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A

a - Variable in class neurord.numeric.math.Matrix
 
aboutXRotation(double) - Static method in class neurord.geom.Geom
 
aboutYRotation(double) - Static method in class neurord.geom.Geom
 
aboutZRotation(double) - Static method in class neurord.geom.Geom
 
abssum(int[]) - Static method in class neurord.util.ArrayUtil
 
action - Variable in class neurord.model.SDRun
 
AdaptiveGridCalc - Class in neurord.numeric.grid
 
AdaptiveGridCalc(int, SDRun) - Constructor for class neurord.numeric.grid.AdaptiveGridCalc
 
add(Position) - Method in class neurord.geom.GPosition
 
add(Vector) - Method in class neurord.geom.GVector
 
add(Object) - Method in class neurord.model.Reaction
 
add(double) - Method in class neurord.numeric.math.Matrix
 
add(Matrix) - Method in class neurord.numeric.math.Matrix
 
add(TriangleStrip) - Method in class neurord.numeric.morph.TrianglesSet
 
addDependent(NextEventQueue.NextEvent, String[], boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
addElement(VolumeElement) - Method in class neurord.numeric.morph.VolumeGrid
 
addElements(List<? extends VolumeElement>) - Method in class neurord.numeric.morph.VolumeGrid
 
addFileAppender(String) - Static method in class neurord.util.CustomFileAppender
 
addFloatValued(ArrayList<FloatValued>) - Method in class neurord.model.ConcentrationSet
 
addFloatValued(ArrayList<FloatValued>) - Method in class neurord.model.SurfaceDensitySet
 
addLibraryPaths(String...) - Static method in class neurord.util.LibUtil
Add a path to java.library.path
addNeighbor(MorphPoint) - Method in class neurord.model.MorphPoint
 
addNeighbor(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
addNormals(ArrayList<float[]>) - Method in class neurord.numeric.morph.TriangleStrip
 
addOffsetChild(MorphPoint) - Method in class neurord.model.MorphPoint
 
addOffsetChild(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
addPoint(double, double, double, double, double, double) - Method in class neurord.numeric.morph.TriangleStrip
 
addPositions(ArrayList<float[]>) - Method in class neurord.numeric.morph.TriangleStrip
 
addRelations(HashMap<Integer, ArrayList<NextEventQueue.NextEvent>>, String[], boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
addRelations(HashMap<Integer, ArrayList<NextEventQueue.NextEvent>>, String[], boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
addRelations(HashMap<Integer, ArrayList<NextEventQueue.NextEvent>>, String[], boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
addRelations(HashMap<Integer, ArrayList<NextEventQueue.NextEvent>>, String[], boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
addResultWriter(ResultWriter) - Method in class neurord.numeric.BaseCalc
 
addReverse(NextEventQueue.NextEvent) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
addTo(ArrayList<StimulationTable.Stimulation>, int, InjectionStim) - Static method in class neurord.numeric.chem.StimulationTable.Stimulation
 
advance(double, double) - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
advance(double, double) - Method in class neurord.numeric.grid.DeterministicGridCalc
 
advance(double, double) - Method in class neurord.numeric.grid.GridCalc
 
advance(double, double, double, int[][], List<IGridCalc.Happening>) - Method in class neurord.numeric.grid.NextEventQueue
Execute an event if the next event is before tstop.
advance(double, double) - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
advance() - Method in class neurord.numeric.pool.DeterministicPoolCalc
 
advance() - Method in class neurord.numeric.pool.ForwardEulerPoolCalc
 
advance() - Method in class neurord.numeric.pool.ForwardExponentialPoolCalc
 
advance() - Method in class neurord.numeric.pool.ImplicitEulerPoolCalc
 
advance() - Method in class neurord.numeric.pool.RungeKutta4PoolCalc
 
advance() - Method in class neurord.numeric.pool.SemiImplicitEulerPoolCalc
 
algoID - Variable in class neurord.numeric.BaseCalc
 
algorithm - Variable in class neurord.model.SDRun
 
alignTop(TreePoint, TreePoint, double) - Method in class neurord.numeric.morph.TreePoint
 
all_settings - Static variable in class neurord.util.Settings
 
alongArea - Variable in class neurord.numeric.morph.VolumeElement
 
angleBetween(Vector, Vector) - Static method in class neurord.geom.Geom
 
append(LogEvent) - Method in class neurord.util.CustomFileAppender
 
apply(Movable) - Method in class neurord.geom.GTranslation
 
Arithmetic - Class in neurord.numeric.math
Arithmetic functions.
Arithmetic() - Constructor for class neurord.numeric.math.Arithmetic
Makes this class non instantiable, but still let's others inherit from it.
ArrayUtil - Class in neurord.util
 
ArrayUtil() - Constructor for class neurord.util.ArrayUtil
 
at - Variable in class neurord.model.EndPoint
 
at - Variable in class neurord.model.Section
 
atFraction - Variable in class neurord.model.EndPoint
 
augmentProperties(Properties) - Static method in class neurord.util.Settings
 
AVAGADRO - Static variable in class neurord.phys.Phys
 
average(Matrix[], Matrix[], double) - Static method in class neurord.numeric.math.Matrix
 
average(Matrix, Matrix, double) - Static method in class neurord.numeric.math.Matrix
 
avgAbs() - Method in class neurord.numeric.math.Column
 

B

BaseCalc - Class in neurord.numeric
Units: concentrations are expressed in nM and volumes in cubic microns So, in these units, one Litre is 10^15 and a 1M solution is 10^9.
BaseCalc(int, SDRun) - Constructor for class neurord.numeric.BaseCalc
 
BaseCalc.algorithm_t - Enum in neurord.numeric
 
BaseCalc.distribution_t - Enum in neurord.numeric
 
BaseCalc.output_t - Enum in neurord.numeric
 
baseGrid(TreePoint, TreePoint, String) - Method in class neurord.disc.DiscBoxer
 
baseGrid(TreePoint, TreePoint, String) - Method in class neurord.disc.DiscSplitter
 
binomial(double, long) - Static method in class neurord.numeric.math.Arithmetic
Efficiently returns the binomial coefficient, often also referred to as "n over k" or "n choose k".
binomial(long, long) - Static method in class neurord.numeric.math.Arithmetic
Efficiently returns the binomial coefficient, often also referred to as "n over k" or "n choose k".
Binomial - Class in neurord.numeric.math
Binomial distribution; See the math definition and animated definition.
Binomial(RandomGenerator) - Constructor for class neurord.numeric.math.Binomial
Constructs a binomial distribution.
binomial - Variable in class neurord.numeric.stochastic.StepGenerator
 
BinomialLike - Interface in neurord.numeric.math
 
BinomialTable - Class in neurord.numeric.stochastic
 
boundary - Variable in class neurord.numeric.morph.VolumeElement
 
BranchTest - Class in neurord.examples.branch
 
BranchTest() - Constructor for class neurord.examples.branch.BranchTest
 
BranchTest3 - Class in neurord.examples.branch
 
BranchTest3() - Constructor for class neurord.examples.branch.BranchTest3
 
buildGrid(double, HashMap<String, Double>) - Method in class neurord.disc.DiscBoxer
 
buildGrid() - Method in class neurord.disc.DiscSplitter
 
buildGrid(TreePoint[], double[], double, double, HashMap<String, Double>) - Static method in class neurord.disc.LineBoxer
 
buildGrid(TreePoint[], double, HashMap<String, Double>, double[], VolumeGrid.geometry_t, double) - Static method in class neurord.disc.TreeBoxDiscretizer
 
buildGrid(double, HashMap<String, Double>, double[], double) - Method in class neurord.disc.TreeCurvedElementDiscretizer
 

C

c_pm - Variable in class neurord.numeric.math.Poisson
 
cable - Class in neurord.neuroml
 
cable() - Constructor for class neurord.neuroml.cable
 
cable - Variable in class neurord.neuroml.segment
 
cableGroups - Variable in class neurord.neuroml.cell
 
cables - Variable in class neurord.neuroml.cell
 
cables - Variable in class neurord.neuroml.MorphMLCableGroup
 
calcPropensity() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
calcPropensity() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
calcPropensity() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
calculatePropensity(int[], int[], int[], int[], int[], double, double, int[]) - Static method in class neurord.numeric.grid.AdaptiveGridCalc
 
calculatePropensity(int[], int[], int[], int[], int[], double, double, int[]) - Static method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
calculation - Variable in class neurord.model.SDRun
 
ceil(double) - Static method in class neurord.numeric.math.Arithmetic
Returns the smallest long >= value.
cell - Class in neurord.neuroml
 
cell() - Constructor for class neurord.neuroml.cell
 
cells - Variable in class neurord.neuroml.morphml
 
center - Variable in class neurord.numeric.morph.VolumeElement
 
characters(char[], int, int) - Method in class neurord.xml.ModelReader.NamespaceFiller
 
chbevl(double, double[], int) - Static method in class neurord.numeric.math.Arithmetic
Evaluates the series of Chebyshev polynomials Ti at argument x/2.
checkHasPositions() - Method in class neurord.model.Segment
 
checkResolved(HashMap<String, Segment>) - Method in class neurord.model.Segment
 
child(T, int) - Method in class neurord.numeric.grid.NextEventQueue.PriorityTree
 
close() - Method in class neurord.numeric.BaseCalc
 
close() - Method in interface neurord.numeric.grid.ResultWriter
 
close() - Method in class neurord.numeric.grid.ResultWriterHDF5
 
close(IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
close() - Method in class neurord.numeric.grid.ResultWriterText
 
close() - Static method in class neurord.util.CustomFileAppender
 
closeTrial(IGridCalc) - Method in interface neurord.numeric.grid.ResultWriter
 
closeTrial(int, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
closeTrial(IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
closeTrial(IGridCalc) - Method in class neurord.numeric.grid.ResultWriterText
 
cog(Position[]) - Static method in class neurord.geom.Geom
 
Column - Class in neurord.numeric.math
 
Column(int) - Constructor for class neurord.numeric.math.Column
 
Column(double[]) - Constructor for class neurord.numeric.math.Column
 
COLUMN - Static variable in class neurord.numeric.math.Matrix
 
conc - Variable in class neurord.inter.SDState
 
Concentration - Class in neurord.model
 
Concentration() - Constructor for class neurord.model.Concentration
 
concentrations - Variable in class neurord.model.ConcentrationSet
 
ConcentrationSet - Class in neurord.model
 
ConcentrationSet() - Constructor for class neurord.model.ConcentrationSet
 
concentrationSets - Variable in class neurord.model.InitialConditions
 
concs_times_count - Variable in class neurord.numeric.grid.ResultWriterHDF5.PopulationOutput
 
configureConsoleLogging() - Static method in class neurord.util.Logging
 
configureFileLogging(String) - Static method in class neurord.util.Logging
 
connections - Variable in class neurord.numeric.morph.VolumeElement
 
copy() - Method in class neurord.numeric.math.Column
 
copy() - Method in class neurord.numeric.math.Matrix
 
copy(int[][], int[][]) - Static method in class neurord.util.ArrayUtil
 
copy(double[][], double[][]) - Static method in class neurord.util.ArrayUtil
 
copyMat() - Method in class neurord.numeric.math.Matrix
 
coupleTo(VolumeElement, double) - Method in class neurord.numeric.morph.VolumeElement
 
create(int[][], RandomGenerator, StepGenerator, VolumeGrid, ReactionTable, StimulationTable, boolean, double, double, boolean, String) - Static method in class neurord.numeric.grid.NextEventQueue
 
createAppender(String, String, String, String, String, String, String, String, Layout<? extends Serializable>, Filter, String, String, Configuration) - Static method in class neurord.util.CustomFileAppender
 
createExtensibleArray(String, Group, Datatype, String, String, String, long...) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
createTrial(int) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
crossProduct(Vector, Vector) - Static method in class neurord.geom.Geom
 
crudeExpOf(double) - Method in class neurord.numeric.math.Matrix
 
CuboidVolumeElement - Class in neurord.numeric.morph
 
CuboidVolumeElement(String, String, String, Position[], Position[], double, Position, double, double, double, double, double) - Constructor for class neurord.numeric.morph.CuboidVolumeElement
 
curvedElements() - Method in class neurord.model.Discretization
 
CurvedVolumeElement - Class in neurord.numeric.morph
 
CurvedVolumeElement(String, String, String, Position[], Position[], double, Position, double, double) - Constructor for class neurord.numeric.morph.CurvedVolumeElement
 
CurvedVolumeSlice - Class in neurord.disc
 
CurvedVolumeSlice(double, double, double) - Constructor for class neurord.disc.CurvedVolumeSlice
 
CustomFileAppender - Class in neurord.util
 

D

dead - Variable in class neurord.numeric.morph.TreePoint
 
decrementBy(Column) - Method in class neurord.numeric.math.Column
 
deltaZ - Variable in class neurord.numeric.morph.VolumeElement
 
dependencies - Variable in class neurord.model.OutputScheme
 
dependent() - Method in interface neurord.numeric.grid.IGridCalc.Event
 
dependent() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
depth2D - Variable in class neurord.model.SDRun
 
description() - Method in interface neurord.numeric.grid.IGridCalc.Event
 
description() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
deserialize(String, Long) - Static method in class neurord.model.SDRun
 
deserialize(File, Long) - Static method in class neurord.model.SDRun
 
det() - Method in class neurord.numeric.math.Matrix
 
DeterministicGridCalc - Class in neurord.numeric.grid
 
DeterministicGridCalc(int, SDRun) - Constructor for class neurord.numeric.grid.DeterministicGridCalc
 
DeterministicPoolCalc - Class in neurord.numeric.pool
 
DeterministicPoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.DeterministicPoolCalc
 
