# # ChangeLog for molecuilder # # Generated by Trac 1.6 # Sep 25, 2025, 7:59:59 PM Fri, 02 Oct 2009 13:02:26 GMT Frederik Heber [2aea0b] * .gitignore (modified) * molecuilder/src/tesselationunittest.cpp (added) * molecuilder/src/tesselationunittest.hpp (added) new tesselation unit test - excluded some more files (mostly ecut ... Thu, 20 Aug 2009 15:40:49 GMT Saskia Metzler [bc3953] * molecuilder/src/atom.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) Ticket 17: Write new function molecule::CopyMoleculeFromSubRegion() Thu, 20 Aug 2009 11:35:19 GMT Saskia Metzler [6c6d84] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) Ticket 16: Unit tests for Vector::RotateVector(), additionally fixing ... Thu, 20 Aug 2009 07:48:07 GMT Frederik Heber [84b811] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Merge branch 'ConcaveHull' of ... Wed, 19 Aug 2009 14:31:29 GMT Frederik Heber [78dac6] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) Smaller fixes, but convex tesselation not working yet - ... Wed, 19 Aug 2009 12:30:21 GMT Frederik Heber [daf5d6] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/leastsquaremin.cpp (added) * molecuilder/src/leastsquaremin.hpp (added) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (added) * molecuilder/src/vectorunittest.hpp (added) Merge branch 'VectorUnitTest' into ConcaveHull Wed, 19 Aug 2009 12:23:05 GMT Frederik Heber [6c09a4] * molecuilder/src/Makefile.am (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) VectorUnitTest extended to Projections and Line intersection, some ... Wed, 19 Aug 2009 12:22:08 GMT Frederik Heber [66ce7a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Replaced Vector::Projection() by Vector::ScalarProduct() - ... Tue, 18 Aug 2009 13:59:11 GMT Saskia Metzler [d6b011] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Ticket 15: new function RemoveDegeneratedTriangles() Added functions ... Tue, 18 Aug 2009 08:48:06 GMT Frederik Heber [da84d6] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/leastsquaremin.cpp (added) * molecuilder/src/leastsquaremin.hpp (added) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (added) * molecuilder/src/vectorunittest.hpp (added) Incorporation of Unit test on class Vector. - new file ... Tue, 18 Aug 2009 08:42:39 GMT Frederik Heber [27459a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Further bugfixes to three-step-procedure in convex envelope, not yet ... Mon, 17 Aug 2009 13:20:16 GMT Saskia Metzler [48cd93] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Ticket 14: Rename .._.. functions in boundary.cpp Mon, 17 Aug 2009 10:48:03 GMT Frederik Heber [3de1d2] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) Rewrite of ConvexizeNonconvexEnvelope() with three steps: Remove ... Mon, 17 Aug 2009 10:30:53 GMT Frederik Heber [eb58a7] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) documentation, some renames (..Triangle.. -> ..Tesselation..) and a ... Mon, 17 Aug 2009 10:29:03 GMT Frederik Heber [844cf5] * molecuilder/src/builder.cpp (modified) Sorted the menu list in ParseCommandLineParamaters() and print volume ... Thu, 13 Aug 2009 20:31:12 GMT Frederik Heber [d6d226d] * molecuilder/doc/userguide.xml (added) First version of the user guide in xml (docbook format) - ... Thu, 13 Aug 2009 20:30:07 GMT Frederik Heber [ada6d2] * molecuilder/configure.ac (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/doc/molecuilder.xml.in (added) Manpage is created via xmlto with a docbook stylesheet. - Hooks in ... Mon, 10 Aug 2009 16:11:47 GMT Frederik Heber [70c4567] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) New function ConvexizeNonconvexEnvelope() to calculate the volume of ... Sat, 08 Aug 2009 19:25:28 GMT Frederik Heber [0cf171] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) BUGFIXes to Find_convex_... and Find_non_convex_... algorithms - ... Sat, 08 Aug 2009 19:22:28 GMT Frederik Heber [51abbe] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(), NonConvex tesselation is now clocked. Sat, 08 Aug 2009 19:19:23 GMT Frederik Heber [0ee99dc] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) BUGFIXES to some vector functions. - Vector::MakeNormalVector() ... ... Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber [e0521b] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) new stream operator with just one parameter and virtual destructor Fri, 07 Aug 2009 12:50:27 GMT Frederik Heber [67fced] * molecuilder/src/TAGS (deleted) * util/depcomp (deleted) * util/install-sh (deleted) excluded unimportant stuff, depcomp and install-sh from util Fri, 07 Aug 2009 12:48:06 GMT Frederik Heber [609e48] * molecuilder/src/boundary.cpp (modified) output of terminating special property comment in .r3d file had no ... Fri, 07 Aug 2009 12:46:27 GMT Frederik Heber [ef5521] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) BUGFIX: PointCloud implementation in molecule stopped one before ... Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber [0fc0b5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Test case of filling a simulation domain with water included. Fri, 07 Aug 2009 09:12:19 GMT Frederik Heber [8f9a8e] * molecuilder/src/tesselation.cpp (modified) FIX: We have to check whether we create a degenerate triangle also on ... Tue, 04 Aug 2009 13:55:11 GMT Frederik Heber [d93bb24] * molecuilder/src/builder.cpp (modified) FillWithMolecule() for testing built into ParseCommandLine() Tue, 04 Aug 2009 13:53:55 GMT Frederik Heber [7aa922] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) find_(non)_convex_border TesselStruct is not free'd anymore, ... Tue, 04 Aug 2009 13:48:57 GMT Frederik Heber [eeefb3] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Fixes for concave hull creation - fixed ... Tue, 04 Aug 2009 13:47:05 GMT Frederik Heber [04dcc0] * molecuilder/src/molecules.cpp (modified) Smaller FIXES to molecule class - new pointer TesselStruct was not ... Mon, 03 Aug 2009 20:21:05 GMT Frederik Heber [f4a346] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (added) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (added) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.hpp (added) Merge branch 'TesselationRefactoring' into ConcaveHull Conflicts: ... Mon, 03 Aug 2009 18:58:46 GMT Frederik Heber [0e2190] * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * util/depcomp (modified) * util/install-sh (modified) Merge branch 'ConcaveHull' of ... Mon, 03 Aug 2009 16:48:46 GMT Saskia Metzler [e8de2e] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) Adding functions IsInnerAtom() and IsInnerPoint() which can check ... Mon, 03 Aug 2009 16:48:00 GMT Saskia Metzler [dc162d] * molecuilder/src/molecules.hpp (modified) Compare and output operator for atom takes const argumen Mon, 03 Aug 2009 16:45:38 GMT Saskia Metzler [a87d5e6] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) new function LinkedCell::GetNeighbourBounds() - ... Mon, 03 Aug 2009 16:44:16 GMT Saskia Metzler [3219a0] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) new function isNull(), output operator takes const argument Mon, 03 Aug 2009 16:43:42 GMT Saskia Metzler [b65771] * molecuilder/src/atom.cpp (modified) output operator now takes const argument Mon, 03 Aug 2009 15:26:32 GMT Frederik Heber [eb167d] * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) Some minor fixes with regards to what needs to be included where and ... Mon, 03 Aug 2009 15:09:12 GMT Frederik Heber [4dca8e] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (added) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/verbose.hpp (added) definitions for class element and verbose moved to their own header ... Mon, 03 Aug 2009 14:58:43 GMT Frederik Heber [e78824] * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) class config definitions moved to their own header file. NOTE: ... Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber [834ff3] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.hpp (modified) Huge refactoring of Tesselation routines, but not finished yet. - ... Mon, 03 Aug 2009 08:10:09 GMT Frederik Heber [4e4940] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) We are one step further in fixing the convex hull: There are two ... Tue, 28 Jul 2009 13:02:51 GMT Frederik Heber [3dc682] * molecuilder/src/boundary.cpp (modified) Convex tesselation is now working also for heptan. But the convex ... Tue, 28 Jul 2009 13:01:15 GMT Frederik Heber [da5c7c] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) New function Vector::NormSquared() and Angle checks whether Norm's ... Tue, 28 Jul 2009 10:33:53 GMT Frederik Heber [78b45a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) ConvexTesselation working again. - File was not written, as NULL ... Mon, 27 Jul 2009 14:53:57 GMT Frederik Heber [dd69cc] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/molecules.cpp (modified) FIX: DetermineCenterOfAll() did point in wrong direction, convex ... Mon, 27 Jul 2009 14:22:20 GMT Frederik Heber [63443f] * molecuilder/src/config.cpp (modified) BUGFIX: config::Load() added atoms in wrong order, hence resulting in ... Mon, 27 Jul 2009 14:08:27 GMT Frederik Heber [a0fb02] * molecuilder/src/builder.cpp (modified) BUGFIX: ManipulateAtoms() had mol = NULL - in ManipulateAtoms() the ... Mon, 27 Jul 2009 14:07:25 GMT Frederik Heber [0ac84df] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/vector.cpp (modified) BUGFIX: molecule::ReturnFullMatrixforSymmetric had it still all ... Mon, 27 Jul 2009 08:16:03 GMT Frederik Heber [53d153] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Split VolumeOfConvexEnvelope() into find_convex_border() and ... Fri, 24 Jul 2009 10:38:32 GMT Frederik Heber [c3a303] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) * 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/parser.hpp (modified) * pcp/Makefile.am (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) * util/src/average.cpp (modified) * util/src/dynamicANOVA.sh.in (modified) Merge branch 'master' into ConcaveHull Conflicts: ... Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber [a048fa] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.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 (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 14:04:47 GMT Frederik Heber [47548d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) Merge branch 'AtomRemoval' Conflicts: ... Thu, 23 Jul 2009 13:53:01 GMT Frederik Heber [1f6efb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 13:45:24 GMT Frederik Heber [f39735] * .gitignore (modified) * molecuilder/src/#border.cpp# (deleted) * molecuilder/src/#makefile# (deleted) * molecuilder/src/#molecules.hpp# (deleted) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (added) * molecuilder/src/linkedcell.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) Merge branch 'MultipleMolecules' Conflicts: ... Thu, 23 Jul 2009 12:32:48 GMT Frederik Heber [560995] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/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 [1b2aa1] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.