#
# ChangeLog for src/builder.cpp
#
# Generated by Trac 1.4.4
# Dec 27, 2024, 7:40:46 AM

Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber <heber@…> [e138de]
	* src/Makefile.am (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_graphnode.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/errorlogger.cpp (moved)
	* src/errorlogger.hpp (moved)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/log.cpp (modified)
	* src/log.hpp (modified)
	* src/logger.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/test/ActOnAlltest.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/stackclassunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)

	Huge change from ofstream * (const) out --> Log().

	- first shift ...


Wed, 04 Nov 2009 18:15:10 GMT Frederik Heber <heber@…> [7ea9e6]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/vector.cpp (modified)

	Periodic variants of AnalysisPair...() implemented.

	- BUGFIX: ...


Wed, 04 Nov 2009 14:54:31 GMT Frederik Heber <heber@…> [a5551b]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)

	Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass ...


Wed, 04 Nov 2009 12:57:24 GMT Frederik Heber <heber@…> [f4e1f5]
	* src/builder.cpp (modified)

	Closing ticket #47, case 'C' uses biggest molecule as surface for ...


Tue, 03 Nov 2009 14:34:02 GMT Frederik Heber <heber@…> [ae38fb]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)

	Fixing not created adjacency list, partially fixing subgraph ...


Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber <heber@…> [7218f8]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)

	Several memory bugfixes (thx valgrind).

	- main() - shortened case ...


Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber <heber@…> [fa649a]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)

	Small changes.

	- VolumeOfConvexEnvelope() - setprecision corrected ...


Fri, 30 Oct 2009 16:09:29 GMT Frederik Heber <heber@…> [34e0013]
	* src/bondgraph.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule_graph.cpp (modified)

	BondGraph is initialized within config::Load(), as it has to happen ...


Fri, 30 Oct 2009 15:49:38 GMT Frederik Heber <heber@…> [b21a64]
	* src/bondgraph.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)

	BondGraph is parsed if command line switch '-g' is given.

	- ...


Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber <heber@…> [b70721]
	* src/Makefile.am (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/bondgraph.cpp (added)
	* src/bondgraph.hpp (added)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (added)
	* src/unittests/bondgraphunittest.hpp (added)

	New class BondGraph.

	- BondGraph parses a file containing bond ...


Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber <heber@…> [776b64]
	* configure.ac (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Huge refactoring to make const what is const (ticket #38), continued. ...


Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber <heber@…> [266237]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/builder.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/listofbondsunittest.cpp (added)
	* src/unittests/listofbondsunittest.hpp (added)

	Huge refactoring: molecule::ListOfBondsPerAtom and ...


Sat, 17 Oct 2009 17:06:42 GMT Frederik Heber <heber@…> [44a59b]
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Renamed and rewritten CreateAdjacencyList2().

	- rename ...


Sat, 17 Oct 2009 16:54:46 GMT Frederik Heber <heber@…> [09048c]
	* src/analysis_correlation.hpp (modified)
	* src/builder.cpp (modified)

	Added case 'C' to ParseCommandLineOptions with ...


Thu, 15 Oct 2009 08:10:10 GMT Frederik Heber <heber@…> [db6bf74]
	* src/builder.cpp (modified)
	* src/periodentafel.cpp (modified)

	Fixed two memory leaks.

	- FIX: if the element database could not be ...


Fri, 09 Oct 2009 12:30:54 GMT Frederik Heber <heber@…> [c111db]
	* Makefile.am (modified)
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (moved)
	* src/unittests/ActOnAllUnitTest.hpp (moved)
	* src/unittests/ActOnAlltest.hpp (moved)
	* src/unittests/Makefile.am (added)
	* src/unittests/memoryallocatorunittest.cpp (moved)
	* src/unittests/memoryallocatorunittest.hpp (moved)
	* src/unittests/memoryusageobserverunittest.cpp (moved)
	* src/unittests/memoryusageobserverunittest.hpp (moved)
	* src/unittests/tesselationunittest.cpp (moved)
	* src/unittests/tesselationunittest.hpp (moved)
	* src/unittests/vectorunittest.cpp (moved)
	* src/unittests/vectorunittest.hpp (moved)

	Merge branch 'new-delete-conversion' into CodeRefactoring
 ...


Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber <heber@…> [f66195]
	* src/ActOnAllUnitTest.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/element.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/lists.hpp (added)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/tesselationunittest.hpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* src/verbose.hpp (modified)

	forward declarations used to untangle interdependet classes.

	- ...


Wed, 07 Oct 2009 15:04:23 GMT Saskia Metzler <metzler@…> [be90f1]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/unittests/Makefile.am (added)
	* src/unittests/memoryallocatorunittest.cpp (moved)
	* src/unittests/memoryallocatorunittest.hpp (moved)
	* src/unittests/memoryusageobserverunittest.cpp (moved)
	* src/unittests/memoryusageobserverunittest.hpp (moved)
	* src/unittests/tesselationunittest.cpp (moved)
	* src/unittests/tesselationunittest.hpp (moved)
	* src/unittests/vectorunittest.cpp (moved)
	* src/unittests/vectorunittest.hpp (moved)

	temp commit


Tue, 06 Oct 2009 17:56:15 GMT Frederik Heber <heber@…> [ebcade]
	* src/builder.cpp (modified)
	* tests/Makefile.am (modified)
	* tests/regression/Fragmentation/1/pre/test.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment0.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment0.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment1.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment1.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment2.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment2.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment3.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment3.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment4.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment4.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragmentAdjacency.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentForces-Factors.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentKeySets.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentOrderAtSite.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentTE-Factors.dat (added)
	* tests/regression/Fragmentation/2/post/test.conf (added)
	* tests/regression/Fragmentation/2/pre/test.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (added)
	* tests/regression/Fragmentation/3/pre/test.conf (added)
	* tests/regression/Graph/1/post/test.conf (added)
	* tests/regression/Graph/1/pre/test.conf (added)
	* tests/regression/Simple_configuration/1/post/test.xyz (added)
	* tests/regression/Simple_configuration/2/post/test.conf (added)
	* tests/regression/Simple_configuration/2/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/2/pre/test.xyz (added)
	* tests/regression/Simple_configuration/3/post/test.conf (added)
	* tests/regression/Simple_configuration/3/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/4/post/test.conf (added)
	* tests/regression/Simple_configuration/4/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/4/pre/test.conf (added)
	* tests/regression/Simple_configuration/5/post/test.conf (added)
	* tests/regression/Simple_configuration/5/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/5/pre/test.conf (added)
	* tests/regression/Simple_configuration/6/pre/empty.conf (added)
	* tests/regression/Simple_configuration/7/pre/test.conf (added)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/1/post/test.conf (added)
	* tests/regression/Tesselation/1/pre/test.conf (added)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.dat (added)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/2/post/test.conf (added)
	* tests/regression/Tesselation/2/pre/test.conf (added)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/3/post/tecplot.phy (added)
	* tests/regression/Tesselation/3/post/test.conf (added)
	* tests/regression/Tesselation/3/pre/test.conf (added)
	* tests/regression/Tesselation/4/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/4/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/4/post/test.conf (added)
	* tests/regression/Tesselation/4/pre/test.conf (added)
	* tests/testsuite.at (modified)

	Extended the testsuite to encompass the vital areas of molecuilder.
 ...


Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber <heber@…> [cee0b57]
	* src/Makefile.am (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.hpp (modified)
	* src/graph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (added)
	* src/molecule_fragmentation.cpp (added)
	* src/molecule_geometry.cpp (added)
	* src/molecule_graph.cpp (added)
	* src/molecule_pointcloud.cpp (added)
	* src/moleculelist.cpp (modified)
	* src/verbose.cpp (modified)

	class molecule implementation split up into six separate parts.

