//MassCenter centers in in the center of mass of oref. Mass must be
//A column vector. Returns the centered matrix and the displacement matrix.
func MassCenter(in, oref *v3.Matrix, mass *mat64.Dense) (*v3.Matrix, *v3.Matrix, error) {
or, _ := oref.Dims()
ir, _ := in.Dims()
if mass == nil { //just obtain the geometric center
tmp := ones(or)
mass = mat64.NewDense(or, 1, tmp) //gnOnes(or, 1)
}
ref := v3.Zeros(or)
ref.Copy(oref)
gnOnesvector := gnOnes(1, or)
f := func() { ref.ScaleByCol(ref, mass) }
if err := gnMaybe(gnPanicker(f)); err != nil {
return nil, nil, CError{err.Error(), []string{"v3.Matrix.ScaleByCol", "MassCenter"}}
}
ref2 := v3.Zeros(1)
g := func() { ref2.Mul(gnOnesvector, ref) }
if err := gnMaybe(gnPanicker(g)); err != nil {
return nil, nil, CError{err.Error(), []string{"v3.gOnesVector", "MassCenter"}}
}
ref2.Scale(1.0/mass.Sum(), ref2)
returned := v3.Zeros(ir)
returned.Copy(in)
returned.SubVec(returned, ref2)
/* for i := 0; i < ir; i++ {
if err := returned.GetRowVector(i).Subtract(ref2); err != nil {
return nil, nil, err
}
}
*/
return returned, ref2, nil
}
//CenterOfMass returns the center of mass the atoms represented by the coordinates in geometry
//and the masses in mass, and an error. If mass is nil, it calculates the geometric center
func CenterOfMass(geometry *v3.Matrix, mass *mat64.Dense) (*v3.Matrix, error) {
if geometry == nil {
return nil, CError{"goChem: nil matrix to get the center of mass", []string{"CenterOfMass"}}
}
gr, _ := geometry.Dims()
if mass == nil { //just obtain the geometric center
tmp := ones(gr)
mass = mat64.NewDense(gr, 1, tmp) //gnOnes(gr, 1)
}
tmp2 := ones(gr)
gnOnesvector := mat64.NewDense(1, gr, tmp2) //gnOnes(1, gr)
ref := v3.Zeros(gr)
ref.ScaleByCol(geometry, mass)
ref2 := v3.Zeros(1)
ref2.Mul(gnOnesvector, ref)
ref2.Scale(1.0/mass.Sum(), ref2)
return ref2, nil
}