#
# ChangeLog for src
#
# Generated by Trac 1.6
# May 23, 2025, 12:31:48 PM

Mon, 05 Oct 2009 14:59:11 GMT Frederik Heber <heber@…> [c0917c]
	* src/builder.cpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/memoryusageobserverunittest.cpp (modified)
	* src/memoryusageobserverunittest.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:50:43 GMT metzler <metzler@…> [b66c22]
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Mon, 05 Oct 2009 14:35:06 GMT Frederik Heber <heber@…> [41194a]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:12:18 GMT metzler <metzler@…> [c30180]
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Fri, 02 Oct 2009 13:02:26 GMT Frederik Heber <heber@…> [0227a9]
	* src/tesselationunittest.cpp (added)
	* src/tesselationunittest.hpp (added)

	new tesselation unit test

	- excluded some more files (mostly ecut ...


Mon, 21 Sep 2009 11:48:42 GMT Saskia Metzler <metzler@…> [29812d]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)

	Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free ...


Thu, 20 Aug 2009 15:40:49 GMT Saskia Metzler <metzler@…> [89c8b2]
	* src/atom.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Ticket 17: Write new function molecule::CopyMoleculeFromSubRegion()


Thu, 20 Aug 2009 11:35:19 GMT Saskia Metzler <metzler@…> [78b73c]
	* src/vector.cpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Ticket 16: Unit tests for Vector::RotateVector(), additionally fixing ...


Thu, 20 Aug 2009 07:48:07 GMT Frederik Heber <heber@…> [34e0592]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.hpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Wed, 19 Aug 2009 14:31:29 GMT Frederik Heber <heber@…> [1d9b7aa]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)

	Smaller fixes, but convex tesselation not working yet

	- ...


Wed, 19 Aug 2009 12:30:21 GMT Frederik Heber <heber@…> [99c484]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/leastsquaremin.cpp (added)
	* src/leastsquaremin.hpp (added)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (added)
	* src/vectorunittest.hpp (added)

	Merge branch 'VectorUnitTest' into ConcaveHull


Wed, 19 Aug 2009 12:23:05 GMT Frederik Heber <heber@…> [ef9df36]
	* src/Makefile.am (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	VectorUnitTest extended to Projections and Line intersection, some ...


Wed, 19 Aug 2009 12:22:08 GMT Frederik Heber <heber@…> [658efb]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	Replaced Vector::Projection() by Vector::ScalarProduct()

	- ...


Tue, 18 Aug 2009 13:59:11 GMT Saskia Metzler <metzler@…> [7c14ec]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Ticket 15: new function RemoveDegeneratedTriangles()
	Added functions ...


Tue, 18 Aug 2009 08:48:06 GMT Frederik Heber <heber@…> [54a746]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/leastsquaremin.cpp (added)
	* src/leastsquaremin.hpp (added)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (added)
	* src/vectorunittest.hpp (added)

	Incorporation of Unit test on class Vector.

	- new file ...


Tue, 18 Aug 2009 08:42:39 GMT Frederik Heber <heber@…> [0077b5]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Further bugfixes to three-step-procedure in convex envelope, not yet ...


Mon, 17 Aug 2009 13:20:16 GMT Saskia Metzler <metzler@…> [f1cccd]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Ticket 14: Rename .._.. functions in boundary.cpp


Mon, 17 Aug 2009 10:48:03 GMT Frederik Heber <heber@…> [093645]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)

	Rewrite of ConvexizeNonconvexEnvelope() with three steps: Remove ...


Mon, 17 Aug 2009 10:30:53 GMT Frederik Heber <heber@…> [16d866]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	documentation, some renames (..Triangle.. -> ..Tesselation..) and a ...


Mon, 17 Aug 2009 10:29:03 GMT Frederik Heber <heber@…> [86381b]
	* src/builder.cpp (modified)

	Sorted the menu list in ParseCommandLineParamaters() and print volume ...


Mon, 10 Aug 2009 16:11:47 GMT Frederik Heber <heber@…> [08ef35]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	New function ConvexizeNonconvexEnvelope() to calculate the volume of ...


