A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels

A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.     

An efficient linear scaling procedure for constructing localized orbitals of large molecules based on the one-particle density matrix

We have developed a linear-scaling algorithm for obtaining the Boys localized molecular orbitals from the one-particle density matrix. The algorithm is made up of two steps: the Cholesky decomposition of the density matrix to obtain Cholesky molecular orbitals and the subsequent Boys localization process. Linear-scaling algorithms have been proposed to achieve linear-scaling calculations of these two steps, based on the sparse matrix technique and the locality of the Cholesky molecular orbitals. The present algorithm has been applied to compute the Boys localized orbitals in a number of systems including α-helix peptides, water clusters, and protein molecules. Illustrative calculations demonstrate that the computational time of obtaining Boys localized orbitals with the present algorithm is asymptotically linear with increasing the system size.     

Bringing about matrix sparsity in linear-scaling electronic structure calculations

The performance of linear-scaling electronic structure calculations depends critically on matrix sparsity. This article gives an overview of different strategies for removal of small matrix elements, with emphasis on schemes that allow for rigorous control of errors. In particular, a novel scheme is proposed that has significantly smaller computational overhead compared with the Euclidean norm-based truncation scheme of Rubensson et al. (J Comput Chem 2009, 30, 974) while still achieving the desired asymptotic behavior required for linear scaling. Small matrix elements are removed while ensuring that the Euclidean norm of the error matrix stays below a desired value, so that the resulting error in the occupied subspace can be controlled. The efficiency of the new scheme is investigated in benchmark calculations for water clusters including up to 6523 water molecules. Furthermore, the foundation of matrix sparsity is investigated. This includes a study of the decay of matrix element magnitude with distance between basis function centers for different molecular systems and different methods. The studied methods include Hartree–Fock and density functional theory using both pure and hybrid functionals. The relation between band gap and decay properties of the density matrix is also discussed.     

Linear-scaling localized-density-matrix method for the ground and excited states of one-dimensional molecular systems

A linear-scaling localized-density-matrix (LDM) method is developed to evaluate the ground-state reduced single-electron density matrices of one-dimensional molecular systems. The new method may be combined with the existing linear-scaling LDM method for the excited states (Yokojima and Chen, Chem. Phys. Lett. 292 (1998) 379), and thus leads to a linear-scaling calculation method for the properties of both the ground and excited states. The combined method is applied to the polyacetylene oligomers and the linear-scaling of the total computational time is clearly demonstrated.     

Gaussian and finite-element Coulomb method for the fast evaluation of Coulomb integrals

The authors propose a new linear-scaling method for the fast evaluation of Coulomb integrals with Gaussian basis functions called the Gaussian and finite-element Coulomb (GFC) method. In this method, the Coulomb potential is expanded in a basis of mixed Gaussian and finite-element auxiliary functions that express the core and smooth Coulomb potentials, respectively. Coulomb integrals can be evaluated by three-center one-electron overlap integrals among two Gaussian basis functions and one mixed auxiliary function. Thus, the computational cost and scaling for large molecules are drastically reduced. Several applications to molecular systems show that the GFC method is more efficient than the analytical integration approach that requires four-center two-electron repulsion integrals. The GFC method realizes a near linear scaling for both one-dimensional alanine alpha-helix chains and three-dimensional diamond pieces.     

Density functional theory for systems of very many atoms

The standard Kohn-Sham formulation of density functional theory (DFT ) is limited, for practical reasons, to systems of less than about 50-100 atoms. The computational effort scales as N, where N_at is the number of atoms and 2 < α > 3. (By comparison, conventional configuration interaction methods are limited to 5-10 atom systems.) This article deals with the prospect of practical methods that scale linearly in N_at and may thus allow calculations for systems of 10³-104 atoms. The physical reason (“near-sightedness”) for linear scaling is presented. Implementations of linear scaling DFT by the use of generalized Wannier functions or the one-particle density matrix are discussed. © 1995 John Wiley & Sons, Inc.     

An atomic orbital-based reformulation of energy gradients in second-order Møller-Plesset perturbation theory

A fully atomic orbital (AO)-based reformulation of second-order M?ller-Plesset perturbation theory (MP2) energy gradients is introduced, which provides the basis for reducing the computational scaling with the molecular size from the fifth power to linear. Our formulation avoids any transformation between the AO and the molecular orbital (MO) basis and employs pseudodensity matrices similar to the AO-MP2 energy expressions within the Laplace scheme for energies. The explicit computation of perturbed one-particle density matrices emerging in the new AO-based gradient expression is avoided by reformulating the Z-vector method of Handy and Schaefer [J. Chem. Phys. 81, 5031 (1984)] within a density matrix-based scheme.     

Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach

The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree-Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N(3)) scaling order within HF theory to an n.O(N'(3)) one, where n is the number of fragments and N', the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful.     

