[med-svn] [cain] 02/06: Imported Upstream version 1.10+dfsg
Andreas Tille
tille at debian.org
Sat May 28 05:48:51 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cain.
commit e772f3eaffaa4d1cf350cc3cb5f738d3de71831d
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 17 22:37:08 2015 +0100
Imported Upstream version 1.10+dfsg
---
src/solvers/HomogeneousDirect2DSearch.d | 39 ---------
src/solvers/HomogeneousDirect2DSearchBubbleSort.d | 44 ----------
src/solvers/HomogeneousDirect2DSearchSorted.d | 44 ----------
.../HomogeneousDirectAllReactions2DSearch.d | 41 ---------
src/solvers/HomogeneousDirectBinarySearch.d | 34 --------
.../HomogeneousDirectBinarySearchRecursiveCdf.d | 35 --------
src/solvers/HomogeneousDirectBinarySearchSorted.d | 41 ---------
.../HomogeneousDirectCompositionRejection.d | 39 ---------
src/solvers/HomogeneousDirectLinearSearch.d | 39 ---------
.../HomogeneousDirectLinearSearchBubbleSort.d | 43 ----------
.../HomogeneousDirectLinearSearchDelayedUpdate.d | 39 ---------
src/solvers/HomogeneousDirectLinearSearchSorted.d | 45 ----------
.../HomogeneousDirectRejectionBinsSplitting.d | 45 ----------
src/solvers/HomogeneousFirstReaction.d | 29 -------
src/solvers/HomogeneousFirstReactionAbsoluteTime.d | 31 -------
src/solvers/HomogeneousFirstReactionInfluence.d | 31 -------
...usHistogramFinalHypoexponentialDirect2DSearch.d | 38 ---------
src/solvers/HomogeneousHistogramsAverage.d | 43 ----------
src/solvers/HomogeneousHistogramsAverageAps.d | 44 ----------
.../HomogeneousHistogramsAverageElapsedTime.d | 46 ----------
src/solvers/HomogeneousHistogramsDirect2DSearch.d | 43 ----------
src/solvers/HomogeneousHistogramsDirectTree.d | 42 ----------
.../HomogeneousHistogramsMultiTimeDirect2DSearch.d | 44 ----------
...sHistogramsTransientDirectTreeExponentialLast.d | 44 ----------
...HistogramsTransientDirectTreeExponentialLimit.d | 44 ----------
...ogramsTransientDirectTreeHypoexponentialLimit.d | 45 ----------
...togramsTransientDirectTreeNormalApproximation.d | 45 ----------
.../HomogeneousHybridDirectTauLeapingForward.d | 51 ------------
.../HomogeneousHybridDirectTauLeapingMidpoint.d | 51 ------------
.../HomogeneousHybridDirectTauLeapingRungeKutta4.d | 51 ------------
.../HomogeneousNextReactionBinaryHeapGibsonBruck.d | 37 ---------
.../HomogeneousNextReactionBinaryHeapPair.d | 37 ---------
.../HomogeneousNextReactionBinaryHeapPointer.d | 37 ---------
src/solvers/HomogeneousNextReactionHashing.d | 37 ---------
.../HomogeneousNextReactionHashingGenericList.d | 39 ---------
.../HomogeneousNextReactionHashingGenericVector.d | 39 ---------
src/solvers/HomogeneousNextReactionHashingVector.d | 39 ---------
src/solvers/HomogeneousNextReactionLinearSearch.d | 38 ---------
.../HomogeneousNextReactionLinearSearchPointer.d | 36 --------
.../HomogeneousNextReactionLinearSearchUnrolled.d | 39 ---------
.../HomogeneousNextReactionPartitionCostAdaptive.d | 38 ---------
.../HomogeneousNextReactionPartitionFixedSize.d | 38 ---------
.../HomogeneousNextReactionPartitionPropensities.d | 38 ---------
.../HomogeneousNextReactionPartitionSizeAdaptive.d | 38 ---------
src/solvers/HomogeneousOdeReactionFixedForward.d | 19 -----
src/solvers/HomogeneousOdeReactionFixedMidpoint.d | 19 -----
.../HomogeneousOdeReactionFixedRungeKutta4.d | 19 -----
...HomogeneousOdeReactionFixedRungeKuttaCashKarp.d | 20 -----
.../HomogeneousOdeReactionRungeKuttaCashKarp.d | 19 -----
src/solvers/HomogeneousTauLeapingFixedForward.d | 41 ---------
src/solvers/HomogeneousTauLeapingFixedMidpoint.d | 41 ---------
.../HomogeneousTauLeapingFixedRungeKutta4.d | 41 ---------
src/solvers/HomogeneousTauLeapingForward.d | 41 ---------
.../HomogeneousTauLeapingForwardNoCorrection.d | 41 ---------
.../HomogeneousTauLeapingImplicitFixedEuler.d | 97 ----------------------
src/solvers/HomogeneousTauLeapingMidpoint.d | 41 ---------
.../HomogeneousTauLeapingMidpointNoCorrection.d | 41 ---------
src/solvers/HomogeneousTauLeapingRungeKutta4.d | 41 ---------
.../HomogeneousTauLeapingRungeKutta4NoCorrection.d | 42 ----------
src/solvers/HomogeneousTauLeapingSalFixedLinear.d | 42 ----------
src/solvers/HomogeneousTauLeapingSalLinear.d | 42 ----------
src/solvers/HomogeneousTrajectoryTreeFull.d | 31 -------
62 files changed, 2458 deletions(-)
diff --git a/src/solvers/HomogeneousDirect2DSearch.d b/src/solvers/HomogeneousDirect2DSearch.d
deleted file mode 100644
index 3bee515..0000000
--- a/src/solvers/HomogeneousDirect2DSearch.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousDirect2DSearch.o HomogeneousDirect2DSearch.d : HomogeneousDirect2DSearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirect2DSearchBubbleSort.d b/src/solvers/HomogeneousDirect2DSearchBubbleSort.d
deleted file mode 100644
index 4219e78..0000000
--- a/src/solvers/HomogeneousDirect2DSearchBubbleSort.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousDirect2DSearchBubbleSort.o HomogeneousDirect2DSearchBubbleSort.d : \
- HomogeneousDirect2DSearchBubbleSort.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearchBubbleSort.h \
- ../numerical/random/discrete/DgPmfOrderedPairPointer.h \
- ../numerical/random/discrete/../../../ads/iterator/TransformIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/AdaptedIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/../functor/index.h \
- ../numerical/random/discrete/../../../ads/functor/select.h \
- ../numerical/random/discrete/../../../ext/pair.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ads/counter/CounterWithReset.h \
- ../numerical/random/discrete/../../../ads/counter/Counter.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirect2DSearchSorted.d b/src/solvers/HomogeneousDirect2DSearchSorted.d
deleted file mode 100644
index 19f23aa..0000000
--- a/src/solvers/HomogeneousDirect2DSearchSorted.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousDirect2DSearchSorted.o HomogeneousDirect2DSearchSorted.d : HomogeneousDirect2DSearchSorted.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearchSorted.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchSortedStatic.h \
- ../numerical/random/discrete/DgPmfOrderedPairPointer.h \
- ../numerical/random/discrete/../../../ads/iterator/TransformIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/AdaptedIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/../functor/index.h \
- ../numerical/random/discrete/../../../ads/functor/select.h \
- ../numerical/random/discrete/../../../ext/pair.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ads/counter/CounterWithReset.h \
