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We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser(XFEL)pulses.In our scheme,molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states.We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses.The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics,providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.