Real-time time-dependent density functional theory using density fitting and the continuous fast multipole method

An implementation of real-time time-dependent density functional theory (RT-TDDFT) within the TURBOMOLE program package is reported using Gaussian-type orbitals as basis functions, second and fourth order Magnus propagator, and the self-consistent field as well as the predictor–corrector time integration schemes. The Coulomb contribution to the Kohn–Sham matrix is calculated combining density fitting approximation and the continuous fast multipole method. Performance of the implementation is benchmarked for molecular systems with different sizes and dimensionalities. For linear alkane chains, the wall time for density matrix time propagation step is comparable to the Kohn-Sham (KS) matrix construction. However, for larger two- and three-dimensional molecules, with up to about 5,000 basis functions, the computational effort of RT-TDDFT calculations is dominated by the KS matrix evaluation. In addition, the maximum time step is evaluated using a set of small molecules of different polarities. The photoabsorption spectra of several molecular systems calculated using RT-TDDFT are compared to those obtained using linear response time-dependent density functional theory and coupled cluster methods.     

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients

A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian‐type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange‐correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn–Sham matrix formation. © 2016 Wiley Periodicals, Inc.     

Dispersion energy from density-fitted density susceptibilities of singles and doubles coupled cluster theory

A new method of calculation of the second-order dispersion energy is proposed. It is based on the Longuet-Higgins formula [Faraday Discuss. Chem. Soc. 40, 7 (1965)], which describes the dispersion interaction in terms of frequency-dependent density susceptibilities of monomers. In this study, the density susceptibilities are obtained from the coupled cluster theory at the singles and doubles level. Density fitting is applied in order to reduce the computational effort for the evaluation of density susceptibilities. It is shown that density fitting improves the scaling of the computational resources with molecular size by one order of magnitude without affecting the accuracy of the resulting dispersion energy. Numerical results are presented for several van der Waals molecules to illustrate the performance of the new approach.     

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Stress tensor

A full implementation of the analytical stress tensor for periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian-type orbitals as basis functions. It is the extension of the implementation of analytical energy gradients (Lazarski et al., Journal of Computational Chemistry 2016, 37, 2518–2526) to the stress tensor for the purpose of optimization of lattice vectors. Its key component is the efficient calculation of the Coulomb contribution by combining density fitting approximation and continuous fast multipole method. For the exchange-correlation (XC) part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097–3104) is extended to XC weight derivatives and stress tensor. The computational efficiency and favorable scaling behavior of the stress tensor implementation are demonstrated for various model systems. The overall computational effort for energy gradient and stress tensor for the largest systems investigated is shown to be at most two and a half times the computational effort for the Kohn–Sham matrix formation. © 2019 Wiley Periodicals, Inc.     

Linear-scaling quantum mechanical methods for excited states

The poor scaling of many existing quantum mechanical methods with respect to the system size hinders their applications to large systems. In this tutorial review, we focus on latest research on linear-scaling or O(N) quantum mechanical methods for excited states. Based on the locality of quantum mechanical systems, O(N) quantum mechanical methods for excited states are comprised of two categories, the time-domain and frequency-domain methods. The former solves the dynamics of the electronic systems in real time while the latter involves direct evaluation of electronic response in the frequency-domain. The localized density matrix (LDM) method is the first and most mature linear-scaling quantum mechanical method for excited states. It has been implemented in time- and frequency-domains. The O(N) time-domain methods also include the approach that solves the time-dependent Kohn-Sham (TDKS) equation using the non-orthogonal localized molecular orbitals (NOLMOs). Besides the frequency-domain LDM method, other O(N) frequency-domain methods have been proposed and implemented at the first-principles level. Except one-dimensional or quasi-one-dimensional systems, the O(N) frequency-domain methods are often not applicable to resonant responses because of the convergence problem. For linear response, the most efficient O(N) first-principles method is found to be the LDM method with Chebyshev expansion for time integration. For off-resonant response (including nonlinear properties) at a specific frequency, the frequency-domain methods with iterative solvers are quite efficient and thus practical. For nonlinear response, both on-resonance and off-resonance, the time-domain methods can be used, however, as the time-domain first-principles methods are quite expensive, time-domain O(N) semi-empirical methods are often the practical choice. Compared to the O(N) frequency-domain methods, the O(N) time-domain methods for excited states are much more mature and numerically stable, and have been applied widely to investigate the dynamics of complex molecular systems.     

