source: molecuilder/src

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Diff Rev Age Author Log Message
(edit) @d93bb24   16 years FrederikHeber FillWithMolecule() for testing built into ParseCommandLine() JansCluster_water
(edit) @7aa922   16 years FrederikHeber find_(non)_convex_border TesselStruct is not free'd anymore, …
(edit) @eeefb3   16 years FrederikHeber Fixes for concave hull creation - fixed …
(edit) @04dcc0   16 years FrederikHeber Smaller FIXES to molecule class - new pointer TesselStruct was not …
(edit) @f4a346   16 years FrederikHeber Merge branch 'TesselationRefactoring' into ConcaveHull Conflicts: …
(edit) @0e2190   16 years FrederikHeber Merge branch 'ConcaveHull' of …
(edit) @e8de2e   16 years Saskia Metzler Adding functions IsInnerAtom() and IsInnerPoint() which can check …
(edit) @dc162d   16 years Saskia Metzler Compare and output operator for atom takes const argumen
(edit) @a87d5e6   16 years Saskia Metzler new function LinkedCell::GetNeighbourBounds() - …
(edit) @3219a0   16 years Saskia Metzler new function isNull(), output operator takes const argument
(edit) @b65771   16 years Saskia Metzler output operator now takes const argument
(edit) @eb167d   16 years FrederikHeber Some minor fixes with regards to what needs to be included where and …
(edit) @4dca8e   16 years FrederikHeber definitions for class element and verbose moved to their own header …
(edit) @e78824   16 years FrederikHeber class config definitions moved to their own header file. NOTE: …
(edit) @834ff3   16 years FrederikHeber Huge refactoring of Tesselation routines, but not finished yet. - new …
(edit) @4e4940   16 years FrederikHeber We are one step further in fixing the convex hull: There are two …
(edit) @3dc682   16 years FrederikHeber Convex tesselation is now working also for heptan. But the convex hull …
(edit) @da5c7c   16 years FrederikHeber New function Vector::NormSquared() and Angle checks whether Norm's are …
(edit) @78b45a   16 years FrederikHeber ConvexTesselation working again. - File was not written, as NULL was …
(edit) @dd69cc   16 years FrederikHeber FIX: DetermineCenterOfAll() did point in wrong direction, convex …
(edit) @63443f   16 years FrederikHeber BUGFIX: config::Load() added atoms in wrong order, hence resulting in …
(edit) @a0fb02   16 years FrederikHeber BUGFIX: ManipulateAtoms() had mol = NULL - in ManipulateAtoms() the …
(edit) @0ac84df   16 years FrederikHeber BUGFIX: molecule::ReturnFullMatrixforSymmetric had it still all wrong. …
(edit) @53d153   16 years FrederikHeber Split VolumeOfConvexEnvelope() into find_convex_border() and …
(edit) @c3a303   16 years FrederikHeber Merge branch 'master' into ConcaveHull Conflicts: …
(edit) @a048fa   16 years FrederikHeber fixed indentation from tabs to two spaces.
(edit) @47548d   16 years FrederikHeber Merge branch 'AtomRemoval' Conflicts: molecuilder/src/builder.cpp …
(edit) @1f6efb   16 years FrederikHeber fixed indentation from tabs to two spaces.
(edit) @f39735   16 years FrederikHeber Merge branch 'MultipleMolecules' Conflicts: …
(edit) @560995   16 years FrederikHeber Fix indentation from tabs to two spaces to prepare merging with …
(edit) @1b2aa1   16 years FrederikHeber Fix indentation from tab to two spaces. The trouble was caused at the …
(edit) @307290   16 years FrederikHeber Merge branch 'ConstrainedMolecularDynamics' Conflicts: …
(edit) @59a745   16 years FrederikHeber Merge branch 'test' Conflicts: molecuilder/src/analyzer.cpp …
(edit) @3b470f   16 years FrederikHeber Merge branch 'Thermostat' Conflicts: .gitignore Makefile.am …
(edit) @09f4dc   16 years FrederikHeber Merge branch 'HessianMatrix'
(edit) @2218dca   16 years FrederikHeber Merge branch 'GraphRefactoring'
(edit) @c95b69   16 years FrederikHeber BUGFIX: Due to stupid mistake, first atom was overlooked in periodic …
(edit) @88b936   16 years FrederikHeber new class ConfigFileBuffer and new overloaded function …
(edit) @598f76   16 years FrederikHeber BUGFIX: molecule::Output...() routines wrote elements beginning with 0 …
(edit) @22f587   16 years FrederikHeber XYZ and config files now store the atoms in the same order as they are …
(edit) @6fb785   16 years FrederikHeber molecule::CenterInBox puts atoms now periodically into the given box, …
(edit) @a8c8ba   16 years FrederikHeber FIX: Now tries each of the axis direction to find a starting triangle …
(edit) @8bbe43   16 years FrederikHeber Lots of changes to the number of output messages. As the finding of …
(edit) @438506   16 years FrederikHeber Fixed all of the remaining memory leaks due to …
(edit) @ab7b5e7   16 years FrederikHeber Memory leak fix: ParseCommandLineOptions() and main() free'd mol twice …
(edit) @bd86e8   16 years FrederikHeber Changed the unsatisfactory PathToDatabases construct, removing warning …
(edit) @c12297   16 years FrederikHeber fixed compiler warning: deprecated conversion from string const to …
(edit) @669a7e   16 years FrederikHeber fixed compiler warning by changing int to size_t because C++ STL …
(edit) @61e92a   16 years FrederikHeber Removed unneeded variables