DetTest - Class in neurord.examples.NOEPAC
 
DetTest() - Constructor for class neurord.examples.NOEPAC.DetTest
 
dgx - Variable in class neurord.numeric.morph.TreePoint
 
dgy - Variable in class neurord.numeric.morph.TreePoint
 
diameter - Variable in class neurord.neuroml.MorphMLPoint
 
dim() - Method in class neurord.numeric.math.Matrix
 
DiscBoxer - Class in neurord.disc
 
DiscBoxer(TreePoint[], double[]) - Constructor for class neurord.disc.DiscBoxer
 
discFill(Position, Position, String, String, double[], double) - Method in class neurord.disc.CurvedVolumeSlice
 
discFill(Position, Position, String, String) - Method in class neurord.numeric.morph.VolumeSlice
 
Discretization - Class in neurord.model
 
Discretization() - Constructor for class neurord.model.Discretization
 
DiscretizedSpine - Class in neurord.disc
 
DiscretizedSpine(double[], double[], String[], String[]) - Constructor for class neurord.disc.DiscretizedSpine
 
DiscSplitter - Class in neurord.disc
 
DiscSplitter(TreePoint[], double, HashMap<String, Double>, double[], double) - Constructor for class neurord.disc.DiscSplitter
 
distal - Variable in class neurord.neuroml.segment
 
distanceBetween(Position, Position) - Static method in class neurord.geom.Geom
 
distanceBetween(double[], double[]) - Static method in class neurord.geom.Geom
 
distanceTo(MorphPoint) - Method in class neurord.model.MorphPoint
 
distanceTo(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
distribution - Variable in class neurord.model.SDRun
 
distribution - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
dl - Variable in class neurord.numeric.math.Poisson
 
dotProduct(Vector, Vector) - Static method in class neurord.geom.Geom
 
double_t - Static variable in class neurord.numeric.grid.ResultWriterHDF5
 
doubleFactorials - Static variable in class neurord.numeric.math.Arithmetic
 
DoubleListAdapter - Class in neurord.xml
 
DoubleListAdapter() - Constructor for class neurord.xml.DoubleListAdapter
 
DoubleMatrixAdapter - Class in neurord.xml
 
DoubleMatrixAdapter() - Constructor for class neurord.xml.DoubleMatrixAdapter
 
dpcInit() - Method in class neurord.numeric.pool.DeterministicPoolCalc
 
dpcInit() - Method in class neurord.numeric.pool.ImplicitEulerPoolCalc
 
dr - Variable in class neurord.numeric.math.Poisson
 
dummy - Static variable in class neurord.util.CustomFileAppender
 
dump() - Method in class neurord.numeric.math.Matrix
 
duration - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 

E

effectiveRate(double, double) - Method in class neurord.numeric.chem.StimulationTable.Stimulation
 
element() - Method in interface neurord.numeric.grid.IGridCalc.Event
"source" voxel number
element() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
element2() - Method in interface neurord.numeric.grid.IGridCalc.Event
"target" voxel number (different from source only for diffusion)
element2() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
element2() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
element2() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
ElementConnection - Class in neurord.numeric.morph
 
ElementConnection(VolumeElement, VolumeElement, double) - Constructor for class neurord.numeric.morph.ElementConnection
 
end - Variable in class neurord.model.Segment
 
end - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
endElement(String, String, String) - Method in class neurord.xml.ModelReader.NamespaceFiller
 
EndPoint - Class in neurord.model
 
EndPoint(String, double, double, double, double) - Constructor for class neurord.model.EndPoint
 
endPosition(Vector) - Static method in class neurord.geom.Geom
 
endtime() - Method in class neurord.numeric.grid.GridCalc
 
error(SAXParseException) - Method in class neurord.xml.ModelReader.NamespaceFiller
 
ev1vec(int) - Method in class neurord.numeric.math.Matrix
 
event_number() - Method in interface neurord.numeric.grid.IGridCalc.Event
Index in the sequential numbering of all events
event_number() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
event_number() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 
event_number() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
event_statistics - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
event_type() - Method in interface neurord.numeric.grid.IGridCalc.Event
 
event_type() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
event_type() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
event_type() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
event_type() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
eventCount() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
eventCount() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
eventCount() - Method in class neurord.numeric.grid.GridCalc
 
eventCount() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
events - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_cache - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_event - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_extent - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_kind - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_original - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_time - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
events_waited - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
expOf(double) - Method in class neurord.numeric.math.Matrix
 
exponential(double) - Method in class neurord.numeric.math.MersenneTwister
 
exponential(double) - Method in interface neurord.numeric.math.RandomGenerator
A number from the probability distribution [ t ≥ 0] a exp(-at)
exposedArea - Variable in class neurord.numeric.morph.VolumeElement
 
extendExtensibleArray(H5ScalarDS, long) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
extent() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
extent() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 
extent - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
extent: how many "instances" of this event are scheduled to occur.

F

f1 - Variable in class neurord.numeric.math.Poisson
 
f2 - Variable in class neurord.numeric.math.Poisson
 
f4 - Variable in class neurord.numeric.math.Poisson
 
f5 - Variable in class neurord.numeric.math.Poisson
 
factorial(int) - Static method in class neurord.numeric.math.Arithmetic
Instantly returns the factorial k!.
FALLBACK - Static variable in class neurord.util.Settings
 
filename - Variable in class neurord.model.OutputSet
 
FileUtil - Class in neurord.util
 
FileUtil() - Constructor for class neurord.util.FileUtil
 
fill(int[][], int) - Static method in class neurord.util.ArrayUtil
 
fill(double[][], double) - Static method in class neurord.util.ArrayUtil
 
fill(int[][][], int) - Static method in class neurord.util.ArrayUtil
 
filterElementsByLabel(String) - Method in class neurord.numeric.morph.VolumeGrid
 
findBracket(double[], double) - Static method in class neurord.util.ArrayUtil
 
findNearest(TreePoint, TreePoint) - Method in class neurord.disc.SegmentSlicer
 
FitConstraints - Class in neurord.model
 
FitConstraints() - Constructor for class neurord.model.FitConstraints
 
fitConstraints - Variable in class neurord.model.InitialConditions
 
fix() - Method in class neurord.numeric.morph.VolumeGrid
 
flatten() - Method in class neurord.numeric.math.Matrix
 
flatten(double[][], int) - Static method in class neurord.util.ArrayUtil
 
flatten(int[][], long, int) - Static method in class neurord.util.ArrayUtil
 
flatten(int[][][], long, int) - Static method in class neurord.util.ArrayUtil
 
flatten(int[], int[][][], int, int) - Static method in class neurord.util.ArrayUtil
 
flip() - Method in class neurord.numeric.morph.TriangleStrip
 
FloatValued - Interface in neurord.inter
 
floor(double) - Static method in class neurord.numeric.math.Arithmetic
Returns the largest long <= value.
flushEvents(double, boolean) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
flushPopulation(double) - Method in class neurord.numeric.grid.ResultWriterHDF5.PopulationOutput
 
footer() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
footer() - Method in class neurord.numeric.grid.GridCalc
 
footer() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
footer() - Method in class neurord.numeric.grid.StochasticGridCalc
 
formatSide(ArrayList<? extends SpecieRef>) - Static method in class neurord.model.Reaction
 
formatTimespan(long) - Static method in class neurord.util.TimeUtil
 
ForwardEulerPoolCalc - Class in neurord.numeric.pool
 
ForwardEulerPoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.ForwardEulerPoolCalc
 
ForwardExponentialPoolCalc - Class in neurord.numeric.pool
 
ForwardExponentialPoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.ForwardExponentialPoolCalc
 
fractAlongParent - Variable in class neurord.neuroml.cable
 
fromString(String) - Static method in enum neurord.numeric.morph.VolumeGrid.geometry_t
 
fromToVector(Position, Position) - Static method in class neurord.geom.Geom
 
fromZRotation(Vector) - Static method in class neurord.geom.Geom
 

G

gammln(double) - Method in class neurord.numeric.math.MersenneTwister
 
gammln(double) - Method in interface neurord.numeric.math.RandomGenerator
 
gammln(double) - Static method in class neurord.numeric.math.RandomMath
 
gaussian() - Method in class neurord.numeric.math.MersenneTwister
 
gaussian() - Method in interface neurord.numeric.math.RandomGenerator
 
gaussianRV() - Static method in class neurord.numeric.math.NRRandom
 
generateBinomial(int, double) - Method in class neurord.numeric.math.Binomial
* Binomial-Distribution - Acceptance Rejection/Inversion * * * Acceptance Rejection method combined with Inversion for * generating Binomial random numbers with parameters * n (number of trials) and p (probability of success).
generateID(String) - Static method in class neurord.model.Specie
 
Geom - Class in neurord.geom
 
Geom() - Constructor for class neurord.geom.Geom
 
get() - Method in class neurord.numeric.grid.NextEventQueue.Numbering
 
getAlgorithm() - Method in class neurord.model.SDRun
 
getAlongArea() - Method in class neurord.numeric.morph.VolumeElement
 
getArea(Position[]) - Static method in class neurord.geom.Geom
 
getAreaIndexes(String[]) - Method in class neurord.numeric.morph.VolumeGrid
 
getAsElementsText() - Method in class neurord.numeric.morph.VolumeGrid
 
getAsPlainText() - Method in class neurord.numeric.morph.VolumeElement
 
getAsTableText() - Method in class neurord.numeric.morph.VolumeGrid
 
getAsText() - Method in class neurord.numeric.morph.VolumeElement
 
getAsText() - Method in class neurord.numeric.morph.VolumeGrid
 
getAttribute(H5File, String, String) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
getBalancedSlices(double, int) - Method in class neurord.disc.SegmentSlicer
 
getBoundaries() - Method in class neurord.disc.DiscretizedSpine
 
getBoundary() - Method in class neurord.numeric.morph.VolumeElement
 
getCalc(int, SDRun) - Method in enum neurord.SDCalcType
 
getColumn(int) - Method in class neurord.numeric.math.Matrix
 
getColumnData() - Method in class neurord.numeric.math.Matrix
 
getConc1() - Method in class neurord.inter.SDState
 
getConc2() - Method in class neurord.inter.SDState
 
getConcentrations() - Method in class neurord.numeric.StaticCalc
 
getConcentrationSets() - Method in class neurord.model.InitialConditions
 
getConnections() - Method in class neurord.numeric.morph.VolumeElement
 
getContactArea() - Method in class neurord.numeric.morph.ElementConnection
 
getData() - Method in class neurord.inter.SDState
 
getData() - Method in class neurord.numeric.math.Column
 
getDefaultMaxElementSide() - Method in class neurord.model.Discretization
 
getDeltaZ() - Method in class neurord.numeric.morph.VolumeElement
 
getDensity() - Method in class neurord.numeric.morph.SpinePopulation
 
getDiffusionConstant() - Method in class neurord.model.Specie
 
getDiffusionConstants() - Method in class neurord.numeric.chem.ReactionTable
 
getDiscretization() - Method in class neurord.model.SDRun
 
getDistal() - Method in class neurord.neuroml.segment
 
getDistribution() - Method in class neurord.model.InjectionStim
 
getDuration() - Method in class neurord.model.InjectionStim
 
getDX() - Method in class neurord.geom.GVector
 
getDX() - Method in interface neurord.geom.Vector
 
getDY() - Method in class neurord.geom.GVector
 
getDY() - Method in interface neurord.geom.Vector
 
getDZ() - Method in class neurord.geom.GVector
 
getDZ() - Method in interface neurord.geom.Vector
 
getElement(int) - Method in class neurord.numeric.morph.VolumeGrid
 
getElement(int) - Method in class neurord.numeric.morph.VolumeLine
 
getElement(int, int) - Method in class neurord.numeric.morph.VolumeSlice
 
getElementA() - Method in class neurord.numeric.morph.ElementConnection
 
getElementB() - Method in class neurord.numeric.morph.ElementConnection
 
getElementConcentrations() - Method in class neurord.numeric.StaticCalc
 
getElementRegion(int) - Method in class neurord.numeric.morph.VolumeGrid
 
getElementRegions() - Method in class neurord.numeric.morph.VolumeGrid
 
getElements() - Method in class neurord.disc.CurvedVolumeSlice
 
getElements() - Method in class neurord.numeric.morph.VolumeLine
 
getElements() - Method in class neurord.numeric.morph.VolumeSlice
 
getElementsInRegion(String) - Method in class neurord.numeric.morph.VolumeGrid
 
getElementVolumes() - Method in class neurord.numeric.morph.VolumeGrid
 
getEnd() - Method in class neurord.model.InjectionStim
 
getEnd() - Method in class neurord.model.Segment
 
getEndTime() - Method in class neurord.model.SDRun
 
getEnvironmentVariable(String, int) - Static method in class neurord.util.Settings
 
getEvents() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
getEvents() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
getEvents() - Method in interface neurord.numeric.grid.IGridCalc
 
getEvents() - Method in class neurord.numeric.grid.NextEventQueue
 
getEvents() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
getEventStatistics() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
getEventStatistics() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
getEventStatistics() - Method in interface neurord.numeric.grid.IGridCalc
 
getEventStatistics() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
getExposedArea() - Method in class neurord.numeric.morph.VolumeElement
 
getExposedAreas() - Method in class neurord.numeric.morph.VolumeGrid
 
getFinal() - Method in interface neurord.inter.Transitional
 
getFinal() - Method in class neurord.neuroml.cell
 
getFinal() - Method in class neurord.neuroml.morphml
 
getFirstOverlap(double[], double[][]) - Method in class neurord.numeric.morph.VolumeLine
 
getFixedStepDt() - Method in class neurord.model.SDRun
 
getFixedWidthSlices(double, HashMap<String, Double>) - Method in class neurord.disc.SegmentSlicer
 
getFloatValuedElements() - Method in class neurord.model.InitialConditions
 
getForwardRate() - Method in class neurord.model.Reaction
 
getGeometry() - Method in class neurord.model.SDRun
 
getGridNumbers(int[][], int[], int[], IGridCalc) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
getGridPartConc(int, int) - Method in class neurord.numeric.grid.DeterministicGridCalc
 
getGridPartConc(int, int) - Method in interface neurord.numeric.grid.IGridCalc
 
getGridPartConc(int, int) - Method in class neurord.numeric.grid.StochasticGridCalc
 
getGridPartNumb(int, int) - Method in class neurord.numeric.grid.DeterministicGridCalc
 
