# # ChangeLog for molecuilder # # Generated by Trac 1.6 # Dec 8, 2025, 4:33:26 AM Fri, 19 Dec 2008 16:21:11 GMT Christian Neuen [edf4a0] * molecuilder/src/boundary.cpp (modified) Switched choice process to Ball angle completely. Problem remains. ... Thu, 18 Dec 2008 17:21:34 GMT Christian Neuen [2b7a1a] * molecuilder/src/boundary.cpp (modified) First change to Ball angle as criteria, however, change sucks. Wed, 17 Dec 2008 15:56:07 GMT Christian Neuen [87c8e7] * molecuilder/src/boundary.cpp (modified) Solved possible problem with Second quadrant overhaul Tue, 16 Dec 2008 18:39:28 GMT Christian Neuen [313dff] * molecuilder/configure.ac (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * pcp/configure.ac (modified) * util/configure.ac (modified) Tesselation starts to look good, minor discrepancies are still there ... Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen [5a447f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) Atom indices are now correctly processed. Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen [735468] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/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 [db177a] * molecuilder/src/border.cpp (deleted) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) several changes, now output is created, quality unknown Wed, 03 Dec 2008 14:18:10 GMT Christian Neuen [3e20fe] * molecuilder/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 [e0c5b1] * molecuilder/src/#border.cpp# (added) * molecuilder/src/#makefile# (added) * molecuilder/src/#molecules.hpp# (added) * molecuilder/src/.#border.cpp (added) * molecuilder/src/.#molecules.hpp (added) * molecuilder/src/TAGS (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) Multiple changes to boundary, currently not fully operational. ... Thu, 27 Nov 2008 09:59:27 GMT Christian Neuen [f5b58e] * molecuilder/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 [6b3826] * molecuilder/src/border.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/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 [a709c4] * molecuilder/src/border.cpp (added) Construction of border triangles of non convex point set Sat, 18 Oct 2008 14:03:57 GMT Frederik Heber [59f86c] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and ... Fri, 17 Oct 2008 13:24:10 GMT Frederik Heber [f5d7e1] * molecuilder/src/molecules.cpp (modified) molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, ... Fri, 17 Oct 2008 13:22:38 GMT Frederik Heber [fa2d7d] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) Analyzer now writes usable plot and data files for shielding ... Fri, 17 Oct 2008 13:20:42 GMT Frederik Heber [f89a9e] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::Save() and config::SaveMPQC() now take string for filename, ... Thu, 16 Oct 2008 09:27:59 GMT Frederik Heber [7f1d3e] * molecuilder/tests/testsuite.at (modified) * util/depcomp (modified) * util/install-sh (modified) New tests that check that if subsequent arguments to certain cmd ... Thu, 16 Oct 2008 09:27:17 GMT Frederik Heber [136e89] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): All cases now make thorough checks ... Thu, 16 Oct 2008 09:26:48 GMT Frederik Heber [88e31c] * molecuilder/src/periodentafel.cpp (modified) periodentafel::LoadPeriodentafel(): if other dbs fail, we just give a ... Thu, 16 Oct 2008 09:25:56 GMT Frederik Heber [45105b] * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) New function IsValidNumber(): checks whether a command line argument ... Wed, 15 Oct 2008 18:20:51 GMT Frederik Heber [93d0ee] * molecuilder/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 [b248ca] * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) new function AppendOutputFile() for appending to output files whereas ... Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber [a7e452] * molecuilder/src/molecules.cpp (modified) molecule::VerletForceIntegration() different code, same algorithm ... Tue, 14 Oct 2008 19:14:10 GMT Frederik Heber [7a3724] * molecuilder/src/boundary.cpp (modified) new version of Tesselation::GuessStartingTriangle() seems to fix ... Tue, 14 Oct 2008 13:26:02 GMT Frederik Heber [51d33c5] * molecuilder/src/boundary.cpp (modified) BUGFIX: Tesselation::AddPoint() always increased ... Sun, 12 Oct 2008 15:58:48 GMT Frederik Heber [45d5cc] * molecuilder/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 [139f8c] * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/valence.db (modified) corrected number of valence orbitals for Calcium (2 -> 4) and ... Sat, 11 Oct 2008 16:07:28 GMT Frederik Heber [1e5e16] * molecuilder/src/molecules.cpp (modified) molecule::AddHydrogenReplacementAtom() returns false on missing ... Fri, 10 Oct 2008 13:38:46 GMT Frederik Heber [372c4cd] * molecuilder/src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... Fri, 10 Oct 2008 13:38:41 GMT Frederik Heber [31ed7d] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber [5a78f5] * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ... Thu, 11 Sep 2008 13:25:47 GMT Frederik Heber [4917ddd] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::DoWannier