source: src@ 36166d

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
../
unittests 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
UIElements 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
test 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
Shapes 205d9b   15 years Till Crueger Added missing const to Shape::isInside() method
Patterns 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
Parser 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Legacy 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
Helpers f0f1cc   15 years Till Crueger Simplified the #ifdef and #define structure in MemDebug.hpp
Exceptions 325390   15 years Till Crueger Started work on basic matrix class to be used with Vector class
Descriptors 6d574a   15 years Till Crueger Replaced several old-style asserts with more usable ASSERTs
Actions 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
World_calculations.hpp 595 bytes ​ 0e2a47   15 years Till Crueger Added overloaded methods for all methods in the world taking an …
World.hpp 8.6 KB ​ 84c494   15 years Till Crueger Made the world store the cell_size within a Box object.
World.cpp 7.6 KB ​ 84c494   15 years Till Crueger Made the world store the cell_size within a Box object.
version.h 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
verbose.hpp 1.4 KB ​ 90f680   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
verbose.cpp 2.5 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
VectorSet.hpp 1.7 KB ​ 014475   15 years Till Crueger Made all places use the periodicDistance() and …
VectorSet.cpp 246 bytes ​ cb16fe   15 years Till Crueger Added a mixin that allows specifying methods for complete sets of vectors.
vector_ops.hpp 223 bytes ​ 42a101   15 years Till Crueger Removed RotateVector() function in favor of Line::rotateVector() …
vector_ops.cpp 2.8 KB ​ 3dcb1f   15 years Till Crueger Added two functions to Box class to translate Vectors from Box-Space …
vector.hpp 3.2 KB ​ 4b94bb   15 years Till Crueger Moved Vector-Matrix operations to matrix class
vector.cpp 12.4 KB ​ 4b94bb   15 years Till Crueger Moved Vector-Matrix operations to matrix class
valence.db 1.6 KB ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
types.hpp 412 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
triangleintersectionlist.hpp 1.6 KB ​ 8db598   15 years FrederikHeber New class TriangleIntersection List and (hopefully) final fix of …
triangleintersectionlist.cpp 6.2 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
ThermoStatContainer.hpp 859 bytes ​ a3fded   15 years FrederikHeber New class ThermoStatContainer containing all parameters and changes to …
ThermoStatContainer.cpp 1.3 KB ​ 43dad6   15 years FrederikHeber Introducing (but not yet incorporated) FormatParser specializations …
tesselationhelpers.hpp 4.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
tesselationhelpers.cpp 43.5 KB ​ 24c35a   15 years FrederikHeber Removed unused variables. Signed-off-by: Frederik Heber …
tesselation.hpp 16.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
tesselation.cpp 232.4 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
stackclass.hpp 8.1 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Space.hpp 1.0 KB ​ ccf826   15 years Till Crueger Removed Vector::mirror() in favour of Plane::mirror()
Space.cpp 482 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
Plane.hpp 1.9 KB ​ 27ac00   15 years Till Crueger Made the line-plane intersection method take a line instead of two vectors
Plane.cpp 6.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
periodentafel.hpp 2.1 KB ​ 61745cc   15 years FrederikHeber BUGFIX: LoadPeriodentafel() did not close files and elements have to …
periodentafel.cpp 15.3 KB ​ f34c23   15 years FrederikHeber MEMFIX: Periodentafel constructor would instantiate stringstreams in …
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
parser.cpp 46.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
orbitals.db 474 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
moleculelist.cpp 47.2 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_template.hpp 16.3 KB ​ 273382   15 years Till Crueger Prepared interface of Vector Class for transition to VectorComposites
molecule_pointcloud.cpp 1.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_graph.cpp 65.7 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_geometry.cpp 17.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_fragmentation.cpp 78.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule_dynamics.cpp 34.5 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule.hpp 22.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
molecule.cpp 46.1 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Matrix.hpp 2.3 KB ​ cd82ec   15 years Till Crueger Improved comments of matrix class
Matrix.cpp 5.0 KB ​ 4b94bb   15 years Till Crueger Moved Vector-Matrix operations to matrix class
Makefile.am 9.3 KB ​ 456341   15 years Till Crueger Moved all Exceptions and Matrix class from LinAlg module back to main …
logger.hpp 752 bytes ​ aee1a3   15 years Till Crueger Made logger class use the new Singleton framework
logger.cpp 1.4 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. - …
log.cpp 1.5 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
linkedcell.hpp 2.4 KB ​ ffe885   15 years FrederikHeber BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of …
linkedcell.cpp 14.0 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
