Alistair Rendell: Publications

    Under Review

  1. W. Armstrong and A.P. Rendell, "Reinforcement Learning for Automated Performance Tuning: Initial Evaluation for Sparse Matrix Format Selection", The Third international Workshop on Automatic Performance Tuning (IWAPT08), (submitted).

    2008

  2. Alistair P Rendell, Joseph Antony, Warren Armstrong, Pete Janes and Rui Yang, "Building Fast, Reliable and Adaptive Software for Computational Science", SciDAC 2008 (In Press)
  3. E.C. McCreath, A. El Zein, J. Imholz, A.P. Rendell and E. Wong, "Using the Cell Broadband Engine and NVIDIA 8800 GPU for Computational Science Applications: A Particle Dynamics Comparison", International Symposium on Applied Computing and Computational Science (ACCS 2008) (Accepted June 08).
  4. J.Cai, A.P. Rendell, P. Strazdins, H.J. Wong, "Performance Models for Cluster-Enabled OpenMP Implementations", 13th IEEE Asia-Pacific Computer Systems Architecture Conference (accepted, May 08).
  5. P.P. Janes and A.P. Rendell, "Including Rigorous Numerical Bounds in Quantum Chemistry Calculations: Gaussian Integral Evaluation", 2008 IEEE 11th International Conference on Computational Science and Engineering (accepted, Apr 08).
  6. A. El Zein, E. McCreath, A.P. Rendell and A. Smola, "Performance Evaluation of the NVIDIA GeForce 8800 GTX GPU for Machine Learning", 2008 Int. Conf. Computational Science (accepted, Feb 08).
  7. H.J. Wong, J. Cai, A.P. Rendell and P. Strazdins,"Micro-Benchmarks for Cluster OpenMP Implementations: Memory Consistency Costs", 2008 International Workshop on OpenMP, LNCS 60-70, 5004 (2008).
  8. R. Yang, J. Antony, P. P. Janes and A. P. Rendell, "Memory and Thread Placement Effects as a Function of Cache Usage: A Study of the Gaussian Chemistry Code on the SunFire X4600 M2", International Symposium on Parallel Architectures, Algorithms, and Networks, 31-36, 2008 {http://doi.ieeecomputersociety.org/10.1109/I-SPAN.2008.13}
  9. J. Antony, M.J. Frisch and A.P. Rendell, "Modelling the Performance of the Gaussian Computational Chemistry Code on x86 Architectures". In Modeling, Simulation and Optimization of Complex Processes, Proceedings of the Third International Conference on High Performance Scientific Computing, March 6-10, 2006 Hanoi, Vietnam. Eds H.G. Bock, E. Kostina, H.X Phu and R. Rannacher, Springer-Verlag Berlin Heidelberg, 2008. ISBN 978-3-540-79408-0. Pages 49-58. PDF

    2007

  10. H'sien J. Wong and A.P. Rendell, "The design of MPI Based Distributed Shared Memory Systems to Support OpenMP on Clusters" Cluster07, IEEE Catalog Number 07EX1855C, 231-240, (2007)
  11. A.P. Rendell, B. Clarke, P. Janes, J. Milthorpe, and R. Yang, "Interval Arithmetic and Computational Science: Rounding and Truncation Errors in N-Body Methods", International Conference on Computational Science and its Applications (ICCSA), IEEE Conference Proceedings (DOI 10.1109/ICCSA.2007.49), 457-466 (2007).
  12. R. Yang, A.P. Rendell, M.J. Frisch, "On the use of Incomplete LU Decomposition as a Preconditioning Technique for Density Fitting in Electronic Structure Computations", International Conference on Computational Science and its Applications, LNCS 4705, 265-280 (2007).
  13. R. Yang, A.P. Rendell and M.J. Frisch, "Automatically generated coulomb-fitting basis sets: Design and accuracy for systems containing H to Kr", Journal of Chemical Physics, 127, 074102-074102-14 (2007).
  14. R. Yang and A.P. Rendell, "Ga Cleaning of Al2O3 Substrate: Low Coverage Adsorption of Ga on a Hydrogen Contaminated alpha-Al2O3(0001) Surface", J. Phys. Chem C, 3384-3392, 111 (2007).

