# # ChangeLog for src # # Generated by Trac 1.6 # May 23, 2025, 4:23:26 PM Fri, 09 May 2008 12:50:42 GMT Frederik Heber [f30216] * src/Makefile.am (modified) * src/joiner.cpp (modified) joiner now writes ENERGYPERFRAGMENT file for adaptive BOSSANOVA Fri, 09 May 2008 12:50:16 GMT Frederik Heber [bf2db1] * src/datacreator.cpp (modified) CreateDataFragment(): endline after datum in header Fri, 09 May 2008 12:49:46 GMT Frederik Heber [396d06] * src/defs.hpp (modified) ENERGYPERFRAGMENT without ".dat" Fri, 09 May 2008 12:49:30 GMT Frederik Heber [6f6a8e] * src/parser.cpp (modified) some comments for where "F" and where "E" terms are created 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 15:26:55 GMT Frederik Heber [da5355] * src/molecules.hpp (modified) new functions MoleculeLeafClass::AssignKeySetsToFragment() and ... Thu, 08 May 2008 15:25:00 GMT Frederik Heber [df2fca] * src/molecules.cpp (modified) FragmentMolecule(): abstractized AssignKeySetsToFragments() and ... Thu, 08 May 2008 15:22:41 GMT Frederik Heber [d2a294] * src/moleculelist.cpp (modified) new function FillListOfLocalAtoms() checks whether List needs filling ... 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 12:45:25 GMT Frederik Heber [4a54f3] * src/molecules.hpp (modified) new functions MoleculeLeafClass::Count() and ... Thu, 08 May 2008 12:41:47 GMT Frederik Heber [386aa2] * src/moleculelist.cpp (modified) FillBondStructureFromReference: previous == NULL was bad idea, new ... Thu, 08 May 2008 12:04:42 GMT Frederik Heber [9fcf47] * src/molecules.cpp (modified) * src/molecules.hpp (modified) new function molecule::CheckOrderAtSite and ... Thu, 08 May 2008 12:02:43 GMT Frederik Heber [c82f3d] * src/moleculelist.cpp (modified) new function MoleculeLeafClass::FillBondStructureFromReference that ... Thu, 08 May 2008 12:01:42 GMT Frederik Heber [8f75a4] * src/helpers.hpp (modified) new function CreateFatherLookupTable Creates a lookup table for ... Thu, 08 May 2008 12:00:24 GMT Frederik Heber [fe5589] * src/parser.cpp (modified) Matrix::ParseMatrix()L: comment makes it clearer at what fragment ... 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 ... Wed, 07 May 2008 13:35:09 GMT Frederik Heber [db066d] * src/parser.cpp (modified) changed comments a bit Tue, 06 May 2008 09:48:00 GMT Frederik Heber [7b4261] * src/parser.cpp (modified) MatrixContainer::MatrixContainer() debug message fixes only, ... 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 16:54:44 GMT Frederik Heber [3c4b08] * src/parser.cpp (modified) joiner crashed due to incorrect destructing of MatrixContainer, ... 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 15:18:27 GMT Frederik Heber [bd6579] * src/helpers.cpp (modified) Free(): only set to NULL if it was free'd otherwise it is already Fri, 02 May 2008 15:18:05 GMT Frederik Heber [3b15bb] * src/parser.cpp (modified) ~MatrixContainer(): Bugfix - Free if Matrix[MatrixCounter] would also ... 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 12:31:38 GMT Frederik Heber [260934] * src/builder.cpp (modified) Velocities were not correctly handled, also not in fragments 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 07:45:23 GMT Frederik Heber [4885953] * src/builder.cpp (modified) * src/defs.hpp (modified) changed config file to first argument again and standard config name ... Tue, 29 Apr 2008 07:41:20 GMT Frederik Heber [04980c] * src/config.cpp (modified) bugfix: configpath and -name are not set to empty string. Tue, 29 Apr 2008 07:16:32 GMT Frederik Heber [6590bee] * src/builder.cpp (modified) bugfix in main: without arguments, code would crash due to access of ... 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 ... Tue, 29 Apr 2008 06:57:59 GMT Frederik Heber [2910e0] * src/builder.cpp (modified) Comply with test again: help and version command options exit at once ... Tue, 29 Apr 2008 06:30:38 GMT Frederik Heber [5b15ab] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.hpp (modified) config::Load..() now get filename instead of pointer to file, bugfix ... 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 ... Mon, 28 Apr 2008 09:18:10 GMT Frederik Heber [08f1a0] * src/analyzer.cpp (modified) main(): thrown out unused stringstreams prefix and line Mon, 28 Apr 2008 07:16:42 GMT Frederik Heber [a8aac8d] * src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): various ofstream gathered into a ... 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 ... Sun, 27 Apr 2008 12:59:40 GMT Frederik Heber [206887] * src/molecules.hpp (modified) Load/StorePeriodentafel(): filename as parameter, if NULL default ... Sun, 27 Apr 2008 12:59:18 GMT Frederik Heber [73f80e] * src/builder.cpp (modified) new elementsdb-switch and command line options parsing parts moved ... Sun, 27 Apr 2008 12:53:53 GMT Frederik Heber [cf959d] * src/periodentafel.cpp (modified) Load/StorePeriodentafel(): filename as parameter, if NULL default ... Fri, 25 Apr 2008 13:54:51 GMT Frederik Heber [dbe929] * src/builder.cpp (modified) Huge rewrite of initial command line parsing config file argument ... Fri, 25 Apr 2008 13:52:38 GMT Frederik Heber [7151c4] * src/defs.hpp (modified) added VERSIONSTRING Fri, 25 Apr 2008 13:52:05 GMT Frederik Heber [267e95] * src/periodentafel.cpp (modified) LoadPeriodentafel(): no more outputs of parsed elements Thu, 24 Apr 2008 17:03:14 GMT Frederik Heber [6dea43] * src/helpers.hpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) ADDHYDROGEN and HAVE_DEBUG fix: config.h was not yet included ... 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 ...