- ../numerical/random/discrete/../../../ads/counter/Counter.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectAllReactions2DSearch.d b/src/solvers/HomogeneousDirectAllReactions2DSearch.d
deleted file mode 100644
index 6ab6ebf..0000000
--- a/src/solvers/HomogeneousDirectAllReactions2DSearch.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousDirectAllReactions2DSearch.o HomogeneousDirectAllReactions2DSearch.d : \
- HomogeneousDirectAllReactions2DSearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirectAllReactions.ipp ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectBinarySearch.d b/src/solvers/HomogeneousDirectBinarySearch.d
deleted file mode 100644
index b1b050e..0000000
--- a/src/solvers/HomogeneousDirectBinarySearch.d
+++ /dev/null
@@ -1,34 +0,0 @@
-HomogeneousDirectBinarySearch.o HomogeneousDirectBinarySearch.d : HomogeneousDirectBinarySearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorBinarySearch.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectBinarySearchRecursiveCdf.d b/src/solvers/HomogeneousDirectBinarySearchRecursiveCdf.d
deleted file mode 100644
index 6f87af4..0000000
--- a/src/solvers/HomogeneousDirectBinarySearchRecursiveCdf.d
+++ /dev/null
@@ -1,35 +0,0 @@
-HomogeneousDirectBinarySearchRecursiveCdf.o HomogeneousDirectBinarySearchRecursiveCdf.d : \
- HomogeneousDirectBinarySearchRecursiveCdf.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorBinarySearchRecursiveCdf.h \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/DiscreteGeneratorBinarySearchRecursiveCdf.ipp \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectBinarySearchSorted.d b/src/solvers/HomogeneousDirectBinarySearchSorted.d
deleted file mode 100644
index e7541fc..0000000
--- a/src/solvers/HomogeneousDirectBinarySearchSorted.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousDirectBinarySearchSorted.o HomogeneousDirectBinarySearchSorted.d : \
- HomogeneousDirectBinarySearchSorted.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorBinarySearchSorted.h \
- ../numerical/random/discrete/DgPmfOrderedPairPointer.h \
- ../numerical/random/discrete/../../../ads/iterator/TransformIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/AdaptedIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/../functor/index.h \
- ../numerical/random/discrete/../../../ads/functor/select.h \
- ../numerical/random/discrete/../../../ext/pair.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ads/counter/CounterWithReset.h \
- ../numerical/random/discrete/../../../ads/counter/Counter.h \
- ../numerical/random/discrete/../../../array/StaticArrayOfArrays.h \
- ../numerical/random/discrete/../../../array/../ext/vector.h \
- ../numerical/random/discrete/../../../array/StaticArrayOfArrays.ipp \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectCompositionRejection.d b/src/solvers/HomogeneousDirectCompositionRejection.d
deleted file mode 100644
index 1514e02..0000000
--- a/src/solvers/HomogeneousDirectCompositionRejection.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousDirectCompositionRejection.o HomogeneousDirectCompositionRejection.d : \
- HomogeneousDirectCompositionRejection.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorCompositionRejection.h \
- ../numerical/random/discrete/DiscreteGeneratorCompositionRejectionStatic.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectLinearSearch.d b/src/solvers/HomogeneousDirectLinearSearch.d
deleted file mode 100644
index 86cb5d6..0000000
--- a/src/solvers/HomogeneousDirectLinearSearch.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousDirectLinearSearch.o HomogeneousDirectLinearSearch.d : HomogeneousDirectLinearSearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorLinearSearch.h \
- ../numerical/random/discrete/DgPmfAndSum.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectLinearSearchBubbleSort.d b/src/solvers/HomogeneousDirectLinearSearchBubbleSort.d
deleted file mode 100644
index a94881b..0000000
--- a/src/solvers/HomogeneousDirectLinearSearchBubbleSort.d
+++ /dev/null
@@ -1,43 +0,0 @@
-HomogeneousDirectLinearSearchBubbleSort.o HomogeneousDirectLinearSearchBubbleSort.d : \
- HomogeneousDirectLinearSearchBubbleSort.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorLinearSearchBubbleSort.h \
- ../numerical/random/discrete/DgPmfAndSumOrderedPairPointer.h \
- ../numerical/random/discrete/DgPmfOrderedPairPointer.h \
- ../numerical/random/discrete/../../../ads/iterator/TransformIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/AdaptedIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/../functor/index.h \
- ../numerical/random/discrete/../../../ads/functor/select.h \
- ../numerical/random/discrete/../../../ext/pair.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectLinearSearchDelayedUpdate.d b/src/solvers/HomogeneousDirectLinearSearchDelayedUpdate.d
deleted file mode 100644
index 095b4d1..0000000
--- a/src/solvers/HomogeneousDirectLinearSearchDelayedUpdate.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousDirectLinearSearchDelayedUpdate.o HomogeneousDirectLinearSearchDelayedUpdate.d : \
- HomogeneousDirectLinearSearchDelayedUpdate.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorLinearSearchDelayedUpdate.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectLinearSearchSorted.d b/src/solvers/HomogeneousDirectLinearSearchSorted.d
deleted file mode 100644
index 35be400..0000000
--- a/src/solvers/HomogeneousDirectLinearSearchSorted.d
+++ /dev/null
@@ -1,45 +0,0 @@
-HomogeneousDirectLinearSearchSorted.o HomogeneousDirectLinearSearchSorted.d : \
- HomogeneousDirectLinearSearchSorted.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorLinearSearchSorted.h \
- ../numerical/random/discrete/DgPmfAndSumOrderedPairPointer.h \
- ../numerical/random/discrete/DgPmfOrderedPairPointer.h \
- ../numerical/random/discrete/../../../ads/iterator/TransformIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/AdaptedIterator.h \
- ../numerical/random/discrete/../../../ads/iterator/../functor/index.h \
- ../numerical/random/discrete/../../../ads/functor/select.h \
- ../numerical/random/discrete/../../../ext/pair.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../../../ads/counter/CounterWithReset.h \
- ../numerical/random/discrete/../../../ads/counter/Counter.h \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousDirectRejectionBinsSplitting.d b/src/solvers/HomogeneousDirectRejectionBinsSplitting.d
deleted file mode 100644
index 434ae68..0000000
--- a/src/solvers/HomogeneousDirectRejectionBinsSplitting.d
+++ /dev/null
@@ -1,45 +0,0 @@
