Utilizing high performance computing for chemistry: parallel computational chemistry.

Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.

Scalar relativistic explicitly correlated R12 methods.

Combinations of explicitly correlated R12 wave functions with relativistic Douglas-Kroll-Hess (DKH) Hamiltonians are discussed. We considered several ways to incorporate the relativistic terms into the second-order Moller-Plesset R12 method and applied them to the helium isoelectronic series to investigate their accuracy and numerical stability. Among the approaches are the evaluation of the relativistic terms via double resolution-of-the-identity and the explicit evaluation of all terms up to O(c(-4)) using the Pauli Hamiltonian. Numerical collapse of the latter can be avoided if the R12 amplitudes are determined by Kato's cusp condition. Closed formulas for new two-electron integrals that include the mass-velocity term have been derived and implemented into the LIBINT2 integral library. The proposed approaches are not restricted to DKH and can be combined with other one- and two-component relativistic Hamiltonians.

Calculation of chemical reaction energies using the AM05 density functional.

We present results that compare the accuracy of the AM05 density functional (Armiento and Mattsson, Phys Rev B 2005, 72, 085108; Mattsson et al., J Chem Phys 2008, 128, 084714) to a set of chemical reaction energies. The reactions were generated from the singlet species in the well-known G2 test suite (Curtiss et al., J Chem Phys 1991; Curtiss et al., J Chem Phys 1997; 106, 1063). Our results show that, in general, the AM05 functional performs nearly as well as the other "pure" density functionals, but none of these perform as well as the hybrid B3LYP functional. These results are nonetheless encouraging because the AM05 functional arises from very simple assumptions, and does not require the calculation of the Hartree-Fock exchange integrals.

Components for integral evaluation in quantum chemistry.

Sharing low-level functionality between software packages enables more rapid development of new capabilities and reduces the duplication of work among development groups. Using the component approach advocated by the Common Component Architecture Forum, we have designed a flexible interface for sharing integrals between quantum chemistry codes. Implementation of these interfaces has been undertaken within the Massively Parallel Quantum Chemistry package, exposing both the IntV3 and Cints/Libint integrals packages to component applications. Benchmark timings for Hartree-Fock calculations demonstrate that the overhead due to the added interface code varies significantly, from less than 1% for small molecules with large basis sets to nearly 10% for larger molecules with smaller basis sets. Correlated calculations and density functional approaches encounter less severe performance overheads of less than 5%. While these overheads are acceptable, additional performance losses occur when arbitrary implementation details, such as integral ordering within buffers, must be handled. Integral reordering is observed to add an additional overhead as large as 12%; hence, a common standard for such implementation details is desired for optimal performance.

PSI3: an open-source Ab Initio electronic structure package.

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.

Local Møller-Plesset Perturbation Theory: A Massively Parallel Algorithm.

A massively parallel algorithm is presented for computation of energies with local second-order Møller-Plesset (LMP2) perturbation theory. Both the storage requirement and the computational time scale linearly with the molecular size. The parallel algorithm is designed to be scalable, employing a distributed data scheme for the two-electron integrals, avoiding communication bottlenecks, and distributing tasks in all computationally significant steps. A sparse data representation and a set of generalized contraction routines have been developed to allow efficient massively parallel implementation using distributed sparse multidimensional arrays. High parallel efficiency of the algorithm is demonstrated for applications employing up to 100 processors.

Component-based integration of chemistry and optimization software.

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

Second-order Møller-Plesset theory with linear R12 terms (MP2-R12) revisited: auxiliary basis set method and massively parallel implementation.

Ab initio electronic structure approaches in which electron correlation explicitly appears have been the subject of much recent interest. Because these methods accelerate the rate of convergence of the energy and properties with respect to the size of the one-particle basis set, they promise to make accuracies of better than 1 kcal/mol computationally feasible for larger chemical systems than can be treated at present with such accuracy. The linear R12 methods of Kutzelnigg and co-workers are currently the most practical means to include explicit electron correlation. However, the application of such methods to systems of chemical interest faces severe challenges, most importantly, the still steep computational cost of such methods. Here we describe an implementation of the second-order Møller-Plesset method with terms linear in the interelectronic distances (MP2-R12) which has a reduced computational cost due to the use of two basis sets. The use of two basis sets in MP2-R12 theory was first investigated recently by Klopper and Samson and is known as the auxiliary basis set (ABS) approach. One of the basis sets is used to describe the orbitals and another, the auxiliary basis set, is used for approximating matrix elements occurring in the exact MP2-R12 theory. We further extend the applicability of the approach by parallelizing all steps of the integral-direct MP2-R12 energy algorithm. We discuss several variants of the MP2-R12 method in the context of parallel execution and demonstrate that our implementation runs efficiently on a variety of distributed memory machines. Results of preliminary applications indicate that the two-basis (ABS) MP2-R12 approach cannot be used safely when small basis sets (such as augmented double- and triple-zeta correlation consistent basis sets) are utilized in the orbital expansion. Our results suggest that basis set reoptimization or further modifications of the explicitly correlated ansatz and/or standard approximations for matrix elements are necessary in order to make the MP2-R12 method sufficiently accurate when small orbital basis sets are used. The computer code is a part of the latest public release of Sandia's Massively Parallel Quantum Chemistry program available under GNU General Public License.