# # ChangeLog for / # # Generated by Trac 1.6 # Jun 11, 2025, 11:20:43 PM Mon, 03 Aug 2009 16:48:46 GMT Saskia Metzler [8c54a3] * src/boundary.cpp (modified) * src/boundary.hpp (modified) Adding functions IsInnerAtom() and IsInnerPoint() which can check ... Mon, 03 Aug 2009 16:48:00 GMT Saskia Metzler [ee1b16] * src/molecules.hpp (modified) Compare and output operator for atom takes const argumen Mon, 03 Aug 2009 16:45:38 GMT Saskia Metzler [0f4538] * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) new function LinkedCell::GetNeighbourBounds() - ... Mon, 03 Aug 2009 16:44:16 GMT Saskia Metzler [9c20aa] * src/vector.cpp (modified) * src/vector.hpp (modified) new function isNull(), output operator takes const argument Mon, 03 Aug 2009 16:43:42 GMT Saskia Metzler [321a11] * src/atom.cpp (modified) output operator now takes const argument Thu, 09 Jul 2009 13:33:39 GMT Frederik Heber [a37350] * src/boundary.cpp (modified) FIX: Now tries each of the axis direction to find a starting triangle ... Thu, 09 Jul 2009 12:02:46 GMT Frederik Heber [8cede7] * src/boundary.cpp (modified) * src/linkedcell.cpp (modified) Lots of changes to the number of output messages. As the finding of ... Thu, 09 Jul 2009 11:40:14 GMT Frederik Heber [b65901] * src/boundary.cpp (modified) Fixed all of the remaining memory leaks due to ... 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 10:38:53 GMT Frederik Heber [1c6081] * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) fixed compiler warning: deprecated conversion from string const to ... Thu, 09 Jul 2009 10:38:34 GMT Frederik Heber [70c333f] * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/ellipsoid.hpp (modified) fixed compiler warning by changing int to size_t because C++ STL ... 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 Thu, 09 Jul 2009 10:22:05 GMT Frederik Heber [542ab3] * src/boundary.cpp (modified) Removed unnecessary code - Choose_preferable_third_point() - ... Thu, 09 Jul 2009 09:45:00 GMT Frederik Heber [86234b] * src/boundary.cpp (modified) * src/boundary.hpp (modified) BUGFIX: Memory leak due to special triangles and similar lines in ... Tue, 07 Jul 2009 14:48:21 GMT Frederik Heber [018741] * src/boundary.cpp (modified) FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when ... Tue, 07 Jul 2009 09:12:54 GMT Frederik Heber [f0ebac] * src/boundary.cpp (modified) BUGFIX: Initial edge for starting triangle may be up to TWICE the ... 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 08:12:28 GMT Frederik Heber [02da9e] * src/vector.cpp (modified) BUGFIX: Numerical imprecision forced check of bounds for acos() ... 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 ... Tue, 07 Jul 2009 06:49:32 GMT Frederik Heber [3d919e] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.hpp (modified) All of Saskia Metzler's changes so far to remove bugs from ... Thu, 02 Apr 2009 16:42:53 GMT Frederik Heber [ca2587] * src/boundary.cpp (modified) * src/moleculelist.cpp (modified) * src/molecules.hpp (modified) Framework for embedding one molecule into another, now the embedding ... 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 ... Fri, 06 Feb 2009 09:48:09 GMT Frederik Heber [124df1] * src/boundary.cpp (modified) Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list Fri, 06 Feb 2009 09:44:15 GMT Frederik Heber [e1bc68] * src/linkedcell.cpp (added) * src/linkedcell.hpp (added) New file and class LinkedCell that contains the linked cell ... Mon, 29 Dec 2008 12:29:21 GMT Frederik Heber [6d4a76] * src/boundary.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Merge branch 'ConcaveHull' of ... 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 ... Tue, 23 Dec 2008 13:28:05 GMT Christian Neuen [23e09b] * src/boundary.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) fancy commit Tue, 23 Dec 2008 13:06:36 GMT Frederik Heber [02bfde] * src/boundary.cpp (modified) Merge branch 'ConcaveHull' of ... Tue, 23 Dec 2008 11:22:57 GMT Frederik Heber [44fd95] * src/boundary.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Cleaned up all debugging output Tue, 23 Dec 2008 11:21:29 GMT Christian Neuen [196a5a] * src/boundary.cpp (modified) BallAngel enhanced, added new alternative direction for issues with ... Fri, 19 Dec 2008 16:21:11 GMT Christian Neuen [7c6712] * src/boundary.cpp (modified) Switched choice process to Ball angle completely. Problem remains. ... Thu, 18 Dec 2008 17:21:34 GMT Christian Neuen [e9fa06f] * src/boundary.cpp (modified) First change to Ball angle as criteria, however, change sucks. Wed, 17 Dec 2008 15:56:07 GMT Christian Neuen [10af0d] * src/boundary.cpp (modified) Solved possible problem with Second quadrant overhaul Tue, 16 Dec 2008 18:39:28 GMT Christian Neuen [e4ea46] * configure.ac (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Tesselation starts to look good, minor discrepancies are still there ... Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen [caf5d6] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.cpp (modified) Atom indices are now correctly processed. 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 Wed, 03 Dec 2008 14:18:10 GMT Christian Neuen [f683fe] * src/ReMapDBondFileFromXYZ.py (added) Parses a pdb and xyz file and decideds which atoms are in both and ... Wed, 03 Dec 2008 14:12:05 GMT Christian Neuen [69eb71] * src/#border.cpp# (added) * src/#makefile# (added) * src/#molecules.hpp# (added) * src/.#border.cpp (added) * src/.#molecules.hpp (added) * src/TAGS (added) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecules.cpp (modified) * src/molecules.hpp (modified) * src/vector.cpp (modified) Multiple changes to boundary, currently not fully operational. ... Thu, 27 Nov 2008 09:59:27 GMT Christian Neuen [1ffa21] * src/border.cpp (modified) The border.cpp contains the same functions as the changes in ... Thu, 27 Nov 2008 09:55:08 GMT Christian Neuen [03648b] * src/border.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) In vector a function for calculation of the vector-(cross-)product ... Tue, 25 Nov 2008 15:05:07 GMT Christian Neuen [51695c] * src/border.cpp (added) Construction of border triangles of non convex point set 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 13:24:10 GMT Frederik Heber [65de9b] * src/molecules.cpp (modified) molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, ... Fri, 17 Oct 2008 13:22:38 GMT Frederik Heber [4ee3df] * src/analyzer.cpp (modified) * src/datacreator.cpp (modified) Analyzer now writes usable plot and data files for shielding ... 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 09:27:59 GMT Frederik Heber [f00693] * tests/testsuite.at (modified) New tests that check that if subsequent arguments to certain cmd ... Thu, 16 Oct 2008 09:27:17 GMT Frederik Heber [a8b9d61] * src/builder.cpp (modified) ParseCommandLineOptions(): All cases now make thorough checks ... Thu, 16 Oct 2008 09:26:48 GMT Frederik Heber [52f5d5] * src/periodentafel.cpp (modified) periodentafel::LoadPeriodentafel(): if other dbs fail, we just give a ... Thu, 16 Oct 2008 09:25:56 GMT Frederik Heber [e198c7] * src/helpers.cpp (modified) * src/helpers.hpp (modified) New function IsValidNumber(): checks whether a command line argument ... Wed, 15 Oct 2008 18:20:51 GMT Frederik Heber [95634f] * src/analyzer.cpp (modified) Analyzer now prints usable ShieldingsPAS data and plot files (so that ... Wed, 15 Oct 2008 18:20:40 GMT Frederik Heber [19f3d6] * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) new function AppendOutputFile() for appending to output files whereas ... Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber [57d8b0] * src/molecules.cpp (modified) molecule::VerletForceIntegration() different code, same algorithm ... Tue, 14 Oct 2008 19:14:10 GMT Frederik Heber [2b4a40] * src/boundary.cpp (modified) new version of Tesselation::GuessStartingTriangle() seems to fix ... Tue, 14 Oct 2008 13:26:02 GMT Frederik Heber [ca8073] * src/boundary.cpp (modified) BUGFIX: Tesselation::AddPoint() always increased ... Sun, 12 Oct 2008 15:58:48 GMT Frederik Heber [ec7ba8] * src/config.cpp (modified) changed basis set for mpqc from STO-3G to 3-21G (more stable with ... Sat, 11 Oct 2008 16:07:45 GMT Frederik Heber [9fc556] * src/Hbondangle.db (modified) * src/Hbonddistance.db (modified) * src/orbitals.db (modified) * src/valence.db (modified) corrected number of valence orbitals for Calcium (2 -> 4) and ... Sat, 11 Oct 2008 16:07:28 GMT Frederik Heber [74a65e] * src/molecules.cpp (modified) molecule::AddHydrogenReplacementAtom() returns false on missing ... Fri, 10 Oct 2008 13:38:46 GMT Frederik Heber [617b53] * src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... Fri, 10 Oct 2008 13:38:41 GMT Frederik Heber [1e8243] * src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... 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 13:25:47 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, ...