-HomogeneousDirectRejectionBinsSplitting.o HomogeneousDirectRejectionBinsSplitting.d : \
- HomogeneousDirectRejectionBinsSplitting.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGeneratorRejectionBinsSplitting.h \
- ../numerical/random/discrete/DiscreteGeneratorRejectionBinsSplittingStatic.h \
- ../numerical/random/discrete/DgBinConstants.h \
- ../numerical/random/discrete/../uniform/Default.h \
- ../numerical/random/discrete/../../../ads/algorithm/sort.h \
- ../numerical/random/discrete/../../../ads/algorithm/Triplet.h \
- ../numerical/random/discrete/../../../ads/algorithm/../functor/compose.h \
- ../numerical/random/discrete/../../../ads/algorithm/../functor/select.h \
- ../numerical/random/discrete/../../../ads/algorithm/sort.ipp \
- ../numerical/random/discrete/../../../ads/functor/compare_handle.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/DiscreteGeneratorRejectionBinsSplittingStatic.ipp \
- ../numerical/random/discrete/DiscreteGeneratorRejectionBinsSplitting.ipp \
- HomogeneousDirect.ipp ../stochastic/Direct.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousFirstReaction.d b/src/solvers/HomogeneousFirstReaction.d
deleted file mode 100644
index e8ec2c4..0000000
--- a/src/solvers/HomogeneousFirstReaction.d
+++ /dev/null
@@ -1,29 +0,0 @@
-HomogeneousFirstReaction.o HomogeneousFirstReaction.d : HomogeneousFirstReaction.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/FirstReaction.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/FirstReaction.ipp \
- HomogeneousFirstReaction.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousFirstReactionAbsoluteTime.d b/src/solvers/HomogeneousFirstReactionAbsoluteTime.d
deleted file mode 100644
index 821b618..0000000
--- a/src/solvers/HomogeneousFirstReactionAbsoluteTime.d
+++ /dev/null
@@ -1,31 +0,0 @@
-HomogeneousFirstReactionAbsoluteTime.o HomogeneousFirstReactionAbsoluteTime.d : \
- HomogeneousFirstReactionAbsoluteTime.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/FirstReactionAbsoluteTime.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/FirstReactionAbsoluteTime.ipp \
- HomogeneousFirstReaction.ipp ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousFirstReactionInfluence.d b/src/solvers/HomogeneousFirstReactionInfluence.d
deleted file mode 100644
index d98f977..0000000
--- a/src/solvers/HomogeneousFirstReactionInfluence.d
+++ /dev/null
@@ -1,31 +0,0 @@
-HomogeneousFirstReactionInfluence.o HomogeneousFirstReactionInfluence.d : \
- HomogeneousFirstReactionInfluence.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/FirstReactionInfluence.h ../stochastic/FirstReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/FirstReaction.ipp \
- ../stochastic/FirstReactionInfluence.ipp HomogeneousFirstReaction.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramFinalHypoexponentialDirect2DSearch.d b/src/solvers/HomogeneousHistogramFinalHypoexponentialDirect2DSearch.d
deleted file mode 100644
index 384087b..0000000
--- a/src/solvers/HomogeneousHistogramFinalHypoexponentialDirect2DSearch.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousHistogramFinalHypoexponentialDirect2DSearch.o HomogeneousHistogramFinalHypoexponentialDirect2DSearch.d : \
- HomogeneousHistogramFinalHypoexponentialDirect2DSearch.cc \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/discrete/../uniform/Default.h \
- ../numerical/random/discrete/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/discrete/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- HomogeneousHistogramFinalHypoexponentialDirect.ipp \
- ../stochastic/HistogramFinalHypoexponentialDirect.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/HistogramsPackedArray.h ../stochastic/HistogramsPacked.h \
- ../stochastic/HistogramReference.h ../stochastic/TimeEpochOffset.h \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsAverage.d b/src/solvers/HomogeneousHistogramsAverage.d
deleted file mode 100644
index 59d35da..0000000
--- a/src/solvers/HomogeneousHistogramsAverage.d
+++ /dev/null
@@ -1,43 +0,0 @@
-HomogeneousHistogramsAverage.o HomogeneousHistogramsAverage.d : HomogeneousHistogramsAverage.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsAverage.ipp ../stochastic/HistogramsAverage.h \
- ../stochastic/HistogramsAverageBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsAveragePackedArray.h \
- ../stochastic/HistogramsAveragePacked.h \
- ../stochastic/HistogramReference.h ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsAverageAps.d b/src/solvers/HomogeneousHistogramsAverageAps.d
deleted file mode 100644
index cc55aeb..0000000
--- a/src/solvers/HomogeneousHistogramsAverageAps.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousHistogramsAverageAps.o HomogeneousHistogramsAverageAps.d : HomogeneousHistogramsAverageAps.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsAverageAps.ipp \
- ../stochastic/HistogramsAverageAps.h \
- ../stochastic/HistogramsAverageBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsAveragePackedArray.h \
- ../stochastic/HistogramsAveragePacked.h \
- ../stochastic/HistogramReference.h ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsAverageElapsedTime.d b/src/solvers/HomogeneousHistogramsAverageElapsedTime.d
deleted file mode 100644
index d6c382b..0000000
--- a/src/solvers/HomogeneousHistogramsAverageElapsedTime.d
+++ /dev/null
@@ -1,46 +0,0 @@
-HomogeneousHistogramsAverageElapsedTime.o HomogeneousHistogramsAverageElapsedTime.d : \
- HomogeneousHistogramsAverageElapsedTime.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsAverageElapsedTime.ipp \
- ../stochastic/HistogramsAverageElapsedTime.h \
- ../stochastic/HistogramsAverageBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsAveragePackedArray.h \
- ../stochastic/HistogramsAveragePacked.h \
- ../stochastic/HistogramReference.h \
- ../stochastic/modifiedRecordedSpecies.h ../stochastic/ReactionSet.h \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsDirect2DSearch.d b/src/solvers/HomogeneousHistogramsDirect2DSearch.d
deleted file mode 100644
index 68f9038..0000000
--- a/src/solvers/HomogeneousHistogramsDirect2DSearch.d
+++ /dev/null
@@ -1,43 +0,0 @@
-HomogeneousHistogramsDirect2DSearch.o HomogeneousHistogramsDirect2DSearch.d : \
- HomogeneousHistogramsDirect2DSearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsDirect.ipp ../stochastic/HistogramsDirect.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsDirectTree.d b/src/solvers/HomogeneousHistogramsDirectTree.d
deleted file mode 100644
index d56abd2..0000000
--- a/src/solvers/HomogeneousHistogramsDirectTree.d
+++ /dev/null
@@ -1,42 +0,0 @@
