source: src@ 436f04

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
../
Actions d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
Descriptors 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
Exceptions 325390   15 years Till Crueger Started work on basic matrix class to be used with Vector class
Helpers f0f1cc   15 years Till Crueger Simplified the #ifdef and #define structure in MemDebug.hpp
Legacy 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
Parser 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
Patterns 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
test 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
UIElements daa5f1   15 years Till Crueger Added forgotten include in TextWindow.hpp
unittests 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
analysis_bonds.cpp 11.0 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
analysis_bonds.hpp 1.4 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
analysis_correlation.cpp 22.7 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
analysis_correlation.hpp 5.2 KB ​ c78d44   15 years FrederikHeber Change to PairCorrelation...() functions, accept now vector<element *> …
analyzer.cpp 33.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom.cpp 9.9 KB ​ ad2b411   15 years FrederikHeber atom::getId() should be a const function as it changes nothing in the …
atom.hpp 3.6 KB ​ ad2b411   15 years FrederikHeber atom::getId() should be a const function as it changes nothing in the …
atom_atominfo.cpp 586 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_atominfo.hpp 1.0 KB ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
atom_bondedparticle.cpp 5.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_bondedparticle.hpp 1.3 KB ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
atom_bondedparticleinfo.cpp 393 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_bondedparticleinfo.hpp 1012 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
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   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnodeinfo.cpp 479 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_graphnodeinfo.hpp 1.4 KB ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_particleinfo.cpp 841 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_particleinfo.hpp 990 bytes ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_trajectoryparticle.cpp 9.9 KB ​ a3fded   15 years FrederikHeber New class ThermoStatContainer containing all parameters and changes to …
atom_trajectoryparticle.hpp 2.1 KB ​ b453f9   15 years FrederikHeber Begun with ticket #38 (make const what is const). - basically all …
atom_trajectoryparticleinfo.cpp 474 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_trajectoryparticleinfo.hpp 973 bytes ​ cb16fe   15 years Till Crueger Added a mixin that allows specifying methods for complete sets of vectors.
bond.cpp 3.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 5.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
bondgraph.hpp 1.6 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
boundary.cpp 50.0 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
boundary.hpp 2.8 KB ​ 775d133   15 years FrederikHeber Filling has a MaxDistance, somes changes to the Correlation Analysis. …
builder.cpp 6.5 KB ​ 326bbe   15 years FrederikHeber Legacy/oldmenu is no more. - TextWindow::TextWindow() now properly …
CommandLineParser.cpp 3.4 KB ​ 4f7f34e   15 years FrederikHeber ParseCommandLineOptions() is not used anymore. - new Actions …
CommandLineParser.hpp 2.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
config.cpp 99.1 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
config.hpp 4.0 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
ConfigFileBuffer.cpp 5.3 KB ​ 1b2d30   15 years FrederikHeber Extended PcpParser, completed MpqcParser. - BUGFIX: …
ConfigFileBuffer.hpp 1.1 KB ​ 43dad6   15 years FrederikHeber Introducing (but not yet incorporated) FormatParser specializations …
datacreator.cpp 35.8 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
datacreator.hpp 5.0 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
defs.hpp 4.9 KB ​ b48ba6   15 years FrederikHeber Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered …
element.cpp 1.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
element.hpp 2.0 KB ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
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 ​ c94eeb   15 years Till Crueger Replaced several double* that were used as Matrixes with actuall …
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
errorlogger.cpp 1.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
errorlogger.hpp 807 bytes ​ ed58ad   15 years Till Crueger Made the errorLogger use the new Singleton framework
graph.cpp 3.8 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
graph.hpp 2.9 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
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 7.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
gslvector.hpp 1.9 KB ​ 0c7ed8   15 years Till Crueger Passed the internal gsl_vector structure from Vector to …
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 ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
helpers.hpp 5.2 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
info.cpp 754 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
info.hpp 609 bytes ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
joiner.cpp 11.6 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
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 6.3 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Line.hpp 964 bytes ​ 5589858   15 years Till Crueger Added methods to construct orthogonal planes from lines and vice versa
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 14.0 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
linkedcell.hpp 2.4 KB ​ ffe885   15 years FrederikHeber BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of …
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 1.4 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
logger.hpp 752 bytes ​ aee1a3   15 years Till Crueger Made logger class use the new Singleton framework
Makefile.am 7.0 KB ​ 325390   15 years Till Crueger Started work on basic matrix class to be used with Vector class
Matrix.cpp 4.3 KB ​ 436f04   15 years Till Crueger Added a method that allows faster setting of matrix elements using …
Matrix.hpp 1.1 KB ​ 436f04   15 years Till Crueger Added a method that allows faster setting of matrix elements using …
memoryallocator.cpp 988 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
memoryallocator.hpp 4.1 KB ​ f2bb0f   15 years Till Crueger FIX: Repaired memory smashing in CreateAdjacencyList BROKEN: …
memoryusageobserver.cpp 2.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
memoryusageobserver.hpp 1.3 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
molecule.cpp 46.3 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
molecule.hpp 22.3 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
molecule_dynamics.cpp 34.7 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
molecule_fragmentation.cpp 79.0 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
molecule_geometry.cpp 18.3 KB ​ d10eb6   15 years Till Crueger Made the ReturnFullMatrixForSymmetric return a Matrix object directely …
molecule_graph.cpp 65.7 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
molecule_pointcloud.cpp 1.8 KB ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
molecule_template.hpp 16.3 KB ​ 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
moleculelist.cpp 47.4 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
parser.cpp 45.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 15.3 KB ​ f34c23   15 years FrederikHeber MEMFIX: Periodentafel constructor would instantiate stringstreams in …
periodentafel.hpp 2.1 KB ​ 61745cc   15 years FrederikHeber BUGFIX: LoadPeriodentafel() did not close files and elements have to …
Plane.cpp 6.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Plane.hpp 1.9 KB ​ 27ac00   15 years Till Crueger Made the line-plane intersection method take a line instead of two vectors
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 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 ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
tesselation.cpp 230.2 KB ​ 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
tesselation.hpp 15.9 KB ​ 8f215d   15 years Till Crueger Simplified tesselation.cpp by allowing direct access to derived …
tesselationhelpers.cpp 40.2 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
tesselationhelpers.hpp 3.8 KB ​ 71b20e   15 years FrederikHeber Attempt to fix the embedding. Basically it would be working, but …
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 6.2 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
triangleintersectionlist.hpp 1.6 KB ​ 8db598   15 years FrederikHeber New class TriangleIntersection List and (hopefully) final fix of …
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 16.7 KB ​ 63d2b8   15 years Till Crueger Removed unused Vector::KeepPeriodic() method.
vector.hpp 3.7 KB ​ 63d2b8   15 years Till Crueger Removed unused Vector::KeepPeriodic() method.
vector_ops.cpp 2.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
vector_ops.hpp 223 bytes ​ 42a101   15 years Till Crueger Removed RotateVector() function in favor of Line::rotateVector() …
VectorSet.cpp 246 bytes ​ cb16fe   15 years Till Crueger Added a mixin that allows specifying methods for complete sets of vectors.
VectorSet.hpp 1.1 KB ​ cb16fe   15 years Till Crueger Added a mixin that allows specifying methods for complete sets of vectors.
verbose.cpp 2.5 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
verbose.hpp 1.4 KB ​ 90f680   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
version.h 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
World.cpp 7.5 KB ​ 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
World.hpp 8.5 KB ​ 43dad6   15 years FrederikHeber Introducing (but not yet incorporated) FormatParser specializations …
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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