linearsystemofequations.hpp 1.1 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
linearsystemofequations.cpp 3.6 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
Line.hpp 1019 bytes ​ f932b7   15 years Till Crueger Added a method to calculate the intersection of a line with the unit sphere
Line.cpp 6.8 KB ​ f932b7   15 years Till Crueger Added a method to calculate the intersection of a line with the unit sphere
leastsquaremin.hpp 950 bytes ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
leastsquaremin.cpp 719 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
joiner.cpp 11.6 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
info.hpp 609 bytes ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
info.cpp 754 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
helpers.hpp 5.2 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
helpers.cpp 4.0 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Hbonddistance.db 282 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
Hbondangle.db 251 bytes ​ 274d45   15 years FrederikHeber FIX: Atoms were stored not in the sequence they were loaded. 1. The …
gslvector.hpp 1.9 KB ​ 0c7ed8   15 years Till Crueger Passed the internal gsl_vector structure from Vector to …
gslvector.cpp 7.9 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 …
gslmatrix.cpp 7.3 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 …
graph.cpp 3.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
errorlogger.hpp 807 bytes ​ ed58ad   15 years Till Crueger Made the errorLogger use the new Singleton framework
errorlogger.cpp 1.9 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 …
ellipsoid.cpp 17.0 KB ​ 5108e1   15 years Till Crueger Removed MatrixMultiplication() method from Vector class
elements_db.hpp 322 bytes ​ 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 4.1 KB ​ 4eb4fe   15 years FrederikHeber "-e <db path>" not necessary anymore. Removed necessity of specifying …
element.hpp 2.0 KB ​ ead4e6   15 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
element.cpp 1.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
defs.hpp 4.9 KB ​ b48ba6   15 years FrederikHeber Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered …
datacreator.hpp 5.0 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
datacreator.cpp 35.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
ConfigFileBuffer.hpp 1.1 KB ​ 43dad6   15 years FrederikHeber Introducing (but not yet incorporated) FormatParser specializations …
ConfigFileBuffer.cpp 5.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
config.hpp 4.0 KB ​ 35b698   15 years FrederikHeber BIG CHANGE: config::load and config::save in ParseCommandLineOptions() …
config.cpp 99.2 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
CommandLineParser.hpp 6.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
CommandLineParser.cpp 3.4 KB ​ 4f7f34e   15 years FrederikHeber ParseCommandLineOptions() is not used anymore. - new Actions …
builder.cpp 7.1 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Box.hpp 2.0 KB ​ 7ac4af   15 years Till Crueger Added an optimized version of the Box::explode() method for n=1
Box.cpp 3.3 KB ​ 7ac4af   15 years Till Crueger Added an optimized version of the Box::explode() method for n=1
boundary.hpp 2.8 KB ​ 775d133   15 years FrederikHeber Filling has a MaxDistance, somes changes to the Correlation Analysis. …
boundary.cpp 50.0 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
bondgraph.hpp 1.6 KB ​ 97ebf8   15 years FrederikHeber Added all commands defined in ParseCommandLineOptions() as Actions. - …
bondgraph.cpp 5.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bond.cpp 3.7 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
atom_trajectoryparticleinfo.hpp 973 bytes ​ cb16fe   15 years Till Crueger Added a mixin that allows specifying methods for complete sets of vectors.
atom_trajectoryparticleinfo.cpp 474 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom_trajectoryparticle.hpp 2.2 KB ​ ef7d30   15 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
atom_trajectoryparticle.cpp 9.9 KB ​ ef7d30   15 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
atom_particleinfo.hpp 990 bytes ​ 68f03d   15 years Till Crueger FIX: Memory corruption in particleInfo class
atom_particleinfo.cpp 810 bytes ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
atom_graphnodeinfo.hpp 1.4 KB ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_graphnodeinfo.cpp 448 bytes ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
atom_graphnode.hpp 846 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnode.cpp 1.1 KB ​ 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_bondedparticleinfo.cpp 393 bytes ​ 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_bondedparticle.cpp 5.9 KB ​ 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_atominfo.cpp 586 bytes ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
atom.hpp 3.6 KB ​ c550dd   15 years Till Crueger Removed the VectorIsInParallelepiped in favor of more general methods …
atom.cpp 9.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
analyzer.cpp 33.9 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
analysis_correlation.hpp 5.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
analysis_correlation.cpp 22.4 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_bonds.cpp 11.3 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
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