source: src@ fc192f

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 Candidate_v1.7.0 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
../
unittests 6f5dfe   15 years FrederikHeber Added boost::filesystem usage for input files. - parameters for …
UIElements 2a6a2c   15 years FrederikHeber Removed MapOfActions::populateActions(). - Action prototypes are now …
Thermostats 14c57a   15 years Till Crueger Made all parts of the programm use the new thermostat structure
test 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Shapes 9c1c89   15 years FrederikHeber FIX: all ...:getHomogeneousPointsOnSurface() now have size_t instead …
Patterns 2a6a2c   15 years FrederikHeber Removed MapOfActions::populateActions(). - Action prototypes are now …
Parser bd2390   15 years FrederikHeber BUGFIX: new boost::filesystem led to non-parsing of files. - BUGFIX: …
LinearAlgebra e3e6e2   15 years FrederikHeber Added BoxVector class. BoxVector is simply a Vector with a different …
Helpers bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Exceptions f8982c   15 years FrederikHeber FIX: NotInvertibleException.hpp was present twice.
Descriptors bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Actions fc192f   15 years FrederikHeber Added paramdescriptions to the .def of all Actions. - option …
World_calculations.hpp 595 bytes ​ 0e2a47   16 years Till Crueger Added overloaded methods for all methods in the world taking an …
World.hpp 13.0 KB ​ 5f1d5b8   15 years FrederikHeber BUGFIX: fixed undefined ref to …
World.cpp 21.9 KB ​ 654394   15 years FrederikHeber MEMFIX: World::numMoleculeDefragSkips and World::lastMoleculePoolSize …
version.h 103 bytes ​ 5f8660a   15 years FrederikHeber Changed PACKAGENAME and version. - rename ESPACKVersion in …
valence.db 1.6 KB ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
types.hpp 412 bytes ​ ead4e6   16 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
triangleintersectionlist.hpp 1.6 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
triangleintersectionlist.cpp 6.7 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
ThermoStatContainer.hpp 828 bytes ​ 14c57a   15 years Till Crueger Made all parts of the programm use the new thermostat structure
ThermoStatContainer.cpp 3.3 KB ​ 14c57a   15 years Till Crueger Made all parts of the programm use the new thermostat structure
TesselPoint.hpp 495 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
TesselPoint.cpp 917 bytes ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
tesselationhelpers.hpp 3.7 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
tesselationhelpers.cpp 40.0 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
tesselation.hpp 8.3 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
tesselation.cpp 189.2 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
stackclass.hpp 8.1 KB ​ 952f38   15 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   17 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
PointCloud.hpp 892 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
PointCloud.cpp 652 bytes ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
periodentafel.hpp 2.1 KB ​ e5c0a1   15 years Till Crueger Made the periodentafel return only "const element *" instead of …
periodentafel.cpp 15.3 KB ​ 9f99b3   15 years FrederikHeber MEMFIX: periodentafel::LoadElementsDatabase() leaked memory. - if …
parser.hpp 4.8 KB ​ f66195   16 years FrederikHeber forward declarations used to untangle interdependet classes. - …
parser.cpp 46.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
moleculelist.cpp 36.1 KB ​ 9c7e0f   15 years FrederikHeber deleted function MoleculeListClass::flipChosen() and …
molecule_pointcloud.cpp 2.3 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
molecule_graph.cpp 66.5 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
molecule_geometry.cpp 14.7 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
molecule_fragmentation.cpp 80.0 KB ​ 32ea56   15 years Till Crueger Removed last occurences of molecule::SetIndexedArrayForEachAtomTo()
molecule_dynamics.cpp 31.6 KB ​ 32ea56   15 years Till Crueger Removed last occurences of molecule::SetIndexedArrayForEachAtomTo()
molecule.hpp 13.5 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
molecule.cpp 39.5 KB ​ 76ff55   15 years FrederikHeber BUGFIX: molecule::CopyMolecule() was broken. fixes: - for loop over …
Makefile.am 14.7 KB ​ 8df74d   15 years FrederikHeber Split off all ...Query and ...Pipe boilerplate classes. - each …
lists.hpp 3.5 KB ​ d3347e   16 years Till Crueger FIX: repaired compiler problems for latest refactoring
linkedcell.hpp 5.6 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
linkedcell.cpp 12.2 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
leastsquaremin.hpp 950 bytes ​ ead4e6   16 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
leastsquaremin.cpp 1.0 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
joiner.cpp 12.0 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Hbonddistance.db 282 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
Hbondangle.db 251 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
graph.hpp 3.0 KB ​ d4103c8   15 years Till Crueger Removed opening of namespace from molecule.hpp
graph.cpp 4.1 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
Formula.hpp 3.3 KB ​ 426f2a   15 years Till Crueger Added a method to enumerate formulas
Formula.cpp 14.7 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
ellipsoid.hpp 1.2 KB ​ e138de   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
ellipsoid.cpp 17.4 KB ​ bcf653   15 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 …
elements_db.cpp 8.3 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
elements.db 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
element.hpp 2.5 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
element.cpp 3.9 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
defs.hpp 5.1 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
defs.cpp 4.2 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
datacreator.hpp 5.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
datacreator.cpp 36.2 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
ConfigFileBuffer.cpp 5.7 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
config.hpp 3.7 KB ​ 8d1dd4   15 years Till Crueger Removed obsolete load methods from config class
config.cpp 74.6 KB ​ 9e7813   15 years Till Crueger Removed ActOnAllAtoms from config.cpp
CommandLineParser.hpp 6.1 KB ​ 53d01c   15 years FrederikHeber Renamed dir Actions/CmdAction -> Actions/CommandAction, renamed class …
CommandLineParser.cpp 3.4 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
CandidateForTesselation.hpp 1.2 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
CandidateForTesselation.cpp 7.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
builder.cpp 7.8 KB ​ 4cf323d   15 years FrederikHeber Renamed QT -> Qt in files, dirs, and class names.
