An efficient implementation of the "cluster-in-molecule" approach for local electron correlation calculations

An efficient implementation of the "cluster-in-molecule" (CIM) approach is presented for performing local electron correlation calculations in a basis of orthogonal occupied and virtual localized molecular orbitals (LMOs). The main idea of this approach is that significant excitation amplitudes can be approximately obtained by solving the coupled cluster (or Moller-Plesset perturbation theory) equations of a series of "clusters," each of which contains a subset of occupied and virtual LMOs. In the present implementation, we have proposed a simple approach for constructing virtual LMOs of clusters, and new ways of constructing clusters and extracting the correlation contributions from calculations on clusters, which are more efficient than those suggested in the original work. More importantly, linear scaling of computational time of the CIM approach is achieved by evaluating the transformed two-electron integrals over LMOs using simple truncation techniques in limited operations (independent of the molecular size). With typical thresholds, for a variety of molecules our test calculations demonstrate that more than 99% of the conventional MP2 or coupled cluster with doubles correlation energies can be recovered in the present CIM approach.     

Divide-and-conquer local correlation approach to the correlation energy of large molecules

A divide-and-conquer local correlation approach for correlation energy calculations on large molecules is proposed for any post-Hartree-Fock correlation method. The main idea of this approach is to decompose a large system into various fragments capped by their local environments. The total correlation energy of the whole system can be approximately obtained as the summation of correlation energies from all capped fragments, from which correlation energies from all adjacent caps are removed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations for a wide range of molecules using the 6-31G or 6-31G( * *) basis set demonstrate that this simple approach recovers more than 99.0% of the conventional second-order Moller-Plesset perturbation theory and coupled cluster with single and double excitations correlation energies.     

A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules

We describe an alternative fragment-based method, the localized molecular-orbital assembler method, for Hartree-Fock (HF) calculations of macromolecules. In this approach, a large molecule is divided into many small-size fragments, each of which is capped by its local surroundings. Then the conventional HF calculations are preformed on these capped fragments (or subsystems) and the canonical molecular orbitals of these systems are transferred into localized molecular orbitals (LMOs). By assembling the LMOs of these subsystems into a set of LMOs of the target molecule, the total density matrix of the target molecule is constructed and correspondingly the HF energy or other molecular properties can be approximately computed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations with double-zeta and polarized double-zeta basis sets demonstrate that the present approach is able to reproduce the conventional HF energies within a few millihartrees for a broad range of molecules.     

A natural linear scaling coupled-cluster method

It is shown that using an appropriate localized molecular orbital (LMO) basis, one is able to calculate coupled-cluster singles and doubles (CCSD) wave functions and energies for very large systems by performing full CCSD calculations on small subunits only. This leads to a natural linear scaling coupled-cluster method (NLSCC), in which total correlation energies of extended systems are evaluated as the sum of correlation energy contributions from individual small subunits within that system. This is achieved by defining local occupied orbital correlation energies. These are quantities, which in the LMO basis become transferable between similar molecular fragments. Conventional small scale existing molecular CCSD codes are all that is needed, the local correlation effect being simply transmitted via the appropriate LMO basis. Linear scaling of electronic correlation energy calculations is thus naturally achieved using the NLSCC approach, which in principle can treat nonperiodic extended systems of infinite basis set size. Results are shown for alkanes and several polyglycine molecules and the latter compared to recent results obtained via an explicit large scale LCCSD calculation. (c) 2004 American Institute of Physics.     

Coupled-cluster singles and doubles for extended systems

Coupled-cluster theory with connected single and double excitation operators (CCSD) and related approximations, such as linearized CCSD, quadratic configuration interaction with single and double excitation operators, coupled-cluster with connected double excitation operator (CCD), linearized CCD, approximate CCD, and second- and third-order many-body perturbation theories, are formulated and implemented for infinitely extended one-dimensional systems (polymers), on the basis of the periodic boundary conditions and distance-based screening of integrals, density matrix elements, and excitation amplitudes. The variation of correlation energies with the truncation radii of short- and long-range lattice sums and with the number of wave vector sampling points in the first Brillouin zone is examined for polyethylene, polyacetylene, and polyyne, and is shown to be a function of the degree of pi-electron conjugation or the fundamental band gaps. The t2 and t1 amplitudes in the atomic orbital (AO) basis are obtained by first computing the t amplitudes in the Bloch-orbital basis and subsequently back-transforming them into the AO basis. The plot of these AO-based t amplitudes as a function of unit cells also indicates that the t2 amplitudes of polyacetylene and polyyne exhibit appreciably slower decay than those of polyethylene, although the asymptotic decay behavior is invariably 1/r3. The AO-based t1 amplitudes appear to correlate strongly with the electronic structure, and they decay seemingly exponentially for polyethylene whereas they stay at a constant magnitude across the seventh nearest neighbors of polyacetylene and polyyne, which attests to far reaching effects of nondynamical electron correlation mediated by orbital rotation. Nonetheless, the unit cell contributions to the correlation energies taper below 10(-6) hartree after 15 A for all three polymers. The basis set dependence of the decay behavior of t2 amplitudes is also examined for linear hydrogen fluoride polymer (HF)infinity and linear beryllium polymer (Be)infinity employing the STO-3G, 6-31G, and 6-31G* basis sets, and proves to be rather small.     