implemented that is parsed from config file, ... Thu, 11 Sep 2008 13:08:18 GMT Frederik Heber [55ebd0] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): Command line option "-E" for changing an ... Tue, 09 Sep 2008 15:32:16 GMT Frederik Heber [8e52aa] * molecuilder/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 [79cd79] * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new function: molecule::OutputTemperatureFromTrajectories() stores ... Tue, 09 Sep 2008 07:46:15 GMT Frederik Heber [ec4e84] * molecuilder/configure.ac (modified) * pcp/configure.ac (modified) * util/configure.ac (modified) configure BUGFIX: GSL may be linked against cblas_... functions or ... Sat, 06 Sep 2008 16:21:31 GMT Frederik Heber [b21e1f] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did ... Sat, 06 Sep 2008 15:08:32 GMT Frederik Heber [d473c3] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which ... Sat, 06 Sep 2008 15:06:51 GMT Frederik Heber [f9cd68] * molecuilder/src/builder.cpp (modified) BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the ... Fri, 05 Sep 2008 17:09:39 GMT Frederik Heber [5887ed] * molecuilder/src/builder.cpp (modified) SaveConfig() now also stores an MPQC input file. ... Fri, 05 Sep 2008 17:02:18 GMT Frederik Heber [dfc1c7] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/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 [0f508c] * molecuilder/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 [55e916] * molecuilder/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 [181f9e] * molecuilder/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 [830971] * molecuilder/src/molecules.cpp (modified) molecule::ScanForPeriodicCorrection() two printfs were commented out Fri, 29 Aug 2008 10:39:17 GMT Frederik Heber [ff74f7] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::SaveMPQC() included in headers and used in ... Fri, 29 Aug 2008 10:12:00 GMT Frederik Heber [2c536c] * molecuilder/src/config.cpp (modified) new function SaveMPQC(), bugfixes in ParseForParameter() ... Mon, 18 Aug 2008 10:55:30 GMT Frederik Heber [8e2a42] * molecuilder/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 [04c868] * molecuilder/src/molecules.cpp (modified) tiny comments and docu update for FragmentMolecule() Mon, 18 Aug 2008 08:57:58 GMT Frederik Heber [644ba1] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Adaptivity fixes, MD by VerletForceIntegration introduced, MD ... Mon, 18 Aug 2008 08:35:40 GMT Frederik Heber [e6971b] * molecuilder/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 [7b67a3] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) Splitting MatrrixContainer::ParseMatrix in ParseMatrix ParseMatrix ... Mon, 18 Aug 2008 08:27:34 GMT Frederik Heber [d24e8f0] * molecuilder/src/analyzer.cpp (modified) Time analysis is back in Mon, 18 Aug 2008 08:25:28 GMT Frederik Heber [3d4088] * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/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 [67f102] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/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 [8f8621] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/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 [0a08df] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Scaffold of new function: VerletForceIntegration() - does MD step by ... Wed, 06 Aug 2008 08:50:52 GMT Frederik Heber [e8dd4d] * molecuilder/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 [e6372f] * molecuilder/src/datacreator.cpp (modified) * molecuilder/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 [7670cab] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new test function CheckForConnectedSubgraph() and bigger rewrite of ... Wed, 30 Jul 2008 14:16:21 GMT Frederik Heber [ec947b] * molecuilder/src/molecules.cpp (modified) CyclicStructureAnalysis(): BUGFIX - BFSStack may be empty if we can't ... Wed, 30 Jul 2008 13:11:30 GMT Frederik Heber [d49416] * molecuilder/src/molecules.cpp (modified) 2 BUGFIXES: CreateAdjacencyList() and CyclicStructureAnalysis() ... Mon, 28 Jul 2008 14:41:22 GMT Frederik Heber [126934] * molecuilder/src/atom.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms ... Mon, 28 Jul 2008 14:18:25 GMT Frederik Heber [3f805d] * molecuilder/src/molecules.cpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set ... Mon, 28 Jul 2008 13:47:52 GMT Frederik Heber [39651f] * molecuilder/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 [747b10] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, ... Thu, 24 Jul 2008 14:00:19 GMT Frederik Heber [db3ea3] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) BIG change: Hcorrection included and bugfix of analyzer (wrt forces) ... Thu, 24 Jul 2008 13:58:40 GMT Frederik Heber [b3eb8e] * molecuilder/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 [0f7a85] * molecuilder/src/periodentafel.cpp (modified) * molecuilder/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 [ed5f58] * molecuilder/src/molecules.hpp (modified) * molecuilder/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 [23b4aa] * molecuilder/src/molecules.cpp (modified) StoreKeySetFile(): removed unncessary iterator "ende" storing Tue, 08 Jul 2008 13:12:55 GMT Frederik Heber [6beb99] * molecuilder/src/molecules.cpp (modified) * pcp/src/ions.c (modified) changed verbosity a bit Fri, 27 Jun 2008 21:14:58 GMT Frederik Heber [375dcf] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (added) * pcp/src/perturbed.c (modified) introduced shieldings to analyzer and joiner both now handle ... Mon, 23 Jun 2008 11:25:09 GMT Frederik Heber [d7b1bf] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): new option 'O' centers system at origin ... Mon, 23 Jun 2008 11:23:50 GMT Frederik Heber [329d0f] * molecuilder/src/molecules.cpp (modified) StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond ... Sun, 22 Jun 2008 13:39:41 GMT Frederik Heber [7a40c8] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' ... Sun, 22 Jun 2008 13:27:47 GMT Frederik Heber [cccac6] * .gitignore (modified) * m4/ac_doxygen.m4 (added) * molecuilder/src/parser.cpp (modified) * pcp/src/output.c (modified) * util/src/NanoCreator.c (modified) Merge branch 'bisect' into AdaptiveMolecuilder Fri, 20 Jun 2008 08:08:13 GMT Frederik Heber [42bdb2] * molecuilder/src/parser.cpp (modified) MatrixContainer::ParseMatrix(): BUGFIX - line_s_.eof() Bug was ... Fri, 20 Jun 2008 07:08:31 GMT Frederik Heber [b73d28] * molecuilder/src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): boundary is now 2.5 Angstroem ... Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber [1f9f1b] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/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 [0779a9] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * util/src/CalculateDensity.sh (modified) * util/src/CalculateMass.sh (modified) some mor changes to fine-tune the cluster generation. Sadly, ... Fri, 13 Jun 2008 09:18:57 GMT Frederik Heber [3f0c46] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Final touches for Create Clusters in water repetition in ... Thu, 12 Jun 2008 19:34:36 GMT Frederik Heber [7fcea6] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Smaller fixes CreateClustersinWater is now PrepareClustersinWater ... Thu, 12 Jun 2008 19:14:46 GMT Frederik Heber [e292c10] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) VolumeOfConvexEnvelope: Works! VolumeOfConvexEnvelope has been ... Thu, 12 Jun 2008 19:14:32 GMT Frederik Heber [9185c8] * molecuilder/src/helpers.hpp (modified) cosmetics Thu, 12 Jun 2008 19:13:43 GMT Frederik Heber [dcf51d] * molecuilder/src/boundary.cpp (added) * molecuilder/src/boundary.hpp (added) * molecuilder/src/periodentafel.cpp (modified) StorePeriodentafel(): BUGFIX - there still was elements.db instead of ... Tue, 10 Jun 2008 11:31:03 GMT Frederik Heber [364fc0] * molecuilder/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 [2259f4] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) VolumeOfConvexEnvelope() finished and tested with SiOH4, ... Tue, 10 Jun 2008 11:21:13 GMT Frederik Heber [ffcf49] * molecuilder/src/builder.cpp (modified) fastparse enabled by "-n" Tue, 10 Jun 2008 11:20:12 GMT Frederik Heber [b9a995] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) some new functions: vector::vector(), vector::ProjectOntoPlane(), ... Tue, 10 Jun 2008 11:15:52 GMT Frederik Heber [68fbb5] * m4/ac_doxygen.m4 (deleted) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Revert "some new functions: vector::vector(), ... Tue, 10 Jun 2008 11:13:41 GMT Frederik Heber [c4a0a2] * molecuilder/src/config.cpp (modified) enabled fast parsing (-n) config::Load(): the repetition and ... Tue, 10 Jun 2008 11:11:22 GMT Frederik Heber [d11f22] * m4/ac_doxygen.m4 (added) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) some new functions: vector::vector(), vector::ProjectOntoPlane(), ... Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber [32b6dc] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/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 [a89a22] * molecuilder/src/vector.cpp (modified) these are all smaller fixes due to extensively enabled compiler ... Sat, 07 Jun 2008 13:20:30 GMT Frederik Heber [75793b2] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/parser.cpp (modified) these are all smaller fixes due to extensively enabled compiler ... Sat, 07 Jun 2008 13:16:19 GMT Frederik Heber [02bc3c] * molecuilder/configure.ac (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (added) * pcp/configure.ac (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (added) * util/configure.ac (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (added) new aclocal macro with controles all the enable- ... Mon, 02 Jun 2008 10:28:29 GMT Frederik Heber [0cc323] * molecuilder/src/helpers.hpp (modified) needed for strncat and companions for gcc-4.3.0 Fri, 30 May 2008 15:48:16 GMT Frederik Heber [807e8a] * molecuilder/configure.ac (modified) * pcp/configure.ac (modified) * pcp/src/perturbed.c (modified) libblas needed for libgsl is now found via AC_SEARCH_LIB and list ... Fri, 30 May 2008 13:51:53 GMT Frederik Heber [eefb8e] * molecuilder/src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): return of ...