RMS Distance

The root mean square distance calculates the particle offset for all frames. This examples uses the 3-dimensional Positions (all) input.

Note

As of this version (0.12c), Positions (all) do not work for incrementally loaded trajectories.

Source code (Error checking omitted):

#include <array>
#include <cmath>
#include <vector>

//@in fcnt pcnt 3
double* positions = 0;
//@in 6
double* bbox = 0;

//@out fcnt
double* rms = 0;
std::vector<double> _rms;

//@var
int fcnt = 1;
//@var
int pcnt = 1;

void vec(double* to, double* frm, double* v, double* b) {
    for (int a = 0; a < 3; a++) {
        const double l = std::abs(b[a*2] - b[a*2+1]);
        v[a] = (to[a] - frm[a]) / l;
        v[a] -= std::round(v[a]);
        v[a] *= l;
    }
}
void add(double* a, double* b, double* v) {
    v[0] = a[0] + b[0];
    v[1] = a[1] + b[1];
    v[2] = a[2] + b[2];
}
double len2(double* a) {
    return a[0]*a[0] + a[1]*a[1] + a[2]*a[2];
}

//@entry
void Execute() {
    _rms.resize(fcnt, 0);
    rms = _rms.data();
    rms[0] = 0;

    std::vector<std::array<double, 3>> offset(pcnt), offset_sum(pcnt);

    double* pposo = positions;
    for (int f = 1; f < fcnt; f++) {
        double* ppos = pposo + pcnt * 3;
        for (int p = 0; p < pcnt; p++) {
            auto oft = offset[p].data();
            auto ofts = offset_sum[p].data();
            vec(ppos + p * 3, pposo + p * 3, oft, bbox);
            add(ofts, oft, ofts);
            rms[f] += len2(ofts);
        }
        rms[f] = std::sqrt(rms[f] / pcnt);
        pposo = ppos;
    }
}