    2006

  15. W. Armstrong, P. Christen, E. McCreath, A.P. Rendell, "Dynamic Algorithm Selection Using Reinforcement Learning", Proceedings of the International Workshop on Integrating AI and Data Mining (AIDM 2006), 18-24, IEEE Publications (ISBN 0-7695-2730-2, Digital Object Identifier: 10.1109/AIDM.2006.9) 2006.
  16. J. Antony, P.P. Janes and A.P. Rendell, "Exploring Thread and Memory Placement on NUMA Architectures: Solaris and Linux, UltraSPARC/FirePlane and Opteron/HyperTransport", 13th IEEE International Conference on High Performance Computing, Lecture Notes in Computer Science, 338-352, 4297 (2006).
  17. R. Yang and A.P. Rendell, "First Principles Study of Gallium Atoms adsorption on the alpha-Al2O3(0001) Surface", J. Phys. Chem B, 9608-9618, 110 (2006).
  18. A.P. Rendell "A Project Based Approach to Teaching Parallel Systems", 2006 International Conference on Computational Science, Lecture Notes in Computer Science 155-160, 3992 (2006).
  19. A.P. Rendell, B. Clarke and J. Milthorpe, "Interval Arithmetic and Computational Science: Performance Considerations", 2006 International Conference on Computational Science, Lecture Notes in Computer Science 218-225, 3991 (2006)

    2005

  20. J. Milthorpe and A.P. Rendell, "Learning to Live with Errors: A Fresh Look at Floating-Point Computation", Proceedings of the Third Australian Undergraduate Computing Conference, 34-41, Canberra 2005 (ISBN 0-9757173-1-6)
  21. J. Roper and A.P. Rendell, "Introducing Design Patterns, Graphical User Interfaces and Threads within the Context of a High Performance Computing Application", Lecture Notes in Computer Science, Springer Verlag, Springer Verlag, 3515, 18 (2005)
  22. H.J Wong and A.P. Rendell, "The SCore Cluster Enabled OpenMP Environment: Performance Prospects for Computational Science" Lecture Notes in Computer Science, Springer Verlag, Springer Verlag, 3514, 1067 (2005)
  23. H.J. Wong and A.P. Rendell, "Optimizing Performance for SCore Cluster Enabled OpenMP Applications: Solving the Laplace Equation and Performing Fourier Transform", Proceedings of The 4th International Workshop on OpenMP: Experiences and Implementations, Tsukuba, Japan, Jan 20-21, 2005.

    2004

  24. D. Tsifakis, A.P. Rendell, P.E. Strazdins, "Cache Oblivious Matrix Transposition: Simulation and Experiment", 4th International Conference on Computational Science, Lecture Notes in Computer Science, Springer Verlag, 3037, 17-25 (2004)
  25. A. Bliznyuk and A.P. Rendell, "Electronic Effects in Biomolecular SImulations: Investigation of the KcsA Potassium Ion Channel", J. Phys. Chem. B. 13866-13873, v108, 2004

    2003

  26. N. Robertson and A.P. Rendell, "OpenMP and NUMA Architectures I: Investigating Memory Placement on the SGI Origin 3000", 3rd International Conference on Computational Science, Lecture Notes in Computer Science, Springer Verlag, 2660, 648-656 (2003)
  27. J.R. Reimers, W.A. Shapley, A.P. Rendell and N.S. Hush, "Modelling the bacterial photsynthetic reaction centre 6. Use of density functional theory to determine the nature of vibronic coupling between the four lowest energy electronic states of the special pair radical cation", J. Chem. Phys. 119, 3249-3261 (2003)
  28. R.M. Olson, M.W. Schmidt, M.S. Gordon and A.P. Rendell, "Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model", Proceedings of SC03, 2003.

