source: src@ d74077

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 d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
Descriptors d6e719   15 years FrederikHeber BUGFIX: some Molecule...Descriptors::find() function copied the …
Exceptions 0b0a20   15 years FrederikHeber Inserted all possible queries into MapOfActions. - …
Helpers 7067bd6   15 years Till Crueger Made all methods of the range struct explicitly inline
Legacy d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
Parser d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
Patterns b2d8d0   15 years FrederikHeber Registry pattern split off of ActionRegistry, the latter converted to …
Shapes 205d9b   15 years Till Crueger Added missing const to Shape::isInside() method
test 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
UIElements d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
unittests d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
analysis_bonds.cpp 11.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
analysis_bonds.hpp 1.4 KB ​ bfd839   15 years FrederikHeber Changed and added counting of hydrogen bonds to menu. - …
analysis_correlation.cpp 21.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
analysis_correlation.hpp 5.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
analyzer.cpp 33.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
atom.cpp 10.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom.hpp 3.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_atominfo.cpp 3.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_atominfo.hpp 2.6 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticle.cpp 6.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_bondedparticle.hpp 1.4 KB ​ d74077   15 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_bondedparticleinfo.hpp 1020 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_graphnode.cpp 1.1 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_graphnode.hpp 846 bytes ​ e138de   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnodeinfo.cpp 442 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_graphnodeinfo.hpp 1.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.cpp 780 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_particleinfo.hpp 1014 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticle.cpp 10.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticle.hpp 2.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
atom_trajectoryparticleinfo.cpp 474 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_trajectoryparticleinfo.hpp 981 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
bond.cpp 3.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
bond.hpp 2.0 KB ​ b9947d   16 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 5.9 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
bondgraph.hpp 1.6 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
boundary.cpp 50.8 KB ​ d74077   15 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
BoundaryLineSet.cpp 10.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryLineSet.hpp 1.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryMaps.hpp 2.1 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPointSet.cpp 2.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPointSet.hpp 646 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.cpp 9.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryPolygonSet.hpp 1.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryTriangleSet.cpp 16.9 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
BoundaryTriangleSet.hpp 1.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
Box.cpp 3.4 KB ​ 0ae36b   15 years FrederikHeber Box::isInside() now uses MYEPSILON as additional boundary of the [0,1) …
Box.hpp 2.1 KB ​ 0ff6b5   15 years FrederikHeber Box::isInside() function added to check whether a given vector is …
builder.cpp 7.0 KB ​ b9c847   15 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
CandidateForTesselation.cpp 7.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
CandidateForTesselation.hpp 1.1 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
CommandLineParser.cpp 3.1 KB ​ 192f6e   15 years FrederikHeber FIX: Removed positional action "input". - BUG: This caused that input …
CommandLineParser.hpp 6.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
config.cpp 99.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
config.hpp 4.0 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
ConfigFileBuffer.cpp 5.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
datacreator.cpp 35.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
datacreator.hpp 5.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
defs.hpp 5.0 KB ​ 127a8e   15 years Till Crueger Improved managing of Ids in the World - Improved algorithm for …
element.cpp 1.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
element.hpp 2.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
elements.db 4.1 KB ​ 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.hpp 322 bytes ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
ellipsoid.cpp 17.1 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
ellipsoid.hpp 1.2 KB ​ e138de   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
errorlogger.cpp 2.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
errorlogger.hpp 805 bytes ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
Formula.cpp 13.1 KB ​ ee86a0   15 years Till Crueger Simplyfied formula parsing using range objects
Formula.hpp 3.0 KB ​ d8a0ec   15 years Till Crueger Made the Formula array resize itself in both directions - resizing …
graph.cpp 3.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
graph.hpp 3.0 KB ​ d4103c8   15 years Till Crueger Removed opening of namespace from molecule.hpp
gslmatrix.cpp 7.3 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