-HomogeneousHistogramsDirectTree.o HomogeneousHistogramsDirectTree.d : HomogeneousHistogramsDirectTree.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsDirectTree.ipp \
- ../stochastic/HistogramsDirectTree.h ../stochastic/HistogramsBase.h \
- ../stochastic/Direct.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsMultiTimeDirect2DSearch.d b/src/solvers/HomogeneousHistogramsMultiTimeDirect2DSearch.d
deleted file mode 100644
index 0ca9bd4..0000000
--- a/src/solvers/HomogeneousHistogramsMultiTimeDirect2DSearch.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousHistogramsMultiTimeDirect2DSearch.o HomogeneousHistogramsMultiTimeDirect2DSearch.d : \
- HomogeneousHistogramsMultiTimeDirect2DSearch.cc \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../numerical/random/exponential/../uniform/Default.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsMultiTimeDirect.ipp \
- ../stochastic/HistogramsMultiTimeDirect.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLast.d b/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLast.d
deleted file mode 100644
index 4930703..0000000
--- a/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLast.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousHistogramsTransientDirectTreeExponentialLast.o HomogeneousHistogramsTransientDirectTreeExponentialLast.d : \
- HomogeneousHistogramsTransientDirectTreeExponentialLast.cc \
- ../stochastic/HomogeneousHistogramsTransientDirectTreeExponentialLast.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsTransientDirect.ipp \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLimit.d b/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLimit.d
deleted file mode 100644
index ae6cda7..0000000
--- a/src/solvers/HomogeneousHistogramsTransientDirectTreeExponentialLimit.d
+++ /dev/null
@@ -1,44 +0,0 @@
-HomogeneousHistogramsTransientDirectTreeExponentialLimit.o HomogeneousHistogramsTransientDirectTreeExponentialLimit.d : \
- HomogeneousHistogramsTransientDirectTreeExponentialLimit.cc \
- ../stochastic/HomogeneousHistogramsTransientDirectTreeExponentialLimit.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsTransientDirect.ipp \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.d b/src/solvers/HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.d
deleted file mode 100644
index e67415e..0000000
--- a/src/solvers/HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.d
+++ /dev/null
@@ -1,45 +0,0 @@
-HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.o HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.d : \
- HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.cc \
- ../stochastic/HomogeneousHistogramsTransientDirectTreeHypoexponentialLimit.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../stochastic/../numerical/random/hypoexponential/HypoexponentialDistributionDistinctDynamicMinimumParameters.h \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsTransientDirect.ipp \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHistogramsTransientDirectTreeNormalApproximation.d b/src/solvers/HomogeneousHistogramsTransientDirectTreeNormalApproximation.d
deleted file mode 100644
index 916bc23..0000000
--- a/src/solvers/HomogeneousHistogramsTransientDirectTreeNormalApproximation.d
+++ /dev/null
@@ -1,45 +0,0 @@
-HomogeneousHistogramsTransientDirectTreeNormalApproximation.o HomogeneousHistogramsTransientDirectTreeNormalApproximation.d : \
- HomogeneousHistogramsTransientDirectTreeNormalApproximation.cc \
- ../stochastic/HomogeneousHistogramsTransientDirectTreeNormalApproximation.h \
- ../stochastic/HistogramsBase.h ../stochastic/Direct.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/Direct.ipp ../stochastic/HistogramsPackedArray.h \
- ../stochastic/HistogramsPacked.h ../stochastic/HistogramReference.h \
- ../stochastic/../numerical/random/hypoexponential/HypoexponentialDistributionNormalApproximation.h \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearch.h \
- ../numerical/random/discrete/DiscreteGenerator2DSearchStatic.h \
- ../numerical/random/discrete/DgPmf.h \
- ../numerical/random/discrete/../../../ext/vector.h \
- ../numerical/random/discrete/linearSearch.h \
- ../numerical/random/discrete/../../../loki/static_check.h \
- ../numerical/random/discrete/../../../loki/TypeManip.h \
- ../numerical/random/discrete/linearSearch.ipp \
- ../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- HomogeneousHistogramsTransientDirect.ipp \
- ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHybridDirectTauLeapingForward.d b/src/solvers/HomogeneousHybridDirectTauLeapingForward.d
deleted file mode 100644
index 32317c9..0000000
--- a/src/solvers/HomogeneousHybridDirectTauLeapingForward.d
+++ /dev/null
@@ -1,51 +0,0 @@
-HomogeneousHybridDirectTauLeapingForward.o HomogeneousHybridDirectTauLeapingForward.d : \
- HomogeneousHybridDirectTauLeapingForward.cc \
- HomogeneousHybridDirectTauLeaping.ipp \
- ../stochastic/HybridDirectTauLeaping.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TauLeapingDynamic.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../uniform/Default.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeapingDynamic.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/../numerical/random/discrete/DiscreteGeneratorDynamic.h \
- ../stochastic/../numerical/random/discrete/linearSearch.h \
- ../stochastic/../numerical/random/discrete/../../../loki/static_check.h \
- ../stochastic/../numerical/random/discrete/../../../loki/TypeManip.h \
- ../stochastic/../numerical/random/discrete/linearSearch.ipp \
- ../stochastic/../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/discrete/../../../ext/vector.h \
- ../stochastic/HybridDirectTauLeaping.ipp \
- ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHybridDirectTauLeapingMidpoint.d b/src/solvers/HomogeneousHybridDirectTauLeapingMidpoint.d
deleted file mode 100644
index ea35723..0000000
--- a/src/solvers/HomogeneousHybridDirectTauLeapingMidpoint.d
+++ /dev/null
@@ -1,51 +0,0 @@
-HomogeneousHybridDirectTauLeapingMidpoint.o HomogeneousHybridDirectTauLeapingMidpoint.d : \
- HomogeneousHybridDirectTauLeapingMidpoint.cc \
- HomogeneousHybridDirectTauLeaping.ipp \
- ../stochastic/HybridDirectTauLeaping.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TauLeapingDynamic.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../uniform/Default.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeapingDynamic.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/../numerical/random/discrete/DiscreteGeneratorDynamic.h \
- ../stochastic/../numerical/random/discrete/linearSearch.h \
