- Molecuilder-devel

[SCM] MoleCuilder branch Candidate_v1.4.9 deleted. v1.4.8-54-g0516fd9
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.9 has been deleted was 0516fd9f440d63cdfbb63b946c9933f28f304b68 ----------------------------------------------------------------------- 0516fd9f440d63cdfbb63b946c9933f28f304b68 Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9 ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-gf40d8dd
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_ConvexizeNonconvexEnvelope has been deleted was f40d8dd765907294031f269bb2aee70f44522f5f ----------------------------------------------------------------------- f40d8dd765907294031f269bb2aee70f44522f5f TESTS: Extended Tesselations tests to convex case. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder annotated tag v1.4.9 created. v1.4.9
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The annotated tag, v1.4.9 has been created at ed071df08976dd4a9e83a9dcd39827e1d10dc656 (tag) tagging 42344903478721db21dff3e7385e7c5f037aff66 (commit) replaces v1.4.8 tagged by Frederik Heber on Wed Oct 22 23:40:06 2014 +0200 - Log ----------------------------------------------------------------- Convex envelopes and thereby volume measurments are fully working. Trajectories no longer need to be consecutive (we store time step and position) Some new actions and small fixes. Userguide now contains explanation of every present Action. This version contains the following branches: 33ee996 Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured) 78c9509 GUI_Enhancements (fixed appearance of QtHomologyList widget) c7fe90c Experiment_AmyloseWater (new TranslateToOriginAction eases rotations) 46ce1c8 Dynamic_Molecules (trajectories stored as map, not vector) 9d1320c Refactoring_PotentialActions (split FitPotentialAction, extracted save and load potentials) bbf6dcd MirrorAtoms (new MirrorAtoms action) 054d47f ActionFixes (fixing AtomByIdAction) 9bce964 CodeCheck_ActionInUserguide (check that every Action appears in user guide) Frederik Heber (56): VersionAction also prints to log, not only to status. DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. Added CodeChecks test that every action appears in the userguide. DOCU: Added all missing Actions to userguide. DOCU: Fixed all missing links in userguide. FIX: (Not)AtomByIdAction would fail with assert if not atoms are present. FIX: atom's copy cstor does not need to copy positions, ... again. Added AverageMoleculeForceAction for measuring average force acting on a molecule. Added TranslateToOriginAction. Changed how trajectories are stored, not as vecor but as map. FIX: World::setTime() now first copies Bondgraph and then sets the time. Added AtomMirrorAction. Merge branch 'ActionFixes' into Candidate_v1.4.9 Merge branch 'MirrorAtoms' into Candidate_v1.4.9 Split FitPotentialAction into two actions. Extracted ParsePotentialsAction from FitCompoundPotentialAction. Extracted SavePotentialsAction. Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Merge branch 'DynamicMolecules' into Candidate_v1.4.9 Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 FIX: QtHomologyList's plot widget was too high (and fixed). FIX: Added Boost::MultiIndexContainer check for MemDebug. MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d. FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. FIX: Raster3D needs header.r3d, which had been missing so far. FIX: Changed all performCriticalExit() into ASSERT() in tesselation. FIX: AddTesselationLine() would only work in initial tesselation phase. FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. DOCUFIX: Corrected formula for general tetrahedron in docu. Changed some verbosities in Tesselation code. FIX: Reduced verbosity noise from Line::getIntersection(). FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly. FIX: Filling of non-convex polygon with only minimal angles did not work. Added Tesselation::IsPointBelowSurroundingPolygon(). FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong. FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector. FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface(). Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface() FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop. Rewrote ConvexizeNonconvexEnvelope(). FIX: GainMap is used to store the concavity angle, we flip now always most concave. FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization. ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface(). Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction. DOCU: Added extensive explanation how convexization works. Added tcl scripts for viewing and debugging convexized surfaces. Added SphereRadius parameter to ConvexEnvelopeAction. Convex-envelope has debug parameter DoOutputEveryStep. TESTFIX: Regression test Tesselation/BigConvex is now working. TESTS: Extended Tesselations tests to convex case. Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9 MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere. DISTFIX: POTENTIALSOURCES was overwritten, not added to. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch stable updated. v1.4.8-56-g4234490
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, stable has been updated via 42344903478721db21dff3e7385e7c5f037aff66 (commit) via e63edb93a800204ca8a32bfc45eed103c7679210 (commit) via 0516fd9f440d63cdfbb63b946c9933f28f304b68 (commit) via 33ee9960e3c188eaa1d7490c6b14994fbd779863 (commit) via 565695bc8823d4df417f859cee34ed9b17e3b0b8 (commit) via 5f7b95f1f29d4009517dae2f5ef5ae993e846ce8 (commit) via bcb83114d92eb11cccb67975f4967b7fb251de3d (commit) via 991c35d557cd7eb1196fd569a74860662f03eeb6 (commit) via 8544b32bd227c145f76c3bf5a30ca16c01e9a7d9 (commit) via e2396e6d7030fd404f25afa9b5e8d1e1bc72bdb8 (commit) via aac19f2bb7cdef195d60c2e090de27fd193f1ee9 (commit) via 2ef2cc3b3e76c8ecb94ddaddfb1203081ea07eb0 (commit) via 81ffd87c0c1926d2a925cdbb620380e16e421cbe (commit) via d289c64b86bc28a435d03cdf4f3ece926c6debf6 (commit) via 6da9e995abeca059d65efd473cd2ac3eacf8279d (commit) via 30ce7d21a0bc0d344058826d689837a313b01efd (commit) via 77eec57c5ebcc041fb7d83112c887c95824f977d (commit) via e26c3533deedb0298b184037987b587e4d718562 (commit) via d45a5bfcf5b03614dc189256f1861f31e819f103 (commit) via 32d7e4e99ad240050c6936e8be2d5450c409f996 (commit) via d33bb8a2c2523a42b0a9e36768e551c57c340cbc (commit) via f1ae15bf748d2c4746bb9ed901593b75d8a44b1f (commit) via c2c786e40198b3b955ca9b66593dd013bd531b2e (commit) via 6d52807f7b413a18b8d814ac5501fdce735fcdea (commit) via b8d21539ab1899769efb705f4de59ef647f234b1 (commit) via dfe0549d4ce8433fde1acf2f7886d20fc1f0174a (commit) via 75d42ad5b96258a67afde9aa02cf39b04a4f6059 (commit) via c2f30642d960bd67dc5b7bca66d267525a8f58ab (commit) via bb86bd850f990066e79d37a776337c627624df65 (commit) via 613790861011df25a40877f5c6bfb2156def7a8c (commit) via cead3fe0679f2e6b3b53a7300f42efde4b3cc552 (commit) via cfb9c59bbf7a92a53173e5044b42303e74361093 (commit) via 1b6cec8a7217342cc34f00da7084bcec75e948a3 (commit) via 7d320c29fb3cf5f18317f1e2370bbf89802448e4 (commit) via 4da4defddffa2503040fe329681f55b1f6f8c856 (commit) via 3b179825d4e6f17bd22fbd7f880f59cc7fd8924e (commit) via 5c8807e908af52740778a67bac4173280b6d141b (commit) via b119a092aa1848936f8c80974f857ded3c098885 (commit) via 9e1bfbc27ee42cdb562491c7e51fdb9da26faaf0 (commit) via 0ea063beb1f1de6945df69f74ce759aab7643539 (commit) via f1eabd03d00ab44fb84ebc758d0ebfc85d6dee6d (commit) via 98d166e8fbc83bccb5843ecc5d4296f2c25488c0 (commit) via 2ed3bf3dd38da578e40e717928f565e66746d252 (commit) via 7acbfc4fee584acd54942911e6d4b9c73149b2c7 (commit) via bbf6dcd010a0439f2e1a441678550e5a56e1cf30 (commit) via 46ce1c8a9f9a6af80b7fcf736dcf57f11b47f8b7 (commit) via 8cc22fe4af9577450a3d00a92ea000018b14b366 (commit) via c7fe90cd467a73a0ef32b5c631534b2928c0b926 (commit) via f4b626a1fbf68b80e642bace1770e5577aeed6d8 (commit) via 7a7b3408459dae333637248d2b3e0bebed301975 (commit) via 054d47f3558f3549e6480280882111c4df74ad9f (commit) via 9bce96471db8bac23510c29ddaa7dbcabf15d765 (commit) via f73e0644af36b981af22685b57300f77cb7b0937 (commit) via c62e275561001d2ecd22b8489ac47810fd64e5ce (commit) via 2a6d8c7977c1f749091ead256bcca349538a8b59 (commit) via ced7f04bae3c2939e0888dfb7559e4b0f342a808 (commit) from 7f6a2fc9f64c88371654df745552167f0e0e3a9c (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 42344903478721db21dff3e7385e7c5f037aff66 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 22 20:07:11 2014 +0200 DISTFIX: POTENTIALSOURCES was overwritten, not added to. commit e63edb93a800204ca8a32bfc45eed103c7679210 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 22 20:05:30 2014 +0200 MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere. - check for not checking the same key again was broken, causing the invalid read error. This is fixed by correcting the check. - also fixed occurence in FitParticleChargesAction. ----------------------------------------------------------------------- Summary of changes: LinearAlgebra/src/LinearAlgebra/Line.cpp | 22 +- configure.ac | 1 + doc/userguide/userguide.xml | 1582 ++++++++++++++++---- m4/boost.m4 | 6 + src/Actions/ActionQueue.cpp | 13 +- .../AnalysisAction/AverageMoleculeForceAction.cpp | 95 ++ .../AnalysisAction/AverageMoleculeForceAction.def | 29 + .../AnalysisAction/AverageMoleculeForceAction.hpp | 21 + src/Actions/AtomAction/MirrorAction.cpp | 117 ++ src/Actions/AtomAction/MirrorAction.def | 40 + src/Actions/AtomAction/MirrorAction.hpp | 22 + src/Actions/AtomAction/TranslateToOriginAction.cpp | 108 ++ src/Actions/AtomAction/TranslateToOriginAction.def | 34 + src/Actions/AtomAction/TranslateToOriginAction.hpp | 22 + src/Actions/CommandAction/VersionAction.cpp | 1 + src/Actions/GlobalListOfActions.hpp | 12 +- src/Actions/Makefile.am | 30 +- .../MoleculeAction/ForceAnnealingAction.cpp | 1 - .../MoleculeAction/VerletIntegrationAction.cpp | 12 +- .../PotentialAction/FitCompoundPotentialAction.cpp | 123 ++ .../PotentialAction/FitCompoundPotentialAction.def | 49 + .../PotentialAction/FitCompoundPotentialAction.hpp | 22 + .../PotentialAction/FitParticleChargesAction.cpp | 7 +- src/Actions/PotentialAction/FitPotentialAction.cpp | 275 +--- src/Actions/PotentialAction/FitPotentialAction.def | 15 +- .../PotentialAction/ParsePotentialsAction.cpp | 114 ++ .../PotentialAction/ParsePotentialsAction.def | 37 + .../PotentialAction/ParsePotentialsAction.hpp | 22 + .../PotentialAction/SavePotentialsAction.cpp | 100 ++ .../PotentialAction/SavePotentialsAction.def | 36 + .../PotentialAction/SavePotentialsAction.hpp | 22 + .../SelectionAction/Atoms/AtomByIdAction.cpp | 2 +- .../SelectionAction/Atoms/NotAtomByIdAction.cpp | 2 +- .../TesselationAction/ConvexEnvelopeAction.cpp | 32 +- .../TesselationAction/ConvexEnvelopeAction.def | 16 +- src/Actions/UndoRedoHelpers.cpp | 12 +- src/Actions/UndoRedoHelpers.hpp | 9 +- src/Atom/TesselPoint.cpp | 12 +- src/Atom/TesselPoint.hpp | 4 +- src/Atom/atom.cpp | 23 +- src/Atom/atom.hpp | 4 +- src/Atom/atom_atominfo.cpp | 499 +++---- src/Atom/atom_atominfo.hpp | 18 +- src/Atom/atom_bondedparticle.cpp | 80 +- src/Atom/atom_bondedparticleinfo.cpp | 52 +- src/Atom/atom_bondedparticleinfo.hpp | 17 +- src/Atom/unittests/AtomObserverUnitTest.cpp | 3 +- src/Fragmentation/Exporters/HydrogenPool.cpp | 2 +- .../Exporters/SaturationDistanceMaximizer.hpp | 4 +- src/LinkedCell/unittests/stubs/TesselPointStub.cpp | 4 +- src/Potentials/Makefile.am | 7 + src/Potentials/PotentialTrainer.cpp | 217 +++ src/Potentials/PotentialTrainer.hpp | 52 + src/Potentials/Specifics/ConstantPotential.cpp | 2 +- .../Specifics/FourBodyPotential_Improper.cpp | 2 +- .../Specifics/FourBodyPotential_Torsion.cpp | 2 +- .../Specifics/ManyBodyPotential_Tersoff.cpp | 2 +- .../Specifics/PairPotential_Harmonic.cpp | 2 +- .../Specifics/PairPotential_LennardJones.cpp | 2 +- src/Potentials/Specifics/PairPotential_Morse.cpp | 2 +- .../Specifics/ThreeBodyPotential_Angle.cpp | 2 +- src/Tesselation/BoundaryLineSet.cpp | 3 +- src/Tesselation/BoundaryPointSet.cpp | 2 +- src/Tesselation/BoundaryTriangleSet.cpp | 27 +- src/Tesselation/CandidateForTesselation.cpp | 16 +- src/Tesselation/boundary.cpp | 233 +++- src/Tesselation/boundary.hpp | 2 +- src/Tesselation/tesselation.cpp | 1355 ++++++++++------- src/Tesselation/tesselation.hpp | 14 +- src/Tesselation/tesselationhelpers.cpp | 26 +- src/Tesselation/triangleintersectionlist.cpp | 18 +- .../Views/Qt4/Plotting/QSeisPlotPage.cpp | 43 +- .../Views/Qt4/Plotting/QSeisPlotPage.hpp | 6 + src/UIElements/Views/Qt4/QtHomologyList.cpp | 20 +- src/World.cpp | 21 +- src/documentation/constructs/tesselation.dox | 66 +- src/molecule_geometry.cpp | 19 +- tests/CodeChecks/Makefile.am | 1 + .../testsuite-action_present_in_userguide.at | 42 + tests/CodeChecks/testsuite.at | 4 +- tests/Python/AllActions/options.dat | 6 + .../testsuite-1_2-dimethoxyethane.at | 40 - .../testsuite-1_2-dimethylbenzene.at | 40 - .../testsuite-2-methylcyclohexanone.at | 40 - .../pre/1_2-dimethoxyethane.xyz | 0 .../testsuite-1_2-dimethoxyethane.at | 40 + .../pre/1_2-dimethylbenzene.xyz | 0 .../testsuite-1_2-dimethylbenzene.at | 42 + .../pre/2-methylcyclohexanone.xyz | 0 .../testsuite-2-methylcyclohexanone.at | 40 + .../pre/N_N-dimethylacetamide.xyz | 0 .../testsuite-N_N-dimethylacetamide.at | 40 + tests/Tesselations/Convex/amylose/pre/amylose.pdb | 470 ++++++ .../Convex/amylose/testsuite-amylose.at | 40 + .../{ => Convex}/benzene/pre/benzene.xyz | 0 .../Convex/benzene/testsuite-benzene.at | 42 + .../{ => Convex}/cholesterol/pre/cholesterol.xyz | 0 .../Convex/cholesterol/testsuite-cholesterol.at | 40 + .../{ => Convex}/cycloheptane/pre/cycloheptane.xyz | 0 .../Convex/cycloheptane/testsuite-cycloheptane.at | 40 + .../pre/dimethyl_bromomalonate.xyz | 0 .../testsuite-dimethyl_bromomalonate.at | 40 + .../{ => Convex}/glucose/pre/glucose.xyz | 0 .../Convex/glucose/testsuite-glucose.at | 40 + .../{ => Convex}/heptan/pre/heptan.xyz | 0 .../Tesselations/Convex/heptan/testsuite-heptan.at | 40 + .../{ => Convex}/isoleucine/pre/isoleucine.xyz | 0 .../Convex/isoleucine/testsuite-isoleucine.at | 40 + .../{ => Convex}/neohexane/pre/neohexane.xyz | 0 .../Convex/neohexane/testsuite-neohexane.at | 40 + .../{ => Convex}/proline/pre/proline.xyz | 0 .../Convex/proline/testsuite-proline.at | 40 + .../{ => Convex}/putrescine/pre/putrescine.xyz | 0 .../Convex/putrescine/testsuite-putrescine.at | 40 + .../tartaric_acid/pre/tartaric_acid.xyz | 0 .../tartaric_acid/testsuite-tartaric_acid.at | 42 + tests/Tesselations/Makefile.am | 90 +- .../testsuite-N_N-dimethylacetamide.at | 40 - .../NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-2.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-25.