# # ChangeLog for molecuilder # # Generated by Trac 1.6 # Dec 7, 2025, 3:24:42 PM Mon, 12 Oct 2009 12:10:43 GMT Frederik Heber [ff9879] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) First half of molecule_fragmentation.cpp refactoring. - new ... Mon, 12 Oct 2009 10:30:02 GMT Frederik Heber [7c2f6b] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) Complete refactoring of molecule_dynamics.cpp - new small ... Fri, 09 Oct 2009 14:35:14 GMT Frederik Heber [104cf4] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) First half of molecule_dynamics.cpp is refactored into smaller parts. ... Fri, 09 Oct 2009 12:30:54 GMT Frederik Heber [e71890] * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (moved) * molecuilder/src/unittests/ActOnAllUnitTest.hpp (moved) * molecuilder/src/unittests/ActOnAlltest.hpp (moved) * molecuilder/src/unittests/Makefile.am (added) * molecuilder/src/unittests/memoryallocatorunittest.cpp (moved) * molecuilder/src/unittests/memoryallocatorunittest.hpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved) * molecuilder/src/unittests/tesselationunittest.cpp (moved) * molecuilder/src/unittests/tesselationunittest.hpp (moved) * molecuilder/src/unittests/vectorunittest.cpp (moved) * molecuilder/src/unittests/vectorunittest.hpp (moved) Merge branch 'new-delete-conversion' into CodeRefactoring ... Fri, 09 Oct 2009 12:08:24 GMT Frederik Heber [682229] * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/unittests/Makefile.am (added) * molecuilder/src/unittests/memoryallocatorunittest.cpp (moved) * molecuilder/src/unittests/memoryallocatorunittest.hpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved) * molecuilder/src/unittests/tesselationunittest.cpp (moved) * molecuilder/src/unittests/tesselationunittest.hpp (moved) * molecuilder/src/unittests/vectorunittest.cpp (moved) * molecuilder/src/unittests/vectorunittest.hpp (moved) Merge branch 'new-delete-conversion' of ... Fri, 09 Oct 2009 11:57:41 GMT Frederik Heber [3efb4a] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) Implementing templated iterators done for molecule.cpp - new ... Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber [17b3a5c] * molecuilder/src/ActOnAllUnitTest.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/lists.hpp (added) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (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/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/tesselationunittest.hpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/src/verbose.hpp (modified) forward declarations used to untangle interdependet classes. - ... Wed, 07 Oct 2009 15:35:17 GMT metzler [afbb6c0] * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/unittests/Makefile.am (modified) Ticket 30: Put molecuilder unit tests in their own subfolder in src Wed, 07 Oct 2009 15:04:23 GMT Saskia Metzler [53f32e] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/unittests/Makefile.am (added) * molecuilder/src/unittests/memoryallocatorunittest.cpp (moved) * molecuilder/src/unittests/memoryallocatorunittest.hpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved) * molecuilder/src/unittests/tesselationunittest.cpp (moved) * molecuilder/src/unittests/tesselationunittest.hpp (moved) * molecuilder/src/unittests/vectorunittest.cpp (moved) * molecuilder/src/unittests/vectorunittest.hpp (moved) temp commit Wed, 07 Oct 2009 14:29:57 GMT Frederik Heber [70b7aa] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/molecule.cpp (modified) used forward declaration to untangle atom and bond declarations, ... Wed, 07 Oct 2009 13:18:59 GMT Frederik Heber [972706] * molecuilder/src/molecule.cpp (modified) molecule::CountElements() changed to use ... Wed, 07 Oct 2009 13:16:13 GMT Frederik Heber [0cd3b2] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new ... Wed, 07 Oct 2009 13:11:28 GMT Frederik Heber [567b7f] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) In molecule::OutputTrajectories() ActOnAllAtoms() with new function ... Tue, 06 Oct 2009 17:57:01 GMT Frederik Heber [8ffe32] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (added) More functions of molecule now use templated iterators. - the ... Tue, 06 Oct 2009 17:56:15 GMT Frederik Heber [a4644b] * molecuilder/src/builder.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/regression/Fragmentation/1/pre/test.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment0.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment0.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment1.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment1.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment2.