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Apra, Edoardo

Publications and source records attributed to Apra, Edoardo.

49 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures

Coupled cluster singles and doubles (CCSD) algorithm has been optimized in NWChem software package. This modification alleviated the communication bottleneck and provided from 2- to 5-fold speedup in the CCSD iteration time depending on the problem size and available memory. Sustained 0.60 petaflop/sec performance on CCSD(T) calculation has been obtained on NCSA Blue Waters. This number included all stages of the calculation from initialization till termination, iterative computation of single and double excitations, and perturbative accounting for triple excitations. In the section of perturbative triples alone, the computation maintained 1.18 petaflop/sec performance level. CCSD computations have been performed on Guanine-Cytosine deoxydinucleotide monophosphate (GC-dDMP) to probe the conformational energy difference in DNA single strand in A- and B-conformations. The computation revealed significant discrepancy between CCSD and classical force fields in prediction of relative energy of A- and B-conformations of GC-dDMP.

calculations↗
DOE OSTI2013

Computational approaches to the chemical conversion of carbon dioxide

The conversion of CO2 into fuels and chemicals is viewed as an attractive route for controlling the atmospheric concentration of this greenhouse gas and recycling it, but its industrial application is limited by the low selectivity and activity of the current catalysts. Theoretical modeling, in particular density-functional theory (DFT) simulations, provides a powerful and effective tool to discover chemical reaction mechanisms and design new catalysts for the chemical conversion of CO2, overcoming the repetitious and time/labor consuming trial-and-error experimental processes. In this article we give a comprehensive survey of recent advances on mechanism determination by DFT calculations for the catalytic hydrogenation of CO2 into CO, CH4, CH3OH, and HCOOH, and CO2 methanation, as well as the photo- and electrochemical reduction of CO2. DFT-guided design procedures of new catalytic systems are also reviewed, and challenges and perspectives in this field are outlined.

Cheng, Daojian↗
DOE OSTI2013

Coexistence of Weak Ferromagnetism and Polar Lattice Distortion in Epitaxial NiTiO 3 thin films of the LiNbO 3 -Type Structure

We report the magnetic and structural characteristics of epitaxial NiTiO 3 films grown by pulsed laser deposition that are isostructural with acentric LiNbO 3 (space group R3c). Optical second harmonic generation and magnetometry demonstrate lattice polarization at room temperature and weak ferromagnetism below 250 K, respectively. These results appear to be consistent with earlier predictions from first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LiNbO 3 structure. This acentric form of NiTiO 3 is believed to be one of the rare examples of ferroelectrics exhibiting weak ferromagnetism generated by a Dzyaloshinskii-Moriya interaction.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2013

Noniterative Multireference Coupled Cluster Methods on Heterogeneous CPU-GPU Systems

A novel parallel algorithm for non-iterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [K. Bhaskaran-Nair, J.Brabec, E. Aprà, H.J.J. van Dam, J. Pittner, K. Kowalski, J. Chem. Phys. 137, 094112 (2012)] with the possibility of accelerating numerical calculations using graphics processing unit (GPU) is presented. We discuss the performance of this algorithm on the example of the MRCCSD(T) method (iterative singles and doubles and perturbative triples), where the corrections due to triples are added to the diagonal elements of the MRCCSD (iterative singles and doubles) effective Hamiltonian matrix. The performance of the combined RLP/GPU algorithm is illustrated on the example of the Brillouin-Wigner (BW) and Mukherjee (Mk) state-specific MRCCSD(T) formulations.

Brillouin-Wigner↗
DOE OSTI2012

CO Oxidation by Subnanometer AgxAu3–x Supported Clusters via Density Functional Theory Simulations

The activity of AgxAu3–x/MgO(100) clusters in CO oxidation is investigated computationally via systematic sampling techniques. It is found that these subnanometer species transform after ligand adsorption into reaction complexes which catalyze CO oxidation through a variety of different mechanisms, occurring via both Langmuir–Hinshelwood and Eley–Rideal paths and in some cases directly involving the oxide support. The alloyed Ag2Au1 cluster is proposed as the best catalyst in terms of efficiency and robustness.

caculations↗
DOE OSTI2012

Implementation of the multireference Brillouin-Wigner and Mukherjee’s coupled cluster methods with non-iterative triple excitations utilizing reference-level parallelism

In this paper we discuss the performance of the non-iterative State-Specific Mul- tireference Coupled Cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with the exact full configuration interaction results (FCI) for small systems (H2O, N2, and Be3). For larger systems (naphthyne isomers and -carotene), the non-iterative BW-MRCCSD(T) and Mk-MRCCSD(T) methods are compared against the results obtained with the single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of pro- cessor groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Runtime Techniques to Enable a Highly-Scalable Global Address Space Model for Petascale Computing

Over the past decade, the trajectory to the petascale has been built on increased complexity and scale of the underlying parallel architectures. Meanwhile, software developers have struggled to provide tools that maintain the productivity of computational science teams using these new systems. In this regard, Global Address Space (GAS) programming models provide a straightforward and easy to use addressing model, which can lead to improved productivity. However, the scalability of GAS depends directly on the design and implementation of the runtime system on the target petascale distributed-memory architecture. In this paper, we describe the design, implementation, and optimization of the Aggregate Remote Memory Copy Interface (ARMCI) runtime library on the Cray XT5 2.3 PetaFLOPs computer at Oak Ridge National Laboratory. We optimized our implementation with the flow intimation technique that we have introduced in this paper. Our optimized ARMCI implementation improves scalability of both the Global Arrays programming model and a real-world chemistry application—NWChem—from small jobs up through 180,000 cores.

