source: molecuilder/src

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Diff Rev Age Author Log Message
(edit) @aa8542   15 years FrederikHeber BUGFIX: BondGraphUnitTest was not working. Changes: - atoms are now …
(edit) @543ce4   16 years FrederikHeber Huge change from ofstream * (const) out --> Log(). - first shift was …
(edit) @ec70ec   16 years FrederikHeber Merge branch 'CodeRefactoring' of …
(edit) @5f1d021   16 years FrederikHeber Periodic variants of AnalysisPair...() implemented. - BUGFIX: …
(edit) @20895b   16 years FrederikHeber Extension to the periodic boundary case for analysis_correlation.cpp …
(edit) @c1b76e   16 years FrederikHeber config::Load() refactored: Dissection into connected subgraphs -> …
(edit) @e1900f   16 years FrederikHeber Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass …
(edit) @4efdad   16 years FrederikHeber BUGFIX: Allocated one molecule too much in config::Load(). - Count() …
(edit) @a3ffb44   16 years FrederikHeber Closing ticket #47, case 'C' uses biggest molecule as surface for pair …
(edit) @c1b4a4   16 years FrederikHeber "not working parsed molecule into subgraph splitting"-BUG fixed, …
(edit) @08b88b   16 years FrederikHeber Fixing not created adjacency list, partially fixing subgraph …
(edit) @5f9f8b   16 years FrederikHeber Removed libmolecuilder linking from unit tests where only some few …
(edit) @8bc524   16 years FrederikHeber Several memory bugfixes (thx valgrind). - main() - shortened case …
(edit) @df0520   16 years FrederikHeber Small changes. - VolumeOfConvexEnvelope() - setprecision corrected - …
(edit) @245826   16 years FrederikHeber BondGraph is initialized within config::Load(), as it has to happen …
(edit) @b84ab4   16 years FrederikHeber BondGraph is parsed if command line switch '-g' is given. - …
(edit) @96d8dc   16 years Saskia Metzler Ticket 43 Create a logging class The verbosity level can now be …
(edit) @5f697c   16 years FrederikHeber New class BondGraph. - BondGraph parses a file containing bond …
(edit) @bc8155   16 years FrederikHeber Test code is moved to its own source subdirectory: test. - …
(edit) @92fc40   16 years FrederikHeber Added Unit test for StackClass. - was former …
(edit) @dbc152   16 years FrederikHeber Refactored StackClass with respect to tickets #38, #4. - #38 make …
(edit) @6d7651   16 years FrederikHeber Refactored tesselationhelpers.cpp with respect to ticket #38 (make …
(edit) @069034   16 years FrederikHeber class config, ConfigFileBuffer, periodentafel and Vector are …
(edit) @a9b2a0a   16 years FrederikHeber Huge refactoring to make const what is const (ticket #38), continued. …
(edit) @55a71b   16 years FrederikHeber analyzer.cpp and boundary.cpp refactored. - ticket #39 is done with …
(edit) @8b6ee4   16 years FrederikHeber Begun with ticket #4 (shorten constructors) on class atom and class …
(edit) @94d0ad   16 years FrederikHeber Begun with ticket #38 (make const what is const). - basically all …
(edit) @2e6aa1   16 years FrederikHeber ..._CPPFLAGS and ..._LDFLAGS in unittests/Makefile.am put into global …
(edit) @2e2a70   16 years FrederikHeber Refactored atom.cpp into multiple files. After the class atom was …
(edit) @3b0ba2   16 years FrederikHeber iostream was missing in vector includes.
(edit) @6b937bd   16 years FrederikHeber Huge Refactoring: class atom split up into several inherited classes. …
(edit) @99bed3   16 years FrederikHeber Added BFSAccounting and DFSAccounting structures and all functions use …
(edit) @e60069   16 years FrederikHeber Refactored molecule::BuildInducedSubgraph() - new functions …
(edit) @9897787   16 years FrederikHeber Refactored molecule::BreadthFirstSearchAdd() - new function: …
(edit) @312ba2   16 years FrederikHeber Refactored CheckAdjacencyFileAgainstMolecule(). - new functions: …
(edit) @6e250f   16 years FrederikHeber Removed ResetAllAtomNumbers(), replaced by templated SetAtomValueToValue().
