Advances in Scalable Computational Chemistry: NWChem
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N. Govind | K. Kowalski | T. P. Straatsma | E. J. Bylaska | H.J.J. van Dam | N. Govind | W. A. de Jong | M. Valiev | T. Straatsma | K. Kowalski | N. Govind | E. Bylaska | W. A. Jong | M. Valiev | H. V. Dam
[1] M. Plesset,et al. Note on an Approximation Treatment for Many-Electron Systems , 1934 .
[2] Karol Kowalski,et al. The active-space equation-of-motion coupled-cluster methods for excited electronic states: Full EOMCCSDt , 2001 .
[3] Marcel Nooijen,et al. Many‐body similarity transformations generated by normal ordered exponential excitation operators , 1996 .
[4] Marat Valiev,et al. A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction. , 2009, Journal of the American Chemical Society.
[5] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[6] Robert J. Harrison,et al. Parallel Douglas-Kroll Energy and Gradients in NWChem. Estimating Scalar Relativistic Effects Using Douglas-Kroll Contracted Basis Sets. , 2001 .
[7] M. Dupuis,et al. An ab initio model of electron transport in hematite (α-Fe2O3) basal planes , 2003 .
[8] T. P. Straatsma,et al. Treatment of rotational isomers in free energy evaluations. Analysis of the evaluation of free energy differences by molecular dynamics simulations of systems with rotational isomeric states , 1989 .
[9] R. Parr. Density-functional theory of atoms and molecules , 1989 .
[10] Nelson,et al. Plane-wave electronic-structure calculations on a parallel supercomputer. , 1993, Physical review. B, Condensed matter.
[11] H. Berendsen,et al. ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS , 1977 .
[12] Mark S. Gordon,et al. General atomic and molecular electronic structure system , 1993, J. Comput. Chem..
[13] Niranjan Govind,et al. Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem. , 2009, Journal of chemical theory and computation.
[14] Michael C. Zerner,et al. The linked singles and doubles model: An approximate theory of electron correlation based on the coupled‐cluster ansatz , 1982 .
[15] Karol Kowalski,et al. Parallel computation of coupled-cluster hyperpolarizabilities. , 2009, The Journal of chemical physics.
[16] Rodney J. Bartlett,et al. A new method for excited states: Similarity transformed equation-of-motion coupled-cluster theory , 1997 .
[17] Henrik Koch,et al. Coupled cluster response functions , 1990 .
[18] Marat Valiev,et al. Large-scale parallel calculations with combined coupled cluster and molecular mechanics formalism: Excitation energies of zinc–porphyrin in aqueous solution , 2008 .
[19] Hess,et al. Applicability of the no-pair equation with free-particle projection operators to atomic and molecular structure calculations. , 1985, Physical review. A, General physics.
[20] Henry F. Schaefer,et al. A new implementation of the full CCSDT model for molecular electronic structure , 1988 .
[21] Evert Jan Baerends,et al. Relativistic regular two‐component Hamiltonians , 1993 .
[22] F. Nogueira,et al. A primer in density functional theory , 2003 .
[23] Tjerk P. Straatsma,et al. NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..
[24] R. Bartlett,et al. A full coupled‐cluster singles and doubles model: The inclusion of disconnected triples , 1982 .
[25] R. Bartlett,et al. Coupled-cluster theory in quantum chemistry , 2007 .
[26] A. J. Sadlej,et al. Reduced-size polarized basis sets for calculations of molecular electric properties. IV. First-row transition metals , 2007 .
[27] J. Hammond,et al. Dynamic polarizabilities of polyaromatic hydrocarbons using coupled-cluster linear response theory. , 2007, The Journal of chemical physics.
[28] S. Grimme. Semiempirical hybrid density functional with perturbative second-order correlation. , 2006, The Journal of chemical physics.
[29] Donald C. Comeau,et al. The equation-of-motion coupled-cluster method. Applications to open- and closed-shell reference states , 1993 .
[30] Steven E. J. Bell,et al. Reduced–size polarized basis sets for calculations of molecular electric properties. III. Second–row atoms , 2005 .
[31] N. Oliphant,et al. Coupled‐cluster method truncated at quadruples , 1991 .
[32] S. Hirata. Tensor Contraction Engine: Abstraction and Automated Parallel Implementation of Configuration-Interaction, Coupled-Cluster, and Many-Body Perturbation Theories , 2003 .