Computer Science↗
DOE OSTI2012

Parallel implementation of multireference coupled-cluster theories based on the reference-level parallelism

A novel algorithm for implementing general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski-Monkhorst exponential Ansatz [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] is introduced. The proposed algorithm utilizes processor groups to calculate the equations for the MRCC amplitudes. In the basic formulation each processor group constructs the equations related to a specific subset of references. By flexible choice of processor groups and subset of reference-specific sufficiency conditions designated to a given group one can assure optimum utilization of available computing resources. The performance of this algorithm is illustrated on the examples of the Brillouin-Wigner and Mukherjee MRCC methods with singles and doubles (BW-MRCCSD and Mk-MRCCSD). A significant improvement in scalability and in reduction of time to solution is reported with respect to recently reported parallel implementation of the BW-MRCCSD formalism [J.Brabec, H.J.J. van Dam, K. Kowalski, J. Pittner, Chem. Phys. Lett. 514, 347 (2011)].

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2011

Scalable implementations of accurate excited-state coupled cluster theories: application of high-level methods to porphyrin based systems

The development of reliable tools for excited-state simulations is emerging as an extremely powerful computational chemistry tool for understanding complex processes in the broad class of light harvesting systems and optoelectronic devices. Over the last years we have been developing equation of motion coupled cluster (EOMCC) methods capable of tackling these problems. In this paper we discuss the parallel performance of EOMCC codes which provide accurate description of the excited-state correlation effects. Two aspects are discuss in details: (1) a new algorithm for the iterative EOMCC methods based on the novel task scheduling algorithms, and (2) parallel algorithms for the non-iterative methods describing the effect of triply excited configurations. We demonstrate that the most computationally intensive non-iterative part can take advantage of 210,000 cores of the Cray XT5 system at OLCF. In particular, we demonstrate the importance of non-iterative many-body methods for achieving experimental level of accuracy for several porphyrin-based system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Laser Spectroscopic and Theoretical Studies of Encapsulation Complexes of Calix[4]arene

The complexes between the host calix[4]arene (C4A) and various guest molecules such as NH3, N2, CH4, and C2H2 have been investigated via experimental and theoretical methods. The S1-S0 electronic spectra of these guest-host complexes are observed by mass-selected resonant two-photon ionization (R2PI) and laser induced fluorescence (LIF) spectroscopy. The infrared (IR) spectra of the complexes formed in molecular beams are obtained by IR-UV double resonance (IR-UV DR) and IR photodissociation (IRPD) spectroscopy. The supramolecular structures of the complexes are investigated by electronic structure methods (density functional and second order perturbation theory). The current results for the various molecular guests are put in perspective with the previously reported ones for the C4A-Rare Gas (Rg) (Phys. Chem. Chem. Phys. 2007, 126, 141101) and C4A-H2O complexes (J. Phys. Chem. A, 2010, 114, 2967). The electronic spectra of the complexes of C4A with N2, CH4 and C2H2 exhibit red-shifts of similar magnitudes with the ones observed for the C4A-Rg complexes, whereas the complexes of C4A with H2O and NH3 show much larger red-shifts. Most of the IR-UV DR spectra of the complexes, except for C4A-C2H2, show a broad hydrogen bonded OH stretching band with a peak at ~3160 cm-1. The analysis of the experimental results, in agreement with the ones resulted from the electronic structure calculations, suggest that C4A preferentially forms endo-complexes with all the guest species reported in this study. We discuss the similarities and differences of the structures, binding energies and the nature of the interaction between the C4A host and the various guest species. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy

08 HYDROGEN↗
DOE OSTI2011

Role of Many-Body Effects in Describing Low-Lying Excited States of pi-Conjugated Chromophores: High-Level Equation-of-Motion Coupled-Cluster Studies of Fused Porphyrin Systems

The unusual photophysical properties of the pi-conjugated chrompohores makes them potential building blocks of various molecular devices. In particular, significant narrowing of the HOMO-LUMO gaps can be observed as an effect of functionalization chromophores with polycyclic aromatic hydrocabrons (PAHs). In this paper we present equation-of-motion coupled cluster calculations for vertical excitation energies of several functionalized forms of porphyrins. The results of free-base porphyrin (FBP) clearly demonstrate significant differences between functionalization of FBP with one- (anthracene) and two-dimensional (coronene) structures. We also compare the EOMCC results with the experimentally available results for the anthracene fused zinc porphyrin. The impact of various-type correlation effects is illustrated on several benchmark models where the comparison with the experiment is possible. In particular, we demonstrate that for all excited states considered in this paper, all of them being dominated by single excitations, the inclusion of triply excited configurations is crucial for attaining qualitative agreement with the experiment. We also demonstrate the parallel performance of the most computationally intensive part of the completely renormalized EOMCCSD(T) approach (CR-EOMCCSD(T)) across 120,000 cores.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2010

High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at the MP2 and CCSD(T) levels of theory and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17 the CCSD(T) calculations confirm the previously found at the MP2 level of theory "interior" arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