source: src@ 6670a97

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 6670a97   15 years FrederikHeber Change to testsuite as verbosity is now defined as (-v 3) not as …
Descriptors 6e97e5   15 years Till Crueger Added a generic Iterator that can be used to iterate only over certain …
Exceptions 3cdd16   15 years Till Crueger Added more Exceptions to the project to signal differen Math erorrs
Helpers 28c351   15 years FrederikHeber FIX: strncpy was lacking cstring include.
Legacy 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
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 5079a0   15 years FrederikHeber Actions put into libMolecuilderActions, UIElements into …
unittests 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
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 19.3 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
analysis_correlation.hpp 5.2 KB ​ 58ed4a   15 years FrederikHeber Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - …
analyzer.cpp 33.9 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
atom.cpp 9.4 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
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 ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
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 ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
atom_graphnode.hpp 846 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnodeinfo.cpp 477 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_graphnodeinfo.hpp 1.4 KB ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_particleinfo.cpp 833 bytes ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
atom_particleinfo.hpp 909 bytes ​ 46d958   15 years Till Crueger Made the world solely responsible for creating and destroying atoms.
atom_trajectoryparticle.cpp 9.7 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
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 ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 5.9 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
bondgraph.hpp 1.6 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
boundary.cpp 50.8 KB ​ b5c2d7   15 years FrederikHeber Don't exit when no starting triangle has been found. - The issue is …
boundary.hpp 2.8 KB ​ 775d133   15 years FrederikHeber Filling has a MaxDistance, somes changes to the Correlation Analysis. …
builder.cpp 115.7 KB ​ eff648   15 years FrederikHeber BUGFIX: In ParseCommandLineOptions() -v and -V were mixed. - …
CommandLineParser.cpp 1.8 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
CommandLineParser.hpp 1.7 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
config.cpp 106.4 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
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 6.7 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
helpers.hpp 5.4 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
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 ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
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.cpp 412 bytes ​ 46d958   15 years Till Crueger Made the world solely responsible for creating and destroying atoms.
lists.hpp 4.1 KB ​ 46d958   15 years Till Crueger Made the world solely responsible for creating and destroying atoms.
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 6.6 KB ​ 5079a0   15 years FrederikHeber Actions put into libMolecuilderActions, UIElements into …
memoryallocator.hpp 4.1 KB ​ 3e50ff   15 years FrederikHeber cstdlib header was missing, necessary for free, malloc and calloc …
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 46.2 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
molecule.hpp 21.4 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
molecule_dynamics.cpp 34.6 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
molecule_fragmentation.cpp 78.1 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
molecule_geometry.cpp 17.6 KB ​ 673c7f   15 years FrederikHeber BUGFIX: molecule::DetermineCenterOfAll() was broken for single atom. …
molecule_graph.cpp 62.8 KB ​ e5ad5c   15 years FrederikHeber BUGFIX: BondGraphUnitTest was not working. Changes: - atoms are now …
molecule_pointcloud.cpp 2.1 KB ​ 71b20e   15 years FrederikHeber Attempt to fix the embedding. Basically it would be working, but …
molecule_template.hpp 16.8 KB ​ 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
moleculelist.cpp 48.2 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
orbitals.db 442 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
parser.cpp 47.5 KB ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
periodentafel.cpp 13.5 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
periodentafel.hpp 2.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
Plane.cpp 6.8 KB ​ fa5a6a   15 years Till Crueger Added unittests for planes
Plane.hpp 1.6 KB ​ fa5a6a   15 years Till Crueger Added unittests for planes
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 ​ a67d19   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
tesselation.cpp 230.1 KB ​ b8d4a3   15 years Saskia Metzler Tremolo format parser
tesselation.hpp 16.0 KB ​ ce70970   15 years FrederikHeber FIX: Tesselation::FindStartingTriangle() returns false when no …
tesselationhelpers.cpp 40.0 KB ​ 1513a74   15 years Till Crueger Declared the Vector class as single point spaces
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 ​ fa5a6a   15 years Till Crueger Added unittests for planes
vector.hpp 3.7 KB ​ fa5a6a   15 years Till Crueger Added unittests for planes
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 7.2 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
World.hpp 8.2 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
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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