getGridPartNumb(int, int) - Method in interface neurord.numeric.grid.IGridCalc
 
getGridPartNumb(int, int) - Method in class neurord.numeric.grid.StochasticGridCalc
 
getGroupID() - Method in class neurord.numeric.morph.VolumeElement
 
getGroupID(int) - Method in class neurord.numeric.morph.VolumeGrid
 
getHappenings() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
getHappenings() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
getHappenings() - Method in interface neurord.numeric.grid.IGridCalc
 
getHappenings() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
getHeadings() - Method in class neurord.numeric.morph.VolumeElement
 
getIBox(double) - Method in class neurord.numeric.morph.VolumeSlice
 
getID() - Method in class neurord.model.Reaction
 
getID() - Method in class neurord.model.Segment
 
getID() - Method in class neurord.model.Specie
 
getID() - Method in class neurord.model.SpineAllocation
 
getID() - Method in class neurord.neuroml.cable
 
getID() - Method in class neurord.neuroml.MorphMLPoint
 
getID() - Method in class neurord.neuroml.segment
 
getID() - Method in class neurord.numeric.morph.SpinePopulation
 
getID() - Method in class neurord.numeric.morph.SpineProfile
 
getIdentifier() - Method in interface neurord.model.IOutputSet
 
getIdentifier() - Method in class neurord.model.OutputSet
 
getIdentifier() - Method in class neurord.model.SDRun
 
getIncrementRateMatrix(Column) - Method in class neurord.numeric.chem.ReactionTable
 
getIndex() - Method in class neurord.model.Specie
 
getIndicesOfOutputSpecies(String[]) - Method in interface neurord.model.IOutputSet
 
getIndicesOfOutputSpecies(String[]) - Method in class neurord.model.OutputSet
 
getIndicesOfOutputSpecies(String[]) - Method in class neurord.model.SDRun
 
getInitialConditions() - Method in class neurord.model.SDRun
 
getInjectionSite() - Method in class neurord.model.InjectionStim
 
getInterTrainInterval() - Method in class neurord.model.InjectionStim
 
getJBox(double) - Method in class neurord.numeric.morph.VolumeSlice
 
getLabel() - Method in class neurord.neuroml.cable
 
getLabel() - Method in class neurord.neuroml.meta
 
getLabel() - Method in class neurord.numeric.morph.TreePoint
 
getLabel() - Method in class neurord.numeric.morph.VolumeElement
 
getLabel(int) - Method in class neurord.numeric.morph.VolumeGrid
 
getLabels() - Method in class neurord.disc.DiscretizedSpine
 
getLabels() - Method in class neurord.numeric.morph.SpineProfile
 
getLength() - Method in class neurord.numeric.morph.TriangleStrip
 
getLocalDelta(TreePoint, TreePoint) - Method in class neurord.disc.Resolution
 
getManifest() - Static method in class neurord.util.Settings
 
getMarshaller(T) - Method in class neurord.xml.ModelReader
 
getMaxAspectRatio() - Method in class neurord.model.Discretization
 
getMorphMLCell() - Method in class neurord.neuroml.morphml
 
getMorphology() - Method in class neurord.model.SDRun
 
getName() - Method in class neurord.model.Reaction
 
getName() - Method in class neurord.model.Specie
 
getName() - Method in class neurord.neuroml.cable
 
getName() - Method in class neurord.neuroml.MorphMLCableGroup
 
getName() - Method in class neurord.neuroml.segment
 
getNamesOfOutputSpecies() - Method in interface neurord.model.IOutputSet
 
getNamesOfOutputSpecies() - Method in class neurord.model.OutputSet
 
getNamesOfOutputSpecies() - Method in class neurord.model.SDRun
 
getNanoMolarConcentration() - Method in class neurord.model.Concentration
 
getNanoMolarConcentration(String) - Method in class neurord.model.ConcentrationSet
 
getNanoMolarConcentration() - Method in class neurord.model.NanoMolarity
 
getNanoMolarConcentration() - Method in class neurord.model.NumberDensity
 
getNazimuthals() - Method in class neurord.disc.CurvedVolumeSlice
 
getNeighbors() - Method in class neurord.model.MorphPoint
 
getNeighbors() - Method in class neurord.numeric.morph.TreePoint
 
getNel() - Method in class neurord.numeric.StaticCalc
 
getNormal(Position[]) - Static method in class neurord.geom.Geom
 
getNormals() - Method in class neurord.numeric.morph.TrianglesSet
 
getNReaction() - Method in class neurord.numeric.chem.ReactionTable
 
getNSpec() - Method in class neurord.numeric.StaticCalc
 
getNSpecies() - Method in class neurord.numeric.chem.ReactionTable
 
getNumber() - Method in class neurord.numeric.morph.VolumeElement
 
getNumberElements() - Method in class neurord.numeric.grid.GridCalc
 
getNumberElements() - Method in interface neurord.numeric.grid.IGridCalc
 
getNumTrains() - Method in class neurord.model.InjectionStim
 
getOffsetChildren() - Method in class neurord.model.MorphPoint
 
getOffsetChildren() - Method in class neurord.numeric.morph.TreePoint
 
getOnset() - Method in class neurord.model.InjectionStim
 
getOption(CommandLine, String, int) - Static method in class neurord.util.Settings
 
getOption(CommandLine, String, boolean) - Static method in class neurord.util.Settings
 
getOption(CommandLine, String, double) - Static method in class neurord.util.Settings
 
getOption(CommandLine, String, File) - Static method in class neurord.util.Settings
 
getOutputInterval(double) - Method in interface neurord.model.IOutputSet
 
getOutputInterval(double) - Method in class neurord.model.OutputSet
 
getOutputInterval(double) - Method in class neurord.model.SDRun
 
getOutputInterval() - Method in class neurord.model.SDRun
 
getOutputSets() - Method in class neurord.model.SDRun
 
getParent() - Method in class neurord.numeric.morph.TreePoint
 
getParentID() - Method in class neurord.neuroml.segment
 
getParticleCount() - Method in class neurord.numeric.BaseCalc
 
getParticleCount() - Method in class neurord.numeric.grid.GridCalc
 
getParticleCount() - Method in class neurord.numeric.pool.ForwardEulerPoolCalc
 
getParticleCount() - Method in class neurord.numeric.pool.ForwardExponentialPoolCalc
 
getParticleCount() - Method in class neurord.numeric.pool.ImplicitEulerPoolCalc
 
getParticleCount() - Method in class neurord.numeric.pool.RungeKutta4PoolCalc
 
getParticleCount() - Method in class neurord.numeric.pool.SemiImplicitEulerPoolCalc
 
getParticleCount() - Method in class neurord.numeric.StaticCalc
 
getPerElementCouplingConstants() - Method in class neurord.numeric.morph.VolumeGrid
 
getPerElementNeighbors() - Method in class neurord.numeric.morph.VolumeGrid
 
getPeriod() - Method in class neurord.model.InjectionStim
 
getPopulation() - Method in class neurord.model.SDRun
 
getPopulations() - Method in class neurord.numeric.morph.SpineDistribution
 
getPositions() - Method in class neurord.numeric.morph.TrianglesSet
 
getPower() - Method in class neurord.model.SpecieRef
The order in reaction (propensity is proportional to the number of molecules raised to this power).
getProductIndices() - Method in class neurord.model.Reaction
Returns an array [2 x nspecies] containing products and their counts (n) in reaction.
getProductIndices() - Method in class neurord.numeric.chem.ReactionTable
 
getProductionColumn(Column) - Method in class neurord.numeric.chem.ReactionTable
 
getProductionMatrix() - Method in class neurord.numeric.chem.ReactionTable
 
getProductStoichiometry() - Method in class neurord.numeric.chem.ReactionTable
The number of particles created in the reaction (by specie).
getProfile() - Method in class neurord.model.SpineType
 
getProfile() - Method in class neurord.numeric.morph.SpinePopulation
 
getProgramVersion() - Static method in class neurord.util.Settings
 
getProperties() - Static method in class neurord.util.Settings
 
getProperty(String) - Static method in class neurord.util.Settings
 
getProperty(String, String, int) - Static method in class neurord.util.Settings
 
getProperty(String, String, boolean) - Static method in class neurord.util.Settings
 
getProperty(String, String, double) - Static method in class neurord.util.Settings
 
getProperty(String, String, String) - Static method in class neurord.util.Settings
 
getPropertyList(String, String, String...) - Static method in class neurord.util.Settings
 
getProximal() - Method in class neurord.neuroml.segment
 
getR() - Method in class neurord.neuroml.MorphMLPoint
 
getRadii(int) - Method in class neurord.disc.CurvedVolumeSlice
 
getRadius() - Method in class neurord.numeric.morph.TreePoint
 
getRAElement(int, int) - Method in class neurord.disc.CurvedVolumeSlice
 
getRate() - Method in class neurord.model.InjectionStim
 
getRateColumn(Column) - Method in class neurord.numeric.chem.ReactionTable
 
getRates() - Method in class neurord.model.InjectionStim
 
getRates() - Method in class neurord.numeric.chem.ReactionTable
 
getRawSibling(String) - Method in class neurord.numeric.grid.ResultWriterText
 
getReactantIndices() - Method in class neurord.model.Reaction
Returns an array [2 x nspecies] containing reactants and their counts (n) in reaction.
getReactantIndices() - Method in class neurord.numeric.chem.ReactionTable
 
getReactantPowers() - Method in class neurord.numeric.chem.ReactionTable
Propensity powers for true second- and higher-order reactions.
getReactantStoichiometry() - Method in class neurord.numeric.chem.ReactionTable
The number of particles destroyed in the reaction (by specie).
getReactionSignature(int[], int[], int[], int[], String[]) - Static method in class neurord.numeric.chem.ReactionTable
 
getReactionTable() - Method in class neurord.model.SDRun
 
getRegion() - Method in class neurord.model.ConcentrationSet
 
getRegion() - Method in interface neurord.model.IOutputSet
 
getRegion() - Method in class neurord.model.OutputSet
 
getRegion() - Method in interface neurord.model.Regional
 
getRegion() - Method in class neurord.model.SDRun
 
getRegion() - Method in class neurord.model.SurfaceDensitySet
 
getRegion() - Method in class neurord.numeric.morph.VolumeElement
 
getRegionConcentration(String, String[]) - Method in class neurord.model.InitialConditions
 
getRegionConcentration(String) - Method in class neurord.model.SDRun
 
getRegionConcentrations() - Method in class neurord.model.SDRun
 
getRegionLabels() - Method in class neurord.numeric.morph.VolumeGrid
 
getRegions() - Method in class neurord.disc.DiscretizedSpine
 
getRegions() - Method in class neurord.numeric.morph.SpineProfile
 
getRegionSurfaceDensities() - Method in class neurord.model.SDRun
 
getRegionSurfaceDensity(String, String[]) - Method in class neurord.model.InitialConditions
 
getRegionSurfaceDensity(String) - Method in class neurord.model.SDRun
 
getResolutionHM() - Method in class neurord.model.Discretization
 
getReverseRate() - Method in class neurord.model.Reaction
 
getReversiblePairs() - Method in class neurord.numeric.chem.ReactionTable
Returns an array of indicies of the "other" reaction.
getRootName(File) - Static method in class neurord.util.FileUtil
 
getRotatedPosition(Position, Position) - Method in class neurord.geom.GRotation
 
getRotatedPosition(Position) - Method in class neurord.geom.GRotation
 
getRotatedPosition(Position) - Method in interface neurord.geom.Rotation
 
getRotatedPosition(Position, Position) - Method in interface neurord.geom.Rotation
 
getRotatedVector(Vector) - Method in class neurord.geom.GRotation
 
getRotatedVector(Vector) - Method in interface neurord.geom.Rotation
 
getRow(int) - Method in class neurord.numeric.math.Matrix
 
getSeed() - Static method in class neurord.numeric.math.NRRandom
 
getSegments() - Method in class neurord.neuroml.cell
 
getSibling(String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
getSiblingFile(String) - Method in class neurord.numeric.grid.ResultWriterText
 
getSideArea() - Method in class neurord.numeric.morph.VolumeElement
 
getSimulationSeed() - Method in class neurord.numeric.BaseCalc
 
getSimulationSeed() - Method in interface neurord.numeric.grid.IGridCalc
 
getSource() - Method in class neurord.numeric.BaseCalc
 
getSource() - Method in interface neurord.numeric.grid.IGridCalc
 
getSpecieID() - Method in class neurord.model.SpecieRef
 
getSpecieIndex(String) - Method in class neurord.numeric.chem.ReactionTable
 
getSpecieIndexes(String[]) - Method in class neurord.numeric.StaticCalc
 
getSpecies() - Method in class neurord.model.InjectionStim
 
getSpecies() - Method in class neurord.model.ReactionScheme
 
getSpecies() - Method in class neurord.model.SDRun
 
getSpecies() - Method in class neurord.numeric.chem.ReactionTable
 
getSpineDistribution() - Method in class neurord.model.Morphology
 
getStart() - Method in class neurord.model.Segment
 
getStartTime() - Method in class neurord.model.SDRun
 
getStatistics() - Method in class neurord.model.SDRun
 
getStatisticsInterval() - Method in class neurord.model.SDRun
 
getStimsForInterval(double, double) - Method in class neurord.numeric.chem.StimulationTable
 
getStimulations() - Method in class neurord.numeric.chem.StimulationTable
 
getStimulationTable() - Method in class neurord.model.SDRun
 
getStimulationTargets() - Method in class neurord.model.SDRun
 
getStochDiffMorphology() - Method in class neurord.neuroml.cell
 
getStochDiffSegment(HashMap<String, String>) - Method in class neurord.neuroml.segment
 
getStochiometry() - Method in class neurord.model.SpecieRef
The stochiometry (number of molecules consumed during a reaction).
getStripLengths() - Method in class neurord.numeric.morph.TrianglesSet
 