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/parser.hpp (modified) * molecuilder/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 [307290] * molecuilder/src/molecules.cpp (modified) Merge branch 'ConstrainedMolecularDynamics' Conflicts: ... Thu, 23 Jul 2009 11:31:00 GMT Frederik Heber [59a745] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) Merge branch 'test' Conflicts: ... Thu, 23 Jul 2009 11:23:59 GMT Frederik Heber [3b470f] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.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) * pcp/Makefile.am (modified) * util/src/average.cpp (modified) Merge branch 'Thermostat' Conflicts: .gitignore ... Thu, 23 Jul 2009 09:14:18 GMT Frederik Heber [09f4dc] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * util/src/AdaptiveANOVA.sh.in (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) * util/src/CreateFromXYZ.sh.in (modified) * util/src/SortByRings.sh.in (modified) Merge branch 'HessianMatrix' Thu, 23 Jul 2009 09:11:01 GMT Frederik Heber [2218dca] * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) Merge branch 'GraphRefactoring' Fri, 10 Jul 2009 21:19:23 GMT Frederik Heber [c95b69] * molecuilder/src/molecules.cpp (modified) BUGFIX: Due to stupid mistake, first atom was overlooked in periodic ... Fri, 10 Jul 2009 21:01:40 GMT Frederik Heber [88b936] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new class ConfigFileBuffer and new overloaded function ... Fri, 10 Jul 2009 20:20:09 GMT Frederik Heber [598f76] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::Output...() routines wrote elements beginning with ... Fri, 10 Jul 2009 14:29:56 GMT Frederik Heber [22f587] * molecuilder/src/molecules.cpp (modified) XYZ and config files now store the atoms in the same order as they ... Fri, 10 Jul 2009 12:48:05 GMT Frederik Heber [6fb785] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) molecule::CenterInBox puts atoms now periodically into the given box, ... Thu, 09 Jul 2009 13:33:39 GMT Frederik Heber [a8c8ba] * molecuilder/src/boundary.cpp (modified) FIX: Now tries each of the axis direction to find a starting triangle ... Thu, 09 Jul 2009 12:02:46 GMT Frederik Heber [8bbe43] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) Lots of changes to the number of output messages. As the finding of ... Thu, 09 Jul 2009 11:40:14 GMT Frederik Heber [438506] * molecuilder/src/boundary.cpp (modified) Fixed all of the remaining memory leaks due to ... Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber [ab7b5e7] * molecuilder/src/builder.cpp (modified) Memory leak fix: ParseCommandLineOptions() and main() free'd mol ... Thu, 09 Jul 2009 11:01:08 GMT Frederik Heber [bd86e8] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) Changed the unsatisfactory PathToDatabases construct, removing ... Thu, 09 Jul 2009 10:38:53 GMT Frederik Heber [c12297] * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) fixed compiler warning: deprecated conversion from string const to ... Thu, 09 Jul 2009 10:38:34 GMT Frederik Heber [669a7e] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) fixed compiler warning by changing int to size_t because C++ STL ... Thu, 09 Jul 2009 10:31:05 GMT Frederik Heber [61e92a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Removed unneeded variables Thu, 09 Jul 2009 10:22:05 GMT Frederik Heber [12cf763] * molecuilder/src/boundary.cpp (modified) Removed unnecessary code - Choose_preferable_third_point() - ... Thu, 09 Jul 2009 09:45:00 GMT Frederik Heber [49c774] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) BUGFIX: Memory leak due to special triangles