source: src@ 435065

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Name Size Rev Age Author Last Change
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Actions 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
Descriptors 170ba6   14 years FrederikHeber BUGFIX: MoleculeOrderDescription was not working in reverse because of …
Dynamics 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
Exceptions 266875   14 years FrederikHeber FIX: ParserError did not adhere to naming convention. - excepetions …
Graph 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
Helpers ce5f05   14 years FrederikHeber Moved Shading and EdgeType from defs.hpp to bond.hpp, getColor from …
LinearAlgebra a5028f   14 years FrederikHeber RandomNumberGeneratorFactory is now used instead of rand() throughout …
Parser 1bfc8e   14 years FrederikHeber Removed ThermostatContainer instance from config, instance from World …
RandomNumbers c14c78   14 years FrederikHeber Some bugfixes for RandomNumber... stuff. - BUGFIX: Asserts contained …
Shapes e5bf2b   14 years FrederikHeber removed CPPUNIT_LIBS/FLAGS from most Makefile.am and LIBS/libs -> …
Thermostats 056e70   14 years FrederikHeber Suffixed getters and setters for AtomInfo trajecories with AtStep. - …
UIElements fa60dd   14 years FrederikHeber Removed molecule::GetName() usage in QtMoleculeView. - in …
unittests 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
analysis_bonds.cpp 12.3 KB ​ 735b1c   14 years FrederikHeber ParticleInfo::ParticleInfo_nr is protected and accessed via …
analysis_bonds.hpp 1.4 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
analysis_correlation.cpp 25.9 KB ​ 9d83b6   14 years FrederikHeber BondedParticleInfo now has vector<BondList> - vector<BondList> …
analysis_correlation.hpp 7.2 KB ​ 92e5cb   14 years FrederikHeber Refactored Output..Correlation...() code into a single templated one. …
analyzer.cpp 34.1 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
atom.cpp 11.6 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
atom.hpp 4.3 KB ​ e2373df   14 years FrederikHeber TesselPoint, Atom and AtomInfo have virtual UpdateSteps() to allow …
atom_atominfo.cpp 18.3 KB ​ 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
atom_atominfo.hpp 7.8 KB ​ 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
atom_bondedparticle.cpp 9.1 KB ​ 4b5cf8   14 years FrederikHeber BondedParticle::OutputBondOfAtom() now takes stream to print to.
atom_bondedparticle.hpp 1.6 KB ​ 4b5cf8   14 years FrederikHeber BondedParticle::OutputBondOfAtom() now takes stream to print to.
atom_bondedparticleinfo.cpp 2.3 KB ​ 38c44b   14 years FrederikHeber Added verbosity to AppendTrajectoryStep() of BondedParticle.
atom_bondedparticleinfo.hpp 2.5 KB ​ 1e6249   14 years FrederikHeber BondedParticle has virtual UpdateSteps() to allow consistent extending …
atom_graphnode.cpp 1.5 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
atom_graphnode.hpp 913 bytes ​ f9183b   14 years FrederikHeber BUGFIX: graph info per bond is now output nicely. - added operator<< …
atom_graphnodeinfo.cpp 758 bytes ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 1.2 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
atom_particleinfo.hpp 1.4 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
AtomicInfo.cpp 1.7 KB ​ bce72c   14 years FrederikHeber AtomicInfo::AtomicVelocity and ::AtomicForce are now private. - …
AtomicInfo.hpp 770 bytes ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
AtomSet.hpp 5.4 KB ​ 8009ce   14 years FrederikHeber Rewrote OutputTemperature into a functor in Dynamics/ - formerly …
bond.cpp 4.5 KB ​ ce5f05   14 years FrederikHeber Moved Shading and EdgeType from defs.hpp to bond.hpp, getColor from …
bond.hpp 2.2 KB ​ ce5f05   14 years FrederikHeber Moved Shading and EdgeType from defs.hpp to bond.hpp, getColor from …
boundary.cpp 62.5 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
boundary.hpp 2.6 KB ​ 34c43a   14 years FrederikHeber Bigger change: Replaced PointCloud by PointCloudAdaptor. - PointCloud …
BoundaryLineSet.cpp 10.6 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
BoundaryLineSet.hpp 1.5 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
BoundaryMaps.hpp 3.2 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
BoundaryPointSet.cpp 3.1 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
BoundaryPointSet.hpp 1.3 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
BoundaryPolygonSet.cpp 9.6 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
BoundaryPolygonSet.hpp 1.8 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
BoundaryTriangleSet.cpp 17.3 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
BoundaryTriangleSet.hpp 1.7 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
Box.cpp 7.8 KB ​ 528b3e   14 years FrederikHeber Added conversion functions to VectorValue and BoxValue and changed …
Box.hpp 2.9 KB ​ 528b3e   14 years FrederikHeber Added conversion functions to VectorValue and BoxValue and changed …
builder.cpp 3.4 KB ​ f4d063   14 years FrederikHeber MEMFIX: MemDebug ignores all unknown sources. Removed all dependencies …
builder_init.cpp 6.7 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
builder_init.hpp 418 bytes ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
CandidateForTesselation.cpp 7.7 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
CandidateForTesselation.hpp 1.3 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
config.cpp 72.9 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
config.hpp 3.6 KB ​ f71baf   14 years FrederikHeber Made BondGraph an instance of World, removed from config. - BondGraph …
