# # ChangeLog for src/builder.cpp # # Generated by Trac 1.4.4 # Dec 28, 2024, 12:57:14 AM Thu, 25 Sep 2008 17:57:19 GMT Frederik Heber [62f793] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) thermostats enumerator, necessary variables included in class config, ... 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 13:08:18 GMT Frederik Heber [4f2335] * src/builder.cpp (modified) ParseCommandLineOptions(): Command line option "-E" for changing an ... 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 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. ... 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 ... 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 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 ... 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 ... 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 ... 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 ... Sun, 22 Jun 2008 13:39:41 GMT Frederik Heber [256520] * src/builder.cpp (modified) ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' ... 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 ... Tue, 10 Jun 2008 11:21:13 GMT Frederik Heber [233e33] * src/builder.cpp (modified) fastparse enabled by "-n" 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 ... 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, ... 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 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 11:15:32 GMT Frederik Heber [ca2b83] * src/builder.cpp (modified) command line parsing outsourced to ParseCommandLineOptions(), cases ... 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 14:20:08 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, 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 07:45:23 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 07:16:32 GMT Frederik Heber [6590bee] * src/builder.cpp (modified) bugfix in main: without arguments, code would crash due to access of ... Tue, 29 Apr 2008 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 ... 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 ... 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, 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 ...