Uses of Class
ffx.numerics.math.Double3

Packages that use Double3

Package	Description
ffx.numerics.atomic	The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.numerics.math	The Math package implements complex numbers, a software square root, and vector operations.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.

Uses of Double3 in ffx.numerics.atomic

Methods in ffx.numerics.atomic that return Double3

Modifier and Type	Method	Description
Double3	AtomicDoubleArray3D.get(int index)	Get the Double3 at the specified index.

Methods in ffx.numerics.atomic with parameters of type Double3

Modifier and Type	Method	Description
void	AtomicDoubleArray3D.add(int threadID, int index, Double3 d3)	Add to the double arrays at the specified index the given Double3.
void	AtomicDoubleArray3D.set(int threadID, int index, Double3 d3)	Set the double arrays at the specified index to the given Double3.
void	AtomicDoubleArray3D.sub(int threadID, int index, Double3 d3)	Subtracts from the double arrays at the specified index the given Double3.

Uses of Double3 in ffx.numerics.math

Methods in ffx.numerics.math that return Double3

Modifier and Type	Method	Description
Double3	Double3.add(Double3 b)	Finds the sum of this Double3 with b.
Double3	Double3.addI(Double3 b)	Finds the sum of this Double3 with b in place.
Double3	Double3.copy()	Returns a new copy of this Double3.
Double3	Double3.fma(double b, Double3 c)	Compute this * b + c and return the result in a new Double3.
Double3	Double3.fmaI(double b, Double3 c)	Compute this * b + c and return the result in a new Double3.
Double3	Double3.normalize()	Normalize this Double3.
Double3	Double3.normalizeI()	Normalize this Double3 in place.
Double3	Double3.scale(double d)	Scales a Double3.
Double3	Double3.scaleI(double d)	Scales a Double3 in place.
Double3	Double3.set(double[] b)	Set the value of this Double3.
Double3	Double3.set(double x, double y, double z)	Set the value of this Double3.
Double3	Double3.set(Double3 b)	Set the value of this Double3.
Double3	Double3.sqrt()	Square roots values in Double3.
Double3	Double3.sqrtI()	Square roots values in Double3 in place.
Double3	Double3.square()	Squares values in Double3.
Double3	Double3.squareI()	Squares values in Double3 in place.
Double3	Double3.sub(Double3 b)	Finds the difference between two vectors.
Double3	Double3.subI(Double3 b)	Finds the difference between two vectors.
Double3	Double3.X(Double3 b)	Cross product of this Double3 with b.
Double3	Double3.XI(Double3 b)	In-place Cross product of this Double3 with b.

Methods in ffx.numerics.math with parameters of type Double3

Modifier and Type	Method	Description
Double3	Double3.add(Double3 b)	Finds the sum of this Double3 with b.
Double3	Double3.addI(Double3 b)	Finds the sum of this Double3 with b in place.
double	Double3.angle(Double3 b)	Angle of this Double3 with b.
double	Double3.dist(Double3 b)	Finds the Euclidean distance between two positions.
double	Double3.dist2(Double3 b)	Finds the square of the Euclidean distance between two positions.
double	Double3.dot(Double3 b)	Finds the dot product between two vectors.
Double3	Double3.fma(double b, Double3 c)	Compute this * b + c and return the result in a new Double3.
Double3	Double3.fmaI(double b, Double3 c)	Compute this * b + c and return the result in a new Double3.
Double3	Double3.set(Double3 b)	Set the value of this Double3.
Double3	Double3.sub(Double3 b)	Finds the difference between two vectors.
Double3	Double3.subI(Double3 b)	Finds the difference between two vectors.
Double3	Double3.X(Double3 b)	Cross product of this Double3 with b.
Double3	Double3.XI(Double3 b)	In-place Cross product of this Double3 with b.

Uses of Double3 in ffx.potential.bonded

Methods in ffx.potential.bonded that return Double3

Modifier and Type	Method	Description
Double3	Atom.getXYZ()	getXYZ