ConfigFileBuffer.cpp 7.1 KB ​ 6a465e   14 years FrederikHeber Rewrote LoadMolecule() for PcpParser. - LoadMolecule() rewritten as …
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   14 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
datacreator.cpp 36.2 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
datacreator.hpp 5.1 KB ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
element.cpp 4.0 KB ​ 67c92b   14 years FrederikHeber Added Electronegativity database and member value to class element. - …
element.hpp 2.6 KB ​ 67c92b   14 years FrederikHeber Added Electronegativity database and member value to class element. - …
elements.db 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
elements_db.cpp 9.6 KB ​ 67c92b   14 years FrederikHeber Added Electronegativity database and member value to class element. - …
elements_db.hpp 434 bytes ​ 67c92b   14 years FrederikHeber Added Electronegativity database and member value to class element. - …
ellipsoid.cpp 18.7 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
Formula.cpp 14.9 KB ​ 266875   14 years FrederikHeber FIX: ParserError did not adhere to naming convention. - excepetions …
Formula.hpp 3.5 KB ​ 266875   14 years FrederikHeber FIX: ParserError did not adhere to naming convention. - excepetions …
graph.cpp 4.1 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
graph.hpp 3.1 KB ​ 03c77c   14 years FrederikHeber bonds::previous and ::next removed, lists.hpp deleted. - the last of …
Hbondangle.db 251 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
Hbonddistance.db 282 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
IPointCloud.hpp 670 bytes ​ caa06ef   14 years FrederikHeber Added name to PointCloudAdaptor, set by constructor. - name is used …
joiner.cpp 12.0 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
linkedcell.cpp 12.0 KB ​ 3738f0   14 years FrederikHeber Moved molecule::CreateAdjacencyList over to class BondGraph. to make …
linkedcell.hpp 2.7 KB ​ 3738f0   14 years FrederikHeber Moved molecule::CreateAdjacencyList over to class BondGraph. to make …
Makefile.am 12.6 KB ​ 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
molecule.cpp 40.1 KB ​ 8009ce   14 years FrederikHeber Rewrote OutputTemperature into a functor in Dynamics/ - formerly …
molecule.hpp 11.0 KB ​ 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
molecule_dynamics.cpp 971 bytes ​ 435065   14 years FrederikHeber Rewrote VerletForceIntegration into a functor in Dynamics/. - we now …
molecule_fragmentation.cpp 82.7 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
molecule_geometry.cpp 18.0 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
molecule_graph.cpp 58.1 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
moleculelist.cpp 36.8 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
parser.cpp 47.1 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
parser.hpp 4.8 KB ​ b23e26   14 years FrederikHeber Added operator<< for MatrixContainer class.
periodentafel.cpp 16.7 KB ​ 03c77c   14 years FrederikHeber bonds::previous and ::next removed, lists.hpp deleted. - the last of …
periodentafel.hpp 2.1 KB ​ 67c92b   14 years FrederikHeber Added Electronegativity database and member value to class element. - …
PointCloudAdaptor.hpp 2.0 KB ​ caa06ef   14 years FrederikHeber Added name to PointCloudAdaptor, set by constructor. - name is used …
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
SubspaceFactorizer.cpp 16.1 KB ​ a5028f   14 years FrederikHeber RandomNumberGeneratorFactory is now used instead of rand() throughout …
tesselation.cpp 187.9 KB ​ 5309ba   14 years FrederikHeber Renamed ParticleInfo_nr back to Nr. - Note that this mostly affected …
tesselation.hpp 7.9 KB ​ 34c43a   14 years FrederikHeber Bigger change: Replaced PointCloud by PointCloudAdaptor. - PointCloud …
tesselationhelpers.cpp 40.2 KB ​ 735b1c   14 years FrederikHeber ParticleInfo::ParticleInfo_nr is protected and accessed via …
tesselationhelpers.hpp 3.7 KB ​ 34c43a   14 years FrederikHeber Bigger change: Replaced PointCloud by PointCloudAdaptor. - PointCloud …
TesselPoint.cpp 1.2 KB ​ ba5215   14 years FrederikHeber Extended BoundaryPointSet by functions to directly access TesselPoint …
TesselPoint.hpp 1.3 KB ​ ba5215   14 years FrederikHeber Extended BoundaryPointSet by functions to directly access TesselPoint …
ThermoStatContainer.cpp 3.4 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
ThermoStatContainer.hpp 828 bytes ​ 14c57a   14 years Till Crueger Made all parts of the programm use the new thermostat structure
triangleintersectionlist.cpp 6.7 KB ​ ad011c   14 years FrederikHeber CodePatterns places all includes now in subfolder CodePatterns/. - …
triangleintersectionlist.hpp 1.6 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
types.hpp 482 bytes ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
valence.db 1.6 KB ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
version.h 103 bytes ​ 5f8660a   14 years FrederikHeber Changed PACKAGENAME and version. - rename ESPACKVersion in …
World.cpp 22.9 KB ​ 632508   14 years FrederikHeber Moved files bondgraph.?pp -> Graph/BondGraph.?pp.
World.hpp 13.6 KB ​ f71baf   14 years FrederikHeber Made BondGraph an instance of World, removed from config. - BondGraph …
World_calculations.hpp 689 bytes ​ 56f73b   14 years FrederikHeber Added config.h also to all header files, code check test ascertain …
WorldTime.cpp 772 bytes ​ 6bb605   14 years FrederikHeber Worldtime now has static CurrentTime and static (inline) …
WorldTime.hpp 1.8 KB ​ 9d83b6   14 years FrederikHeber BondedParticleInfo now has vector<BondList> - vector<BondList> …
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