getSubmembranes() - Method in class neurord.numeric.morph.VolumeGrid
 
getSurfaceBoundary() - Method in class neurord.numeric.morph.VolumeElement
 
getSurfaceDensity(String) - Method in class neurord.model.SurfaceDensitySet
 
getSurfaceLayers() - Method in class neurord.model.Discretization
 
getTable() - Static method in class neurord.numeric.stochastic.BinomialTable
 
getTargetIDs() - Method in class neurord.numeric.chem.StimulationTable
 
getTargetRegion() - Method in class neurord.numeric.morph.SpinePopulation
 
getText3D() - Method in class neurord.numeric.morph.CurvedVolumeElement
 
getTopArea() - Method in class neurord.numeric.morph.VolumeElement
 
getTotalPreserved() - Method in class neurord.model.FitConstraints
 
getTotalPreserved() - Method in class neurord.model.InitialConditions
 
getToVector(Position) - Static method in class neurord.geom.Geom
 
getTranslated(Position) - Method in class neurord.geom.GTranslation
 
getTranslated(Position) - Method in interface neurord.geom.Translation
 
getTreePoints() - Method in class neurord.model.Morphology
 
getTrial(int) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
getUnitNormal(Position[]) - Static method in class neurord.geom.Geom
 
getValue() - Method in interface neurord.inter.FloatValued
 
getValue() - Method in class neurord.model.NanoMolarity
 
getValue() - Method in class neurord.model.NumberDensity
 
getValue() - Method in class neurord.model.PicoSD
 
getVolume() - Method in class neurord.numeric.morph.VolumeElement
 
getVolumeGrid() - Method in class neurord.model.SDRun
 
getVolumes() - Method in class neurord.numeric.StaticCalc
 
getWidths() - Method in class neurord.disc.DiscretizedSpine
 
getWidths() - Method in class neurord.numeric.morph.SpineProfile
 
getWork() - Method in class neurord.numeric.morph.TreePoint
 
getX() - Method in class neurord.geom.GPosition
 
getX() - Method in interface neurord.geom.Position
 
getX() - Method in class neurord.neuroml.MorphMLPoint
 
getX() - Method in class neurord.numeric.morph.TreePoint
 
getX() - Method in class neurord.numeric.morph.VolumeElement
 
getX(int) - Method in class neurord.numeric.morph.VolumeSlice
 
getXPts() - Method in class neurord.numeric.morph.SpineProfile
 
getY() - Method in class neurord.geom.GPosition
 
getY() - Method in interface neurord.geom.Position
 
getY() - Method in class neurord.neuroml.MorphMLPoint
 
getY() - Method in class neurord.numeric.morph.TreePoint
 
getY() - Method in class neurord.numeric.morph.VolumeElement
 
getY(int) - Method in class neurord.numeric.morph.VolumeSlice
 
getZ() - Method in class neurord.geom.GPosition
 
getZ() - Method in interface neurord.geom.Position
 
getZ() - Method in class neurord.neuroml.MorphMLPoint
 
getZ() - Method in class neurord.numeric.morph.TreePoint
 
getZ() - Method in class neurord.numeric.morph.VolumeElement
 
GPosition - Class in neurord.geom
 
GPosition(double, double, double) - Constructor for class neurord.geom.GPosition
 
GPosition(Position) - Constructor for class neurord.geom.GPosition
 
GPosition() - Constructor for class neurord.geom.GPosition
 
GridCalc - Class in neurord.numeric.grid
 
GridCalc(int, SDRun) - Constructor for class neurord.numeric.grid.GridCalc
 
gridData() - Method in class neurord.numeric.morph.VolumeGrid
 
GRotation - Class in neurord.geom
 
GRotation() - Constructor for class neurord.geom.GRotation
 
GRotation(int, double) - Constructor for class neurord.geom.GRotation
 
group - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
groupID - Variable in class neurord.numeric.morph.VolumeElement
 
grv() - Static method in class neurord.numeric.math.NRRandom
 
GTranslation - Class in neurord.geom
 
GTranslation(Position) - Constructor for class neurord.geom.GTranslation
 
GTranslation(Vector) - Constructor for class neurord.geom.GTranslation
 
GVector - Class in neurord.geom
 
GVector(double, double, double) - Constructor for class neurord.geom.GVector
 
GVector(Position) - Constructor for class neurord.geom.GVector
 
GVector(double[]) - Constructor for class neurord.geom.GVector
 
GVector(Vector) - Constructor for class neurord.geom.GVector
 
GVector() - Constructor for class neurord.geom.GVector
 

H

Happening(int, IGridCalc.HappeningKind, int, double, double, double) - Constructor for class neurord.numeric.grid.NextEventQueue.Happening
 
hasElement(int, int) - Method in class neurord.numeric.morph.VolumeSlice
 
hasNeighbor(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
hasOffsetChildren() - Method in class neurord.model.MorphPoint
 
hasOffsetChildren() - Method in class neurord.numeric.morph.TreePoint
 
hasPosition() - Method in class neurord.model.MorphPoint
 
hasRegion() - Method in class neurord.model.ConcentrationSet
 
hasRegion() - Method in interface neurord.model.Regional
 
hasRegion() - Method in class neurord.model.SurfaceDensitySet
 
help_exit(Options, boolean) - Static method in class neurord.StochDiff
 

I

ic_loader - Variable in class neurord.reduce.Reducer
 
ICTest - Class in neurord.examples.ictest
 
ICTest() - Constructor for class neurord.examples.ictest.ICTest
 
id - Variable in class neurord.model.Reaction
 
id - Variable in class neurord.model.Segment
 
id - Variable in class neurord.model.SpineType
 
id - Variable in class neurord.neuroml.cable
 
id - Variable in class neurord.neuroml.morphml
 
id - Variable in class neurord.neuroml.MorphMLPoint
 
id - Variable in class neurord.neuroml.segment
 
identise() - Method in class neurord.numeric.math.Matrix
 
identity() - Method in class neurord.numeric.math.Matrix
 
IGridCalc - Interface in neurord.numeric.grid
 
IGridCalc.Event - Interface in neurord.numeric.grid
 
IGridCalc.EventType - Enum in neurord.numeric.grid
 
IGridCalc.Happening - Interface in neurord.numeric.grid
 
IGridCalc.HappeningKind - Enum in neurord.numeric.grid
 
ImplicitEulerPoolCalc - Class in neurord.numeric.pool
 
ImplicitEulerPoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.ImplicitEulerPoolCalc
 
ImportException - Exception in neurord.neuroml
 
ImportException() - Constructor for exception neurord.neuroml.ImportException
 
importLines(ArrayList<VolumeLine>) - Method in class neurord.numeric.morph.VolumeGrid
 
importSlices(ArrayList<VolumeSlice>) - Method in class neurord.numeric.morph.VolumeGrid
 
importSmoothSlices(ArrayList<CurvedVolumeSlice>) - Method in class neurord.numeric.morph.VolumeGrid
 
increment(int, double) - Method in class neurord.numeric.math.Column
 
incrementBy(double) - Method in class neurord.numeric.math.Column
 
incrementBy(double[]) - Method in class neurord.numeric.math.Column
 
incrementBy(Column) - Method in class neurord.numeric.math.Column
 
index() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
index() - Method in interface neurord.numeric.grid.NextEventQueue.Node
 
init() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
init() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
init() - Method in class neurord.numeric.grid.GridCalc
 
init(String) - Method in interface neurord.numeric.grid.ResultWriter
 
init(String) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
init(String) - Method in class neurord.numeric.grid.ResultWriterText
 
init() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
init() - Method in class neurord.numeric.grid.StochasticGridCalc
 
init() - Method in class neurord.numeric.pool.DeterministicPoolCalc
 
init() - Method in class neurord.numeric.StaticCalc
 
initEvents() - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
initEventStatistics(boolean, IGridCalc, int) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
InitialConditions - Class in neurord.model
 
InitialConditions() - Constructor for class neurord.model.InitialConditions
 
initPopulation(int, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
initPopulation(int[][], SDRun) - Method in class neurord.numeric.grid.StochasticGridCalc
 
InjectionStim - Class in neurord.model
 
InjectionStim(String, String, Double, Double, Double, Double, Double) - Constructor for class neurord.model.InjectionStim
 
int_t - Static variable in class neurord.numeric.grid.ResultWriterHDF5
 
interiorPointConnect(Segment, double, MorphPoint) - Method in class neurord.model.EndPoint
 
interpInAtFor(double[], double[], double[]) - Static method in class neurord.util.ArrayUtil
 
intersect(int[], int...) - Static method in class neurord.util.ArrayUtil
 
interval - Variable in class neurord.model.Statistics
 
intlog(int) - Static method in class neurord.numeric.grid.GridCalc
 
inverse() - Method in class neurord.numeric.math.Matrix
 
invert() - Method in class neurord.numeric.math.Matrix
 
iota(int) - Static method in class neurord.util.ArrayUtil
 
IOutputSet - Interface in neurord.model
 
isContinuation() - Method in class neurord.numeric.grid.ResultWriterText
 
isCuboid() - Method in class neurord.numeric.morph.VolumeGrid
 
isCurved() - Method in class neurord.numeric.morph.VolumeGrid
 
isEndPoint() - Method in class neurord.numeric.morph.TreePoint
 
isSubmembrane() - Method in class neurord.numeric.morph.VolumeElement
 
items - Variable in class neurord.neuroml.meta
 
iwork - Variable in class neurord.numeric.morph.TreePoint
 

J

javaExecutable(Class) - Static method in class neurord.util.Settings
 

K

k1 - Variable in class neurord.numeric.math.Poisson
 
k2 - Variable in class neurord.numeric.math.Poisson
 
k4 - Variable in class neurord.numeric.math.Poisson
 
k5 - Variable in class neurord.numeric.math.Poisson
 
kind() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
kind() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 

L

l_my - Variable in class neurord.numeric.math.Poisson
 
label - Variable in class neurord.model.MorphPoint
 
label - Variable in class neurord.model.Section
 
label - Variable in class neurord.numeric.morph.TreePoint
 
label - Variable in class neurord.numeric.morph.VolumeElement
 
largestNeighborNot(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
leap - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
leap: when the event was generated as an "exact" event (false), or "leap" event (true).
leap_count(double, double, boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
leap_count(double, double, boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
leap_count(double, double, boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
leap_min_jump - Variable in class neurord.model.SDRun
How many times our calculated allowed leap must be longer than normal event waiting time, for us to choose leaping.
leap_time(double) - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
Calculate leap_time based on the limit on variance and expected extents.
leap_time(double) - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
leap_time(double) - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
length(Vector) - Static method in class neurord.geom.Geom
 
length_units - Variable in class neurord.neuroml.morphml
 
lengthUnits - Variable in class neurord.neuroml.morphml
 
LibUtil - Class in neurord.util
 
LibUtil() - Constructor for class neurord.util.LibUtil
 
LineBoxer - Class in neurord.disc
 
LineBoxer() - Constructor for class neurord.disc.LineBoxer
 
lineFill(Position, Position, String, String) - Method in class neurord.numeric.morph.VolumeLine
 
listToRegionMap(List<T>) - Static method in class neurord.model.InitialConditions
 
littlestChild(T) - Method in class neurord.numeric.grid.NextEventQueue.PriorityTree
 
ll - Variable in class neurord.numeric.math.Poisson
 
llll - Variable in class neurord.numeric.math.Poisson
 
LN_PARTICLES_PUVC - Static variable in class neurord.numeric.BaseCalc
 
lnp - Variable in class neurord.numeric.stochastic.NGoTable
 
loadFromFile(File, File, int, double) - Static method in class neurord.model.SDRun
 
loadModel(File, int, double) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
locate(int, SpineDistribution, double, VolumeGrid) - Static method in class neurord.disc.SpineLocator
 
locateBetween(TreePoint, TreePoint, double) - Method in class neurord.numeric.morph.TreePoint
 
log - Static variable in class neurord.model.InjectionStim
 
log - Static variable in class neurord.model.Reaction
 
log - Static variable in class neurord.model.Specie
 
log - Static variable in class neurord.numeric.grid.AdaptiveGridCalc
 
log - Static variable in class neurord.numeric.grid.GridCalc
 
log - Static variable in class neurord.numeric.grid.NextEventQueue
 
log - Static variable in class neurord.numeric.grid.ResultWriterHDF5
 
log - Static variable in class neurord.numeric.grid.StochasticGridCalc
 
log(double, double) - Static method in class neurord.numeric.math.Arithmetic
Returns logbasevalue.
log - Static variable in class neurord.SDCalc
 
log(double[]) - Static method in class neurord.util.ArrayUtil
 
log(double[][]) - Static method in class neurord.util.ArrayUtil
 
log - Static variable in class neurord.util.TimeUtil
 
log - Static variable in class neurord.xml.ModelReader
 
log10(double) - Static method in class neurord.numeric.math.Arithmetic
Returns log10value.
log2(double) - Static method in class neurord.numeric.math.Arithmetic
Returns log2value.
logArray(int) - Static method in class neurord.util.ArrayUtil
 
logFactorial(int) - Static method in class neurord.numeric.math.Arithmetic
Returns log(k!).
logFactorials - Static variable in class neurord.numeric.math.Arithmetic
 
Logging - Class in neurord.util
 
Logging() - Constructor for class neurord.util.Logging
 
long_t - Static variable in class neurord.numeric.grid.ResultWriterHDF5
 
longFactorial(int) - Static method in class neurord.numeric.math.Arithmetic
Instantly returns the factorial k!.
longFactorials - Static variable in class neurord.numeric.math.Arithmetic
 
lr - Variable in class neurord.numeric.math.Poisson
 
LU() - Method in class neurord.numeric.math.Matrix
 
lubksb(Column) - Method in class neurord.numeric.math.Matrix
 
lubksb(double[]) - Method in class neurord.numeric.math.Matrix
 
LUSolve(double[][], double[]) - Static method in class neurord.numeric.math.Matrix
 
