source: src@ 052bfd8

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 052bfd8   14 years FrederikHeber Added MENUNAME and MENUPOSITION to each Action's .def. - MENUNAME is …
Descriptors bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Exceptions f8982c   14 years FrederikHeber FIX: NotInvertibleException.hpp was present twice.
Helpers bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
LinearAlgebra e3e6e2   14 years FrederikHeber Added BoxVector class. BoxVector is simply a Vector with a different …
Parser bd2390   14 years FrederikHeber BUGFIX: new boost::filesystem led to non-parsing of files. - BUGFIX: …
Patterns 2a6a2c   14 years FrederikHeber Removed MapOfActions::populateActions(). - Action prototypes are now …
Shapes 9c1c89   14 years FrederikHeber FIX: all ...:getHomogeneousPointsOnSurface() now have size_t instead …
test 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Thermostats 14c57a   14 years Till Crueger Made all parts of the programm use the new thermostat structure
UIElements 2a6a2c   14 years FrederikHeber Removed MapOfActions::populateActions(). - Action prototypes are now …
unittests 6f5dfe   14 years FrederikHeber Added boost::filesystem usage for input files. - parameters for …
analysis_bonds.cpp 11.8 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
analysis_bonds.hpp 1.4 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
analysis_correlation.cpp 21.7 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
analysis_correlation.hpp 5.3 KB ​ 146cff2   14 years FrederikHeber FIX: include <cmath> missing in some files.
analyzer.cpp 34.1 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom.cpp 11.9 KB ​ e8a21f   14 years Till Crueger Added an atom::getNr() method to atom class
atom.hpp 4.0 KB ​ e8a21f   14 years Till Crueger Added an atom::getNr() method to atom class
atom_atominfo.cpp 3.7 KB ​ 1f8337   14 years Till Crueger Moved AtomInfo::getMass() method to class atom to avoid problems with …
atom_atominfo.hpp 2.7 KB ​ 1f8337   14 years Till Crueger Moved AtomInfo::getMass() method to class atom to avoid problems with …
atom_bondedparticle.cpp 6.6 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
atom_bondedparticle.hpp 1.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticleinfo.cpp 696 bytes ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_bondedparticleinfo.hpp 1020 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnode.cpp 1.5 KB ​ f9183b   14 years FrederikHeber BUGFIX: graph info per bond is now output nicely. - added operator<< …
atom_graphnode.hpp 913 bytes ​ f9183b   14 years FrederikHeber BUGFIX: graph info per bond is now output nicely. - added operator<< …
atom_graphnodeinfo.cpp 753 bytes ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 1.0 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_particleinfo.hpp 1014 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticle.cpp 4.9 KB ​ a3948b   14 years Till Crueger Removed unused TrajectoryParticle::CorrectVelocity() method
atom_trajectoryparticle.hpp 1.6 KB ​ a3948b   14 years Till Crueger Removed unused TrajectoryParticle::CorrectVelocity() method
atom_trajectoryparticleinfo.cpp 775 bytes ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_trajectoryparticleinfo.hpp 1009 bytes ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
AtomicInfo.cpp 1.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
AtomicInfo.hpp 700 bytes ​ e41c48   14 years FrederikHeber RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() is …
AtomSet.hpp 3.6 KB ​ 5ac690   14 years Till Crueger Added a method to the AtomSetMixin that allows adding a velocity to …
bond.cpp 4.1 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 6.7 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
bondgraph.hpp 1.5 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
boundary.cpp 58.5 KB ​ eee966   14 years FrederikHeber New Action FillVoidWithMoleculeAction. - in contrast to …
boundary.hpp 2.5 KB ​ eee966   14 years FrederikHeber New Action FillVoidWithMoleculeAction. - in contrast to …
BoundaryLineSet.cpp 10.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryLineSet.hpp 1.5 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryMaps.hpp 3.1 KB ​ 6b5657   14 years FrederikHeber Decoupled typedef for some STL maps used in boundary.cpp from those …
BoundaryPointSet.cpp 2.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryPointSet.hpp 646 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.cpp 9.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryPolygonSet.hpp 1.7 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryTriangleSet.cpp 17.3 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryTriangleSet.hpp 1.7 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
Box.cpp 6.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Box.hpp 2.5 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
builder.cpp 7.8 KB ​ 4cf323d   14 years FrederikHeber Renamed QT -> Qt in files, dirs, and class names.