- ../stochastic/../numerical/random/discrete/../../../loki/static_check.h \
- ../stochastic/../numerical/random/discrete/../../../loki/TypeManip.h \
- ../stochastic/../numerical/random/discrete/linearSearch.ipp \
- ../stochastic/../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/discrete/../../../ext/vector.h \
- ../stochastic/HybridDirectTauLeaping.ipp \
- ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousHybridDirectTauLeapingRungeKutta4.d b/src/solvers/HomogeneousHybridDirectTauLeapingRungeKutta4.d
deleted file mode 100644
index 1ccc8bf..0000000
--- a/src/solvers/HomogeneousHybridDirectTauLeapingRungeKutta4.d
+++ /dev/null
@@ -1,51 +0,0 @@
-HomogeneousHybridDirectTauLeapingRungeKutta4.o HomogeneousHybridDirectTauLeapingRungeKutta4.d : \
- HomogeneousHybridDirectTauLeapingRungeKutta4.cc \
- HomogeneousHybridDirectTauLeaping.ipp \
- ../stochastic/HybridDirectTauLeaping.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TauLeapingDynamic.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../uniform/Default.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeapingDynamic.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/../numerical/random/discrete/DiscreteGeneratorDynamic.h \
- ../stochastic/../numerical/random/discrete/linearSearch.h \
- ../stochastic/../numerical/random/discrete/../../../loki/static_check.h \
- ../stochastic/../numerical/random/discrete/../../../loki/TypeManip.h \
- ../stochastic/../numerical/random/discrete/linearSearch.ipp \
- ../stochastic/../numerical/random/discrete/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/discrete/../../../ext/vector.h \
- ../stochastic/HybridDirectTauLeaping.ipp \
- ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionBinaryHeapGibsonBruck.d b/src/solvers/HomogeneousNextReactionBinaryHeapGibsonBruck.d
deleted file mode 100644
index 583510f..0000000
--- a/src/solvers/HomogeneousNextReactionBinaryHeapGibsonBruck.d
+++ /dev/null
@@ -1,37 +0,0 @@
-HomogeneousNextReactionBinaryHeapGibsonBruck.o HomogeneousNextReactionBinaryHeapGibsonBruck.d : \
- HomogeneousNextReactionBinaryHeapGibsonBruck.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionBinaryHeapPair.d b/src/solvers/HomogeneousNextReactionBinaryHeapPair.d
deleted file mode 100644
index ce272f8..0000000
--- a/src/solvers/HomogeneousNextReactionBinaryHeapPair.d
+++ /dev/null
@@ -1,37 +0,0 @@
-HomogeneousNextReactionBinaryHeapPair.o HomogeneousNextReactionBinaryHeapPair.d : \
- HomogeneousNextReactionBinaryHeapPair.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionBinaryHeapPointer.d b/src/solvers/HomogeneousNextReactionBinaryHeapPointer.d
deleted file mode 100644
index 0c7a716..0000000
--- a/src/solvers/HomogeneousNextReactionBinaryHeapPointer.d
+++ /dev/null
@@ -1,37 +0,0 @@
-HomogeneousNextReactionBinaryHeapPointer.o HomogeneousNextReactionBinaryHeapPointer.d : \
- HomogeneousNextReactionBinaryHeapPointer.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionHashing.d b/src/solvers/HomogeneousNextReactionHashing.d
deleted file mode 100644
index 988f3d2..0000000
--- a/src/solvers/HomogeneousNextReactionHashing.d
+++ /dev/null
@@ -1,37 +0,0 @@
-HomogeneousNextReactionHashing.o HomogeneousNextReactionHashing.d : HomogeneousNextReactionHashing.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueHashing.h \
- ../ads/indexedPriorityQueue/HashingChaining.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionHashingGenericList.d b/src/solvers/HomogeneousNextReactionHashingGenericList.d
deleted file mode 100644
index 40b005a..0000000
--- a/src/solvers/HomogeneousNextReactionHashingGenericList.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousNextReactionHashingGenericList.o HomogeneousNextReactionHashingGenericList.d : \
- HomogeneousNextReactionHashingGenericList.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueHashing.h \
- ../ads/indexedPriorityQueue/HashingChaining.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- ../ads/indexedPriorityQueue/HashingChainingGeneric.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionHashingGenericVector.d b/src/solvers/HomogeneousNextReactionHashingGenericVector.d
deleted file mode 100644
index 1939e52..0000000
--- a/src/solvers/HomogeneousNextReactionHashingGenericVector.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousNextReactionHashingGenericVector.o HomogeneousNextReactionHashingGenericVector.d : \
- HomogeneousNextReactionHashingGenericVector.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueHashing.h \
- ../ads/indexedPriorityQueue/HashingChaining.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- ../ads/indexedPriorityQueue/HashingChainingGeneric.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionHashingVector.d b/src/solvers/HomogeneousNextReactionHashingVector.d
deleted file mode 100644
index e1412d9..0000000
--- a/src/solvers/HomogeneousNextReactionHashingVector.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousNextReactionHashingVector.o HomogeneousNextReactionHashingVector.d : \
- HomogeneousNextReactionHashingVector.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueHashing.h \
- ../ads/indexedPriorityQueue/HashingChaining.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- ../ads/indexedPriorityQueue/HashingChainingVector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionLinearSearch.d b/src/solvers/HomogeneousNextReactionLinearSearch.d
deleted file mode 100644
index cb656e1..0000000
--- a/src/solvers/HomogeneousNextReactionLinearSearch.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousNextReactionLinearSearch.o HomogeneousNextReactionLinearSearch.d : \
- HomogeneousNextReactionLinearSearch.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearchSimple.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- ../ads/indexedPriorityQueue/../../loki/TypeManip.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionLinearSearchPointer.d b/src/solvers/HomogeneousNextReactionLinearSearchPointer.d
deleted file mode 100644
index c02dd70..0000000
--- a/src/solvers/HomogeneousNextReactionLinearSearchPointer.d
+++ /dev/null
@@ -1,36 +0,0 @@
-HomogeneousNextReactionLinearSearchPointer.o HomogeneousNextReactionLinearSearchPointer.d : \
- HomogeneousNextReactionLinearSearchPointer.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionLinearSearchUnrolled.d b/src/solvers/HomogeneousNextReactionLinearSearchUnrolled.d
deleted file mode 100644
index 81aecf8..0000000
--- a/src/solvers/HomogeneousNextReactionLinearSearchUnrolled.d
+++ /dev/null
@@ -1,39 +0,0 @@
