source: src@ 579a81

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 bb4408   15 years FrederikHeber BUGFIX: Removed adding of parsed atoms in LoadXyzAction. - a molecule …
Descriptors bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
Exceptions bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
Helpers b0b086   15 years FrederikHeber BUGFIX: Fixed unity target. - MemDebug.cpp has to appear before any …
LinearAlgebra bc8a41   15 years Till Crueger Added a warning to keep people from using VectorContent directly
Parser bb4408   15 years FrederikHeber BUGFIX: Removed adding of parsed atoms in LoadXyzAction. - a molecule …
Patterns 5f1d5b8   15 years FrederikHeber BUGFIX: fixed undefined ref to …
Shapes bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
test 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Thermostats 579a81   15 years Till Crueger Added a basic self-descriptive structure for Thermostats
UIElements 26cf17   15 years FrederikHeber Added Formula WidgetItem to QTWorldView. - int are converted to …
unittests 31fb1d   15 years FrederikHeber (un)select-atoms-inside-cuboid: cuboid may be rotated. - …
analysis_bonds.cpp 11.5 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
analysis_bonds.hpp 1.4 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
analysis_correlation.cpp 21.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
analysis_correlation.hpp 5.3 KB ​ e5c0a1   15 years Till Crueger Made the periodentafel return only "const element *" instead of …
analyzer.cpp 33.9 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom.cpp 11.2 KB ​ fa7989   15 years FrederikHeber FIX: World::destroyMolecule(mol *) - assert that pointer is not NULL. …
atom.hpp 3.8 KB ​ e41c48   15 years FrederikHeber RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() is …
atom_atominfo.cpp 3.5 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_atominfo.hpp 2.7 KB ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
atom_bondedparticle.cpp 6.3 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_bondedparticle.hpp 1.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticleinfo.cpp 466 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_bondedparticleinfo.hpp 1020 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnode.cpp 1.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_graphnode.hpp 846 bytes ​ e138de   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnodeinfo.cpp 523 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 844 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_particleinfo.hpp 1014 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticle.cpp 10.2 KB ​ 7329c3   15 years Till Crueger Removed obsolete method for summing up temperature
atom_trajectoryparticle.hpp 2.3 KB ​ 7329c3   15 years Till Crueger Removed obsolete method for summing up temperature
atom_trajectoryparticleinfo.cpp 545 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
atom_trajectoryparticleinfo.hpp 1009 bytes ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
AtomicInfo.cpp 1.4 KB ​ e41c48   15 years FrederikHeber RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() is …
AtomicInfo.hpp 700 bytes ​ e41c48   15 years FrederikHeber RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() is …
AtomSet.hpp 2.4 KB ​ ddc85b   15 years Till Crueger Added a method that allows calculation of the total temperature of a …
bond.cpp 3.8 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
bond.hpp 2.0 KB ​ b9947d   16 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 6.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
bondgraph.hpp 1.4 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
boundary.cpp 51.0 KB ​ 6b5657   15 years FrederikHeber Decoupled typedef for some STL maps used in boundary.cpp from those …
boundary.hpp 2.3 KB ​ 6b5657   15 years FrederikHeber Decoupled typedef for some STL maps used in boundary.cpp from those …
BoundaryLineSet.cpp 10.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
BoundaryLineSet.hpp 1.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryMaps.hpp 3.1 KB ​ 6b5657   15 years FrederikHeber Decoupled typedef for some STL maps used in boundary.cpp from those …
BoundaryPointSet.cpp 2.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
BoundaryPointSet.hpp 646 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.cpp 9.3 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
BoundaryPolygonSet.hpp 1.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryTriangleSet.cpp 17.1 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
BoundaryTriangleSet.hpp 1.7 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
Box.cpp 6.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
Box.hpp 2.5 KB ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
builder.cpp 7.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
CandidateForTesselation.cpp 7.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