    2002

  29. P.L. Cummins, S.P. Greatbanks, A.P Rendell and J.E. Gready ''Computational methods for the study of enzymic reaction mechanisms. 1. Application to the hydride transfer step in the catalysis of dihydrofolate reductase'', J Phys Chem B 106, 9934-9944 (2002)
  30. S.J.Titmuss, P.L. Cummins, A.P. Rendell, A.A. Bliznyuk and J.E. Gready, ''Comparison of Linear-Scaling Semiempirical Methods and Combined Quantum Mechanical/Molecular Mechanical Methods for Enzymic Reactions II: An Energy Decomposition Analysis'', J. Comp. Chem., b23, 1314-1322, (2002).
  31. P.L. Cummins, S.J. Titmuss, D. Jayatilaka, A.A. Bliznyuk, A.P. Rendell and J.E. Gready ''Comparison of Semiempirical and ab initio Quantum Mechanical Decomposition Analyses for the Interaction Energy between Molecules'' Chem. Phys. Letts. v352, 245-251 (2002).

    2001

  32. A.A. Bliznyuk, A.P. Rendell, T.W. Allen, and S-H. Chung, ''The Potassium Ion Channell: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential'', J. Phys. Chem. B, v105, 12673-12679 (2001).

    2000

  33. S.R. Gadre, K. Babu, and A.P. Rendell, ``Electrostatics for Exploring Hydration Patterns of Molecules:3. Uracil'', J. Phys. Chem A, v104, 8976-8982 (2000).
  34. S.J. Titmuss, P.L. Cummins, J.E. Gready, A.A. Bliznyuk, and A.P. Rendell, ``Comparison of Linear Scaling Semiempirical Methods and Combined Quantum Mechanical/Molecular Mechanical Methods Applied to Enzyme Reactions'', Chem. Phys. Lett., v320, 169-176 (2000).
  35. S.P. Greatbanks, J.E. Gready, A.C. Limaye and A.P. Rendell, ``Comparison of Enzyme Polarization of Ligands and Charge- Transfer Effects for Dihydrofolate Reductase using Point- Charge Embedded ab initio QM and Linear-Scaling Semiempirical QM Methods'', J. Comp. Chem. v21, 788-811 (2000).
  36. T.W. Allen, A. Bliznyuk, A.P. Rendell, S. Kuyucak, S.-H. Chung ``The Potassium Channel: Structure, selectivity and diffusion'' J. Chem. Phys. v112, 8191-8204 (2000).
  37. A.P. Rendell A. Bliznyuk, T. Huber, R.H. Nobes, E.V. Akhmatskaya, H.A. Freuchtl, P.W.-C. Kung, V. Milman, H. Lung, ``Computational Chemistry on Fujitsu Vector-Parallel Processors: Development and Performance of Applications Software'', Parallel Computing, v26, 887-911 (2000).
  38. R.N. Nobes, A.P Rendell and J. Nieplocha, ``Computational Chemistry on Fujitsu Vector-Parallel Processors: Hardware and Programming environment'', Parallel Computing, v26, 869-886 (2000).