[33] Martins,et al. Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.
[34] Josef Paldus,et al. Correlation Problems in Atomic and Molecular Systems. IV. Extended Coupled-Pair Many-Electron Theory and Its Application to the B H 3 Molecule , 1972 .
[35] Sriram Krishnamoorthy,et al. Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer. , 2010, The Journal of chemical physics.
[36] Tomasz Janowski,et al. Efficient Parallel Implementation of the CCSD External Exchange Operator and the Perturbative Triples (T) Energy Calculation. , 2008, Journal of chemical theory and computation.
[37] Marat Valiev,et al. Combined quantum mechanical and molecular mechanics studies of the electron-transfer reactions involving carbon tetrachloride in solution. , 2008, The journal of physical chemistry. A.
[38] M. Head‐Gordon,et al. A fifth-order perturbation comparison of electron correlation theories , 1989 .
[39] Tjerk P. Straatsma,et al. NWChem: Exploiting parallelism in molecular simulations , 2000 .
[40] K. Rosso,et al. Self-Exchange Electron Transfer Kinetics and Reduction Potentials for Anthraquinone Disulfonate , 2004 .
[41] D. Truhlar,et al. Quantum mechanical methods for enzyme kinetics. , 2003, Annual review of physical chemistry.
[42] N. Nakatsuji,et al. Cluster expansion of the wavefunction. Excited states , 1978 .
[43] Henry F. Schaefer,et al. On the evaluation of analytic energy derivatives for correlated wave functions , 1984 .
[44] Marat Valiev,et al. Interactions of Cl- and OH radical in aqueous solution. , 2009, The journal of physical chemistry. A.
[45] R. Bartlett,et al. The coupled‐cluster single, double, triple, and quadruple excitation method , 1992 .
[46] K. Brueckner,et al. Many-Body Problem for Strongly Interacting Particles. II. Linked Cluster Expansion , 1955 .
[47] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[48] M. Ratner. Molecular electronic-structure theory , 2000 .
[49] T. Straatsma,et al. Multiconfiguration thermodynamic integration , 1991 .
[50] F. Coester,et al. Bound states of a many-particle system , 1958 .
[51] N. Govind,et al. Electric Field Gradients Calculated from Two-Component Hybrid Density Functional Theory Including Spin-Orbit Coupling. , 2010, Journal of chemical theory and computation.
[52] Blöchl,et al. Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.
[53] U. Singh,et al. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .
[54] Kimihiko Hirao,et al. Cluster expansion of the wavefunction. Symmetry-adapted-cluster expansion, its variational determination, and extension of open-shell orbital theory , 1978 .
[55] Robert A. van de Geijn,et al. SUMMA: Scalable Universal Matrix Multiplication Algorithm , 1995 .
[56] Tomasz Janowski,et al. Quantum chemistry in parallel with PQS , 2009, J. Comput. Chem..
[57] Roland Lindh,et al. Utilizing high performance computing for chemistry: parallel computational chemistry. , 2010, Physical chemistry chemical physics : PCCP.
[58] Marvin Douglas,et al. Quantum electrodynamical corrections to the fine structure of helium , 1971 .
[59] Poul Jørgensen,et al. The second-order approximate coupled cluster singles and doubles model CC2 , 1995 .
[60] Johannes Grotendorst,et al. Modern methods and algorithms of quantum chemistry , 2000 .
[61] Tjerk P. Straatsma,et al. Load balancing of molecular dynamics simulation with NWChem , 2001, IBM Syst. J..
[62] A. Szabo,et al. Modern quantum chemistry , 1982 .
[63] Warren E. Pickett,et al. Pseudopotential methods in condensed matter applications , 1989 .
[64] Mark S. Gordon,et al. A Novel Approach to Parallel Coupled Cluster Calculations: Combining Distributed and Shared Memory Techniques for Modern Cluster Based Systems , 2007 .
[65] Hamann. Generalized norm-conserving pseudopotentials. , 1989, Physical review. B, Condensed matter.
[66] A. Lipton,et al. A QM/MM approach to interpreting 67Zn solid-state NMR data in zinc proteins. , 2008, Journal of the American Chemical Society.