Møller-Plesset (MP2) perturbation theory for large molecules

Summary A novel formulation of MP2 theory is presented which starts from the Laplace transform MP2 ansatz, and subsequently moves from a molecular orbital (MO) representation to an atomic orbital (AO) representation. Consequently, the new formulation is denoted AO-MP2. As in traditional MP2 approaches electron repulsion integrals still need to be transformed. Strict bounds on the individual MP2 energy contribution of each intermediate four-index quantity allow to screen off numerically insignificant integrals with a single threshold parameter. Implicit in our formulation is a bound to two-particle density matrix elements. For small molecules the computational cost for AO-MP2 calculations is about a factor of 100 higher than for traditional MO-based approaches, but due to screening the computational effort in larger systems will only grow with the fourth power of the size of the system (or less) as is demonstrated both in theory and in application. MP2 calculations on (non-metallic) crystalline systems seem to be a feasible extension of the Laplace transform approach. In large molecules the AO-MP2 ansatz allows massively parallel MP2 calculations without input/output of four-index quantities provided that each processor has in-core memory for a limited number of two-index quantities. Energy gradient formulas for the AO-MP2 approach are derived.Dedicated to Prof. W. Kutzelnigg whose books on theoretical chemistry aroused my interest in this field     

New method for direct linear-scaling calculation of electron density of proteins

A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.     

Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Mo̸ller-Plesset perturbation theory

Many approximations have been developed to help deal with the O(N(4)) growth of the electron repulsion integral (ERI) tensor, where N is the number of one-electron basis functions used to represent the electronic wavefunction. Of these, the density fitting (DF) approximation is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to molecular size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decomposition to obtain a low-rank approximation to density fitting (tensor hypercontraction density fitting or THC-DF). This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling reduction for second- and third-order perturbation theory (MP2 and MP3), showing that both can be carried out in O(N(4)) operations. This should be compared to the usual scaling behavior of O(N(5)) and O(N(6)) for MP2 and MP3, respectively. The THC-DF technique can also be applied to other methods in electronic structure theory, such as coupled-cluster and configuration interaction, promising significant gains in computational efficiency and storage reduction.     

An efficient local coupled cluster method for accurate thermochemistry of large systems

An efficient local coupled cluster method with single and double excitation operators and perturbative treatment of triple excitations [DF-LCCSD(T)] is described. All required two-electron integrals are evaluated using density fitting approximations. These have a negligible effect on the accuracy but reduce the computational effort by 1-2 orders of magnitude, as compared to standard integral-direct methods. Excitations are restricted to local subsets of non-orthogonal virtual orbitals (domain approximation). Depending on distance criteria, the correlated electron pairs are classified into strong, close, weak, and very distant pairs. Only strong pairs, which typically account for more than 90% of the correlation energy, are optimized in the LCCSD treatment. The remaining close and weak pairs are approximated by LMP2 (local second-order Mo?ller-Plesset perturbation theory); very distant pairs are neglected. It is demonstrated that the accuracy of this scheme can be significantly improved by including the close pair LMP2 amplitudes in the LCCSD equations, as well as in the perturbative treatment of the triples excitations. Using this ansatz for the wavefunction, the evaluation and transformation of the two-electron integrals scale cubically with molecular size. If local density fitting approximations are activated, this is reduced to linear scaling. The LCCSD iterations scale quadratically, but linear scaling can be achieved by neglecting some terms involving contractions of single excitations. The accuracy and efficiency of the method is systematically tested using various approximations, and calculations for molecules with up to 90 atoms and 2636 basis functions are presented.     

Correlated holes and their relationships with reduced density matrices and cumulants

This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.     

Linear scaling density fitting

Two modifications of the resolution of the identity (RI)/density fitting (DF) approximations are presented. First, we apply linear scaling and J-engine techniques to speed up traditional DF. Second, we develop an algorithm that produces local, accurate fits with effort that scales linearly with system size. The fits produced are continuous, differentiable, well-defined, and do not require preset fitting domains. This metric-independent technique for producing a priori local fits is shown to be accurate and robust even for large systems. Timings are presented for linear scaling RI/DF calculations on large one-, two-, and three-dimensional carbon systems.     

Tighter multipole-based integral estimates and parallel implementation of linear-scaling AO-MP2 theory

Within an atomic-orbital-based (AO-based) formulation of second-order M?ller-Plesset perturbation theory (MP2), we present a novel screening procedure which allows us to preselect numerically significant two-electron integrals more efficiently, especially for large basis sets. The screening is based on our recently introduced multipole-based integral estimates (MBIE) method [J. Chem. Phys., 2005, 123, 184102], that allows to exploit the 1/R(4) or 1/R(6) coupling between electronic charge distributions in transformed integral products within AO-MP2. In this way, linear scaling is attained with fully-controlled numerical accuracy. Furthermore, a parallel implementation of our linear-scaling AO-MP2 method is described, which also allows us to perform calculations with larger basis sets. First calculations reveal that for e.g. linear alkanes the scaling of the number of required transformed integral products is almost equal for 6-31G* and cc-pVTZ basis sets. Using the improved MBIE screening, the largest parallel calculation was performed for a ribozyme fragment consisting of 497 atoms and 5697 basis functions, while our largest AO-MP2 calculation was performed for a stacked DNA system (16 base pairs) comprising 1052 atoms and 10 674 basis functions on a single processor.