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We describe a method to compute photon-matter interaction and atomic dynamicswith X-ray lasers using a hybrid code based on classical molecular dynamics andcollisional-radiative calculations. The forces between the atoms aredynamically computed based on changes to their electronic occupations and thefree electron cloud created due to the irradiation of photons in the X-rayspectrum. The rapid transition from neutral solid matter to dense plasma phaseallows the use of screened potentials, which reduces the number of non-bondedinteractions required to compute. In combination with parallelisation throughdomain decomposition, large-scale molecular dynamics and ionisation induced byX-ray lasers can be followed. This method is applicable for large enoughsamples (solids, liquids, proteins, viruses, atomic clusters and crystals) thatwhen exposed to an X-ray laser pulse turn into a plasma in the first fewfemtoseconds of the interaction. We show several examples of the applicabilityof the method and we quantify the sizes that the method is suitable for. Forlarge systems, we investigate non-thermal heating and scattering of bulk water,which we compare to previous experiments. We simulate molecular dynamics of aprotein crystal induced by an X-ray pump, X-ray probe scheme, and find goodagreement of the damage dynamics with experiments. For single particle imaging,we simulate ultrafast dynamics of a methane cluster exposed to a femtosecondX-ray laser. In the context of coherent diffractive imaging we study thefragmentation as given by an X-ray pump X-ray probe setup to understand theevolution of radiation damage.

MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics