The GAMESS-UK electronic structure package: algorithms, developments and applications

A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offers a wide range of quantum mechanical wavefunctions, capable of treating systems ranging from closed-shell molecules through to the species involved in complex reaction mechanisms. The availability of a wide variety of correlation methods provides the necessary functionality to tackle a number of chemically important tasks, ranging from geometry optimization and transition-state location to the treatment of solvation effects and the prediction of excited state spectra. With the availability of relativistic ECPs and the development of ZORA, such calculations may be performed on the entire Periodic Table, including the lanthanides. Emphasis is given to the DFT module, which has been extensively developed in recent years, and a number of other, novel features of the program. The parallelization strategy used in the program is outlined, and detailed speedup results are given. Applications of the code in the areas of enzyme and zeolite catalysis and in spectroscopy are described.

[1]  Julia E. Rice,et al.  An efficient closed-shell singles and doubles coupled-cluster method , 1988 .

[2]  B. Roos,et al.  A new method for large-scale Cl calculations , 1972 .

[3]  Paul J. Lewi,et al.  Inhibition and substrate recognition – a computational approach applied to HIV protease , 2003, J. Comput. Aided Mol. Des..

[4]  J. H. van Lenthe,et al.  TURTLE - A gradient VBSCF Program. Theory and Studies of Aromaticity , 2002 .

[5]  J. H. van Lenthe,et al.  The direct CI method , 2006 .

[6]  M. Palmer,et al.  The electronic states of benzene and the azines. I. The parent compound benzene. Correlation of vacuum UV and electron scattering data with ab initio CI studies , 1989 .

[7]  Bernard R. Brooks,et al.  Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method , 2002 .

[8]  Joop H. van Lenthe,et al.  Software news and updates , 2001, J. Comput. Chem..

[9]  J. G. Snijders,et al.  Gradients in the ab initio scalar zeroth-order regular approximation (ZORA) approach , 2000 .

[10]  V. Lebedev,et al.  A QUADRATURE FORMULA FOR THE SPHERE OF THE 131ST ALGEBRAIC ORDER OF ACCURACY , 1999 .

[11]  H. Schaefer,et al.  The analytic configuration interaction gradient method: Application to the cyclic and open isomers of the S3 molecule , 1986 .

[12]  Anthony J. Stone,et al.  Distributed multipole analysis, or how to describe a molecular charge distribution , 1981 .

[13]  R. Lathe.  Phd by thesis , 1988, Nature.

[14]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[15]  David E. Bernholdt,et al.  Parallel computational chemistry made easier: The development of NWChem , 1995 .

[16]  P. Jørgensen,et al.  Walking on potential energy surfaces , 1983 .

[17]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals , 1985 .

[18]  H. Schaefer,et al.  Unified theoretical treatment of analytic first and second energy derivatives in open-shell Hartree—Fock theory , 1982 .

[19]  Robert J. Buenker,et al.  A new table-direct configuration interaction method for the evaluation of Hamiltonian matrix elements in a basis of linear combinations of spin-adapted functions , 1995 .

[20]  Peter Pulay,et al.  Convergence and efficiency of the valence bond self-consistent field method , 1991 .

[21]  Robert J. Harrison,et al.  Global Arrays: a portable "shared-memory" programming model for distributed memory computers , 1994, Proceedings of Supercomputing '94.

[22]  M. Palmer,et al.  The electronic states of the azines. IV. Pyrazine, studied by VUV absorption, near-threshold electron energy-loss spectroscopy and ab initio multi-reference configuration interaction calculations , 1991 .

[23]  Rodney J. Bartlett,et al.  Multi-reference averaged quadratic coupled-cluster method: a size-extensive modification of multi-reference CI , 1993 .

[24]  B. Roos,et al.  A simple method for the evaluation of the second-order-perturbation energy from external double-excitations with a CASSCF reference wavefunction , 1982 .

[25]  J. Connolly,et al.  On first‐row diatomic molecules and local density models , 1979 .

[26]  J. V. Lenthe,et al.  ON THE EVALUATION OF NON-ORTHOGONAL MATRIX ELEMENTS , 1991 .

[27]  A. H. de Vries,et al.  Implementation of reaction field methods in quantum chemistry computer codes , 1995, J. Comput. Chem..

[28]  B. Roos,et al.  MCSCF–CI calculations of the ground state potential curves of LiH, Li2, and F2 , 1981 .

[29]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[30]  J. H. van Lenthe,et al.  The valence‐bond self‐consistent field method (VB–SCF): Theory and test calculations , 1983 .

[31]  M. F. Guest,et al.  The eletronic states of the azines. III, Pyrimidine, studied by VUV absorption, near-threshold electron energy-loss spectroscopy and ab initio multi-reference configuration calculations , 1990 .

[32]  Warren J. Hehre,et al.  Computation of electron repulsion integrals involving contracted Gaussian basis functions , 1978 .

[33]  James Demmel,et al.  ScaLAPACK: A Portable Linear Algebra Library for Distributed Memory Computers - Design Issues and Performance , 1995, PARA.

