# # ChangeLog for molecuilder/src/atom.cpp # # Generated by Trac 1.6 # Sep 22, 2025, 12:11:49 PM Wed, 07 Apr 2010 15:45:38 GMT Tillmann Crueger [71910a] * molecuilder/src/Exceptions/CustomException.cpp (added) * molecuilder/src/Exceptions/CustomException.hpp (added) * molecuilder/src/Exceptions/LinearDependenceException.cpp (added) * molecuilder/src/Exceptions/LinearDependenceException.hpp (added) * molecuilder/src/Helpers/fast_functions.hpp (added) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (added) * molecuilder/src/Plane.hpp (added) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/gslmatrix.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/linearsystemofequations.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (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/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.hpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vector_ops.cpp (added) * molecuilder/src/vector_ops.hpp (added) Made data internal data-structure of vector class private - ... Wed, 10 Mar 2010 17:51:48 GMT Tillmann Crueger [4c60ef] * molecuilder/src/Actions/AtomsCalculation_impl.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.cpp (modified) * molecuilder/src/Descriptors/MoleculeDescriptor.cpp (modified) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Patterns/Singleton.hpp (added) * molecuilder/src/Patterns/Singleton_impl.hpp (added) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/WorldIterators.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_atominfo.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.cpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added generic singleton Pattern that can be inherited to any class ... Thu, 04 Mar 2010 10:33:44 GMT Tillmann Crueger [f058ef] * molecuilder/src/Descriptors/MoleculeIdDescriptor.cpp (added) * molecuilder/src/Descriptors/MoleculeIdDescriptor.hpp (added) * molecuilder/src/Descriptors/MoleculeIdDescriptor_impl.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (moved) * molecuilder/src/unittests/AtomDescriptorTest.hpp (moved) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.cpp (added) * molecuilder/src/unittests/MoleculeDescriptorTest.hpp (added) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added methods to query Molecules by ID Wed, 03 Mar 2010 17:47:40 GMT Tillmann Crueger [3746aeb] * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) Added mechanisms that allow reuse of IDs and changing Ids of Atoms Wed, 24 Feb 2010 16:21:12 GMT Tillmann Crueger [7bfc19] * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/atom_particleinfo.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/lists.cpp (added) * molecuilder/src/lists.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/DescriptorUnittest.cpp (modified) * molecuilder/src/unittests/DescriptorUnittest.hpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.hpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Made the world solely responsible for creating and destroying atoms. Fri, 05 Feb 2010 15:19:27 GMT Tillmann Crueger [d2d8f5] * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/atom_particleinfo.hpp (modified) Made all atoms register themselves with the world upon creation Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber [543ce4] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_graphnode.hpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (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/element.cpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/errorlogger.cpp (moved) * molecuilder/src/errorlogger.hpp (moved) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/log.hpp (modified) * molecuilder/src/logger.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (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/periodentafel.cpp (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/test/ActOnAlltest.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/stackclassunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) Huge change from ofstream * (const) out --> Log(). - first shift ... Tue, 27 Oct 2009 11:45:23 GMT Frederik Heber [8b6ee4] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) Begun with ticket #4 (shorten constructors) on class atom and class ... Tue, 27 Oct 2009 08:54:44 GMT Frederik Heber [94d0ad] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/atom_particleinfo.hpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/atom_trajectoryparticle.