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At least 253 records · Page 14

The hydrogen abstraction reaction O({sup 3}P) + CH{sub 4}: A new analytical potential energy surface based on fit to ab initio calculations

Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole set of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of H{sub 2} Eley-Rideal abstraction from W(110): Sensitivity to the representation of the molecule-surface potential

Dynamics of the Eley-Rideal (ER) abstraction of H{sub 2} from W(110) is analyzed by means of quasi-classical trajectory calculations. Simulations are based on two different molecule-surface potential energy surfaces (PES) constructed from Density Functional Theory results. One PES is obtained by fitting, using a Flexible Periodic London-Eyring-Polanyi-Sato (FPLEPS) functional form, and the other by interpolation through the corrugation reducing procedure (CRP). Then, the present study allows us to elucidate the ER dynamics sensitivity on the PES representation. Despite some sizable discrepancies between both H+H/W(110) PESs, the obtained projectile-energy dependence of the total ER cross sections are qualitatively very similar ensuring that the main physical ingredients are captured in both PES models. The obtained distributions of the final energy among the different molecular degrees of freedom barely depend on the PES model, being most likely determined by the reaction exothermicity. Therefore, a reasonably good agreement with the measured final vibrational state distribution is observed in spite of the pressure and material gaps between theoretical and experimental conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A reactant-coordinate-based wave packet method for full-dimensional state-to-state quantum dynamics of tetra-atomic reactions: Application to both the abstraction and exchange channels in the H + H 2 O reaction

Here, an efficient and accurate wave packet method is proposed for the calculation of the state-to-state S -matrix elements in bimolecular reactions involving four atoms. This approach propagates an initial state specific wave packet in reactant Jacobi coordinates. The projection in product channels is carried out on projection planes, which have one less degree of freedom, by transforming both the time-dependent wave packet and final product states into a set of intermediate coordinates. This reactant-coordinate-based method is more efficient than product-coordinate-based methods because it typically requires a smaller number of basis functions or grid points and allows the determination of S -matrix elements for multiple product channels from a single propagation. This method is demonstrated in calculating the ( J tot = 0) state-to-state S -matrix elements for both the abstraction and exchange channels of the H + H 2 O reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Full-dimensional global potential energy surfaces describing abstraction and exchange for the H + H{sub 2}S reaction

For the H + H{sub 2}S system, ∼34 000 data points are sampled over a large configuration space including both abstraction and exchange channels, and calculated at the level of explicitly correlated unrestricted coupled cluster method with singles, doubles, and perturbative triples excitations with the augmented correlation-consistent polarized triple zeta basis set (UCCSD(T)-F12a/aug-cc-pVTZ). The data set was fit using the newly proposed permutation invariant polynomial-neural network (PIP-NN) method with three different vectors as the input: two redundant sets of PIPs, one with the maximum order four (PES-I) and one with the maximum order three (PES-II), and nine non-redundant PIPs (PES-III). All these PESs show small fitting errors and essentially the same performance in representing the title system. Various kinetics and dynamical properties are calculated using the tunneling corrected transition state theory and quasi-classical trajectory, and compared with available experimental results. At a collision energy of 10 kcal/mol, both the H{sub 2} and SH products are found to be internally cold, with ∼20% of H{sub 2} at its first vibrational excited state, while SH is essentially a spectator. The angular distributions of the products are mainly in backward with considerable contributions from sideway direction. In addition, analytical partial derivatives of any PIP-NN PES with respect to the coordinates of atoms are derived by making use of the monomial symmetrization algorithm [Z. Xie and J. M. Bowman, J. Chem. Theory Comput. 6, 26–34 (2010)]. It can not only accelerate the evaluation of the derivatives, but also improve the energy convergence significantly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Introducing Weirs: An Abstraction for Next Generation Streaming Workflows

In HPC applications, it is widely understood that in situ systems will play a significant role in next generation systems. The rate that next-generation leadership machines will be able to generate data will exceed the bandwidths of the planned I/O systems, leading to a need for in situ processing of the resulting data to reduce it. There have been a number of techniques proposed for in situ workflow systems; we are concerned here specifically with the needs of publish/subscribe or streaming-based approaches, which allow the in situ system to be composed of completely separate executables running concurrently on the hardware. In this paper we introduce an abstract known as a Weir. A weir is a useful mechanism to control state in a point to point streaming workflow in the absence of a third party publish subscribe system.

