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New algebraic formulation of density functional calculation

COMPUTER PHYSICS COMMUNICATIONS 2000年第1-2期128卷 1-45页

作者： Ismail-Beigi, S Arias, TA Cornell Univ Atom & Solid State Phys Lab Ithaca NY 14853 USA MIT Dept Phys Cambridge MA 02139 USA MIT Elect Res Lab Cambridge MA 02139 USA

This article addresses a fundamental problem faced by the community employing single-particle ab initio methods: the lack of an effective formalism for the rapid exploration and exchange of new methods. To rectify this, we introduce a new, basis-set independent, matrix-based formulation of generalized density functional theories which reduces the development, implementation, and dissemination of new techniques to the derivation and transcription of a few lines of algebra. This new framework enables us to concisely demystify the inner workings of fully functional, highly efficient modern ab initio codes and to give complete instructions for their construction for calculations employing arbitrary basis sets. Within this framework, we also discuss in full detail a variety of leading-edge techniques, minimization algorithms, and highly efficient computational kernels for use with scalar as well as shared and distributed-memory supercomputer architectures. (C) 2000 published by Elsevier Science B.V. All rights reserved.

关键词： density-functional theory ab initio calculations electronic structure methods electronic structure calculations high performance computing parallel computing computer languages

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Extended Ewald summation technique

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COMPUTER PHYSICS COMMUNICATIONS 2016年 206卷 64-68页

作者： Kylanpaa, Ilkka Rasanen, Esa Tampere Univ Technol Dept Phys POB 692 FI-33101 Tampere Finland

We present a technique to improve the accuracy and to reduce the computational labor in the calculation of long-range interactions in systems with periodic boundary conditions. We extend the well-known Ewald method by using a linear combination of screening Gaussian charge distributions instead of only one. This enables us to find faster converging real-space and reciprocal space summations. The combined simplicity and efficiency of our method is demonstrated, and the scheme is readily applicable to large-scale periodic simulations, classical as well as quantum. Moreover, apart from the required a priori optimization the method is straightforward to include in most routines based on the Ewald method within, e.g., density-functional, molecular dynamics, and quantum Monte Carlo calculations. (C) 2016 Elsevier B.V. All rights reserved.

关键词： Long-range interactions electronic structure methods Molecular dynamics

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Binary SCF:: GAMESS improvements for energy evaluation based on SCF methods

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COMPUTER PHYSICS COMMUNICATIONS 2006年第1期174卷 1-16页

作者： de Matos, J Bortolato, E Camilo, A Martini, JA Gonçalves, RAL de Souza, PSL Univ Estadual Ponta Grossa Dept Phys BR-84030900 Ponta Grossa PR Brazil Univ Estadual Ponta Grossa Dept Comp BR-84030900 Ponta Grossa PR Brazil Univ Estadual Maringa Dept Comp BR-87020900 Maringa Parana Brazil Univ Sao Paulo ICMC SCE BR-13560970 Sao Carlos SP Brazil

This paper describes a new algorithm that improves computational efficiency for energy evaluation in GAMESS, named Binary SCF (BitSCF). This algorithm is based on the Conventional Self Consistent Field (CSCF) method and it presents two main innovations. The first one is the use of a bit map for the control of the 2e(-) integrals evaluated and previously stored in disk. The bit map reduces disk demand significantly when storing 2e(-) integrals. The second innovation is the use of i-loop balancing, a new proposal for static workload distribution through the nodes. The i-loop balancing optimizes parallelism in GAMESS, reducing an important sequential portion of its source code. The results obtained confirm a reduction of up to 49% in the disk demand for the 2e(-) integrals storage, considering different simulated molecules on a 13-node Beowulf cluster and 6-31G and STO-6G basis set. The total and CPU times stay below the times obtained with the GAMESS CSCF method for larger molecules. The total execution and CPU times were equivalent at the CSCF times for smaller molecules. The results show an improvement in the GAMESS scalability as well as a better cost vs. benefit relationship when executing the program. (c) 2005 Elsevier B.V. All rights reserved.

