Dear @chenjianqi,
A similar issue has been addressed in the past in this post:Cosmic ray showers - Geometry and Materials - FLUKA User Forum, which I invite you to have a look to. The parameters used in the atmloc have an impact on the construction of the local geometry, particularly of the definition of the cones which constraint the atmospheric layers. Please note that using a geomagnetic cutoff acceptance too high prevents the routine to generate output files (.geo, .sur, etc).
Please note that the example provided with the FLUKA distribution is relative to Tsukuba (36N° 140E°). Using those coordinates in the atmloc produce a very similar geometry to the one provided with FLUKA.
Hope that helps.
Regards,
Angelo