# # ChangeLog for / # # Generated by Trac 1.4.4 # Dec 29, 2024, 8:07:47 AM Thu, 25 Sep 2008 17:50:17 GMT Frederik Heber [7ce307] * src/Makefile.am (modified) Some files were missing in the repository pseudopotentials and the ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [795a54] * src/molecules.cpp (modified) molecule::MinimiseConstrainedPotential(): Extension of search and ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [c30cda] * src/molecules.cpp (modified) molecule::MinimiseConstrainedPotential() : Minimisation is fixed ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [85bac0] * src/builder.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Implemented molecule::LinearInterpolationBetweenConfiguration(). ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [a1fe77] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Basic implementation of Constrained MD is done, missing testing. Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [6e9353] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) Constrained Molecular Dynamics: two new functions ... Thu, 11 Sep 2008 13:25:47 GMT Frederik Heber [18913c] * src/config.cpp (modified) * src/molecules.hpp (modified) config::DoWannier implemented that is parsed from config file, ... Thu, 11 Sep 2008 13:08:18 GMT Frederik Heber [4f2335] * src/builder.cpp (modified) ParseCommandLineOptions(): Command line option "-E" for changing an ... Tue, 09 Sep 2008 15:32:16 GMT Frederik Heber [2985c8] * src/vector.cpp (modified) BUGFIX: Normalize() would try to normalize a zero vector which ended ... 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 ... Tue, 09 Sep 2008 07:46:15 GMT Frederik Heber [bd3e55] * configure.ac (modified) configure BUGFIX: GSL may be linked against cblas_... functions or ... 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 ... Sat, 06 Sep 2008 15:06:51 GMT Frederik Heber [d1fc7f] * src/builder.cpp (modified) BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the ... Fri, 05 Sep 2008 17:09:39 GMT Frederik Heber [a8aadf6] * src/builder.cpp (modified) SaveConfig() now also stores an MPQC input file. ... Fri, 05 Sep 2008 17:02:18 GMT Frederik Heber [ed060e] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.hpp (modified) moved all definitions from boundary.hpp to molecules.hpp, and renamed ... Wed, 03 Sep 2008 17:28:31 GMT Frederik Heber [7e27e7] * src/config.cpp (modified) BUGFIX: config::load() parses endlessly if there are no atoms in the ... Tue, 02 Sep 2008 12:06:14 GMT Frederik Heber [dd8cf8] * src/builder.cpp (modified) FIX: ExitFlag not defaults to 0, and set specifically to 1 in the ... Tue, 02 Sep 2008 12:05:31 GMT Frederik Heber [7e07cf] * src/config.cpp (modified) fix: in config::edit() the loop asking for cell values had the wrong ... Fri, 29 Aug 2008 10:39:59 GMT Frederik Heber [3dcd14] * src/molecules.cpp (modified) molecule::ScanForPeriodicCorrection() two printfs were commented out Fri, 29 Aug 2008 10:39:17 GMT Frederik Heber [c1fc22] * src/moleculelist.cpp (modified) * src/molecules.hpp (modified) config::SaveMPQC() included in headers and used in ... Fri, 29 Aug 2008 10:12:00 GMT Frederik Heber [6b8b57] * src/config.cpp (modified) new function SaveMPQC(), bugfixes in ParseForParameter() ... Mon, 18 Aug 2008 10:55:30 GMT Frederik Heber [ab3a0e] * tests/testsuite.at (modified) Fixed second test (main_pcp_linux was not written anymore, hence ... 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 ... Mon, 18 Aug 2008 08:35:40 GMT Frederik Heber [f05407] * src/analyzer.cpp (modified) analyzer has been adapted to the aforementioned change in the calling ... Mon, 18 Aug 2008 08:35:11 GMT Frederik Heber [8f019c] * src/analyzer.cpp (modified) * src/helpers.cpp (modified) * src/joiner.cpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) Splitting MatrrixContainer::ParseMatrix in ParseMatrix ParseMatrix ... Mon, 18 Aug 2008 08:27:34 GMT Frederik Heber [f3dc4c] * src/analyzer.cpp (modified) Time analysis is back in Mon, 18 Aug 2008 08:25:28 GMT Frederik Heber [9e5a04d] * src/Hbondangle.db (modified) * src/Hbonddistance.db (modified) * src/orbitals.db (modified) Included missing silicon and took more or lesss sensible values for ... 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 ... Wed, 06 Aug 2008 08:50:52 GMT Frederik Heber [b4b7c3] * src/analyzer.cpp (modified) pcp.speed is parsed and analyzed again (Time matrices). This was ... Wed, 06 Aug 2008 08:37:04 GMT Frederik Heber [fb9364] * src/datacreator.cpp (modified) * src/parser.cpp (modified) The entries in the Header of ForceMatrix are now separated by tabs, ... 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 13:47:52 GMT Frederik Heber [b61043] * src/builder.cpp (modified) Removed Output of parsed elements db (does work well, so not ... 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) ... Thu, 24 Jul 2008 13:58:40 GMT Frederik Heber [c685eb] * src/builder.cpp (modified) adding atom: element is now first, not last parameter and output ... Thu, 24 Jul 2008 13:56:00 GMT Frederik Heber [82cd9f] * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) BUGFIX: elements.db is now using path instead of file elements ... Wed, 09 Jul 2008 13:33:57 GMT Frederik Heber [7d96c6] * src/molecules.hpp (modified) * src/vector.hpp (modified) class vector was wrongly still in molecules.hpp instead of vector.hpp 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 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 ...