关键词： GAMESS SCF energy evaluation 2e(-) integrals electronic structure methods parallel computing high performance computing

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The object-oriented DFT program library S/PHI/nX

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COMPUTER PHYSICS COMMUNICATIONS 2011年第3期182卷 543-554页

作者： Boeck, S. Freysoldt, C. Dick, A. Ismer, L. Neugebauer, J. Max Planck Inst Eisenforsch GmbH D-40237 Dusseldorf Germany

In order to simplify the development and implementation process of quantum mechanical algorithms, we developed a set of object-oriented C++ libraries which can exploit modern computer architectures. The libraries are characterized as follows: (i) State-of-the-art computer science techniques have been applied or developed in this work to provide language elements to express algebraic expressions efficiently on modern computer platforms. (ii) Quantum mechanical algorithms are crucial in the field of materials research. The new libraries support the Dirac notation to implement such algorithms in the native language of physicists. (iii) The libraries are completed by elements to express equations of motions efficiently which is required for implementing structural algorithms such as molecular dynamics. Based on these libraries we introduce the DFT program package S/PHI/nX. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Density-functional theory Ab initio calculations electronic structure methods electronic structure calculations High performance computing Computer languages

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Coupled Cluster Green's function formulations based on the effective Hamiltonians

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MOLECULAR PHYSICS 2020年第19-20期118卷

作者： Bauman, Nicholas P. Peng, Bo Kowalski, Karol Pacific Northwest Natl Lab William R Wiley Environm Mol Sci Lab Battelle K8-91POB 999 Richland WA 99352 USA Pacific Northwest Natl Lab Adv Comp Math & Data Div Battelle Richland WA 99352 USA

We demonstrate that the effective Hamiltonians obtained with the downfolding procedure based on double unitary coupled cluster (DUCC) ansatz can be used in the context of Green's function coupled cluster (GFCC) formalism to calculate spectral functions of molecular systems. This combined approach (DUCC-GFCC) provides a significant reduction of numerical effort and good agreement with the corresponding all-orbital GFCC methods in energy windows that are consistent with the choice of active space. These features are demonstrated on the example of four benchmark systems: , , CO, and trans-1,3-butadiene, where DUCC-GFCC calculations were performed for active spaces of various sizes. [GRAPHICS] .

关键词： Coupled cluster Green's function electronic structure methods

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Combinatorial-computational-chemoinformatics (C³) approach to finding and analyzing low-energy tautomers

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2010年第6-7期24卷 627-638页

作者： Haranczyk, Maciej Gutowski, Maciej Univ Calif Berkeley Lawrence Berkeley Lab Computat Res Div Berkeley CA 94720 USA Heriot Watt Univ Chem Sch Engn & Phys Sci Edinburgh EH14 4AS Midlothian Scotland

Finding the most stable tautomer or a set of low-energy tautomers of molecules is critical in many aspects of molecular modelling or virtual screening experiments. Enumeration of low-energy tautomers of neutral molecules in the gas-phase or typical solvents can be performed by applying available organic chemistry knowledge. This kind of enumeration is implemented in a number of software packages and it is relatively reliable. However, in esoteric cases such as charged molecules in uncommon, non-aqueous solvents there is simply not enough available knowledge to make reliable predictions of low energy tautomers. Over the last few years we have been developing an approach to address the latter problem and we successfully applied it to discover the most stable anionic tautomers of nucleic acid bases that might be involved in the process of DNA damage by low-energy electrons and in charge transfer through DNA. The approach involves three steps: (1) combinatorial generation of a library of tautomers, (2) energy-based screening of the library using electronic structure methods, and (3) analysis of the information generated in step (2). In steps 1-3 we employ combinatorial, computational and chemoinformatics techniques, respectively. Therefore, this hybrid approach is named "Combinatorial*Computational*Chemoinformatics", or just abbreviated as C-3 (or C-cube) approach. This article summarizes our developments and most interesting methodological aspects of the C-3 approach. It can serve as an example how to identify the most stable tautomers of molecular systems for which common chemical knowledge had not been sufficient to make definite predictions.

关键词： Tautomer Combinatorial approach electronic structure methods Chemoinformatics

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Ab initio molecular dynamics studies of the OH + D₂ → HOD plus D reaction: Direct classical trajectory calculations by MP2

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CHEMICAL PHYSICS 2008年第1-3期354卷 142-147页

作者： Tian, Xiaofeng Gao, Tao He, Na Zhang, Zhihui Sichuan Univ Inst Atom & Mol Phys Chengdu 610065 Peoples R China

The mechanism and dynamics of the reaction of OH with D-2 have been investigated using electronic structure methods. A Hessian based method with updating was used to integrate the trajectories. The calculations of geometries and energies in the present work were at B3LYP/cc-PVDZ, MP2/cc-PVDZ and HF/6-311++G(2df,2pd) levels. The direct classical trajectory calculations were at the MP2/cc-PVDZ level. The distribution of averaged product translational energies was in good agreement with the experimental data. but the percentage in distribution of the vibrational energies in the present calculations was lower by 11% than the experiment. This call be attributed to the difference in the reverse reaction barrier height and total available energy between calculations and experiment. (C) 2008 Elsevier B.V, All rights reserved.

