source: src@ 05a97c

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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Views 24a5e0   15 years Till Crueger Added -Wall flag and fixed several small hickups
unittests b64313   15 years Till Crueger Improved Observer Framework to include methods to report the state - …
UIElements dbb474   15 years Till Crueger Improved Doxygen documentation
test e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
Patterns c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
Menu 24a5e0   15 years Till Crueger Added -Wall flag and fixed several small hickups
Legacy ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
Helpers 80c63d   15 years Till Crueger Added more functionality to custom asserts. - Asserts allow now …
Descriptors 57adc7   15 years Till Crueger Added methods to query Molecules by ID
Actions dbb474   15 years Till Crueger Improved Doxygen documentation
WorldIterators.cpp 3.6 KB ​ 1c51c8   15 years Till Crueger Added methods for querying molecules using descriptors
World_calculations.hpp 595 bytes ​ 0e2a47   15 years Till Crueger Added overloaded methods for all methods in the world taking an …
World.hpp 9.0 KB ​ 88d586   15 years Till Crueger Added mechanisms that allow reuse of IDs and changing Ids of Atoms
World.cpp 7.0 KB ​ f2bb0f   15 years Till Crueger FIX: Repaired memory smashing in CreateAdjacencyList BROKEN: …
version.h 98 bytes ​ f34def   15 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
verbose.hpp 1.4 KB ​ 89f768   15 years FrederikHeber BUGFIX: Output is again indented, errorLogger prefixes according to …
verbose.cpp 2.2 KB ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
vector.hpp 4.0 KB ​ b84d5d   15 years FrederikHeber FIX: operator implementation of Vector algebra was wrong and caused …
vector.cpp 38.8 KB ​ b84d5d   15 years FrederikHeber FIX: operator implementation of Vector algebra was wrong and caused …
valence.db 1.5 KB ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
tesselationhelpers.hpp 3.8 KB ​ 71b20e   15 years FrederikHeber Attempt to fix the embedding. Basically it would be working, but …
tesselationhelpers.cpp 40.4 KB ​ c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
tesselation.hpp 14.7 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
tesselation.cpp 209.8 KB ​ c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
stackclass.hpp 8.0 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
ReMapDBondFileFromXYZ.py 5.9 KB ​ f683fe   16 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
periodentafel.hpp 1.4 KB ​ fb73b8   15 years FrederikHeber class config, ConfigFileBuffer, periodentafel and Vector are …
periodentafel.cpp 9.9 KB ​ 49e1ae   15 years FrederikHeber cstring header was missing in files, supplying definition of strlen, …
parser.hpp 4.8 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
parser.cpp 47.0 KB ​ 244a84   15 years FrederikHeber GetDistanceToSurface() separated, filling now with water instead of …
orbitals.db 442 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
moleculelist.cpp 46.2 KB ​ ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
molecule_template.hpp 15.9 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
molecule_pointcloud.cpp 1.7 KB ​ c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
molecule_graph.cpp 60.9 KB ​ 05a97c   15 years Till Crueger Replaced some error conditions with ASSERTs
molecule_geometry.cpp 17.8 KB ​ ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
molecule_fragmentation.cpp 78.2 KB ​ ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
molecule_dynamics.cpp 34.8 KB ​ ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
molecule.hpp 22.0 KB ​ c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
molecule.cpp 45.9 KB ​ 05a97c   15 years Till Crueger Replaced some error conditions with ASSERTs
memoryusageobserver.hpp 1.3 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
memoryusageobserver.cpp 2.9 KB ​ 3e50ff   15 years FrederikHeber cstdlib header was missing, necessary for free, malloc and calloc …
memoryallocator.hpp 4.1 KB ​ f2bb0f   15 years Till Crueger FIX: Repaired memory smashing in CreateAdjacencyList BROKEN: …
Makefile.am 5.7 KB ​ 75ac0c   15 years Till Crueger Added custom Assert makro that allows ignoring asserts
logger.hpp 756 bytes ​ 06c7a3   15 years Saskia Metzler Ticket 43 Create a logging class The verbosity level can now be …
logger.cpp 1.7 KB ​ 89f768   15 years FrederikHeber BUGFIX: Output is again indented, errorLogger prefixes according to …
log.hpp 272 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
log.cpp 689 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
lists.hpp 3.5 KB ​ d3347e   15 years Till Crueger FIX: repaired compiler problems for latest refactoring
linkedcell.hpp 2.1 KB ​ 776b64   15 years FrederikHeber Huge refactoring to make const what is const (ticket #38), continued. …
linkedcell.cpp 8.9 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
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 ​ f60610   15 years FrederikHeber Wrapper class for gsl_linalg along with working Unit test. - new …
leastsquaremin.hpp 944 bytes ​ 776b64   15 years FrederikHeber Huge refactoring to make const what is const (ticket #38), continued. …
leastsquaremin.cpp 684 bytes ​ 776b64   15 years FrederikHeber Huge refactoring to make const what is const (ticket #38), continued. …