	- ...


Mon, 05 Oct 2009 17:21:58 GMT Frederik Heber <heber@…> [c26f44]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/builder.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/molecules.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationunittest.cpp (modified)
	* tests/testsuite.at (modified)

	Fixed testsuite, removed some minor bugs.

	- ...


Mon, 05 Oct 2009 16:05:53 GMT Frederik Heber <heber@…> [a33931]
	* 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/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Merge branch 'ConcaveHull' into ConvexHull

	Conflicts:

	        ...


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, 28 Sep 2009 18:41:52 GMT Frederik Heber <heber@…> [f7f7a4]
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Implemenation of embedding merge, untested. LinearInterpolation now ...


Fri, 21 Aug 2009 12:17:52 GMT Frederik Heber <heber@…> [d4fa23]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	New function RemoveAllBoundaryPoints() for sequentially removing all ...


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 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()

	- ...


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 10:29:03 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 19:22:28 GMT Frederik Heber <heber@…> [8bb475f]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(), NonConvex tesselation is now clocked.


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

	Test case of filling a simulation domain with water included.


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

	FillWithMolecule() for testing built into ParseCommandLine()


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

	Huge refactoring of Tesselation routines, but not finished yet.

	- ...


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

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


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

	ConvexTesselation working again.

	- File was not written, as NULL ...


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

	BUGFIX: ManipulateAtoms() had mol = NULL

	- in ManipulateAtoms() the ...


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

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


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

	Merge branch 'master' into ConcaveHull

	Conflicts:

	        ...


Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber <heber@…> [042f82]
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)

	fixed indentation from tabs to two spaces.


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

	Merge branch 'AtomRemoval'

	Conflicts:

	        ...


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

	fixed indentation from tabs to two spaces.


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

	Merge branch 'MultipleMolecules'

	Conflicts:

	        ...


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

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


Thu, 23 Jul 2009 12:14:13 GMT Frederik Heber <heber@…> [437922]
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/defs.hpp (modified)
	* src/joiner.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)

	Fix indentation from tab to two spaces.

	The trouble was caused at ...


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

	Merge branch 'Thermostat'

	Conflicts:

	        .gitignore
	        ...


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

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


Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber <heber@…> [e72001]
	* src/builder.cpp (modified)

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


Thu, 09 Jul 2009 11:01:08 GMT Frederik Heber <heber@…> [989bf6]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)

	Changed the unsatisfactory PathToDatabases construct, removing ...


Thu, 09 Jul 2009 10:31:05 GMT Frederik Heber <heber@…> [4777e9]
	* src/analyzer.cpp (modified)
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)

	Removed unneeded variables


Tue, 07 Jul 2009 08:17:53 GMT Frederik Heber <heber@…> [ce4d22]
	* src/builder.cpp (modified)

	BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere
 ...


Tue, 07 Jul 2009 08:11:47 GMT Frederik Heber <heber@…> [260b2f]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)

	Cosmetical changes in Find_third_point_for_tesselation() and ...


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

	Removing of atoms via command line possible

	-R switchs allows for ...


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

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


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

	removed lots of warnings due to unused variables

	This arose due to ...


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

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


Thu, 02 Apr 2009 16:42:36 GMT Frederik Heber <heber@…> [ca3ccc]
	* src/builder.cpp (modified)

	simple switched order for edit molecule to be in alphabetical
	ordering


Thu, 02 Apr 2009 16:12:54 GMT Frederik Heber <heber@…> [1907a7]
	* src/atom.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Basic implementation of Multiple molecules.

	builder.cpp:
	 - ...


Tue, 10 Feb 2009 12:04:37 GMT Frederik Heber <heber@…> [d8b94a]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.hpp (modified)

	Gaussian basis for MPQC input files can now be specified with -B ...


