Modified to determine the distance between atom and the z-axis and checked to see if that is within the diameter of the beams - this makes sense since the beams are crossed and the condition that the distance be smaller than the beam diameter holds only along the y-axis.
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@ -9,7 +9,7 @@ function T = computeTimeSpentInInteractionRegion(this, r)
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T = 0;
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NumberOfTimeSteps = int64(this.SimulationTime/this.TimeStep);
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for n = 1:(NumberOfTimeSteps - 1)
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dr = Helper.calculateDistanceFromPointToLine(r(n+1, :), [0 0 0], [1 0 0]);
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dr = Helper.calculateDistanceFromPointToLine(r(n+1, :), [0 0 0], [0 0 1]);
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if dr < this.CoolingBeamRadius
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A = 1;
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else
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