source: src@ 3bc926

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 9eb7580   14 years FrederikHeber Renamed Matrix setter functions to unify naming. - Matrix::one -> …
Descriptors bcf653   14 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Exceptions d5240d   14 years FrederikHeber FIX: Linking to non-system boost is working now. - FIX: …
Helpers cfc53b   14 years FrederikHeber Added template function toString(), is included in Assert.hpp. - …
LinearAlgebra 3bc926   14 years FrederikHeber Extended MatrixContent class. - MatrixContent formerly has been just …
Parser d5240d   14 years FrederikHeber FIX: Linking to non-system boost is working now. - FIX: …
Patterns ae21cbd   14 years FrederikHeber MEMFIX: new function AddStaticEntitiestoIgnoreList() for putting …
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 d2b28f   14 years FrederikHeber Added missing MemDebug include to various implementation files.
UIElements 9eb7580   14 years FrederikHeber Renamed Matrix setter functions to unify naming. - Matrix::one -> …
unittests 3bc926   14 years FrederikHeber Extended MatrixContent class. - MatrixContent formerly has been just …
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 1.7 KB ​ d2b28f   14 years FrederikHeber Added missing MemDebug include to various implementation files.
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 ​ 9eb7580   14 years FrederikHeber Renamed Matrix setter functions to unify naming. - Matrix::one -> …
Box.hpp 2.5 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
builder.cpp 9.0 KB ​ c82d0c   14 years FrederikHeber MenuDescription is now a singleton. - also all Maps are static …
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 …
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 12.2 KB ​ d5240d   14 years FrederikHeber FIX: Linking to non-system boost is working now. - FIX: …
molecule.cpp 39.6 KB ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
molecule.hpp 13.3 KB ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
molecule_dynamics.cpp 31.6 KB ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
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 ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
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 22.3 KB ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
World.hpp 13.2 KB ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
World_calculations.hpp 619 bytes ​ e4afb4   14 years FrederikHeber Huge refactoring: Introduction of Traits to Actions. This change is …
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