when a ball is thrown in upward direction --how can it be a negative displacement?
You have the choice to say that the axis perpendicular to the ground points upward or downward (i.e., in the direction of gravity). It is purely arbitrary and won't affect the results, provided that the convention chosen is strictly adhered to: once you've chosen which way is positive, stick to it!
It is an arbitrary choice. Having made a choice one simply has to be consistent.
If one were considering a situation where one is standing on the ground throwing a ball upwards so that all distances are up, it would be sensible and simplest to say up is positive.
If one were throwing objects off the top of a tower so that most of the displacements were below the starting point, one could well choose to take the starting point at the top of the tower as zero and make the downwards direction positive. Then, if one did throw a ball upwards, its displacement would be negative until it fell past the top of the tower.
is toward gravity +ve ?
Yes, if the throwing the ball upwards results in a negative displacement, then the force of gravity is postive.
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