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OP, the landlord generally can not charge 100% of the cost of replacement carpet. Be aware, though, that many judges will allow a much higher percentage of the replacement cost if replacement is needed because of destruction done by the tenant. Not the whole cost of replacing, but a bigger percentage of the cost than if replacement was due to plain old wearing out due to old age with some accidental stains.
I know a landlord who had to replace carpet because the tenant was rebuilding motorcycle engines in the living room. The judge in that case allowed the entire cost of replacement to be charged to the tenant because it was so far removed from normal wear and tear or accidental damage. Pets tearing the carpet and leaving a lot of urine stains is some fairly extreme damage.
I suggest that you wait and see what the landlord bills for the damage. I haven't seen your carpet so I don't know how bad it is, but in my units, my carpet cleaner is a genius. He can get out all sorts of smells and he can patch torn carpet so you can't see where it was repaired. I have had more than one tenant thinking they would have to pay to replace carpet when all they got was the bill for cleaning, deodorizing, and an additional $25 for a patch job.
If the carpet has to be replaced, expect the cost of carpet and pad to be prorated. The cost of sealing the subfloor because of urine stains will be 100% your cost.
You might want to clean the house so it is spotless and the carpet is the only damage. If you do that, your landlord will be in a much better mood. If you leave the rest of the house dirty or damaged, plus the pet ruined carpet, your landlord is very likely to go after you for every penny he can legally charge.