source: src

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(edit) @5d18f3   7 weeks frederik.heber FIX: PotentialTrainer did not heed take-best correctly. - we used the … Candidate_v1.7.0 stable
(edit) @85dd16   7 weeks frederik.heber Adds new tab "All potentials". - tab lists all potentials from … Candidate_v1.7.0 stable
(edit) @a4b917   7 weeks frederik.heber Adds add and remove potential actions. - DOC: Adds missing actions to … Candidate_v1.7.0 stable
(edit) @a0d8aa   2 months frederik.heber PotentialFactory exposes particle type numbers. - Also, potentials … Candidate_v1.7.0 stable
(edit) @e83114   2 months frederik.heber StreamFactory_EmpiricalPotential creates potential instances with … Candidate_v1.7.0 stable
(edit) @72b6d7   2 months frederik.heber SerializablePotential's parameters_t is taken from FunctionModel. - … Candidate_v1.7.0 stable
(edit) @5a255af   2 months frederik.heber FIX: deserialized EmpiricalPotential lacked parameters. - with the … Candidate_v1.7.0 stable
(edit) @476781   2 months frederik.heber FIX: fixes several issues in QtHomologyList related to plotting. - … Candidate_v1.7.0 stable
(edit) @a93896   2 months frederik.heber Ignores pyMoleCuilder import in python script. - TEST: LoadSession … Candidate_v1.7.0 stable
(edit) @463bfb   3 months frederik.heber FIX: SaturateAction had typo in default. - this originated in 2390e63956. Candidate_v1.7.0 stable
(edit) @780bfa   3 months frederik.heber FIX: FormatParserStorage did not add parser instance on SetOutput. - … Candidate_v1.7.0 stable
(edit) @bcc29ca   3 months frederik.heber Splits off Undo mark actions. - Undo action has again no parameters … Candidate_v1.7.0 stable
(edit) @e0feb3   3 months frederik.heber Increases size of icons in toolbar. Candidate_v1.7.0 stable
(edit) @9cdab3   3 months frederik.heber Adds context menu "atom" to GLWorldView. Candidate_v1.7.0 stable
(edit) @ae9ad6   3 months frederik.heber Removes check in FragmentationAutomation's ReceiveResults. - we can … Candidate_v1.7.0 stable
(edit) @454b555   3 months frederik.heber Improved includes for Qt classes. - QT_CFLAGS needs to be set in … Candidate_v1.7.0 stable
(edit) @ce666c   3 months frederik.heber Adds double/triple H bond distance and angle for S, P. - these are … Candidate_v1.7.0 stable
(edit) @641550   3 months frederik.heber FIX: Fixes GetBondLength off-by-one. - in ad09292f6 we overlooked … Candidate_v1.7.0 stable
(edit) @c41ce0   3 months frederik.heber Adds qt_size and qt_position arguments to control Qt window size. - … Candidate_v1.7.0 stable
(edit) @6294b6   3 months frederik.heber MPQCJob mutes output on verbosity level 0 and unmutes else. - we … Candidate_v1.7.0 stable
(edit) @c099dc   3 months frederik.heber SetParserParameters prints old and new params. Candidate_v1.7.0 stable
(edit) @19832d   20 months frederik.heber BondGraph: returns 1. instead of -1. on miss. - when the symmetric … Candidate_v1.7.0 stable
(edit) @9782e20   20 months frederik.heber BondifyAction: added undo/redo. - DOC: fixed small typo in Action's … Candidate_v1.7.0 stable
(edit) @ad0929   20 months frederik.heber FIX: BondGraph::GetBondLength() accessed off by one. Candidate_v1.7.0 stable
(edit) @399c69   20 months frederik.heber Rewrote AddAction to use UndoRedoHelpers. Candidate_v1.7.0 stable
(edit) @0427d1   20 months frederik.heber FIX: ActionQueue no locked on CurrentAction access. - … Candidate_v1.7.0 stable
(edit) @5a479d   22 months frederik.heber Added python actions to generate all graph6 strings. - graph6 strings … Candidate_v1.7.0 stable
(edit) @44ce58   2 years frederik.heber FIX: solves xcb issues under ubuntu 22.04. - under Ubuntu 22.04 (with … Candidate_v1.7.0 stable
(edit) @d91a8f   3 years frederik.heber Added ClearHomologiesAction. - this is necessary during sampling … Candidate_v1.7.0 stable
(edit) @fb08cc   3 years frederik.heber Increases precision of distance-energy table. - PotentialTrainer's … Candidate_v1.7.0 stable
(edit) @80bf6e   3 years frederik.heber FIX: GeneratePotentialsAction generates all combination. Merge with … Candidate_v1.7.0 stable
(edit) @78e5cf   3 years frederik.heber Graph6Writer::write_elementlist uses least connected non-hydrogen. - … Candidate_v1.7.0 stable
(edit) @c8a442   3 years frederik.heber FIX: posix:time needs to use milliseconds. - floating-point seconds … Candidate_v1.7.0 stable
