#
# ChangeLog for molecuilder/src
#
# Generated by Trac 1.6
# Dec 9, 2025, 2:32:46 AM

Fri, 09 Oct 2009 12:08:24 GMT Frederik Heber <heber@…> [682229]
	* molecuilder/Makefile.am (modified)
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/memoryusageobserver.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (added)
	* molecuilder/src/unittests/memoryallocatorunittest.cpp (moved)
	* molecuilder/src/unittests/memoryallocatorunittest.hpp (moved)
	* molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved)
	* molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved)
	* molecuilder/src/unittests/tesselationunittest.cpp (moved)
	* molecuilder/src/unittests/tesselationunittest.hpp (moved)
	* molecuilder/src/unittests/vectorunittest.cpp (moved)
	* molecuilder/src/unittests/vectorunittest.hpp (moved)

	Merge branch 'new-delete-conversion' of ...


Wed, 07 Oct 2009 15:35:17 GMT metzler <metzler@…> [afbb6c0]
	* molecuilder/Makefile.am (modified)
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/unittests/Makefile.am (modified)

	Ticket 30: Put molecuilder unit tests in their own subfolder in src


Wed, 07 Oct 2009 15:04:23 GMT Saskia Metzler <metzler@…> [53f32e]
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (added)
	* molecuilder/src/unittests/memoryallocatorunittest.cpp (moved)
	* molecuilder/src/unittests/memoryallocatorunittest.hpp (moved)
	* molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved)
	* molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved)
	* molecuilder/src/unittests/tesselationunittest.cpp (moved)
	* molecuilder/src/unittests/tesselationunittest.hpp (moved)
	* molecuilder/src/unittests/vectorunittest.cpp (moved)
	* molecuilder/src/unittests/vectorunittest.hpp (moved)

	temp commit


Tue, 06 Oct 2009 11:15:50 GMT metzler <metzler@…> [729279]
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/memoryusageobserver.hpp (modified)
	* molecuilder/src/memoryusageobserverunittest.cpp (modified)
	* molecuilder/src/memoryusageobserverunittest.hpp (modified)

	#22 Write a critical exit function


Mon, 05 Oct 2009 15:43:25 GMT Frederik Heber <heber@…> [89eff5]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)

	new/delete conversion.

	mode change only, nothing else.


Mon, 05 Oct 2009 15:42:20 GMT Frederik Heber <heber@…> [5dda23]
	* molecuilder/src/analyzer.cpp (modified)

	New/delete conversion.

	82: "main" missing in msg


Mon, 05 Oct 2009 14:59:11 GMT Frederik Heber <heber@…> [bf497f]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/memoryusageobserver.hpp (modified)
	* molecuilder/src/memoryusageobserverunittest.cpp (modified)
	* molecuilder/src/memoryusageobserverunittest.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:50:43 GMT metzler <metzler@…> [39d983]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (added)
	* molecuilder/src/memoryusageobserver.hpp (added)
	* molecuilder/src/memoryusageobserverunittest.cpp (added)
	* molecuilder/src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Mon, 05 Oct 2009 14:35:06 GMT Frederik Heber <heber@…> [7794d8]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/memoryallocator.hpp (added)
	* molecuilder/src/memoryallocatorunittest.cpp (added)
	* molecuilder/src/memoryallocatorunittest.hpp (added)
	* molecuilder/src/memoryusageobserver.cpp (added)
	* molecuilder/src/memoryusageobserver.hpp (added)
	* molecuilder/src/memoryusageobserverunittest.cpp (added)
	* molecuilder/src/memoryusageobserverunittest.hpp (added)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:12:18 GMT metzler <metzler@…> [14db08]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (added)
	* molecuilder/src/memoryusageobserver.hpp (added)
	* molecuilder/src/memoryusageobserverunittest.cpp (added)
	* molecuilder/src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Fri, 02 Oct 2009 13:02:26 GMT Frederik Heber <heber@…> [2aea0b]
	* .gitignore (modified)
	* molecuilder/src/tesselationunittest.cpp (added)
	* molecuilder/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@…> [390a2b]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/memoryallocator.hpp (added)
	* molecuilder/src/memoryallocatorunittest.cpp (added)
	* molecuilder/src/memoryallocatorunittest.hpp (added)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/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@…> [bc3953]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/vectorunittest.cpp (modified)
	* molecuilder/src/vectorunittest.hpp (modified)

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


Thu, 20 Aug 2009 11:35:19 GMT Saskia Metzler <metzler@…> [6c6d84]
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vectorunittest.cpp (modified)
	* molecuilder/src/vectorunittest.hpp (modified)

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


Thu, 20 Aug 2009 07:48:07 GMT Frederik Heber <heber@…> [84b811]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Wed, 19 Aug 2009 14:31:29 GMT Frederik Heber <heber@…> [78dac6]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)

	Smaller fixes, but convex tesselation not working yet

	- ...