(edit) @f444ce   16 years FrederikHeber Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr. …
(edit) @c9f639   16 years FrederikHeber Refactored molecule::CyclicStructureAnalysis() - new functions: …
(edit) @77894f   16 years FrederikHeber Refactored molecule::DepthFirstSearchAnalysis() - new functions: …
(edit) @872b51   16 years FrederikHeber Huge refactoring: molecule::ListOfBondsPerAtom and …
(edit) @b0ee98   16 years FrederikHeber Refactored CreateAdjacencyList(). - new auxiliary functions: …
(edit) @aec775   16 years FrederikHeber Extended class LinkedCell to handle a relative offset to current cell. …
(edit) @bee48d   16 years FrederikHeber Renamed and rewritten CreateAdjacencyList2(). - rename …
(edit) @d70bf6   16 years FrederikHeber Added case 'C' to ParseCommandLineOptions with CorrelationToSurface(). …
(edit) @921097   16 years FrederikHeber Templated version of flip now operates with references instead of …
(edit) @25e34b   16 years FrederikHeber LoadMolecule externalized from Load() - new function …
(edit) @e72287   16 years FrederikHeber Functions to output correlations directly added. - new …
(edit) @543794   16 years FrederikHeber flip() is now templated. Signed-off-by: Frederik Heber …
(edit) @746bb4   16 years FrederikHeber Fixed two memory leaks. - FIX: if the element database could not be …
(edit) @13ecff   16 years FrederikHeber Unit tests AnalysisCorrelation is done. - four carbon atoms were …
(edit) @a2db10   16 years FrederikHeber performCriticalExit() must not be defined static. Note that static …
(edit) @c419f2   16 years FrederikHeber UnitTest AnalysisCorrelationToSurface revealed two bugs: - BUGFIX: if …
(edit) @6f9d14   16 years FrederikHeber Check whether map is not NULL in GetMinMax() and BinData(). …
(edit) @57cfb7   16 years FrederikHeber Pair correlation analysis added. - new file analysis_correlation.cpp …
(edit) @9f73db   16 years FrederikHeber Fixed broken test "Fragmentation - Fragmentation". - BUGFIX: Code was …
(edit) @082da1   16 years FrederikHeber Refactored molecule::FragmentBOSSANOVA(). - renamed functions: …
(edit) @ae65ac   16 years FrederikHeber Refactored molecule::PowerSetGenerator(). - new functions are: …
(edit) @cf4b78   16 years FrederikHeber Rewritten molecule::molecule::SPFragmentGenerator() - new functions …
(edit) @ff9879   16 years FrederikHeber First half of molecule_fragmentation.cpp refactoring. - new template …
(edit) @7c2f6b   16 years FrederikHeber Complete refactoring of molecule_dynamics.cpp - new small functions: …
(edit) @104cf4   16 years FrederikHeber First half of molecule_dynamics.cpp is refactored into smaller parts. …
(edit) @e71890   16 years FrederikHeber Merge branch 'new-delete-conversion' into CodeRefactoring Conflicts: …
(edit) @682229   16 years FrederikHeber Merge branch 'new-delete-conversion' of …
(edit) @3efb4a   16 years FrederikHeber Implementing templated iterators done for molecule.cpp - new …
(edit) @17b3a5c   16 years FrederikHeber forward declarations used to untangle interdependet classes. - …
(edit) @afbb6c0   16 years Saskia Metzler Ticket 30: Put molecuilder unit tests in their own subfolder in src
(edit) @53f32e   16 years Saskia Metzler temp commit
(edit) @70b7aa   16 years FrederikHeber used forward declaration to untangle atom and bond declarations, …
(edit) @972706   16 years FrederikHeber molecule::CountElements() changed to use …
(edit) @0cd3b2   16 years FrederikHeber in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new …
(edit) @567b7f   16 years FrederikHeber In molecule::OutputTrajectories() ActOnAllAtoms() with new function …
(edit) @8ffe32   16 years FrederikHeber More functions of molecule now use templated iterators. - the …
(edit) @a4644b   16 years FrederikHeber Extended the testsuite to encompass the vital areas of molecuilder. - …
(edit) @729279   16 years Saskia Metzler #22 Write a critical exit function
(edit) @f92d00   16 years FrederikHeber class molecule implementation split up into six separate parts. - …
(edit) @3746440   16 years FrederikHeber new function Vector::WrapPeriodically() and …
(edit) @dcbdf2   16 years FrederikHeber New function atom::CorrectFactor() and atom::EqualsFather(). - are …
(edit) @d40b96   16 years FrederikHeber even the class of the member function can be templated, see …
(edit) @4bc937   16 years FrederikHeber Member functions of Vector class may be called while going over an …
(edit) @424d1ce   16 years FrederikHeber Merge branch 'ConvexHull' into ActOnAll Conflicts: …
(edit) @9c32a1   16 years FrederikHeber Included BOOST library MPL into autoconf setup.
(edit) @58808e   16 years FrederikHeber Fixed testsuite, removed some minor bugs. - …
(edit) @8afe31   16 years FrederikHeber Merge branch 'ConcaveHull' into ConvexHull Conflicts: .gitignore …
(edit) @89eff5   16 years FrederikHeber new/delete conversion. mode change only, nothing else.
(edit) @5dda23   16 years FrederikHeber New/delete conversion. 82: "main" missing in msg
(edit) @bf497f   16 years FrederikHeber Merge branch 'ConcaveHull' of …
(edit) @39d983   16 years Saskia Metzler #19 Observe memory usage
(edit) @7794d8   16 years FrederikHeber Merge branch 'ConcaveHull' of …
(edit) @ef36b84   16 years FrederikHeber ActOnAll is a test (not in the molecuilder source tree, but as a …
(edit) @14db08   16 years Saskia Metzler #19 Observe memory usage
(edit) @daf956   16 years FrederikHeber Fixes to the (Non)ConvexTesselation, working with …
(edit) @fca6e7   16 years FrederikHeber FIX of Vector::GetIntersectionWithPlane() - Direction was not …
(edit) @2aea0b   16 years FrederikHeber new tesselation unit test - excluded some more files (mostly ecut and …
(edit) @60cbe5   16 years FrederikHeber Various fixes and attempt to get convex hull working. - …
(edit) @bb56cf   16 years FrederikHeber new function CalculateVolumeofGeneralTetraeder(). - is used when a …
(edit) @01e6c5   16 years FrederikHeber Small fixes. - FIX: atom::~atom(): Name is free'd - config::Load(): …
(edit) @606dfb   16 years FrederikHeber Implemenation of embedding merge, untested. LinearInterpolation now …
(edit) @6f1551   16 years FrederikHeber LinkedCell has another constructor initialised from LinkedNodes (list …
(edit) @f2dfc5   16 years FrederikHeber Added Tesselation unit test - new file tesselationunittest with …
(edit) @390a2b   16 years Saskia Metzler Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free …
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