and similar lines in ... Tue, 07 Jul 2009 14:48:21 GMT Frederik Heber [30212a8] * molecuilder/src/boundary.cpp (modified) FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when ... Tue, 07 Jul 2009 09:12:54 GMT Frederik Heber [a811a0] * molecuilder/src/boundary.cpp (modified) BUGFIX: Initial edge for starting triangle may be up to TWICE the ... Tue, 07 Jul 2009 08:17:53 GMT Frederik Heber [d98327] * molecuilder/src/builder.cpp (modified) BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere ... Tue, 07 Jul 2009 08:12:28 GMT Frederik Heber [54de04] * molecuilder/src/vector.cpp (modified) BUGFIX: Numerical imprecision forced check of bounds for acos() ... Tue, 07 Jul 2009 08:11:47 GMT Frederik Heber [eeae5b] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) Cosmetical changes in Find_third_point_for_tesselation() and ... Tue, 07 Jul 2009 06:49:32 GMT Frederik Heber [d2639f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.hpp (modified) All of Saskia Metzler's changes so far to remove bugs from ... Fri, 03 Jul 2009 14:25:17 GMT Frederik Heber [ea9696] * molecuilder/src/builder.cpp (modified) Removing of atoms via command line possible -R switchs allows for ... Wed, 03 Jun 2009 16:16:37 GMT Frederik Heber [378e87] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) BUGFIX: RemoveAtom() would remove the iterator, ... Fri, 10 Apr 2009 23:28:39 GMT Frederik Heber [a41b50] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/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 [bb12e7] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/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 [37a050] * molecuilder/src/builder.cpp (modified) fixes due to changes in molecule structure (Center...()) and merge ... Wed, 08 Apr 2009 11:27:50 GMT Frederik Heber [d618b5] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Lots of bugfixes, some name changes and new functions BUGFIX: - ... Wed, 08 Apr 2009 11:25:03 GMT Frederik Heber [8b05c6] * molecuilder/src/moleculelist.cpp (modified) MoleculeListClass::Enumerate() lists center and size of molecule, fix ... Thu, 02 Apr 2009 16:42:53 GMT Frederik Heber [899029f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) Framework for embedding one molecule into another, now the embedding ... Thu, 02 Apr 2009 16:42:36 GMT Frederik Heber [3021d93] * molecuilder/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 [c830e8e] * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Basic implementation of Multiple molecules. builder.cpp: - ... Tue, 10 Feb 2009 12:04:37 GMT Frederik Heber [451d7a] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/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 [f23d7d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/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 [97c751] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) Chi integration had some copy&paste error Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber [e08f45] * .gitignore (modified) * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * molecuilder/ChangeLog (modified) * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/doc/Doxyfile (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (modified) * molecuilder/src/.#border.cpp (deleted) * molecuilder/src/.