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-3.dat | 0 .../NonConvexEnvelope-1_2-dimethoxyethane-4.dat | 0 .../pre/1_2-dimethoxyethane.xyz | 0 .../testsuite-1_2-dimethoxyethane.at | 40 + .../NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-2.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-25.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-3.dat | 0 .../NonConvexEnvelope-1_2-dimethylbenzene-4.dat | 0 .../pre/1_2-dimethylbenzene.xyz | 0 .../testsuite-1_2-dimethylbenzene.at | 40 + ...NonConvexEnvelope-2-methylcyclohexanone-1.5.dat | 0 ...NonConvexEnvelope-2-methylcyclohexanone-2.5.dat | 0 .../NonConvexEnvelope-2-methylcyclohexanone-2.dat | 0 .../NonConvexEnvelope-2-methylcyclohexanone-25.dat | 0 ...NonConvexEnvelope-2-methylcyclohexanone-3.5.dat | 0 .../NonConvexEnvelope-2-methylcyclohexanone-3.dat | 0 .../NonConvexEnvelope-2-methylcyclohexanone-4.dat | 0 .../pre/2-methylcyclohexanone.xyz | 0 .../testsuite-2-methylcyclohexanone.at | 40 + ...NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat | 0 ...NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat | 0 .../NonConvexEnvelope-N_N-dimethylacetamide-2.dat | 0 .../NonConvexEnvelope-N_N-dimethylacetamide-25.dat | 0 ...NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat | 0 .../NonConvexEnvelope-N_N-dimethylacetamide-3.dat | 0 .../NonConvexEnvelope-N_N-dimethylacetamide-4.dat | 0 .../pre/N_N-dimethylacetamide.xyz | 0 .../testsuite-N_N-dimethylacetamide.at | 40 + .../benzene/post/NonConvexEnvelope-benzene-1.5.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-2.5.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-2.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-25.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-3.5.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-3.dat | 0 .../benzene/post/NonConvexEnvelope-benzene-4.dat | 0 .../NonConvex}/benzene/pre/benzene.xyz | 0 .../NonConvex/benzene/testsuite-benzene.at | 40 + .../post/NonConvexEnvelope-cholesterol-1.5.dat | 0 .../post/NonConvexEnvelope-cholesterol-2.5.dat | 0 .../post/NonConvexEnvelope-cholesterol-2.dat | 0 .../post/NonConvexEnvelope-cholesterol-25.dat | 0 .../post/NonConvexEnvelope-cholesterol-3.5.dat | 0 .../post/NonConvexEnvelope-cholesterol-3.dat | 0 .../post/NonConvexEnvelope-cholesterol-4.dat | 0 .../NonConvex}/cholesterol/pre/cholesterol.xyz | 0 .../NonConvex/cholesterol/testsuite-cholesterol.at | 40 + .../post/NonConvexEnvelope-cycloheptane-1.5.dat | 0 .../post/NonConvexEnvelope-cycloheptane-2.5.dat | 0 .../post/NonConvexEnvelope-cycloheptane-2.dat | 0 .../post/NonConvexEnvelope-cycloheptane-25.dat | 0 .../post/NonConvexEnvelope-cycloheptane-3.5.dat | 0 .../post/NonConvexEnvelope-cycloheptane-3.dat | 0 .../post/NonConvexEnvelope-cycloheptane-4.dat | 0 .../NonConvex}/cycloheptane/pre/cycloheptane.xyz | 0 .../cycloheptane/testsuite-cycloheptane.at | 40 + ...onConvexEnvelope-dimethyl_bromomalonate-1.5.dat | 0 ...onConvexEnvelope-dimethyl_bromomalonate-2.5.dat | 0 .../NonConvexEnvelope-dimethyl_bromomalonate-2.dat | 0 ...NonConvexEnvelope-dimethyl_bromomalonate-25.dat | 0 ...onConvexEnvelope-dimethyl_bromomalonate-3.5.dat | 0 .../NonConvexEnvelope-dimethyl_bromomalonate-3.dat | 0 .../NonConvexEnvelope-dimethyl_bromomalonate-4.dat | 0 .../pre/dimethyl_bromomalonate.xyz | 0 .../testsuite-dimethyl_bromomalonate.at | 40 + .../glucose/post/NonConvexEnvelope-glucose-1.5.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-2.5.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-2.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-25.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-3.5.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-3.dat | 0 .../glucose/post/NonConvexEnvelope-glucose-4.dat | 0 .../NonConvex}/glucose/pre/glucose.xyz | 0 .../NonConvex/glucose/testsuite-glucose.at | 40 + .../heptan/post/NonConvexEnvelope-heptan-1.5.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-2.5.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-2.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-25.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-3.5.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-3.dat | 0 .../heptan/post/NonConvexEnvelope-heptan-4.dat | 0 .../NonConvex}/heptan/pre/heptan.xyz | 0 .../NonConvex/heptan/testsuite-heptan.at | 40 + .../post/NonConvexEnvelope-isoleucine-1.5.dat | 0 .../post/NonConvexEnvelope-isoleucine-2.5.dat | 0 .../post/NonConvexEnvelope-isoleucine-2.dat | 0 .../post/NonConvexEnvelope-isoleucine-25.dat | 0 .../post/NonConvexEnvelope-isoleucine-3.5.dat | 0 .../post/NonConvexEnvelope-isoleucine-3.dat | 0 .../post/NonConvexEnvelope-isoleucine-4.dat | 0 .../NonConvex}/isoleucine/pre/isoleucine.xyz | 0 .../NonConvex/isoleucine/testsuite-isoleucine.at | 40 + .../post/NonConvexEnvelope-neohexane-1.5.dat | 0 .../post/NonConvexEnvelope-neohexane-2.5.dat | 0 .../post/NonConvexEnvelope-neohexane-2.dat | 0 .../post/NonConvexEnvelope-neohexane-25.dat | 0 .../post/NonConvexEnvelope-neohexane-3.5.dat | 0 .../post/NonConvexEnvelope-neohexane-3.dat | 0 .../post/NonConvexEnvelope-neohexane-4.dat | 0 .../NonConvex}/neohexane/pre/neohexane.xyz | 0 .../NonConvex/neohexane/testsuite-neohexane.at | 40 + .../proline/post/NonConvexEnvelope-proline-1.5.dat | 0 .../proline/post/NonConvexEnvelope-proline-2.5.dat | 0 .../proline/post/NonConvexEnvelope-proline-2.dat | 0 .../proline/post/NonConvexEnvelope-proline-25.dat | 0 .../proline/post/NonConvexEnvelope-proline-3.5.dat | 0 .../proline/post/NonConvexEnvelope-proline-3.dat | 0 .../proline/post/NonConvexEnvelope-proline-4.dat | 0 .../NonConvex}/proline/pre/proline.xyz | 0 .../NonConvex/proline/testsuite-proline.at | 40 + .../post/NonConvexEnvelope-putrescine-1.5.dat | 0 .../post/NonConvexEnvelope-putrescine-2.5.dat | 0 .../post/NonConvexEnvelope-putrescine-2.dat | 0 .../post/NonConvexEnvelope-putrescine-25.dat | 0 .../post/NonConvexEnvelope-putrescine-3.5.dat | 0 .../post/NonConvexEnvelope-putrescine-3.dat | 0 .../post/NonConvexEnvelope-putrescine-4.dat | 0 .../NonConvex}/putrescine/pre/putrescine.xyz | 0 .../NonConvex/putrescine/testsuite-putrescine.at | 40 + .../post/NonConvexEnvelope-tartaric_acid-1.5.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-2.5.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-2.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-25.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-3.5.