-HomogeneousNextReactionLinearSearchUnrolled.o HomogeneousNextReactionLinearSearchUnrolled.d : \
- HomogeneousNextReactionLinearSearchUnrolled.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearchUnrolled.h \
- ../ads/indexedPriorityQueue/../algorithm/extremeElement.h \
- ../ads/indexedPriorityQueue/../algorithm/extremeElement.ipp \
- ../ads/indexedPriorityQueue/../../loki/TypeManip.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionPartitionCostAdaptive.d b/src/solvers/HomogeneousNextReactionPartitionCostAdaptive.d
deleted file mode 100644
index 9a69698..0000000
--- a/src/solvers/HomogeneousNextReactionPartitionCostAdaptive.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousNextReactionPartitionCostAdaptive.o HomogeneousNextReactionPartitionCostAdaptive.d : \
- HomogeneousNextReactionPartitionCostAdaptive.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearchCostAdaptive.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearch.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionPartitionFixedSize.d b/src/solvers/HomogeneousNextReactionPartitionFixedSize.d
deleted file mode 100644
index 082a67e..0000000
--- a/src/solvers/HomogeneousNextReactionPartitionFixedSize.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousNextReactionPartitionFixedSize.o HomogeneousNextReactionPartitionFixedSize.d : \
- HomogeneousNextReactionPartitionFixedSize.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearchFixedSize.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearch.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionPartitionPropensities.d b/src/solvers/HomogeneousNextReactionPartitionPropensities.d
deleted file mode 100644
index 43d67ed..0000000
--- a/src/solvers/HomogeneousNextReactionPartitionPropensities.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousNextReactionPartitionPropensities.o HomogeneousNextReactionPartitionPropensities.d : \
- HomogeneousNextReactionPartitionPropensities.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearchPropensities.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearch.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousNextReactionPartitionSizeAdaptive.d b/src/solvers/HomogeneousNextReactionPartitionSizeAdaptive.d
deleted file mode 100644
index 7484168..0000000
--- a/src/solvers/HomogeneousNextReactionPartitionSizeAdaptive.d
+++ /dev/null
@@ -1,38 +0,0 @@
-HomogeneousNextReactionPartitionSizeAdaptive.o HomogeneousNextReactionPartitionSizeAdaptive.d : \
- HomogeneousNextReactionPartitionSizeAdaptive.cc \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearchSizeAdaptive.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueuePartitionLinearSearch.h \
- ../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../ads/indexedPriorityQueue/../../ext/vector.h \
- HomogeneousNextReaction.ipp ../stochastic/NextReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/TimeEpochOffset.h ../stochastic/NextReaction.ipp \
- ../stochastic/ReactionPriorityQueue.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueLinearSearch.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../numerical/random/exponential/Default.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousOdeReactionFixedForward.d b/src/solvers/HomogeneousOdeReactionFixedForward.d
deleted file mode 100644
index e884b18..0000000
--- a/src/solvers/HomogeneousOdeReactionFixedForward.d
+++ /dev/null
@@ -1,19 +0,0 @@
-HomogeneousOdeReactionFixedForward.o HomogeneousOdeReactionFixedForward.d : \
- HomogeneousOdeReactionFixedForward.cc HomogeneousOdeReaction.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp ../stochastic/../ext/vector.h \
- ../stochastic/../loki/TypeManip.h ../stochastic/Reaction.ipp \
- ../stochastic/ReactionSet.ipp ../stochastic/OdeReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp ../stochastic/State.ipp \
- ../stochastic/OdeReaction.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousOdeReactionFixedMidpoint.d b/src/solvers/HomogeneousOdeReactionFixedMidpoint.d
deleted file mode 100644
index 1fa35df..0000000
--- a/src/solvers/HomogeneousOdeReactionFixedMidpoint.d
+++ /dev/null
@@ -1,19 +0,0 @@
-HomogeneousOdeReactionFixedMidpoint.o HomogeneousOdeReactionFixedMidpoint.d : \
- HomogeneousOdeReactionFixedMidpoint.cc HomogeneousOdeReaction.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp ../stochastic/../ext/vector.h \
- ../stochastic/../loki/TypeManip.h ../stochastic/Reaction.ipp \
- ../stochastic/ReactionSet.ipp ../stochastic/OdeReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp ../stochastic/State.ipp \
- ../stochastic/OdeReaction.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousOdeReactionFixedRungeKutta4.d b/src/solvers/HomogeneousOdeReactionFixedRungeKutta4.d
deleted file mode 100644
index a5e80bc..0000000
--- a/src/solvers/HomogeneousOdeReactionFixedRungeKutta4.d
+++ /dev/null
@@ -1,19 +0,0 @@
-HomogeneousOdeReactionFixedRungeKutta4.o HomogeneousOdeReactionFixedRungeKutta4.d : \
- HomogeneousOdeReactionFixedRungeKutta4.cc HomogeneousOdeReaction.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp ../stochastic/../ext/vector.h \
- ../stochastic/../loki/TypeManip.h ../stochastic/Reaction.ipp \
- ../stochastic/ReactionSet.ipp ../stochastic/OdeReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp ../stochastic/State.ipp \
- ../stochastic/OdeReaction.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousOdeReactionFixedRungeKuttaCashKarp.d b/src/solvers/HomogeneousOdeReactionFixedRungeKuttaCashKarp.d
deleted file mode 100644
index aa520f5..0000000
--- a/src/solvers/HomogeneousOdeReactionFixedRungeKuttaCashKarp.d
+++ /dev/null
@@ -1,20 +0,0 @@
-HomogeneousOdeReactionFixedRungeKuttaCashKarp.o HomogeneousOdeReactionFixedRungeKuttaCashKarp.d : \
- HomogeneousOdeReactionFixedRungeKuttaCashKarp.cc \
- HomogeneousOdeReaction.ipp ../stochastic/Propensities.h \
- ../stochastic/ReactionSet.h ../stochastic/Reaction.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp ../stochastic/../ext/vector.h \
- ../stochastic/../loki/TypeManip.h ../stochastic/Reaction.ipp \
- ../stochastic/ReactionSet.ipp ../stochastic/OdeReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp ../stochastic/State.ipp \
- ../stochastic/OdeReaction.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousOdeReactionRungeKuttaCashKarp.d b/src/solvers/HomogeneousOdeReactionRungeKuttaCashKarp.d
deleted file mode 100644
index aa2f2ad..0000000
--- a/src/solvers/HomogeneousOdeReactionRungeKuttaCashKarp.d
+++ /dev/null
@@ -1,19 +0,0 @@
-HomogeneousOdeReactionRungeKuttaCashKarp.o HomogeneousOdeReactionRungeKuttaCashKarp.d : \
