#
# ChangeLog for tests/regression/Molecules
#
# Generated by Trac 1.4.4
# Jan 2, 2025, 7:23:51 PM

Tue, 01 Mar 2011 13:17:07 GMT Frederik Heber <heber@…> [0cbad2]
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.def (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* tests/regression/Molecules/BondFile/post/test.pdb (added)
	* tests/regression/Molecules/BondFile/pre/silica.dbond.0000 (added)
	* tests/regression/Molecules/BondFile/pre/silica.pov1.0000.pdb (added)
	* tests/regression/Molecules/BondFile/pre/test.dbond (modified)
	* tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (modified)

	Moved molecule::CreateAdjacencyListFromDbondFile() over to BondGraph ...


Tue, 01 Mar 2011 12:49:28 GMT Frederik Heber <heber@…> [3738f0]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/AtomSet.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* tests/Fragmentations/defs.in (modified)
	* tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified)
	* tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified)
	* tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified)
	* tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified)

	Moved molecule::CreateAdjacencyList over to class BondGraph.

	to ...


Thu, 24 Feb 2011 19:47:41 GMT Frederik Heber <heber@…> [6a465e]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (modified)
	* src/config.cpp (modified)
	* tests/regression/Molecules/SaveTemperature/post/test.ekin (modified)

	Rewrote LoadMolecule() for PcpParser.

	- LoadMolecule() rewritten as ...


Wed, 09 Feb 2011 20:04:56 GMT Frederik Heber <heber@…> [acd638]
	* src/Parser/TremoloParser.cpp (modified)
	* tests/regression/Molecules/Copy/post/tensid.data (added)
	* tests/regression/Molecules/Copy/pre/tensid.data (added)
	* tests/regression/Molecules/Copy/pre/tensid.potentials (added)
	* tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified)

	BUGFIX: copied atoms were not correctly stored with respect to Type, ...


Fri, 04 Feb 2011 19:11:51 GMT Frederik Heber <heber@…> [967b3c]
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.def (modified)
	* tests/regression/Analysis/AngularDipoleCorrelation-DiscreteAngles/testsuite-analysis-angular-dipole-correlation-discrete-angles.at (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Molecules/BondFile/pre/test.conf (moved)
	* tests/regression/Molecules/BondFile/pre/test.dbond (moved)
	* tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (added)
	* tests/regression/Molecules/Copy/post/test-copy.xyz (moved)
	* tests/regression/Molecules/Copy/pre/test.xyz (moved)
	* tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (added)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/post/test.conf (moved)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/pre/test.conf (moved)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (added)
	* tests/regression/Molecules/RotateAroundOrigin/post/test-rotated-xYz20.xyz (moved)
	* tests/regression/Molecules/RotateAroundOrigin/post/test-rotated-z180.xyz (moved)
	* tests/regression/Molecules/RotateAroundOrigin/post/test-rotated-z360.xyz (moved)
	* tests/regression/Molecules/RotateAroundOrigin/post/test-rotated-z90.xyz (moved)
	* tests/regression/Molecules/RotateAroundOrigin/pre/test.xyz (moved)
	* tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (added)
	* tests/regression/Molecules/RotateAroundSelf/post/test-rotated-xYz20.xyz (moved)
	* tests/regression/Molecules/RotateAroundSelf/post/test-rotated-z180.xyz (moved)
	* tests/regression/Molecules/RotateAroundSelf/post/test-rotated-z360.xyz (moved)
	* tests/regression/Molecules/RotateAroundSelf/post/test-rotated-z90.xyz (moved)
	* tests/regression/Molecules/RotateAroundSelf/pre/test.xyz (moved)
	* tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (added)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-xYz20.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z180.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z360.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z90.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-xYz20.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z180.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z360.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z90.xyz (moved)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (added)
	* tests/regression/Molecules/SaveAdjacency/post/test.adj (moved)
	* tests/regression/Molecules/SaveAdjacency/pre/test.conf (moved)
	* tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (added)
	* tests/regression/Molecules/SaveBonds/post/test.dbond (moved)
	* tests/regression/Molecules/SaveBonds/pre/test.conf (added)
	* tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (added)
	* tests/regression/Molecules/SaveTemperature/post/test.ekin (moved)
	* tests/regression/Molecules/SaveTemperature/pre/test.conf (moved)
	* tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (added)
	* tests/regression/Molecules/Translation-Periodic/post/test.conf (moved)
	* tests/regression/Molecules/Translation-Periodic/pre/test.conf (moved)
	* tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (added)
	* tests/regression/Molecules/Translation/post/test.conf (moved)
	* tests/regression/Molecules/Translation/post/test2.conf (moved)
	* tests/regression/Molecules/Translation/pre/test.conf (moved)
	* tests/regression/Molecules/Translation/pre/test2.conf (moved)
	* tests/regression/Molecules/Translation/testsuite-molecules-translation.at (added)
	* tests/regression/Molecules/VerletIntegration/pre/test.conf (moved)
	* tests/regression/Molecules/VerletIntegration/pre/test.forces (moved)
	* tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (added)
	* tests/regression/Molecules/testsuite-molecules.at (added)
	* tests/regression/testsuite-molecules.at (deleted)
	* tests/regression/testsuite.at (modified)