joiner.cpp 11.4 KB ​ 49e1ae   15 years FrederikHeber cstring header was missing in files, supplying definition of strlen, …
info.hpp 609 bytes ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
info.cpp 693 bytes ​ 8725ed   15 years FrederikHeber New Info class that contains a global verbosity level, increased per …
helpers.hpp 3.2 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
helpers.cpp 7.6 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
Hbonddistance.db 204 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
Hbondangle.db 180 bytes ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
gslvector.hpp 1.1 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
gslvector.cpp 3.6 KB ​ 2793ef   15 years FrederikHeber FIX - GSLVector::Set() return value was double instead of void. …
gslmatrix.hpp 1.4 KB ​ 1f61b6   15 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
gslmatrix.cpp 7.2 KB ​ 93c8ed   15 years FrederikHeber MEMLEAK: mismatched delete/free, matrix in GSLMatrix::Transpose() was …
graph.hpp 2.9 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
graph.cpp 3.7 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
errorlogger.hpp 811 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
errorlogger.cpp 2.3 KB ​ c5f836   15 years FrederikHeber bugfix to errorLogger and some error verbosity changes. - BUGFIX: …
ellipsoid.hpp 1.2 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
ellipsoid.cpp 16.6 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
elements.db 4.4 KB ​ 6ac7ee   16 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
element.hpp 1.9 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
element.cpp 1.6 KB ​ d5af3e   15 years FrederikHeber FIX: constructor of element now is shortened and all its member …
defs.hpp 5.1 KB ​ 7042f45   15 years Till Crueger Changed the type of AtomIds and MoleculeIds to an opaque type
datacreator.hpp 5.0 KB ​ f66195   15 years FrederikHeber forward declarations used to untangle interdependet classes. - …
datacreator.cpp 35.6 KB ​ 1f2217   15 years Till Crueger Small fixes
config.hpp 4.5 KB ​ 235bed   15 years Till Crueger Moved saveConfig method from oldmenu to a method inside config class
config.cpp 104.0 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
builder.cpp 98.0 KB ​ ea7176   15 years Till Crueger FIX: Made AtomCount a Cacheable so that the number of atoms in a …
boundary.hpp 2.8 KB ​ 9473f6   15 years FrederikHeber FillBoxWithMolecule now allows boundary between filler molecules and …
boundary.cpp 50.0 KB ​ c72112   15 years Till Crueger Repaired GetMAxId() method of molecule
bondgraph.hpp 1.4 KB ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
bondgraph.cpp 5.7 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
bond.hpp 2.0 KB ​ b9947d   15 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
bond.cpp 3.6 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
atom_trajectoryparticleinfo.hpp 912 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_trajectoryparticleinfo.cpp 441 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_trajectoryparticle.hpp 2.1 KB ​ b453f9   15 years FrederikHeber Begun with ticket #38 (make const what is const). - basically all …
atom_trajectoryparticle.cpp 9.7 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
atom_particleinfo.hpp 909 bytes ​ 46d958   15 years Till Crueger Made the world solely responsible for creating and destroying atoms.
atom_particleinfo.cpp 682 bytes ​ 24a5e0   15 years Till Crueger Added -Wall flag and fixed several small hickups
atom_graphnodeinfo.hpp 1.4 KB ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_graphnodeinfo.cpp 477 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_graphnode.hpp 846 bytes ​ e138de   15 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
atom_graphnode.cpp 1.0 KB ​ 717e0c   15 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
atom_bondedparticleinfo.hpp 1012 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_bondedparticleinfo.cpp 360 bytes ​ 6b919f8   15 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
atom_bondedparticle.hpp 1.3 KB ​ 1f1b23   15 years FrederikHeber Possibility to store all bonds to file added. So far we only could …
atom_bondedparticle.cpp 5.4 KB ​ 1f1b23   15 years FrederikHeber Possibility to store all bonds to file added. So far we only could …
atom_atominfo.hpp 1011 bytes ​ f16a4b   15 years Till Crueger Added Descriptor that allows querying of atoms by their type
atom_atominfo.cpp 528 bytes ​ f16a4b   15 years Till Crueger Added Descriptor that allows querying of atoms by their type
atom.hpp 3.5 KB ​ 57adc7   15 years Till Crueger Added methods to query Molecules by ID
atom.cpp 9.5 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
analyzer.cpp 33.7 KB ​ 49e1ae   15 years FrederikHeber cstring header was missing in files, supplying definition of strlen, …
analysis_correlation.hpp 5.2 KB ​ 790807   15 years FrederikHeber Output....Correlation() don't prepend header line with '#', BinData() …
analysis_correlation.cpp 18.7 KB ​ 24725c   15 years Till Crueger FIX: repaired PairCorrelation() by using IDs assigned by the world …
analysis_bonds.hpp 820 bytes ​ 220cf37   15 years FrederikHeber Two new bond analysis functions. - GetMaxMinMeanBondCount() - …
analysis_bonds.cpp 2.4 KB ​ 9879f6   15 years FrederikHeber Huge Refactoring due to class molecule now being an STL container. - …
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