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-3.dat | 0 .../post/NonConvexEnvelope-tartaric_acid-4.dat | 0 .../NonConvex}/tartaric_acid/pre/tartaric_acid.xyz | 0 .../tartaric_acid/testsuite-tartaric_acid.at | 40 + tests/Tesselations/benzene/testsuite-benzene.at | 40 - .../cholesterol/testsuite-cholesterol.at | 40 - .../cycloheptane/testsuite-cycloheptane.at | 40 - .../testsuite-dimethyl_bromomalonate.at | 40 - tests/Tesselations/glucose/testsuite-glucose.at | 40 - tests/Tesselations/heptan/testsuite-heptan.at | 40 - .../isoleucine/testsuite-isoleucine.at | 40 - .../Tesselations/neohexane/testsuite-neohexane.at | 40 - tests/Tesselations/proline/testsuite-proline.at | 40 - .../putrescine/testsuite-putrescine.at | 40 - .../tartaric_acid/testsuite-tartaric_acid.at | 40 - tests/Tesselations/testsuite.at | 82 +- .../regression/Atoms/Mirror/post/test-mirrored.xyz | 5 + tests/regression/Atoms/Mirror/post/test.xyz | 5 + tests/regression/Atoms/Mirror/pre/test.xyz | 5 + .../Atoms/Mirror/testsuite-atoms-mirror.at | 53 + .../post/test-shifted-weighted.xyz | 5 + .../TranslationToOrigin/post/test-shifted.xyz | 5 + .../Atoms/TranslationToOrigin/post/test.xyz | 5 + .../Atoms/TranslationToOrigin/pre/test.xyz | 5 + .../testsuite-atoms-translation-to-origin.at | 65 + tests/regression/Atoms/testsuite-atoms.at | 6 + tests/regression/Makefile.am | 2 + .../testsuite-potential-fit-potential.at | 96 +- .../Tesselation/BigConvex/post/ConvexEnvelope.dat | 90 ++ .../Tesselation/BigConvex/post/ConvexEnvelope.r3d | 277 ++++ .../BigConvex/post/NonConvexEnvelope.dat | 123 -- .../BigConvex/post/NonConvexEnvelope.r3d | 321 ---- .../Tesselation/BigConvex/post/test.conf | 147 -- .../testsuite-tesselation-big-convex-envelope.at | 7 +- .../testsuite-tesselation-convex-envelope.at | 4 +- utils/developer/raster3d/header.r3d | 20 + utils/developer/tcl/analyseconvexizing.tcl | 161 ++ utils/developer/tcl/convexizing.tcl | 79 + 287 files changed, 7014 insertions(+), 2961 deletions(-) create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.def create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp create mode 100644 src/Actions/AtomAction/MirrorAction.cpp create mode 100644 src/Actions/AtomAction/MirrorAction.def create mode 100644 src/Actions/AtomAction/MirrorAction.hpp create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.cpp create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.def create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.hpp create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.cpp create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.def create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.hpp create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.cpp create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.def create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.hpp create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.cpp create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.def create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.hpp create mode 100644 src/Potentials/PotentialTrainer.cpp create mode 100644 src/Potentials/PotentialTrainer.hpp create mode 100644 tests/CodeChecks/testsuite-action_present_in_userguide.at delete mode 100644 tests/Tesselations/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at delete mode 100644 tests/Tesselations/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at delete mode 100644 tests/Tesselations/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at rename tests/Tesselations/{ => Convex}/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (100%) create mode 100644 tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at rename tests/Tesselations/{ => Convex}/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (100%) create mode 100644 tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at rename tests/Tesselations/{ => Convex}/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (100%) create mode 100644 tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at rename tests/Tesselations/{ => Convex}/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (100%) create mode 100644 tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at create mode 100644 tests/Tesselations/Convex/amylose/pre/amylose.pdb create mode 100644 tests/Tesselations/Convex/amylose/testsuite-amylose.at rename tests/Tesselations/{ => Convex}/benzene/pre/benzene.xyz (100%) create mode 100644 tests/Tesselations/Convex/benzene/testsuite-benzene.at rename tests/Tesselations/{ => Convex}/cholesterol/pre/cholesterol.xyz (100%) create mode 100644 tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at rename tests/Tesselations/{ => Convex}/cycloheptane/pre/cycloheptane.xyz (100%) create mode 100644 tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at rename tests/Tesselations/{ => Convex}/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (100%) create mode 100644 tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at rename tests/Tesselations/{ => Convex}/glucose/pre/glucose.xyz (100%) create mode 100644 tests/Tesselations/Convex/glucose/testsuite-glucose.at rename tests/Tesselations/{ => Convex}/heptan/pre/heptan.xyz (100%) create mode 100644 tests/Tesselations/Convex/heptan/testsuite-heptan.at rename tests/Tesselations/{ => Convex}/isoleucine/pre/isoleucine.xyz (100%) create mode 100644 tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at rename tests/Tesselations/{ => Convex}/neohexane/pre/neohexane.xyz (100%) create mode 100644 tests/Tesselations/Convex/neohexane/testsuite-neohexane.at rename tests/Tesselations/{ => Convex}/proline/pre/proline.xyz (100%) create mode 100644 tests/Tesselations/Convex/proline/testsuite-proline.at rename tests/Tesselations/{ => Convex}/putrescine/pre/putrescine.xyz (100%) create mode 100644 tests/Tesselations/Convex/putrescine/testsuite-putrescine.at rename tests/Tesselations/{ => Convex}/tartaric_acid/pre/tartaric_acid.xyz (100%) create mode 100644 tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at delete mode 100644 tests/Tesselations/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/benzene/pre/benzene.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/benzene/testsuite-benzene.at rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/cholesterol/pre/cholesterol.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/cycloheptane/pre/cycloheptane.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/glucose/pre/glucose.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/glucose/testsuite-glucose.at rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/heptan/pre/heptan.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/heptan/testsuite-heptan.at rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/isoleucine/pre/isoleucine.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/neohexane/pre/neohexane.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/proline/pre/proline.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/proline/testsuite-proline.at rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/putrescine/pre/putrescine.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-1.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-25.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.5.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.dat (100%) rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-4.dat (100%) copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/tartaric_acid/pre/tartaric_acid.xyz (100%) create mode 100644 tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at delete mode 100644 tests/Tesselations/benzene/testsuite-benzene.at delete mode 100644 tests/Tesselations/cholesterol/testsuite-cholesterol.at delete mode 100644 tests/Tesselations/cycloheptane/testsuite-cycloheptane.at delete mode 100644 tests/Tesselations/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at delete mode 100644 tests/Tesselations/glucose/testsuite-glucose.at delete mode 100644 tests/Tesselations/heptan/testsuite-heptan.at delete mode 100644 tests/Tesselations/isoleucine/testsuite-isoleucine.at delete mode 100644 tests/Tesselations/neohexane/testsuite-neohexane.at delete mode 100644 tests/Tesselations/proline/testsuite-proline.at delete mode 100644 tests/Tesselations/putrescine/testsuite-putrescine.at delete mode 100644 tests/Tesselations/tartaric_acid/testsuite-tartaric_acid.at create mode 100644 tests/regression/Atoms/Mirror/post/test-mirrored.xyz create mode 100644 tests/regression/Atoms/Mirror/post/test.xyz create mode 100644 tests/regression/Atoms/Mirror/pre/test.xyz create mode 100644 tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test.xyz create mode 100644 tests/regression/Atoms/TranslationToOrigin/pre/test.xyz create mode 100644 tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at create mode 100644 tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.dat create mode 100644 tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.r3d delete mode 100644 tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.dat delete mode 100644 tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.r3d delete mode 100644 tests/regression/Tesselation/BigConvex/post/test.conf create mode 100644 utils/developer/raster3d/header.r3d create mode 100644 utils/developer/tcl/analyseconvexizing.tcl create mode 100644 utils/developer/tcl/convexizing.tcl hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Candidate_v1.4.9 created. v1.4.8-54-g0516fd9