Sat, 08 Aug 2009 19:25:28 GMT Frederik Heber <heber@…> [5c7bf8]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	BUGFIXes to Find_convex_... and Find_non_convex_... algorithms

	- ...


Sat, 08 Aug 2009 19:22:28 GMT Frederik Heber <heber@…> [8bb475f]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(), NonConvex tesselation is now clocked.


Sat, 08 Aug 2009 19:19:23 GMT Frederik Heber <heber@…> [46670d]
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	BUGFIXES to some vector functions.

	- Vector::MakeNormalVector() ... ...


Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber <heber@…> [055861]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	new stream operator with just one parameter and virtual destructor


Fri, 07 Aug 2009 12:50:27 GMT Frederik Heber <heber@…> [8d31ce]
	* src/TAGS (deleted)

	excluded unimportant stuff, depcomp and install-sh from util


Fri, 07 Aug 2009 12:48:06 GMT Frederik Heber <heber@…> [133d56]
	* src/boundary.cpp (modified)

	output of terminating special property comment in .r3d file had no ...


Fri, 07 Aug 2009 12:46:27 GMT Frederik Heber <heber@…> [1999d8]
	* src/linkedcell.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	BUGFIX: PointCloud implementation in molecule stopped one before ...


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.


Fri, 07 Aug 2009 09:12:19 GMT Frederik Heber <heber@…> [1953f9]
	* src/tesselation.cpp (modified)

	FIX: We have to check whether we create a degenerate triangle also on ...


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

	FillWithMolecule() for testing built into ParseCommandLine()


Tue, 04 Aug 2009 13:53:55 GMT Frederik Heber <heber@…> [ef0e6d]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)

	find_(non)_convex_border TesselStruct is not free'd anymore, ...


Tue, 04 Aug 2009 13:48:57 GMT Frederik Heber <heber@…> [62bb91]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Fixes for concave hull creation

	- fixed ...


Tue, 04 Aug 2009 13:47:05 GMT Frederik Heber <heber@…> [03e57a]
	* src/molecules.cpp (modified)

	Smaller FIXES to molecule class

	- new pointer TesselStruct was not ...


Mon, 03 Aug 2009 20:21:05 GMT Frederik Heber <heber@…> [ab1932]
	* 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/config.hpp (added)
	* src/element.cpp (modified)
	* src/element.hpp (added)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/helpers.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (added)
	* src/tesselation.hpp (added)
	* src/tesselationhelpers.cpp (added)
	* src/tesselationhelpers.hpp (added)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.hpp (added)

	Merge branch 'TesselationRefactoring' into ConcaveHull

	Conflicts:
 ...


Mon, 03 Aug 2009 18:58:46 GMT Frederik Heber <heber@…> [0dbddc]
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 03 Aug 2009 16:48:46 GMT Saskia Metzler <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 <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 <metzler@…> [0f4538]
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)

	new function LinkedCell::GetNeighbourBounds()

	- ...


Mon, 03 Aug 2009 16:44:16 GMT Saskia Metzler <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 <metzler@…> [321a11]
	* src/atom.cpp (modified)

	output operator now takes const argument


Mon, 03 Aug 2009 15:26:32 GMT Frederik Heber <heber@…> [edb93c]
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/config.hpp (modified)
	* src/helpers.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)

	Some minor fixes with regards to what needs to be included where and ...


Mon, 03 Aug 2009 15:09:12 GMT Frederik Heber <heber@…> [cd4ccc]
	* src/Makefile.am (modified)
	* src/atom.hpp (modified)
	* src/bond.hpp (modified)
	* src/config.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (added)
	* src/helpers.hpp (modified)
	* src/molecules.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/verbose.hpp (added)

	definitions for class element and verbose moved to their own header ...


Mon, 03 Aug 2009 14:58:43 GMT Frederik Heber <heber@…> [a80fbdf]
	* src/Makefile.am (modified)
	* src/boundary.hpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	class config definitions moved to their own header file.

	NOTE: ...


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 13:02:51 GMT Frederik Heber <heber@…> [e1589e]
	* src/boundary.cpp (modified)

	Convex tesselation is now working also for heptan. But the convex ...