[67] Peter Pulay,et al. Parallel Calculation of Coupled Cluster Singles and Doubles Wave Functions Using Array Files. , 2007, Journal of chemical theory and computation.
[68] Kenneth B. Wiberg,et al. Analysis of the effect of electron correlation on charge density distributions , 1992 .
[69] Peter Pulay,et al. High accuracy benchmark calculations on the benzene dimer potential energy surface , 2007 .
[70] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[71] Anna I. Krylov,et al. Size-consistent wave functions for bond-breaking: the equation-of-motion spin-flip model , 2001 .
[72] Eric J. Bylaska,et al. Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems , 2002 .
[73] Scott B. Baden,et al. Parallel implementation of γ‐point pseudopotential plane‐wave DFT with exact exchange , 2011, J. Comput. Chem..
[74] Rodney J. Bartlett,et al. The equation-of-motion coupled-cluster method: Excitation energies of Be and CO , 1989 .
[75] V. Kellö,et al. Medium-size polarized basis sets for high-level-correlated calculations of molecular electric properties , 1991 .
[76] J A McCammon,et al. Theoretical calculations of relative affinities of binding. , 1991, Methods in enzymology.
[77] Karol Kowalski,et al. Coupled cluster calculations for static and dynamic polarizabilities of C60. , 2008, The Journal of chemical physics.
[78] V. Tipparaju,et al. Role of Many-Body Effects in Describing Low-Lying Excited States of π-Conjugated Chromophores: High-Level Equation-of-Motion Coupled-Cluster Studies of Fused Porphyrin Systems. , 2011, Journal of chemical theory and computation.
[79] Kimihiko Hirao,et al. The higher-order Douglas–Kroll transformation , 2000 .
[80] T. Straatsma,et al. Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes , 2008 .
[81] Marat Valiev,et al. Hybrid approach for free energy calculations with high-level methods: application to the SN2 reaction of CHCl3 and OH- in water. , 2007, The Journal of chemical physics.
[82] Scott B. Baden,et al. Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second , 2009 .
[83] R J Bartlett,et al. Parallel implementation of electronic structure energy, gradient, and Hessian calculations. , 2008, The Journal of chemical physics.
[84] Marat Valiev,et al. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. , 2007 .
[85] Robert J. Harrison,et al. Parallel direct four-index transformations , 1996 .
[86] R. Bartlett,et al. The full CCSDT model for molecular electronic structure , 1987 .
[87] Marat Valiev,et al. Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment. , 2006, The Journal of chemical physics.
[88] Michael W. Schmidt,et al. A natural orbital diagnostic for multiconfigurational character in correlated wave functions , 1999 .
[89] Mark S. Gordon,et al. Coupled cluster algorithms for networks of shared memory parallel processors , 2007, Comput. Phys. Commun..
[90] J. Cizek. On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell-Type Expansion Using Quantum-Field Theoretical Methods , 1966 .
[91] K. Dyall. An exact separation of the spin‐free and spin‐dependent terms of the Dirac–Coulomb–Breit Hamiltonian , 1994 .
[92] Karol Kowalski,et al. New coupled-cluster methods with singles, doubles, and noniterative triples for high accuracy calculations of excited electronic states. , 2004, The Journal of chemical physics.
[93] D. Bernholdt,et al. Large-scale correlated electronic structure calculations: the RI-MP2 method on parallel computers , 1996 .
[94] Theresa L Windus,et al. Thermodynamic properties of the C5, C6, and C8 n-alkanes from ab initio electronic structure theory. , 2005, The journal of physical chemistry. A.
[95] T. Straatsma,et al. Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation , 2009, Proteins.
[96] W. J. Stevens,et al. Effective Potentials in Molecular Quantum Chemistry , 1984 .
[97] F. Coester,et al. Short-range correlations in nuclear wave functions , 1960 .
[98] John F. Stanton,et al. The equation of motion coupled‐cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties , 1993 .
[99] J. Hammond,et al. Coupled-cluster dynamic polarizabilities including triple excitations. , 2008, The Journal of chemical physics.
[100] Hiroshi Nakatsuji,et al. Cluster expansion of the wavefunction. Electron correlations in ground and excited states by SAC (symmetry-adapted-cluster) and SAC CI theories , 1979 .
[101] T. Straatsma,et al. Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration , 1994 .
[102] T. H. Dunning. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .