#
# ChangeLog for src/builder.cpp
#
# Generated by Trac 1.6
# May 24, 2025, 5:05:37 PM

Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber <heber@…> [f3278b]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Test case of filling a simulation domain with water included.


Tue, 04 Aug 2009 13:55:11 GMT Frederik Heber <heber@…> [9f97c5]
	* src/builder.cpp (modified)

	FillWithMolecule() for testing built into ParseCommandLine()


Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber <heber@…> [357fba]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (added)
	* src/bond.cpp (modified)
	* src/bond.hpp (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (added)
	* src/tesselation.hpp (added)
	* src/tesselationhelpers.cpp (added)
	* src/tesselationhelpers.hpp (added)
	* src/vector.hpp (modified)

	Huge refactoring of Tesselation routines, but not finished yet.

	- ...


Mon, 03 Aug 2009 08:10:09 GMT Frederik Heber <heber@…> [2319ed]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	We are one step further in fixing the convex hull: There are two ...


Tue, 28 Jul 2009 10:33:53 GMT Frederik Heber <heber@…> [a567c3]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)

	ConvexTesselation working again.

	- File was not written, as NULL ...


Mon, 27 Jul 2009 14:08:27 GMT Frederik Heber <heber@…> [b6d8a9]
	* src/builder.cpp (modified)

	BUGFIX: ManipulateAtoms() had mol = NULL

	- in ManipulateAtoms() the ...


Mon, 27 Jul 2009 08:16:03 GMT Frederik Heber <heber@…> [d30402]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	Split VolumeOfConvexEnvelope() into find_convex_border() and ...


Fri, 24 Jul 2009 10:38:32 GMT Frederik Heber <heber@…> [36ec71]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/defs.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (added)
	* src/joiner.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	Merge branch 'master' into ConcaveHull

	Conflicts:

	        ...


Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber <heber@…> [042f82]
	* 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/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (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/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)

	fixed indentation from tabs to two spaces.


Thu, 23 Jul 2009 14:04:47 GMT Frederik Heber <heber@…> [51c910]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)

	Merge branch 'AtomRemoval'

	Conflicts:

	        ...


Thu, 23 Jul 2009 13:53:01 GMT Frederik Heber <heber@…> [375b458]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)

	fixed indentation from tabs to two spaces.


Thu, 23 Jul 2009 13:45:24 GMT Frederik Heber <heber@…> [d067d45]
	* src/#border.cpp# (deleted)
	* src/#makefile# (deleted)
	* src/#molecules.hpp# (deleted)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.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/element.cpp (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 (added)
	* src/linkedcell.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)

	Merge branch 'MultipleMolecules'

	Conflicts:

	        ...


Thu, 23 Jul 2009 12:32:48 GMT Frederik Heber <heber@…> [ce5ac3]
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/helpers.cpp (modified)
	* src/molecules.cpp (modified)
	* src/parser.cpp (modified)
	* src/vector.cpp (modified)
	* src/verbose.cpp (modified)

	Fix indentation from tabs to two spaces to prepare merging with ...


Thu, 23 Jul 2009 12:14:13 GMT Frederik Heber <heber@…> [437922]
	* 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/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)
	* src/periodentafel.cpp (modified)

	Fix indentation from tab to two spaces.

	The trouble was caused at ...


Thu, 23 Jul 2009 11:23:59 GMT Frederik Heber <heber@…> [631dcb]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/defs.hpp (modified)
	* src/joiner.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Merge branch 'Thermostat'

	Conflicts:

	        .gitignore
	        ...


Fri, 10 Jul 2009 12:48:05 GMT Frederik Heber <heber@…> [21c017]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	molecule::CenterInBox puts atoms now periodically into the given box, ...


Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber <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 <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 <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 <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 <heber@…> [260b2f]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)

	Cosmetical changes in Find_third_point_for_tesselation() and ...


Fri, 03 Jul 2009 14:25:17 GMT Frederik Heber <heber@…> [a5b2c3a]
	* src/builder.cpp (modified)

	Removing of atoms via command line possible

	-R switchs allows for ...


Wed, 03 Jun 2009 16:16:37 GMT Frederik Heber <heber@…> [c54da3]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)

	BUGFIX: RemoveAtom() would remove the iterator, ...


Fri, 10 Apr 2009 23:28:02 GMT Frederik Heber <heber@…> [09af1b]
	* src/analyzer.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/ellipsoid.cpp (modified)

	removed lots of warnings due to unused variables

	This arose due to ...


Wed, 08 Apr 2009 11:35:42 GMT Frederik Heber <heber@…> [63f06e]
	* src/builder.cpp (modified)

	fixes due to changes in molecule structure (Center...()) and merge ...


Thu, 02 Apr 2009 16:42:36 GMT Frederik Heber <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 <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 <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 23:17:38 GMT Frederik Heber <heber@…> [2746be]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.hpp (modified)

	Basis for MPQC can now be specified via command line switch

	 * -B ...


Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber <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 21:46:58 GMT Frederik Heber <heber@…> [cc2ee5]
	* 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/graph.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (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)

	Just a temporary commit


Mon, 29 Dec 2008 12:25:04 GMT Frederik Heber <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 <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 <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 <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 <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 <heber@…> [a8b9d61]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(): All cases now make thorough checks ...


Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber <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, 09 Oct 2008 18:27:56 GMT Frederik Heber <heber@…> [df793a]
	* 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, 25 Sep 2008 17:57:19 GMT Frederik Heber <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 <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 <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 <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 <heber@…> [4f2335]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(): Command line option "-E" for changing an ...


Tue, 09 Sep 2008 08:37:07 GMT Frederik Heber <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 <heber@…> [d1fc7f]
	* src/builder.cpp (modified)

	BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the ...


Fri, 05 Sep 2008 17:09:39 GMT Frederik Heber <heber@…> [a8aadf6]
	* src/builder.cpp (modified)

	SaveConfig() now also stores an MPQC input file.
 ...


Tue, 02 Sep 2008 12:06:14 GMT Frederik Heber <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 <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 <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 <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 <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 <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 <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 <heber@…> [1f066fe]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(): new option 'O' centers system at origin
 ...


Sun, 22 Jun 2008 13:39:41 GMT Frederik Heber <heber@…> [256520]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' ...


Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber <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 <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 <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 <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 <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 <heber@…> [233e33]
	* src/builder.cpp (modified)

	fastparse enabled by "-n"


Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber <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 <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 <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 <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 <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 <heber@…> [ca2b83]
	* src/builder.cpp (modified)

	command line parsing outsourced to ParseCommandLineOptions(), cases ...


Fri, 16 May 2008 13:35:43 GMT Frederik Heber <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 ...