#
# ChangeLog for molecuilder/src/molecules.hpp
#
# Generated by Trac 1.4.4
# Apr 15, 2025, 6:41:20 PM

Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber <heber@…> [32b6dc]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Mon, 26 May 2008 10:52:00 GMT Frederik Heber <heber@…> [5eb05a]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Fri, 23 May 2008 09:17:19 GMT Frederik Heber <heber@…> [f75030]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/verbose.cpp (modified)

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


Wed, 21 May 2008 09:24:54 GMT Frederik Heber <heber@…> [725869]
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (added)

	new header file for the vector class, new operators +=,*=,*,+


Fri, 09 May 2008 14:20:08 GMT Frederik Heber <heber@…> [0716ff4]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	MinimumRingSize is now an array over all atoms

	Each entry in ...


Thu, 08 May 2008 17:31:04 GMT Frederik Heber <heber@…> [a3ff7b2]
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	molecule::CheckOrderAtSite() now interprets negative Orders as ...


Thu, 08 May 2008 16:18:07 GMT Frederik Heber <heber@…> [461e93]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	molecule::CheckOrderAtSite() returns bool and used as threshold ...


Thu, 08 May 2008 15:52:11 GMT Frederik Heber <heber@…> [d88597]
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	new function molecule::CreateMappingLabelsToConfigSequence() creates ...


Thu, 08 May 2008 15:39:36 GMT Frederik Heber <heber@…> [2b79c3]
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in ...


Thu, 08 May 2008 15:26:55 GMT Frederik Heber <heber@…> [169b24]
	* molecuilder/src/molecules.hpp (modified)

	new functions MoleculeLeafClass::AssignKeySetsToFragment() and ...


Thu, 08 May 2008 12:45:25 GMT Frederik Heber <heber@…> [7b80a5]
	* molecuilder/src/molecules.hpp (modified)

	new functions MoleculeLeafClass::Count() and ...


Thu, 08 May 2008 12:04:42 GMT Frederik Heber <heber@…> [9c3496]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	new function molecule::CheckOrderAtSite and ...


Wed, 07 May 2008 14:46:33 GMT Frederik Heber <heber@…> [a01955]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	rewritten CyclicStructureAnalysis(): uses DFS spanning tree and ...


Wed, 07 May 2008 13:38:13 GMT Frederik Heber <heber@…> [d50d2a]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/stackclass.hpp (added)

	AtomStackClass -> template <typename T> StackClass<T> change in new ...


Mon, 05 May 2008 16:19:05 GMT Frederik Heber <heber@…> [115bf4]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.cpp (modified)

	ForcesFile and TEFactors are _needed_, reincorporated. ...


Fri, 02 May 2008 13:25:48 GMT Frederik Heber <heber@…> [c75363]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	HUGE REWRITE to allow for adaptive increase of the bond order, first ...


Tue, 29 Apr 2008 12:19:51 GMT Frederik Heber <heber@…> [c510a7]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* pcp/src/defs.h (modified)
	* pcp/src/helpers.c (modified)
	* pcp/src/init.c (modified)
	* pcp/src/ions.c (modified)
	* pcp/src/opt.c (modified)
	* pcp/src/output.c (modified)
	* pcp/src/perturbed.c (modified)
	* pcp/src/pseudo.c (modified)
	* pcp/src/wannier.c (modified)

	char lengths of 255 and MAXDUMMYSTRING replaced with define ...


Tue, 29 Apr 2008 07:55:34 GMT Frederik Heber <heber@…> [307fd1]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	Store/CheckAdj...() now also incorporate bond order to check against.


Tue, 29 Apr 2008 07:04:59 GMT Frederik Heber <heber@…> [7b1cea]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	configname is also stored in config structure, GetDefaultPath by ...


Tue, 29 Apr 2008 06:30:38 GMT Frederik Heber <heber@…> [f5306f]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	config::Load..() now get filename instead of pointer to file, bugfix ...


