#
# ChangeLog for molecuilder/src/builder.cpp
#
# Generated by Trac 1.6
# Sep 20, 2025, 9:07:38 PM

Fri, 17 Oct 2008 13:20:42 GMT Frederik Heber <heber@…> [f89a9e]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/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@…> [136e89]
	* molecuilder/src/builder.cpp (modified)

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


Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber <heber@…> [5a78f5]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Thu, 11 Sep 2008 13:08:18 GMT Frederik Heber <heber@…> [55ebd0]
	* molecuilder/src/builder.cpp (modified)

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


Tue, 09 Sep 2008 08:37:07 GMT Frederik Heber <heber@…> [79cd79]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Sat, 06 Sep 2008 15:06:51 GMT Frederik Heber <heber@…> [f9cd68]
	* molecuilder/src/builder.cpp (modified)

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


Fri, 05 Sep 2008 17:09:39 GMT Frederik Heber <heber@…> [5887ed]
	* molecuilder/src/builder.cpp (modified)

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


Tue, 02 Sep 2008 12:06:14 GMT Frederik Heber <heber@…> [55e916]
	* molecuilder/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@…> [644ba1]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Wed, 06 Aug 2008 09:02:01 GMT Frederik Heber <heber@…> [8f8621]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/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@…> [0a08df]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)

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


Mon, 28 Jul 2008 13:47:52 GMT Frederik Heber <heber@…> [39651f]
	* molecuilder/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@…> [b3eb8e]
	* molecuilder/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@…> [375dcf]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/parser.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (added)
	* pcp/src/perturbed.c (modified)

	introduced shieldings to analyzer and joiner

	both now handle ...


Mon, 23 Jun 2008 11:25:09 GMT Frederik Heber <heber@…> [d7b1bf]
	* molecuilder/src/builder.cpp (modified)

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


Sun, 22 Jun 2008 13:39:41 GMT Frederik Heber <heber@…> [7a40c8]
	* molecuilder/src/builder.cpp (modified)

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


Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber <heber@…> [1f9f1b]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/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@…> [0779a9]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* util/src/CalculateDensity.sh (modified)
	* util/src/CalculateMass.sh (modified)

	some mor changes to fine-tune the cluster generation.

	Sadly, ...


Fri, 13 Jun 2008 09:18:57 GMT Frederik Heber <heber@…> [3f0c46]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)

	Final touches for Create Clusters in water

	repetition in ...


Thu, 12 Jun 2008 19:34:36 GMT Frederik Heber <heber@…> [7fcea6]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)

	Smaller fixes

	CreateClustersinWater is now PrepareClustersinWater ...


Thu, 12 Jun 2008 19:14:46 GMT Frederik Heber <heber@…> [e292c10]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/molecules.cpp (modified)
	* molecuilder/src/molecules.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	VolumeOfConvexEnvelope: Works!

	VolumeOfConvexEnvelope has been ...


Tue, 10 Jun 2008 11:21:13 GMT Frederik Heber <heber@…> [ffcf49]
	* molecuilder/src/builder.cpp (modified)

	fastparse enabled by "-n"


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 ...


Fri, 30 May 2008 10:42:49 GMT Frederik Heber <heber@…> [9e831e]
	* molecuilder/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@…> [8b486e]
	* molecuilder/src/builder.cpp (modified)

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


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 11:15:32 GMT Frederik Heber <heber@…> [3ce105]
	* molecuilder/src/builder.cpp (modified)

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


Fri, 16 May 2008 13:35:43 GMT Frederik Heber <heber@…> [0e348e]
	* molecuilder/src/builder.cpp (modified)

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


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 ...


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 07:45:23 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 07:16:32 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 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 ...


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 ...


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, 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 ...