Localized molecular orbital studies of certain compounds with [A_3X_3] six-membered rings

The localized molecular orbitals (LMOs) of certain quasi-aromatic organic and inor-ganic molecules with six-membered rings have been calculated by virtue of the ab initio methodusing STO-3G and 4-31G basis sets as well as the CNDO/2 method. It is shown that there existsextensively-delocalized p-pπ bonding in these quasi-aromatic systems. The localized pictures ofthe π-type LMOs for the heterocyclic and homocyclic systems from the σ-π localization schemeare discussed. The Generator Orbital approach is utilized to account for the bonding patterns.     

Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method

The fragment molecular orbital (FMO) method was combined with the second order M?ller-Plesset (MP2) perturbation theory. The accuracy of the method using the 6-31G(*) basis set was tested on (H(2)O)(n), n=16,32,64; alpha-helices and beta-strands of alanine n-mers, n=10,20,40; as well as on (H(2)O)(n), n=16,32,64 using the 6-31 + + G(**) basis set. Relative to the regular MP2 results that could be afforded, the FMO2-MP2 error in the correlation energy did not exceed 0.003 a.u., the error in the correlation energy gradient did not exceed 0.000 05 a.u./bohr and the error in the correlation contribution to dipole moment did not exceed 0.03 debye. An approximation reducing computational load based on fragment separation was introduced and tested. The FMO2-MP2 method demonstrated nearly linear scaling and drastically reduced the memory requirements of the regular MP2, making possible calculations with several thousands basis functions using small Pentium clusters. As an example, (H(2)O)(64) with the 6-31 + + G(**) basis set (1920 basis functions) can be run in 1 Gbyte RAM and it took 136 s on a 40-node Pentium4 cluster.     

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.     

NH3…H2O体系氢键团簇结构的从头计算方案比较

对H2O，NH3单分子以及反式线性NH3…H2O双分子团簇应用HF，DFT，MR2，CCD ，QCISD等从头计算方法在不同的基组水平上进行几何结构优化和氨—水分子间相 互作用能计算。比较实验值和计算结果表明：对氨—水体系，MP2／6-31+G^**方法 能够满足氢键N-0键长误差为0．004nm，键角∠NOH误差为1°，NH3…H2O相互作用 能△E与CCD和QCISD偏差2．1kJ／mol计算精度的要求，并有较合理的计算代价。     

Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE

We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.     

Parallel, linear-scaling building-block and embedding method based on localized orbitals and orbital-specific basis sets

We present a linear scaling method for the energy minimization step of semiempirical and first-principles Hartree-Fock and Kohn-Sham calculations. It is based on the self-consistent calculation of the optimum localized orbitals of any localization method of choice and on the use of orbital-specific basis sets. The full set of localized orbitals of a large molecule is seen as an orbital mosaic where each tessera is made of only a few of them. The orbital tesserae are computed out of a set of embedded cluster pseudoeigenvalue coupled equations which are solved in a building-block self-consistent fashion. In each iteration, the embedded cluster equations are solved independently of each other and, as a result, the method is parallel at a high level of the calculation. In addition to full system calculations, the method enables to perform simpler, much less demanding embedded cluster calculations, where only a fraction of the localized molecular orbitals are variational while the rest is frozen, taking advantage of the transferability of the localized orbitals of a given localization method between similar molecules. Monitoring single point energy calculations of large poly(ethylene oxide) molecules and three dimensional carbon monoxide clusters using an extended Huckel Hamiltonian are presented.     

Scaling factors for vibrational frequencies and zero-point vibrational energies of some recently developed exchange-correlation functionals

The scaling factors for the vibrational frequencies and zero-point vibrational energies evaluated at various combinations of recently developed exchange-correlation functionals and various basis sets are reported. The exchange-correlation functionals considered are B972, B98, HCTH, OLYP, O3LYP, G96LYP, PBE0 and VSXC functionals; the basis sets employed are 3-21G, 6-31G*, 6-31G**, 6-31+G, 6-311G*, 6-311G**, 6-311G(df,p), 6-311+G(df,p), cc-pVDZ and aug-cc-pVDZ. The experimental harmonic frequencies of 122 small molecules and the zero-point vibrational energies of 39 small molecules are used to determine the scaling factors through the least-square fitting procedure. It was found that the scaling factors do not depend significantly on the basis sets considered. The vibrational frequency scaling factors evaluated by using the B98 and PBE0 functionals are recommended on the basis of smallest root mean square error. The zero-point vibrational energy scaling factors evaluated from the B972 functional with Pople's double-zeta basis set and the HCTH functional with Pople's triple-zeta basis set are recommended on the basis of smallest root mean square error.     

