[med-svn] [cain] 06/07: Merge tag 'upstream/1.10+dfsg'
Andreas Tille
tille at debian.org
Thu Dec 17 21:35:55 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cain.
commit 6771116c8739d92b9ee3295a0920fb9f84d00b64
Merge: 157b5ac b846fde
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 17 22:29:12 2015 +0100
Merge tag 'upstream/1.10+dfsg'
Upstream version 1.10+dfsg
src/solvers/HomogeneousDirect.ipp | 250 ++++++++++++++++++++
src/solvers/HomogeneousDirect2DSearch.cc | 11 +
src/solvers/HomogeneousDirect2DSearch.d | 39 ++++
src/solvers/HomogeneousDirect2DSearchBubbleSort.cc | 11 +
src/solvers/HomogeneousDirect2DSearchBubbleSort.d | 44 ++++
src/solvers/HomogeneousDirect2DSearchSorted.cc | 11 +
src/solvers/HomogeneousDirect2DSearchSorted.d | 44 ++++
src/solvers/HomogeneousDirectAllReactions.ipp | 257 +++++++++++++++++++++
.../HomogeneousDirectAllReactions2DSearch.cc | 11 +
.../HomogeneousDirectAllReactions2DSearch.d | 41 ++++
src/solvers/HomogeneousDirectBinarySearch.cc | 12 +
src/solvers/HomogeneousDirectBinarySearch.d | 34 +++
.../HomogeneousDirectBinarySearchRecursiveCdf.cc | 13 ++
.../HomogeneousDirectBinarySearchRecursiveCdf.d | 35 +++
src/solvers/HomogeneousDirectBinarySearchSorted.cc | 14 ++
src/solvers/HomogeneousDirectBinarySearchSorted.d | 41 ++++
.../HomogeneousDirectCompositionRejection.cc | 12 +
.../HomogeneousDirectCompositionRejection.d | 39 ++++
src/solvers/HomogeneousDirectLinearSearch.cc | 12 +
src/solvers/HomogeneousDirectLinearSearch.d | 39 ++++
.../HomogeneousDirectLinearSearchBubbleSort.cc | 12 +
.../HomogeneousDirectLinearSearchBubbleSort.d | 43 ++++
.../HomogeneousDirectLinearSearchDelayedUpdate.cc | 12 +
.../HomogeneousDirectLinearSearchDelayedUpdate.d | 39 ++++
src/solvers/HomogeneousDirectLinearSearchSorted.cc | 14 ++
src/solvers/HomogeneousDirectLinearSearchSorted.d | 45 ++++
.../HomogeneousDirectRejectionBinsSplitting.cc | 13 ++
.../HomogeneousDirectRejectionBinsSplitting.d | 45 ++++
src/solvers/HomogeneousFirstReaction.cc | 20 ++
src/solvers/HomogeneousFirstReaction.d | 29 +++
src/solvers/HomogeneousFirstReaction.ipp | 193 ++++++++++++++++
.../HomogeneousFirstReactionAbsoluteTime.cc | 22 ++
src/solvers/HomogeneousFirstReactionAbsoluteTime.d | 31 +++
src/solvers/HomogeneousFirstReactionInfluence.cc | 22 ++
src/solvers/HomogeneousFirstReactionInfluence.d | 31 +++
...ogeneousHistogramFinalHypoexponentialDirect.ipp | 193 ++++++++++++++++
...sHistogramFinalHypoexponentialDirect2DSearch.cc | 9 +
...usHistogramFinalHypoexponentialDirect2DSearch.d | 38 +++
src/solvers/HomogeneousHistogramsAverage.cc | 11 +
src/solvers/HomogeneousHistogramsAverage.d | 43 ++++
src/solvers/HomogeneousHistogramsAverage.ipp | 207 +++++++++++++++++
src/solvers/HomogeneousHistogramsAverageAps.cc | 11 +
src/solvers/HomogeneousHistogramsAverageAps.d | 44 ++++
src/solvers/HomogeneousHistogramsAverageAps.ipp | 207 +++++++++++++++++
.../HomogeneousHistogramsAverageElapsedTime.cc | 11 +
.../HomogeneousHistogramsAverageElapsedTime.d | 46 ++++
.../HomogeneousHistogramsAverageElapsedTime.ipp | 207 +++++++++++++++++