Mon, 28 Apr 2008 13:53:54 GMT Frederik Heber <heber@…> [661288]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	Atoms in the fragments in the configs are again ordered as first ...


Mon, 28 Apr 2008 10:41:40 GMT Frederik Heber <heber@…> [34d37c]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	storing and comparing Adjacency outsourced into two new functions.
 ...


Mon, 28 Apr 2008 09:22:38 GMT Frederik Heber <heber@…> [2614f83]
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	FragmentMolecule(): Adjacency store/check and parsing of KeySetFile ...


Sun, 27 Apr 2008 12:59:40 GMT Frederik Heber <heber@…> [c72cbe]
	* molecuilder/src/molecules.hpp (modified)

	Load/StorePeriodentafel(): filename as parameter, if NULL default ...


Thu, 24 Apr 2008 17:03:14 GMT Frederik Heber <heber@…> [77da65]
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/parser.hpp (modified)

	ADDHYDROGEN and HAVE_DEBUG fix: config.h was not yet included
 ...


Wed, 23 Apr 2008 17:33:51 GMT Frederik Heber <heber@…> [090299]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

	molecuilder reads and stored ion velocities

	Class atom has new ...


Fri, 18 Apr 2008 11:26:42 GMT Frederik Heber <heber@…> [a0bcf1]
	* AUTHORS (added)
	* COPYING (added)
	* ChangeLog (added)
	* Makefile.am (added)
	* NEWS (added)
	* README (added)
	* autogen.sh (added)
	* configure.ac (added)
	* molecuilder/AUTHORS (added)
	* molecuilder/ChangeLog (added)
	* molecuilder/Makefile.am (added)
	* molecuilder/NEWS (added)
	* molecuilder/README (added)
	* molecuilder/autogen.sh (added)
	* molecuilder/configure.ac (added)
	* molecuilder/doc/Doxyfile (added)
	* molecuilder/doc/Makefile.am (added)
	* molecuilder/m4/ac_doxygen.m4 (added)
	* molecuilder/src/Hbondangle.db (added)
	* molecuilder/src/Hbonddistance.db (added)
	* molecuilder/src/Makefile.am (added)
	* molecuilder/src/analyzer.cpp (added)
	* molecuilder/src/atom.cpp (added)
	* molecuilder/src/bond.cpp (added)
	* molecuilder/src/builder.cpp (added)
	* molecuilder/src/config.cpp (added)
	* molecuilder/src/datacreator.cpp (added)
	* molecuilder/src/datacreator.hpp (added)
	* molecuilder/src/defs.hpp (added)
	* molecuilder/src/element.cpp (added)
	* molecuilder/src/elements.db (added)
	* molecuilder/src/graph.cpp (added)
	* molecuilder/src/helpers.cpp (added)
	* molecuilder/src/helpers.hpp (added)
	* molecuilder/src/joiner.cpp (added)
	* molecuilder/src/moleculelist.cpp (added)
	* molecuilder/src/molecules.cpp (added)
	* molecuilder/src/molecules.hpp (added)
	* molecuilder/src/orbitals.db (added)
	* molecuilder/src/parser.cpp (added)
	* molecuilder/src/parser.hpp (added)
	* molecuilder/src/periodentafel.cpp (added)
	* molecuilder/src/valence.db (added)
	* molecuilder/src/vector.cpp (added)
	* molecuilder/src/verbose.cpp (added)
	* pcp/AUTHORS (added)
	* pcp/CHANGES (added)
	* pcp/ChangeLog (added)
	* pcp/Makefile.am (added)
	* pcp/NEWS (added)