LUSolve(Column) - Method in class neurord.numeric.math.Matrix
 
lvprod(double[]) - Method in class neurord.numeric.math.Matrix
 

M

m - Variable in class neurord.numeric.math.Poisson
 
main(String[]) - Static method in class neurord.examples.branch.BranchTest
 
main(String[]) - Static method in class neurord.examples.branch.BranchTest3
 
main(String[]) - Static method in class neurord.examples.ictest.ICTest
 
main(String[]) - Static method in class neurord.examples.morphsurf.MSTest
 
main(String[]) - Static method in class neurord.examples.morphtest.MorphTest
 
main(String[]) - Static method in class neurord.examples.NOEPAC.DetTest
 
main(String[]) - Static method in class neurord.examples.plane.PlaneTest
 
main(String[]) - Static method in class neurord.examples.regions.RegionsTest
 
main(String[]) - Static method in class neurord.examples.restart.ReduceTest
 
main(String[]) - Static method in class neurord.examples.restart.RestartTest
 
main(String[]) - Static method in class neurord.examples.smoothvolume.SmoothVolumeTest
 
main(String[]) - Static method in class neurord.examples.volume.VolumeTest
 
main(String[]) - Static method in class neurord.numeric.math.MersenneTwister
 
main(String[]) - Static method in class neurord.numeric.stochastic.BinomialTable
 
main(String[]) - Static method in class neurord.numeric.stochastic.NGoTable
 
main(String...) - Static method in class neurord.numeric.stochastic.StepGenerator
 
main(String[]) - Static method in class neurord.numeric.stochastic.TimeTests
 
main(String[]) - Static method in class neurord.reduce.Reduce
 
main(String[]) - Static method in class neurord.SDGaussianProblem
 
main(String[]) - Static method in class neurord.SDTest1Stoch
 
main(String[]) - Static method in class neurord.SDTest4
 
main(String[]) - Static method in class neurord.SDTestDet
 
main(String[]) - Static method in class neurord.SDTestStoch
 
main(String[]) - Static method in class neurord.SDTestStochA
 
main(String[]) - Static method in class neurord.SDTestSuite1A
 
main(String[]) - Static method in class neurord.SDTestSuite2A
 
main(String[]) - Static method in class neurord.SDTestSuite3A
 
main(String[]) - Static method in class neurord.StochDiff
 
main(String...) - Static method in class neurord.xml.ModelReader
 
make_equation(double, double, int[], int[], int[], int[], int[], int[], int[], int[], String) - Static method in class neurord.numeric.grid.SecondOrderSolver
 
makeCopy() - Method in class neurord.numeric.morph.TreePoint
 
makePopulation(double) - Method in class neurord.model.SpineAllocation
 
makeProfile() - Method in class neurord.model.SpineType
 
makeRanges() - Method in class neurord.numeric.morph.VolumeLine
 
makeReactionTable() - Method in class neurord.model.ReactionScheme
 
makeRegionConcentrations(String[], String[]) - Method in class neurord.model.InitialConditions
 
makeRegionSurfaceDensities(String[], String[]) - Method in class neurord.model.InitialConditions
 
marshal(List<Double>) - Method in class neurord.xml.DoubleListAdapter
 
marshal(DoubleMatrix) - Method in class neurord.xml.DoubleMatrixAdapter
 
marshal(List<String>) - Method in class neurord.xml.StringListAdapter
 
marshal(String) - Method in class neurord.xml.StringTrimAdapter
 
marshall(T, Writer) - Method in class neurord.xml.ModelReader
 
marshall(T, OutputStream) - Method in class neurord.xml.ModelReader
 
marshall(T, String) - Method in class neurord.xml.ModelReader
 
marshall(T) - Method in class neurord.xml.ModelReader
 
Matrix - Class in neurord.numeric.math
 
Matrix(int) - Constructor for class neurord.numeric.math.Matrix
 
Matrix(int, int) - Constructor for class neurord.numeric.math.Matrix
 
Matrix(double[][]) - Constructor for class neurord.numeric.math.Matrix
 
Matrix(int, double[]) - Constructor for class neurord.numeric.math.Matrix
 
maxAbsElt() - Method in class neurord.numeric.math.Matrix
 
MaxElementSide - Class in neurord.model
 
MaxElementSide() - Constructor for class neurord.model.MaxElementSide
 
maxLength(String...) - Static method in class neurord.util.ArrayUtil
 
maxLength(double[]...) - Static method in class neurord.util.ArrayUtil
 
maxLength(int[]...) - Static method in class neurord.util.ArrayUtil
 
maxLength(int[][]...) - Static method in class neurord.util.ArrayUtil
 
MEAN_MAX - Static variable in class neurord.numeric.math.Poisson
 
MersenneTwister - Class in neurord.numeric.math
 
MersenneTwister() - Constructor for class neurord.numeric.math.MersenneTwister
 
MersenneTwister(long) - Constructor for class neurord.numeric.math.MersenneTwister
 
meta - Class in neurord.neuroml
 
meta() - Constructor for class neurord.neuroml.meta
 
meta_group - Variable in class neurord.neuroml.cable
 
meta_name - Variable in class neurord.neuroml.MetaItem
 
meta_property - Variable in class neurord.neuroml.MetaItem
 
meta_tag - Variable in class neurord.neuroml.MetaItem
 
meta_value - Variable in class neurord.neuroml.MetaItem
 
MetaItem - Class in neurord.neuroml
 
MetaItem(String) - Constructor for class neurord.neuroml.MetaItem
 
metas - Variable in class neurord.neuroml.meta
 
midpoint(Position, Position) - Static method in class neurord.geom.Geom
 
min(double[]) - Static method in class neurord.util.ArrayUtil
 
MINUS_ONE - Static variable in class neurord.numeric.grid.NextEventQueue
 
MINUS_ONE_PLUS_ONE - Static variable in class neurord.numeric.grid.NextEventQueue
 
mode - Variable in class neurord.numeric.stochastic.NGoTable
 
model - Variable in class neurord.numeric.grid.ResultWriterHDF5
 
model() - Method in class neurord.numeric.grid.ResultWriterHDF5
 
ModelReader<T> - Class in neurord.xml
 
ModelReader(Class<T>) - Constructor for class neurord.xml.ModelReader
 
ModelReader.NamespaceFiller - Class in neurord.xml
 
morphml - Class in neurord.neuroml
 
morphml() - Constructor for class neurord.neuroml.morphml
 
MorphMLCableGroup - Class in neurord.neuroml
 
MorphMLCableGroup() - Constructor for class neurord.neuroml.MorphMLCableGroup
 
MorphMLPoint - Class in neurord.neuroml
 
MorphMLPoint() - Constructor for class neurord.neuroml.MorphMLPoint
 
MorphMLProperties - Class in neurord.neuroml
 
MorphMLProperties() - Constructor for class neurord.neuroml.MorphMLProperties
 
Morphology - Class in neurord.model
 
Morphology() - Constructor for class neurord.model.Morphology
 
MorphPoint - Class in neurord.model
 
MorphPoint() - Constructor for class neurord.model.MorphPoint
 
MorphPoint(String, double, double, double, double) - Constructor for class neurord.model.MorphPoint
 
MorphTest - Class in neurord.examples.morphtest
 
MorphTest() - Constructor for class neurord.examples.morphtest.MorphTest
 
Movable - Interface in neurord.geom
 
movePerp(TreePoint, TreePoint, double) - Method in class neurord.numeric.morph.TreePoint
 
moveTo(double, double, double) - Method in class neurord.geom.GPosition
 
moveTo(double, double, double) - Method in interface neurord.geom.Movable
 
mpyBy(double) - Method in class neurord.numeric.math.Matrix
 
mpyBy(Matrix) - Method in class neurord.numeric.math.Matrix
 
MSTest - Class in neurord.examples.morphsurf
 
MSTest() - Constructor for class neurord.examples.morphsurf.MSTest
 
multiplyBy(double) - Method in class neurord.numeric.math.Matrix
 
multiplyInto(double[]) - Method in class neurord.numeric.math.Matrix
 
multiuplyBy(double) - Method in class neurord.numeric.math.Column
 
my_last - Variable in class neurord.numeric.math.Poisson
 
my_old - Variable in class neurord.numeric.math.Poisson
 

N

n - Variable in class neurord.numeric.stochastic.NGoTable
 
name - Variable in class neurord.model.OutputSpecie
 
name - Variable in class neurord.model.Reaction
 
name - Variable in class neurord.neuroml.cable
 
name - Variable in class neurord.neuroml.cell
 
name - Variable in class neurord.neuroml.MetaItem
 
name - Variable in class neurord.neuroml.morphml
 
name - Variable in class neurord.neuroml.MorphMLCableGroup
 
name - Variable in class neurord.neuroml.segment
 
name - Variable in class neurord.numeric.morph.TreePoint
 
NamespaceFiller(HashMap<String, String>...) - Constructor for class neurord.xml.ModelReader.NamespaceFiller
 
NanoMolarity - Class in neurord.model
 
NanoMolarity() - Constructor for class neurord.model.NanoMolarity
 
nbr - Variable in class neurord.numeric.morph.TreePoint
 
ncm(int, int) - Method in class neurord.numeric.stochastic.BinomialTable
 
ncm_l(int, int) - Method in class neurord.numeric.stochastic.BinomialTable
 
negate() - Method in class neurord.numeric.math.Matrix
 
negate(int[]) - Static method in class neurord.util.ArrayUtil
 
neighborize(TreePoint, TreePoint) - Static method in class neurord.numeric.morph.TreePoint
 
neighborize() - Method in class neurord.numeric.morph.VolumeLine
 
nel - Variable in class neurord.inter.SDState
 
nel - Variable in class neurord.numeric.grid.GridCalc
 
NeuroMLBase - Class in neurord.neuroml
 
NeuroMLBase() - Constructor for class neurord.neuroml.NeuroMLBase
 
neurord - package neurord
Stochastic diffusion segments of dendrits with spines.
neurord.disc - package neurord.disc
These are various ways of turning a morphology into a set of elements of constrained volume.
neurord.examples.branch - package neurord.examples.branch
 
neurord.examples.ictest - package neurord.examples.ictest
 
neurord.examples.morphsurf - package neurord.examples.morphsurf
 
neurord.examples.morphtest - package neurord.examples.morphtest
 
neurord.examples.NOEPAC - package neurord.examples.NOEPAC
 
neurord.examples.plane - package neurord.examples.plane
 
neurord.examples.regions - package neurord.examples.regions
 
neurord.examples.restart - package neurord.examples.restart
 
neurord.examples.smoothvolume - package neurord.examples.smoothvolume
 
neurord.examples.volume - package neurord.examples.volume
 
neurord.geom - package neurord.geom
Just some geometry - positions, vectors, translations and rotations.
neurord.inter - package neurord.inter
 
neurord.model - package neurord.model
These classes represent the model as it is stored in the input files.
neurord.neuroml - package neurord.neuroml
 
neurord.numeric - package neurord.numeric
 
neurord.numeric.chem - package neurord.numeric.chem
Species and reactions
neurord.numeric.grid - package neurord.numeric.grid
SteppedStochasticCalc contains the particle number based calculation with fixed timesteps where a number of diffusion events and reactions is generated for each reaction, volume and volume-volume connection at each timestep.
neurord.numeric.math - package neurord.numeric.math
Just some linear algebra.
neurord.numeric.morph - package neurord.numeric.morph
Representation of the morphology and discretized mesh for computational purposes.
neurord.numeric.pool - package neurord.numeric.pool
These are deterministic calculations for a single mixed pool.
neurord.numeric.stochastic - package neurord.numeric.stochastic
These are the functions for the innner loops of the calculation.
neurord.phys - package neurord.phys
 
neurord.reduce - package neurord.reduce
 
neurord.util - package neurord.util
Various utilities todo with file handling, string processing etc.
neurord.xml - package neurord.xml
 
NEURORD_NS - Static variable in class neurord.xml.ModelReader
 
NextEventQueue - Class in neurord.numeric.grid
 
NextEventQueue(RandomGenerator, StepGenerator, int[][], boolean, double, double) - Constructor for class neurord.numeric.grid.NextEventQueue
Use create() instead, this is public only for testing.
NextEventQueue.Happening - Class in neurord.numeric.grid
 
NextEventQueue.NextDiffusion - Class in neurord.numeric.grid
 
NextEventQueue.NextEvent - Class in neurord.numeric.grid
 
NextEventQueue.NextReaction - Class in neurord.numeric.grid
 
NextEventQueue.NextStimulation - Class in neurord.numeric.grid
 
NextEventQueue.Node - Interface in neurord.numeric.grid
 
NextEventQueue.Numbering - Class in neurord.numeric.grid
 
NextEventQueue.PriorityTree<T extends NextEventQueue.Node> - Class in neurord.numeric.grid
 
nextInt(int, double) - Method in class neurord.numeric.math.Binomial
Returns a random number from the distribution with the given parameters n and p; bypasses the internal state.
nextInt(int, double) - Method in interface neurord.numeric.math.BinomialLike
 
nextInt(double) - Method in class neurord.numeric.math.Poisson
Returns a random number from the distribution; bypasses the internal state.
nextInt(int, double) - Method in class neurord.numeric.math.Poisson
 
nextRandom() - Static method in class neurord.numeric.math.NRRandom
 
nGo(double) - Method in class neurord.numeric.stochastic.NGoTable
 
nGo(int, double) - Method in class neurord.numeric.stochastic.StepGenerator
 
nGoBS(double) - Method in class neurord.numeric.stochastic.NGoTable
 
NGoTable - Class in neurord.numeric.stochastic
Table of cumulative probabilities of a certain number of successes from the total number of events when the probability of success is given.
NGoTable(int, double, BaseCalc.distribution_t) - Constructor for class neurord.numeric.stochastic.NGoTable
 