Wed, 19 Aug 2009 12:30:21 GMT Frederik Heber <heber@…> [daf5d6]
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/leastsquaremin.cpp (added)
	* molecuilder/src/leastsquaremin.hpp (added)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/vectorunittest.cpp (added)
	* molecuilder/src/vectorunittest.hpp (added)

	Merge branch 'VectorUnitTest' into ConcaveHull


Wed, 19 Aug 2009 12:23:05 GMT Frederik Heber <heber@…> [6c09a4]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/vectorunittest.cpp (modified)
	* molecuilder/src/vectorunittest.hpp (modified)

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


Wed, 19 Aug 2009 12:22:08 GMT Frederik Heber <heber@…> [66ce7a]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

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

	- ...


Tue, 18 Aug 2009 13:59:11 GMT Saskia Metzler <metzler@…> [d6b011]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

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


Tue, 18 Aug 2009 08:48:06 GMT Frederik Heber <heber@…> [da84d6]
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/leastsquaremin.cpp (added)
	* molecuilder/src/leastsquaremin.hpp (added)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/vectorunittest.cpp (added)
	* molecuilder/src/vectorunittest.hpp (added)

	Incorporation of Unit test on class Vector.

	- new file ...


Tue, 18 Aug 2009 08:42:39 GMT Frederik Heber <heber@…> [27459a]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/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@…> [48cd93]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

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


Mon, 17 Aug 2009 10:48:03 GMT Frederik Heber <heber@…> [3de1d2]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)

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


Mon, 17 Aug 2009 10:30:53 GMT Frederik Heber <heber@…> [eb58a7]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

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


Mon, 17 Aug 2009 10:29:03 GMT Frederik Heber <heber@…> [844cf5]
	* molecuilder/src/builder.cpp (modified)

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


Mon, 10 Aug 2009 16:11:47 GMT Frederik Heber <heber@…> [70c4567]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

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


Sat, 08 Aug 2009 19:25:28 GMT Frederik Heber <heber@…> [0cf171]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

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

	- ...


Sat, 08 Aug 2009 19:22:28 GMT Frederik Heber <heber@…> [51abbe]
	* molecuilder/src/builder.cpp (modified)

	ParseCommandLineOptions(), NonConvex tesselation is now clocked.


Sat, 08 Aug 2009 19:19:23 GMT Frederik Heber <heber@…> [0ee99dc]
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	BUGFIXES to some vector functions.

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


Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber <heber@…> [e0521b]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/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@…> [67fced]
	* molecuilder/src/TAGS (deleted)
	* util/depcomp (deleted)
	* util/install-sh (deleted)

	excluded unimportant stuff, depcomp and install-sh from util


Fri, 07 Aug 2009 12:48:06 GMT Frederik Heber <heber@…> [609e48]
	* molecuilder/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@…> [ef5521]
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

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


Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber <heber@…> [0fc0b5]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/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@…> [8f9a8e]
	* molecuilder/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@…> [d93bb24]
	* molecuilder/src/builder.cpp (modified)

	FillWithMolecule() for testing built into ParseCommandLine()


Tue, 04 Aug 2009 13:53:55 GMT Frederik Heber <heber@…> [7aa922]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/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@…> [eeefb3]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	Fixes for concave hull creation

	- fixed ...


Tue, 04 Aug 2009 13:47:05 GMT Frederik Heber <heber@…> [04dcc0]
	* molecuilder/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@…> [f4a346]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (added)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (added)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (added)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/element.hpp (added)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/ellipsoid.hpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (added)
	* molecuilder/src/tesselation.hpp (added)
	* molecuilder/src/tesselationhelpers.cpp (added)
	* molecuilder/src/tesselationhelpers.hpp (added)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/verbose.hpp (added)

	Merge branch 'TesselationRefactoring' into ConcaveHull

	Conflicts:
 ...


Mon, 03 Aug 2009 18:58:46 GMT Frederik Heber <heber@…> [0e2190]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* util/depcomp (modified)
	* util/install-sh (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 03 Aug 2009 16:48:46 GMT Saskia Metzler <metzler@…> [e8de2e]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)

	Adding functions IsInnerAtom() and IsInnerPoint() which can check ...


