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The natural orbital functional theory (NOFT) has emerged as an alternative formalism to both density functional (DF) and wavefunction methods. In NOFT, the electronic structure is described in terms of the natural orbitals (NOs) and their occupation numbers (ONs). The approximate NOFs have proven to be more accurate than those of the density for systems with a significant multiconfigurational character, on one side, and scale better with the number of basis functions than correlated wavefunction methods, on the other side. A challenging task in NOFT is to efficiently perform orbital optimization. In this article we present DoNOF, our open source implementation based on diagonalizations that allows to obtain the resulting orbitals automatically orthogonal. The one-particle reduced-density matrix (1RDM) of the ensemble of pure-spin states provides the proper description of spin multiplets. The capabilities of the code are tested on the water molecule, namely, geometry optimization, natural and canonical representations of molecular orbitals, ionization potential, and electric moments. In DoNOF, the electron-pair-based NOFs developed in our group PNOF5, PNOF7 and PNOF7s are implemented. These JKL-only NOFs take into account most non-dynamic effects plus intrapair-dynamic electron correlation, but lack a significant part of interpair-dynamic correlation. Correlation corrections are estimated by the single-reference NOF-MP2 method that simultaneously calculates static and dynamic electron correlations taking as a reference the Slater determinant formed with the NOs of a previous PNOF calculation. The NOF-MP2 method is used to analyze the potential energy surface (PES) and the binding energy for the symmetric dissociation of the water molecule, and compare it with accurate wavefunction-based methods.