(edit) @1c0b0b   3 years frederik.heber Graph6Writer::write_elementlist uses BFS from boundary atom. - the … Candidate_v1.7.0 stable
(edit) @0daef6   3 years frederik.heber Added missing boost_chrono lib dep. Candidate_v1.7.0 stable
(edit) @30def8   3 years frederik.heber FIX: CommandLineParser's implicit argument does not work anymore. Candidate_v1.7.0 stable
(edit) @f71fc8   3 years frederik.heber FIX: SphericalPointDistribution used wrong type in default return. Candidate_v1.7.0 stable
(edit) @82e5fb   4 years frederik.heber Added option error-file to fit potential actions. - DOCU: Added … Candidate_v1.7.0 stable
(edit) @889067e   4 years frederik.heber Added force-overwrite to OutputAsAction. - DOCU: Also added … Candidate_v1.7.0 stable
(edit) @4b2207   4 years frederik.heber FIX: SaveEnergiesAction did not use correct units. - temperature was … Candidate_v1.7.0 stable
(edit) @20fc6f   4 years frederik.heber FIX: PotentialTrainer always ignored take-best-of param. Candidate_v1.7.0 stable
(edit) @9b0dcd   4 years frederik.heber Added potential-list argument to GeneratePotentialsAction. - DOCU: … Candidate_v1.7.0 stable
(edit) @c98620   4 years frederik.heber FIX: StreamFactory did not set BindingModel. - we streamed into a … Candidate_v1.7.0 stable
(edit) @698185   4 years frederik.heber FIX: Smaller fixes to CompoundPotential. Candidate_v1.7.0 stable
(edit) @55c494   4 years frederik.heber Added GeneratePotentialsAction. - this generates all potential … Candidate_v1.7.0 stable
(edit) @c4afdf3   4 years frederik.heber Extended BindingModel by comparators. - this allows placing them in … Candidate_v1.7.0 stable
(edit) @3f8238   4 years frederik.heber Added number of particle types getter to EmpiricalPotential. Candidate_v1.7.0 stable
(edit) @0c8989   4 years frederik.heber Enhanced assert message for IndexedVectors. Candidate_v1.7.0 stable
(edit) @923ce2   4 years frederik.heber Added get_masses to python functionality. Candidate_v1.7.0 stable
(edit) @ecc050   4 years frederik.heber pyMoleCuilder's wait() has return value. - tells whether actions have … Candidate_v1.7.0 stable
(edit) @8c9cce   4 years frederik.heber Numpy exporters are fully operational. - TESTS: added test on working … Candidate_v1.7.0 stable
(edit) @7ca7d5d   4 years frederik.heber Adding NUMPY cppflags, ldflags, and libs. Candidate_v1.7.0 stable
(edit) @7b1824   4 years frederik.heber Exporting numpy getter/setter for positions, velocities, forces. Candidate_v1.7.0 stable
(edit) @6b7765   4 years frederik.heber Added small lib to capture stdout and stderr in jupyter. - we need to … Candidate_v1.7.0 stable
(edit) @999eaf   5 years frederik.heber Added EvaluateStabilityAction to estimate a molecule's stability. - … Candidate_v1.7.0 stable
(edit) @5aa337   5 years frederik.heber FIX: HomologyGraph did not heed bond degree correctly. - the graph … Candidate_v1.7.0 stable
(edit) @564f17   5 years frederik.heber Extended HomologyContainer::value_t by fragment energy. - renamed … Candidate_v1.7.0 stable
(edit) @e0e77e   5 years frederik.heber Switch off defragmenting of World's atomic id pool. - with increased … Candidate_v1.7.0 stable
(edit) @2390e6   5 years frederik.heber SaturateAction may use outer shell information. - when considering … Candidate_v1.7.0 stable
(edit) @87c1cc   5 years frederik.heber FIX: NotAtomByElementAction used atom ptr instead of ids for undo state. Candidate_v1.7.0 stable
(edit) @d54e37   5 years frederik.heber FIX: PopAtomAction must not store atom ptr but atom ids for undoing. Candidate_v1.7.0 stable
(edit) @7df863   5 years frederik.heber Added repr to all boost python vector instances. Candidate_v1.7.0 stable
(edit) @7d2ee1   5 years frederik.heber ActionHistory's marked states is now a stack. - i.e. multiple marks … Candidate_v1.7.0 stable
(edit) @0fbea3   5 years frederik.heber FIX: set all analysis actions hasUndo to false. - none of these … Candidate_v1.7.0 stable
(edit) @0ec9f5   5 years frederik.heber Added UndoMarkAction. NOTE: This action is necessary as not all … Candidate_v1.7.0 stable
(edit) @5061d9   5 years frederik.heber Added action to print selected atoms as graph6 string. - added … Candidate_v1.7.0 stable
(edit) @cd79d0   5 years frederik.heber Undo and Redo state debug info about involved action. Candidate_v1.7.0 stable
