source: src@ f6bd32

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 f6bd32   15 years FrederikHeber Case 'o' is now handled by CommandLineUI. - As of now, multiple …
Descriptors 31b09e   15 years FrederikHeber Added new MoleculeDescriptor by name. - molecule Ids are rather …
Exceptions 3cdd16   15 years Till Crueger Added more Exceptions to the project to signal differen Math erorrs
Helpers f2f4ae   15 years Till Crueger Made the memory debugger thread safe
Legacy 104524   15 years FrederikHeber Changed PairCorrelationAction to incorporate all three cases and …
Parser 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
Patterns 033a05   15 years Till Crueger Small improvements to Observer code
test 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
UIElements 77b2d7   15 years FrederikHeber Cases 't' and 'T' are now handled by CommandLineUI. - TESTFIX: both …
unittests c78d44   15 years FrederikHeber Change to PairCorrelation...() functions, accept now vector<element *> …
analysis_bonds.cpp 11.0 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
analysis_bonds.hpp 1.4 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
analysis_correlation.cpp 22.9 KB ​ 58bbd3   15 years FrederikHeber Cases 'C' are now handled by CommandLineUI. - TESTFIX: …
analysis_correlation.hpp 5.2 KB ​ c78d44   15 years FrederikHeber Change to PairCorrelation...() functions, accept now vector<element *> …
analyzer.cpp 33.9 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
atom.cpp 9.4 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
atom.hpp 3.6 KB ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
atom_atominfo.cpp 553 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
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 ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_bondedparticle.hpp 1.3 KB ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
atom_bondedparticleinfo.cpp 360 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
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 ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_graphnode.hpp 846 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnodeinfo.cpp 446 bytes ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
atom_graphnodeinfo.hpp 1.4 KB ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_particleinfo.cpp 808 bytes ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_particleinfo.hpp 990 bytes ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_trajectoryparticle.cpp 9.7 KB ​ c7a473   15 years FrederikHeber Added cased '-P' (force integration) to testsuite. - this is …
atom_trajectoryparticle.hpp 2.1 KB ​ b453f9   15 years FrederikHeber Begun with ticket #38 (make const what is const). - basically all …
atom_trajectoryparticleinfo.cpp 441 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_trajectoryparticleinfo.hpp 912 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
bond.cpp 3.6 KB ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 5.8 KB ​ bd6bfa   15 years FrederikHeber Fixes after first,last removal. - BUGFIX: …
bondgraph.hpp 1.6 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
boundary.cpp 50.0 KB ​ accebe   15 years FrederikHeber Fix of PrepareClustersInWater (at least it does not stumble over …
boundary.hpp 2.8 KB ​ 775d133   15 years FrederikHeber Filling has a MaxDistance, somes changes to the Correlation Analysis. …
builder.cpp 94.8 KB ​ f6bd32   15 years FrederikHeber Case 'o' is now handled by CommandLineUI. - As of now, multiple …
CommandLineParser.cpp 3.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
CommandLineParser.hpp 2.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
config.cpp 105.6 KB ​ 42af9e   15 years FrederikHeber MEMFIXES: no more default saving/loading of element's db, …
config.hpp 4.5 KB ​ 235bed   15 years Till Crueger Moved saveConfig method from oldmenu to a method inside config class
datacreator.cpp 35.8 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
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 ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
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 ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
elements_db.hpp 322 bytes ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
ellipsoid.cpp 16.9 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
errorlogger.cpp 1.9 KB ​ 90f680   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
errorlogger.hpp 807 bytes ​ ed58ad   15 years Till Crueger Made the errorLogger use the new Singleton framework
graph.cpp 3.8 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
graph.hpp 2.9 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
gslmatrix.cpp 7.2 KB ​ 0a4f7f   15 years Till Crueger Made data internal data-structure of vector class private - Replaced …
gslmatrix.hpp 1.4 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
gslvector.cpp 7.7 KB ​ b11d3b   15 years FrederikHeber Added operators and state checkers to GSLVector. - added operators …
gslvector.hpp 1.8 KB ​ b11d3b   15 years FrederikHeber Added operators and state checkers to GSLVector. - added operators …
Hbondangle.db 180 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
Hbonddistance.db 204 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
helpers.cpp 5.4 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
helpers.hpp 5.3 KB ​ 0de7e8   15 years FrederikHeber FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: …
