Example #1
0
File: xtc.go Project: rmera/gochem
//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
}
Example #2
0
File: xtc.go Project: rmera/gochem
/*NextConc takes a slice of bools and reads as many frames as elements the list has
form the trajectory. The frames are discarted if the corresponding elemetn of the slice
* is false. The function returns a slice of channels through each of each of which
* a *matrix.DenseMatrix will be transmited*/
func (X *XTCObj) NextConc(frames []*v3.Matrix) ([]chan *v3.Matrix, error) {
	if X.buffSize < len(frames) {
		X.setConcBuffer(len(frames))
	}
	if X.natoms == 0 {
		return nil, Error{TrajUnIni, X.filename, []string{"NextConc"}, true}
	}
	framechans := make([]chan *v3.Matrix, len(frames)) //the slice of chans that will be returned
	cnatoms := C.int(X.natoms)
	used := false
	for key, val := range frames {
		//cCoords:=X.concBuffer[key]
		worked := C.get_coords(X.fp, &X.concBuffer[key][0], cnatoms)
		//Error handling
		if worked == 11 {
			if used == false {
				X.readable = false
				return nil, newlastFrameError(X.filename, "NextConc") //This is not really an error and
			} else { //should be catched in the calling function
				X.readable = false
				return framechans, newlastFrameError(X.filename, "NextConc") //same
			}
		}
		if worked != 0 {
			X.readable = false
			return nil, Error{ReadError, X.filename, []string{"NextConc"}, true}
		}
		if val == nil {
			framechans[key] = nil //ignored frame
			continue
		}
		used = true
		framechans[key] = make(chan *v3.Matrix)
		//Now the parallel part
		go func(natoms int, cCoords []C.float, goCoords *v3.Matrix, pipe chan *v3.Matrix) {
			r, c := goCoords.Dims()
			for j := 0; j < r; j++ {
				for k := 0; k < c; k++ {
					l := k + (3 * j)
					goCoords.Set(j, k, (10 * float64(cCoords[l]))) //nm to Angstroms
				}
			}
			pipe <- goCoords
		}(X.natoms, X.concBuffer[key], val, framechans[key])
	}
	return framechans, nil
}