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There are some details with your code, the main reason that it isn't running is because of this line return np.sum(xAcc), np.sum(yAcc), you calculated a matrix of accelerations from the interactions between all the particles where you added the acceleration of one particle and the inverse of that acceleration to the other, since the mass of all particles is the same then the accelerations are the same, then you sum all the elements of the matrix, so all the terms cancel out, and instead of returning the acceleration of each particle you return the sum of the accelerations of ALL the particles, and given that they all have the same mass, is just 0, even if it was not 0 it would have been wrong because you where mixing them all, so all the particles would have the same acceleration and move in the same direction.

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In that same function you have also something that can be improved, you have something like

Based on your code I can't understand why do have to declareglobal xAcc in this way. You don't seem to use it anywhere outside of the function.

In any case, the line xPositions[i, :] = x will not help you to change your xAcc size, because it was declared earlier at xPositions = np.zeros((number_of_steps, 3)).

I see that xAcc = np.zeros((xPositions.size, xPositions.size), dtype=object) is declared as a square matrix (3000, 3000), and at this line return np.sum(xAcc, axis=0), np.sum(yAcc, axis=0) you reduced it at only one axis, so that's why you get xAcc as a vector of length 3000. Maybe reducing at another axis will help in your case np.sum(xAcc), in this way you will get an array of lenth 3.

It would be helpful to see the problem at hand.