#
# ChangeLog for /
#
# Generated by Trac 1.6
# Nov 24, 2025, 4:01:44 PM

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 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 ...


Thu, 27 Nov 2008 09:55:08 GMT Christian Neuen <neuen@…> [03648b]
	* src/border.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	In vector a function for calculation of the vector-(cross-)product ...


Tue, 25 Nov 2008 15:05:07 GMT Christian Neuen <neuen@…> [51695c]
	* src/border.cpp (added)

	Construction of border triangles of non convex point set


Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber <heber@…> [72744a]
	* src/analyzer.cpp (modified)

	Analyzer now produces data file with Frobenius norm of hessian
	matrix.


Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber <heber@…> [376f97]
	* src/parser.cpp (modified)

	Added some commentary to HessianMatrix::SumSubHessians to ease
	debugging


Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber <heber@…> [05d2b2]
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)

	Implemented Frobenius norm calculation for class HessianMatrix
 ...


Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber <heber@…> [b12a35]
	* src/analyzer.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	HessianMatrix implemented fully, but not yet working, probably due to ...


Thu, 30 Oct 2008 16:13:32 GMT Frederik Heber <heber@…> [674220]
	* src/analyzer.cpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.hpp (modified)

	Implemented analysis of magnetic susceptibilites.

	This is very ...


Thu, 30 Oct 2008 16:12:57 GMT Frederik Heber <heber@…> [5621c3]
	* src/graph.cpp (modified)
	* src/graph.hpp (added)

	Begin of implementing classes Graph, SubGraph, Node and Edge.

	So ...


Thu, 30 Oct 2008 01:01:04 GMT Frederik Heber <heber@…> [cc36a5]
	* src/analyzer.cpp (modified)

	Analyzer now produces data file with Frobenius norm of hessian
	matrix.


Thu, 30 Oct 2008 00:59:40 GMT Frederik Heber <heber@…> [2e6e7a]
	* src/graph.cpp (modified)
	* src/graph.hpp (added)

	Begin of implementing classes Graph, SubGraph, Node and Edge.

	So ...


Thu, 30 Oct 2008 00:56:02 GMT Frederik Heber <heber@…> [a8f53c4]
	* src/parser.cpp (modified)

	Added some commentary to HessianMatrix::SumSubHessians to ease
	debugging


Thu, 30 Oct 2008 00:55:19 GMT Frederik Heber <heber@…> [234af2]
	* src/analyzer.cpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.hpp (modified)

	Implemented analysis of magnetic susceptibilites.

	This is very ...


Wed, 29 Oct 2008 14:54:54 GMT Frederik Heber <heber@…> [84fc91]
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)

	Implemented Frobenius norm calculation for class HessianMatrix
 ...


Sun, 19 Oct 2008 13:57:23 GMT Frederik Heber <heber@…> [eeec8f]
	* src/analyzer.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	HessianMatrix implemented fully, but not yet working, probably due to ...


Sat, 18 Oct 2008 15:05:54 GMT Frederik Heber <heber@…> [f731ae]
	* src/analyzer.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/joiner.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	ColumnCounter -> *ColumnCounter

	columns of the MatrixContainer ...


Sat, 18 Oct 2008 14:06:51 GMT Frederik Heber <heber@…> [85d278]
	* src/joiner.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	Introduced new class HessianMatrix derived from MatrixContainer, ...


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 13:24:10 GMT Frederik Heber <heber@…> [65de9b]
	* src/molecules.cpp (modified)

	molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, ...


Fri, 17 Oct 2008 13:22:38 GMT Frederik Heber <heber@…> [4ee3df]
	* src/analyzer.cpp (modified)
	* src/datacreator.cpp (modified)

	Analyzer now writes usable plot and data files for shielding ...


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 09:27:59 GMT Frederik Heber <heber@…> [f00693]
	* tests/testsuite.at (modified)

	New tests that check that if subsequent arguments to certain cmd ...


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

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


Thu, 16 Oct 2008 09:26:48 GMT Frederik Heber <heber@…> [52f5d5]
	* src/periodentafel.cpp (modified)

	periodentafel::LoadPeriodentafel(): if other dbs fail, we just give a ...


Thu, 16 Oct 2008 09:25:56 GMT Frederik Heber <heber@…> [e198c7]
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)

	New function IsValidNumber(): checks whether a command line argument ...


Wed, 15 Oct 2008 18:20:51 GMT Frederik Heber <heber@…> [95634f]
	* src/analyzer.cpp (modified)

	Analyzer now prints usable ShieldingsPAS data and plot files (so that ...