by git＠ins.uni-bonn.de 20 Oct '14

20 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.9 has been created at 0516fd9f440d63cdfbb63b946c9933f28f304b68 (commit) - Log ----------------------------------------------------------------- commit 0516fd9f440d63cdfbb63b946c9933f28f304b68 Merge: 3b17982 33ee996 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 19 19:13:32 2014 +0200 Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9 commit 33ee9960e3c188eaa1d7490c6b14994fbd779863 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:00:11 2014 +0200 TESTS: Extended Tesselations tests to convex case. - moved all present tests to NonConvex folder, added same set but including amylose in Convex folder. commit 565695bc8823d4df417f859cee34ed9b17e3b0b8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 16 16:34:13 2014 +0200 TESTFIX: Regression test Tesselation/BigConvex is now working. commit 5f7b95f1f29d4009517dae2f5ef5ae993e846ce8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:47:03 2014 +0200 Convex-envelope has debug parameter DoOutputEveryStep. - this writes for each convexization step a distinct tesselation file. - added parameter to ConvexizeNonconvexEnvelope(). commit bcb83114d92eb11cccb67975f4967b7fb251de3d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:24:30 2014 +0200 Added SphereRadius parameter to ConvexEnvelopeAction. commit 991c35d557cd7eb1196fd569a74860662f03eeb6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:34:55 2014 +0200 Added tcl scripts for viewing and debugging convexized surfaces. commit 8544b32bd227c145f76c3bf5a30ca16c01e9a7d9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:55:44 2014 +0200 DOCU: Added extensive explanation how convexization works. - updated userguide for convex-envelope. commit e2396e6d7030fd404f25afa9b5e8d1e1bc72bdb8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 10:44:54 2014 +0200 Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction. commit aac19f2bb7cdef195d60c2e090de27fd193f1ee9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:27:36 2014 +0200 ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface(). - with this convexization of a nonconvex tesselated surface seems to be robustly working as we can now deal also with points with degeneracies. commit 2ef2cc3b3e76c8ecb94ddaddfb1203081ea07eb0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 18:14:39 2014 +0200 FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization. commit 81ffd87c0c1926d2a925cdbb620380e16e421cbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 15:08:11 2014 +0200 FIX: GainMap is used to store the concavity angle, we flip now always most concave. - this overrules prior flipping those that gives greatest gain in volume. commit d289c64b86bc28a435d03cdf4f3ece926c6debf6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 16:34:41 2014 +0200 Rewrote ConvexizeNonconvexEnvelope(). - now works for some sphere radii on amylose (e.g. 40 and 50). - we first remove all points that are only attached to concave lines. - also, we always flip the baseline (i.e. add a general tetraeder to the non-convex volume) for concave lines when the tetraeder does not intersect with present triangles. commit 6da9e995abeca059d65efd473cd2ac3eacf8279d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:31:18 2014 +0200 FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop. - even if a triangle pair is not removed, it must still be removed from the degenerated list or we run into infinite loops. commit 30ce7d21a0bc0d344058826d689837a313b01efd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 09:37:06 2014 +0200 Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface() - also added new functions Tesselation::RemoveFullConcavePointFromTesselatedSurface() and Tesselation::CheckAllConcaveInPolygon(). commit 77eec57c5ebcc041fb7d83112c887c95824f977d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:38:17 2014 +0200 FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface(). commit e26c3533deedb0298b184037987b587e4d718562 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 14:46:36 2014 +0200 FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector. - with the point to be removed we have a very good measure for a vector pointing inside. Before we used the average of all normal vectors. commit d45a5bfcf5b03614dc189256f1861f31e819f103 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:55:26 2014 +0200 FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong. - replaced code by using present function for tetrahedron calculation with center of gravity as fourth point when going over all boundary triangles. - TESTFIX: volume change in convex regression test. commit 32d7e4e99ad240050c6936e8be2d5450c409f996 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 08:57:30 2014 +0200 FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. - before we just took the average of the normal vector of both present triangles as guide. Now, we check the intersection of the fourth endpoint on the plane of the first triangle and decide by on which side of the three boundary lines the intersection lies whether to flip the normal vectors sign for the associated (new) triangle or not. commit d33bb8a2c2523a42b0a9e36768e551c57c340cbc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 14 18:37:03 2014 +0200 Added Tesselation::IsPointBelowSurroundingPolygon(). - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks whether point is below. commit f1ae15bf748d2c4746bb9ed901593b75d8a44b1f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 12:27:57 2014 +0200 FIX: Filling of non-convex polygon with only minimal angles did not work. - when removing points from non-convex boundary and we encounter non-convex polygons, we must pick smallest angles but close to the non-convex site! commit c2c786e40198b3b955ca9b66593dd013bd531b2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:43:03 2014 +0200 FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly. - FIX: Very last node was removed twice due to StartNode = EndNode setting. commit 6d52807f7b413a18b8d814ac5501fdce735fcdea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:38:16 2014 +0200 FIX: Reduced verbosity noise from Line::getIntersection(). - removed use of info and toned down verbosity levels (which are so low because of now missing info). commit