info.cpp 721 bytes ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
info.hpp 609 bytes ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
joiner.cpp 11.6 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
leastsquaremin.cpp 686 bytes ​ 0a4f7f   15 years Till Crueger Made data internal data-structure of vector class private - Replaced …
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
Line.cpp 632 bytes ​ 6f646d   15 years Till Crueger Added a line class that represents one dimensional subspaces
Line.hpp 493 bytes ​ 6f646d   15 years Till Crueger Added a line class that represents one dimensional subspaces
linearsystemofequations.cpp 3.6 KB ​ 0a4f7f   15 years Till Crueger Made data internal data-structure of vector class private - Replaced …
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 ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
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 1.4 KB ​ 90f680   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
log.hpp 323 bytes ​ 58ed4a   15 years FrederikHeber Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - …
logger.cpp 1.4 KB ​ aee1a3   15 years Till Crueger Made logger class use the new Singleton framework
logger.hpp 752 bytes ​ aee1a3   15 years Till Crueger Made logger class use the new Singleton framework
Makefile.am 6.9 KB ​ 31b09e   15 years FrederikHeber Added new MoleculeDescriptor by name. - molecule Ids are rather …
memoryallocator.cpp 955 bytes ​ a844d8   55 years (none)
memoryallocator.hpp 4.1 KB ​ f2bb0f   15 years Till Crueger FIX: Repaired memory smashing in CreateAdjacencyList BROKEN: …
memoryusageobserver.cpp 2.9 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
memoryusageobserver.hpp 1.3 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
molecule.cpp 46.9 KB ​ 387b36   15 years FrederikHeber Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() …
molecule.hpp 22.3 KB ​ bd6bfa   15 years FrederikHeber Fixes after first,last removal. - BUGFIX: …
molecule_dynamics.cpp 34.6 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
molecule_fragmentation.cpp 79.5 KB ​ 0de7e8   15 years FrederikHeber FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: …
molecule_geometry.cpp 18.3 KB ​ 7fd416   15 years FrederikHeber FIX: CorrelationToSurface() was broken. - DOCU: …
molecule_graph.cpp 65.7 KB ​ 0de7e8   15 years FrederikHeber FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: …
molecule_pointcloud.cpp 1.5 KB ​ 6ef0a4   15 years FrederikHeber Removed Info objects from the small pointcloud implementation …
molecule_template.hpp 16.3 KB ​ 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
moleculelist.cpp 47.3 KB ​ 58bbd3   15 years FrederikHeber Cases 'C' are now handled by CommandLineUI. - TESTFIX: …
orbitals.db 442 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
parser.cpp 45.7 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 15.1 KB ​ 61745cc   15 years FrederikHeber BUGFIX: LoadPeriodentafel() did not close files and elements have to …
periodentafel.hpp 2.1 KB ​ 61745cc   15 years FrederikHeber BUGFIX: LoadPeriodentafel() did not close files and elements have to …
Plane.cpp 7.0 KB ​ d4c9ae   15 years Till Crueger Removed the DistanceToPlane method in the Vector class in favor of a …
Plane.hpp 1.6 KB ​ d4c9ae   15 years Till Crueger Removed the DistanceToPlane method in the Vector class in favor of a …
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 317 bytes ​ 005e18   15 years Till Crueger Added const correctness to plane class and simplified interface
Space.hpp 420 bytes ​ 005e18   15 years Till Crueger Added const correctness to plane class and simplified interface
stackclass.hpp 8.1 KB ​ 920c70   15 years FrederikHeber Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and …
tesselation.cpp 230.4 KB ​ accebe   15 years FrederikHeber Fix of PrepareClustersInWater (at least it does not stumble over …
tesselation.hpp 15.9 KB ​ 8f215d   15 years Till Crueger Simplified tesselation.cpp by allowing direct access to derived …
tesselationhelpers.cpp 40.2 KB ​ 15b670   15 years FrederikHeber Testfixes for Tesselations/1-3 and bugfixes for …
tesselationhelpers.hpp 3.8 KB ​ 71b20e   15 years FrederikHeber Attempt to fix the embedding. Basically it would be working, but …
triangleintersectionlist.cpp 6.1 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
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 1.5 KB ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
vector.cpp 18.7 KB ​ eddea2   15 years FrederikHeber Added case '-T' (periodic translation) to testsuite. - BUGFIX: …
vector.hpp 3.7 KB ​ d4c9ae   15 years Till Crueger Removed the DistanceToPlane method in the Vector class in favor of a …
vector_ops.cpp 6.9 KB ​ fa5a6a   15 years Till Crueger Added unittests for planes
vector_ops.hpp 431 bytes ​ 0a4f7f   15 years Till Crueger Made data internal data-structure of vector class private - Replaced …
verbose.cpp 2.5 KB ​ 90f680   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
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 7.1 KB ​ 387b36   15 years FrederikHeber Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() …
World.hpp 8.3 KB ​ 387b36   15 years FrederikHeber Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() …
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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