# # ChangeLog for / # # Generated by Trac 1.4.4 # Dec 26, 2024, 2:29:35 PM Fri, 27 Jun 2008 21:14:58 GMT Frederik Heber [68cb0f] * src/Makefile.am (modified) * src/analyzer.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/defs.hpp (modified) * src/element.cpp (modified) * src/joiner.cpp (modified) * src/molecules.hpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (added) introduced shieldings to analyzer and joiner both now handle ... Mon, 23 Jun 2008 11:25:09 GMT Frederik Heber [1f066fe] * src/builder.cpp (modified) ParseCommandLineOptions(): new option 'O' centers system at origin ... Mon, 23 Jun 2008 11:23:50 GMT Frederik Heber [f14a52] * src/molecules.cpp (modified) StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond ... Sun, 22 Jun 2008 13:39:41 GMT Frederik Heber [256520] * src/builder.cpp (modified) ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' ... Sun, 22 Jun 2008 13:27:47 GMT Frederik Heber [8a3e45] * src/parser.cpp (modified) Merge branch 'bisect' into AdaptiveMolecuilder Fri, 20 Jun 2008 08:08:13 GMT Frederik Heber [d250b2] * src/parser.cpp (modified) MatrixContainer::ParseMatrix(): BUGFIX - line_s_.eof() Bug was ... Fri, 20 Jun 2008 07:08:31 GMT Frederik Heber [d427bd] * src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): boundary is now 2.5 Angstroem ... 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 ... Fri, 13 Jun 2008 14:26:50 GMT Frederik Heber [edb650] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) some mor changes to fine-tune the cluster generation. Sadly, ... Fri, 13 Jun 2008 09:18:57 GMT Frederik Heber [318bfd] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) Final touches for Create Clusters in water repetition in ... Thu, 12 Jun 2008 19:34:36 GMT Frederik Heber [6c5812] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) Smaller fixes CreateClustersinWater is now PrepareClustersinWater ... 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 ... Thu, 12 Jun 2008 19:14:32 GMT Frederik Heber [bc84e47] * src/helpers.hpp (modified) cosmetics Thu, 12 Jun 2008 19:13:43 GMT Frederik Heber [8eb17a] * src/boundary.cpp (added) * src/boundary.hpp (added) * src/periodentafel.cpp (modified) StorePeriodentafel(): BUGFIX - there still was elements.db instead of ... Tue, 10 Jun 2008 11:31:03 GMT Frederik Heber [cdee6b] * src/config.cpp (modified) fastparse was not yet working for more than one ion type moved ... 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, ... Tue, 10 Jun 2008 11:21:13 GMT Frederik Heber [233e33] * src/builder.cpp (modified) fastparse enabled by "-n" Tue, 10 Jun 2008 11:20:12 GMT Frederik Heber [498a9f] * src/vector.cpp (modified) * src/vector.hpp (modified) some new functions: vector::vector(), vector::ProjectOntoPlane(), ... Tue, 10 Jun 2008 11:15:52 GMT Frederik Heber [3dfad8] * src/vector.cpp (modified) * src/vector.hpp (modified) Revert "some new functions: vector::vector(), ... Tue, 10 Jun 2008 11:13:41 GMT Frederik Heber [62c16c] * src/config.cpp (modified) enabled fast parsing (-n) config::Load(): the repetition and ... Tue, 10 Jun 2008 11:11:22 GMT Frederik Heber [17ce5c] * src/vector.cpp (modified) * src/vector.hpp (modified) some new functions: vector::vector(), vector::ProjectOntoPlane(), ... 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 ... Sat, 07 Jun 2008 13:21:33 GMT Frederik Heber [65684f] * src/vector.cpp (modified) these are all smaller fixes due to extensively enabled compiler ... Sat, 07 Jun 2008 13:20:30 GMT Frederik Heber [fa40b5] * src/analyzer.cpp (modified) * src/bond.