Mon, 03 Aug 2009 16:48:00 GMT Saskia Metzler <metzler@…> [dc162d]
	* molecuilder/src/molecules.hpp (modified)

	Compare and output operator for atom takes const argumen


Mon, 03 Aug 2009 16:45:38 GMT Saskia Metzler <metzler@…> [a87d5e6]
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)

	new function LinkedCell::GetNeighbourBounds()

	- ...


Mon, 03 Aug 2009 16:44:16 GMT Saskia Metzler <metzler@…> [3219a0]
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	new function isNull(), output operator takes const argument


Mon, 03 Aug 2009 16:43:42 GMT Saskia Metzler <metzler@…> [b65771]
	* molecuilder/src/atom.cpp (modified)

	output operator now takes const argument


Mon, 03 Aug 2009 15:26:32 GMT Frederik Heber <heber@…> [eb167d]
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/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@…> [4dca8e]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/element.hpp (added)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/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@…> [e78824]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (added)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/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@…> [834ff3]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (added)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (added)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/ellipsoid.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/tesselation.cpp (added)
	* molecuilder/src/tesselation.hpp (added)
	* molecuilder/src/tesselationhelpers.cpp (added)
	* molecuilder/src/tesselationhelpers.hpp (added)
	* molecuilder/src/vector.hpp (modified)

	Huge refactoring of Tesselation routines, but not finished yet.

	- ...


Mon, 03 Aug 2009 08:10:09 GMT Frederik Heber <heber@…> [4e4940]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/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@…> [3dc682]
	* molecuilder/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@…> [da5c7c]
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/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@…> [78b45a]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)

	ConvexTesselation working again.

	- File was not written, as NULL ...


Mon, 27 Jul 2009 14:53:57 GMT Frederik Heber <heber@…> [dd69cc]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)

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


Mon, 27 Jul 2009 14:22:20 GMT Frederik Heber <heber@…> [63443f]
	* molecuilder/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@…> [a0fb02]
	* molecuilder/src/builder.cpp (modified)

	BUGFIX: ManipulateAtoms() had mol = NULL

	- in ManipulateAtoms() the ...


Mon, 27 Jul 2009 14:07:25 GMT Frederik Heber <heber@…> [0ac84df]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

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


Mon, 27 Jul 2009 08:16:03 GMT Frederik Heber <heber@…> [53d153]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)

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


Fri, 24 Jul 2009 10:38:32 GMT Frederik Heber <heber@…> [c3a303]
	* .gitignore (modified)
	* Makefile.am (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/datacreator.hpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/graph.cpp (modified)
	* molecuilder/src/graph.hpp (added)
	* 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)
	* pcp/Makefile.am (modified)
	* util/src/CalculateDensity.sh.in (modified)
	* util/src/CalculateMass.sh.in (modified)
	* util/src/average.cpp (modified)
	* util/src/dynamicANOVA.sh.in (modified)

	Merge branch 'master' into ConcaveHull

	Conflicts:

	        ...


Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber <heber@…> [a048fa]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/ellipsoid.hpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (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)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/verbose.cpp (modified)

	fixed indentation from tabs to two spaces.


Thu, 23 Jul 2009 14:04:47 GMT Frederik Heber <heber@…> [47548d]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* util/src/CalculateDensity.sh.in (modified)
	* util/src/CalculateMass.sh.in (modified)

	Merge branch 'AtomRemoval'

	Conflicts:

	        ...


Thu, 23 Jul 2009 13:53:01 GMT Frederik Heber <heber@…> [1f6efb]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)

	fixed indentation from tabs to two spaces.


Thu, 23 Jul 2009 13:45:24 GMT Frederik Heber <heber@…> [f39735]
	* .gitignore (modified)
	* molecuilder/src/#border.cpp# (deleted)
	* molecuilder/src/#makefile# (deleted)
	* molecuilder/src/#molecules.hpp# (deleted)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/datacreator.hpp (modified)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (added)
	* molecuilder/src/ellipsoid.hpp (added)
	* molecuilder/src/graph.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/linkedcell.cpp (added)
	* molecuilder/src/linkedcell.hpp (added)
	* 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)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/verbose.cpp (modified)
	* util/src/NanoCreator.c (modified)
	* util/src/NanoCreator.h (modified)

	Merge branch 'MultipleMolecules'

	Conflicts:

	        ...


