source: src@ ba9f5b

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 ed6dd8   14 years FrederikHeber FIX: newly parsed-in atoms should always end up in their own molecule …
Descriptors 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
Exceptions 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Helpers 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
Legacy bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
Parser 86cff86   14 years FrederikHeber InputAction now parses all possible formats, not only pcp. - new …
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 b9c847   14 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
unittests 86cff86   14 years FrederikHeber InputAction now parses all possible formats, not only pcp. - new …
analysis_bonds.cpp 11.3 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
analysis_bonds.hpp 1.4 KB ​ bfd839   15 years FrederikHeber Changed and added counting of hydrogen bonds to menu. - …
analysis_correlation.cpp 22.9 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
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 ​ ef7d30   14 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
atom_trajectoryparticle.hpp 2.2 KB ​ ef7d30   14 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
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 50.4 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
boundary.hpp 2.8 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
builder.cpp 7.0 KB ​ b9c847   14 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
CommandLineParser.cpp 3.1 KB ​ 192f6e   14 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 99.1 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 17.0 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
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 5.5 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
helpers.hpp 5.3 KB ​ 0de7e8   15 years FrederikHeber FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: …
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 13.9 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
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 9.0 KB ​ f8be39   14 years wildenhues Fix .git-version rule. * src/Makefile.am ($(srcdir)/.git-version): …
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 46.4 KB ​ 906822   15 years Till Crueger Removed forgotten debug message
molecule.hpp 22.2 KB ​ c27778   14 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_dynamics.cpp 34.5 KB ​ ef7d30   14 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
molecule_fragmentation.cpp 79.2 KB ​ c27778   14 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_geometry.cpp 18.5 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
molecule_graph.cpp 65.8 KB ​ c27778   14 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
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 46.4 KB ​ c27778   14 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
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 ​ 8e0c63   14 years FrederikHeber MEMFIX: MatrixContainer::MatrixContainer() made some initial …
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 232.5 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
tesselation.hpp 16.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
tesselationhelpers.cpp 43.5 KB ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
tesselationhelpers.hpp 4.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
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 ​ bdc91e   14 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
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 18.3 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
vector.hpp 3.6 KB ​ 0c7ed8   15 years Till Crueger Passed the internal gsl_vector structure from Vector to …
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 7.7 KB ​ b9c847   14 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
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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