use shallow atmosphere in amip

[szy21]

Purpose

The nightly AMIP breaks with deep atmosphere, so I set it to shallow atmosphere now. See #1183
shallow atmosphere build: https://buildkite.com/clima/climacoupler-coarse-nightly-amip/builds/250

To-do

Content

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• I have read and checked the items on the review checklist.

[juliasloan25]

In the long term, will we want to use shallow or deep atmosphere?

[akshaysridhar]

In the long term, will we want to use shallow or deep atmosphere?

Deep atmosphere (this is now default in the atmos configurations)