src/solvers/HomogeneousHistogramsDirect.ipp | 190 +++++++++++++++
src/solvers/HomogeneousHistogramsDirect2DSearch.cc | 11 +
src/solvers/HomogeneousHistogramsDirect2DSearch.d | 43 ++++
src/solvers/HomogeneousHistogramsDirectTree.cc | 11 +
src/solvers/HomogeneousHistogramsDirectTree.d | 42 ++++
src/solvers/HomogeneousHistogramsDirectTree.ipp | 197 ++++++++++++++++
.../HomogeneousHistogramsMultiTimeDirect.ipp | 195 ++++++++++++++++
...HomogeneousHistogramsMultiTimeDirect2DSearch.cc | 11 +
.../HomogeneousHistogramsMultiTimeDirect2DSearch.d | 44 ++++
.../HomogeneousHistogramsTransientDirect.ipp | 184 +++++++++++++++
...HistogramsTransientDirectTreeExponentialLast.cc | 25 ++
...sHistogramsTransientDirectTreeExponentialLast.d | 44 ++++
...istogramsTransientDirectTreeExponentialLimit.cc | 25 ++
...HistogramsTransientDirectTreeExponentialLimit.d | 44 ++++
...gramsTransientDirectTreeHypoexponentialLimit.cc | 26 +++
...ogramsTransientDirectTreeHypoexponentialLimit.d | 45 ++++
...ogramsTransientDirectTreeNormalApproximation.cc | 26 +++
...togramsTransientDirectTreeNormalApproximation.d | 45 ++++
src/solvers/HomogeneousHybridDirectTauLeaping.ipp | 181 +++++++++++++++
.../HomogeneousHybridDirectTauLeapingForward.cc | 7 +
.../HomogeneousHybridDirectTauLeapingForward.d | 51 ++++
.../HomogeneousHybridDirectTauLeapingMidpoint.cc | 7 +
.../HomogeneousHybridDirectTauLeapingMidpoint.d | 51 ++++
...HomogeneousHybridDirectTauLeapingRungeKutta4.cc | 7 +
.../HomogeneousHybridDirectTauLeapingRungeKutta4.d | 51 ++++
src/solvers/HomogeneousNextReaction.ipp | 246 ++++++++++++++++++++
...HomogeneousNextReactionBinaryHeapGibsonBruck.cc | 11 +
.../HomogeneousNextReactionBinaryHeapGibsonBruck.d | 37 +++
.../HomogeneousNextReactionBinaryHeapPair.cc | 9 +
.../HomogeneousNextReactionBinaryHeapPair.d | 37 +++
.../HomogeneousNextReactionBinaryHeapPointer.cc | 9 +
.../HomogeneousNextReactionBinaryHeapPointer.d | 37 +++
src/solvers/HomogeneousNextReactionHashing.cc | 11 +
src/solvers/HomogeneousNextReactionHashing.d | 37 +++
.../HomogeneousNextReactionHashingGenericList.cc | 15 ++
.../HomogeneousNextReactionHashingGenericList.d | 39 ++++
.../HomogeneousNextReactionHashingGenericVector.cc | 14 ++
.../HomogeneousNextReactionHashingGenericVector.d | 39 ++++
.../HomogeneousNextReactionHashingVector.cc | 13 ++
src/solvers/HomogeneousNextReactionHashingVector.d | 39 ++++
src/solvers/HomogeneousNextReactionLinearSearch.cc | 9 +
src/solvers/HomogeneousNextReactionLinearSearch.d | 38 +++
.../HomogeneousNextReactionLinearSearchPointer.cc | 9 +
.../HomogeneousNextReactionLinearSearchPointer.d | 36 +++
.../HomogeneousNextReactionLinearSearchUnrolled.cc | 9 +
.../HomogeneousNextReactionLinearSearchUnrolled.d | 39 ++++
...HomogeneousNextReactionPartitionCostAdaptive.cc | 12 +
.../HomogeneousNextReactionPartitionCostAdaptive.d | 38 +++
.../HomogeneousNextReactionPartitionFixedSize.cc | 10 +
.../HomogeneousNextReactionPartitionFixedSize.d | 38 +++
...HomogeneousNextReactionPartitionPropensities.cc | 10 +
.../HomogeneousNextReactionPartitionPropensities.d | 38 +++
...HomogeneousNextReactionPartitionSizeAdaptive.cc | 12 +
