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The dense neutron-rich matter found in supernovae and neutron stars is expected to form complex nonuniform phases referred to as nuclear pasta. The pasta shapes depend on density, temperature and proton fraction and determine many transport properties in supernovae and neutron star crusts. We use two recently developed hybrid CPU/GPU codes to perform large scale molecular dynamics (MD) simulations with $51200$ and $409600$ nucleons of nuclear pasta. From the output of the MD simulations we characterize the topology and compute two observables, the radial distribution function $g(r)$ and the structure factor $S(q)$, for systems with proton fractions $Y_p=0.10, 0.20, 0.30$ and $0.40$ at about one third of nuclear saturation density and temperatures near $1.0$ MeV. We observe that the two lowest proton fraction systems simulated, $Y_p=0.10$ and $0.20$, equilibrate quickly and form liquid-like structures. Meanwhile, the two higher proton fraction systems, $Y_p=0.30$ and $0.40$, take a longer time to equilibrate and organize themselves in solid-like periodic structures. Furthermore, the $Y_p=0.40$ system is made up of slabs, lasagna phase, interconnected by defects while the $Y_p=0.30$ systems consist of a stack of perforated plates, the nuclear waffle phase. The periodic configurations observed in our MD simulations for proton fractions $Y_pge0.30$ have important consequences for the structure factors $S(q)$ of protons and neutrons, which relate to many transport properties of supernovae and neutron star crust. A detailed study of the waffle phase and how its structure depends on temperature, size of the simulation and the screening length showed that finite-size effects appear to be under control and, also, that the plates in the waffle phase merge at temperatures slightly above $1.0$ MeV and the holes in the plates form an hexagonal lattice at temperatures slightly lower than $1.0$ MeV.
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