A local second-order Møller-Plesset method with localized orbitals: a parallelized efficient electron correlation method

Using orthogonal localized occupied orbitals we have developed and implemented a parallelized local second-order M?ller-Plesset (MP2) method based on the idea developed by Head-Gordon and co-workers. A subset of nonorthogonal correlation functions (the orbital domain) was assigned to each of the localized occupied orbitals using a distance criterion and excitations from localized occupied orbitals that were arranged into subsets. The correlation energy was estimated using a partial diagonalization and an iterative efficient method for solving large-scale linear equations. Some illustrative calculations are provided for molecules with up to 1484 Cartesian basis sets. The orbital domain sizes were found to be independent of the molecular size, and the present local MP2 method covered about 98%-99% of the correlation energy of the conventional canonical MP2 method.     

Application of many-body perturbation theory in the localized representation for the all-trans conjugated polyenes

Ab initio self-consistent field (SCF ) calculations are performed with the standard 6-31G* basis set for all-trans conjugated oligomers C_2n+2H_2n+4. The canonical occupied and virtual molecular orbitals (MO s) are separately localized by unitary transformations. Due to the localization, the perturbation operator is partitioned into two-particle and into single-particle terms; the MBPT is, therefore, a double-perturbation expansion in this case. By using the localized representation of the MBPT , the correlation energy contributions can be partitioned into local and nonlocal effects. It can be shown that the local effects are very important and well transferable, which makes possible the calculation of the correlation energy of larger molecules if the localized molecular orbitals (occupied and virtual) of smaller related molecules are known. © 1994 John Wiley & Sons, Inc.     

Kohn-Sham Density Matrix and the Kernel Energy MethodSCI北大核心CSCD

The kernel energy method(KEM) has been shown to provide fast and accurate molecular energy calculations for molecules at their equilibrium geometries.KEM breaks a molecule into smaller subsets,called kernels,for the purposes of calculation.The results from the kernels are summed according to an expression characteristic of KEM to obtain the full molecule energy.A generalization of the kernel expansion to density matrices provides the full molecule density matrix and orbitals.In this study,the kernel expansion for the density matrix is examined in the context of density functional theory(DFT) Kohn-Sham(KS) calculations.A kernel expansion for the one-body density matrix analogous to the kernel expansion for energy is defined,and is then converted into a normalizedprojector by using the Clinton algorithm.Such normalized projectors are factorizable into linear combination of atomic orbitals(LCAO) matrices that deliver full-molecule Kohn-Sham molecular orbitals in the atomic orbital basis.Both straightforward KEM energies and energies from a normalized,idempotent density matrix obtained from a density matrix kernel expansion to which the Clinton algorithm has been applied are compared to reference energies obtained from calculations on the full system without any kernel expansion.Calculations were performed both for a simple proof-of-concept system consisting of three atoms in a linear configuration and for a water cluster consisting of twelve water molecules.In the case of the proof-of-concept system,calculations were performed using the STO-3 G and6-31 G(d,p) bases over a range of atomic separations,some very far from equilibrium.The water cluster was calculated in the 6-31 G(d,p) basis at an equilibrium geometry.The normalized projector density energies are more accurate than the straightforward KEM energy results in nearly all cases.In the case of the water cluster,the energy of the normalized projector is approximately four times more accurate than the straightforward KEM energy result.The KS density matrices of this study are applicable to quantum crystallography.     

Hybrid correlation models based on active-space partitioning: seeking accurate O(N5) ab initio methods for bond breaking

Moller-Plesset second-order (MP2) perturbation theory remains the least expensive standard ab initio method that includes electron correlation, scaling as O(N5) with the number of molecular orbitals N. Unfortunately, when restricted Hartree-Fock orbitals are employed, the potential energy curves calculated with this method are of little use at large interatomic separations because of the divergent behavior of MP2 in these regions. In our previous study [J. Chem. Phys. 122, 234110 (2005)] we combined the MP2 method with the singles and doubles coupled cluster (CCSD) method to produce a hybrid method that retains the computational scaling of MP2 and improves dramatically the shape of the MP2 curves. In this work we expand the hybrid methodology to several other schemes. We investigate a new, improved MP2-CCSD method as well as a few other O(N5) methods related to the Epstein-Nesbet pair correlation theory. Nonparallelity errors across the dissociation curve as well as several spectroscopic constants are computed for BH, HF, H2O, CH+, CH4, and Li2 molecules with the 6-31G* basis set and compared with the corresponding full configuration interaction results. We show that among the O(N5) methods considered, our new hybrid MP2-CCSD method is the most accurate and significantly outperforms MP2 not only at large interatomic separations, but also near equilibrium geometries.     

Hydrogen bonding and dimeric self-association of 2-pyrrolidinone: An ab initio study

Ab initio calculations on the different associated structures of 2-pyrrolidinone with water and with itself were carried out using 3-21G and 6-31G^* basis sets at the Hartree–Fock level, including electron correlation using second-order Møller–Plesset perturbation theory. The calculated free energy changes for the intermolecular hydrogen bonded dimer and hydrated species indicated that the molecular systems with cyclic dimerization and association with two water molecules are dominant. The results are compared to the available experimental data in the literature.