[Molecuilder-devel] [SCM] branch stable updated. v1.5.1
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- Log -----------------------------------------------------------------
commit 69a4206f578e3716755e03e48a082cebd3b0db64
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jan 21 13:48:19 2016 +0100
Set version to 1.5.1.
- MoleCuilder library is now 15:1:0.
- Codename "Volleyball" (the 5-1 formation in volleyball has only a single
setter with five possible attackers).
commit 9ae11c8ffa4dc0d34f93a07bcb120ad35c686947
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Feb 6 23:38:33 2016 +0100
DEBIANFIX: requiring libcodepatterns instead of ..-dev variant.
commit 3690e473417f286de3e772d934f7ae47120b763c
Merge: d1831e6 62d092e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Feb 2 18:50:29 2016 +0100
Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1
commit d1831e68610ffad961ff27e9f13c54a4ae810a1d
Merge: e387509 b61bd5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Feb 2 18:50:22 2016 +0100
Merge branch 'Fix_debianpackage' into Candidate_v1.5.1
commit e38750985965a330bae6c625523a373491b95349
Merge: d26fb76 dace6c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jan 31 13:47:23 2016 +0100
Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.1
commit d26fb7625dde5c4fa08b01ff2fa421d45b545931
Merge: 6a922b1 2f429ef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jan 31 13:47:12 2016 +0100
Merge branch 'Better_HBondDistances' into Candidate_v1.5.1
commit 6a922b176cac1093a59e5316e5fc5f8b18a99813
Merge: 9a8a6bb e39e7a3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jan 31 13:47:04 2016 +0100
Merge branch 'Molecule_Enhanced_BoundingBox' into Candidate_v1.5.1
commit 9a8a6bb95a3a7a6f0fa93fc6a5b64041d47de9c7
Merge: 08d9df7 ceaab1d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jan 31 13:46:56 2016 +0100
Merge branch 'AtomAlwaysHasMolecule' into Candidate_v1.5.1
commit e39e7a39013eb9930f8d044d1a2c5297df13da96
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Aug 31 14:38:50 2015 +0200
Implemented more efficient per-molecule bounding box information.
- molecule now has internal bimaps to know the extent of itself in a cheap way,
right map needs to be multiset_of to allow for non-unique values.
- moved BoundingBoxInfo from GLMolObject to molecule.
- is itself a Cacheable and is requested from GLMoleculeObject_molecule on new
channel BoundingBoxChanged.
- Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved.
- in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry.
commit e3e52ab3453d1812f2502d0534b424543c3505e8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jan 30 18:46:50 2016 +0100
FIX: BondGraph::Createdjacency compare atoms on position in memory.
- this caused every and again failures in tests as an atom with an earlier id
might end up at a "later" memory position resulting in flipped positions in
e.g. PDB CONECT entries (regression tests molecules remove failed).
-----------------------------------------------------------------------
Summary of changes:
LinearAlgebra-debug.pc.in | 2 +-
MoleCuilder.pc.in | 1 +
configure.ac | 56 +++--
debian/changelog | 16 +-
debian/control | 18 +-
debian/copyright | 2 +-
m4/ax_codepatterns.m4 | 14 +-
m4/qwt.m4 | 6 +
makeDebianPackage.sh | 3 +-
src/Actions/AtomAction/AddAction.cpp | 113 ++++++---
src/Actions/AtomAction/AddAction.def | 4 +-
src/Actions/AtomAction/SaturateAction.cpp | 2 +-
.../AnalyseFragmentationResultsAction.cpp | 40 +++-
.../FragmentationAction/FragmentationAction.cpp | 15 +-
.../FragmentationAutomationAction.cpp | 8 +-
.../FragmentationAutomationAction.def | 11 +-
.../WorldAction/SetBoundaryConditionsAction.def | 2 +-
src/Atom/atom.cpp | 5 +-
src/Element/element.cpp | 4 +-
src/Element/elements_db.cpp | 50 ++--
src/Element/unittests/ElementUnitTest.cpp | 4 +-
.../Automation/ResultContainer_impl.hpp | 2 +-
.../Automation/VMGFragmentController.cpp | 9 +-