关键词： Barrier height MP2 electronic structure methods Direct classical trajectory calculations BOMD

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Theoretical enthalpies of formation and structural characterisation of halogenated nitromethanes and isomeric halomethyl nitrites

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CHEMICAL PAPERS 2012年第12期66卷 1157-1165页

作者： Kosmas, Agnie Mylona Ntivas, Aristeidis Liaska, Stavroula Papayannis, Demetrios K. Univ Ioannina Dept Chem GR-45110 Ioannina Greece Univ Ioannina Dept Mat Sci GR-45110 Ioannina Greece

The structural, energetic, and thermochemical properties of a number of halogenated nitromethanes, CH (n) X3-n NO2, and the isomeric nitrites, CH (n) X3-n ONO, are investigated, using theoretical ab initio and density functional theory (DFT) electronic structure methods. Analysis of the results and comparison with the maternal species, nitromethane, CH3NO2, and methyl nitrite, CH3ONO, reveal strong dependence of the molecular properties on the halogen induction effect. Opposite trends are obtained in the C-N and C-O bond dissociation energies (BDE) upon halogenation and higher stabilities are calculated for the trans-nitrite isomers, in contrast with the plain alkyl families where the nitroalkanes are the most stable species. Formation enthalpies, Delta H (f) (a"') , at 298 K are calculated for all halogenated isomers.

关键词： halogenated methyl nitrates electronic structure methods halogen induction effect relative energy enthalpy of formation

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Charge and Energy Transfer Dynamics in Molecular Systems 4

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2023年

作者： Oliver Kühn Volkhard May

Charge and Energy Transfer Dynamics in Molecular Systems Comprehensive resource offering knowledge on charge and energy transfer dynamics in molecular systems and nanostructures Charge and Energy Transfer Dynamics in ... 详细信息

ISBN: (数字)9783527696277

ISBN: (纸本)9783527339785

关键词： electronic molecular state vibrational molecular states molecular Schrödinger equation Born–Oppenheimer separation electronic structure methods Hartree–Fock equations open wave packets interaction representation energy transfer textbook

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“You Are Young and Can Afford to Do Something Stupid.”: Fostering an Understanding of electronic Spin in Chemistry

“You Are Young and Can Afford to Do Something Stupid.”: Fo...

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作者： Joyce, Justin P. Colorado State University

学位级别：Ph.D., Doctor of Philosophy

In this dissertation I develop tools with electronic structure methods to resolve electronic spin as the inciting property of diverse chemical phenomena. The content is organized as follows:Chapter 1 provides the historical context of the events leading to the conception of electronic spin. I align the application of this intrinsic quantum mechanical property with advancing the impact of chemistry. The Chapters dedicated to my research are separated by their focus of closed- or open-shell electronic systems. The sections are predicated with a theoretical method that provides quantitative and visual insight into the electron-electron interactions. The methods developed with model systems are then extended to new results garnered from close collaboration with experimental *** Chapter 2 we characterize the impact of the Pauli Exclusion principle on the relative stability of the structural isomers of octane (C8H18). We develop that the asymmetry of the electronic wavefunction exerts a complementary relationship with respect to the strain and stability of chemical systems. This is demonstrated with respect to both the magnification of medium-range electron correlation and the reduction of vibrational enthalpy via exchange repulsion. We refer to the dynamic interplay between these forces as a Gestalt interaction. Most of the text and graphics have been previously published, its reference provided as follows: Joyce, J.P.; Shores, M.P.; Rappé, A.K.: Phys. Chem. Chem. Phys., 2020, 22, *** Chapter 3 we extend the principle of complementarity developed in Chapter 2 to the relative stability of the labile spin states of octahedral Fe2+ coordination complexes. This establishes the analogous impact of geminal and cis-contacts on the electronic energy of structural and spin isomers, respectively. In the tradition of Pauling, we develop an empirical structural parameter based on the principle of s-p hybridization that is benchmarked with experimental crystallo

关键词： electronic spin electronic structure methods Chemical phenomena C8H18 Pauli Exclusion principle

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