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A factor of 2 is missing when summing the partial components (for i != j terms) to give the total F(Q,t)/S(Q,w). A possible solution is to use this code at the end of the coherent block in the finalize function:

        if pair[0] == pair[1]:
            self._outputData["f(q,t)_coh_total"][:] += self._outputData["f(q,t)_coh_weighted_%s%s" % pair][:]
            self._outputData["s(q,f)_coh_total"][:] += self._outputData["s(q,f)_coh_weighted_%s%s" % pair][:]
        else:
            self._outputData["f(q,t)_coh_total"][:] += 2*self._outputData["f(q,t)_coh_weighted_%s%s" % pair][:]
            self._outputData["s(q,f)_coh_total"][:] += 2*self._outputData["s(q,f)_coh_weighted_%s%s" % pair][:]