source: molecuilder/src/molecules.cpp

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Diff Rev Age Author Log Message
(edit) @e0c5b1   17 years neuen Multiple changes to boundary, currently not fully operational. …
(edit) @f5d7e1   17 years FrederikHeber molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, …
(edit) @a7e452   17 years FrederikHeber molecule::VerletForceIntegration() different code, same algorithm …
(edit) @1e5e16   17 years FrederikHeber molecule::AddHydrogenReplacementAtom() returns false on missing …
(edit) @31ed7d   17 years FrederikHeber BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in output …
(edit) @5a78f5   17 years FrederikHeber BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected …
(edit) @79cd79   17 years FrederikHeber new function: molecule::OutputTemperatureFromTrajectories() stores …
(edit) @b21e1f   17 years FrederikHeber BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did only …
(edit) @d473c3   17 years FrederikHeber BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which …
(edit) @830971   17 years FrederikHeber molecule::ScanForPeriodicCorrection() two printfs were commented out
(edit) @04c868   17 years FrederikHeber tiny comments and docu update for FragmentMolecule() MDTrajectoriesAndVerlet
(edit) @644ba1   17 years FrederikHeber Adaptivity fixes, MD by VerletForceIntegration introduced, MD …
(edit) @67f102   17 years FrederikHeber config::Save() and config::Load() parse MD steps into and out of …
(edit) @8f8621   17 years FrederikHeber Rename of class vector to Vector to avoid conflict with vector from STL.
(edit) @0a08df   17 years FrederikHeber Scaffold of new function: VerletForceIntegration() - does MD step by …
(edit) @7670cab   17 years FrederikHeber new test function CheckForConnectedSubgraph() and bigger rewrite of …
(edit) @ec947b   17 years FrederikHeber CyclicStructureAnalysis(): BUGFIX - BFSStack may be empty if we can't …
(edit) @d49416   17 years FrederikHeber 2 BUGFIXES: CreateAdjacencyList() and CyclicStructureAnalysis() …
(edit) @126934   17 years FrederikHeber CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms …
(edit) @3f805d   17 years FrederikHeber CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set …
(edit) @747b10   17 years FrederikHeber CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, as …
(edit) @db3ea3   17 years FrederikHeber BIG change: Hcorrection included and bugfix of analyzer (wrt forces) … JoinAnalysis_works_for_forces
(edit) @23b4aa   17 years FrederikHeber StoreKeySetFile(): removed unncessary iterator "ende" storing
(edit) @6beb99   17 years FrederikHeber changed verbosity a bit
(edit) @329d0f   17 years FrederikHeber StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond …
(edit) @1f9f1b   17 years FrederikHeber BUGFIX: If other databases could not be loaded, no error was produced, …
(edit) @e292c10   17 years FrederikHeber VolumeOfConvexEnvelope: Works! VolumeOfConvexEnvelope has been …
(edit) @2259f4   17 years FrederikHeber VolumeOfConvexEnvelope() finished and tested with SiOH4, …
(edit) @32b6dc   17 years FrederikHeber Working version of PAS transformation (tested on C-S-H cluster) and …
(edit) @94b458   17 years FrederikHeber BUGFIX: line.erase() threw exception with illegal line end Found by …
(edit) @5eb05a   17 years FrederikHeber molecule::CreateAdjacencyList() now needs IsAngstroem as parameter …
(edit) @f75030   17 years FrederikHeber Lots of for loops now count in reverse order where it does not matter, …
(edit) @927aba   17 years FrederikHeber new function CenterInBox, some char* converted to string CenterInBox …
(edit) @cc6dfb   17 years FrederikHeber CyclicStructureAnalysis(): forget to check whether we actually have …
(edit) @0716ff4   17 years FrederikHeber MinimumRingSize is now an array over all atoms Each entry in …
(edit) @a3ff7b2   17 years FrederikHeber molecule::CheckOrderAtSite() now interprets negative Orders as …
(edit) @461e93   17 years FrederikHeber molecule::CheckOrderAtSite() returns bool and used as threshold …
(edit) @d88597   17 years FrederikHeber new function molecule::CreateMappingLabelsToConfigSequence() creates …
(edit) @2b79c3   17 years FrederikHeber new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in …
(edit) @ea84ed   17 years FrederikHeber FragmentMolecule(): abstractized AssignKeySetsToFragments() and …
(edit) @08fd83   17 years FrederikHeber MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling of …
(edit) @9c3496   17 years FrederikHeber new function molecule::CheckOrderAtSite and …
(edit) @a01955   17 years FrederikHeber rewritten CyclicStructureAnalysis(): uses DFS spanning tree and …
(edit) @d50d2a   17 years FrederikHeber AtomStackClass -> template <typename T> StackClass<T> change in new …
(edit) @0e8321   17 years FrederikHeber KeySetFile is stored without an additional last tab on each line
(edit) @115bf4   17 years FrederikHeber ForcesFile and TEFactors are _needed_, reincorporated. UniqueFragments …
(edit) @30fda2   17 years FrederikHeber commenting in header changed for the four main functions that …
(edit) @c75363   17 years FrederikHeber HUGE REWRITE to allow for adaptive increase of the bond order, first …
(edit) @c510a7   17 years FrederikHeber char lengths of 255 and MAXDUMMYSTRING replaced with define …
(edit) @307fd1   17 years FrederikHeber Store/CheckAdj...() now also incorporate bond order to check against.
(edit) @7b1cea   17 years FrederikHeber configname is also stored in config structure, GetDefaultPath by …
(edit) @661288   17 years FrederikHeber Atoms in the fragments in the configs are again ordered as first …
(edit) @e565a8   17 years FrederikHeber removed some output lines (commented-out) mostly in …
(edit) @8efbfc   17 years FrederikHeber FragmentMolecule(): status variable used when checking adjacency file …
(edit) @d982bb   17 years FrederikHeber All filenames (const char *) have been transferred to defs.hpp …
(edit) @34d37c   17 years FrederikHeber storing and comparing Adjacency outsourced into two new functions. …
(edit) @2614f83   17 years FrederikHeber FragmentMolecule(): Adjacency store/check and parsing of KeySetFile …
(edit) @16cd31   17 years FrederikHeber AddXYZFile(): Bugfix - if element could not be parsed (e.g. elements …
(edit) @e58fcb7   17 years FrederikHeber FragmentMolecule(): debug messages removed for ADDHYDROGEN
(edit) @da83f8   17 years FrederikHeber added --enable-optimization, thrown -g -O specifics out of …
(edit) @090299   17 years FrederikHeber molecuilder reads and stored ion velocities Class atom has new …
(add) @a0bcf1   17 years FrederikHeber -initial commit -Minimum set of files needed from ESPACK SVN …
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