    1984-99

  39. S.P. Greatbanks, J.E. Gready, A.C. Limaye and A.P. Rendell, ``Enzyme Polarization of Substrates and Cofactor of Dihydrofolate Reductase by Different Theoretical Methods'', Proteins v37, 157-165 (1999)
  40. A.A. Bliznyuk and A.P. Rendell, ``Faster Semiempirical Gradients'', J. Comp. Chem. v20, 629-635 (1999)
  41. S.R. Gadre, S.S. Pundlik, A.C. Limaye and A.P. Rendell, ``Electrostatic Investigation of Metal Cation binding to DNA Bases and Base Pairs'', Chemical Communications, 573 (1998)
  42. G.D. Fletcher, A.P. Rendell and P. Sherwood, ``A parallel second-order Moller-Plesset gradient'', Molecular Physics, V91, 431 (1997).
  43. R. Kobayashi and A.P. Rendell, ``A direct coupled cluster algorithm for massively parallel computers'', Chem. Phys. Lett. 265, 1 (1997)
  44. A.T. Wong, R.J. Harrison and A.P. Rendell, ``Parallel Direct Four-Index Transformations'', Theoret. Chim. Acta.'' Theor Chim Acta 93, 317 (1996).
  45. T.J. Lee, M. Head-Gordon, and A.P. Rendell, ``Investigation of a Diagonostic for Perturbation Theory. Comparison of the T1 Diagnostic of Coupled-Cluster Theory'', Chem. Phys. Lett. 243, 402 (1995).
  46. T.J. Lee, S.C. Racine, J.E. Rice and A.P. Rendell, ``On the Orbital Contribution to Analytical Derivatives of Perturbation Theory Energies'', Mole. Phys. 85, 561 (1995).
  47. A.P. Rendell, ``Diagonalisation Free SCF'', Chem. Phys. Lett. 229, 204 (1994).
  48. A.P. Rendell and T.J. Lee, ``Coupled-Cluster Theory Employing Approximate Integrals: An Approach to Avoid the Input/Output and Storage Bottlenecks'', J. Chem. Phys., 101, 400 (1994).
  49. T.J. Lee, A.P. Rendell, K.G. Dyall and D. Jayatilaka, ``Open-Shell Restricted Hartree-Fock Perturbation Theory: Some Considerations and Comparisons'', J. Chem. Phys., 100, 7400 (1994).
  50. J.S. Francisco, S.P. Sander, T.J. Lee and A.P. Rendell, ``Structures, Relative Stabilities and Spectra of Isomers of HClO2'', J. Phys. Chem., 98, 5644 (1994)
  51. T.J. Lee and A.P. Rendell, ``Ab initio characterization of ClOOH; Implications for atmospheric chemistry'', J. Phys. Chem., 97 6999, (1993).
  52. A. P. Rendell, M.F. Guest and R. A. Kendall, ``A distributed data parallel coupled-cluster algorithm: investigation of the 2-hydroxypyridine/2(1h)-pyridinone tautomerism'' J. Comput. Chem., 14, 1429 (1993).
  53. A. P. Rendell, T.J. Lee, A. Komornicki and S. Wilson, ``Evaluation of the Contributions from Triply Excited Intermediates to the Fourth-Order Perturbation Theory Energy on Intel Distributed Memory Supercomputers'' Theoret. Chim. Acta., 84, 271 (1993).
  54. A. P. Rendell, T.J. Lee and R. Lindh, ``Quantum Chemistry on Parallel Computer Architectures: Coupled-Cluster Theory Applied to the Bending Potential of Fulminic Acid'' Chem. Phys. Letters, 194, 84 (1992).
  55. D. M. Hirst M.F. Guest and A.P. Rendell, ``Ab initio potential-energy curves for molecular ions NeH+ and ArH+'', Mole. Phys., 77, 279 (1992).
  56. P.-A. Malmqvist, B.O. Roos, M. Fulscher and A.P. Rendell, ``An Ab initio Quantum Chemical Study of Vertical Excited Singlet States of Pyrimidine'', Chem. Phys., 162, 359 (1992).
  57. T. J. Lee, A. P. Rendell and P. R. Taylor, ``The Structures, Binding Energies and Vibrational Frequencies of Ca3 and Ca4 --- an Application of the CCSD(T) Method'' Theoret. Chim. Acta., 83, 165 (1992).
  58. M.R.A. Blomberg, P.E.M. Siegbahn, T.J. Lee, A.P. Rendell and J.E. Rice, ``Binding Energies and Bond Distances of Ni(CO)x, x=1-4: an Application of Coupled-Cluster Theory'' J. Chem. Phys., 95, 5898 (1991).
  59. T.J. Lee and A.P. Rendell, ``The structure and energetics of the HCN-HNC transition state'' Chem. Phys. Letters, 177, 491 (1991).