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Begun with ticket #38 (make const what is const). - basically all ... Tue, 20 Oct 2009 08:55:17 GMT Frederik Heber [2e2a70] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_atominfo.cpp (added) * molecuilder/src/atom_atominfo.hpp (added) * molecuilder/src/atom_bondedparticle.cpp (added) * molecuilder/src/atom_bondedparticle.hpp (added) * molecuilder/src/atom_bondedparticleinfo.cpp (added) * molecuilder/src/atom_bondedparticleinfo.hpp (added) * molecuilder/src/atom_graphnode.cpp (added) * molecuilder/src/atom_graphnode.hpp (added) * molecuilder/src/atom_graphnodeinfo.cpp (added) * molecuilder/src/atom_graphnodeinfo.hpp (added) * molecuilder/src/atom_particleinfo.cpp (added) * molecuilder/src/atom_particleinfo.hpp (added) * molecuilder/src/atom_trajectoryparticle.cpp (added) * molecuilder/src/atom_trajectoryparticle.hpp (added) * molecuilder/src/atom_trajectoryparticleinfo.cpp (added) * molecuilder/src/atom_trajectoryparticleinfo.hpp (added) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Refactored atom.cpp into multiple files. After the class atom was ... Mon, 19 Oct 2009 13:09:29 GMT Frederik Heber [6b937bd] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Huge Refactoring: class atom split up into several inherited classes. ... Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber [f444ce] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr. ... Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber [872b51] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/lists.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (added) * molecuilder/src/unittests/listofbondsunittest.hpp (added) Huge refactoring: molecule::ListOfBondsPerAtom and ... 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 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 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 13:16:13 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 ... 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 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, 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, 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 ... 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() 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 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 16:43:42 GMT Saskia Metzler [b65771] * molecuilder/src/atom.cpp (modified) output operator now takes const argument 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 ... 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 11:23:59 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, 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: - ... 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, 29 Dec 2008 21:46:58 GMT Frederik Heber [848729] * .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/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) * 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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) Just a temporary commit Thu, 09 Oct 2008 16:19:39 GMT Frederik Heber [a7b3b8] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/molecules.hpp (modified) Output of atom and bond to stream now is set to const bond/atom Mon, 18 Aug 2008 08:57:58 GMT Frederik Heber [644ba1] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Adaptivity fixes, MD by VerletForceIntegration introduced, MD ... Mon, 28 Jul 2008 14:41:22 GMT Frederik Heber [126934] * molecuilder/src/atom.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms ... Wed, 07 May 2008 13:38:13 GMT Frederik Heber [d50d2a] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/stackclass.hpp (added) AtomStackClass -> template StackClass change in new ... Fri, 02 May 2008 13:25:48 GMT Frederik Heber [c75363] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/vector.cpp (modified) HUGE REWRITE to allow for adaptive increase of the bond order, first ... Wed, 23 Apr 2008 17:33:51 GMT Frederik Heber [090299] * molecuilder/src/atom.