NM_PER_PARTICLE_PUV - Static variable in class neurord.numeric.BaseCalc
 
NMAX - Static variable in class neurord.numeric.stochastic.BinomialTable
 
nnbr - Variable in class neurord.numeric.morph.TreePoint
 
notes - Variable in class neurord.neuroml.cell
 
NOTICE - Static variable in class neurord.util.Logging
 
nreaction - Variable in class neurord.numeric.chem.ReactionTable
 
NRRandom - Class in neurord.numeric.math
 
NRRandom() - Constructor for class neurord.numeric.math.NRRandom
 
nspec - Variable in class neurord.inter.SDState
 
nspec - Variable in class neurord.numeric.grid.GridCalc
 
number - Variable in class neurord.model.NumberDensity
 
number - Variable in class neurord.numeric.morph.VolumeElement
 
NumberDensity - Class in neurord.model
 
NumberDensity() - Constructor for class neurord.model.NumberDensity
 
Numbering() - Constructor for class neurord.numeric.grid.NextEventQueue.Numbering
 

O

on - Variable in class neurord.model.EndPoint
 
onset - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
oppositeNeighbor(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
optionCount(CommandLine, String[], String, String) - Static method in class neurord.util.Settings
 
orientAC(TreePoint, TreePoint[]) - Static method in class neurord.disc.TreeUtil
 
original_wait() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
original_wait() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 
original_wait - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
time: original wait time.
output - Variable in class neurord.model.SDRun
 
output - Variable in class neurord.numeric.grid.ResultWriterHDF5
 
outputFile() - Method in interface neurord.numeric.grid.ResultWriter
 
outputFile - Variable in class neurord.numeric.grid.ResultWriterHDF5
 
outputFile() - Method in class neurord.numeric.grid.ResultWriterHDF5
 
outputFile() - Method in class neurord.numeric.grid.ResultWriterText
 
outputInterval - Variable in class neurord.model.OutputSet
 
outputQuantity - Variable in class neurord.model.SDRun
 
OutputScheme - Class in neurord.model
 
OutputScheme() - Constructor for class neurord.model.OutputScheme
 
outputScheme - Variable in class neurord.model.SDRun
 
OutputSet - Class in neurord.model
 
OutputSet() - Constructor for class neurord.model.OutputSet
 
outputSets - Variable in class neurord.model.OutputScheme
 
OutputSpecie - Class in neurord.model
 
OutputSpecie() - Constructor for class neurord.model.OutputSpecie
 
outputSpecieIndices(String, List<String>, String[]) - Static method in class neurord.model.OutputSet
 
outputSpecies - Variable in class neurord.model.OutputSet
 
overrideRuntime(double) - Method in class neurord.model.SDRun
 
overrideStatistics(String, Double) - Method in class neurord.model.SDRun
 

P

p - Variable in class neurord.numeric.math.Poisson
 
p0 - Variable in class neurord.numeric.math.Poisson
 
p1 - Variable in class neurord.numeric.math.Poisson
 
p2 - Variable in class neurord.numeric.math.Poisson
 
p3 - Variable in class neurord.numeric.math.Poisson
 
p4 - Variable in class neurord.numeric.math.Poisson
 
p5 - Variable in class neurord.numeric.math.Poisson
 
p6 - Variable in class neurord.numeric.math.Poisson
 
parent - Variable in class neurord.neuroml.segment
 
parent(T) - Method in class neurord.numeric.grid.NextEventQueue.PriorityTree
 
parent - Variable in class neurord.numeric.morph.TreePoint
 
parentizeFrom(TreePoint, TreePoint[]) - Static method in class neurord.disc.TreeUtil
 
partBranchOffset - Variable in class neurord.numeric.morph.TreePoint
 
PARTICLES_PUASD - Static variable in class neurord.numeric.BaseCalc
 
PARTICLES_PUVC - Static variable in class neurord.numeric.BaseCalc
 
period - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
Phys - Class in neurord.phys
 
Phys() - Constructor for class neurord.phys.Phys
 
pick(int[], int[]) - Static method in class neurord.util.ArrayUtil
 
PicoSD - Class in neurord.model
 
PicoSD() - Constructor for class neurord.model.PicoSD
 
planeConnect(CurvedVolumeSlice) - Method in class neurord.disc.CurvedVolumeSlice
 
planeConnect(VolumeLine) - Method in class neurord.numeric.morph.VolumeLine
 
planeConnect(VolumeSlice) - Method in class neurord.numeric.morph.VolumeSlice
 
PlaneTest - Class in neurord.examples.plane
 
PlaneTest() - Constructor for class neurord.examples.plane.PlaneTest
 
plus(double) - Method in class neurord.numeric.math.Column
 
plus(Column) - Method in class neurord.numeric.math.Column
 
PLUS_ONE - Static variable in class neurord.numeric.grid.NextEventQueue
 
poidev(double, MersenneTwister) - Static method in class neurord.numeric.math.RandomMath
 
poisson(double) - Method in class neurord.numeric.math.MersenneTwister
 
Poisson - Class in neurord.numeric.math
Poisson distribution (quick); See the math definition and animated definition.
Poisson(RandomGenerator) - Constructor for class neurord.numeric.math.Poisson
Constructs a poisson distribution.
poisson(double) - Method in interface neurord.numeric.math.RandomGenerator
 
poisson - Variable in class neurord.numeric.stochastic.StepGenerator
 
poisson(double) - Method in class neurord.numeric.stochastic.StepGenerator
 
poissonInt(double, MersenneTwister) - Static method in class neurord.numeric.math.RandomMath
 
population - Variable in class neurord.numeric.grid.ResultWriterHDF5.LoadModelResult
 
PopulationOutput(Group, String, int[], int[]) - Constructor for class neurord.numeric.grid.ResultWriterHDF5.PopulationOutput
 
populations - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
populations - Variable in class neurord.numeric.morph.SpineDistribution
 
position(double, double, double) - Static method in class neurord.geom.Geom
 
Position - Interface in neurord.geom
 
positivize() - Method in class neurord.numeric.math.Column
 
power(int) - Method in class neurord.numeric.math.Matrix
 
pp - Variable in class neurord.numeric.math.Poisson
 
preferConcs() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
preferConcs() - Method in interface neurord.numeric.grid.IGridCalc
 
preferConcs() - Method in class neurord.numeric.grid.StochasticGridCalc
 
prepareCalc(int) - Method in class neurord.SDCalc
 
PreserveTotal - Class in neurord.model
 
PreserveTotal() - Constructor for class neurord.model.PreserveTotal
 
preserveTotals - Variable in class neurord.model.FitConstraints
 
print() - Method in class neurord.numeric.chem.ReactionTable
 
print() - Method in class neurord.numeric.math.Column
 
print() - Method in class neurord.numeric.math.Matrix
 
print(int) - Method in class neurord.numeric.stochastic.BinomialTable
 
print() - Method in class neurord.numeric.stochastic.NGoTable
 
printAvailableSettings(PrintStream) - Static method in class neurord.util.Settings
 
printconc(double[][]) - Method in class neurord.reduce.Reducer
 
PriorityTree() - Constructor for class neurord.numeric.grid.NextEventQueue.PriorityTree
 
ProbabilityTable - Class in neurord.numeric.stochastic
 
ProbabilityTable() - Constructor for class neurord.numeric.stochastic.ProbabilityTable
 
prod(Matrix) - Method in class neurord.numeric.math.Matrix
 
Product - Class in neurord.model
 
Product() - Constructor for class neurord.model.Product
 
product(long[]) - Static method in class neurord.util.ArrayUtil
 
productPopulation() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
properties - Variable in class neurord.neuroml.segment
 
propertyOverrides() - Method in class neurord.xml.ModelReader
 
proximal - Variable in class neurord.neuroml.segment
 
pruneFrom(String, int, double) - Method in class neurord.numeric.grid.ResultWriterText
this expects each record to begin with max, and then have a time field as the idx'th element of the line.

Q

q - Variable in class neurord.numeric.math.Poisson
 
Q10 - Variable in class neurord.model.Reaction
 

R

r - Variable in class neurord.model.MorphPoint
 
r1 - Variable in class neurord.numeric.math.Poisson
 
r2 - Variable in class neurord.numeric.math.Poisson
 
r4 - Variable in class neurord.numeric.math.Poisson
 
r5 - Variable in class neurord.numeric.math.Poisson
 
r_peerPoint - Variable in class neurord.model.MorphPoint
 
radiiDiffer(MorphPoint) - Method in class neurord.model.EndPoint
 
random() - Method in class neurord.numeric.math.Matrix
 
random() - Method in class neurord.numeric.math.MersenneTwister
 
random() - Static method in class neurord.numeric.math.NRRandom
 
random() - Method in interface neurord.numeric.math.RandomGenerator
 
randomGenerator - Variable in class neurord.numeric.math.Binomial
 
randomGenerator - Variable in class neurord.numeric.math.Poisson
 
RandomGenerator - Interface in neurord.numeric.math
 
randomIndexFromColumn(int) - Method in class neurord.numeric.math.Matrix
 
randomIndexFromColumn(int, double) - Method in class neurord.numeric.math.Matrix
 
randomIndexFromOffsetColumn(int, int) - Method in class neurord.numeric.math.Matrix
 
randomise() - Method in class neurord.numeric.math.Matrix
 
RandomMath - Class in neurord.numeric.math
 
RandomMath() - Constructor for class neurord.numeric.math.RandomMath
 
RandomProvider - Class in neurord.numeric.math
 
RandomProvider() - Constructor for class neurord.numeric.math.RandomProvider
 
rate - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
Reactant - Class in neurord.model
 
Reactant() - Constructor for class neurord.model.Reactant
 
reactant_stoichiometry() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
reactantPopulation() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
reactants() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
Reaction - Class in neurord.model
 
Reaction() - Constructor for class neurord.model.Reaction
 
ReactionScheme - Class in neurord.model
 
ReactionScheme() - Constructor for class neurord.model.ReactionScheme
 
reactionStep(int[], int[], int, int) - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
ReactionTable - Class in neurord.numeric.chem
 
ReactionTable(int, String[], double[]) - Constructor for class neurord.numeric.chem.ReactionTable
 
readSibling(String) - Method in class neurord.numeric.grid.ResultWriterText
 
readState(String) - Static method in class neurord.inter.StateReader
 
readStateString(String) - Static method in class neurord.inter.StateReader
 
readStringFromFile(File) - Static method in class neurord.util.FileUtil
 
rect2rvprod(double[], double[], double[]) - Method in class neurord.numeric.math.Matrix
 
Reduce - Class in neurord.reduce
 
Reduce() - Constructor for class neurord.reduce.Reduce
 
reduce() - Method in class neurord.reduce.Reducer
 
Reducer - Class in neurord.reduce
 
Reducer(SDRun, SDState) - Constructor for class neurord.reduce.Reducer
 
ReduceTest - Class in neurord.examples.restart
 
ReduceTest() - Constructor for class neurord.examples.restart.ReduceTest
 
redundant() - Method in class neurord.model.MorphPoint
 
region - Variable in class neurord.model.ConcentrationSet
 
region - Variable in class neurord.model.MaxElementSide
 
region - Variable in class neurord.model.OutputSet
 
region - Variable in class neurord.model.Segment
 
region - Variable in class neurord.model.SurfaceDensitySet
 
region - Variable in class neurord.numeric.morph.VolumeElement
 
Regional - Interface in neurord.model
 
regionClass - Variable in class neurord.model.Section
 
regionClassWith(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
RegionsTest - Class in neurord.examples.regions
 
RegionsTest() - Constructor for class neurord.examples.regions.RegionsTest
 
reinit() - Method in class neurord.numeric.StaticCalc
 
removeDeadNeighbors() - Method in class neurord.numeric.morph.TreePoint
 
removeNeighbor(MorphPoint) - Method in class neurord.model.MorphPoint
 
removeNeighbor(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
replaceNeighbor(TreePoint, TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
replaceNeighborLabels(MorphPoint, MorphPoint) - Method in class neurord.model.MorphPoint
 
resetEventStatistics() - Method in class neurord.numeric.grid.AdaptiveGridCalc
 
resetEventStatistics() - Method in class neurord.numeric.grid.DeterministicGridCalc
 
resetEventStatistics() - Method in class neurord.numeric.grid.GridCalc
 
resetEventStatistics() - Method in class neurord.numeric.grid.SteppedStochasticGridCalc
 
reshape(int[], int, int) - Static method in class neurord.util.ArrayUtil
 
Resolution - Class in neurord.disc
 
Resolution(double, HashMap<String, Double>) - Constructor for class neurord.disc.Resolution
 
resolve(HashMap<String, Segment>, MorphPoint) - Method in class neurord.model.EndPoint
 
resolve(double) - Method in class neurord.model.Morphology
 
resolve(HashMap<String, Specie>) - Method in class neurord.model.Reaction
 
resolve(HashMap<String, Segment>) - Method in class neurord.model.Segment
 
resolve(HashMap<String, SpineType>) - Method in class neurord.model.SpineAllocation
 
RestartTest - Class in neurord.examples.restart
 
RestartTest() - Constructor for class neurord.examples.restart.RestartTest
 
results - Variable in class neurord.numeric.BaseCalc
 
results - Variable in class neurord.SDCalc
 
ResultWriter - Interface in neurord.numeric.grid
 
ResultWriterHDF5 - Class in neurord.numeric.grid
 
ResultWriterHDF5(File, IOutputSet, List<? extends IOutputSet>, String[], VolumeGrid) - Constructor for class neurord.numeric.grid.ResultWriterHDF5
 