CandidateForTesselation.hpp 1.2 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
CommandLineParser.cpp 3.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
CommandLineParser.hpp 6.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
config.cpp 99.6 KB ​ 2b7d1b   15 years FrederikHeber Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into …
config.hpp 4.0 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
ConfigFileBuffer.cpp 5.5 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
datacreator.cpp 36.0 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
datacreator.hpp 5.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
defs.cpp 4.0 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
defs.hpp 5.1 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
element.cpp 2.8 KB ​ ae959a   15 years FrederikHeber element::group, period, block converted from char[] to std::string. - …
element.hpp 2.0 KB ​ ae959a   15 years FrederikHeber element::group, period, block converted from char[] to std::string. - …
elements.db 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
elements_db.cpp 8.1 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
elements_db.hpp 322 bytes ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
ellipsoid.cpp 17.2 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
ellipsoid.hpp 1.2 KB ​ e138de   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
Formula.cpp 14.5 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
Formula.hpp 3.3 KB ​ 426f2a   15 years Till Crueger Added a method to enumerate formulas
graph.cpp 3.9 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
graph.hpp 3.0 KB ​ d4103c8   15 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 11.8 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
leastsquaremin.cpp 802 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
linkedcell.cpp 14.0 KB ​ ff58f1   15 years FrederikHeber BUGFIX: fixed initializer list sequence of LinkedCell.
linkedcell.hpp 2.4 KB ​ 57f243   15 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
Makefile.am 13.4 KB ​ 194649   15 years Till Crueger Added class structure to represent thermostats
molecule.cpp 39.7 KB ​ 900402   15 years Till Crueger Made the molecule::OutputTemperatureFromTrajectories() method use the …
molecule.hpp 20.4 KB ​ a7a087   15 years FrederikHeber new function World::changeMoleculeId(). - copied from changeAtomId() …
molecule_dynamics.cpp 34.7 KB ​ c743f8   15 years Till Crueger Removed some more invocations of ActOnAllAtoms
molecule_fragmentation.cpp 79.3 KB ​ c743f8   15 years Till Crueger Removed some more invocations of ActOnAllAtoms
molecule_geometry.cpp 14.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
molecule_graph.cpp 66.1 KB ​ c743f8   15 years Till Crueger Removed some more invocations of ActOnAllAtoms
molecule_pointcloud.cpp 1.9 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
molecule_template.hpp 14.0 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
moleculelist.cpp 36.1 KB ​ 2b7d1b   15 years FrederikHeber Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into …
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
parser.cpp 46.3 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
parser.hpp 4.8 KB ​ f66195   16 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 15.1 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
periodentafel.hpp 2.1 KB ​ e5c0a1   15 years Till Crueger Made the periodentafel return only "const element *" instead of …
PointCloud.cpp 422 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
PointCloud.hpp 892 bytes ​ d74077   15 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   15 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
tesselation.cpp 188.8 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
tesselation.hpp 7.9 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
tesselationhelpers.cpp 39.8 KB ​ a19d73e   15 years FrederikHeber FIX: GetCenterofCircumcircle() has check for division by zero.
tesselationhelpers.hpp 3.7 KB ​ 88b400   15 years FrederikHeber converted #define's to enums, consts and typedefs [Meyers, "Effective …
TesselPoint.cpp 687 bytes ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
TesselPoint.hpp 495 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
ThermoStatContainer.cpp 1.5 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
ThermoStatContainer.hpp 800 bytes ​ ea2c76   15 years Till Crueger Removed definition of unused method in ThermostatContainer class
triangleintersectionlist.cpp 6.4 KB ​ bf3817   15 years FrederikHeber Added ifdef HAVE_CONFIG and config.h include to each and every cpp …
triangleintersectionlist.hpp 1.6 KB ​ d74077   15 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 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
World.cpp 21.6 KB ​ 5f1d5b8   15 years FrederikHeber BUGFIX: fixed undefined ref to …
World.hpp 13.0 KB ​ 5f1d5b8   15 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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