[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.8-56-g4234490

23 Oct 2014

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- Log -----------------------------------------------------------------
commit 42344903478721db21dff3e7385e7c5f037aff66
Author: Frederik Heber <heber@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@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
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 .../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
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 .../NonConvex}/neohexane/pre/neohexane.xyz         |    0
 .../NonConvex/neohexane/testsuite-neohexane.at     |   40 +
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 .../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
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 .../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 -
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 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

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[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.8-56-g4234490

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