ResultWriterHDF5.LoadModelResult - Class in neurord.numeric.grid
 
ResultWriterHDF5.PopulationOutput - Class in neurord.numeric.grid
 
ResultWriterHDF5.Trial - Class in neurord.numeric.grid
 
resultWriters - Variable in class neurord.numeric.BaseCalc
 
resultWriters - Variable in class neurord.SDCalc
 
ResultWriterText - Class in neurord.numeric.grid
 
ResultWriterText(File, IOutputSet, List<? extends IOutputSet>, String[], VolumeGrid, boolean) - Constructor for class neurord.numeric.grid.ResultWriterText
 
reverse - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
 
reverse_is_leaping - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
 
rnGo(double) - Method in class neurord.numeric.stochastic.NGoTable
 
root - Variable in class neurord.numeric.grid.ResultWriterHDF5
 
rotate(Rotation) - Method in class neurord.numeric.morph.TrianglesSet
 
rotate(Rotation) - Method in class neurord.numeric.morph.TriangleStrip
 
rotateAbout(Movable, Position) - Method in class neurord.geom.GRotation
 
rotateAbout(Movable, Position) - Method in interface neurord.geom.Rotation
 
Rotation - Interface in neurord.geom
 
round(double) - Method in class neurord.numeric.math.Matrix
 
round() - Method in class neurord.numeric.math.Matrix
 
round(double) - Method in class neurord.numeric.math.MersenneTwister
 
round(double) - Method in interface neurord.numeric.math.RandomGenerator
Randomly round up or down, so the average is @mean.
ROW - Static variable in class neurord.numeric.math.Matrix
 
run() - Method in class neurord.numeric.BaseCalc
 
run() - Method in class neurord.SDCalc
 
RungeKutta4PoolCalc - Class in neurord.numeric.pool
 
RungeKutta4PoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.RungeKutta4PoolCalc
 
rvprod(double[]) - Method in class neurord.numeric.math.Matrix
 
rvprodOneElt(double[], int) - Method in class neurord.numeric.math.Matrix
 

S

scoeff_ki - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
 
SDCalc - Class in neurord
 
SDCalc(SDRun, File) - Constructor for class neurord.SDCalc
 
SDCalcType - Enum in neurord
 
SDGaussianProblem - Class in neurord
 
SDGaussianProblem() - Constructor for class neurord.SDGaussianProblem
 
SDRun - Class in neurord.model
 
SDRun() - Constructor for class neurord.model.SDRun
 
sdRun - Variable in class neurord.numeric.BaseCalc
 
sds - Variable in class neurord.model.SurfaceDensitySet
 
sdSets - Variable in class neurord.model.InitialConditions
 
SDState - Class in neurord.inter
 
SDState() - Constructor for class neurord.inter.SDState
 
SDTest1Stoch - Class in neurord
 
SDTest1Stoch() - Constructor for class neurord.SDTest1Stoch
 
SDTest4 - Class in neurord
 
SDTest4() - Constructor for class neurord.SDTest4
 
SDTestDet - Class in neurord
 
SDTestDet() - Constructor for class neurord.SDTestDet
 
SDTestStoch - Class in neurord
 
SDTestStoch() - Constructor for class neurord.SDTestStoch
 
SDTestStochA - Class in neurord
 
SDTestStochA() - Constructor for class neurord.SDTestStochA
 
SDTestSuite1A - Class in neurord
 
SDTestSuite1A() - Constructor for class neurord.SDTestSuite1A
 
SDTestSuite2A - Class in neurord
 
SDTestSuite2A() - Constructor for class neurord.SDTestSuite2A
 
SDTestSuite3A - Class in neurord
 
SDTestSuite3A() - Constructor for class neurord.SDTestSuite3A
 
SecondOrderSolver - Class in neurord.numeric.grid
 
SecondOrderSolver(int[], int[], String, double, double, double) - Constructor for class neurord.numeric.grid.SecondOrderSolver
 
Section - Class in neurord.model
 
Section() - Constructor for class neurord.model.Section
 
sections - Variable in class neurord.model.SpineType
 
seed - Variable in class neurord.numeric.grid.ResultWriterHDF5.LoadModelResult
 
Segment - Class in neurord.model
 
Segment() - Constructor for class neurord.model.Segment
 
segment - Class in neurord.neuroml
 
segment() - Constructor for class neurord.neuroml.segment
 
segmentIDWith(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
SegmentMerger - Class in neurord.disc
 
SegmentMerger() - Constructor for class neurord.disc.SegmentMerger
 
segments - Variable in class neurord.model.Morphology
 
segments - Variable in class neurord.neuroml.cell
 
SegmentSlicer - Class in neurord.disc
divided into segments either with fixed lengths or with equal integral of the square root of the radiusr.
SegmentSlicer(TreePoint[]) - Constructor for class neurord.disc.SegmentSlicer
 
self_leap_limit(int[]) - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
Make sure that the propensity of *this* reaction does not change too much.
SemiImplicitEulerPoolCalc - Class in neurord.numeric.pool
 
SemiImplicitEulerPoolCalc(int, SDRun) - Constructor for class neurord.numeric.pool.SemiImplicitEulerPoolCalc
 
serialize() - Method in class neurord.model.SDRun
 
serializeSWC() - Method in class neurord.numeric.morph.TreeWriter
 
set(int, int, double) - Method in class neurord.numeric.math.Matrix
 
setAttribute(HObject, String, String) - Static method in class neurord.numeric.grid.ResultWriterHDF5
Utility functions ******************
setAttribute(HObject, String, long) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
setBodyValue(String) - Method in class neurord.neuroml.MetaItem
 
setDims(int, int) - Method in class neurord.numeric.math.Matrix
 
setEvent(int, boolean, double, double) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
setIDWith(MorphPoint, String) - Method in class neurord.model.MorphPoint
 
setIDWith(TreePoint, String) - Method in class neurord.numeric.morph.TreePoint
 
setIndex(int) - Method in class neurord.model.Specie
 
setIndex(int) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
setIndex(int) - Method in interface neurord.numeric.grid.NextEventQueue.Node
 
setLabel(String) - Method in class neurord.numeric.morph.TreePoint
 
setLogLevel(LoggerContext, String, Level) - Static method in class neurord.util.Logging
 
setLogLevels() - Static method in class neurord.util.Logging
Set log4j2 log levels based on properties: log.<logger-name>=info|debug|warning|...
setName(String) - Method in class neurord.neuroml.MetaItem
 
setNumber(int) - Method in class neurord.numeric.morph.VolumeElement
 
setPositionIndexes(int, int) - Method in class neurord.numeric.morph.CurvedVolumeElement
 
setRadius(double) - Method in class neurord.numeric.morph.TreePoint
 
setReactionData(int, int[][], int[][], double, boolean) - Method in class neurord.numeric.chem.ReactionTable
 
setRegionWith(MorphPoint, String) - Method in class neurord.model.MorphPoint
 
setRegionWith(TreePoint, String) - Method in class neurord.numeric.morph.TreePoint
 
setSeed(long) - Method in class neurord.numeric.math.MersenneTwister
 
setSeed(int) - Static method in class neurord.numeric.math.NRRandom
 
setSegment(Segment) - Method in class neurord.model.MorphPoint
 
setSubAreaOf(TreePoint) - Method in class neurord.numeric.morph.TreePoint
 
Settings - Class in neurord.util
 
setTriangles(int[], float[][], float[][]) - Method in class neurord.numeric.morph.CurvedVolumeElement
 
setValue(double) - Method in interface neurord.inter.FloatValued
 
setValue(double) - Method in class neurord.model.NanoMolarity
 
setValue(double) - Method in class neurord.model.NumberDensity
 
setValue(double) - Method in class neurord.model.PicoSD
 
setValue(String) - Method in class neurord.neuroml.MetaItem
 
setWork(int) - Method in class neurord.numeric.morph.TreePoint
 
SHARED_DIFF_PARTICLES - Static variable in class neurord.numeric.grid.SteppedStochasticGridCalc
 
short_str_t - Static variable in class neurord.numeric.grid.ResultWriterHDF5
 
showFit(double[], double[]) - Method in class neurord.reduce.Reducer
 
siblings - Variable in class neurord.numeric.grid.ResultWriterText
 
sideArea - Variable in class neurord.numeric.morph.VolumeElement
 
sim - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
simulationSeed - Variable in class neurord.model.SDRun
 
SINGLE_VOXEL - Static variable in class neurord.model.Discretization
 
site - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
size() - Method in class neurord.numeric.math.Column
 
size() - Method in class neurord.numeric.morph.VolumeGrid
 
SmoothVolumeTest - Class in neurord.examples.smoothvolume
 
SmoothVolumeTest() - Constructor for class neurord.examples.smoothvolume.SmoothVolumeTest
 
soleRegion() - Method in class neurord.numeric.morph.TreePoint
 
Sp(String) - Method in class neurord.numeric.math.Matrix
 
span(double, double, int) - Static method in class neurord.util.ArrayUtil
 
specids - Variable in class neurord.inter.SDState
 
Specie - Class in neurord.model
 
Specie() - Constructor for class neurord.model.Specie
 
specieID - Variable in class neurord.model.Concentration
 
specieID - Variable in class neurord.model.InjectionStim
 
specieID - Variable in class neurord.model.PicoSD
 
specieID - Variable in class neurord.model.PreserveTotal
 
SpecieRef - Class in neurord.model
 
SpecieRef() - Constructor for class neurord.model.SpecieRef
 
species - Variable in class neurord.numeric.chem.StimulationTable.Stimulation
 
species - Variable in class neurord.numeric.grid.GridCalc
 
species - Variable in class neurord.numeric.grid.ResultWriterHDF5.LoadModelResult
 
speciesMatch(String[], String[]) - Static method in class neurord.model.SDRun
 
SpineAllocation - Class in neurord.model
 
SpineAllocation() - Constructor for class neurord.model.SpineAllocation
 
SpineDistribution - Class in neurord.numeric.morph
 
SpineDistribution(SpinePopulation[]) - Constructor for class neurord.numeric.morph.SpineDistribution
 
SpineLocator - Class in neurord.disc
 
SpineLocator() - Constructor for class neurord.disc.SpineLocator
 
SpinePopulation - Class in neurord.numeric.morph
 
SpinePopulation(String, SpineProfile, String, double) - Constructor for class neurord.numeric.morph.SpinePopulation
 
SpineProfile - Class in neurord.numeric.morph
 
SpineProfile(String, double[], double[], String[], String[]) - Constructor for class neurord.numeric.morph.SpineProfile
 
spineSeed - Variable in class neurord.model.SDRun
 
SpineType - Class in neurord.model
 
SpineType() - Constructor for class neurord.model.SpineType
 
spineTypes - Variable in class neurord.model.Morphology
 
start - Variable in class neurord.model.Segment
 
startElement(String, String, String, Attributes) - Method in class neurord.xml.ModelReader.NamespaceFiller
 
stat_count(String, String[]) - Method in class neurord.numeric.grid.NextEventQueue
 
stat_index() - Method in interface neurord.numeric.grid.IGridCalc.Event
 
stat_index() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
stat_index_description() - Method in interface neurord.numeric.grid.IGridCalc.Event
 
stat_index_description() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
StateReader - Class in neurord.inter
 
StateReader() - Constructor for class neurord.inter.StateReader
 
StaticCalc - Class in neurord.numeric
 
StaticCalc(int, SDRun) - Constructor for class neurord.numeric.StaticCalc
 
statistics - Variable in class neurord.model.SDRun
 
Statistics - Class in neurord.model
 
Statistics() - Constructor for class neurord.model.Statistics
 
statistics_times - Variable in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
StepGenerator - Class in neurord.numeric.stochastic
 
StepGenerator(RandomGenerator) - Constructor for class neurord.numeric.stochastic.StepGenerator
 
SteppedStochasticGridCalc - Class in neurord.numeric.grid
 
SteppedStochasticGridCalc(int, SDRun) - Constructor for class neurord.numeric.grid.SteppedStochasticGridCalc
 
stepResiduals(Column, Column, double) - Method in class neurord.numeric.chem.ReactionTable
 
stepSize() - Method in class neurord.model.SDRun
 
Stimulation(int, String, BaseCalc.distribution_t, int, double, double, double, double, double, double) - Constructor for class neurord.numeric.chem.StimulationTable.Stimulation
 
stimulations - Variable in class neurord.model.StimulationSet
 
StimulationSet - Class in neurord.model
 
StimulationSet() - Constructor for class neurord.model.StimulationSet
 
StimulationTable - Class in neurord.numeric.chem
 
StimulationTable(List<InjectionStim>, ReactionTable) - Constructor for class neurord.numeric.chem.StimulationTable
 
StimulationTable.Stimulation - Class in neurord.numeric.chem
 
stirlingCorrection(int) - Static method in class neurord.numeric.math.Arithmetic
Returns the StirlingCorrection.
StochasticGridCalc - Class in neurord.numeric.grid
 
StochasticGridCalc(int, SDRun) - Constructor for class neurord.numeric.grid.StochasticGridCalc
 