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment2.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment3.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment3.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment4.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment4.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentAdjacency.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentForces-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentKeySets.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentOrderAtSite.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentTE-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/test.conf (added) * molecuilder/tests/regression/Fragmentation/2/pre/test.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment0.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment1.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment2.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment3.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment4.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/test.conf (added) * molecuilder/tests/regression/Graph/1/post/test.conf (added) * molecuilder/tests/regression/Graph/1/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/1/post/test.xyz (added) * molecuilder/tests/regression/Simple_configuration/2/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/2/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/2/pre/test.xyz (added) * molecuilder/tests/regression/Simple_configuration/3/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/3/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/4/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/4/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/4/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/5/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/5/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/5/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/6/pre/empty.conf (added) * molecuilder/tests/regression/Simple_configuration/7/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/1/post/test.conf (added) * molecuilder/tests/regression/Tesselation/1/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/2/post/test.conf (added) * molecuilder/tests/regression/Tesselation/2/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/3/post/tecplot.phy (added) * molecuilder/tests/regression/Tesselation/3/post/test.conf (added) * molecuilder/tests/regression/Tesselation/3/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/4/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/4/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/4/post/test.conf (added) * molecuilder/tests/regression/Tesselation/4/pre/test.conf (added) * molecuilder/tests/testsuite.at (modified) Extended the testsuite to encompass the vital areas of molecuilder. ... Tue, 06 Oct 2009 11:15:50 GMT metzler [729279] * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/memoryusageobserverunittest.cpp (modified) * molecuilder/src/memoryusageobserverunittest.hpp (modified) #22 Write a critical exit function Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber [f92d00] * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (added) * molecuilder/src/molecule_fragmentation.cpp (added) * molecuilder/src/molecule_geometry.cpp (added) * molecuilder/src/molecule_graph.cpp (added) * molecuilder/src/molecule_pointcloud.cpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/verbose.cpp (modified) class molecule implementation split up into six separate parts. - ... Mon, 05 Oct 2009 22:09:51 GMT Frederik Heber [3746440] * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) new function Vector::WrapPeriodically() and ... Mon, 05 Oct 2009 22:08:57 GMT Frederik Heber [dcbdf2] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (moved) * molecuilder/src/molecule.hpp (moved) New function atom::CorrectFactor() and atom::EqualsFather(). - are ... Mon, 05 Oct 2009 21:14:28 GMT Frederik Heber [d40b96] * molecuilder/src/ActOnAllUnitTest.cpp (modified) * molecuilder/src/ActOnAlltest.hpp (modified) even the class of the member function can be templated, see ... Mon, 05 Oct 2009 20:51:24 GMT Frederik Heber [4bc937] * molecuilder/src/ActOnAllUnitTest.cpp (modified) * molecuilder/src/ActOnAllUnitTest.hpp (modified) * molecuilder/src/ActOnAlltest.