[34]  M. Guest,et al.  The molecular and electronic states of 1,2,4,5-tetrazine studied by VUV absorption, near-threshold electron energy-loss spectroscopy and ab initio multi-reference configuration interaction studies , 1997 .

[35]  W Smith,et al.  DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.

[36]  H. Bernhard Schlegel,et al.  An efficient algorithm for calculating ab initio energy gradients using s, p Cartesian Gaussians , 1982 .

[37]  J. V. Lenthe,et al.  Trends in Cyclopentadienyl - Main-Group-Metal Bonding , 2003 .

[38]  J. H. van Lenthe,et al.  The ZORA formalism applied to the Dirac-Fock equation , 1995 .

[39]  Michael J. Frisch,et al.  Achieving linear scaling in exchange-correlation density functional quadratures , 1996 .

[40]  C. W. Murray,et al.  Quadrature schemes for integrals of density functional theory , 1993 .

[41]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[42]  John R. Sabin,et al.  On some approximations in applications of Xα theory , 1979 .

[43]  Jack Dongarra,et al.  LAPACK's user's guide , 1992 .

[44]  P. M. Rodger,et al.  DL_POLY: Application to molecular simulation , 2002 .

[45]  S. Peyerimhoff,et al.  Comparison of various CI treatments for the description of potential curves for the lowest three states of O2 , 1972 .

[46]  S. C. Rogers,et al.  QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .

[47]  V. R. Saunders,et al.  On methods for converging open-shell Hartree-Fock wave-functions , 1974 .

[48]  Matt Challacombe,et al.  Linear scaling computation of the Fock matrix. V. Hierarchical Cubature for numerical integration of the exchange-correlation matrix , 2000 .

[49]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi , 1985 .

[50]  H. M. Vinkers,et al.  SYNOPSIS: SYNthesize and OPtimize System in Silico. , 2003, Journal of medicinal chemistry.

[51]  Henry F. Schaefer,et al.  On the evaluation of analytic energy derivatives for correlated wave functions , 1984 .

[52]  Evert Jan Baerends,et al.  Numerical integration for polyatomic systems , 1992 .

[53]  Alistair P. Rendell,et al.  A parallel vectorized implementation of triple excitations in CCSD(T): application to the binding energies of the AlH3, AlH2F, AlHF2 and AlF3 dimers , 1991 .

[54]  Philippe C. Hiberty,et al.  Compact valence bond functions with breathing orbitals: Application to the bond dissociation energies of F2 and FH , 1994 .

[55]  Miss A.O. Penney.  (b) , 1974, The New Yale Book of Quotations.

[56]  Krishnan Raghavachari,et al.  Gaussian-2 theory for molecular energies of first- and second-row compounds , 1991 .

[57]  M. Vincent,et al.  Computer simulation of zeolite structure and reactivity using embedded cluster methods , 1997 .

[58]  Dennis R. Salahub,et al.  Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation , 1992 .

[59]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations , 1984 .

[60]  G. te Velde,et al.  Three‐dimensional numerical integration for electronic structure calculations , 1988 .

[61]  P. Pulay.  Convergence acceleration of iterative sequences. the case of scf iteration , 1980 .

[62]  Robert J. Harrison,et al.  Shared Memory Programming in Metacomputing Environments: The Global Array Approach , 1997, The Journal of Supercomputing.

[63]  Marvin Douglas,et al.  Quantum electrodynamical corrections to the fine structure of helium , 1971 .

[64]  F. Weinhold,et al.  Natural population analysis , 1985 .

[65]  James Demmel,et al.  ScaLAPACK: A Portable Linear Algebra Library for Distributed Memory Computers - Design Issues and Performance , 1995, Proceedings of the 1996 ACM/IEEE Conference on Supercomputing.

[66]  M. Guest,et al.  The electronic states and molecular properties of 1,2,3-triazine studied by VUV absorption, near-threshold electron energy-loss spectroscopy and ab initio multi-reference configuration interaction studies , 1998 .

[67]  Ph. Durand,et al.  Regular Two-Component Pauli-Like Effective Hamiltonians in Dirac Theory , 1986 .

[68]  Julia E. Rice,et al.  The closed‐shell coupled cluster single and double excitation (CCSD) model for the description of electron correlation. A comparison with configuration interaction (CISD) results , 1987 .

[69]  Robert J. Harrison,et al.  An efficient implementation of the full-CI method using an (n–2)-electron projection space , 1989 .

[70]  Benny G. Johnson,et al.  An implementation of analytic second derivatives of the gradient‐corrected density functional energy , 1994 .

[71]  L. Curtiss,et al.  Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint , 1988 .

[72]  Per E. M. Siegbahn,et al.  Direct configuration interaction with a reference state composed of many reference configurations , 1980 .

[73]  P. Durand,et al.  A theoretical method to determine atomic pseudopotentials for electronic structure calculations of molecules and solids , 1975 .