Wed, 15 Oct 2008 18:20:40 GMT Frederik Heber <heber@…> [19f3d6]
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)

	new function AppendOutputFile() for appending to output files whereas ...


Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber <heber@…> [57d8b0]
	* src/molecules.cpp (modified)

	molecule::VerletForceIntegration() different code, same algorithm ...


Tue, 14 Oct 2008 19:14:10 GMT Frederik Heber <heber@…> [2b4a40]
	* src/boundary.cpp (modified)

	new version of Tesselation::GuessStartingTriangle() seems to fix ...


Tue, 14 Oct 2008 13:26:02 GMT Frederik Heber <heber@…> [ca8073]
	* src/boundary.cpp (modified)

	BUGFIX: Tesselation::AddPoint() always increased ...


Sun, 12 Oct 2008 15:58:48 GMT Frederik Heber <heber@…> [ec7ba8]
	* src/config.cpp (modified)

	changed basis set for mpqc from STO-3G to 3-21G (more stable with ...


Sat, 11 Oct 2008 16:07:45 GMT Frederik Heber <heber@…> [9fc556]
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/orbitals.db (modified)
	* src/valence.db (modified)

	corrected number of valence orbitals for Calcium (2 -> 4) and ...


Sat, 11 Oct 2008 16:07:28 GMT Frederik Heber <heber@…> [74a65e]
	* src/molecules.cpp (modified)

	molecule::AddHydrogenReplacementAtom() returns false on missing ...


Fri, 10 Oct 2008 13:39:58 GMT Frederik Heber <heber@…> [edcda5]
	* src/moleculelist.cpp (modified)

	BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ...


Fri, 10 Oct 2008 13:39:54 GMT Frederik Heber <heber@…> [4158ba]
	* src/molecules.cpp (modified)

	BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ...


Fri, 10 Oct 2008 13:38:46 GMT Frederik Heber <heber@…> [617b53]
	* src/moleculelist.cpp (modified)

	BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ...


Fri, 10 Oct 2008 13:38:41 GMT Frederik Heber <heber@…> [1e8243]
	* src/molecules.cpp (modified)

	BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ...


Fri, 10 Oct 2008 13:36:06 GMT Frederik Heber <heber@…> [fcbfc8]
	* src/moleculelist.cpp (modified)

	BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ...


Fri, 10 Oct 2008 13:32:33 GMT Frederik Heber <heber@…> [ad85c2]
	* src/molecules.cpp (modified)

	BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ...


Thu, 09 Oct 2008 18:29:34 GMT Frederik Heber <heber@…> [41f151]
	* 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 18:29:03 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, 09 Oct 2008 16:19:39 GMT Frederik Heber <heber@…> [ba4432]
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/molecules.hpp (modified)

	Output of atom and bond to stream now is set to const bond/atom


Sun, 28 Sep 2008 17:55:04 GMT Frederik Heber <heber@…> [aa5702]
	* src/analyzer.cpp (modified)
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)

	corrected molecule::VerletForceIntegration() and analyzer creates ...


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, 25 Sep 2008 17:57:02 GMT Frederik Heber <heber@…> [16a52b]
	* src/defs.hpp (modified)

	Lots of conversion factors for various units

	Were taken from PCP defs.h


Thu, 25 Sep 2008 17:50:17 GMT Frederik Heber <heber@…> [7ce307]
	* src/Makefile.am (modified)

	Some files were missing in the repository

	pseudopotentials and the ...


Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber <heber@…> [795a54]
	* src/molecules.cpp (modified)

	molecule::MinimiseConstrainedPotential(): Extension of search and ...


Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber <heber@…> [c30cda]
	* src/molecules.cpp (modified)

	molecule::MinimiseConstrainedPotential() : Minimisation is fixed
 ...


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 13:25:47 GMT Frederik Heber <heber@…> [18913c]
	* src/config.cpp (modified)
	* src/molecules.hpp (modified)

	config::DoWannier implemented that is parsed from config file, ...


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 15:32:16 GMT Frederik Heber <heber@…> [2985c8]
	* src/vector.cpp (modified)

	BUGFIX: Normalize() would try to normalize a zero vector which ended ...


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 ...


Tue, 09 Sep 2008 07:46:15 GMT Frederik Heber <heber@…> [bd3e55]
	* configure.ac (modified)

	configure BUGFIX: GSL may be linked against cblas_... functions or ...


Sat, 06 Sep 2008 16:21:31 GMT Frederik Heber <heber@…> [deac6c]
	* src/molecules.cpp (modified)

	BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did ...


Sat, 06 Sep 2008 15:08:32 GMT Frederik Heber <heber@…> [a6b7fb]
	* src/config.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which ...


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.
 ...