	Changed regression testsuite structure of Molecules.

	- all numbered ...


Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber <heber@…> [1a7fd2]
	* src/Actions/Makefile.am (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (added)
	* src/Actions/MoleculeAction/CopyAction.def (added)
	* src/Actions/MoleculeAction/CopyAction.hpp (added)
	* tests/regression/Molecules/11/post/test-copy.xyz (added)
	* tests/regression/Molecules/11/pre/test.xyz (added)
	* tests/regression/testsuite-molecules.at (modified)

	New Action MoleculeAction/CopyAction.


Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber <heber@…> [b5cf6c]
	* src/bondgraph.cpp (modified)
	* tests/regression/Molecules/2/post/test.adj (modified)

	BUGFIX: BondGraph::max_distance is used for LinkedCell cell length ...


Fri, 06 Aug 2010 16:56:59 GMT Frederik Heber <heber@…> [327364]
	* tests/regression/Molecules/8/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/8/pre/test.conf (deleted)
	* tests/regression/testsuite-molecules.at (modified)

	Rotate to PAS is fixed.

	- was marked BROKEN before in test case, is ...


Fri, 06 Aug 2010 16:49:14 GMT Frederik Heber <heber@…> [31db5b]
	* tests/regression/Molecules/10/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/10/pre/test.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/9/pre/test.xyz (added)
	* tests/regression/testsuite-molecules.at (modified)

	Added test cases for Actions rotate-origin and rotate-self.


Wed, 07 Jul 2010 11:53:05 GMT Frederik Heber <heber@…> [86cff86]
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* tests/regression/Domain/6/post/test-x.xyz (moved)
	* tests/regression/Domain/6/post/test-y.xyz (moved)
	* tests/regression/Domain/6/post/test-z.xyz (moved)
	* tests/regression/Domain/6/post/test.xyz (moved)
	* tests/regression/Fragmentation/2/post/BondFragment0.xyz (moved)
	* tests/regression/Fragmentation/2/post/BondFragment1.xyz (moved)
	* tests/regression/Fragmentation/2/post/BondFragment2.xyz (moved)
	* tests/regression/Fragmentation/2/post/BondFragment3.xyz (moved)
	* tests/regression/Fragmentation/2/post/BondFragment4.xyz (moved)
	* tests/regression/Molecules/6/post/test2.conf (moved)
	* tests/regression/Molecules/6/pre/test2.conf (added)
	* tests/regression/Simple_configuration/2/post/test.in (moved)
	* tests/regression/Simple_configuration/2/post/test.xyz (moved)
	* tests/regression/Simple_configuration/3/post/test.in (moved)
	* tests/regression/Simple_configuration/3/post/test.xyz (moved)
	* tests/regression/Simple_configuration/3/post/test2.conf (moved)
	* tests/regression/Simple_configuration/3/post/test2.in (added)
	* tests/regression/Simple_configuration/3/post/test2.xyz (added)
	* tests/regression/Simple_configuration/4/post/test.conf.xyz (deleted)
	* tests/regression/Simple_configuration/4/post/test.xyz (added)
	* tests/regression/Simple_configuration/4/pre/test.xyz (added)
	* tests/regression/Simple_configuration/5/post/test.in (moved)
	* tests/regression/Simple_configuration/5/post/test.xyz (moved)
	* tests/regression/Simple_configuration/8/post/test.xyz (moved)
	* tests/regression/Simple_configuration/8/post/test.xyz-sorted (added)
	* tests/regression/testsuite-domain.at (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	InputAction now parses all possible formats, not only pcp.

	- new ...