(edit) @12cf763   16 years FrederikHeber Removed unnecessary code - Choose_preferable_third_point() - already …
(edit) @49c774   16 years FrederikHeber BUGFIX: Memory leak due to special triangles and similar lines in …
(edit) @30212a8   16 years FrederikHeber FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when we … TesselationWORKING
(edit) @a811a0   16 years FrederikHeber BUGFIX: Initial edge for starting triangle may be up to TWICE the …
(edit) @d98327   16 years FrederikHeber BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere Some …
(edit) @54de04   16 years FrederikHeber BUGFIX: Numerical imprecision forced check of bounds for acos() …
(edit) @eeae5b   16 years FrederikHeber Cosmetical changes in Find_third_point_for_tesselation() and …
(edit) @d2639f   16 years FrederikHeber All of Saskia Metzler's changes so far to remove bugs from Tesselation …
(edit) @ea9696   16 years FrederikHeber Removing of atoms via command line possible -R switchs allows for the …
(edit) @378e87   16 years FrederikHeber BUGFIX: RemoveAtom() would remove the iterator, molecule::RemoveAtom() …
(edit) @a41b50   16 years FrederikHeber return type of MoleculeListClass::insert is now void instead of bool …
(edit) @bb12e7   16 years FrederikHeber removed lots of warnings due to unused variables This arose due to …
(edit) @37a050   16 years FrederikHeber fixes due to changes in molecule structure (Center...()) and merge …
(edit) @d618b5   16 years FrederikHeber Lots of bugfixes, some name changes and new functions BUGFIX: - …
(edit) @8b05c6   16 years FrederikHeber MoleculeListClass::Enumerate() lists center and size of molecule, fix …
(edit) @899029f   16 years FrederikHeber Framework for embedding one molecule into another, now the embedding …
(edit) @3021d93   16 years FrederikHeber simple switched order for edit molecule to be in alphabetical ordering
(edit) @c830e8e   16 years FrederikHeber Basic implementation of Multiple molecules. builder.cpp: - …
(edit) @451d7a   17 years FrederikHeber Gaussian basis for MPQC input files can now be specified with -B …
(edit) @f23d7d   17 years FrederikHeber Basis for MPQC can now be specified via command line switch * -B is …
(edit) @97c751   17 years FrederikHeber Chi integration had some copy&paste error
(edit) @e08f45   17 years FrederikHeber Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull Conflicts: …
(edit) @dafe43   17 years FrederikHeber Merge ../espack3
(edit) @d3d15c   17 years FrederikHeber Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list
(edit) @95183e   17 years FrederikHeber New file and class LinkedCell that contains the linked cell algorithms …
(edit) @848729   17 years FrederikHeber Just a temporary commit
(edit) @3d9045   17 years FrederikHeber Merge branch 'ConcaveHull' of …
(edit) @eec6c8   17 years FrederikHeber Now we also produce Raster3D output files additionally to TecPlot ones …
(edit) @2ac928   17 years neuen fancy commit
(edit) @fe3c9a   17 years FrederikHeber Merge branch 'ConcaveHull' of …
(edit) @07c050   17 years FrederikHeber Cleaned up all debugging output
(edit) @56a489   17 years neuen BallAngel enhanced, added new alternative direction for issues with …
(edit) @edf4a0   17 years neuen Switched choice process to Ball angle completely. Problem remains. …
(edit) @2b7a1a   17 years neuen First change to Ball angle as criteria, however, change sucks.
(edit) @87c8e7   17 years neuen Solved possible problem with Second quadrant overhaul
(edit) @313dff   17 years neuen Tesselation starts to look good, minor discrepancies are still there …
(edit) @5a447f   17 years neuen Atom indices are now correctly processed.
(edit) @735468   17 years neuen Another update w.r.t. the Tesselation. Some signs switched, but atom …
(edit) @db177a   17 years neuen several changes, now output is created, quality unknown
(edit) @3e20fe   17 years neuen Parses a pdb and xyz file and decideds which atoms are in both and …
(edit) @e0c5b1   17 years neuen Multiple changes to boundary, currently not fully operational. …
(edit) @f5b58e   17 years neuen The border.cpp contains the same functions as the changes in boundary, …
(edit) @6b3826   17 years neuen In vector a function for calculation of the vector-(cross-)product has …
(edit) @a709c4   17 years neuen Construction of border triangles of non convex point set
(edit) @6ce722   17 years FrederikHeber Analyzer now produces data file with Frobenius norm of hessian matrix.
(edit) @ab64f4   17 years FrederikHeber Added some commentary to HessianMatrix::SumSubHessians to ease debugging
(edit) @95628a   17 years FrederikHeber Implemented Frobenius norm calculation for class HessianMatrix …
(edit) @f98e5a   17 years FrederikHeber HessianMatrix implemented fully, but not yet working, probably due to …
(edit) @002351   17 years FrederikHeber Implemented analysis of magnetic susceptibilites. This is very …
(edit) @650212   17 years FrederikHeber Begin of implementing classes Graph, SubGraph, Node and Edge. So far …
(edit) @d40e32   17 years FrederikHeber Analyzer now produces data file with Frobenius norm of hessian matrix.
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