Theresa L. Windus

General atomic and molecular electronic structure system

A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines.

Basis Set Exchange: A Community Database for Computational Sciences

Basis sets are some of the most important input data for computational models in the chemistry, materials, biology, and other science domains that utilize computational quantum mechanics methods. Providing a shared, Web-accessible environment where researchers can not only download basis sets in their required format but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a Web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.

6-31G* basis set for atoms K through Zn

Medium basis sets based upon contractions of Gaussian primitives are developed for the third-row elements K through Zn. The basis functions generalize the 6-31G and 6-31G* sets commonly used for atoms up to Ar. They use six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split-valence pair of three and one primitives for valence orbitals, which are 4s and 5p for atoms K and Ca, and 4s, 4p, and 3d for atoms Sc through Zn. A 6-31G* set is formed by adding a single set of Gaussian polarization functions to the 6-31G set. They are Cartesian d-functions for atoms K and Ca, and Cartesian f-functions for atoms Sc through Zn. Comparison with experimental data shows relatively good agreement with bond lengths and angles for representative vapor-phase metal complexes.

High performance computational chemistry: An overview of NWChem a distributed parallel application☆

NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. The architecture facilitates rapid development and portability of fully distributed application modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.

A Component Architecture for High-Performance Scientific Computing

The Common Component Architecture (CCA) provides a means for software developers to manage the complexity of large-scale scientific simulations and to move toward a plug-and-play environment for high-performance coputing. In the scientific computing context, component models also promote collaboration using independently developed software, thereby allowing particular individals or groups to focus on the aspects of greatest interest to them. The CCA supports parallel and distributed coputing as well as local high-performance connections between components in a language-independent manner. The design places minimal requirements on components and thus facilitates the integration of existing code into the CCA environment. The CCA model imposes minimal ovehead to minimize the impact on application performance. The focus on high performance distinguishes the CCA from most other component models. The CCA is being applied within an increasing range of disciplines, including cobustion research, global climate simulation, and computtional chemistry.

Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State†

Ab initio nonadiabatic dynamics simulations are reported for thymine with focus on the S(2) --> S(1) deactivation using the state-averaged CASSCF method. Supporting calculations have been performed on vertical excitations, S(1) and S(2) minima, and minima on the crossing seam using the MS-CASPT2, RI-CC2, MR-CIS, and MR-CISD methods. The photodynamical process starts with a fast (<100 fs) planar relaxation from the S(2) pipi* state into the pi(O)pi* minimum of the S(2) state. The calculations demonstrate that two pi-excited states (denoted pipi* and pi(O)pi*) are actually involved in this stage. The time in reaching the S(2)/S(1) intersections, through which thymine can deactivate to S(1), is delayed by both the change in character between the states as well as the flatness of the S(2) surface. This deactivation occurs in an average time of 2.6 ps at the lowest-energy region of the crossing seam. After that, thymine relaxes to the npi* minimum of the S(1) state, where it remains until the transfer to the ground state takes place. The present dynamics simulations show that not only the pi(O)pi* S(2) trapping but also the trapping in the npi* S(1) minimum contribute to the elongation of the excited-state lifetime of thymine.

Uncontracted rys quadrature implementation of up to G functions on graphical processing units

An implementation is presented of an uncontracted Rys quadrature algorithm for electron repulsion integrals, including up to g functions on graphical processing units (GPUs). The general GPU programming model, the challenges associated with implementing the Rys quadrature on these highly parallel emerging architectures, and a new approach to implementing the quadrature are outlined. The performance of the implementation is evaluated for single and double precision on two different types of GPU devices. The performance obtained is on par with the matrix-vector routine from the CUDA basic linear algebra subroutines (CUBLAS) library.

A collaborative informatics infrastructure for multi-scale science

The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information in support of systems-based research and is applying it within combustion science. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information.

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method

Benchmark timings are presented for the fragment molecular orbital method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 basis functions, using second order perturbation theory and an augmented and polarized double-ζ basis set, takes ∼7 min on 131 072 cores.

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.