b8d21539ab1899769efb705f4de59ef647f234b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:03 2014 +0200 Changed some verbosities in Tesselation code. - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet. - also to CandidateForTesselation, TriangleIntersectionList, tesselation, tesselation helpers and boundary code. commit dfe0549d4ce8433fde1acf2f7886d20fc1f0174a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:28:44 2014 +0200 DOCUFIX: Corrected formula for general tetrahedron in docu. - also code now matches with formula to avoid further confusion, although the result does not change by that. commit 75d42ad5b96258a67afde9aa02cf39b04a4f6059 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:23:50 2014 +0200 FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. - AddTesselationLine() now returns whether new or present line was used. - FIX: Last inner line in closed polygon has been added by one but last triangle already, we added it twice. commit c2f30642d960bd67dc5b7bca66d267525a8f58ab Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:24:52 2014 +0200 FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. commit bb86bd850f990066e79d37a776337c627624df65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:25:23 2014 +0200 FIX: AddTesselationLine() would only work in initial tesselation phase. - the CandidateForTesselation instance is NULL when we convexize and this was not correctly processed by AddTesselationLine(). commit 613790861011df25a40877f5c6bfb2156def7a8c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:20 2014 +0200 FIX: Changed all performCriticalExit() into ASSERT() in tesselation. commit cead3fe0679f2e6b3b53a7300f42efde4b3cc552 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:56:24 2014 +0200 FIX: Raster3D needs header.r3d, which had been missing so far. commit cfb9c59bbf7a92a53173e5044b42303e74361093 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit 1b6cec8a7217342cc34f00da7084bcec75e948a3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 22 22:10:11 2014 +0200 FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. commit 7d320c29fb3cf5f18317f1e2370bbf89802448e4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:40:10 2014 +0200 MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d. commit 4da4defddffa2503040fe329681f55b1f6f8c856 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:35:04 2014 +0200 FIX: Added Boost::MultiIndexContainer check for MemDebug. - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation with Ubuntu 14.04. commit 3b179825d4e6f17bd22fbd7f880f59cc7fd8924e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 13:19:18 2014 +0200 FIX: QtHomologyList's plot widget was too high (and fixed). - also the sizes of splitter's children in QtHomologyList are now stored to settings (as QsizePolicy does not have an effect on a splitter). commit 5c8807e908af52740778a67bac4173280b6d141b Merge: b119a09 c7fe90c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 19 19:12:11 2014 +0200 Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 Conflicts: doc/userguide/userguide.xml tests/regression/Atoms/testsuite-atoms.at - mirror-atoms and translate-to-origins occupied the same places. commit b119a092aa1848936f8c80974f857ded3c098885 Merge: 9e1bfbc 46ce1c8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 19 19:10:16 2014 +0200 Merge branch 'DynamicMolecules' into Candidate_v1.4.9 commit 9e1bfbc27ee42cdb562491c7e51fdb9da26faaf0 Merge: 2ed3bf3 0ea063b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 19 19:09:30 2014 +0200 Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 commit 0ea063beb1f1de6945df69f74ce759aab7643539 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 09:54:12 2014 +0200 Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials removed. - Fit...Actions do not store anymore. - TESTFIX: potential regression tests now use save-potentials and compare against stored file. commit f1eabd03d00ab44fb84ebc758d0ebfc85d6dee6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 09:39:58 2014 +0200 Extracted ParsePotentialsAction from FitCompoundPotentialAction. commit 98d166e8fbc83bccb5843ecc5d4296f2c25488c0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 22:38:05 2014 +0200 Split FitPotentialAction into two actions. - FitPotentialAction fits just a single potential. - new FitCompoundPotentialAction fits via a potential file. - PotentialTrainer contains all helper functions and common code and is only compiled when CONDLEVMAR. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Candidate_v1.4.9 deleted. v1.4.8-21-g78c9509
by git＠ins.uni-bonn.de 20 Oct '14

20 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.9 has been deleted was 78c9509cba8ec6569d3fee2987607785743b7e09 ----------------------------------------------------------------------- 78c9509cba8ec6569d3fee2987607785743b7e09 FIX: QtHomologyList's plot widget was too high (and fixed). ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-gf40d8dd
by git＠ins.uni-bonn.de 17 Oct '14

17 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_ConvexizeNonconvexEnvelope has been created at f40d8dd765907294031f269bb2aee70f44522f5f (commit) - Log ----------------------------------------------------------------- commit f40d8dd765907294031f269bb2aee70f44522f5f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:00:11 2014 +0200 TESTS: Extended Tesselations tests to convex case. - moved all present tests to NonConvex folder, added same set but including amylose in Convex folder. commit 5dcf7f15dc3a3f0a8e49f6cb75fac6944dff7a1b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 16 16:34:13 2014 +0200 TESTFIX: Regression test Tesselation/BigConvex is now working. commit fe2aa94863b0c598bfc0fe9a836c274cad414aba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:47:03 2014 +0200 Convex-envelope has debug parameter DoOutputEveryStep. - this writes for each convexization step a distinct tesselation file. - added parameter to ConvexizeNonconvexEnvelope(). commit caf1c49fd6d0d3ea742cfcd9465a27bb2586e1bd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:24:30 2014 +0200 Added SphereRadius parameter to ConvexEnvelopeAction. commit 424aa9f2367194493c6a2dfd66eef6addc0f8bcd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:34:55 2014 +0200 Added tcl scripts for viewing and debugging convexized surfaces. commit 81c536e142093bc4778cdced24084570dad28dc0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:55:44 2014 +0200 DOCU: Added extensive explanation how convexization works. - updated userguide for convex-envelope. commit 5c69254ae69e4c974ce0f37d9f92e7af7e38400a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 10:44:54 2014 +0200 Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction. commit 14fafa978ad8f073e3f6bfc71896bed224bc275c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:27:36 2014 +0200 ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface(). - with this convexization of a nonconvex tesselated surface seems to be robustly working as we can now deal also with points with degeneracies. commit 20c18051dace481e30b64e5ba906d722ba28b834 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 18:14:39 2014 +0200 FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization. commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 15:08:11 2014 +0200 FIX: GainMap is used to store the concavity angle, we