You read the clause. If it was properly written, it will tell you exactly how the bonus/penalty is to be calculated. The contract may even include examples.
In contractual terms, a penalty clause is specifically there to encourage the other party to finish the contract, and to punish that party if there is a breach. Penalty clauses are not calculated with respect to a genuine estimate of the losses that will be incurred by the contracting party. If there is a genuine attempt to estimate damages, and you agree to them, it is called liquidated damages. The courts will ignore a penalty clause because it is unfair, and calculate the actual damage you cause the other party.