source: molecuilder/src

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Diff Rev Age Author Log Message
(edit) @328418d   16 years FrederikHeber BUGFIX: MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() - …
(edit) @a83171   16 years FrederikHeber Default molecule name can be set via command line, BUGFIX: …
(edit) @bd506d   16 years FrederikHeber BUGFIX: FillBoxWithMolecule() - bonds were added after adding of each …
(edit) @9565ec   16 years FrederikHeber singleton class World introduced, contains only cell_size from class …
(edit) @9f03b2   16 years FrederikHeber FIX: allowing empty config files, and filling can deal with no …
(edit) @e49719   16 years FrederikHeber ManipulateAtoms() can turn atoms around bonds again, in …
(edit) @f7b476   16 years FrederikHeber New class TriangleIntersection List and (hopefully) final fix of …
(edit) @075d08   16 years FrederikHeber Bigger change to FillBoxWithMolecule(). - BUG: Position check was …
(edit) @978bcd   16 years FrederikHeber FIX: ParseCommandLineOptions - case 'C' used wrong LC width, case 'F' …
(edit) @c0c33f   16 years FrederikHeber Added Vector Copy constructors, Vector::GetDistanceVectorToPlane() and …
(edit) @b1d8ab5   16 years FrederikHeber Added operators and state checkers to GSLVector. - added operators …
(edit) @850e50   16 years FrederikHeber Filling has a MaxDistance, somes changes to the Correlation Analysis. …
(edit) @2bc06b   16 years FrederikHeber changed case 'C' of ParseCommandLineOptions to allow selecting between …
(edit) @6d0fcaa   16 years FrederikHeber Possibility to store all bonds to file added. So far we only could …
(edit) @1c7aed   16 years FrederikHeber Output....Correlation() don't prepend header line with '#', BinData() …
(edit) @14c0f0   16 years FrederikHeber FIX: FillBoxWithMolecule() - seed of random number generator was not …
(edit) @8d0b25   16 years FrederikHeber Added output of surfacemap in ParseCommandLineOptions(), case 'C' again.
(edit) @478683   16 years FrederikHeber GetDistanceToSurface() separated, filling now with water instead of …
(edit) @551a58   16 years FrederikHeber Merge branch 'FixVersioning3' into Analysis_PairCorrelation Tesselation-DistanceToSurface_WORKING
(edit) @0af58f   16 years FrederikHeber Fixed versioning. - FIX: version.h was falsely excluded in .gitignore …
(edit) @591f15   16 years FrederikHeber BUGFIX: Tesselation::IsInnerPoint() returned wrong result. - We …
(edit) @a922f3   16 years FrederikHeber Merge branch 'FixTemplatedMinMax' into FixFillingWithMolecule
(edit) @1ec554   16 years FrederikHeber Rather use parameter passing by value instead of reference. - We …
(edit) @a34fab   16 years FrederikHeber Unit test for BoundaryTriangleSet member functions added. - for now …
(edit) @1aa2a5   16 years FrederikHeber FillBoxWithMolecule now allows boundary between filler molecules and …
(edit) @252790   16 years FrederikHeber Changed verbosity for Vector::GetIntersectionWithPlane(). - when line …
(edit) @249522   16 years FrederikHeber FillWithMolecule() is now working correctly. - FillWithMolecule() …
(edit) @3dea05   16 years FrederikHeber Templated Min and Max functions added. Signed-off-by: Frederik Heber …
(edit) @8a34e69   16 years FrederikHeber Boolean return value of Tesselation::IsInnerPoint in …
(edit) @49d3e1e   16 years FrederikHeber Small fixes to make checks working again. - Tesselations tests 13 and …
(edit) @afa056   16 years FrederikHeber Removed unnecessary epsilon parameter. - epsilon before was used as a …
(edit) @91b1e79   16 years FrederikHeber Fixed Tesselation::IsInnerPoint() - Both unit tests …
(edit) @d403a1   16 years FrederikHeber InsideOutside unit test of tesselation is working correctly. - FIX: …
(edit) @23f6ec   16 years FrederikHeber BUGFIX - Test was wrong in upper bounds of inside area. - upper …
(edit) @9291f85   16 years FrederikHeber Added Determinant() function to class GSLMatrix. - new function …
(edit) @7b991d   16 years FrederikHeber FIX - GSLVector::Set() return value was double instead of void. …
(edit) @ac6b65   16 years FrederikHeber Vector::GetIntersectionOfTwoLinesOnPlane() rewritten. Use routine …
(edit) @901774   16 years FrederikHeber libgslwrapper.a added to LDADD of most tests. Since Vector class uses …
(edit) @51a8a1   16 years FrederikHeber BUGFIX - GetCenterOfSphere(): condition were not put correctly in …
(edit) @00b5802   16 years FrederikHeber BUGFIX - molecule::MinimiseConstrainedPotential() OldPotential was …
(edit) @70e11d   16 years FrederikHeber Inclusion of config.h was missing. This caused a bug with GSL's …