[74]  M. Guest,et al.  The electronic states of furan studied by VUV absorption, near-threshold electron energy-loss spectroscopy and ab initio multi-reference configuration interaction calculations , 1995 .

[75]  Evert Jan Baerends,et al.  Relativistic regular two‐component Hamiltonians , 1993 .

[76]  Friedrich Biegler-König,et al.  Calculation of the average properties of atoms in molecules. II , 1982 .

[77]  Robert J. Harrison,et al.  Global arrays: A nonuniform memory access programming model for high-performance computers , 1996, The Journal of Supercomputing.

[78]  Sujata Sharma,et al.  Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis , 2000, Nature Structural Biology.

[79]  Roger D. Amos,et al.  Geometric derivatives of excitation energies using SCF and DFT , 1999 .

[80]  S. Hoffmann,et al.  The electronic states of isoxazole studied by VUV absorption, electron energy-loss spectroscopies and ab initio multi-reference configuration interaction calculations , 2004 .

[81]  A. Becke.  A multicenter numerical integration scheme for polyatomic molecules , 1988 .

[82]  I. C. Walker,et al.  The electronic states of the azines. II. Pyridine, studied by VUV absorption, near-threshold electron energy loss spectroscopy and ab initio multi-reference configuration interaction calculations , 1990 .

[83]  Robert J. Gdanitz,et al.  The averaged coupled-pair functional (ACPF): A size-extensive modification of MR CI(SD) , 1988 .

[84]  F. L. Hirshfeld.  Bonded-atom fragments for describing molecular charge densities , 1977 .

[85]  J. H. van Lenthe,et al.  Magnetic properties and aromaticity of o-, m-, and p-benzyne. , 2002, Chemistry.

[86]  Michael Hanrath,et al.  New algorithms for an individually selecting MR-CI program , 1997 .

[87]  Alistair P. Rendell,et al.  Comparison of the quadratic configuration interaction and coupled cluster approaches to electron correlation including the effect of triple excitations , 1990 .

[88]  Michel Dupuis,et al.  Molecular symmetry. II. Gradient of electronic energy with respect to nuclear coordinates , 1978 .

[89]  P. Pulay.  Improved SCF convergence acceleration , 1982 .

[90]  W. Lipscomb,et al.  Perturbed Hartree—Fock Calculations. I. Magnetic Susceptibility and Shielding in the LiH Molecule , 1963 .

[91]  P. Knowles,et al.  An efficient second-order MC SCF method for long configuration expansions , 1985 .

[92]  Graham D. Fletcher,et al.  A parallel second-order Møller-Plesset gradient , 1997 .

[93]  Bernard R. Brooks,et al.  ENZYME MECHANISMS WITH HYBRID QUANTUM AND MOLECULAR MECHANICAL POTENTIALS.I. THEORETICAL CONSIDERATIONS , 1996 .

[94]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[95]  Peter J. Knowles,et al.  Improved radial grids for quadrature in molecular density‐functional calculations , 1996 .

[96]  Michel Dupuis,et al.  Evaluation of molecular integrals over Gaussian basis functions , 1976 .

[97]  S. Mahulikar,et al.  Physica Scripta , 2004 .

[98]  N. Nekrasov.  In the woods of M theory , 1998, hep-th/9810168.

[99]  W. Miller,et al.  ON FINDING TRANSITION STATES , 1981 .

[100]  David E. Bernholdt,et al.  High performance computational chemistry: An overview of NWChem a distributed parallel application , 2000 .

[101]  Peter J. Knowles,et al.  Studies using the CASSCF wavefunction , 1982 .

[102]  J. Baker.  An algorithm for the location of transition states , 1986 .

[103]  P. Sherwood,et al.  Identification and Characterization of Active Sites and Their Catalytic Processes—the Cu/ZnO Methanol Catalyst , 2003 .

[104]  P. Jørgensen,et al.  A multiconfigurational time-dependent hartree-fock approach , 1979 .

[105]  Bernard R. Brooks,et al.  Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase , 2003 .

[106]  James S. Crighton,et al.  Locating transition states , 1984 .

[107]  M. Guest,et al.  Assignment of the electronic states of pyrazole by ab initio multi-reference configuration interaction calculations , 2003 .

[108]  J. Koutecký,et al.  Compact formulation of multiconfigurational response theory. Applications to small alkali metal clusters , 1993 .

[109]  J. G. Snijders,et al.  An ab initio two-component relativistic method including spin- orbit coupling using the regular approximation , 2000 .

[110]  R. Fletcher.  Practical Methods of Optimization , 1988 .

[111]  A. H. Vries,et al.  Direct reaction field force field: A consistent way to connect and combine quantum-chemical and classical descriptions of molecules , 1996 .

[112]  Per E. M. Siegbahn,et al.  Generalizations of the direct CI method based on the graphical unitary group approach. II. Single and double replacements from any set of reference configurations , 1980 .

[113]  J. V. Ortiz.  One‐electron density matrices and energy gradients in the random phase approximation , 1994 .

[114]  R. Naaman,et al.  The structure of small molecules and ions , 1988 .