# # ChangeLog for src/builder.cpp # # Generated by Trac 1.6 # Jan 4, 2026, 9:09:26 PM Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber [e72001] * src/builder.cpp (modified) Memory leak fix: ParseCommandLineOptions() and main() free'd mol ... Thu, 09 Jul 2009 11:01:08 GMT Frederik Heber [989bf6] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.hpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) Changed the unsatisfactory PathToDatabases construct, removing ... Thu, 09 Jul 2009 10:31:05 GMT Frederik Heber [4777e9] * src/analyzer.cpp (modified) * src/builder.cpp (modified) * src/moleculelist.cpp (modified) Removed unneeded variables Tue, 07 Jul 2009 08:17:53 GMT Frederik Heber [ce4d22] * src/builder.cpp (modified) BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere ... Tue, 07 Jul 2009 08:11:47 GMT Frederik Heber [260b2f] * src/boundary.cpp (modified) * src/builder.cpp (modified) Cosmetical changes in Find_third_point_for_tesselation() and ... Thu, 02 Apr 2009 16:42:36 GMT Frederik Heber [ca3ccc] * src/builder.cpp (modified) simple switched order for edit molecule to be in alphabetical ordering 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: - ... Tue, 10 Feb 2009 12:04:37 GMT Frederik Heber [d8b94a] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecules.hpp (modified) Gaussian basis for MPQC input files can now be specified with -B ... 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 ... Mon, 29 Dec 2008 12:25:04 GMT Frederik Heber [12298c] * src/#border.cpp# (deleted) * src/#makefile# (deleted) * src/#molecules.hpp# (deleted) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) Now we also produce Raster3D output files additionally to TecPlot ... 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 ... Thu, 04 Dec 2008 15:15:00 GMT Christian Neuen [a8bcea6] * src/border.cpp (deleted) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) several changes, now output is created, quality unknown Sat, 18 Oct 2008 14:03:57 GMT Frederik Heber [450d63] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and ... Fri, 17 Oct 2008 13:20:42 GMT Frederik Heber [9a5bcd] * src/builder.cpp (modified) * src/config.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.hpp (modified) config::Save() and config::SaveMPQC() now take string for filename, ... Thu, 16 Oct 2008 09:27:17 GMT Frederik Heber [a8b9d61] * src/builder.cpp (modified) ParseCommandLineOptions(): All cases now make thorough checks ... 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 ... 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 ...