  A precise evaluation of the secondary particle production and propagation in
the atmosphere is very important for the atmospheric neutrino oscillation
studies. The issue is addressed with the extension of a previously developed
full 3-Dimensional Monte-Carlo simulation of particle generation and transport
in the atmosphere, to compute the flux of secondary protons, muons and
neutrinos. Recent balloon borne experiments have performed a set of accurate
flux measurements for different particle species at different altitudes in the
atmosphere, which can be used to test the calculations for the atmospheric
neutrino production, and constrain the underlying hadronic models. The
simulation results are reported and compared with the latest flux measurements.
It is shown that the level of precision reached by these experiments could be
used to constrain the nuclear models used in the simulation. The implication of
these results for the atmospheric neutrino flux calculation are discussed.
