source: molecuilder/src

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Diff Rev Age Author Log Message
(edit) @caab20   15 years FrederikHeber Merge branch 'FixWorld_differentdefaultcell_size' into …
(edit) @8758eb   15 years FrederikHeber FIX: cell_size in World has not been set to a default size, i.e. has …
(edit) @732da7   15 years FrederikHeber Merge branch 'FixAnalysisBonds_carbonwrongZ' into …
(edit) @da09739   15 years FrederikHeber FIX: AnalysisBondsUnitTests has been broken due to Z of carbon same as …
(edit) @5a2599   15 years FrederikHeber Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into …
(edit) @424890   15 years FrederikHeber FIX: AnalysisCorrelationToPointUnitTest has been broken due to init of …
(edit) @bb50e0   15 years FrederikHeber Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into …
(edit) @a3c47c   15 years FrederikHeber FIX: AnalysisCorrelationToSurfaceUnitTest has been broken since change …
(edit) @d1829c   15 years FrederikHeber Merge branch 'FixBondGraphUnitTest_hydrogencarbon' into …
(edit) @aa8542   15 years FrederikHeber BUGFIX: BondGraphUnitTest was not working. Changes: - atoms are now …
(edit) @d2390d   15 years FrederikHeber Don't exit when no starting triangle has been found. - The issue is …
(edit) @af20f3   15 years FrederikHeber BUGFIX in Tesselation::FindThirdPointForTesselation() - ThirdPoint of …
(edit) @f07455   15 years FrederikHeber FIX: Tesselation::FindStartingTriangle() returns false when no …
(edit) @424d3fe   15 years FrederikHeber BUGFIX of Tesselation::FindStartingTriangle() - second Point Temporary …
(edit) @447896   15 years FrederikHeber BUGFIX of Tesselation::AddTesselationLine() - comparing Vector against …
(edit) @fda112   15 years FrederikHeber BUGFIX in Tesselation::FindThirdPointForTesselation() - regarding …
(edit) @d22a30   15 years FrederikHeber small changes to tesselation. - …
(edit) @2cd534   15 years FrederikHeber FindNonConvexBorder(): Instead of listing all open lines, just list …
(edit) @423c7b   15 years FrederikHeber Changed verbosity of "sum of angle"-warning in …
(edit) @1f2e46   15 years FrederikHeber Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) …
(edit) @c43766   15 years FrederikHeber Rewrite of tesselation: treatment of degenerated triangles and …
(edit) @7d1633   15 years FrederikHeber Made some remaining cout's "info Log() << Verbose(.)"'s ... - changes …
(edit) @ad98d4   15 years FrederikHeber FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever …
(edit) @60612f   15 years FrederikHeber Memory leak fixes and code cleanup after tesselation rewrite. - …
(edit) @0161a3   15 years FrederikHeber Fixed a warning in BondGraph::LoadBondLengthTable() due to missing …
(edit) @39f41d5   15 years FrederikHeber WriteTecplotFile() checked whether Tesselation::LastTriangle is not NULL.
(edit) @086db0   15 years FrederikHeber Rewrite of tesselation procedure: treatment of degenerated triangles. …
(edit) @342fbc9   15 years FrederikHeber BUGFIXES: LinkedCell::SetIndexToNode() had wrong boundaries in zero …
(edit) @adff53   15 years FrederikHeber FIX: If multiple open lines can be chosen in AddTesselationLine(), …
(edit) @7c2ebb   15 years FrederikHeber New approach to degenerated triangles: Recognize on creation and add …
(edit) @ce0de8   15 years FrederikHeber Renamed AddCandidateTriangle() -> AddCandidatePolygon() - …
(edit) @e34098   15 years FrederikHeber FIX: string instead of string.h was included for strcpy()
(edit) @4283d0   15 years FrederikHeber FIX: changed the order in which triangles are picked next during …
(edit) @a732ff   15 years FrederikHeber Changes to BoundaryTriangleSet and CandidateForTesselation. - …
(edit) @41c00d   15 years FrederikHeber BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of …
(edit) @f7e187   15 years FrederikHeber Full-working LinkedCellUnitTest. - new unit test for class LinkedCell …
(edit) @e760c1   15 years FrederikHeber ofstream operators now check for Name being NULL and print NULL in …
(edit) @ef016c   15 years FrederikHeber changes to LinkedCell::GetNeighbourBounds(), …
(edit) @bd8561   15 years FrederikHeber New Unit test for class LinkedCell. - this is just the skeleton, so …
(edit) @6dd8d3   15 years FrederikHeber LinkedNodes is now declared inside LinkedCell and some new functions. …
(edit) @6250e5   15 years FrederikHeber Enhanced CountHydrogenBridgeBonds() a bit. - new functions …
(edit) @794482   15 years FrederikHeber Moved functions CountBondsOfTwo(), CountBondsOfThree() and …
(edit) @768125   15 years FrederikHeber Added output of test cases for visualization. Is commented out though. …
(edit) @32526c   15 years FrederikHeber BUGFIX: CountHydrogenBridgeBonds() was half-broken, …
(edit) @7e4dc3f   15 years FrederikHeber Implemented counting of bonds over all atoms. - new functions in …
(edit) @ac86192   15 years FrederikHeber Introduced CountHydrogenBridgeBonds() function. - …
(edit) @800dc3   15 years FrederikHeber Merge branch 'FixGeneralizeStoreAdjacencyToFile' into …
(edit) @6acc8e4   15 years FrederikHeber Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered …
(edit) @31ccb6   15 years FrederikHeber molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now …
(edit) @12f57b   15 years FrederikHeber Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - …
(edit) @f87c2a   15 years FrederikHeber BUGFIX: DefaultName of molecule was too small an array. - We saw …
(edit) @6e1853   16 years FrederikHeber BUGFIX: config::SaveTREMOLO() - TREMOLO does not like particle Id 0 - …
(edit) @1540c8c   16 years FrederikHeber Merge branch 'FixDissectIntoSubgraphs_ConstructBondGraphcheck' into …
(edit) @296798   16 years FrederikHeber Merge branch 'FixBinDataStartEnd' into Analysis_PairCorrelation
(edit) @3d575e   16 years FrederikHeber Merge branch 'FixLinkedCellConstructor_Setempytcheck' into …
(edit) @b1c92e   16 years FrederikHeber BUGFIX: in BinData() binmap should be initialized from start to end in …
(edit) @bc46c1   16 years FrederikHeber Merge branch 'FixGetBin_tointeger' into FixBinDataStartEnd
(edit) @dd3a80   16 years FrederikHeber BUGFIX: rounding imprecision let values appear twice in BinMap. - we …
(edit) @328418d   16 years FrederikHeber BUGFIX: MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() - …
(edit) @d8fce3   16 years FrederikHeber BUGFIX: LinkedCell::LinkedCell() - before set->empty() check whether …
(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 …
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