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/parser.cpp (modified) these are all smaller fixes due to extensively enabled compiler ... Sat, 07 Jun 2008 13:16:19 GMT Frederik Heber [a19da5d] * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (added) new aclocal macro with controles all the enable- ... Mon, 02 Jun 2008 10:28:29 GMT Frederik Heber [1f6422] * src/helpers.hpp (modified) needed for strncat and companions for gcc-4.3.0 Fri, 30 May 2008 15:48:16 GMT Frederik Heber [0ba2b0a] * configure.ac (modified) libblas needed for libgsl is now found via AC_SEARCH_LIB and list ... Fri, 30 May 2008 13:51:53 GMT Frederik Heber [5e4058] * src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): return of ... Fri, 30 May 2008 13:50:45 GMT Frederik Heber [95078c] * configure.ac (modified) * src/Makefile.am (modified) AM_CFLAGS thrown out as warnings are added to CFLAGS in configure- ... Fri, 30 May 2008 10:43:34 GMT Frederik Heber [6b33de] * src/periodentafel.cpp (modified) LoadPeriodentafel() mixup of cat and cpy orders prevented loading of ... Fri, 30 May 2008 10:42:49 GMT Frederik Heber [fedd5f] * src/builder.cpp (modified) main(): periode is not printed anymore after parsing cmd options, ... Fri, 30 May 2008 09:03:32 GMT Frederik Heber [4b4d65] * src/config.cpp (modified) for bigger molecules listing of found keywords slows things done ... Mon, 26 May 2008 13:28:28 GMT Frederik Heber [37b5bb] * src/periodentafel.cpp (modified) * tests/testsuite.at (modified) renamed ElementsFileName to PathToDatabases, -e now gives path to ... Mon, 26 May 2008 13:25:38 GMT Frederik Heber [d7d29c] * src/builder.cpp (modified) renamed ElementsFileName to PathToDatabases, -e now gives path to ... Mon, 26 May 2008 13:24:33 GMT Frederik Heber [a2c084] * src/config.cpp (modified) BUGFIX: config files' path in the current working directory would not ... Mon, 26 May 2008 13:23:29 GMT Frederik Heber [4ba4a7] * src/helpers.cpp (modified) BUGFIX: single letter FragmentNumbers gave "\n" as return string. ... Mon, 26 May 2008 13:23:02 GMT Frederik Heber [27c6be] * src/element.cpp (modified) Some sensible starting values for element class construct Mon, 26 May 2008 13:22:31 GMT Frederik Heber [0329bf] * src/defs.hpp (modified) new define LocalPath being the local path for pointers to set to ... Mon, 26 May 2008 13:22:10 GMT Frederik Heber [1e9384] * src/moleculelist.cpp (modified) bit more verbosity on the FragmentNumber Mon, 26 May 2008 13:21:19 GMT Frederik Heber [c9c643] * tests/testsuite.at (modified) fragmentation no more has various methods (dropped ... A) 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 ... Sat, 24 May 2008 12:31:46 GMT Frederik Heber [040f93] * src/Makefile.am (modified) removed specialised CFLAGS for general AM_C(PP)FLAGS that just enable ... 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 11:18:11 GMT Frederik Heber [6097ea] * src/parser.cpp (modified) * src/parser.hpp (modified) ParseMatrix(): char * to string, Contains() hat KeySetContainer:: ... Wed, 21 May 2008 11:15:32 GMT Frederik Heber [ca2b83] * src/builder.cpp (modified) command line parsing outsourced to ParseCommandLineOptions(), cases ... Wed, 21 May 2008 11:14:06 GMT Frederik Heber [a9d254] * src/molecules.cpp (modified) new function CenterInBox, some char* converted to string ... Wed, 21 May 2008 11:13:17 GMT Frederik Heber [3b67a1] * src/Makefile.am (modified) new vector header added to molecuilder_SOURCES Wed, 21 May 2008 11:12:54 GMT Frederik Heber [cf2de5] * src/joiner.cpp (modified) one lousy space added Wed, 21 May 2008 09:24:54 GMT Frederik Heber [342f33f] * src/molecules.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (added) new header file for the vector class, new operators +=,*=,*,+ Fri, 16 May 2008 13:35:43 GMT Frederik Heber [98b1d2] * src/builder.cpp (modified) main(): typo in Usage message, BUGFIX - command line arguments did ... 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 ... Fri, 09 May 2008 13:49:57 GMT Frederik Heber [de293ac] * src/moleculelist.cpp (modified) TranslateIndicesToGlobalIDs() did not check whether FragmentList[..] ... 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 07:55:11 GMT Frederik Heber [1fa5b7] * tests/testsuite.at (modified) config file is again first argument and implemented test of ... 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 07:06:18 GMT Frederik Heber [3c1dfb] * tests/testsuite.at (modified) Full test for fragmentation procedure with readin of the adjacency ... 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 ...