#
# ChangeLog for src
#
# Generated by Trac 1.6
# May 24, 2025, 9:57:12 PM

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


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, 09 Feb 2009 14:18:13 GMT Frederik Heber <heber@…> [a98603]
	* 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# (added)
	* src/#makefile# (added)
	* src/#molecules.hpp# (added)
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/Makefile.am (modified)
	* src/ReMapDBondFileFromXYZ.py (added)
	* src/TAGS (added)
	* 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)

	Merge ../espack3


Fri, 06 Feb 2009 09:48:09 GMT Frederik Heber <heber@…> [124df1]
	* src/boundary.cpp (modified)

	Find_non_convex_border(): calls CreateAdjacencyList() to fill bond
	list


Fri, 06 Feb 2009 09:44:15 GMT Frederik Heber <heber@…> [e1bc68]
	* src/linkedcell.cpp (added)
	* src/linkedcell.hpp (added)

	New file and class LinkedCell that contains the linked cell ...


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 12:29:21 GMT Frederik Heber <heber@…> [6d4a76]
	* src/boundary.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 29 Dec 2008 12:25:04 GMT Frederik Heber <heber@…> [12298c]
	* src/#border.cpp# (deleted)
	* src/#makefile# (deleted)
	* src/#molecules.hpp# (deleted)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	Now we also produce Raster3D output files additionally to TecPlot ...


Tue, 23 Dec 2008 13:28:05 GMT Christian Neuen <neuen@…> [23e09b]
	* src/boundary.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	fancy commit


Tue, 23 Dec 2008 13:06:36 GMT Frederik Heber <heber@…> [02bfde]
	* src/boundary.cpp (modified)

	Merge branch 'ConcaveHull' of ...


Tue, 23 Dec 2008 11:22:57 GMT Frederik Heber <heber@…> [44fd95]
	* src/boundary.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Cleaned up all debugging output


Tue, 23 Dec 2008 11:21:29 GMT Christian Neuen <neuen@…> [196a5a]
	* src/boundary.cpp (modified)

	BallAngel enhanced, added new alternative direction for issues with ...


Fri, 19 Dec 2008 16:21:11 GMT Christian Neuen <neuen@…> [7c6712]
	* src/boundary.cpp (modified)

	Switched choice process to Ball angle completely.
	Problem remains. ...


Thu, 18 Dec 2008 17:21:34 GMT Christian Neuen <neuen@…> [e9fa06f]
	* src/boundary.cpp (modified)

	First change to Ball angle as criteria, however, change sucks.


Wed, 17 Dec 2008 15:56:07 GMT Christian Neuen <neuen@…> [10af0d]
	* src/boundary.cpp (modified)

	Solved possible problem with Second quadrant overhaul


Tue, 16 Dec 2008 18:39:28 GMT Christian Neuen <neuen@…> [e4ea46]
	* configure.ac (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Tesselation starts to look good, minor discrepancies are still there ...


Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen <neuen@…> [caf5d6]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/molecules.cpp (modified)

	Atom indices are now correctly processed.


Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen <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


Wed, 03 Dec 2008 14:18:10 GMT Christian Neuen <neuen@…> [f683fe]
	* src/ReMapDBondFileFromXYZ.py (added)

	Parses a pdb and xyz file and decideds which atoms are in both and ...


Wed, 03 Dec 2008 14:12:05 GMT Christian Neuen <neuen@…> [69eb71]
	* src/#border.cpp# (added)
	* src/#makefile# (added)
	* src/#molecules.hpp# (added)
	* src/.#border.cpp (added)
	* src/.#molecules.hpp (added)
	* src/TAGS (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)

	Multiple changes to boundary, currently not fully operational. ...


Thu, 27 Nov 2008 09:59:27 GMT Christian Neuen <neuen@…> [1ffa21]
	* src/border.cpp (modified)

	The border.cpp contains the same functions as the changes in ...