A5084423147- Parallel Computing and Optimization Techniques
- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Advanced Data Storage Technologies
- Distributed and Parallel Computing Systems
- Advanced NMR Techniques and Applications
- Cloud Computing and Resource Management
- Inorganic Fluorides and Related Compounds
- Quantum Computing Algorithms and Architecture
- Atomic and Molecular Physics
- Interconnection Networks and Systems
- Machine Learning in Materials Science
- Ultrasound Imaging and Elastography
- Embedded Systems Design Techniques
- Numerical Methods and Algorithms
- DNA and Nucleic Acid Chemistry
- Distributed systems and fault tolerance
- Algorithms and Data Compression
- Ultrasound and Hyperthermia Applications
- Mass Spectrometry Techniques and Applications
- Catalytic Processes in Materials Science
- Chaos-based Image/Signal Encryption
- Folate and B Vitamins Research
- Crystallography and molecular interactions
- Microwave Imaging and Scattering Analysis
Flinders University
2020-2023
Australian National University
2010-2020
University of California, Irvine
2012
Daresbury Laboratory
1992-1997
The Research Council
1997
Stockholm University
1991-1992
Lund University
1990-1992
Palo Alto Institute
1992
Ames Research Center
1989-1991
National Aeronautics and Space Administration
1990
A discussion of many the recently implemented features GAMESS (General Atomic and Molecular Electronic Structure System) LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These include fragmentation methods such as fragment molecular orbital, effective potential orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, resolution identity second order perturbation theory. Many new coupled cluster theory have been in GAMESS, multiple levels density functional/tight...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe restricted active space self-consistent-field method, implemented with a split graph unitary group approachPer Aake. Malmqvist, Alistair. Rendell, and Bjoern O. RoosCite this: J. Phys. Chem. 1990, 94, 14, 5477–5482Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/j100377a011https://doi.org/10.1021/j100377a011research-articleACS PublicationsRequest...
The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range practical applications. However, this is computationally difficult problem due to the large size computational domain compared acoustic wavelength. Here, k-space pseudospectral method used reduce number grid points required per wavelength for accurate simulations. model based on coupled first-order equations valid wave in heterogeneous with power law absorption. These are derived from fluid...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of the quadratic configuration interaction and coupled-cluster approaches to electron correlation including effect triple excitationsTimothy J. Lee, Alistair P. Rendell, Peter R. TaylorCite this: Phys. Chem. 1990, 94, 14, 5463–5468Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/j100377a008https://doi.org/10.1021/j100377a008research-articleACS...
By representing orbital products in an expansion basis, certain classes of two-electron integrals are approximated for use CCSD(T) calculations (singles and doubles coupled-cluster plus a perturbational estimate the effects connected triple excitations). This leads to very large reduction disk storage input/output requirements, with usually only modest increase computational effort. The new procedure will allow be undertaken, limited by available processor time. Using molecular basis as...
An efficient formulation of the analytic energy gradient for single and double excitation coupled-cluster method that includes a perturbational estimate effects connected triple excitations, denoted CCSD(T), is presented. The presented here has smaller computational cost than any previous formulation, algebraic manipulations lead to additional savings may be applied generally Mo/ller–Plesset perturbation theory energies. contribution from excitations scales as n3on4v+n4on3v, work needed...
The primary focus of GAMESS over the last 5 years has been development new high-performance codes that are able to take effective and efficient advantage most advanced computer architectures, both CPU accelerators. These efforts include employing density fitting fragmentation methods reduce high scaling well-correlated (e.g., coupled-cluster) as well developing novel can optimal graphical processing units other modern Because accurate wave functions be very complex, an important...
We employ the entire experimentally determined protein structure for KcsA potassium channel from Streptomyces lividans in molecular dynamics calculations to observe hydrated structure, ion solvation, selectivity, multiple configurations, and diffusion. Free energy perturbation display a significant discrimination of ∼9 kT favor larger K+ ion. The forming is very flexible yet unable fully solvate Na+ because its smaller size large solvation energy. There evidence that acidic basic sidechains...
