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The pair-functional principle shows how to construct a unique statistical ensemble of strongly interacting atoms that corresponds to any feasible measured set of X-ray intensities. The ensemble and all its distribution functions are strictly periodic in the crystal lattice, so that each unit cell has exactly the same arrangement of atoms at all times. The mean particle density in the cell is uniform because the ensemble has undefined phases and the origin is not fixed. The atoms in this maximum-entropy ensemble interact through pairwise additive periodic statistical forces within the unit cell. The ensemble average pair-correlation function is matched to the observed originless Patterson function of the crystal. The derived pairing force then becomes approximately proportional to the Ornstein-Zernicke direct correlation function of the ensemble. The atoms have a many-body Boltzmann distribution and the logarithm of the likelihood of any particular conformation is related to its total pairing potential. The pairing potential of a group of atoms acts like a local field in the cell. This property is used in the pair-functional method. Molecular structures can be solved by a direct search in real space for clusters of atoms with high pair potentials. During a successful search, the atoms move from their original random positions to form larger and larger clusters of correctly formed fragments. Finally, every atom belongs to a single cluster, which is the correct solution.