#molecules.hpp (deleted) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/elements.db (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/valence.db (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/atlocal.in (modified) * molecuilder/tests/molecuilder.in (modified) * molecuilder/tests/testsuite.at (modified) * pcp/ChangeLog (modified) * pcp/Makefile.am (modified) * pcp/configure.ac (modified) * pcp/doc/Doxyfile (modified) * pcp/doc/Makefile.am (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (modified) * pcp/m4/acx_mpi.m4 (modified) * pcp/pseudopot/pseudo.01 (modified) * pcp/pseudopot/pseudo.02 (modified) * pcp/pseudopot/pseudo.03 (modified) * pcp/pseudopot/pseudo.04 (modified) * pcp/pseudopot/pseudo.05 (modified) * pcp/pseudopot/pseudo.06 (modified) * pcp/pseudopot/pseudo.07 (modified) * pcp/pseudopot/pseudo.08 (modified) * pcp/pseudopot/pseudo.09 (modified) * pcp/pseudopot/pseudo.10 (modified) * pcp/pseudopot/pseudo.11 (modified) * pcp/pseudopot/pseudo.12 (modified) * pcp/pseudopot/pseudo.13 (modified) * pcp/pseudopot/pseudo.14 (modified) * pcp/pseudopot/pseudo.15 (modified) * pcp/pseudopot/pseudo.16 (modified) * pcp/pseudopot/pseudo.17 (modified) * pcp/pseudopot/pseudo.18 (modified) * pcp/pseudopot/pseudo.19 (modified) * pcp/pseudopot/pseudo.20 (modified) * pcp/pseudopot/pseudo.21 (modified) * pcp/pseudopot/pseudo.22 (modified) * pcp/pseudopot/pseudo.23 (modified) * pcp/pseudopot/pseudo.24 (modified) * pcp/pseudopot/pseudo.25 (modified) * pcp/pseudopot/pseudo.26 (modified) * pcp/pseudopot/pseudo.27 (modified) * pcp/pseudopot/pseudo.28 (modified) * pcp/pseudopot/pseudo.29 (modified) * pcp/pseudopot/pseudo.30 (modified) * pcp/pseudopot/pseudo.31 (modified) * pcp/pseudopot/pseudo.32 (modified) * pcp/pseudopot/pseudo.33 (modified) * pcp/pseudopot/pseudo.34 (modified) * pcp/pseudopot/pseudo.35 (modified) * pcp/pseudopot/pseudo.36 (modified) * pcp/pseudopot/pseudo.37 (modified) * pcp/pseudopot/pseudo.38 (modified) * pcp/pseudopot/pseudo.39 (modified) * pcp/pseudopot/pseudo.40 (modified) * pcp/pseudopot/pseudo.41 (modified) * pcp/pseudopot/pseudo.42 (modified) * pcp/pseudopot/pseudo.43 (modified) * pcp/pseudopot/pseudo.44 (modified) * pcp/pseudopot/pseudo.45 (modified) * pcp/pseudopot/pseudo.46 (modified) * pcp/pseudopot/pseudo.47 (modified) * pcp/pseudopot/pseudo.48 (modified) * pcp/pseudopot/pseudo.49 (modified) * pcp/pseudopot/pseudo.50 (modified) * pcp/pseudopot/pseudo.51 (modified) * pcp/pseudopot/pseudo.52 (modified) * pcp/pseudopot/pseudo.53 (modified) * pcp/pseudopot/pseudo.54 (modified) * pcp/pseudopot/pseudo.55 (modified) * pcp/pseudopot/pseudo.56 (modified) * pcp/pseudopot/pseudo.72 (modified) * pcp/pseudopot/pseudo.73 (modified) * pcp/pseudopot/pseudo.74 (modified) * pcp/pseudopot/pseudo.75 (modified) * pcp/pseudopot/pseudo.76 (modified) * pcp/pseudopot/pseudo.77 (modified) * pcp/pseudopot/pseudo.78 (modified) * pcp/pseudopot/pseudo.79 (modified) * pcp/pseudopot/pseudo.80 (modified) * pcp/src/Makefile.am (modified) * pcp/src/data.h (modified) * pcp/src/defs.h (modified) * pcp/src/density.c (modified) * pcp/src/density.h (modified) * pcp/src/energy.c (modified) * pcp/src/energy.h (modified) * pcp/src/errors.c (modified) * pcp/src/errors.h (modified) * pcp/src/excor.c (modified) * pcp/src/excor.h (modified) * pcp/src/grad.c (modified) * pcp/src/grad.h (modified) * pcp/src/gramsch.c (modified) * pcp/src/gramsch.h (modified) * pcp/src/helpers.c (modified) * pcp/src/helpers.h (modified) * pcp/src/init.c (modified) * pcp/src/init.h (modified) * pcp/src/ions.c (modified) * pcp/src/ions.h (modified) * pcp/src/mergesort2.c (modified) * pcp/src/mergesort2.h (modified) * pcp/src/myfft.c (modified) * pcp/src/myfft.h (modified) * pcp/src/mymath.c (modified) * pcp/src/mymath.h (modified) * pcp/src/opt.c (modified) * pcp/src/opt.h (modified) * pcp/src/output.c (modified) * pcp/src/output.h (modified) * pcp/src/parsetest.c (modified) * pcp/src/pcp.c (modified) * pcp/src/pcp.h (modified) * pcp/src/pdbformat.c (modified) * pcp/src/pdbformat.h (modified) * pcp/src/perturbed.c (modified) * pcp/src/perturbed.h (modified) * pcp/src/pseudo.c (modified) * pcp/src/pseudo.h (modified) * pcp/src/riemann.c (modified) * pcp/src/riemann.h (modified) * pcp/src/run.c (modified) * pcp/src/run.h (modified) * pcp/src/test.c (modified) * pcp/src/wannier.c (modified) * pcp/src/wannier.h (modified) * pcp/tests/Makefile.am (modified) * pcp/tests/atlocal.in (modified) * pcp/tests/pcp.in (modified) * pcp/tests/testsuite.at (modified) * util/ChangeLog (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/doc/Doxyfile (modified) * util/doc/Makefile.am (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (modified) * util/specvisual.cfg (modified) * util/specvisual.net (modified) * util/specvisualOnly.net (modified) * util/src/CreateGaAs.c (modified) * util/src/CreateH2.c (modified) * util/src/GetPdb.c (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) * util/src/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/mergesort.c (modified) * util/src/mergesort.h (modified) * util/src/stochastik.cpp (modified) * util/suffix (modified) * util/tests/Makefile.am (modified) * util/tests/NanoCreator.in (modified) * util/tests/atlocal.in (modified) * util/tests/testsuite.at (modified) * util/visual.cfg (modified) * util/visual.net (modified) * util/visualOnly.net (modified) Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull ... Mon, 09 Feb 2009 14:18:13 GMT Frederik Heber [dafe43] * .gitignore (modified) * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * molecuilder/ChangeLog (modified) * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/doc/Doxyfile (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (modified) * molecuilder/src/#border.cpp# (added) * molecuilder/src/#makefile# (added) * molecuilder/src/#molecules.hpp# (added) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/ReMapDBondFileFromXYZ.py (added) * molecuilder/src/TAGS (added) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/elements.db (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/valence.db (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/atlocal.in (modified) * molecuilder/tests/molecuilder.in (modified) * molecuilder/tests/testsuite.at (modified) * pcp/ChangeLog (modified) * pcp/Makefile.am (modified) * pcp/configure.ac (modified) * pcp/doc/Doxyfile (modified) * pcp/doc/Makefile.am (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (modified) * pcp/m4/acx_mpi.m4 (modified) * pcp/pseudopot/pseudo.01 (modified) * pcp/pseudopot/pseudo.02 (modified) * pcp/pseudopot/pseudo.03 (modified) * pcp/pseudopot/pseudo.04 (modified) * pcp/pseudopot/pseudo.05 (modified) * pcp/pseudopot/pseudo.06 (modified) * pcp/pseudopot/pseudo.07 (modified) * pcp/pseudopot/pseudo.08 (modified) * pcp/pseudopot/pseudo.09 (modified) * pcp/pseudopot/pseudo.10 (modified) * pcp/pseudopot/pseudo.11 (modified) * pcp/pseudopot/pseudo.12 (modified) * pcp/pseudopot/pseudo.13 (modified) * pcp/pseudopot/pseudo.14 (modified) * pcp/pseudopot/pseudo.15 (modified) * pcp/pseudopot/pseudo.16 (modified) * pcp/pseudopot/pseudo.17 (modified) * pcp/pseudopot/pseudo.18 (modified) * pcp/pseudopot/pseudo.19 (modified) * pcp/pseudopot/pseudo.20 (modified) * pcp/pseudopot/pseudo.21 (modified) * pcp/pseudopot/pseudo.22 (modified) * pcp/pseudopot/pseudo.23 (modified) * pcp/pseudopot/pseudo.24 (modified) * pcp/pseudopot/pseudo.25 (modified) * pcp/pseudopot/pseudo.26 (modified) * pcp/pseudopot/pseudo.27 (modified) * pcp/pseudopot/pseudo.28 (modified) * pcp/pseudopot/pseudo.29 (modified) * pcp/pseudopot/pseudo.30 (modified) * pcp/pseudopot/pseudo.31 (modified) * pcp/pseudopot/pseudo.32 (modified) * pcp/pseudopot/pseudo.33 (modified) * pcp/pseudopot/pseudo.34 (modified) * pcp/pseudopot/pseudo.35 (modified) * pcp/pseudopot/pseudo.36 (modified) * pcp/pseudopot/pseudo.37 (modified) * pcp/pseudopot/pseudo.38 (modified) * pcp/pseudopot/pseudo.39 (modified) * pcp/pseudopot/pseudo.40 (modified) * pcp/pseudopot/pseudo.41 (modified) * pcp/pseudopot/pseudo.42 (modified) * pcp/pseudopot/pseudo.43 (modified) * pcp/pseudopot/pseudo.44 (modified) * pcp/pseudopot/pseudo.45 (modified) * pcp/pseudopot/pseudo.46 (modified) * pcp/pseudopot/pseudo.47 (modified) * pcp/pseudopot/pseudo.48 (modified) * pcp/pseudopot/pseudo.49 (modified) * pcp/pseudopot/pseudo.50 (modified) * pcp/pseudopot/pseudo.51 (modified) * pcp/pseudopot/pseudo.52 (modified) * pcp/pseudopot/pseudo.53 (modified) * pcp/pseudopot/pseudo.54 (modified) * pcp/pseudopot/pseudo.55 (modified) * pcp/pseudopot/pseudo.56 (modified) * pcp/pseudopot/pseudo.72 (modified) * pcp/pseudopot/pseudo.73 (modified) * pcp/pseudopot/pseudo.74 (modified) * pcp/pseudopot/pseudo.75 (modified) * pcp/pseudopot/pseudo.76 (modified) * pcp/pseudopot/pseudo.77 (modified) * pcp/pseudopot/pseudo.78 (modified) * pcp/pseudopot/pseudo.79 (modified) * pcp/pseudopot/pseudo.80 (modified) * pcp/src/Makefile.am (modified) * pcp/src/data.h (modified) * pcp/src/defs.h (modified) * pcp/src/density.c (modified) * pcp/src/density.h (modified) * pcp/src/energy.c (modified) * pcp/src/energy.h (modified) * pcp/src/errors.c (modified) * pcp/src/errors.h (modified) * pcp/src/excor.c (modified) * pcp/src/excor.h (modified) * pcp/src/grad.c (modified) * pcp/src/grad.h (modified) * pcp/src/gramsch.c (modified) * pcp/src/gramsch.h (modified) * pcp/src/helpers.c (modified) * pcp/src/helpers.h (modified) * pcp/src/init.c (modified) * pcp/src/init.h (modified) * pcp/src/ions.c (modified) * pcp/src/ions.h (modified) * pcp/src/mergesort2.c (modified) * pcp/src/mergesort2.h (modified) * pcp/src/myfft.c (modified) * pcp/src/myfft.h (modified) * pcp/src/mymath.c (modified) * pcp/src/mymath.h (modified) * pcp/src/opt.c (modified) * pcp/src/opt.h (modified) * pcp/src/output.c (modified) * pcp/src/output.h (modified) * pcp/src/parsetest.c (modified) * pcp/src/pcp.c (modified) * pcp/src/pcp.h (modified) * pcp/src/pdbformat.c (modified) * pcp/src/pdbformat.h (modified) * pcp/src/perturbed.c (modified) * pcp/src/perturbed.h (modified) * pcp/src/pseudo.c (modified) * pcp/src/pseudo.h (modified) * pcp/src/riemann.c (modified) * pcp/src/riemann.h (modified) * pcp/src/run.c (modified) * pcp/src/run.h (modified) * pcp/src/test.c (modified) * pcp/src/wannier.c (modified) * pcp/src/wannier.h (modified) * pcp/tests/Makefile.am (modified) * pcp/tests/atlocal.in (modified) * pcp/tests/pcp.in (modified) * pcp/tests/testsuite.at (modified) * util/ChangeLog (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/doc/Doxyfile (modified) * util/doc/Makefile.am (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (modified) * util/specvisual.cfg (modified) * util/specvisual.net (modified) * util/specvisualOnly.net (modified) * util/src/CreateGaAs.c (modified) * util/src/CreateH2.c (modified) * util/src/GetPdb.c (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) * util/src/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/mergesort.c (modified) * util/src/mergesort.h (modified) * util/src/stochastik.cpp (modified) * util/suffix (modified) * util/tests/Makefile.am (modified) * util/tests/NanoCreator.in (modified) * util/tests/atlocal.in (modified) * util/tests/testsuite.at (modified) * util/visual.cfg (modified) * util/visual.net (modified) * util/visualOnly.net (modified) Merge ../espack3 Fri, 06 Feb 2009 09:48:09 GMT Frederik Heber [d3d15c] * molecuilder/src/boundary.cpp (modified) Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list