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In material contract, for areas such has parking space or overhead tank space(where roof mould exists but there is no wall on 2-3 sides) during square calculation is it still taken has complete square calculated value based on mould or is it generally taken as 50% of mould area during square calculation ? Can somebody throw light on generally accepted practice here ?

Actually I would advise against lump sum (per square feet) calculation. Better to go for item rate contract. Your architect should be able to break tasks into items and you can get quotations from contractors for each item.