flip now always most concave. - this overrules prior flipping those that gives greatest gain in volume. commit 4b54f73aba95c7e3039546e82c9a1df393327308 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 16:34:41 2014 +0200 Rewrote ConvexizeNonconvexEnvelope(). - now works for some sphere radii on amylose (e.g. 40 and 50). - we first remove all points that are only attached to concave lines. - also, we always flip the baseline (i.e. add a general tetraeder to the non-convex volume) for concave lines when the tetraeder does not intersect with present triangles. commit 8d778fa588719f6983eed36294b74582c67f6184 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:31:18 2014 +0200 FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop. - even if a triangle pair is not removed, it must still be removed from the degenerated list or we run into infinite loops. commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 09:37:06 2014 +0200 Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface() - also added new functions Tesselation::RemoveFullConcavePointFromTesselatedSurface() and Tesselation::CheckAllConcaveInPolygon(). commit 633576c77a8f88ab8b74845376e2ab706fdea53a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:38:17 2014 +0200 FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface(). commit ee886b36fc89715a5380053cc9ef0ec633424871 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 14:46:36 2014 +0200 FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector. - with the point to be removed we have a very good measure for a vector pointing inside. Before we used the average of all normal vectors. commit c1c8bc20ece846bb15d0be96187f99a80646eafb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:55:26 2014 +0200 FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong. - replaced code by using present function for tetrahedron calculation with center of gravity as fourth point when going over all boundary triangles. - TESTFIX: volume change in convex regression test. commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 08:57:30 2014 +0200 FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. - before we just took the average of the normal vector of both present triangles as guide. Now, we check the intersection of the fourth endpoint on the plane of the first triangle and decide by on which side of the three boundary lines the intersection lies whether to flip the normal vectors sign for the associated (new) triangle or not. commit 97d98600955169f39319e9ee925d91b2bf88c7d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 14 18:37:03 2014 +0200 Added Tesselation::IsPointBelowSurroundingPolygon(). - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks whether point is below. commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 12:27:57 2014 +0200 FIX: Filling of non-convex polygon with only minimal angles did not work. - when removing points from non-convex boundary and we encounter non-convex polygons, we must pick smallest angles but close to the non-convex site! commit aad7aa64cf795a5b4af656e636efc9d343590816 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:43:03 2014 +0200 FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly. - FIX: Very last node was removed twice due to StartNode = EndNode setting. commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:38:16 2014 +0200 FIX: Reduced verbosity noise from Line::getIntersection(). - removed use of info and toned down verbosity levels (which are so low because of now missing info). commit df82bca737770e1707f61dfafdd306da22481bcf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:03 2014 +0200 Changed some verbosities in Tesselation code. - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet. - also to CandidateForTesselation, TriangleIntersectionList, tesselation, tesselation helpers and boundary code. commit 921e9bcac84adb5c685919dd87089396207a8f67 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:28:44 2014 +0200 DOCUFIX: Corrected formula for general tetrahedron in docu. - also code now matches with formula to avoid further confusion, although the result does not change by that. commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:23:50 2014 +0200 FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. - AddTesselationLine() now returns whether new or present line was used. - FIX: Last inner line in closed polygon has been added by one but last triangle already, we added it twice. commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:24:52 2014 +0200 FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:25:23 2014 +0200 FIX: AddTesselationLine() would only work in initial tesselation phase. - the CandidateForTesselation instance is NULL when we convexize and this was not correctly processed by AddTesselationLine(). commit 4136c923ec473144f05170e1b8b9d4fe976b1c81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:20 2014 +0200 FIX: Changed all performCriticalExit() into ASSERT() in tesselation. commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:56:24 2014 +0200 FIX: Raster3D needs header.r3d, which had been missing so far. commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 22 22:10:11 2014 +0200 FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. commit 52e33b90484b6053378ed709009faea5b574a77a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:40:10 2014 +0200 MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d. commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:35:04 2014 +0200 FIX: Added Boost::MultiIndexContainer check for MemDebug. - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation with Ubuntu 14.04. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-ga87919a
by git＠ins.uni-bonn.de 17 Oct '14

17 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_ConvexizeNonconvexEnvelope has been deleted was a87919ab9cbb43b7e4b635445eed99502f832efe ----------------------------------------------------------------------- a87919ab9cbb43b7e4b635445eed99502f832efe TESTS: Extended Tesselations tests to convex case. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-ga87919a
by git＠ins.uni-bonn.de 17 Oct '14

17 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_ConvexizeNonconvexEnvelope has been created at a87919ab9cbb43b7e4b635445eed99502f832efe (commit) - Log ----------------------------------------------------------------- commit a87919ab9cbb43b7e4b635445eed99502f832efe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:00:11 2014 +0200 TESTS: Extended Tesselations tests to convex case. - moved all present tests to NonConvex folder, added same set but including amylose in Convex folder. commit 39fa01a02f0ec194ce6058e65b277536d9a1fe22 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 16 16:34:13 2014 +0200 TESTFIX: Regression test Tesselation/BigConvex is now working. commit 9155d6ea8290bd7d8d19341219a4e1a486f14e4b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:47:03 2014 +0200 Convex-envelope has debug parameter DoOutputEveryStep. - this writes for each convexization step a distinct tesselation file. - added parameter to ConvexizeNonconvexEnvelope(). commit 649aa9249b6121a2a1190dad8781b8358595257c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:24:30 2014 +0200 Added SphereRadius parameter to ConvexEnvelopeAction. commit ef479b42bd736ec67e8e4b56c777e0a28da02395 