source: src@ 592ccd

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 Candidate_v1.7.0 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 680470   15 years Till Crueger Fixed some missing return statements
Descriptors 4d72e4   15 years Till Crueger Made the World use the new mixin for sets of atoms
Exceptions 0b0a20   15 years FrederikHeber Inserted all possible queries into MapOfActions. - …
Helpers 097902   15 years Till Crueger Made the Programm dump some memory statistics to a file when an …
Legacy bdc91e   15 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
Parser 839e85   15 years Till Crueger Removed some unecessary opened namespaces
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   16 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
UIElements 680470   15 years Till Crueger Fixed some missing return statements
unittests 997b2a   15 years Till Crueger Added one more complex test to formulatest
analysis_bonds.cpp 11.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
analysis_bonds.hpp 1.4 KB ​ bfd839   15 years FrederikHeber Changed and added counting of hydrogen bonds to menu. - …
analysis_correlation.cpp 21.1 KB ​ e65de8   15 years FrederikHeber Fixed all correlations for new selected sets of molecules. - …
analysis_correlation.hpp 5.3 KB ​ e65de8   15 years FrederikHeber Fixed all correlations for new selected sets of molecules. - …
analyzer.cpp 33.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
atom.cpp 10.2 KB ​ 0ba410   15 years Till Crueger made the molecule::Output() method use STL algorithms
atom.hpp 3.6 KB ​ 0ba410   15 years Till Crueger made the molecule::Output() method use STL algorithms
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   16 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   16 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   16 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   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 ​ 6b919f8   16 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_particleinfo.cpp 831 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_particleinfo.hpp 1006 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_trajectoryparticle.cpp 9.9 KB ​ ef7d30   15 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
atom_trajectoryparticle.hpp 2.2 KB ​ aafd77   15 years Till Crueger Removed all inclusions of GSL-Headers from molecule.hpp
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.
AtomSet.hpp 1.9 KB ​ a33ea5   15 years Till Crueger Added a method to the AtomSetMixin that allows mapping arbitrary …
bond.cpp 3.7 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
bond.hpp 2.0 KB ​ b9947d   16 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bondgraph.cpp 5.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
bondgraph.hpp 1.6 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
boundary.cpp 50.4 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
boundary.hpp 2.8 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
Box.cpp 6.1 KB ​ e1ab97   15 years Till Crueger Added a function that allows fast creation of a cuboid box by giving …
Box.hpp 2.5 KB ​ e1ab97   15 years Till Crueger Added a function that allows fast creation of a cuboid box by giving …
builder.cpp 7.1 KB ​ 097902   15 years Till Crueger Made the Programm dump some memory statistics to a file when an …
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 99.1 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
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 ​ 11e206   15 years Till Crueger Removed multiple definitions of some global constants from executeable
element.cpp 1.9 KB ​ 592ccd   15 years Till Crueger Removed some obsolete fields from element class
element.hpp 1.9 KB ​ 592ccd   15 years Till Crueger Removed some obsolete fields from element class
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 ​ 5108e1   15 years Till Crueger Removed MatrixMultiplication() method from Vector class
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 14.4 KB ​ 426f2a   15 years Till Crueger Added a method to enumerate formulas
Formula.hpp 3.3 KB ​ 426f2a   15 years Till Crueger Added a method to enumerate formulas
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   16 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 6.3 KB ​ d9f51c   15 years Till Crueger Added some basic structures for enumeration of STL containers
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   16 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 1.2 KB ​ 8dc761   15 years Till Crueger Added missing header guards in linearsystemofequations.hpp
linkedcell.cpp 14.0 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
linkedcell.hpp 2.4 KB ​ ffe885   16 years FrederikHeber BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of …
lists.hpp 3.5 KB ​ d3347e   16 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 ​ 839e85   15 years Till Crueger Removed some unecessary opened namespaces
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 10.6 KB ​ 796aa6   15 years Till Crueger Added faster unity build target to makefiles - unity build means a …
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 44.3 KB ​ 7baf4a   15 years Till Crueger Made the molecule::OutputTrajectoriesXYZ() and molecule::OutputXYZ() …
molecule.hpp 22.0 KB ​ 0ba410   15 years Till Crueger made the molecule::Output() method use STL algorithms
molecule_dynamics.cpp 34.5 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
molecule_fragmentation.cpp 79.2 KB ​ c27778   15 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_geometry.cpp 17.9 KB ​ 0632c5   15 years Till Crueger Removed some BOOST_FOREACH iterations and replaced with simpler …
molecule_graph.cpp 65.9 KB ​ c27778   15 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_pointcloud.cpp 1.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_template.hpp 16.3 KB ​ 273382   16 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
moleculelist.cpp 46.2 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
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 14.4 KB ​ 592ccd   15 years Till Crueger Removed some obsolete fields from element class
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
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 232.5 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
tesselation.hpp 16.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
tesselationhelpers.cpp 39.1 KB ​ 797126   15 years Till Crueger Removed two more unused functions
tesselationhelpers.hpp 3.7 KB ​ 08d9595   15 years Till Crueger removed GSL-Headers from tesselationhelpers.hpp
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 ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
triangleintersectionlist.hpp 1.6 KB ​ 8db598   16 years FrederikHeber New class TriangleIntersection List and (hopefully) final fix of …
types.hpp 412 bytes ​ ead4e6   16 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 12.5 KB ​ 9d5ddf   15 years Till Crueger Added constructor and destructor to VectorContent struct
vector.hpp 3.3 KB ​ 8e17d6   15 years Till Crueger Added VectorContent types that allow making vectors from views
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
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   16 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
World.cpp 20.8 KB ​ 6cb9c76   15 years Till Crueger Changed order of destruction in World destructor
World.hpp 12.5 KB ​ 4d72e4   15 years Till Crueger Made the World use the new mixin for sets of atoms
World_calculations.hpp 595 bytes ​ 0e2a47   16 years Till Crueger Added overloaded methods for all methods in the world taking an …
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