# # ChangeLog for src/molecules.cpp # # Generated by Trac 1.4.4 # Dec 29, 2024, 7:31:08 AM Thu, 02 Apr 2009 16:12:54 GMT Frederik Heber [1907a7] * src/atom.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Basic implementation of Multiple molecules. builder.cpp: - ... Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber [6ac7ee] * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * doc/Doxyfile (modified) * doc/Makefile.am (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * src/.#border.cpp (deleted) * src/.#molecules.hpp (deleted) * src/Hbondangle.db (modified) * src/Hbonddistance.db (modified) * src/Makefile.am (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/defs.hpp (modified) * src/element.cpp (modified) * src/elements.db (modified) * src/ellipsoid.cpp (added) * src/ellipsoid.hpp (added) * src/graph.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/orbitals.db (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/valence.db (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) * tests/Makefile.am (modified) * tests/atlocal.in (modified) * tests/molecuilder.in (modified) * tests/testsuite.at (modified) Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull ... Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen [caf5d6] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.cpp (modified) Atom indices are now correctly processed. Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen [f714979] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/molecules.cpp (modified) Another update w.r.t. the Tesselation. Some signs switched, but atom ... Wed, 03 Dec 2008 14:12:05 GMT Christian Neuen [69eb71] * src/#border.cpp# (added) * src/#makefile# (added) * src/#molecules.hpp# (added) * src/.#border.cpp (added) * src/.#molecules.hpp (added) * src/TAGS (added) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/vector.cpp (modified) Multiple changes to boundary, currently not fully operational. ... Fri, 17 Oct 2008 13:24:10 GMT Frederik Heber [65de9b] * src/molecules.cpp (modified) molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, ... Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber [57d8b0] * src/molecules.cpp (modified) molecule::VerletForceIntegration() different code, same algorithm ... Sat, 11 Oct 2008 16:07:28 GMT Frederik Heber [74a65e] * src/molecules.cpp (modified) molecule::AddHydrogenReplacementAtom() returns false on missing ... Fri, 10 Oct 2008 13:38:41 GMT Frederik Heber [1e8243] * src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber [3ccc3e] * src/builder.cpp (modified) * src/helpers.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ... Tue, 09 Sep 2008 08:37:07 GMT Frederik Heber [698b04] * src/builder.cpp (modified) * src/defs.hpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) new function: molecule::OutputTemperatureFromTrajectories() stores ... Sat, 06 Sep 2008 16:21:31 GMT Frederik Heber [deac6c] * src/molecules.cpp (modified) BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did ... Sat, 06 Sep 2008 15:08:32 GMT Frederik Heber [a6b7fb] * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which ... Fri, 29 Aug 2008 10:39:59 GMT Frederik Heber [3dcd14] * src/molecules.cpp (modified) molecule::ScanForPeriodicCorrection() two printfs were commented out Mon, 18 Aug 2008 09:02:34 GMT Frederik Heber [19892d] * src/molecules.cpp (modified) tiny comments and docu update for FragmentMolecule() Mon, 18 Aug 2008 08:57:58 GMT Frederik Heber [362b0e] * src/Makefile.am (modified) * src/atom.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Adaptivity fixes, MD by VerletForceIntegration introduced, MD ... Wed, 06 Aug 2008 12:00:18 GMT Frederik Heber [5e0d1f] * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) config::Save() and config::Load() parse MD steps into and out of ... Wed, 06 Aug 2008 09:02:01 GMT Frederik Heber [e9b8bb] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Rename of class vector to Vector to avoid conflict with vector from STL. Wed, 06 Aug 2008 08:59:06 GMT Frederik Heber [d7e30c] * src/builder.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Scaffold of new function: VerletForceIntegration() - does MD step by ... Thu, 31 Jul 2008 14:05:37 GMT Frederik Heber [4aa03a] * src/molecules.cpp (modified) * src/molecules.hpp (modified) new test function CheckForConnectedSubgraph() and bigger rewrite of ... Wed, 30 Jul 2008 14:16:21 GMT Frederik Heber [af6d8f] * src/molecules.cpp (modified) CyclicStructureAnalysis(): BUGFIX - BFSStack may be empty if we can't ... Wed, 30 Jul 2008 13:11:30 GMT Frederik Heber [41baaf] * src/molecules.cpp (modified) 2 BUGFIXES: CreateAdjacencyList() and CyclicStructureAnalysis() ... Mon, 28 Jul 2008 14:41:22 GMT Frederik Heber [683914] * src/atom.