97 MATHEMATICS AND COMPUTING↗

Toward Abstracting the Communication Intent in Applications to Improve Portability and Productivity

Programming with communication libraries such as the Message Passing Interface (MPI) obscures the high-level intent of the communication in an application and makes static communication analysis difficult to do. Compilers are unaware of communication libraries' specifics, leading to the exclusion of communication patterns from any automated analysis and optimizations. To overcome this, communication patterns can be expressed at higher-levels of abstraction and incrementally added to existing MPI applications. In this paper, we propose the use of directives to clearly express the communication intent of an application in a way that is not specific to a given communication library. Our communication directives allow programmers to express communication among processes in a portable way, giving hints to the compiler on regions of computations that can be overlapped with communication and relaxing communication constraints on the ordering, completion and synchronization of the communication imposed by specific libraries such as MPI. The directives can then be translated by the compiler into message passing calls that efficiently implement the intended pattern and be targeted to multiple communication libraries. Thus far, we have used the directives to express point-to-point communication patterns in C, C++ and Fortran applications, and have translated them to MPI and SHMEM.

Mintz, Tiffany M.↗

Compiler verification meets cross-language linking via data abstraction

Many real programs are written in multiple different programming languages, and supporting this pattern creates challenges for formal compiler verification. We describe our Coq verification of a compiler for a high-level language, such that the compiler correctness theorem allows us to derive partial-correctness Hoare-logic theorems for programs built by linking the assembly code output by our compiler and assembly code produced by other means. Our compiler supports such tricky features as storable cross-language function pointers, without giving up the usual benefits of being able to verify different compiler phases (including, in our case, two classic optimizations) independently. Here, the key technical innovation is a mixed operational and axiomatic semantics for the source language, with a built-in notion of abstract data types, such that compiled code interfaces with other languages only through axiomatically specified methods that mutate encapsulated private data, represented in whatever formats are most natural for those languages.

97 MATHEMATICS AND COMPUTING↗

The UPC++ PGAS library for exascale computing. Extended Abstract

We describe UPC++ V1.0, a C++11 library that supports APGAS programming. UPC++ targets distributed data structures where communication is irregular or fine-grained. The key abstractions are global pointers, asynchronous programming via RPC, and futures. Global pointers incorporate ownership information useful in optimizing for locality. Futures capture data readiness state, are useful for scheduling and also enable the programmer to chain operations to execute asynchronously as high-latency dependencies become satisfied, via continuations. The interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and closely resemble those used in modern C++. Communication in UPC++ runs at close to hardware speeds by utilizing the low-overhead GASNet-EX communication library.

97 MATHEMATICS AND COMPUTING↗

VEST: abstract vector calculus simplification in Mathematica

We present a new package, VEST (Vector Einstein Summation Tools), that performs abstract vector calculus computations in Mathematica. Through the use of index notation, VEST is able to reduce scalar and vector expressions of a very general type using a systematic canonicalization procedure. In addition, utilizing properties of the Levi-Civita symbol, the program can derive types of multi-term vector identities that are not recognized by canonicalization, subsequently applying these to simplify large expressions. In a companion paper, we employ VEST in the automation of the calculation of Lagrangians for the single particle guiding center system in plasma physics, a computation which illustrates its ability to handle very large expressions. VEST has been designed to be simple and intuitive to use, both for basic checking of work and more involved computations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Programming Abstractions for Data Locality

The goal of the workshop and this report is to identify common themes and standardize concepts for locality-preserving abstractions for exascale programming models.

97 MATHEMATICS AND COMPUTING↗

Algorithms and Abstractions for Assembly in PDE Codes: Workshop Report

The emergence of high-concurrency architectures offering unprecedented performance has brought many high-performance partial differential equation (PDE) discretization codes to the precipice of a major refactor. To help address this challenge a workshop titled "Algorithms and Abstractions for Assembly in PDE Codes" was held in the Computer Science Research Institute at Sandia National Laboratories on May 12th-14th, 2014. This document summarizes the goals of the workshop and the results of the presentations and subsequent discussions.

97 MATHEMATICS AND COMPUTING↗

Usable Data Abstractions for Next-Generation Scientific Workflows

Data- and computationally-intensive scientific research, such as numerical simulations and inversions or the training of large neural networks in machine learning applications, that are well suited for HPC environments also often require expert insight and evaluation throughout the computation which can be greatly facilitated with the use of interactive computing tools, such as those in the Jupyter ecosystem. HPC workflows and interactive workflows are typically treated as orthogonal, however, the next generation of research will require both. The first challenge we face in this project is thus designing the right level of abstractions to allow interactive capabilities in the JupyterLab environment to allow the working scientist to flexibly explore and query their data at multiple levels, with a minimal amount of customization required of the underlying optimized codes. In addition to these questions regarding the high-level representation of data for interactive use in HPC, we tackled two additional issues that are part of the entire lifecycle of research and that become particularly acute in HPC contexts: how to improve the experience of interfacing with the HPC system's scheduling environment for a scientist focused on exploratory questions, and how can that scientist then best share the results of their work with others in a self-contained, reproducible manner.

97 MATHEMATICS AND COMPUTING↗