Tue, 28 Jul 2009 13:01:15 GMT Frederik Heber <heber@…> [d4d0dd]
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	New function Vector::NormSquared() and Angle checks whether Norm's ...


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 14:53:57 GMT Frederik Heber <heber@…> [fcc9b0]
	* src/boundary.cpp (modified)
	* src/molecules.cpp (modified)

	FIX: DetermineCenterOfAll() did point in wrong direction, convex ...


Mon, 27 Jul 2009 14:22:20 GMT Frederik Heber <heber@…> [3c4f04]
	* src/config.cpp (modified)

	BUGFIX: config::Load() added atoms in wrong order, hence resulting in ...


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 14:07:25 GMT Frederik Heber <heber@…> [a20e6a]
	* src/molecules.cpp (modified)
	* src/vector.cpp (modified)

	BUGFIX: molecule::ReturnFullMatrixforSymmetric had it still all ...


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 11:46:57 GMT Frederik Heber <heber@…> [986c80]
	* src/molecules.cpp (modified)

	Merge branch 'ConstrainedMolecularDynamics'

	Conflicts:

	        ...


Thu, 23 Jul 2009 11:31:00 GMT Frederik Heber <heber@…> [71e7c7]
	* src/analyzer.cpp (modified)
	* src/joiner.cpp (modified)

	Merge branch 'test'

	Conflicts:

	        ...


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
	        ...


Thu, 23 Jul 2009 09:14:18 GMT Frederik Heber <heber@…> [b38b64]
	* src/analyzer.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	Merge branch 'HessianMatrix'


Thu, 23 Jul 2009 09:11:01 GMT Frederik Heber <heber@…> [b77416]
	* src/graph.cpp (modified)
	* src/graph.hpp (added)

	Merge branch 'GraphRefactoring'


Fri, 10 Jul 2009 21:19:23 GMT Frederik Heber <heber@…> [205ccd]
	* src/molecules.cpp (modified)

	BUGFIX: Due to stupid mistake, first atom was overlooked in periodic ...


Fri, 10 Jul 2009 21:01:40 GMT Frederik Heber <heber@…> [d1df9b]
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	new class ConfigFileBuffer and new overloaded function ...


Fri, 10 Jul 2009 20:20:09 GMT Frederik Heber <heber@…> [6cb412]
	* src/molecules.cpp (modified)

	BUGFIX: molecule::Output...() routines wrote elements beginning with ...


Fri, 10 Jul 2009 14:29:56 GMT Frederik Heber <heber@…> [5466f3]
	* src/molecules.cpp (modified)

	XYZ and config files now store the atoms in the same order as they ...


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 13:33:39 GMT Frederik Heber <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 <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 <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 <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 10:38:53 GMT Frederik Heber <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 <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 <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 <heber@…> [542ab3]
	* src/boundary.cpp (modified)

	Removed unnecessary code

	- Choose_preferable_third_point()
	- ...


Thu, 09 Jul 2009 09:45:00 GMT Frederik Heber <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 <heber@…> [018741]
	* src/boundary.cpp (modified)

	FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when ...


Tue, 07 Jul 2009 09:12:54 GMT Frederik Heber <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 <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 <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 <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 <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 ...


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 23:28:39 GMT Frederik Heber <heber@…> [178f92]
	* src/moleculelist.cpp (modified)
	* src/molecules.hpp (modified)

	return type of MoleculeListClass::insert is now void instead of bool ...


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 ...


Wed, 08 Apr 2009 11:27:50 GMT Frederik Heber <heber@…> [d67150]
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Lots of bugfixes, some name changes and new functions

	BUGFIX:
	- ...


Wed, 08 Apr 2009 11:25:03 GMT Frederik Heber <heber@…> [3af1f0]
	* src/moleculelist.cpp (modified)

	MoleculeListClass::Enumerate() lists center and size of molecule, fix ...


Thu, 02 Apr 2009 16:42:53 GMT Frederik Heber <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 <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 23:17:28 GMT Frederik Heber <heber@…> [5bc4d0]
	* src/analyzer.cpp (modified)
	* src/joiner.cpp (modified)

	Chi integration had some copy&paste error