(edit) @0a1461   5 years frederik.heber FIX: Polyhedra of N=3 did not rescale to bondlength in 2nd comp. Candidate_v1.7.0 stable
(edit) @5196ca   5 years frederik.heber Making out-of-bounds access in Element's tables more explicit. Candidate_v1.7.0 stable
(edit) @ff2c52   5 years frederik.heber ParseHomologies action lists values and their energy range per key. - … Candidate_v1.7.0 stable
(edit) @9171d8   5 years frederik.heber Using lowest contribution found in homology container. - also listing … Candidate_v1.7.0 stable
(edit) @1be100   5 years frederik.heber FIX: Several small errors in Graph6Reader. - off-by-one error with … Candidate_v1.7.0 stable
(edit) @d951a5   5 years frederik.heber FIX: Small changes to ChemicalSpaceEvaluatorAction. - discarding … Candidate_v1.7.0 stable
(edit) @0f9eb0   5 years frederik.heber Modified fstream checks to good() or eof(). - not using != or == NULL. Candidate_v1.7.0 stable
(edit) @49874c   5 years frederik.heber FIX: Needed to remove some boost::cref in ..Descriptors. - gcc … Candidate_v1.7.0 stable
(edit) @c30959   5 years frederik.heber BondAddAction also adds to molecule. - NOTE: This basically does … Candidate_v1.7.0 stable
(edit) @e70818   5 years frederik.heber Added getSelectedAtomPositions() python function. Candidate_v1.7.0 stable
(edit) @5fa1e86   5 years frederik.heber Added BondifyAction. - this allows to add non-hydrogen bonds and is … Candidate_v1.7.0 stable
(edit) @51d384a   5 years frederik.heber Added BondedParticle::IsBondedTo that uses current worldtime. Candidate_v1.7.0 stable
(edit) @ea30e6   5 years frederik.heber Added python getters for selected atom ids and elements. Candidate_v1.7.0 stable
(edit) @38bcbe   5 years frederik.heber StretchBondAction will used tabled distances when given distance is … Candidate_v1.7.0 stable
(edit) @4de4f6   5 years frederik.heber Added AtomBondNeighbors selection action. - DOCU: Added to userguide. … Candidate_v1.7.0 stable
(edit) @9f55b9   5 years frederik.heber Extracted functor StretchBondUtil from StretchBondAction. Candidate_v1.7.0 stable
(edit) @f3eb6a   5 years frederik.heber FIX: LinkedCell_model executes deletes right away. - we use the … Candidate_v1.7.0 stable
(edit) @ef0f8f   5 years frederik.heber LinkCell model has name on update for debugging. Candidate_v1.7.0 stable
(edit) @d9e1d1   5 years frederik.heber Extending PairCorrelation to correlate element and set of atoms. - … Candidate_v1.7.0 stable
(edit) @addb51   5 years frederik.heber Add action to clear fragmentation state. Candidate_v1.7.0 stable
(edit) @0ad4781   5 years frederik.heber Added action to randomly select a set of atoms. - needed to make new … Candidate_v1.7.0 stable
(edit) @3f5b0a   5 years frederik.heber Added mutex on changes_present in GLWorldView. - this should prevent … Candidate_v1.7.0 stable
(edit) @b0060a   5 years frederik.heber Making test code python2&3 compatible. Candidate_v1.7.0 stable
(edit) @ba49d8   5 years frederik.heber Removing Ambient and Specular color from Qt4 atoms. - this way the … Candidate_v1.7.0 stable
(edit) @da30ddf   5 years frederik.heber FIX: tooltip in Qt4 menu caused sigsev. - I don't know why it … Candidate_v1.7.0 stable
(edit) @61cc0f   5 years frederik.heber Enhanced verbosity of FragmentationAutomation. Candidate_v1.7.0 stable
(edit) @d40189   5 years frederik.heber OutputTemperature -> OutputEnergies, SaveTemperature -> SaveEnergies. … Candidate_v1.7.0 stable
(edit) @cbbb6a   5 years frederik.heber FIX: AnalyseFragmentationResultsAction ignored prefix mostly. Candidate_v1.7.0 stable
(edit) @26062f   5 years frederik.heber StoreSaturatedFragmentAction may now export to FragmentQueue as well. … Candidate_v1.7.0 stable
(edit) @b56827   5 years frederik.heber Program_options 1.63 behavior breaks. - in program_options with 1.63 … Candidate_v1.7.0 stable
(edit) @1ca493a   5 years frederik.heber Allowing python3 usage. - Init function name changes on python2/3. - … Candidate_v1.7.0 stable
(edit) @912a6f   5 years frederik.heber Adapted to boost 1.64. - need array_wrapper.hpp when using … Candidate_v1.7.0 stable
(edit) @4045d4   5 years frederik.heber FIX: libMolecuilderJobs had hard-coded boost_serialization dep. Candidate_v1.7.0 stable
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