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Register a new userAn efficient basis set representation for calculating electrons in molecules
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The method of McCurdy, Baertschy, and Rescigno, J. Phys. B, 37, R137 (2004) is generalized to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O(N log(N)) multiplication operations, not O(N^4), where N is the number of basis functions; N = n^3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionization potentials are reported for one- (He^+, H_2^+ ), two- (H_2, He), ten- (CH_4) and 56-electron (C_8H_8) systems.
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There are many ways to numerically represent of chemical systems in order to compute their electronic structure. Basis functions may be localized in real-space (atomic orbitals), in momentum-space (plane waves), or in both components of phase-space. Such phase-space localized basis functions in the form of wavelets, have been used for many years in electronic structure. In this paper, we turn to a phase-space localized basis set first introduced by K. G. Wilson. We provide the first full study of this basis and its numerical implementation. To calculate electronic energies of a variety of small molecules and states, we utilize the sum-of-products form, Gaussian quadratures, and introduce methods for selecting sample points from a grid of phase-space localized Wilson basis. Both full configuration interaction and Hartree-Fock implementations are discussed and implemented numerically. As with many grid based methods, describing both tightly bound and diffuse orbitals is challenging so we have considered augmenting the Wilson basis set as projected Slater-type orbitals. We have also compared the Wilson basis set against the recently introduced wavelet transformed Gaussians (gausslets). Throughout, we give comments on the implementation and use small atoms and molecules to illustrate convergence properties of the Wilson basis.
State-of-the-art methods for calculating neutral excitation energies are typically demanding and limited to single electron-hole pairs and their composite plasmons. Here we introduce excitonic density-functional theory (XDFT) a computationally light, generally applicable, first-principles technique for calculating neutral excitations based on generalized constrained DFT. In order to simulate an M-particle excited state of an N-electron system, XDFT automatically optimizes a constraining potential to confine N-M electrons within the ground-state Kohn-Sham valence subspace. We demonstrate the efficacy of XDFT by calculating the lowest single-particle singlet and triplet excitation energies of the well-known Thiel molecular test set, with results which are in excellent agreement with time-dependent DFT. Furthermore, going beyond the capability of adiabatic time-dependent DFT, we show that XDFT can successfully capture double excitations. Overall our method makes optical gaps, excition bindings and oscillator strengths readily accessible at a computational cost comparable to that of standard DFT. As such, XDFT appears as an ideal candidate to work within high-throughput discovery frameworks and within linear-scaling methods for large systems.
Vibrational spectra and wavefunctions of polyatomic molecules can be calculated at low memory cost using low-rank sum-of-product (SOP) decompositions to represent basis functions generated using an iterative eigensolver. Using a SOP tensor format does not determine the iterative eigensolver. The choice of the interative eigensolver is limited by the need to restrict the rank of the SOP basis functions at every stage of the calculation. We have adapted, implemented and compared different reduced-rank algorithms based on standard iterative methods (block-Davidson algorithm, Chebyshev iteration) to calculate vibrational energy levels and wavefunctions of the 12-dimensional acetonitrile molecule. The effect of using low-rank SOP basis functions on the different methods is analyzed and the numerical results are compared with those obtained with the reduced rank block power method introduced in J. Chem. Phys. 140, 174111 (2014). Relative merits of the different algorithms are presented, showing that the advantage of using a more sophisticated method, although mitigated by the use of reduced-rank sum-of-product functions, is noticeable in terms of CPU time.
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of molecular dynamics simulation data. However, MSMs approximate the true dynamics by assuming a Markov chain on a clusters discretization of the state space. This approximation is difficult to make for high-dimensional biomolecular systems, and the quality and reproducibility of MSMs has therefore been limited. Here, we discard the assumption that dynamics are Markovian on the discrete clusters. Instead, we only assume that the full phase- space molecular dynamics is Markovian, and a projection of this full dynamics is observed on the discrete states, leading to the concept of Projected Markov Models (PMMs). Robust estimation methods for PMMs are not yet available, but we derive a practically feasible approximation via Hidden Markov Models (HMMs). It is shown how various molecular observables of interest that are often computed from MSMs can be computed from HMMs / PMMs. The new framework is applicable to both, simulation and single-molecule experimental data. We demonstrate its versatility by applications to educative model systems, an 1 ms Anton MD simulation of the BPTI protein, and an optical tweezer force probe trajectory of an RNA hairpin.
We extend to strongly correlated molecular systems the recently introduced basis-set incompleteness correction based on density-functional theory (DFT) [E. Giner et al., J. Chem. Phys. 149, 194301 (2018)]. This basis-set correction relies on a mapping between wave-function calculations in a finite basis set and range-separated DFT (RSDFT) through the definition of an effective non-divergent interaction corresponding to the electron-electron Coulomb interaction projected in the finite basis set. This enables the use of RSDFT-type complementary density functionals to recover the dominant part of the short-range correlation effects missing in this finite basis set. To study both weak and strong correlation regimes we consider the potential energy curves of the H10, N2, O2, and F2 molecules up to the dissociation limit, and we explore various approximations of complementary functionals fulfilling two key properties: spin-multiplet degeneracy (i.e., independence of the energy with respect to the spin projection Sz) and size consistency. Specifically, we investigate the dependence of the functional on different types of on-top pair densities and spin polarizations. The key result of this study is that the explicit dependence on the on-top pair density allows one to completely remove the dependence on any form of spin polarization without any significant loss of accuracy. Quantitatively, we show that the basis-set correction reaches chemical accuracy on atomization energies with triple-zeta quality basis sets for most of the systems studied here. Also, the present basis-set incompleteness correction provides smooth potential energy curves along the whole range of internuclear distances.
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