Sat, 19 Jun 2010 15:54:47 GMT Frederik Heber <heber@…> [274d45]
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/orbitals.db (modified)
	* src/periodentafel.cpp (modified)
	* src/valence.db (modified)
	* tests/regression/Domain/2/post/test.conf (modified)
	* tests/regression/Domain/3/post/test.conf (modified)
	* tests/regression/Domain/4/post/test.conf (modified)
	* tests/regression/Domain/5/post/test.conf (modified)
	* tests/regression/Filling/1/post/test.conf (modified)
	* tests/regression/Filling/1/pre/test.conf (modified)
	* tests/regression/Molecules/6/post/test.conf (modified)
	* tests/regression/Molecules/6/pre/test.conf (modified)
	* tests/regression/Molecules/7/post/test.conf (modified)
	* tests/regression/Molecules/7/pre/test.conf (modified)
	* tests/regression/Simple_configuration/2/post/test.conf (modified)
	* tests/regression/Simple_configuration/3/post/test.conf (modified)
	* tests/regression/Simple_configuration/4/post/test.conf (modified)
	* tests/regression/Simple_configuration/5/post/test.conf (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* tests/regression/testsuite-tesselation.at (modified)

	FIX: Atoms were stored not in the sequence they were loaded.

	1. The ...


Tue, 01 Jun 2010 08:02:48 GMT Frederik Heber <heber@…> [acf800]
	* src/molecule_graph.cpp (modified)
	* tests/regression/Molecules/2/post/test.adj (modified)
	* tests/regression/Molecules/2/post/test.dbond (modified)
	* tests/regression/Molecules/2/pre/test.conf (modified)

	TESTFIX: Wrong (old) ordering of conf files (IonTyp2 before IonType1) ...


Tue, 01 Jun 2010 07:28:15 GMT Frederik Heber <heber@…> [bd6bfa]
	* src/bondgraph.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* tests/regression/Molecules/6/post/test.conf (modified)
	* tests/regression/Molecules/7/post/test.conf (modified)

	Fixes after first,last removal.

	- BUGFIX: ...


Sun, 30 May 2010 18:28:14 GMT Frederik Heber <heber@…> [d6d6c1]
	* tests/regression/Analysis/5/pre/test.conf (added)
	* tests/regression/Molecules/8/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-m' (principal axis system) to testsuite.


Sun, 30 May 2010 17:29:38 GMT Frederik Heber <heber@…> [eddea2]
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/vector.cpp (modified)
	* tests/regression/Molecules/7/post/test.conf (added)
	* tests/regression/Molecules/7/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-T' (periodic translation) to testsuite.

	- BUGFIX: ...


Sun, 30 May 2010 16:55:04 GMT Frederik Heber <heber@…> [5d12d2]
	* tests/regression/Molecules/6/post/test.conf (added)
	* tests/regression/Molecules/6/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-t' (translation) to testsuite.


Sun, 30 May 2010 16:09:06 GMT Frederik Heber <heber@…> [c7a473]
	* src/atom_trajectoryparticle.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* tests/regression/Molecules/5/pre/test.conf (added)
	* tests/regression/Molecules/5/pre/test.forces (added)
	* tests/regression/testsuite.at (modified)

	Added cased '-P' (force integration) to testsuite.

	- this is ...


Sun, 30 May 2010 15:38:38 GMT Frederik Heber <heber@…> [f8f14d]
	* src/builder.cpp (modified)
	* tests/regression/Molecules/4/post/test.conf (added)
	* tests/regression/Molecules/4/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-L' (linear interpolation) to testsuite.

	- this just ...


Sun, 30 May 2010 15:30:32 GMT Frederik Heber <heber@…> [13bfeb]
	* tests/regression/Molecules/3/post/test.ekin (added)
	* tests/regression/Molecules/3/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-S' (storing temperature) to testsuite.

	- made three ...


Sun, 30 May 2010 15:24:29 GMT Frederik Heber <heber@…> [72e36f]
	* tests/regression/Molecules/2/post/test.adj (added)
	* tests/regression/Molecules/2/post/test.dbond (added)
	* tests/regression/Molecules/2/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added cases '-j' (storing bonds) and '-J' (storing adjacency) to ...


Sun, 30 May 2010 15:18:50 GMT Frederik Heber <heber@…> [c68c90]
	* src/builder.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* tests/regression/Molecules/1/pre/test.conf (added)
	* tests/regression/Molecules/1/pre/test.dbond (added)
	* tests/regression/testsuite.at (modified)

	Added case '-A' (parsing bonds) to testsuite.

	- ...