Mon, 09 Feb 2009 23:17:38 GMT Frederik Heber <heber@…> [2746be]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.hpp (modified)

	Basis for MPQC can now be specified via command line switch

	 * -B ...


Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber <heber@…> [6ac7ee]
	* ChangeLog (modified)
	* Makefile.am (modified)
	* configure.ac (modified)
	* doc/Doxyfile (modified)
	* doc/Makefile.am (modified)
	* m4/ac_doxygen.m4 (modified)
	* m4/acx_compilerflags.m4 (modified)
	* src/.#border.cpp (deleted)
	* src/.#molecules.hpp (deleted)
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/elements.db (modified)
	* src/ellipsoid.cpp (added)
	* src/ellipsoid.hpp (added)
	* src/graph.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/orbitals.db (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/valence.db (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* tests/Makefile.am (modified)
	* tests/atlocal.in (modified)
	* tests/molecuilder.in (modified)
	* tests/testsuite.at (modified)

	Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull
 ...


Mon, 29 Dec 2008 21:46:58 GMT Frederik Heber <heber@…> [cc2ee5]
	* ChangeLog (modified)
	* Makefile.am (modified)
	* configure.ac (modified)
	* doc/Doxyfile (modified)
	* doc/Makefile.am (modified)
	* m4/ac_doxygen.m4 (modified)
	* m4/acx_compilerflags.m4 (modified)
	* src/.#border.cpp (deleted)
	* src/.#molecules.hpp (deleted)
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/elements.db (modified)
	* src/graph.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/orbitals.db (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/valence.db (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* tests/Makefile.am (modified)
	* tests/atlocal.in (modified)
	* tests/molecuilder.in (modified)
	* tests/testsuite.at (modified)

	Just a temporary commit


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

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


Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen <neuen@…> [f714979]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)

	Another update w.r.t. the Tesselation.
	Some signs switched, but atom ...


Thu, 04 Dec 2008 15:15:00 GMT Christian Neuen <neuen@…> [a8bcea6]
	* src/border.cpp (deleted)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	several changes, now output is created, quality unknown


Sat, 18 Oct 2008 14:03:57 GMT Frederik Heber <heber@…> [450d63]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and ...


Fri, 17 Oct 2008 13:20:42 GMT Frederik Heber <heber@…> [9a5bcd]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.hpp (modified)

	config::Save() and config::SaveMPQC() now take string for filename, ...


Thu, 16 Oct 2008 09:27:17 GMT Frederik Heber <heber@…> [a8b9d61]
	* src/builder.cpp (modified)

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


Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber <heber@…> [3ccc3e]
	* src/builder.cpp (modified)
	* src/helpers.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ...


Thu, 09 Oct 2008 18:27:56 GMT Frederik Heber <heber@…> [df793a]
	* src/builder.cpp (modified)
	* src/helpers.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ...


Thu, 25 Sep 2008 17:57:19 GMT Frederik Heber <heber@…> [62f793]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	thermostats enumerator, necessary variables included in class config, ...


Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber <heber@…> [85bac0]
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Implemented molecule::LinearInterpolationBetweenConfiguration().
 ...


Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber <heber@…> [a1fe77]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Basic implementation of Constrained MD is done, missing testing.


Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber <heber@…> [6e9353]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Constrained Molecular Dynamics: two new functions ...


Thu, 11 Sep 2008 13:08:18 GMT Frederik Heber <heber@…> [4f2335]
	* src/builder.cpp (modified)

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


Tue, 09 Sep 2008 08:37:07 GMT Frederik Heber <heber@…> [698b04]
	* src/builder.cpp (modified)
	* src/defs.hpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	new function: molecule::OutputTemperatureFromTrajectories() stores ...


Sat, 06 Sep 2008 15:06:51 GMT Frederik Heber <heber@…> [d1fc7f]
	* src/builder.cpp (modified)

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


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

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


Tue, 02 Sep 2008 12:06:14 GMT Frederik Heber <heber@…> [dd8cf8]
	* src/builder.cpp (modified)

	FIX: ExitFlag not defaults to 0, and set specifically to 1 in the ...