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/molecules.hpp (modified) Member functions of Vector class may be called while going over an ... Mon, 05 Oct 2009 18:45:06 GMT Frederik Heber [424d1ce] * molecuilder/configure.ac (modified) * molecuilder/m4/ax_boost_base.m4 (added) * molecuilder/m4/ax_boost_program_options.m4 (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) * 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/tesselation.cpp (modified) * molecuilder/src/tesselationunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) * molecuilder/tests/testsuite.at (modified) Merge branch 'ConvexHull' into ActOnAll Conflicts: ... Mon, 05 Oct 2009 18:43:43 GMT Frederik Heber [9c32a1] * molecuilder/configure.ac (modified) * molecuilder/m4/ax_boost_base.m4 (added) * molecuilder/m4/ax_boost_program_options.m4 (added) * molecuilder/src/Makefile.am (modified) Included BOOST library MPL into autoconf setup. Mon, 05 Oct 2009 17:21:58 GMT Frederik Heber [58808e] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationunittest.cpp (modified) * molecuilder/tests/testsuite.at (modified) Fixed testsuite, removed some minor bugs. - ... Mon, 05 Oct 2009 16:05:53 GMT Frederik Heber [8afe31] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) * 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/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) Merge branch 'ConcaveHull' into ConvexHull Conflicts: ... Mon, 05 Oct 2009 15:43:25 GMT Frederik Heber [89eff5] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) new/delete conversion. mode change only, nothing else. Mon, 05 Oct 2009 15:42:20 GMT Frederik Heber [5dda23] * molecuilder/src/analyzer.cpp (modified) New/delete conversion. 82: "main" missing in msg Mon, 05 Oct 2009 14:59:11 GMT Frederik Heber [bf497f] * molecuilder/src/builder.cpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/memoryusageobserverunittest.cpp (modified) * molecuilder/src/memoryusageobserverunittest.hpp (modified) Merge branch 'ConcaveHull' of ... Mon, 05 Oct 2009 14:50:43 GMT metzler [39d983] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) #19 Observe memory usage Mon, 05 Oct 2009 14:35:06 GMT Frederik Heber [7794d8] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) Merge branch 'ConcaveHull' of ... Mon, 05 Oct 2009 14:31:35 GMT Frederik Heber [ef36b84] * molecuilder/src/ActOnAllUnitTest.cpp (added) * molecuilder/src/ActOnAllUnitTest.hpp (added) * molecuilder/src/ActOnAlltest.hpp (added) * molecuilder/src/Makefile.am (modified) ActOnAll is a test (not in the molecuilder source tree, but as a ... Mon, 05 Oct 2009 14:12:18 GMT metzler [14db08] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) #19 Observe memory usage Fri, 02 Oct 2009 15:19:51 GMT Frederik Heber [daf956] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Fixes to the (Non)ConvexTesselation, working with ... Fri, 02 Oct 2009 15:18:43 GMT Frederik Heber [fca6e7] * molecuilder/src/vector.cpp (modified) FIX of Vector::GetIntersectionWithPlane() - Direction was not ... 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 ... Mon, 28 Sep 2009 20:00:33 GMT Frederik Heber [60cbe5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Various fixes and attempt to get convex hull working. - ... Mon, 28 Sep 2009 18:46:25 GMT Frederik Heber [bb56cf] * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) new function CalculateVolumeofGeneralTetraeder(). - is used when a ... Mon, 28 Sep 2009 18:43:02 GMT Frederik Heber [01e6c5] * molecuilder/src/atom.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/vectorunittest.cpp (modified) Small fixes. - FIX: atom::~atom(): Name is free'd - ... Mon, 28 Sep 2009 18:41:52 GMT Frederik Heber [606dfb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Implemenation of embedding merge, untested. LinearInterpolation now ... Mon, 28 Sep 2009 18:38:06 GMT Frederik Heber [6f1551] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) LinkedCell has another constructor initialised from LinkedNodes (list ... Mon, 28 Sep 2009 18:31:58 GMT Frederik Heber [f2dfc5] * molecuilder/src/Makefile.am (modified) * molecuilder/src/tesselationunittest.cpp (added) * molecuilder/src/tesselationunittest.hpp (added) Added Tesselation unit test - new file tesselationunittest with ... Mon, 21 Sep 2009 11:48:42 GMT Saskia Metzler [390a2b] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free ... Fri, 21 Aug 2009 12:19:08 GMT Frederik Heber [b73929] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) FIX: Tesselation::RemovePointFromTesselatedSurface() is working ... Fri, 21 Aug 2009 12:17:52 GMT Frederik Heber [8b7e0a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) New function RemoveAllBoundaryPoints() for sequentially removing all ... Fri, 21 Aug 2009 12:17:25 GMT Frederik Heber [5f4960] * molecuilder/src/molecules.cpp (modified) formula typo in molecule::PrincipalAxisSystem() fixed 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: ...