- HomogeneousOdeReactionRungeKuttaCashKarp.cc HomogeneousOdeReaction.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp ../stochastic/../ext/vector.h \
- ../stochastic/../loki/TypeManip.h ../stochastic/Reaction.ipp \
- ../stochastic/ReactionSet.ipp ../stochastic/OdeReaction.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp ../stochastic/State.ipp \
- ../stochastic/OdeReaction.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingFixedForward.d b/src/solvers/HomogeneousTauLeapingFixedForward.d
deleted file mode 100644
index a682091..0000000
--- a/src/solvers/HomogeneousTauLeapingFixedForward.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingFixedForward.o HomogeneousTauLeapingFixedForward.d : \
- HomogeneousTauLeapingFixedForward.cc HomogeneousTauLeaping.ipp \
- ../stochastic/TauLeaping.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingFixedMidpoint.d b/src/solvers/HomogeneousTauLeapingFixedMidpoint.d
deleted file mode 100644
index 87980ca..0000000
--- a/src/solvers/HomogeneousTauLeapingFixedMidpoint.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingFixedMidpoint.o HomogeneousTauLeapingFixedMidpoint.d : \
- HomogeneousTauLeapingFixedMidpoint.cc HomogeneousTauLeaping.ipp \
- ../stochastic/TauLeaping.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingFixedRungeKutta4.d b/src/solvers/HomogeneousTauLeapingFixedRungeKutta4.d
deleted file mode 100644
index 79a7670..0000000
--- a/src/solvers/HomogeneousTauLeapingFixedRungeKutta4.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingFixedRungeKutta4.o HomogeneousTauLeapingFixedRungeKutta4.d : \
- HomogeneousTauLeapingFixedRungeKutta4.cc HomogeneousTauLeaping.ipp \
- ../stochastic/TauLeaping.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingForward.d b/src/solvers/HomogeneousTauLeapingForward.d
deleted file mode 100644
index e220640..0000000
--- a/src/solvers/HomogeneousTauLeapingForward.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingForward.o HomogeneousTauLeapingForward.d : HomogeneousTauLeapingForward.cc \
- HomogeneousTauLeaping.ipp ../stochastic/TauLeaping.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingForwardNoCorrection.d b/src/solvers/HomogeneousTauLeapingForwardNoCorrection.d
deleted file mode 100644
index 2b430ee..0000000
--- a/src/solvers/HomogeneousTauLeapingForwardNoCorrection.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingForwardNoCorrection.o HomogeneousTauLeapingForwardNoCorrection.d : \
- HomogeneousTauLeapingForwardNoCorrection.cc HomogeneousTauLeaping.ipp \
- ../stochastic/TauLeaping.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingImplicitFixedEuler.d b/src/solvers/HomogeneousTauLeapingImplicitFixedEuler.d
deleted file mode 100644
index 92a4e9c..0000000
--- a/src/solvers/HomogeneousTauLeapingImplicitFixedEuler.d
+++ /dev/null
@@ -1,97 +0,0 @@
-HomogeneousTauLeapingImplicitFixedEuler.o HomogeneousTauLeapingImplicitFixedEuler.d : \
- HomogeneousTauLeapingImplicitFixedEuler.cc \
- HomogeneousTauLeapingImplicit.ipp ../stochastic/TauLeapingImplicit.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../uniform/Default.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/poisson/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/../third-party/Eigen/LU \
- ../stochastic/../third-party/Eigen/Core \
- ../stochastic/../third-party/Eigen/src/Core/util/DisableMSVCWarnings.h \
- ../stochastic/../third-party/Eigen/src/Core/util/Macros.h \
- ../stochastic/../third-party/Eigen/src/Core/util/Constants.h \
- ../stochastic/../third-party/Eigen/src/Core/util/ForwardDeclarations.h \
- ../stochastic/../third-party/Eigen/src/Core/util/Meta.h \
- ../stochastic/../third-party/Eigen/src/Core/util/XprHelper.h \
- ../stochastic/../third-party/Eigen/src/Core/util/StaticAssert.h \
- ../stochastic/../third-party/Eigen/src/Core/util/Memory.h \
- ../stochastic/../third-party/Eigen/src/Core/NumTraits.h \
- ../stochastic/../third-party/Eigen/src/Core/MathFunctions.h \
- ../stochastic/../third-party/Eigen/src/Core/GenericPacketMath.h \
- ../stochastic/../third-party/Eigen/src/Core/arch/SSE/PacketMath.h \
- ../stochastic/../third-party/Eigen/src/Core/Functors.h \
- ../stochastic/../third-party/Eigen/src/Core/MatrixBase.h \
- ../stochastic/../third-party/Eigen/src/Core/Coeffs.h \
- ../stochastic/../third-party/Eigen/src/Core/Assign.h \
- ../stochastic/../third-party/Eigen/src/Core/MatrixStorage.h \
- ../stochastic/../third-party/Eigen/src/Core/NestByValue.h \
- ../stochastic/../third-party/Eigen/src/Core/Flagged.h \
- ../stochastic/../third-party/Eigen/src/Core/Matrix.h \
- ../stochastic/../third-party/Eigen/src/Core/Cwise.h \
- ../stochastic/../third-party/Eigen/src/Core/CwiseBinaryOp.h \
- ../stochastic/../third-party/Eigen/src/Core/CwiseUnaryOp.h \
- ../stochastic/../third-party/Eigen/src/Core/CwiseNullaryOp.h \
- ../stochastic/../third-party/Eigen/src/Core/Dot.h \
- ../stochastic/../third-party/Eigen/src/Core/Product.h \
- ../stochastic/../third-party/Eigen/src/Core/DiagonalProduct.h \
- ../stochastic/../third-party/Eigen/src/Core/SolveTriangular.h \
- ../stochastic/../third-party/Eigen/src/Core/MapBase.h \
- ../stochastic/../third-party/Eigen/src/Core/Map.h \
- ../stochastic/../third-party/Eigen/src/Core/Block.h \
- ../stochastic/../third-party/Eigen/src/Core/Minor.h \
- ../stochastic/../third-party/Eigen/src/Core/Transpose.h \
- ../stochastic/../third-party/Eigen/src/Core/DiagonalMatrix.h \
- ../stochastic/../third-party/Eigen/src/Core/DiagonalCoeffs.h \
- ../stochastic/../third-party/Eigen/src/Core/Sum.h \
- ../stochastic/../third-party/Eigen/src/Core/Redux.h \
- ../stochastic/../third-party/Eigen/src/Core/Visitor.h \
- ../stochastic/../third-party/Eigen/src/Core/Fuzzy.h \
- ../stochastic/../third-party/Eigen/src/Core/IO.h \
- ../stochastic/../third-party/Eigen/src/Core/Swap.h \
- ../stochastic/../third-party/Eigen/src/Core/CommaInitializer.h \
- ../stochastic/../third-party/Eigen/src/Core/Part.h \
- ../stochastic/../third-party/Eigen/src/Core/CacheFriendlyProduct.h \
- ../stochastic/../third-party/Eigen/src/Core/util/EnableMSVCWarnings.h \
- ../stochastic/../third-party/Eigen/src/LU/LU.h \
- ../stochastic/../third-party/Eigen/src/LU/Determinant.h \
- ../stochastic/../third-party/Eigen/src/LU/Inverse.h \
- ../stochastic/../third-party/Eigen/Array \
- ../stochastic/../third-party/Eigen/src/Array/CwiseOperators.h \
- ../stochastic/../third-party/Eigen/src/Array/Functors.h \
- ../stochastic/../third-party/Eigen/src/Array/BooleanRedux.h \
- ../stochastic/../third-party/Eigen/src/Array/Select.h \
