77 +- src/Actions/ActionRegistry.hpp | 2 + src/Actions/ActionSequence.cpp | 24 +- src/Actions/ActionSequence.hpp | 8 + src/Actions/Action_impl_header.hpp | 40 +- src/Actions/Action_impl_pre.hpp | 17 +- .../AnalysisAction/CalculateBoundingBoxAction.cpp | 78 - .../AnalysisAction/CalculateBoundingBoxAction.def | 37 - .../AnalysisAction/CalculateBoundingBoxAction.hpp | 22 - .../AnalysisAction/CalculateCellVolumeAction.cpp | 67 - .../AnalysisAction/CalculateCellVolumeAction.def | 35 - .../AnalysisAction/CalculateCellVolumeAction.hpp | 22 - .../AnalysisAction/CalculateMolarMassAction.cpp | 71 - .../AnalysisAction/CalculateMolarMassAction.def | 35 - .../AnalysisAction/CalculateMolarMassAction.hpp | 22 - src/Actions/AtomsCalculation.hpp | 2 + src/Actions/AtomsCalculation_impl.hpp | 9 + src/Actions/Calculation.hpp | 6 +- src/Actions/Calculation_impl.hpp | 10 +- src/Actions/CommandAction/VersionAction.cpp | 1 + src/Actions/FillAction/FillRegularGridAction.cpp | 2 +- .../AnalyseFragmentationResultsAction.cpp | 31 +- .../AnalyseFragmentationResultsAction.def | 2 +- .../FragmentationAction/FragmentationAction.def | 7 +- .../FragmentationAutomationAction.cpp | 19 +- .../FragmentationAutomationAction.def | 2 + .../FragmentationAutomationAction.hpp | 2 +- .../MolecularDynamicsAction.cpp | 36 +- .../MolecularDynamicsAction.def | 2 +- .../MolecularDynamicsAction.hpp | 106 - src/Actions/GlobalListOfActions.hpp | 23 +- .../GraphAction/SubgraphDissectionAction.cpp | 82 +- .../GraphAction/SubgraphDissectionAction.def | 4 +- .../GraphAction/SubgraphDissectionAction.hpp | 108 +- src/Actions/Makefile.am | 33 +- src/Actions/MakroAction.cpp | 42 +- src/Actions/MakroAction.hpp | 25 +- src/Actions/MakroAction_impl_header.hpp | 37 +- src/Actions/MakroAction_impl_pre.hpp | 19 +- src/Actions/ManipulateAtomsProcess.cpp | 10 +- src/Actions/ManipulateAtomsProcess.hpp | 6 +- src/Actions/MethodAction.cpp | 8 + src/Actions/MethodAction.hpp | 2 + .../MoleculeAction/VerletIntegrationAction.def | 2 +- src/Actions/PotentialAction/FitPotentialAction.def | 2 +- src/Actions/Process.cpp | 10 +- src/Actions/Process.hpp | 8 +- src/Actions/Reaction.hpp | 92 - src/Actions/Reaction_impl.hpp | 104 - src/Actions/Reaction_impl_header.hpp | 253 --- src/Actions/Reaction_impl_pre.hpp | 327 ---- .../SelectionAction/Atoms/AtomByIdAction.cpp | 2 + .../SelectionAction/Atoms/NotAtomByIdAction.cpp | 2 + src/Actions/ShapeAction/RemoveShapeAction.cpp | 2 +- src/Actions/ShapeAction/StretchShapeAction.cpp | 8 +- src/Actions/pyMoleCuilder.cpp | 147 -- src/Actions/unittests/ActionSequenceUnitTest.cpp | 18 + src/Analysis/analysis_correlation.cpp | 2 +- src/Atom/atom_atominfo.cpp | 6 +- src/Box.cpp | 9 +- src/Filling/Mesh/CubeMesh.cpp | 2 +- src/Fragmentation/AdaptivityMap.cpp | 2 +- .../Automation/SpecificFragmentController.cpp | 15 + .../Automation/SpecificFragmentController.hpp | 16 +- ...ificFragmentController_ResultContainer_impl.hpp | 8 +- src/Fragmentation/BondsPerShortestPath.cpp | 4 +- src/Fragmentation/Exporters/ExportGraph.cpp | 4 +- src/Fragmentation/Fragmentation.cpp | 51 +- src/Fragmentation/Homology/FragmentEdge.cpp | 6 +- src/Fragmentation/Homology/FragmentNode.cpp | 6 +- src/Fragmentation/Homology/HomologyContainer.hpp | 1 + src/Fragmentation/Homology/HomologyGraph.cpp | 6 +- .../Homology/unittests/FragmentEdgeUnitTest.cpp | 14 +- .../Homology/unittests/stubs/FragmentStub.cpp | 5 +- .../Containers/FragmentationChargeDensity.cpp | 8 - .../Containers/FragmentationChargeDensity.hpp | 6 - .../Containers/FragmentationLongRangeResults.cpp | 3 - .../Containers/FragmentationLongRangeResults.hpp | 4 - .../Containers/FragmentationResultContainer.hpp | 22 +- .../Containers/FragmentationShortRangeResults.cpp | 3 + .../Containers/FragmentationShortRangeResults.hpp | 4 + .../Summation/Containers/MPQCData.hpp | 1 + src/Fragmentation/Summation/IndexSetContainer.cpp | 4 +- src/Fragmentation/Summation/SetValues/Fragment.cpp | 5 +- .../SetValues/unittests/EigenvaluesUnitTest.cpp | 4 +- src/Fragmentation/fragmentation_helpers.cpp | 4 +- src/FunctionApproximation/Extractors.cpp | 2 +- .../FunctionApproximation.cpp | 2 +- src/Graph/CyclicStructureAnalysis.cpp | 114 +- src/Graph/CyclicStructureAnalysis.hpp | 1 + src/Jobs/MPQCCommandJob.cpp | 7 +- src/Jobs/MPQCJob.cpp | 6 +- src/Jobs/VMGJob.cpp | 7 +- src/Jobs/WindowGrid_converter.cpp | 44 +- src/Makefile.am | 3 +- src/Parameters/Parameter_impl.hpp | 5 +- .../Specific/TimeStepPresentValidator.cpp | 6 +- src/Parameters/Value_impl.hpp | 9 +- src/Parameters/unittests/ContinuousValueTest.cpp | 85 +- src/Parameters/unittests/DiscreteValueTest.cpp | 16 +- src/Parser/XmlParser.cpp | 14 +- .../Specifics/FourBodyPotential_Torsion.cpp | 1 + .../Specifics/ThreeBodyPotential_Angle.cpp | 1 + src/Python/Makefile.am | 9 +- src/Python/PythonScripting.cpp | 3 + src/Python/PythonScripting_impl.hpp | 41 +- src/Python/exit.cpp | 51 + src/Python/getBoundingBox.cpp | 68 + src/Python/getDomainVolume.cpp | 56 + src/Python/getSelectedMolarMass.cpp | 61 + src/Python/modules.hpp | 36 + src/Python/reinit.cpp | 53 + src/Python/wait.cpp | 53 + src/Shapes/BaseShapes.cpp | 10 +- src/Tesselation/boundary.cpp | 10 +- src/Tesselation/tesselation.cpp | 16 +- src/Tesselation/tesselationhelpers.cpp | 4 +- src/UIElements/CommandLineUI/CommandLineWindow.cpp | 5 +- src/UIElements/Dialog.cpp | 28 +- src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp | 8 + src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp | 2 + src/UIElements/Qt4/Query/QtQueryList.hpp | 2 +- src/UIElements/Qt4/Query/VectorQtQuery.cpp | 2 +- src/UIElements/UIFactory.hpp | 1 + .../Views/Qt4/Plotting/QSeisPlotPage.cpp | 19 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 4 +- src/UIElements/Views/Qt4/QtTimeLine.cpp | 6 +- src/WorldTime.hpp | 2 +- src/builder.cpp | 4 + src/builder_init.cpp | 7 +- src/builder_init.hpp | 1 - src/cleanUp.cpp | 53 +- src/cleanUp.hpp | 5 +- src/documentation/Makefile.am | 8 + src/documentation/code.dox | 9 +- src/documentation/constructs/actions.dox | 33 +- src/documentation/constructs/atoms.dox | 3 +- src/documentation/constructs/bondgraph.dox | 4 +- src/documentation/constructs/filling.dox | 18 +- src/documentation/constructs/fragmentation.dox | 50 +- src/documentation/constructs/potentials.dox | 7 +- src/documentation/constructs/serialization.dox | 44 +- src/documentation/constructs/shaperegistry.dox | 6 +- src/documentation/constructs/shapes.dox | 6 +- src/documentation/constructs/tesselation.dox | 17 +- src/documentation/constructs/validators.dox | 11 +- src/documentation/copyright.dox | 5 +- src/documentation/fileformats.dox | 4 +- src/documentation/future.dox | 16 +- src/documentation/install.dox | 6 +- src/documentation/launch.dox | 11 +- src/documentation/mainpage.dox | 16 +- src/documentation/tests/code-tests.dox | 6 +- src/documentation/tests/regression-tests.dox | 7 +- src/documentation/userguide.dox | 52 + src/documentation/userinterfaces/commandline.dox | 17 +- src/documentation/userinterfaces/graphical.dox | 23 +- src/documentation/userinterfaces/python.dox | 52 +- src/documentation/userinterfaces/textmenu.dox | 21 +- 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