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The surface geopotential field (PHIS) is read in the dycore's inidat.F90 file. There is logic there which sets PHIS = 0 for ideal physics and aquaplanet configurations. It may be as simple as disabling that logic to allow phis to be read from the topo file. But since that isn't a standard model configuration, it would be wise to grep the source code for the ideal_phys logical variable to identify other potential changes that would be needed.
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