  60. A.P. Rendell, T.J. Lee and A. Komornicki, ``A parallel vectorized implementation of triple excitations in CCSD(T): Application to the binding energies of the AlH3, AlH2F, AlHF2 and AlF3 dimers'' Chem. Phys. Letters, 178, 462 (1991).
  61. T.J. Lee and A.P. Rendell, ``Analytic gradients for coupled-cluster energies that include non-iterative connected triple excitations: application to cis- and trans-HONO'' J. Chem. Phys., 94, 6229 (1991).
  62. A.P. Rendell and T.J. Lee, ``An efficient formulation and implementation of the analytic energy gradient method to the single and double excitation coupled-cluster wave function: application to Cl2O2'' J. Chem. Phys., 94, 6219 (1991).
  63. J.D. Watts, I. Cernusak, J. Noga, R.J. Bartlett, C.W. Bauschlicher, T.J. Lee, A.P. Rendell and P.R. Taylor, ``Triple and quadruple excitation contributions to the bonding in Be clusters: calibration calculations on Be3'' J. Chem. Phys., 93, 8875 (1990).
  64. T.J. Lee, A.P. Rendell and P.R. Taylor, ``Vibrations in small Mg clusters'', J. Chem. Phys., 93, 6636 (1990).
  65. A.P. Rendell, T.J. Lee and P.R. Taylor, ``Vibrational frequencies for Be3 and Be4'', J. Chem. Phys., 92, 7050 (1990).
  66. P.-A. Malmqvist, A.P. Rendell, and B.O. Roos, ``The restricted active space (RAS)SCF method, implementation with a split graph unitary group approach'', J. Phys. Chem., 94, 5477 (1990).
  67. T.J. Lee, A.P. Rendell and P.R. Taylor, ``Comparison of the quadratic configuration interaction and coupled-cluster approaches to electron correlation including the effect of triple excitations'', J. Phys. Chem., 94, 5463 (1990).
  68. S.R. Langhoff, C.W. Bauschlicher, A.P. Rendell, and A. Komornicki, ``Theoretical study of the radiative lifetime of the A1Piu state of C2'', J. Chem. Phys., 92, 3000 (1990).
  69. T.J. Lee, A.P. Rendell and P.R. Taylor, ``Theoretical investigations of the structures and binding energies of Ben and Mgn (n=3-5) clusters'', J. Chem. Phys., 92, 489 (1990).
  70. A.P. Rendell, C.W. Bauschlicher and S.R. Langhoff, ``A theoretical determination of the radiative lifetimes of the A2Sigma+ and B2Delta states of CF'', Chem. Phys. Letters, 163, 354 (1989).
  71. S.R. Langhoff, C.W. Bauschlicher and A.P. Rendell, ``The spectroscopy of MnH'', J. Mol. Spectroc., 138, 108 (1989).
  72. G.B. Bacskay, A.P.L. Rendell and N.S. Hush, ``Ab initio quantum chemical study of the molecular and spectroscopic (infrared and Raman) properties of sulfur dioxide: Comparison with ozone'', J. Chem. Phys., 89, 5721 (1988).
  73. A.P.L. Rendell, G.B. Bacskay and N.S. Hush, ``Electron transfer via dithiaspiroalkane linkages. Nature of long-range through-space electronic coupling in disulfoxide radical cations and bis(metal) complexes and implications for the characterization of the SO bond'', J. Am. Chem. Soc., 110, 8343 (1988).
  74. A.P.L. Rendell, G.B. Bacskay, N.S. Hush and N.C. Handy, ``The analytic configuration interaction gradient method: The calculation of one electron properties'', J. Chem. Phys., 87, 5976 (1987).
  75. A.P.L. Rendell, G.B. Bacskay and N.S. Hush, ``An ab initio quantum chemical study of the hydrogen- and `anti-' hydrogen-bonded HF/ClF and HF/Cl2 dimers'', J. Chem. Phys., 87, 535 (1987).
  76. P.L. Cummins, A.P.L. Rendell, D.J. Swanton, G.B. Bacskay and N.S. Hush, ``The role of electrostatics in molecular interactions: Prediction of shapes and electronic properties of weakly bound complexes'', Int. Rev. Phys. Chem., 5, 139 (1986).
  77. A.P.L. Rendell, G.B. Bacskay and N.S. Hush, ``The validity of electrostatic predictions of the shapes of Van der Waals dimers'', Chem. Phys. Letters, 117, 400 (1985).