Thu, 23 Jul 2009 12:32:48 GMT Frederik Heber <heber@…> [560995]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/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@…> [1b2aa1]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (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)
	* molecuilder/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@…> [307290]
	* molecuilder/src/molecules.cpp (modified)

	Merge branch 'ConstrainedMolecularDynamics'

	Conflicts:

	        ...


Thu, 23 Jul 2009 11:31:00 GMT Frederik Heber <heber@…> [59a745]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/joiner.cpp (modified)

	Merge branch 'test'

	Conflicts:

	        ...


Thu, 23 Jul 2009 11:23:59 GMT Frederik Heber <heber@…> [3b470f]
	* .gitignore (modified)
	* Makefile.am (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (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)
	* pcp/Makefile.am (modified)
	* util/src/average.cpp (modified)

	Merge branch 'Thermostat'

	Conflicts:

	        .gitignore
	        ...


Thu, 23 Jul 2009 09:14:18 GMT Frederik Heber <heber@…> [09f4dc]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/datacreator.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/parser.hpp (modified)
	* util/src/AdaptiveANOVA.sh.in (modified)
	* util/src/CalculateDensity.sh.in (modified)
	* util/src/CalculateMass.sh.in (modified)
	* util/src/CreateFromXYZ.sh.in (modified)
	* util/src/SortByRings.sh.in (modified)

	Merge branch 'HessianMatrix'


Thu, 23 Jul 2009 09:11:01 GMT Frederik Heber <heber@…> [2218dca]
	* molecuilder/src/graph.cpp (modified)
	* molecuilder/src/graph.hpp (added)

	Merge branch 'GraphRefactoring'


Fri, 10 Jul 2009 21:19:23 GMT Frederik Heber <heber@…> [c95b69]
	* molecuilder/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@…> [88b936]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	new class ConfigFileBuffer and new overloaded function ...


Fri, 10 Jul 2009 20:20:09 GMT Frederik Heber <heber@…> [598f76]
	* molecuilder/src/molecules.cpp (modified)

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


Fri, 10 Jul 2009 14:29:56 GMT Frederik Heber <heber@…> [22f587]
	* molecuilder/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@…> [6fb785]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/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@…> [a8c8ba]
	* molecuilder/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@…> [8bbe43]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/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@…> [438506]
	* molecuilder/src/boundary.cpp (modified)

	Fixed all of the remaining memory leaks due to ...


Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber <heber@…> [ab7b5e7]
	* molecuilder/src/builder.cpp (modified)

	Memory leak fix: ParseCommandLineOptions() and main() free'd mol ...


Thu, 09 Jul 2009 11:01:08 GMT Frederik Heber <heber@…> [bd86e8]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)

	Changed the unsatisfactory PathToDatabases construct, removing ...


Thu, 09 Jul 2009 10:38:53 GMT Frederik Heber <heber@…> [c12297]
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/datacreator.hpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/parser.hpp (modified)

	fixed compiler warning: deprecated conversion from string const to ...


Thu, 09 Jul 2009 10:38:34 GMT Frederik Heber <heber@…> [669a7e]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/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@…> [61e92a]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Removed unneeded variables


Thu, 09 Jul 2009 10:22:05 GMT Frederik Heber <heber@…> [12cf763]
	* molecuilder/src/boundary.cpp (modified)

	Removed unnecessary code

	- Choose_preferable_third_point()
	- ...


Thu, 09 Jul 2009 09:45:00 GMT Frederik Heber <heber@…> [49c774]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/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@…> [30212a8]
	* molecuilder/src/boundary.cpp (modified)

	FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when ...


Tue, 07 Jul 2009 09:12:54 GMT Frederik Heber <heber@…> [a811a0]
	* molecuilder/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@…> [d98327]
	* molecuilder/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@…> [54de04]
	* molecuilder/src/vector.cpp (modified)

	BUGFIX: Numerical imprecision forced check of bounds for acos()
 ...


Tue, 07 Jul 2009 08:11:47 GMT Frederik Heber <heber@…> [eeae5b]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)

	Cosmetical changes in Find_third_point_for_tesselation() and ...


Tue, 07 Jul 2009 06:49:32 GMT Frederik Heber <heber@…> [d2639f]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/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@…> [ea9696]
	* molecuilder/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@…> [378e87]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)

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


Fri, 10 Apr 2009 23:28:39 GMT Frederik Heber <heber@…> [a41b50]
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/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@…> [bb12e7]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/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@…> [37a050]
	* molecuilder/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@…> [d618b5]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/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@…> [8b05c6]
	* molecuilder/src/moleculelist.cpp (modified)

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