	* pcp/README (added)
	* pcp/autogen.sh (added)
	* pcp/configure.ac (added)
	* pcp/doc/Doxyfile (added)
	* pcp/doc/Makefile.am (added)
	* pcp/m4/ac_doxygen.m4 (added)
	* pcp/m4/acx_mpi.m4 (added)
	* pcp/src/Makefile.am (added)
	* pcp/src/Makefile.in (added)
	* pcp/src/data.h (added)
	* pcp/src/defs.h (added)
	* pcp/src/density.c (added)
	* pcp/src/density.h (added)
	* pcp/src/energy.c (added)
	* pcp/src/energy.h (added)
	* pcp/src/errors.c (added)
	* pcp/src/errors.h (added)
	* pcp/src/excor.c (added)
	* pcp/src/excor.h (added)
	* pcp/src/grad.c (added)
	* pcp/src/grad.h (added)
	* pcp/src/gramsch.c (added)
	* pcp/src/gramsch.h (added)
	* pcp/src/helpers.c (added)
	* pcp/src/helpers.h (added)
	* pcp/src/init.c (added)
	* pcp/src/init.h (added)
	* pcp/src/ions.c (added)
	* pcp/src/ions.h (added)
	* pcp/src/mergesort2.c (added)
	* pcp/src/mergesort2.h (added)
	* pcp/src/myfft.c (added)
	* pcp/src/myfft.h (added)
	* pcp/src/mymath.c (added)
	* pcp/src/mymath.h (added)
	* pcp/src/opt.c (added)
	* pcp/src/opt.h (added)
	* pcp/src/output.c (added)
	* pcp/src/output.h (added)
	* pcp/src/parsetest.c (added)
	* pcp/src/pcp.c (added)
	* pcp/src/pcp.h (added)
	* pcp/src/pdbformat.c (added)
	* pcp/src/pdbformat.h (added)
	* pcp/src/perturbed.c (added)
	* pcp/src/perturbed.h (added)
	* pcp/src/pseudo.c (added)
	* pcp/src/pseudo.h (added)
	* pcp/src/riemann.c (added)
	* pcp/src/riemann.h (added)
	* pcp/src/run.c (added)
	* pcp/src/run.h (added)
	* pcp/src/test.c (added)
	* pcp/src/wannier.c (added)
	* pcp/src/wannier.h (added)
	* util/AUTHORS (added)
	* util/BOSSEvaluate.pl.in (added)
	* util/ChangeLog (added)
	* util/CreateFromXYZ.sh (added)
	* util/CreateGaAs.c (added)
	* util/CreateH2.c (added)
	* util/GetPdb.c (added)
	* util/Makefile.am (added)
	* util/NEWS (added)
	* util/NanoCreator.c (added)
	* util/NanoCreator.h (added)
	* util/Nanotubes.pl.in (added)
	* util/README (added)
	* util/ReSequenceDX.pl.in (added)
	* util/ReadSrcIon.c (added)
	* util/VibrAlyzer.c (added)
	* util/autogen.sh (added)
	* util/average.cpp (added)
	* util/average_result.sh (added)
	* util/compile (added)
	* util/config2xyz.sh (added)
	* util/configure.ac (added)
	* util/convert2old.sh (added)
	* util/convertpdb.sh (added)
	* util/depcomp (added)
	* util/doc/Doxyfile (added)
	* util/doc/Makefile.am (added)
	* util/gather_all_results.sh (added)
	* util/gather_averaged_results.sh (added)
	* util/gather_result.sh (added)
	* util/grep_shielding.sh (added)
	* util/install-sh (added)
	* util/m4/ac_doxygen.m4 (added)
	* util/meas2pdb.sh (added)
	* util/mergesort.c (added)
	* util/mergesort.h (added)
	* util/specvisual.cfg (added)
	* util/specvisual.net (added)
	* util/specvisualOnly.net (added)
	* util/stochastik.cpp (added)
	* util/suffix (added)
	* util/visual.cfg (added)
	* util/visual.net (added)
	* util/visualOnly.net (added)

	-initial commit
	-Minimum set of files needed from ESPACK SVN ...