.../HomogeneousNextReactionPartitionSizeAdaptive.d | 38 +++
src/solvers/HomogeneousOdeReaction.ipp | 215 +++++++++++++++++
src/solvers/HomogeneousOdeReactionFixedForward.cc | 8 +
src/solvers/HomogeneousOdeReactionFixedForward.d | 19 ++
src/solvers/HomogeneousOdeReactionFixedMidpoint.cc | 8 +
src/solvers/HomogeneousOdeReactionFixedMidpoint.d | 19 ++
.../HomogeneousOdeReactionFixedRungeKutta4.cc | 8 +
.../HomogeneousOdeReactionFixedRungeKutta4.d | 19 ++
...omogeneousOdeReactionFixedRungeKuttaCashKarp.cc | 8 +
...HomogeneousOdeReactionFixedRungeKuttaCashKarp.d | 20 ++
.../HomogeneousOdeReactionRungeKuttaCashKarp.cc | 7 +
.../HomogeneousOdeReactionRungeKuttaCashKarp.d | 19 ++
src/solvers/HomogeneousTauLeaping.ipp | 188 +++++++++++++++
src/solvers/HomogeneousTauLeapingFixedForward.cc | 10 +
src/solvers/HomogeneousTauLeapingFixedForward.d | 41 ++++
src/solvers/HomogeneousTauLeapingFixedMidpoint.cc | 10 +
src/solvers/HomogeneousTauLeapingFixedMidpoint.d | 41 ++++
.../HomogeneousTauLeapingFixedRungeKutta4.cc | 10 +
.../HomogeneousTauLeapingFixedRungeKutta4.d | 41 ++++
src/solvers/HomogeneousTauLeapingForward.cc | 9 +
src/solvers/HomogeneousTauLeapingForward.d | 41 ++++
.../HomogeneousTauLeapingForwardNoCorrection.cc | 9 +
.../HomogeneousTauLeapingForwardNoCorrection.d | 41 ++++
src/solvers/HomogeneousTauLeapingImplicit.ipp | 160 +++++++++++++
.../HomogeneousTauLeapingImplicitFixedEuler.cc | 7 +
.../HomogeneousTauLeapingImplicitFixedEuler.d | 97 ++++++++
src/solvers/HomogeneousTauLeapingMidpoint.cc | 9 +
src/solvers/HomogeneousTauLeapingMidpoint.d | 41 ++++
.../HomogeneousTauLeapingMidpointNoCorrection.cc | 9 +
.../HomogeneousTauLeapingMidpointNoCorrection.d | 41 ++++
src/solvers/HomogeneousTauLeapingRungeKutta4.cc | 9 +
src/solvers/HomogeneousTauLeapingRungeKutta4.d | 41 ++++
...HomogeneousTauLeapingRungeKutta4NoCorrection.cc | 9 +
.../HomogeneousTauLeapingRungeKutta4NoCorrection.d | 42 ++++
src/solvers/HomogeneousTauLeapingSal.ipp | 171 ++++++++++++++
src/solvers/HomogeneousTauLeapingSalFixedLinear.cc | 7 +
src/solvers/HomogeneousTauLeapingSalFixedLinear.d | 42 ++++
src/solvers/HomogeneousTauLeapingSalLinear.cc | 5 +
src/solvers/HomogeneousTauLeapingSalLinear.d | 42 ++++
src/solvers/HomogeneousTrajectoryTreeFull.cc | 190 +++++++++++++++
src/solvers/HomogeneousTrajectoryTreeFull.d | 31 +++
...ogeneousHistogramsSteadyStateDirectTimeSteps.cc | 165 +++++++++++++
.../InhomogeneousHistogramsTransientDirect.cc | 159 +++++++++++++
.../InhomogeneousOdeReactionRungeKuttaCashKarp.cc | 165 +++++++++++++
.../InhomogeneousTimeSeriesAllReactionsDirect.cc | 179 ++++++++++++++
.../InhomogeneousTimeSeriesUniformDirect.cc | 171 ++++++++++++++
src/solvers/Makefile | 66 ++++++
src/solvers/Makefile.compilers | 150 ++++++++++++
src/solvers/Propensities.h | 112 +++++++++
src/solvers/SConstruct | 15 ++
src/solvers/env.py | 54 +++++
src/solvers/input.ipp | 108 +++++++++
src/solvers/msvs.py | 37 +++
src/solvers/vc10vars32.bat | 123 ++++++++++
src/solvers/vcvars32.bat | 1 +
155 files changed, 8309 insertions(+)
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