CandidateForTesselation.cpp 7.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
CandidateForTesselation.hpp 1.2 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
CommandLineParser.cpp 3.4 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
CommandLineParser.hpp 6.1 KB ​ 53d01c   14 years FrederikHeber Renamed dir Actions/CmdAction -> Actions/CommandAction, renamed class …
config.cpp 74.6 KB ​ 9e7813   14 years Till Crueger Removed ActOnAllAtoms from config.cpp
config.hpp 3.7 KB ​ 8d1dd4   14 years Till Crueger Removed obsolete load methods from config class
ConfigFileBuffer.cpp 5.7 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
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 ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
datacreator.hpp 5.0 KB ​ 986ed3   14 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
defs.cpp 4.2 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
defs.hpp 5.1 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
element.cpp 3.9 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
element.hpp 2.5 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
elements.db 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
elements_db.cpp 8.3 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
elements_db.hpp 322 bytes ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
ellipsoid.cpp 17.4 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
Formula.cpp 14.7 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Formula.hpp 3.3 KB ​ 426f2a   14 years Till Crueger Added a method to enumerate formulas
graph.cpp 4.1 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
graph.hpp 3.0 KB ​ d4103c8   14 years Till Crueger Removed opening of namespace from molecule.hpp
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 …
joiner.cpp 12.0 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
leastsquaremin.cpp 1.0 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
linkedcell.cpp 12.2 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
linkedcell.hpp 5.6 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
Makefile.am 14.7 KB ​ 8df74d   14 years FrederikHeber Split off all ...Query and ...Pipe boilerplate classes. - each …
molecule.cpp 39.5 KB ​ 76ff55   14 years FrederikHeber BUGFIX: molecule::CopyMolecule() was broken. fixes: - for loop over …
molecule.hpp 13.5 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
molecule_dynamics.cpp 31.6 KB ​ 32ea56   14 years Till Crueger Removed last occurences of molecule::SetIndexedArrayForEachAtomTo()
molecule_fragmentation.cpp 80.0 KB ​ 32ea56   14 years Till Crueger Removed last occurences of molecule::SetIndexedArrayForEachAtomTo()
molecule_geometry.cpp 14.7 KB ​ 83f176   14 years FrederikHeber Made all member variables of class element private, added accessor …
molecule_graph.cpp 66.5 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
molecule_pointcloud.cpp 2.3 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
moleculelist.cpp 36.1 KB ​ 9c7e0f   14 years FrederikHeber deleted function MoleculeListClass::flipChosen() and …
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
parser.cpp 46.6 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 15.3 KB ​ 9f99b3   14 years FrederikHeber MEMFIX: periodentafel::LoadElementsDatabase() leaked memory. - if …
periodentafel.hpp 2.1 KB ​ e5c0a1   14 years Till Crueger Made the periodentafel return only "const element *" instead of …
PointCloud.cpp 652 bytes ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
PointCloud.hpp 892 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
stackclass.hpp 8.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
tesselation.cpp 189.2 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
tesselation.hpp 8.3 KB ​ af2c424   14 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
tesselationhelpers.cpp 40.0 KB ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
tesselationhelpers.hpp 3.7 KB ​ 88b400   14 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
TesselPoint.cpp 917 bytes ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
TesselPoint.hpp 495 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
ThermoStatContainer.cpp 3.3 KB ​ 14c57a   14 years Till Crueger Made all parts of the programm use the new thermostat structure
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 ​ bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
triangleintersectionlist.hpp 1.6 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
types.hpp 412 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
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 21.9 KB ​ 654394   14 years FrederikHeber MEMFIX: World::numMoleculeDefragSkips and World::lastMoleculePoolSize …
World.hpp 13.0 KB ​ 5f1d5b8   14 years FrederikHeber BUGFIX: fixed undefined ref to …
World_calculations.hpp 595 bytes ​ 0e2a47   15 years Till Crueger Added overloaded methods for all methods in the world taking an …
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