Box.hpp 2.5 KB ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Box.cpp 6.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryTriangleSet.hpp 1.7 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
BoundaryTriangleSet.cpp 17.3 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryPolygonSet.hpp 1.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.cpp 9.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryPointSet.hpp 646 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPointSet.cpp 2.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
BoundaryMaps.hpp 3.1 KB ​ 6b5657   15 years FrederikHeber Decoupled typedef for some STL maps used in boundary.cpp from those …
BoundaryLineSet.hpp 1.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryLineSet.cpp 10.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
boundary.hpp 2.5 KB ​ eee966   15 years FrederikHeber New Action FillVoidWithMoleculeAction. - in contrast to …
boundary.cpp 58.5 KB ​ eee966   15 years FrederikHeber New Action FillVoidWithMoleculeAction. - in contrast to …
bondgraph.hpp 1.5 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
bondgraph.cpp 6.7 KB ​ af2c424   15 years FrederikHeber LinkedCell constructor rewritten. - had to introduce …
bond.hpp 2.0 KB ​ b9947d   16 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bond.cpp 4.1 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
AtomSet.hpp 3.6 KB ​ 5ac690   15 years Till Crueger Added a method to the AtomSetMixin that allows adding a velocity to …
AtomicInfo.hpp 700 bytes ​ e41c48   15 years FrederikHeber RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() is …
AtomicInfo.cpp 1.6 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_trajectoryparticleinfo.hpp 1009 bytes ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
atom_trajectoryparticleinfo.cpp 775 bytes ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_trajectoryparticle.hpp 1.6 KB ​ a3948b   15 years Till Crueger Removed unused TrajectoryParticle::CorrectVelocity() method
atom_trajectoryparticle.cpp 4.9 KB ​ a3948b   15 years Till Crueger Removed unused TrajectoryParticle::CorrectVelocity() method
atom_particleinfo.hpp 1014 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 1.0 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnodeinfo.cpp 753 bytes ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_graphnode.hpp 913 bytes ​ f9183b   15 years FrederikHeber BUGFIX: graph info per bond is now output nicely. - added operator<< …
atom_graphnode.cpp 1.5 KB ​ f9183b   15 years FrederikHeber BUGFIX: graph info per bond is now output nicely. - added operator<< …
atom_bondedparticleinfo.hpp 1020 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticleinfo.cpp 696 bytes ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
atom_bondedparticle.hpp 1.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticle.cpp 6.6 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
atom_atominfo.hpp 2.7 KB ​ 1f8337   15 years Till Crueger Moved AtomInfo::getMass() method to class atom to avoid problems with …
atom_atominfo.cpp 3.7 KB ​ 1f8337   15 years Till Crueger Moved AtomInfo::getMass() method to class atom to avoid problems with …
atom.hpp 4.0 KB ​ e8a21f   15 years Till Crueger Added an atom::getNr() method to atom class
atom.cpp 11.9 KB ​ e8a21f   15 years Till Crueger Added an atom::getNr() method to atom class
analyzer.cpp 34.1 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
analysis_correlation.hpp 5.3 KB ​ 146cff2   15 years FrederikHeber FIX: include <cmath> missing in some files.
analysis_correlation.cpp 21.7 KB ​ bcf653   15 years FrederikHeber Added copyright note to each .cpp file and an extensive one to builder.cpp.
analysis_bonds.hpp 1.4 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
analysis_bonds.cpp 11.8 KB ​ 83f176   15 years FrederikHeber Made all member variables of class element private, added accessor …
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