Augmenting a processor with special hardware that is able to apply Single Instruction Multiple Data(SIMD) at the same time cost effective way of improving performance. It also offers means ratio performance power usage due reduced and more data movement intrinsically lower instruction counts. This paper considers compares NEON SIMD set used on ARM Cortex-A series RISC processors SSE2 found Intel platforms within context Open Computer Vision (OpenCV) library. The obtained using compiler...
Model-based treatment planning and exposimetry for high-intensity focused ultrasound requires the numerical simulation of nonlinear propagation through heterogeneous absorbing media. This is a computationally demanding problem due to large distances travelled by waves relative wavelength highest frequency harmonic. Here, k-space pseudospectral method used solve set coupled partial differential equations equivalent generalised Westervelt equation. The model implemented in C++ parallelised...
A novel implementation of the self-consistent field (SCF) procedure specifically designed for high-performance execution on multiple graphics processing units (GPUs) is presented. The algorithm offloads to GPUs three major computational stages SCF, namely, calculation one-electron integrals, and digestion electron repulsion diagonalization Fock matrix, including SCF acceleration via DIIS. Performance results a variety test molecules basis sets show remarkable speedups with respect...
Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery material science and catalysis. However, a predictive physicochemical characterization these processes often requires accurate quantum chemical modeling complex molecular systems with hundreds thousands atoms. Due computationally demanding nature electronic complexity modern high-performance computing hardware, chemistry...
The harmonic vibrational frequencies of the Be3 and Be4 clusters have been determined using ab initio electronic structure calculations. Large atomic natural orbital (ANO) basis sets used in conjunction with high levels correlation treatment. These include multireference configuration-interaction (MRCI) single double coupled-cluster (CCSD) methods, CCSD method augmented a correction for connected triple excitations [CCSD(T)]. In general, all three treatments agree very well. only substantial...
Electronic structure theory (especially quantum chemistry) has thrived and become increasingly relevant to a broad spectrum of scientific endeavors as the sophistication both computer architectures software engineering advanced. This article provides brief history advances in hardware software, from early days IBM mainframes current emphasis on accelerators modern programming practices.
We present a high-performance, GPU (graphics processing unit)-accelerated algorithm for building the Fock matrix. The is designed efficient calculations on large molecular systems and uses novel dynamic load balancing scheme that maximizes throughput avoids thread divergence could occur due to integral screening. Additionally, code adopts ERI digestion exploits all forms of permutational symmetry, combines efficiently evaluation both Coulomb exchange terms together, eliminates explicit...
A comparative study is presented of the various recently developed open-shell perturbation theories that are based on a restricted Hartree–Fock reference wave function. Included in this issues concerning spin contamination, implementational considerations, and numerical comparisons at second-order theory for equilibrium geometries, vibrational frequencies, singlet–triplet energy differences. Based all these it concluded z-averaged (ZAPT) method to be preferred over other devised spin–orbital...
The accuracy of the single and double excitation coupled-cluster (CCSD) method that includes a perturbational estimate connected triple excitations, denoted CCSD(T), has been tested for some representative transition metal complexes. For both binding energy to ligand bond distance NiCO Ni(CO)2, CCSD(T) yields results in very good agreement with multireference averaged coupled-pair functional (ACPF) calculations. are much better than those obtained using either (CPF) or modified CPF (MCPF)...
The analytic energy gradient for the single and double excitation coupled-cluster (CCSD) wave function has been reformulated implemented in a new set of programs. equations have smaller computational cost than any previously published. iterative solution linear construction effective density matrices are fully vectorized, being based on matrix multiplications. method used to investigate Cl2O2 molecule, which recently postulated as an important intermediate destruction ozone stratosphere. In...
Abstract A second order Møller-Plesset (MP2) energy gradient algorithm for distributed memory parallel computers is described. direct approach used in that integrals are recalculated as required, but the degree of recalculation minimized by exploiting large global typically available on machines. Results, obtained using up to 256 processors Cray T3D show very good scalability, with over 99·5% parallelism.
A systematic investigation of the stepwise hydration uracil has been carried out. The rich molecular electrostatic potential (MESP) topographical features provide clues on probable water binding sites. most noteworthy among these are MESP minima due to carbonyl oxygens where value is negative as well those over ring at which positive. Hydrated structures have obtained employing an electrostatics-based model, EPIC (Electrostatic for Intermolecular Complexation) followed by ab initio...