//Next Reads the next frame in a XTCObj that has been initialized for read
//With initread. If keep is true, returns a pointer to matrix.DenseMatrix
//With the coordinates read, otherwiser, it discards the coordinates and
//returns nil.
func (X *XTCObj) Next(output *v3.Matrix) error {
if !X.Readable() {
return Error{TrajUnIni, X.filename, []string{"Next"}, true}
}
cnatoms := C.int(X.natoms)
worked := C.get_coords(X.fp, &X.cCoords[0], cnatoms)
if worked == 11 {
X.readable = false
return newlastFrameError(X.filename, "Next") //This is not really an error and should be catched in the calling function
}
if worked != 0 {
X.readable = false
return Error{ReadError, X.filename, []string{"Next"}, true}
}
if output != nil { //col the frame
r, c := output.Dims()
if r < (X.natoms) {
panic("Buffer v3.Matrix too small to hold trajectory frame")
}
for j := 0; j < r; j++ {
for k := 0; k < c; k++ {
l := k + (3 * j)
output.Set(j, k, (10 * float64(X.cCoords[l]))) //nm to Angstroms
}
}
return nil
}
return nil //Just drop the frame
}
//MakeWater Creates a water molecule at distance Angstroms from a2, in a direction that is angle radians from the axis defined by a1 and a2.
//Notice that the exact position of the water is not well defined when angle is not zero. One can always use the RotateAbout
//function to move the molecule to the desired location. If oxygen is true, the oxygen will be pointing to a2. Otherwise,
//one of the hydrogens will.
func MakeWater(a1, a2 *v3.Matrix, distance, angle float64, oxygen bool) *v3.Matrix {
water := v3.Zeros(3)
const WaterOHDist = 0.96
const WaterAngle = 52.25
const deg2rad = 0.0174533
w := water.VecView(0) //we first set the O coordinates
w.Copy(a2)
w.Sub(w, a1)
w.Unit(w)
dist := v3.Zeros(1)
dist.Sub(a1, a2)
a1a2dist := dist.Norm(0)
fmt.Println("ala2dist", a1a2dist, distance) ////////////////7777
w.Scale(distance+a1a2dist, w)
w.Add(w, a1)
for i := 0; i <= 1; i++ {
o := water.VecView(0)
w = water.VecView(i + 1)
w.Copy(o)
fmt.Println("w1", w) ////////
w.Sub(w, a2)
fmt.Println("w12", w) ///////////////
w.Unit(w)
fmt.Println("w4", w)
w.Scale(WaterOHDist+distance, w)
fmt.Println("w3", w, WaterOHDist, distance)
o.Sub(o, a2)
t, _ := v3.NewMatrix([]float64{0, 0, 1})
upp := v3.Zeros(1)
upp.Cross(w, t)
fmt.Println("upp", upp, w, t)
upp.Add(upp, o)
upp.Add(upp, a2)
//water.SetMatrix(3,0,upp)
w.Add(w, a2)
o.Add(o, a2)
sign := 1.0
if i == 1 {
sign = -1.0
}
temp, _ := RotateAbout(w, o, upp, deg2rad*WaterAngle*sign)
w.SetMatrix(0, 0, temp)
}
var v1, v2 *v3.Matrix
if angle != 0 {
v1 = v3.Zeros(1)
v2 = v3.Zeros(1)
v1.Sub(a2, a1)
v2.Copy(v1)
v2.Set(0, 2, v2.At(0, 2)+1) //a "random" modification. The idea is that its not colinear with v1
v3 := cross(v1, v2)
v3.Add(v3, a2)
water, _ = RotateAbout(water, a2, v3, angle)
}
if oxygen {
return water
}
//we move things so an hydrogen points to a2 and modify the distance acordingly.
e1 := water.VecView(0)
e2 := water.VecView(1)
e3 := water.VecView(2)
if v1 == nil {
v1 = v3.Zeros(1)
}
if v2 == nil {
v2 = v3.Zeros(1)
}
v1.Sub(e2, e1)
v2.Sub(e3, e1)
axis := cross(v1, v2)
axis.Add(axis, e1)
water, _ = RotateAbout(water, e1, axis, deg2rad*(180-WaterAngle))
v1.Sub(e1, a2)
v1.Unit(v1)
v1.Scale(WaterOHDist, v1)
water.AddVec(water, v1)
return water
}