For each of the N P3HT cations throughout the trajectory, we denote their coordinates as x i P (i = 1, • • • , N ) and find the two F 4 TCNQ anions at x i F 1 , x i F 2 in the same snapshot with closest distances between non-hydrogen atoms to the P3HT cation, since their center of mass distance would not necessarily be small even they form π-π stack. The three molecules form a pair P i = (x i P , x i F 1 , x i F 2 ). By employing the Kabsch transformation K, 41 Q 2 = K1 (P 1 )P 2