StochDiff - Class in neurord
 
StochDiff() - Constructor for class neurord.StochDiff
 
stoichiometry(int[], int[], int[], int[]) - Static method in class neurord.numeric.grid.NextEventQueue
Calculates a joint array of stoichiometries from reactants @ri, @rs and products @pi, @ps.
storeResultIn(Hashtable<Integer, Object>) - Method in class neurord.numeric.BaseCalc
 
stringd(double) - Static method in class neurord.numeric.grid.ResultWriterText
 
stringDims() - Method in class neurord.numeric.math.Matrix
 
stringi(int) - Static method in class neurord.numeric.grid.ResultWriterText
 
stringify(Object) - Static method in class neurord.util.Settings
 
StringListAdapter - Class in neurord.xml
 
StringListAdapter() - Constructor for class neurord.xml.StringListAdapter
 
StringTrimAdapter - Class in neurord.xml
 
StringTrimAdapter() - Constructor for class neurord.xml.StringTrimAdapter
 
subAreaPeer - Variable in class neurord.numeric.morph.TreePoint
 
subPlaneConnect(TreePoint, TreePoint, CurvedVolumeSlice, double) - Method in class neurord.disc.CurvedVolumeSlice
 
subPlaneConnect(TreePoint, TreePoint, VolumeLine, double) - Method in class neurord.numeric.morph.VolumeLine
 
subPlaneConnect(TreePoint, TreePoint, VolumeSlice, double) - Method in class neurord.numeric.morph.VolumeSlice
 
substrate_stoichiometry() - Method in interface neurord.numeric.grid.IGridCalc.Event
Stoichiometries of species, negative on the lhs, positive on the rhs
substrate_stoichiometry() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
substrate_stoichiometry() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
substrate_stoichiometry() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
substrate_stoichiometry() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
substrates() - Method in interface neurord.numeric.grid.IGridCalc.Event
Indices of species on both sides of the reaction
substrates() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
substrates() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
substrates() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
substrates() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
substrates_by_voxel() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
substrates_by_voxel() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
substrates_by_voxel() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
substrates_by_voxel() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
subtract(Matrix) - Method in class neurord.numeric.math.Matrix
 
subtractIdentity() - Method in class neurord.numeric.math.Matrix
 
sum(Matrix) - Method in class neurord.numeric.math.Matrix
 
sum(int[]) - Static method in class neurord.util.ArrayUtil
 
sum(int[][]) - Static method in class neurord.util.ArrayUtil
 
sum(int[][][]) - Static method in class neurord.util.ArrayUtil
 
surfaceBoundary - Variable in class neurord.numeric.morph.VolumeElement
 
SurfaceDensitySet - Class in neurord.model
 
SurfaceDensitySet() - Constructor for class neurord.model.SurfaceDensitySet
 
SWITCH_MEAN - Static variable in class neurord.numeric.math.Poisson
 

T

tag - Variable in class neurord.neuroml.meta
 
time() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
time() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 
time - Variable in class neurord.numeric.grid.NextEventQueue.NextEvent
time: when the event is scheduled to occur.
time() - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
time() - Method in interface neurord.numeric.grid.NextEventQueue.Node
 
times(GRotation) - Method in class neurord.geom.GRotation
 
times(double) - Method in class neurord.numeric.math.Column
 
times(Matrix) - Method in class neurord.numeric.math.Matrix
 
times(Column) - Method in class neurord.numeric.math.Matrix
 
TimeTests - Class in neurord.numeric.stochastic
 
TimeTests() - Constructor for class neurord.numeric.stochastic.TimeTests
 
TimeUtil - Class in neurord.util
 
TimeUtil() - Constructor for class neurord.util.TimeUtil
 
toArray(Collection<? extends Integer>) - Static method in class neurord.util.ArrayUtil
 
toDoubleArray(Collection<Double>) - Static method in class neurord.util.ArrayUtil
 
toIntArray(Collection<Integer>) - Static method in class neurord.util.ArrayUtil
 
tolerance - Variable in class neurord.model.SDRun
Accepted tolerance for adaptive calculations (delta f / f for an algorithm dependent function f).
topArea - Variable in class neurord.numeric.morph.VolumeElement
 
toString() - Method in class neurord.geom.GPosition
 
toString() - Method in class neurord.geom.GVector
 
toString() - Method in class neurord.model.EndPoint
 
toString() - Method in class neurord.model.MorphPoint
 
toString() - Method in class neurord.model.SpecieRef
 
toString() - Method in class neurord.numeric.chem.StimulationTable.Stimulation
 
toString() - Method in class neurord.numeric.grid.NextEventQueue.NextDiffusion
 
toString() - Method in class neurord.numeric.grid.NextEventQueue.NextReaction
 
toString() - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
toString() - Method in class neurord.numeric.morph.ElementConnection
 
toString() - Method in class neurord.numeric.morph.TreePoint
 
toString() - Method in class neurord.numeric.morph.VolumeElement
 
toString() - Method in class neurord.numeric.stochastic.NGoTable
 
toTreePoint() - Method in class neurord.model.MorphPoint
 
transferConnections() - Method in class neurord.model.MorphPoint
 
Transitional - Interface in neurord.inter
 
translate(Translation) - Method in class neurord.numeric.morph.TrianglesSet
 
translate(Translation) - Method in class neurord.numeric.morph.TriangleStrip
 
translation(Position) - Static method in class neurord.geom.Geom
 
Translation - Interface in neurord.geom
 
transpose() - Method in class neurord.numeric.math.Matrix
 
TreeBoxDiscretizer - Class in neurord.disc
 
TreeBoxDiscretizer() - Constructor for class neurord.disc.TreeBoxDiscretizer
 
TreeCurvedElementDiscretizer - Class in neurord.disc
 
TreeCurvedElementDiscretizer(TreePoint[]) - Constructor for class neurord.disc.TreeCurvedElementDiscretizer
 
TreePoint - Class in neurord.numeric.morph
 
TreePoint() - Constructor for class neurord.numeric.morph.TreePoint
 
TreePoint(double, double, double, double) - Constructor for class neurord.numeric.morph.TreePoint
 
TreeUtil - Class in neurord.disc
 
TreeUtil() - Constructor for class neurord.disc.TreeUtil
 
TreeWriter - Class in neurord.numeric.morph
 
TreeWriter(TreePoint[]) - Constructor for class neurord.numeric.morph.TreeWriter
 
trial() - Method in class neurord.numeric.BaseCalc
 
trial() - Method in interface neurord.numeric.grid.IGridCalc
 
Trial(Group) - Constructor for class neurord.numeric.grid.ResultWriterHDF5.Trial
 
trials - Variable in class neurord.numeric.grid.ResultWriterHDF5
 
TrianglesSet - Class in neurord.numeric.morph
 
TrianglesSet() - Constructor for class neurord.numeric.morph.TrianglesSet
 
TriangleStrip - Class in neurord.numeric.morph
 
TriangleStrip() - Constructor for class neurord.numeric.morph.TriangleStrip
 

U

uniformRV() - Static method in class neurord.numeric.math.NRRandom
 
unitX() - Static method in class neurord.geom.Geom
 
unitY() - Static method in class neurord.geom.Geom
 
unitZ() - Static method in class neurord.geom.Geom
 
unmarshal(String) - Method in class neurord.xml.DoubleListAdapter
 
unmarshal(String) - Method in class neurord.xml.DoubleMatrixAdapter
 
unmarshal(String) - Method in class neurord.xml.StringListAdapter
 
unmarshal(String) - Method in class neurord.xml.StringTrimAdapter
 
unmarshall(File, InputSource, HashMap<String, String>) - Method in class neurord.xml.ModelReader
 
unmarshall(File, HashMap<String, String>) - Method in class neurord.xml.ModelReader
 
unmarshall(String, HashMap<String, String>) - Method in class neurord.xml.ModelReader
 
updatePopulation(int, int, int, NextEventQueue.NextEvent) - Method in class neurord.numeric.grid.NextEventQueue
 
updateStatistics(int[][], int) - Method in class neurord.numeric.grid.NextEventQueue.NextEvent
 
used() - Method in class neurord.numeric.math.MersenneTwister
 
used() - Method in interface neurord.numeric.math.RandomGenerator
 

V

value - Variable in class neurord.model.MaxElementSide
 
value - Variable in class neurord.model.NanoMolarity
 
value - Variable in class neurord.model.PicoSD
 
value - Variable in class neurord.model.Statistics
 
value - Variable in class neurord.neuroml.meta
 
value - Variable in class neurord.neuroml.MetaItem
 
valueOf(String) - Static method in enum neurord.numeric.BaseCalc.algorithm_t
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.numeric.BaseCalc.distribution_t
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.numeric.BaseCalc.output_t
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.numeric.grid.IGridCalc.EventType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.numeric.grid.IGridCalc.HappeningKind
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.numeric.morph.VolumeGrid.geometry_t
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neurord.SDCalcType
Returns the enum constant of this type with the specified name.
values() - Static method in enum neurord.numeric.BaseCalc.algorithm_t
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.numeric.BaseCalc.distribution_t
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.numeric.BaseCalc.output_t
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.numeric.grid.IGridCalc.EventType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.numeric.grid.IGridCalc.HappeningKind
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.numeric.morph.VolumeGrid.geometry_t
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum neurord.SDCalcType
Returns an array containing the constants of this enum type, in the order they are declared.
vector(double, double, double) - Static method in class neurord.geom.Geom
 
Vector - Interface in neurord.geom
 
versatile_ngo(int, double) - Method in class neurord.numeric.stochastic.StepGenerator
Return a random variate from one of the distributions appropriate for first-order reactions (binomial or poisson) depending on the distribution_t mode specified when this object was created.
volume - Variable in class neurord.numeric.morph.VolumeElement
 
VolumeElement - Class in neurord.numeric.morph
 
VolumeElement(String, String, String, Position[], Position[], double, Position, double, double, double, double, double) - Constructor for class neurord.numeric.morph.VolumeElement
 
VolumeGrid - Class in neurord.numeric.morph
 
VolumeGrid() - Constructor for class neurord.numeric.morph.VolumeGrid
 
VolumeGrid.geometry_t - Enum in neurord.numeric.morph
 
VolumeLine - Class in neurord.numeric.morph
 
VolumeLine(int, int, double[], double, double) - Constructor for class neurord.numeric.morph.VolumeLine
 
VolumeSlice - Class in neurord.numeric.morph
 
VolumeSlice(double, double) - Constructor for class neurord.numeric.morph.VolumeSlice
 
VolumeTest - Class in neurord.examples.volume
 
VolumeTest() - Constructor for class neurord.examples.volume.VolumeTest
 

W

waited() - Method in interface neurord.numeric.grid.IGridCalc.Happening
 
waited() - Method in class neurord.numeric.grid.NextEventQueue.Happening
 
weightedSample(double[]) - Static method in class neurord.numeric.math.NRRandom
 
width - Variable in class neurord.model.Section
 
writeArray(String, Group, double[][]) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeArray(String, Group, int[][], int) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeConcentration - Variable in class neurord.numeric.BaseCalc
 
writeDependencies() - Method in class neurord.model.SDRun
 
writeEventData(Group, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeEvents(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeEventStatistics(double, IGridCalc) - Method in interface neurord.numeric.grid.ResultWriter
 
writeEventStatistics(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeEventStatistics(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeEventStatistics(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterText
 
writeGrid(VolumeGrid, double, IGridCalc) - Method in interface neurord.numeric.grid.ResultWriter
 
writeGrid(VolumeGrid, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeGrid(VolumeGrid, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterText
 
writeManifest() - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeMap(Group, Set<Map.Entry<Object, Object>>) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeOutputInfo(Group, String, int[], int[]) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeOutputInfo(Group) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeOutputInterval(double, IGridCalc) - Method in interface neurord.numeric.grid.ResultWriter
 
writeOutputInterval(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeOutputInterval(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterText
 
writeOutputScheme(int, double, IGridCalc) - Method in interface neurord.numeric.grid.ResultWriter
 
writeOutputScheme(int, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeOutputScheme(int, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterText
 
writePopulation(double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.PopulationOutput
 
writePopulation(int, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeReactionData(Group, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeRegionLabels(Group, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeSimulationData(IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeSpeciesVector(String, String, Group, String[], int[]) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeStimulationData(Group, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
writeString(String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeStringToFile(String, File) - Static method in class neurord.util.FileUtil
 
writeSWC(File) - Method in class neurord.numeric.morph.TreeWriter
 
writeTo(double[]) - Method in class neurord.numeric.math.Column
 
writeToFinalSiblingFile(String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeToFinalSiblingFile(String, String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeToSiblingFile(String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeToSiblingFile(String, String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeToSiblingFileAndClose(String, String) - Method in class neurord.numeric.grid.ResultWriterText
 
writeVector(String, Group, String...) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeVector(String, Group, double...) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeVector(String, Group, int...) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
writeVector(String, Group, long...) - Method in class neurord.numeric.grid.ResultWriterHDF5
 

X

x - Variable in class neurord.model.MorphPoint
 
x - Variable in class neurord.neuroml.MorphMLPoint
 
X_AXIS - Static variable in class neurord.geom.GRotation
 
xJoined(int...) - Static method in class neurord.util.ArrayUtil
 
xJoined(long...) - Static method in class neurord.util.ArrayUtil
 
xml - Variable in class neurord.numeric.grid.ResultWriterHDF5.LoadModelResult
 
xmlns - Variable in class neurord.neuroml.morphml
 
xmlns_cml - Variable in class neurord.neuroml.morphml
 
xmlns_meta - Variable in class neurord.neuroml.morphml
 
xmlns_mml - Variable in class neurord.neuroml.morphml
 
xmlns_xsi - Variable in class neurord.neuroml.morphml
 
xProjection(Vector) - Static method in class neurord.geom.Geom
 
xRotationAngle(Vector, Vector) - Static method in class neurord.geom.Geom
 
xsi_schemaLocation - Variable in class neurord.neuroml.morphml
 
xyProjection(Vector) - Static method in class neurord.geom.Geom
 
xzRotationAngle(Vector) - Static method in class neurord.geom.Geom
 

Y

y - Variable in class neurord.model.MorphPoint
 
y - Variable in class neurord.neuroml.MorphMLPoint
 
Y_AXIS - Static variable in class neurord.geom.GRotation
 
yzRotationAngle(Vector) - Static method in class neurord.geom.Geom
 

Z

z - Variable in class neurord.model.MorphPoint
 
z - Variable in class neurord.neuroml.MorphMLPoint
 
Z_AXIS - Static variable in class neurord.geom.GRotation
 
zElevation(Vector) - Static method in class neurord.geom.Geom
 
zero() - Method in class neurord.numeric.math.Matrix
 
zProjection(Vector) - Static method in class neurord.geom.Geom
 
zRotationAngle(Vector, Vector) - Static method in class neurord.geom.Geom
 

_

_flatten(double[], double[][], int) - Static method in class neurord.util.ArrayUtil
 
_flatten(int[], int[][], long, int) - Static method in class neurord.util.ArrayUtil
 
_flatten(int[], int[][][], long, int) - Static method in class neurord.util.ArrayUtil
 
_init() - Method in class neurord.numeric.grid.ResultWriterHDF5
 
_loadModel(File, int, Double) - Static method in class neurord.numeric.grid.ResultWriterHDF5
 
_run() - Method in class neurord.numeric.BaseCalc
 
_run() - Method in class neurord.numeric.grid.GridCalc
 
_run() - Method in class neurord.numeric.pool.DeterministicPoolCalc
 
_run() - Method in class neurord.numeric.StaticCalc
 
_update_propensity(boolean) - Method in class neurord.numeric.grid.NextEventQueue.NextStimulation
 
_writeArray(String, Group, H5Datatype, long[], Object) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
_writeGrid(VolumeGrid, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5
 
_writeGrid(VolumeGrid, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
_writeOutput(int, double, IGridCalc) - Method in class neurord.numeric.grid.ResultWriterHDF5.Trial
 
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