Mon, 18 Aug 2008 08:57:58 GMT Frederik Heber <heber@…> [362b0e]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Adaptivity fixes, MD by VerletForceIntegration introduced, MD ...


Wed, 06 Aug 2008 09:02:01 GMT Frederik Heber <heber@…> [e9b8bb]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Rename of class vector to Vector to avoid conflict with vector from
	STL.


Wed, 06 Aug 2008 08:59:06 GMT Frederik Heber <heber@…> [d7e30c]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Scaffold of new function: VerletForceIntegration() - does MD step by ...


Mon, 28 Jul 2008 13:47:52 GMT Frederik Heber <heber@…> [b61043]
	* src/builder.cpp (modified)

	Removed Output of parsed elements db (does work well, so not ...


Thu, 24 Jul 2008 13:58:40 GMT Frederik Heber <heber@…> [c685eb]
	* src/builder.cpp (modified)

	adding atom: element is now first, not last parameter and output ...


Fri, 27 Jun 2008 21:14:58 GMT Frederik Heber <heber@…> [68cb0f]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/joiner.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (added)

	introduced shieldings to analyzer and joiner

	both now handle ...


Mon, 23 Jun 2008 11:25:09 GMT Frederik Heber <heber@…> [1f066fe]
	* src/builder.cpp (modified)

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


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

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


Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber <heber@…> [14d4d4]
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/periodentafel.cpp (modified)

	BUGFIX: If other databases could not be loaded, no error was ...


Fri, 13 Jun 2008 14:26:50 GMT Frederik Heber <heber@…> [edb650]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	some mor changes to fine-tune the cluster generation.

	Sadly, ...


Fri, 13 Jun 2008 09:18:57 GMT Frederik Heber <heber@…> [318bfd]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	Final touches for Create Clusters in water

	repetition in ...


Thu, 12 Jun 2008 19:34:36 GMT Frederik Heber <heber@…> [6c5812]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	Smaller fixes

	CreateClustersinWater is now PrepareClustersinWater ...


Thu, 12 Jun 2008 19:14:46 GMT Frederik Heber <heber@…> [110ceb]
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/defs.hpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	VolumeOfConvexEnvelope: Works!

	VolumeOfConvexEnvelope has been ...


Tue, 10 Jun 2008 11:21:13 GMT Frederik Heber <heber@…> [233e33]
	* src/builder.cpp (modified)

	fastparse enabled by "-n"


Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber <heber@…> [d52ea1b]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Working version of PAS transformation (tested on C-S-H cluster) and ...


Fri, 30 May 2008 10:42:49 GMT Frederik Heber <heber@…> [fedd5f]
	* src/builder.cpp (modified)

	main(): periode is not printed anymore after parsing cmd options, ...


Mon, 26 May 2008 13:25:38 GMT Frederik Heber <heber@…> [d7d29c]
	* src/builder.cpp (modified)

	renamed ElementsFileName to PathToDatabases, -e now gives path to ...


Mon, 26 May 2008 10:52:00 GMT Frederik Heber <heber@…> [a251a3]
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	molecule::CreateAdjacencyList() now needs IsAngstroem as parameter
 ...


Fri, 23 May 2008 09:17:19 GMT Frederik Heber <heber@…> [7f3b9d]
	* src/analyzer.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/vector.cpp (modified)
	* src/verbose.cpp (modified)

	Lots of for loops now count in reverse order where it does not ...


Wed, 21 May 2008 11:15:32 GMT Frederik Heber <heber@…> [ca2b83]
	* src/builder.cpp (modified)

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


Fri, 16 May 2008 13:35:43 GMT Frederik Heber <heber@…> [98b1d2]
	* src/builder.cpp (modified)

	main(): typo in Usage message, BUGFIX - command line arguments did ...