We study the short-distance hadronic matrix elements for $D$-meson mixing with partially quenched $N_f=2+1$ lattice QCD. We use a large set of the MIMD Lattice Computation Collaboration's gauge configurations with $a^2$ tadpole-improved staggered sea quarks and tadpole-improved L\"uscher-Weisz gluons. We use the $a^2$ tadpole-improved action for valence light quarks and the Sheikoleslami-Wohlert action with the Fermilab interpretation for the valence charm quark. Our calculation covers the complete set of five operators needed to constrain new physics models for $D$-meson mixing. We match our matrix elements to the $\overline{\text{MS}}$-NDR scheme evaluated at 3GeV. We report values for the Beneke-Buchalla-Greub-Lenz-Nierste choice of evanescent operators and obtain\begin{align}\left/m_D=& 0.042(4)\text{GeV}^3, \nonumber \\\left/m_D=& -0.078(4)\text{GeV}^3, \nonumber \\\left/m_D=& 0.033(2)\text{GeV}^3, \nonumber \\\left/m_D=& 0.155(10)\text{GeV}^3, \nonumber \\\left/m_D=& 0.058(6)\text{GeV}^3.\nonumber\end{align}
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Short-distance matrix elements for D-meson mixing for 2+1 flavor lattice QCD