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms ... Mon, 28 Jul 2008 14:18:25 GMT Frederik Heber [87e2735] * src/molecules.cpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set ... Mon, 28 Jul 2008 13:45:43 GMT Frederik Heber [958457] * src/molecules.cpp (modified) * src/molecules.hpp (modified) CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, ... Thu, 24 Jul 2008 14:00:19 GMT Frederik Heber [390248] * src/analyzer.cpp (modified) * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/defs.hpp (modified) * src/joiner.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) BIG change: Hcorrection included and bugfix of analyzer (wrt forces) ... Wed, 09 Jul 2008 13:24:20 GMT Frederik Heber [0378e2] * src/molecules.cpp (modified) StoreKeySetFile(): removed unncessary iterator "ende" storing Tue, 08 Jul 2008 13:12:55 GMT Frederik Heber [1b62f3] * src/molecules.cpp (modified) changed verbosity a bit Mon, 23 Jun 2008 11:23:50 GMT Frederik Heber [f14a52] * src/molecules.cpp (modified) StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond ... Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber [14d4d4] * src/builder.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/periodentafel.cpp (modified) BUGFIX: If other databases could not be loaded, no error was ... Thu, 12 Jun 2008 19:14:46 GMT Frederik Heber [110ceb] * src/Makefile.am (modified) * src/builder.cpp (modified) * src/defs.hpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) VolumeOfConvexEnvelope: Works! VolumeOfConvexEnvelope has been ... Tue, 10 Jun 2008 11:21:32 GMT Frederik Heber [49de64] * src/molecules.cpp (modified) * src/molecules.hpp (modified) VolumeOfConvexEnvelope() finished and tested with SiOH4, ... Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber [d52ea1b] * src/builder.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Working version of PAS transformation (tested on C-S-H cluster) and ... Mon, 26 May 2008 13:20:10 GMT Frederik Heber [9a1b84] * src/molecules.cpp (modified) BUGFIX: line.erase() threw exception with illegal line end Found by ... Mon, 26 May 2008 10:52:00 GMT Frederik Heber [a251a3] * src/builder.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) molecule::CreateAdjacencyList() now needs IsAngstroem as parameter ... Fri, 23 May 2008 09:17:19 GMT Frederik Heber [7f3b9d] * src/analyzer.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/vector.cpp (modified) * src/verbose.cpp (modified) Lots of for loops now count in reverse order where it does not ... Wed, 21 May 2008 11:14:06 GMT Frederik Heber [a9d254] * src/molecules.cpp (modified) new function CenterInBox, some char* converted to string ... Fri, 09 May 2008 14:38:27 GMT Frederik Heber [0b05147] * src/molecules.cpp (modified) CyclicStructureAnalysis(): forget to check whether we actually have ... Fri, 09 May 2008 14:20:08 GMT Frederik Heber [fc850d] * src/builder.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) MinimumRingSize is now an array over all atoms Each entry in ... Thu, 08 May 2008 17:31:04 GMT Frederik Heber [5de3c9] * src/defs.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) molecule::CheckOrderAtSite() now interprets negative Orders as ... Thu, 08 May 2008 16:18:07 GMT Frederik Heber [a529de] * src/molecules.cpp (modified) * src/molecules.hpp (modified) molecule::CheckOrderAtSite() returns bool and used as threshold ... Thu, 08 May 2008 15:52:11 GMT Frederik Heber [bf46da] * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) new function molecule::CreateMappingLabelsToConfigSequence() creates ... Thu, 08 May 2008 15:39:36 GMT Frederik Heber [87f6c9] * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in ... Thu, 08 May 2008 15:25:00 GMT Frederik Heber [df2fca] * src/molecules.cpp (modified) FragmentMolecule(): abstractized AssignKeySetsToFragments() and ... Thu, 08 May 2008 12:45:52 GMT Frederik Heber [fc1309] * src/molecules.cpp (modified) MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling ... Thu, 08 May 2008 12:04:42 GMT Frederik Heber [9fcf47] * src/molecules.cpp (modified) * src/molecules.hpp (modified) new function molecule::CheckOrderAtSite and ... Wed, 07 May 2008 14:46:33 GMT Frederik Heber [8d9c38] * src/molecules.cpp (modified) * src/molecules.hpp (modified) rewritten CyclicStructureAnalysis(): uses DFS spanning tree and ... Wed, 07 May 2008 13:38:13 GMT Frederik Heber [6d35e4] * src/Makefile.am (modified) * src/atom.cpp (modified) * src/helpers.hpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/stackclass.hpp (added) AtomStackClass -> template StackClass change in new ... Tue, 06 May 2008 09:45:31 GMT Frederik Heber [63382d] * src/molecules.cpp (modified) KeySetFile is stored without an additional last tab on each line Mon, 05 May 2008 16:19:05 GMT Frederik Heber [2459b1] * src/analyzer.cpp (modified) * src/defs.hpp (modified) * src/joiner.