Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

[1]  Wilfried Meyer,et al.  Ionization energies of water from PNO‐CI calculations , 2009 .

[2]  Jon Baker,et al.  Parallel DFT gradients using the Fourier Transform Coulomb method , 2007, J. Comput. Chem..

[3]  Peter Pulay,et al.  Parallel Calculation of Coupled Cluster Singles and Doubles Wave Functions Using Array Files. , 2007, Journal of chemical theory and computation.

[4]  Tomasz Janowski,et al.  Array files for computational chemistry: MP2 energies , 2007, J. Comput. Chem..

[5]  Yihan Shao,et al.  Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations. , 2006, The Journal of chemical physics.

[6]  K. Hirao,et al.  A dual-level approach to density-functional theory. , 2006, Journal of Chemical Physics.

[7]  Shawn T. Brown,et al.  Efficient computation of the exchange-correlation contribution in the density functional theory through multiresolution. , 2006, The Journal of chemical physics.

[8]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[9]  Parallel implementation of Hartree–Fock and density functional theory analytical second derivatives , 2004 .

[10]  Jon Baker,et al.  An efficient atomic orbital based second-order Møller-Plesset gradient program. , 2004, The Journal of chemical physics.

[11]  Martin Head-Gordon,et al.  Approaching the Basis Set Limit in Density Functional Theory Calculations Using Dual Basis Sets without Diagonalization , 2004 .

[12]  Jon Baker,et al.  Parallel Density Functional Theory Energies using the Fourier Transform Coulomb Method , 2004 .

[13]  M. Malagoli,et al.  The effect of grid quality and weight derivatives in density functional calculations of harmonic vibrational frequencies , 2003 .

[14]  Laszlo Fusti-Molnar,et al.  New developments in the Fourier transform Coulomb method: Efficient and accurate localization of the filtered core functions and implementation of the Coulomb energy forces , 2003 .

[15]  Peter Pulay,et al.  Second-order Møller–Plesset calculations with dual basis sets , 2003 .

[16]  Jon Baker,et al.  Parallel stored‐integral and semidirect Hartree–Fock and DFT methods with data compression , 2003, J. Comput. Chem..

[17]  Peter Pulay,et al.  The Fourier transform Coulomb method: Efficient and accurate calculation of the Coulomb operator in a Gaussian basis , 2002 .

[18]  Jon Baker,et al.  An efficient parallel algorithm for the calculation of canonical MP2 energies , 2002, J. Comput. Chem..

[19]  Jon Baker,et al.  Assessment of the Handy–Cohen optimized exchange density functional for organic reactions , 2002 .

[20]  Frank Jensen,et al.  Polarization consistent basis sets: Principles , 2001 .

[21]  Peter Pulay,et al.  Efficient calculation of canonical MP2 energies , 2001 .

[22]  N. Handy,et al.  Left-right correlation energy , 2001 .

[23]  Jon Baker,et al.  Ab initio quantum chemistry on PC-based parallel supercomputers , 2000, Parallel Comput..

[24]  Donald G. Truhlar,et al.  Adiabatic connection for kinetics , 2000 .

[25]  Matthias Krack,et al.  All-electron ab-initio molecular dynamics , 2000 .

[26]  Michele Parrinello,et al.  The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations , 1999 .

[27]  K. Hirao,et al.  Different bases for different correlation effects: multireference Møller–Plesset perturbation theory in the extended basis function space , 1999 .

[28]  Michael J. Frisch,et al.  Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: II , 1998, J. Comput. Chem..

[29]  Jon Baker,et al.  Molecular energies and properties from density functional theory: Exploring basis set dependence of Kohn—Sham equation using several density functionals , 1997 .

[30]  Peter Pulay,et al.  Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation, multi‐Fock algorithm, and pseudodiagonalization , 1997 .

[31]  Anthony Skjellum,et al.  A High-Performance, Portable Implementation of the MPI Message Passing Interface Standard , 1996, Parallel Comput..

[32]  Eric Schwegler,et al.  Linear scaling computation of the Hartree–Fock exchange matrix , 1996 .

[33]  Marco Häser,et al.  Auxiliary basis sets to approximate Coulomb potentials , 1995 .

[34]  Jack Dongarra,et al.  PVM: Parallel virtual machine: a users' guide and tutorial for networked parallel computing , 1995 .

[35]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[36]  Benny G. Johnson,et al.  The performance of a family of density functional methods , 1993 .

[37]  P Pulay,et al.  Local Treatment of Electron Correlation , 1993 .

[38]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[39]  Hans W. Horn,et al.  Fully optimized contracted Gaussian basis sets for atoms Li to Kr , 1992 .

[40]  Wang,et al.  Accurate and simple analytic representation of the electron-gas correlation energy. , 1992, Physical review. B, Condensed matter.

[41]  M. Frisch,et al.  Computational Bottlenecks in Molecular Orbital Calculations , 1991 .

[42]  Peter Pulay,et al.  Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations , 1990 .

[43]  Dunlap.  Three-center Gaussian-type-orbital integral evaluation using solid spherical harmonics. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[44]  R. Cramer,et al.  Validation of the general purpose tripos 5.2 force field , 1989 .

[45]  Peter Pulay,et al.  The unrestricted natural orbital–complete active space (UNO–CAS) method: An inexpensive alternative to the complete active space–self‐consistent‐field (CAS–SCF) method , 1989 .

[46]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[47]  Svein Saebo,et al.  Avoiding the integral storage bottleneck in LCAO calculations of electron correlation , 1989 .

[48]  Marco Häser,et al.  Improvements on the direct SCF method , 1989 .

[49]  P. Knowles,et al.  An efficient internally contracted multiconfiguration–reference configuration interaction method , 1988 .

[50]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

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

[52]  Peter Pulay,et al.  The local correlation treatment. II. Implementation and tests , 1988 .

[53]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[54]  P. Knowles,et al.  A second order multiconfiguration SCF procedure with optimum convergence , 1985 .

[55]  Peter Pulay,et al.  An efficient reformulation of the closed‐shell self‐consistent electron pair theory , 1984 .

[56]  Henry F. Schaefer,et al.  Analytic second derivative techniques for self-consistent-field wave functions. A new approach to the solution of the coupled perturbed hartree-fock equations , 1983 .

[57]  Peter Pulay,et al.  Second and third derivatives of variational energy expressions: Application to multiconfigurational self‐consistent field wave functions , 1983 .

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

[59]  J. Almlöf,et al.  Principles for a direct SCF approach to LICAO–MOab‐initio calculations , 1982 .

[60]  James J. P. Stewart,et al.  Fast semiempirical calculations , 1982 .

[61]  Hans-Joachim Werner,et al.  The self‐consistent electron pairs method for multiconfiguration reference state functions , 1982 .

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

[63]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[64]  Peter Pulay,et al.  Systematic AB Initio Gradient Calculation of Molecular Geometries, Force Constants, and Dipole Moment Derivatives , 1979 .

[65]  Wilfried Meyer,et al.  Theory of self‐consistent electron pairs. An iterative method for correlated many‐electron wavefunctions , 1976 .

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

[67]  P. C. Hariharan,et al.  The influence of polarization functions on molecular orbital hydrogenation energies , 1973 .

[68]  M. Yoshimine,et al.  Construction of the hamiltonian matrix in large configuration interaction calculations , 1973 .

[69]  D. C. Barker,et al.  The calculation of potential gradients in a moving normal region within a superconducting thin film , 1973 .

[70]  Peter Pulay,et al.  Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules , 1969 .

[71]  Walter Kohn,et al.  Analytic Properties of Bloch Waves and Wannier Functions , 1959 .