source: src@ 8f4df1

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
../
unittests 255971   14 years FrederikHeber Converted libMolecuilder to shared lib via libtool. - joiner and …
UIElements 311d688   14 years FrederikHeber Replaced ostream and iostream includes in header by iosfwd. Note that …
test 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Shapes 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Patterns 311d688   14 years FrederikHeber Replaced ostream and iostream includes in header by iosfwd. Note that …
Parser dddbfe   14 years FrederikHeber FIX: XyzParser::Load() did not create a molecule wherein all atoms …
LinearAlgebra e0ba10   14 years FrederikHeber Added output operator to Line class.
Legacy 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Helpers 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Exceptions f4b5b7   14 years FrederikHeber Created LibMolecuilderExceptions. - is shared. - contains all Exceptions.
Descriptors 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Actions 90bc51   14 years FrederikHeber FIX: RotateAroundSelfByAngleAction also gets position, using a …
World_calculations.hpp 595 bytes ​ 0e2a47   15 years Till Crueger Added overloaded methods for all methods in the world taking an …
World.hpp 12.5 KB ​ 4d72e4   14 years Till Crueger Made the World use the new mixin for sets of atoms
World.cpp 20.8 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
version.h 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
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   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
triangleintersectionlist.hpp 1.6 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
triangleintersectionlist.cpp 6.4 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
ThermoStatContainer.hpp 859 bytes ​ a3fded   15 years FrederikHeber New class ThermoStatContainer containing all parameters and changes to …
ThermoStatContainer.cpp 1.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
TesselPoint.hpp 495 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
TesselPoint.cpp 585 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
tesselationhelpers.hpp 3.6 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
tesselationhelpers.cpp 39.6 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
tesselation.hpp 7.7 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
tesselation.cpp 188.5 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
stackclass.hpp 8.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
PointCloud.hpp 892 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
PointCloud.cpp 320 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
periodentafel.hpp 2.1 KB ​ 389cc8   14 years Till Crueger Used the formual class instead of single variables inside molecule
periodentafel.cpp 14.5 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
parser.cpp 46.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
moleculelist.cpp 46.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
molecule_template.hpp 14.0 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_pointcloud.cpp 1.8 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
molecule_graph.cpp 66.0 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
molecule_geometry.cpp 14.2 KB ​ 4bb63c   14 years FrederikHeber made molecule::DetermineCenterOfGravity() a const member function.
molecule_fragmentation.cpp 79.2 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
molecule_dynamics.cpp 34.6 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
molecule.hpp 20.9 KB ​ 4bb63c   14 years FrederikHeber made molecule::DetermineCenterOfGravity() a const member function.
molecule.cpp 44.5 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Makefile.am 12.7 KB ​ 6e5084   14 years FrederikHeber Fixed PrincipalAxisSystemAction. - …
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
linkedcell.hpp 2.4 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
linkedcell.cpp 13.9 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
leastsquaremin.cpp 733 bytes ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
joiner.cpp 11.6 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
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 3.8 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Formula.hpp 3.3 KB ​ 426f2a   14 years Till Crueger Added a method to enumerate formulas
Formula.cpp 14.4 KB ​ 426f2a   14 years Till Crueger Added a method to enumerate formulas
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
ellipsoid.cpp 17.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
elements_db.hpp 322 bytes ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
elements_db.cpp 8.0 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
elements.db 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
element.hpp 2.0 KB ​ e345e3   14 years Till Crueger Added output operator for element class
element.cpp 1.9 KB ​ e345e3   14 years Till Crueger Added output operator for element class
defs.hpp 5.0 KB ​ 11e206   14 years Till Crueger Removed multiple definitions of some global constants from executeable
datacreator.hpp 5.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
datacreator.cpp 35.9 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
ConfigFileBuffer.cpp 5.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
config.hpp 4.0 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
config.cpp 99.5 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
CommandLineParser.hpp 6.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
CommandLineParser.cpp 3.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
CandidateForTesselation.hpp 1.1 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
CandidateForTesselation.cpp 7.2 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
builder.cpp 7.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
Box.hpp 2.5 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
Box.cpp 6.1 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
BoundaryTriangleSet.hpp 1.7 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryTriangleSet.cpp 17.0 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.hpp 1.7 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.cpp 9.2 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPointSet.hpp 646 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPointSet.cpp 2.3 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryMaps.hpp 2.1 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryLineSet.hpp 1.5 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryLineSet.cpp 10.3 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
boundary.hpp 2.8 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
boundary.cpp 50.9 KB ​ 6e5084   14 years FrederikHeber Fixed PrincipalAxisSystemAction. - …
bondgraph.hpp 1.6 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
bondgraph.cpp 6.0 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bond.cpp 3.7 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
AtomSet.hpp 1.9 KB ​ a33ea5   14 years Till Crueger Added a method to the AtomSetMixin that allows mapping arbitrary …
atom_trajectoryparticleinfo.hpp 1009 bytes ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
atom_trajectoryparticleinfo.cpp 474 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_trajectoryparticle.hpp 2.3 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticle.cpp 10.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
atom_particleinfo.hpp 1014 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 780 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnodeinfo.cpp 442 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_graphnode.hpp 846 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnode.cpp 1.1 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
atom_bondedparticleinfo.hpp 1020 bytes ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticleinfo.cpp 393 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_bondedparticle.hpp 1.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticle.cpp 6.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
atom_atominfo.hpp 2.7 KB ​ 57f243   14 years FrederikHeber Created libMolecuilderLinearAlgebra. - is shared. - contains the …
atom_atominfo.cpp 3.4 KB ​ d74077   14 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom.hpp 3.8 KB ​ 0ba410   14 years Till Crueger made the molecule::Output() method use STL algorithms
atom.cpp 10.8 KB ​ dddbfe   14 years FrederikHeber FIX: XyzParser::Load() did not create a molecule wherein all atoms …
analyzer.cpp 33.9 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
analysis_correlation.hpp 5.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
analysis_correlation.cpp 21.3 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
analysis_bonds.hpp 1.4 KB ​ bfd839   15 years FrederikHeber Changed and added counting of hydrogen bonds to menu. - …
analysis_bonds.cpp 11.5 KB ​ 952f38   14 years FrederikHeber created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> …
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