- ../stochastic/../third-party/Eigen/src/Array/PartialRedux.h \
- ../stochastic/../third-party/Eigen/src/Array/Random.h \
- ../stochastic/../third-party/Eigen/src/Array/Norms.h \
- ../stochastic/TauLeapingImplicit.ipp \
- ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingMidpoint.d b/src/solvers/HomogeneousTauLeapingMidpoint.d
deleted file mode 100644
index 4fd7e92..0000000
--- a/src/solvers/HomogeneousTauLeapingMidpoint.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingMidpoint.o HomogeneousTauLeapingMidpoint.d : HomogeneousTauLeapingMidpoint.cc \
- HomogeneousTauLeaping.ipp ../stochastic/TauLeaping.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingMidpointNoCorrection.d b/src/solvers/HomogeneousTauLeapingMidpointNoCorrection.d
deleted file mode 100644
index 7f75fa0..0000000
--- a/src/solvers/HomogeneousTauLeapingMidpointNoCorrection.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingMidpointNoCorrection.o HomogeneousTauLeapingMidpointNoCorrection.d : \
- HomogeneousTauLeapingMidpointNoCorrection.cc HomogeneousTauLeaping.ipp \
- ../stochastic/TauLeaping.h ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingRungeKutta4.d b/src/solvers/HomogeneousTauLeapingRungeKutta4.d
deleted file mode 100644
index 8ceb02a..0000000
--- a/src/solvers/HomogeneousTauLeapingRungeKutta4.d
+++ /dev/null
@@ -1,41 +0,0 @@
-HomogeneousTauLeapingRungeKutta4.o HomogeneousTauLeapingRungeKutta4.d : HomogeneousTauLeapingRungeKutta4.cc \
- HomogeneousTauLeaping.ipp ../stochastic/TauLeaping.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingRungeKutta4NoCorrection.d b/src/solvers/HomogeneousTauLeapingRungeKutta4NoCorrection.d
deleted file mode 100644
index 0af419c..0000000
--- a/src/solvers/HomogeneousTauLeapingRungeKutta4NoCorrection.d
+++ /dev/null
@@ -1,42 +0,0 @@
-HomogeneousTauLeapingRungeKutta4NoCorrection.o HomogeneousTauLeapingRungeKutta4NoCorrection.d : \
- HomogeneousTauLeapingRungeKutta4NoCorrection.cc \
- HomogeneousTauLeaping.ipp ../stochastic/TauLeaping.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeaping.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingSalFixedLinear.d b/src/solvers/HomogeneousTauLeapingSalFixedLinear.d
deleted file mode 100644
index 62771d0..0000000
--- a/src/solvers/HomogeneousTauLeapingSalFixedLinear.d
+++ /dev/null
@@ -1,42 +0,0 @@
-HomogeneousTauLeapingSalFixedLinear.o HomogeneousTauLeapingSalFixedLinear.d : \
- HomogeneousTauLeapingSalFixedLinear.cc HomogeneousTauLeapingSal.ipp \
- ../stochastic/TauLeapingSal.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/PropensityTimeDerivatives.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeapingSal.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTauLeapingSalLinear.d b/src/solvers/HomogeneousTauLeapingSalLinear.d
deleted file mode 100644
index 4fc2abd..0000000
--- a/src/solvers/HomogeneousTauLeapingSalLinear.d
+++ /dev/null
@@ -1,42 +0,0 @@
-HomogeneousTauLeapingSalLinear.o HomogeneousTauLeapingSalLinear.d : HomogeneousTauLeapingSalLinear.cc \
- HomogeneousTauLeapingSal.ipp ../stochastic/TauLeapingSal.h \
- ../stochastic/Solver.h ../stochastic/State.h \
- ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/PropensityTimeDerivatives.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h \
- ../stochastic/../ads/indexedPriorityQueue/IndexedPriorityQueueBase.h \
- ../stochastic/../ads/indexedPriorityQueue/../../ext/vector.h \
- ../stochastic/../numerical/random/uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/uniform/Default.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h \
- ../stochastic/../numerical/random/poisson/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInversionChopDown.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.h \
- ../stochastic/../numerical/random/poisson/../normal/Default.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.h \
- ../stochastic/../numerical/random/poisson/../normal/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/poisson/../normal/NormalGeneratorZigguratVoss.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorAcceptanceComplementWinrand.ipp \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorNormal.h \
- ../stochastic/../numerical/random/poisson/../../round/round.h \
- ../stochastic/../numerical/random/poisson/PoissonGeneratorInvAcNormSure.ipp \
- ../stochastic/TauLeapingSal.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp input.ipp
diff --git a/src/solvers/HomogeneousTrajectoryTreeFull.d b/src/solvers/HomogeneousTrajectoryTreeFull.d
deleted file mode 100644
index 2bc5424..0000000
--- a/src/solvers/HomogeneousTrajectoryTreeFull.d
+++ /dev/null
@@ -1,31 +0,0 @@
-HomogeneousTrajectoryTreeFull.o HomogeneousTrajectoryTreeFull.d : HomogeneousTrajectoryTreeFull.cc \
- ../stochastic/TrajectoryTreeFull.h ../stochastic/Solver.h \
- ../stochastic/State.h ../stochastic/../array/SparseVector.h \
- ../stochastic/../array/../ads/algorithm/is_sorted.h \
- ../stochastic/../array/../ads/functor/select.h \
- ../stochastic/../array/../ads/iterator/TransformIterator.h \
- ../stochastic/../array/../ads/iterator/AdaptedIterator.h \
- ../stochastic/../array/../ads/iterator/../functor/index.h \
- ../stochastic/../array/../ext/pair.h \
- ../stochastic/../array/SparseVector.ipp \
- ../stochastic/../array/StaticArrayOfArrays.h \
- ../stochastic/../array/../ext/vector.h \
- ../stochastic/../array/StaticArrayOfArrays.ipp \
- ../stochastic/../ext/vector.h ../stochastic/State.ipp \
- ../stochastic/Propensities.h ../stochastic/ReactionSet.h \
- ../stochastic/Reaction.h ../stochastic/../loki/TypeManip.h \
- ../stochastic/Reaction.ipp ../stochastic/ReactionSet.ipp \
- ../stochastic/HistogramsPackedArray.h ../stochastic/HistogramsPacked.h \
- ../stochastic/HistogramReference.h \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- ../stochastic/../numerical/random/exponential/../uniform/ContinuousUniformGenerator.h \
- ../stochastic/../numerical/random/exponential/../uniform/Default.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.h \
- ../stochastic/../numerical/random/exponential/../uniform/DiscreteUniformGeneratorMt19937.ipp \
- ../stochastic/../numerical/random/exponential/ExponentialGeneratorZiggurat.ipp \
- ../stochastic/ReactionSet.h ../stochastic/reactionPropensityInfluence.h \
- ../stochastic/reactionPropensityInfluence.ipp ../ads/timer/Timer.h \
- ../ads/timer/Timer.ipp ../ads/utility/ParseOptionsArguments.h \
- ../ads/utility/ParseOptionsArguments.ipp \
- ../numerical/random/exponential/ExponentialGeneratorZiggurat.h \
- input.ipp
--
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