gslmatrix.hpp 1.4 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
gslvector.cpp 8.0 KB ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
gslvector.hpp 1.9 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
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 …
helpers.cpp 4.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
helpers.hpp 5.2 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
info.cpp 754 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
info.hpp 609 bytes ​ 8725ed   16 years FrederikHeber New Info class that contains a global verbosity level, increased per …
joiner.cpp 11.6 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
leastsquaremin.cpp 719 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
Line.cpp 6.8 KB ​ f932b7   15 years Till Crueger Added a method to calculate the intersection of a line with the unit sphere
Line.hpp 1019 bytes ​ f932b7   15 years Till Crueger Added a method to calculate the intersection of a line with the unit sphere
linearsystemofequations.cpp 3.6 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
linearsystemofequations.hpp 1.1 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
linkedcell.cpp 13.9 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
linkedcell.hpp 2.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
log.cpp 1.5 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
log.hpp 323 bytes ​ 58ed4a   15 years FrederikHeber Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - …
logger.cpp 1.5 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
logger.hpp 750 bytes ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
Makefile.am 10.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
Matrix.cpp 7.0 KB ​ 0eb2dc   15 years Till Crueger Added comparison Operator to matrix class
Matrix.hpp 2.9 KB ​ 0eb2dc   15 years Till Crueger Added comparison Operator to matrix class
MatrixContent.hpp 562 bytes ​ fee079   15 years Till Crueger Added a "forward declaration" of the gsl_matrix struct in file Matrix.hpp
molecule.cpp 44.0 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule.hpp 20.9 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_dynamics.cpp 34.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_fragmentation.cpp 79.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_geometry.cpp 18.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_graph.cpp 65.9 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
molecule_pointcloud.cpp 1.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_template.hpp 14.0 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
moleculelist.cpp 46.2 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
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 ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
parser.hpp 4.8 KB ​ f66195   16 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 14.5 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
periodentafel.hpp 2.1 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
Plane.cpp 6.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Plane.hpp 1.9 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
PointCloud.cpp 320 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
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   17 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
Space.cpp 482 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Space.hpp 1.0 KB ​ ccf826   15 years Till Crueger Removed Vector::mirror() in favour of Plane::mirror()
stackclass.hpp 8.1 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
tesselation.cpp 188.4 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
tesselation.hpp 7.7 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
tesselationhelpers.cpp 39.5 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
tesselationhelpers.hpp 3.6 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
TesselPoint.cpp 585 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
TesselPoint.hpp 495 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
ThermoStatContainer.cpp 1.3 KB ​ 43dad6   15 years FrederikHeber Introducing (but not yet incorporated) FormatParser specializations …
ThermoStatContainer.hpp 859 bytes ​ a3fded   15 years FrederikHeber New class ThermoStatContainer containing all parameters and changes to …
triangleintersectionlist.cpp 6.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
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 …
vector.cpp 12.8 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
vector.hpp 3.3 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
vector_ops.cpp 2.8 KB ​ 3dcb1f   15 years Till Crueger Added two functions to Box class to translate Vectors from Box-Space …
vector_ops.hpp 223 bytes ​ 42a101   15 years Till Crueger Removed RotateVector() function in favor of Line::rotateVector() …
VectorContent.hpp 958 bytes ​ 3dbb9d   15 years Till Crueger Added methods to matrix to create vectors for rows and columns
VectorInterface.cpp 334 bytes ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
VectorInterface.hpp 2.0 KB ​ d74077   15 years FrederikHeber Member variable Vector and element of class atom are now private. - …
VectorSet.hpp 1.7 KB ​ 014475   15 years Till Crueger Made all places use the periodicDistance() and …
verbose.cpp 2.6 KB ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
verbose.hpp 1.4 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
version.h 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
World.cpp 20.7 KB ​ e472eab   15 years FrederikHeber Added new all/none selection actions for atoms and molecules. - new …
World.hpp 12.5 KB ​ e472eab   15 years FrederikHeber Added new all/none selection actions for atoms and molecules. - new …
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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