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 11:34:55 2014 +0200 Added tcl scripts for viewing and debugging convexized surfaces. commit 6290d24872224cd9c67492f61112826d620702e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:55:44 2014 +0200 DOCU: Added extensive explanation how convexization works. - updated userguide for convex-envelope. commit aa2e20d92facf7716a4ff5c79760b2b63f38ef04 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 10:44:54 2014 +0200 Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction. commit 14fafa978ad8f073e3f6bfc71896bed224bc275c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:27:36 2014 +0200 ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface(). - with this convexization of a nonconvex tesselated surface seems to be robustly working as we can now deal also with points with degeneracies. commit 20c18051dace481e30b64e5ba906d722ba28b834 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 18:14:39 2014 +0200 FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization. commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 15:08:11 2014 +0200 FIX: GainMap is used to store the concavity angle, we flip now always most concave. - this overrules prior flipping those that gives greatest gain in volume. commit 4b54f73aba95c7e3039546e82c9a1df393327308 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 4 16:34:41 2014 +0200 Rewrote ConvexizeNonconvexEnvelope(). - now works for some sphere radii on amylose (e.g. 40 and 50). - we first remove all points that are only attached to concave lines. - also, we always flip the baseline (i.e. add a general tetraeder to the non-convex volume) for concave lines when the tetraeder does not intersect with present triangles. commit 8d778fa588719f6983eed36294b74582c67f6184 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 12:31:18 2014 +0200 FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop. - even if a triangle pair is not removed, it must still be removed from the degenerated list or we run into infinite loops. commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 09:37:06 2014 +0200 Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface() - also added new functions Tesselation::RemoveFullConcavePointFromTesselatedSurface() and Tesselation::CheckAllConcaveInPolygon(). commit 633576c77a8f88ab8b74845376e2ab706fdea53a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:38:17 2014 +0200 FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface(). commit ee886b36fc89715a5380053cc9ef0ec633424871 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 8 14:46:36 2014 +0200 FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector. - with the point to be removed we have a very good measure for a vector pointing inside. Before we used the average of all normal vectors. commit c1c8bc20ece846bb15d0be96187f99a80646eafb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:55:26 2014 +0200 FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong. - replaced code by using present function for tetrahedron calculation with center of gravity as fourth point when going over all boundary triangles. - TESTFIX: volume change in convex regression test. commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 08:57:30 2014 +0200 FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. - before we just took the average of the normal vector of both present triangles as guide. Now, we check the intersection of the fourth endpoint on the plane of the first triangle and decide by on which side of the three boundary lines the intersection lies whether to flip the normal vectors sign for the associated (new) triangle or not. commit 97d98600955169f39319e9ee925d91b2bf88c7d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 14 18:37:03 2014 +0200 Added Tesselation::IsPointBelowSurroundingPolygon(). - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks whether point is below. commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 12:27:57 2014 +0200 FIX: Filling of non-convex polygon with only minimal angles did not work. - when removing points from non-convex boundary and we encounter non-convex polygons, we must pick smallest angles but close to the non-convex site! commit aad7aa64cf795a5b4af656e636efc9d343590816 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:43:03 2014 +0200 FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly. - FIX: Very last node was removed twice due to StartNode = EndNode setting. commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 3 11:38:16 2014 +0200 FIX: Reduced verbosity noise from Line::getIntersection(). - removed use of info and toned down verbosity levels (which are so low because of now missing info). commit df82bca737770e1707f61dfafdd306da22481bcf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:03 2014 +0200 Changed some verbosities in Tesselation code. - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet. - also to CandidateForTesselation, TriangleIntersectionList, tesselation, tesselation helpers and boundary code. commit 921e9bcac84adb5c685919dd87089396207a8f67 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 7 09:28:44 2014 +0200 DOCUFIX: Corrected formula for general tetrahedron in docu. - also code now matches with formula to avoid further confusion, although the result does not change by that. commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:23:50 2014 +0200 FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. - AddTesselationLine() now returns whether new or present line was used. - FIX: Last inner line in closed polygon has been added by one but last triangle already, we added it twice. commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:24:52 2014 +0200 FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:25:23 2014 +0200 FIX: AddTesselationLine() would only work in initial tesselation phase. - the CandidateForTesselation instance is NULL when we convexize and this was not correctly processed by AddTesselationLine(). commit 4136c923ec473144f05170e1b8b9d4fe976b1c81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:20 2014 +0200 FIX: Changed all performCriticalExit() into ASSERT() in tesselation. commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 9 10:56:24 2014 +0200 FIX: Raster3D needs header.r3d, which had been missing so far. commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 22 22:10:11 2014 +0200 FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. commit 52e33b90484b6053378ed709009faea5b574a77a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:40:10 2014 +0200 MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d. commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 29 16:35:04 2014 +0200 FIX: Added Boost::MultiIndexContainer check for MemDebug. - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation with Ubuntu 14.04. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0

[SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-g5cfdcf7
by git＠ins.uni-bonn.de 17 Oct '14

17 Oct '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_ConvexizeNonconvexEnvelope has been deleted was 5cfdcf70299145cf832d0ed47f1308237b9e42d6 ----------------------------------------------------------------------- 5cfdcf70299145cf832d0ed47f1308237b9e42d6 TESTS: Extended Tesselations tests to convex case. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0