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) ForcesFile and TEFactors are _needed_, reincorporated. ... Fri, 02 May 2008 13:35:10 GMT Frederik Heber [e6f8b7] * src/molecules.cpp (modified) commenting in header changed for the four main functions that ... Fri, 02 May 2008 13:25:48 GMT Frederik Heber [db942e] * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/builder.cpp (modified) * src/defs.hpp (modified) * src/joiner.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) * src/vector.cpp (modified) HUGE REWRITE to allow for adaptive increase of the bond order, first ... Tue, 29 Apr 2008 12:19:51 GMT Frederik Heber [c750cc] * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/periodentafel.cpp (modified) char lengths of 255 and MAXDUMMYSTRING replaced with define ... Tue, 29 Apr 2008 07:55:34 GMT Frederik Heber [451148] * src/molecules.cpp (modified) * src/molecules.hpp (modified) Store/CheckAdj...() now also incorporate bond order to check against. Tue, 29 Apr 2008 07:04:59 GMT Frederik Heber [b5ecd9] * src/config.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) configname is also stored in config structure, GetDefaultPath by ... Mon, 28 Apr 2008 13:53:54 GMT Frederik Heber [555063] * src/molecules.cpp (modified) * src/molecules.hpp (modified) Atoms in the fragments in the configs are again ordered as first ... Mon, 28 Apr 2008 13:46:05 GMT Frederik Heber [c67e16] * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) removed some output lines (commented-out) mostly in ... Mon, 28 Apr 2008 11:39:07 GMT Frederik Heber [140e34] * src/molecules.cpp (modified) FragmentMolecule(): status variable used when checking adjacency file ... Mon, 28 Apr 2008 11:36:11 GMT Frederik Heber [10f641] * src/defs.hpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) * src/periodentafel.cpp (modified) All filenames (const char *) have been transferred to defs.hpp ... Mon, 28 Apr 2008 10:41:40 GMT Frederik Heber [b0a0c3] * src/molecules.cpp (modified) * src/molecules.hpp (modified) storing and comparing Adjacency outsourced into two new functions. ... Mon, 28 Apr 2008 09:22:38 GMT Frederik Heber [183f35] * src/molecules.cpp (modified) * src/molecules.hpp (modified) FragmentMolecule(): Adjacency store/check and parsing of KeySetFile ... Sun, 27 Apr 2008 13:01:06 GMT Frederik Heber [96838d] * src/molecules.cpp (modified) AddXYZFile(): Bugfix - if element could not be parsed (e.g. elements ... Thu, 24 Apr 2008 17:01:39 GMT Frederik Heber [a16756] * src/molecules.cpp (modified) FragmentMolecule(): debug messages removed for ADDHYDROGEN Thu, 24 Apr 2008 13:52:02 GMT Frederik Heber [d3a46d] * configure.ac (modified) * src/Makefile.am (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecules.cpp (modified) added --enable-optimization, thrown -g -O specifics out of ... Wed, 23 Apr 2008 17:33:51 GMT Frederik Heber [943d02] * src/atom.cpp (modified) * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) molecuilder reads and stored ion velocities Class atom has new ... Fri, 18 Apr 2008 11:26:42 GMT Frederik Heber [14de469] * AUTHORS (added) * ChangeLog (added) * Makefile.am (added) * NEWS (added) * README (added) * autogen.sh (added) * configure.ac (added) * doc/Doxyfile (added) * doc/Makefile.am (added) * m4/ac_doxygen.m4 (added) * src/Hbondangle.db (added) * src/Hbonddistance.db (added) * src/Makefile.am (added) * src/analyzer.cpp (added) * src/atom.cpp (added) * src/bond.cpp (added) * src/builder.cpp (added) * src/config.cpp (added) * src/datacreator.cpp (added) * src/datacreator.hpp (added) * src/defs.hpp (added) * src/element.cpp (added) * src/elements.db (added) * src/graph.cpp (added) * src/helpers.cpp (added) * src/helpers.hpp (added) * src/joiner.cpp (added) * src/moleculelist.cpp (added) * src/molecules.cpp (added) * src/molecules.hpp (added) * src/orbitals.db (added) * src/parser.cpp (added) * src/parser.hpp (added) * src/periodentafel.cpp (added) * src/valence.db (added) * src/vector.cpp (added) * src/verbose.cpp (added) -initial commit -Minimum set of files needed from ESPACK SVN ...