(edit) @2c69a9   16 years FrederikHeber cstdlib header was missing, necessary for free, malloc and calloc …
(edit) @e6fe8a   16 years FrederikHeber cstring header was missing in files, supplying definition of strlen, …
(edit) @247d49   16 years FrederikHeber Wrapper class for gsl_linalg along with working Unit test. - new …
(edit) @e651e7   16 years FrederikHeber Wrapper class for gsl_matrix along with working Unit test. - new …
(edit) @22b47e   16 years FrederikHeber Wrapper class for gsl_vector along with working Unit test. - new …
(edit) @a1acc5   16 years FrederikHeber Attempt to fix the tesselation::IsInnerPoint(). We try the …
(edit) @eda56a   16 years FrederikHeber Changes to FindClosest...ToVector() and use of ..Map,..Set,..List …
(edit) @ff4611   16 years FrederikHeber Attempt to fix the embedding. Basically it would be working, but …
(edit) @f78203   16 years FrederikHeber Smaller fixes. - analysis_correlation.cpp: Info objects created at …
(edit) @0310b8   16 years FrederikHeber Non-convex tesselation seems to be working. Seems like it has been …
(edit) @281324   16 years FrederikHeber Merge branch 'FixTestSuite' into FixDegeneratedTesselation
(edit) @230b16   16 years FrederikHeber Merge branch 'FixVersioning2' into FixDegeneratedTesselation
(edit) @16f34d   16 years FrederikHeber Fixing the testsuite. - Putting performCriticalExit() everywhere …
(edit) @b7f3f3   16 years FrederikHeber Removed --tags as we have signed the "initial_commit" tag. - git …
(edit) @65f1dba   16 years FrederikHeber Fix attempts of the Tesselation. One problem still remains: - …
(edit) @59b70a   16 years FrederikHeber FIX: MatrixContainer::ParseMatrix() should not call …
(edit) @35f733   16 years FrederikHeber BUGFIX: delete(mol) belongs to the commented-out …
(edit) @ef87ee   16 years FrederikHeber Added versioning to each executable. - credits to Ralf Wildenhues for …
(edit) @246a3c   16 years FrederikHeber The finding of the degenerated polygons' endpoints was not yet …
(edit) @ea3627   16 years FrederikHeber Correction of degenerated polygons is working. - Correction of …
(edit) @f7490d   16 years FrederikHeber First compiling version of CorrectDegeneratedPolygons. - several new …
(edit) @65d6b3   16 years FrederikHeber Rename of internal variable due to upcoming name-conflict with …
(edit) @a68d44   16 years FrederikHeber removing automatic dissection on loading, Tesselations test now checks …
(edit) @013ad57   16 years FrederikHeber BUGFIX: testcase heptan was not correctly tesselated, as edges of a …
(edit) @3aa635   16 years FrederikHeber Tesselation::FindStartingTriangle() now also uses …
(edit) @be2997   16 years FrederikHeber Multi-Candidate-Add included and incorporated class Info into …
(edit) @edf611   16 years FrederikHeber New Info class that contains a global verbosity level, increased per …
(edit) @4af89b   16 years FrederikHeber Now the best (in terms of ShortestAngle) baseline is picked among all …
(edit) @1a3354   16 years FrederikHeber BUGFIX atom::CorrectBonDegree() wrongly increased bond degrees. - …
(edit) @cc9225   16 years FrederikHeber Fixes and naming of final Tecplot output file is now molecule name. - …
(edit) @7d1ad9   16 years FrederikHeber bugfix to errorLogger and some error verbosity changes. - BUGFIX: …
(edit) @3d4969   16 years FrederikHeber Fixing ticket #18. - each eLog() << Verbose(0) is now followed by …
(edit) @418117a   16 years FrederikHeber Verbosity corrected for ERROR and WARNING - present ERROR and WARNING …
(edit) @09d3b8   16 years FrederikHeber Attempt to fix tesselation for case 1_2-dimethylbenzene. - The issue …
(edit) @2fbbc96   16 years FrederikHeber Only biggest molecule is tesselated for now in …
(edit) @548cbf   16 years FrederikHeber BUGFIX: Output is again indented, errorLogger prefixes according to …
(edit) @e960b1   16 years FrederikHeber BUGFIX: unnecessary include in header, file not closed in definition …
(edit) @e462b3   16 years FrederikHeber Two new bond analysis functions. - GetMaxMinMeanBondCount() - …
(edit) @1fcedd   16 years FrederikHeber New function bond::GetDistance...() - bond::GetDistance() and …
(edit) @486aa5   16 years FrederikHeber Added config::SavePDB() and config::SaveMPQC(). - note: for CODICE we …
(edit) @341850   16 years FrederikHeber Added initial analysis_bonds.cpp and unit test for Analysis of bonds. …
(edit) @fc420f   16 years FrederikHeber LEAKFIX: FillBoxWithMolecule() had mismatch delete/delete[] - …
(edit) @4ef101   16 years FrederikHeber LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have …
(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 …
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