The ammonia smell is from the ketones you're burning — in other words, you're in ketosis and your body is excreting the waste from the fat it's burning! This is a good thing. For me, the ammonia smell shows up in the toilet and in my breath, but sweat is another way to flush toxins out of the body. If the smell bothers you, try drinking more water. It will dilute the ketones so the smell should be less strong.