source: src@ 389cc8

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
../
unittests 8774c5   15 years Till Crueger Added operator-> for Observed Iterators
UIElements b9c847   15 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
test 273382   16 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 e3d865   15 years Till Crueger Madet the internal iterators provided by the world unobserved
Parser 86cff86   15 years FrederikHeber InputAction now parses all possible formats, not only pcp. - new …
Legacy bdc91e   15 years FrederikHeber MEMFIXES: Tesselation routines were leaking memory. - …
Helpers 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
Exceptions 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
Descriptors 4b6777   15 years Till Crueger Added forgotten include in MoleculePtrDescriptor.cpp
Actions fa0b18   15 years Till Crueger Added Observed and Selectiv iterators over internal Structures of the …
World_calculations.hpp 595 bytes ​ 0e2a47   16 years Till Crueger Added overloaded methods for all methods in the world taking an …
World.hpp 12.2 KB ​ cf0ca1   15 years Till Crueger Added Descriptors that allow description of all Selected molecules
World.cpp 19.5 KB ​ 3839e5   15 years Till Crueger Added iterators over selected atoms and molecules
version.h 98 bytes ​ f34def   16 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
verbose.hpp 1.4 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
verbose.cpp 2.6 KB ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
VectorSet.hpp 1.7 KB ​ 014475   15 years Till Crueger Made all places use the periodicDistance() and …
VectorContent.hpp 958 bytes ​ 3dbb9d   15 years Till Crueger Added methods to matrix to create vectors for rows and columns
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 3.3 KB ​ 8e17d6   15 years Till Crueger Added VectorContent types that allow making vectors from views
vector.cpp 12.5 KB ​ 9d5ddf   15 years Till Crueger Added constructor and destructor to VectorContent struct
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   16 years Till Crueger Made the periodentafel use STL-containers instead of custom llists
triangleintersectionlist.hpp 1.6 KB ​ 8db598   16 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 3.7 KB ​ 08d9595   15 years Till Crueger removed GSL-Headers from tesselationhelpers.hpp
tesselationhelpers.cpp 39.1 KB ​ 797126   15 years Till Crueger Removed two more unused functions
tesselation.hpp 16.1 KB ​ b32dbb   15 years FrederikHeber Fixes and changes to tesselation and concavity measurements. Here, we …
tesselation.cpp 232.5 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   17 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
Plane.hpp 1.9 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
Plane.cpp 6.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
periodentafel.hpp 2.1 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
periodentafel.cpp 14.5 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
parser.hpp 4.8 KB ​ f66195   16 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 46.2 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
molecule_template.hpp 16.3 KB ​ 273382   16 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 65.9 KB ​ c27778   15 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_geometry.cpp 18.0 KB ​ aafd77   15 years Till Crueger Removed all inclusions of GSL-Headers from molecule.hpp
molecule_fragmentation.cpp 79.2 KB ​ c27778   15 years FrederikHeber MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not …
molecule_dynamics.cpp 34.5 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
molecule.hpp 22.0 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
molecule.cpp 44.4 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
MatrixContent.hpp 562 bytes ​ fee079   15 years Till Crueger Added a "forward declaration" of the gsl_matrix struct in file Matrix.hpp
Matrix.hpp 2.9 KB ​ 0eb2dc   15 years Till Crueger Added comparison Operator to matrix class
Matrix.cpp 7.0 KB ​ 0eb2dc   15 years Till Crueger Added comparison Operator to matrix class
Makefile.am 9.6 KB ​ 6f43ab   15 years Till Crueger Added a class that allow simple handling of molecules formulas
logger.hpp 750 bytes ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
logger.cpp 1.5 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
log.hpp 323 bytes ​ 58ed4a   16 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   16 years Till Crueger FIX: repaired compiler problems for latest refactoring
linkedcell.hpp 2.4 KB ​ ffe885   16 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   16 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   16 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   16 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 ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
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 ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
gslvector.cpp 8.0 KB ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
gslmatrix.hpp 1.4 KB ​ 1f61b6   16 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 3.0 KB ​ d4103c8   15 years Till Crueger Removed opening of namespace from molecule.hpp
graph.cpp 3.8 KB ​ 36166d   15 years Till Crueger Removed left over parts from old memory-tracker
Formula.hpp 2.8 KB ​ 6f43ab   15 years Till Crueger Added a class that allow simple handling of molecules formulas
Formula.cpp 7.7 KB ​ 6f43ab   15 years Till Crueger Added a class that allow simple handling of molecules formulas
errorlogger.hpp 805 bytes ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
errorlogger.cpp 2.0 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
ellipsoid.hpp 1.2 KB ​ e138de   16 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 ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
element.cpp 1.7 KB ​ 112b09   15 years Till Crueger Added #include "Helpers/MemDebug.hpp" to all .cpp files
defs.hpp 5.0 KB ​ 127a8e   15 years Till Crueger Improved managing of Ids in the World - Improved algorithm for …
datacreator.hpp 5.0 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
ConfigFileBuffer.hpp 1.1 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
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 99.1 KB ​ 389cc8   15 years Till Crueger Used the formual class instead of single variables inside molecule
CommandLineParser.hpp 6.1 KB ​ 7e6b00   15 years FrederikHeber FIX: Sequence of actions called from command line is now corrected. - …
CommandLineParser.cpp 3.1 KB ​ 192f6e   15 years FrederikHeber FIX: Removed positional action "input". - BUG: This caused that input …
builder.cpp 7.0 KB ​ b9c847   15 years FrederikHeber New SetOutputFormatsAction introduced. Fixes: - World::setDomain() is …
Box.hpp 2.0 KB ​ 7ac4af   15 years Till Crueger Added an optimized version of the Box::explode() method for n=1
Box.cpp 3.1 KB ​ 3bf9e2   15 years Till Crueger Replaced check for Symmetric matrix in Box class with check for …
boundary.hpp 2.8 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
bondgraph.hpp 1.6 KB ​ 986ed3   15 years Till Crueger COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with forwards
bondgraph.cpp 5.9 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 …
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 ​ aafd77   15 years Till Crueger Removed all inclusions of GSL-Headers from molecule.hpp
atom_trajectoryparticle.cpp 9.9 KB ​ ef7d30   15 years FrederikHeber MEMFIX: ForceMatrix in VelocityVerletIntegration had a stupid offset. …
atom_particleinfo.hpp 1006 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_particleinfo.cpp 831 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_graphnodeinfo.cpp 442 bytes ​ 5e8e02   15 years Till Crueger Repaired broken NO_MEMDEBUG build-path
atom_graphnode.hpp 846 bytes ​ e138de   16 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   16 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   16 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 ​ c084cc   15 years Till Crueger Added a method to query the molecule an atom belongs to.
atom.cpp 9.9 KB ​ c084cc   15 years Till Crueger Added a method to query the molecule an atom belongs to.
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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