.../Automation/VMGFragmentController.hpp | 4 +-
src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp | 2 +-
src/Fragmentation/Exporters/SaturatedBond.cpp | 6 +-
src/Fragmentation/Interfragmenter.cpp | 258 ++++++++++++++-------
src/Fragmentation/Interfragmenter.hpp | 72 +++++-
src/Fragmentation/Makefile.am | 7 -
.../Containers/FragmentationLongRangeResults.cpp | 50 +++-
.../Containers/FragmentationLongRangeResults.hpp | 19 +-
.../Containers/FragmentationShortRangeResults.cpp | 2 +-
.../Summation/Containers/MPQCData.hpp | 13 +-
.../Summation/Containers/MPQCDataFused.hpp | 4 +-
src/Fragmentation/Summation/Containers/VMGData.cpp | 4 +-
src/Fragmentation/Summation/Containers/VMGData.hpp | 13 +-
.../Summation/Containers/VMGDataFused.hpp | 10 +-
.../Summation/Containers/VMGDataMap.hpp | 42 +++-
.../Summation/Containers/VMGData_printKeyNames.hpp | 5 +-
.../Summation/Converter/DataConverter.hpp | 39 +++-
src/Fragmentation/Summation/Makefile.am | 7 -
.../Summation/SetValues/FragmentForces.cpp} | 82 ++++---
.../Summation/SetValues/FragmentForces.hpp | 71 ++++++
src/Fragmentation/Summation/SetValues/Makefile.am | 2 +
src/Graph/BondGraph.hpp | 12 +-
src/Jobs/ChargeSmearer.cpp | 166 +++++++++++++
src/Jobs/ChargeSmearer.hpp | 141 +++++++++++
src/Jobs/InterfaceVMGJob.cpp | 59 +++--
src/Jobs/InterfaceVMGJob.hpp | 6 +
src/Jobs/MPQCCommandJob.cpp | 4 +-
src/Jobs/Makefile.am | 9 +-
src/Jobs/VMGJob.cpp | 8 +-
src/Jobs/VMGJob.hpp | 8 +-
src/Jobs/WindowGrid_converter.cpp | 61 +++--
src/Jobs/WindowGrid_converter.hpp | 3 +-
src/Makefile.am | 2 +-
src/Parameters/Specifics/Value_element.cpp | 14 +-
src/Parameters/Specifics/Value_elements.cpp | 16 +-
src/Parser/MpqcParser.cpp | 13 ++
src/Parser/MpqcParser_Parameters.cpp | 24 ++
src/Parser/MpqcParser_Parameters.hpp | 14 ++
src/Parser/unittests/ParserMpqcUnitTest.cpp | 4 +
src/UIElements/CommandLineUI/CommandLineParser.cpp | 4 +-
.../Query/ElementCommandLineQuery.cpp | 15 +-
.../Query/ElementsCommandLineQuery.cpp | 43 +++-
src/UIElements/Makefile.am | 42 +++-
src/UIElements/Views/Qt4/Plotting/Makefile.am | 30 ++-
.../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 12 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 27 +--
src/World.cpp | 2 +-
src/controller_MPQCCommandJob.cpp | 2 +-
src/molecule.cpp | 113 +++++++--
src/molecule.hpp | 75 ++++++
tests/GuiChecks/atlocal.in | 1 +
tests/Python/AllActions/options.dat | 1 +
tests/regression/Atoms/Add/post/test.in | 1 +
tests/regression/Atoms/Add/post/test.pdb | 2 +-
tests/regression/Atoms/Remove/post/test.in | 1 +
.../Atoms/Saturate/post/saturated_carbon.xyz | 10 +-
.../Atoms/Saturate/post/saturated_nitrogen.xyz | 8 +-
tests/regression/Parser/Mpqc/post/doublewater.in | 1 +
tests/regression/Parser/Mpqc/post/empty.in | 1 +
tests/regression/Parser/Mpqc/post/test.in | 1 +
tests/regression/Parser/Mpqc/post/testCLHF.in | 1 +
tests/regression/Parser/Mpqc/post/testCLKS.in | 1 +
tests/regression/Parser/Mpqc/post/testMBPT2.in | 1 +
tests/regression/Parser/Mpqc/post/testMBPT2_R12.in | 1 +
tests/regression/Parser/Mpqc/pre/testCLHF.in | 1 +
tests/regression/Parser/Mpqc/pre/testCLHF_n.in | 1 +
.../Parser/Mpqc/pre/testCLHF_n_ascend_ids.in | 1 +
.../Parser/Mpqc/pre/testCLHF_n_mixed_ids.in | 1 +
tests/regression/Parser/Mpqc/pre/testCLKS.in | 1 +
tests/regression/Parser/Mpqc/pre/testMBPT2.in | 1 +
tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in | 1 +
tests/regression/Parser/Mpqc/pre/water.in | 1 +
.../Parser/SetParameters/Mpqc/post/testCLHF.in | 1 +
.../Parser/SetParameters/Mpqc/pre/testCLHF.in | 1 +
97 files changed, 1638 insertions(+), 431 deletions(-)
copy src/{Jobs/MPQCJob.cpp => Fragmentation/Summation/SetValues/FragmentForces.cpp} (50%)
create mode 100644 src/Fragmentation/Summation/SetValues/FragmentForces.hpp
create mode 100644 src/Jobs/ChargeSmearer.cpp
create mode 100644 src/Jobs/ChargeSmearer.hpp
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