#
# ChangeLog for molecuilder
#
# Generated by Trac 1.6
# Jun 4, 2025, 7:27:49 PM

Tue, 06 May 2008 09:48:00 GMT Frederik Heber <heber@…> [48efc3]
	* molecuilder/src/parser.cpp (modified)

	MatrixContainer::MatrixContainer() debug message fixes only, ...


Tue, 06 May 2008 09:45:31 GMT Frederik Heber <heber@…> [0e8321]
	* molecuilder/src/molecules.cpp (modified)

	KeySetFile is stored without an additional last tab on each line


Mon, 05 May 2008 16:54:44 GMT Frederik Heber <heber@…> [8449ed]
	* molecuilder/src/parser.cpp (modified)

	joiner crashed due to incorrect destructing of MatrixContainer, ...


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 15:18:27 GMT Frederik Heber <heber@…> [38fc0d]
	* molecuilder/src/helpers.cpp (modified)

	Free(): only set to NULL if it was free'd otherwise it is already


Fri, 02 May 2008 15:18:05 GMT Frederik Heber <heber@…> [cffff8]
	* molecuilder/src/parser.cpp (modified)

	~MatrixContainer(): Bugfix - Free if Matrix[MatrixCounter] would also ...


Fri, 02 May 2008 13:35:10 GMT Frederik Heber <heber@…> [30fda2]
	* molecuilder/src/molecules.cpp (modified)

	commenting in header changed for the four main functions that ...


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 12:31:38 GMT Frederik Heber <heber@…> [e936b3]
	* molecuilder/src/builder.cpp (modified)

	Velocities were not correctly handled, also not in fragments

	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 07:55:11 GMT Frederik Heber <heber@…> [16b0c8]
	* molecuilder/tests/testsuite.at (modified)

	config file is again first argument and implemented test of ...


Tue, 29 Apr 2008 07:45:23 GMT Frederik Heber <heber@…> [9bd230]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/defs.hpp (modified)

	changed config file to first argument again and standard config name ...


Tue, 29 Apr 2008 07:41:20 GMT Frederik Heber <heber@…> [7e2c5c]
	* molecuilder/src/config.cpp (modified)

	bugfix: configpath and -name are not set to empty string.


Tue, 29 Apr 2008 07:16:32 GMT Frederik Heber <heber@…> [584691]
	* molecuilder/src/builder.cpp (modified)

	bugfix in main: without arguments, code would crash due to access of ...


Tue, 29 Apr 2008 07:06:18 GMT Frederik Heber <heber@…> [2456db]
	* molecuilder/tests/testsuite.at (modified)

	Full test for fragmentation procedure with readin of the adjacency ...


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 06:57:59 GMT Frederik Heber <heber@…> [36b128]
	* molecuilder/src/builder.cpp (modified)

	Comply with test again: help and version command options exit at once ...


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 13:46:05 GMT Frederik Heber <heber@…> [e565a8]
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)

	removed some output lines (commented-out) mostly in ...


Mon, 28 Apr 2008 11:39:07 GMT Frederik Heber <heber@…> [8efbfc]
	* molecuilder/src/molecules.cpp (modified)

	FragmentMolecule(): status variable used when checking adjacency file ...


Mon, 28 Apr 2008 11:36:11 GMT Frederik Heber <heber@…> [d982bb]
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/parser.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)

	All filenames (const char *) have been transferred to defs.hpp
 ...


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 ...


Mon, 28 Apr 2008 09:18:10 GMT Frederik Heber <heber@…> [bd8439]
	* molecuilder/src/analyzer.cpp (modified)

	main(): thrown out unused stringstreams prefix and line


Mon, 28 Apr 2008 07:16:42 GMT Frederik Heber <heber@…> [23409a]
	* molecuilder/src/moleculelist.cpp (modified)

	OutputConfigForListOfFragments(): various ofstream gathered into a ...


Sun, 27 Apr 2008 13:05:46 GMT Frederik Heber <heber@…> [1ddebb]
	* molecuilder/tests/Makefile.am (added)
	* molecuilder/tests/atlocal.in (added)
	* molecuilder/tests/molecuilder.in (added)
	* molecuilder/tests/testsuite.at (added)
	* pcp/tests/Makefile.am (added)
	* pcp/tests/atlocal.in (added)
	* pcp/tests/pcp.in (added)
	* pcp/tests/testsuite.at (added)
	* util/tests/Makefile.am (added)
	* util/tests/atlocal.in (added)
	* util/tests/testsuite.at (added)

	forgot to commit the actual autotest files listed during last commit, ...


Sun, 27 Apr 2008 13:04:01 GMT Frederik Heber <heber@…> [b5279f0]
	* molecuilder/Makefile.am (modified)
	* molecuilder/configure.ac (modified)
	* pcp/Makefile.am (modified)
	* pcp/configure.ac (modified)
	* util/Makefile.am (modified)
	* util/configure.ac (modified)

	Complete test kit (make check) for the three parts: pcp, molecuilder, ...


Sun, 27 Apr 2008 13:01:06 GMT Frederik Heber <heber@…> [16cd31]
	* molecuilder/src/molecules.cpp (modified)

	AddXYZFile(): Bugfix - if element could not be parsed (e.g. elements ...


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 ...


Sun, 27 Apr 2008 12:59:18 GMT Frederik Heber <heber@…> [a829d1]
	* molecuilder/src/builder.cpp (modified)

	new elementsdb-switch and command line options parsing parts moved ...


Sun, 27 Apr 2008 12:53:53 GMT Frederik Heber <heber@…> [b021e4]
	* molecuilder/src/periodentafel.cpp (modified)

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


Fri, 25 Apr 2008 13:54:51 GMT Frederik Heber <heber@…> [8129de]
	* molecuilder/src/builder.cpp (modified)

	Huge rewrite of initial command line parsing

	config file argument ...


Fri, 25 Apr 2008 13:52:38 GMT Frederik Heber <heber@…> [370060]
	* molecuilder/src/defs.hpp (modified)

	added VERSIONSTRING


Fri, 25 Apr 2008 13:52:05 GMT Frederik Heber <heber@…> [941b66]
	* molecuilder/src/periodentafel.cpp (modified)

	LoadPeriodentafel(): no more outputs of parsed elements


Fri, 25 Apr 2008 10:29:18 GMT Frederik Heber <heber@…> [201832]
	* molecuilder/configure.ac (modified)
	* pcp/configure.ac (modified)

	normal blas (e.g. prefered gotoblas) instead of gslcblas is used in ...


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
 ...


Thu, 24 Apr 2008 17:01:39 GMT Frederik Heber <heber@…> [e58fcb7]
	* molecuilder/src/molecules.cpp (modified)

	FragmentMolecule(): debug messages removed for ADDHYDROGEN


Thu, 24 Apr 2008 16:59:35 GMT Frederik Heber <heber@…> [bd7b85]
	* molecuilder/configure.ac (modified)
	* pcp/configure.ac (modified)
	* util/configure.ac (modified)

	AC_MSG_WARN if both optimization and debug present removed

	As ...


Thu, 24 Apr 2008 13:52:02 GMT Frederik Heber <heber@…> [da83f8]
	* Makefile.am (modified)
	* molecuilder/configure.ac (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* pcp/Makefile.am (modified)
	* pcp/configure.ac (modified)
	* pcp/src/Makefile.am (modified)
	* pcp/src/Makefile.in (modified)
	* pcp/src/helpers.h (modified)
	* util/Makefile.am (modified)
	* util/configure.ac (modified)

	added --enable-optimization, thrown -g -O specifics out of ...


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 ...