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) molecuilder reads and stored ion velocities Class atom has new ... Fri, 18 Apr 2008 11:26:42 GMT Frederik Heber [a0bcf1] * AUTHORS (added) * COPYING (added) * ChangeLog (added) * Makefile.am (added) * NEWS (added) * README (added) * autogen.sh (added) * configure.ac (added) * molecuilder/AUTHORS (added) * molecuilder/ChangeLog (added) * molecuilder/Makefile.am (added) * molecuilder/NEWS (added) * molecuilder/README (added) * molecuilder/autogen.sh (added) * molecuilder/configure.ac (added) * molecuilder/doc/Doxyfile (added) * molecuilder/doc/Makefile.am (added) * molecuilder/m4/ac_doxygen.m4 (added) * molecuilder/src/Hbondangle.db (added) * molecuilder/src/Hbonddistance.db (added) * molecuilder/src/Makefile.am (added) * molecuilder/src/analyzer.cpp (added) * molecuilder/src/atom.cpp (added) * molecuilder/src/bond.cpp (added) * molecuilder/src/builder.cpp (added) * molecuilder/src/config.cpp (added) * molecuilder/src/datacreator.cpp (added) * molecuilder/src/datacreator.hpp (added) * molecuilder/src/defs.hpp (added) * molecuilder/src/element.cpp (added) * molecuilder/src/elements.db (added) * molecuilder/src/graph.cpp (added) * molecuilder/src/helpers.cpp (added) * molecuilder/src/helpers.hpp (added) * molecuilder/src/joiner.cpp (added) * molecuilder/src/moleculelist.cpp (added) * molecuilder/src/molecules.cpp (added) * molecuilder/src/molecules.hpp (added) * molecuilder/src/orbitals.db (added) * molecuilder/src/parser.cpp (added) * molecuilder/src/parser.hpp (added) * molecuilder/src/periodentafel.cpp (added) * molecuilder/src/valence.db (added) * molecuilder/src/vector.cpp (added) * molecuilder/src/verbose.cpp (added) * pcp/AUTHORS (added) * pcp/CHANGES (added) * pcp/ChangeLog (added) * pcp/Makefile.am (added) * pcp/NEWS (added) * pcp/README (added) * pcp/autogen.sh (added) * pcp/configure.ac (added) * pcp/doc/Doxyfile (added) * pcp/doc/Makefile.am (added) * pcp/m4/ac_doxygen.m4 (added) * pcp/m4/acx_mpi.m4 (added) * pcp/src/Makefile.am (added) * pcp/src/Makefile.in (added) * pcp/src/data.h (added) * pcp/src/defs.h (added) * pcp/src/density.c (added) * pcp/src/density.h (added) * pcp/src/energy.c (added) * pcp/src/energy.h (added) * pcp/src/errors.c (added) * pcp/src/errors.h (added) * pcp/src/excor.c (added) * pcp/src/excor.h (added) * pcp/src/grad.c (added) * pcp/src/grad.h (added) * pcp/src/gramsch.c (added) * pcp/src/gramsch.h (added) * pcp/src/helpers.c (added) * pcp/src/helpers.h (added) * pcp/src/init.c (added) * pcp/src/init.h (added) * pcp/src/ions.c (added) * pcp/src/ions.h (added) * pcp/src/mergesort2.c (added) * pcp/src/mergesort2.h (added) * pcp/src/myfft.c (added) * pcp/src/myfft.h (added) * pcp/src/mymath.c (added) * pcp/src/mymath.h (added) * pcp/src/opt.c (added) * pcp/src/opt.h (added) * pcp/src/output.c (added) * pcp/src/output.h (added) * pcp/src/parsetest.c (added) * pcp/src/pcp.c (added) * pcp/src/pcp.h (added) * pcp/src/pdbformat.c (added) * pcp/src/pdbformat.h (added) * pcp/src/perturbed.c (added) * pcp/src/perturbed.h (added) * pcp/src/pseudo.c (added) * pcp/src/pseudo.h (added) * pcp/src/riemann.c (added) * pcp/src/riemann.h (added) * pcp/src/run.c (added) * pcp/src/run.h (added) * pcp/src/test.c (added) * pcp/src/wannier.c (added) * pcp/src/wannier.h (added) * util/AUTHORS (added) * util/BOSSEvaluate.pl.in (added) * util/ChangeLog (added) * util/CreateFromXYZ.sh (added) * util/CreateGaAs.c (added) * util/CreateH2.c (added) * util/GetPdb.c (added) * util/Makefile.am (added) * util/NEWS (added) * util/NanoCreator.c (added) * util/NanoCreator.h (added) * util/Nanotubes.pl.in (added) * util/README (added) * util/ReSequenceDX.pl.in (added) * util/ReadSrcIon.c (added) * util/VibrAlyzer.c (added) * util/autogen.sh (added) * util/average.cpp (added) * util/average_result.sh (added) * util/compile (added) * util/config2xyz.sh (added) * util/configure.ac (added) * util/convert2old.sh (added) * util/convertpdb.sh (added) * util/depcomp (added) * util/doc/Doxyfile (added) * util/doc/Makefile.am (added) * util/gather_all_results.sh (added) * util/gather_averaged_results.sh (added) * util/gather_result.sh (added) * util/grep_shielding.sh (added) * util/install-sh (added) * util/m4/ac_doxygen.m4 (added) * util/meas2pdb.sh (added) * util/mergesort.c (added) * util/mergesort.h (added) * util/specvisual.cfg (added) * util/specvisual.net (added) * util/specvisualOnly.net (added) * util/stochastik.cpp (added) * util/suffix (added) * util/visual.cfg (added) * util/visual.net (added) * util/visualOnly.net (added) -initial commit -Minimum set of files needed from ESPACK SVN ...