We present a polynomial Hybrid Monte Carlo (PHMC) algorithm as an exact simulation algorithm with dynamical Kogut-Susskind fermions. The algorithm uses a Hermitian polynomial approximation for the fractional power of the KS fermion matrix. The systematic error from the polynomial approximation is removed by the Kennedy-Kuti noisy Metropolis test so that the algorithm becomes exact at a finite molecular dynamics step size. We performed numerical tests with $N_f$$=$2 case on several lattice sizes. We found that the PHMC algorithm works on a moderately large lattice of $16^4$ at $beta$$=$5.7, $m$$=$0.02 ($m_{mathrm{PS}}/m_{mathrm{V}}$$sim$0.69) with a reasonable computational time.
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