[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.8-56-g4234490
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- Log -----------------------------------------------------------------
commit 42344903478721db21dff3e7385e7c5f037aff66
Author: Frederik Heber <heber at 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 at 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
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