SeqQuest Bibliography

There have been three generations of codes implementing the method as of this date, and the publications in the following are segregated by which code was employed in the application.

Feibelman’s original slab code

The basic idea of the method used by the codes was originally articulated by Peter J. Feibelman (Sandia) and expressed in a computer code he wrote for slab geometries whose output served as an input to a scattering theory code to study defects and adsorbed atoms or molecules on metal surfaces. The papers below are those specific to that slab code. For applications of the scattering theory method that used output from this code as input, see Feibelman’s publication list.

  • “Efficient Solution of Poisson’s Equation in Linear Combination of Atomic Orbitals (LCAO) Electronic Structure Calculations”
    P.J. Feibelman, J. Chem. Phys. 81, 5864 (1984).
  • “Efficient Solution of Poisson’s Equation in Linear Combination of Atomic Orbitals (LCAO) Calculations of Crystal Electronic Structure”
    P.J. Feibelman, Phys. Rev. B 33, 719 (1986).
  • “Local Orbital Basis for Defect Electronic Structure Calculations of an Al(100) Film”
    P.J. Feibelman, Phys. Rev. B 38, 1849 (1988).
  • “Pulay-type Formula for Surface Stress in a Local Density Functional, Linear Combination of Atomic Orbital Electronic Structure Calculation”
    P.J. Feibelman, Phys. Rev. B 44, 3916 (1991).
  • “Efficient Brillouin-Zone Averaging in Surface Force Calculations”
    P.J. Feibelman, Phys. Rev. B 45, 3842 (1992).
  • “Calculation of Surface Stress in a Linear Combination of Atomic Orbitals Representation”
    P.J. Feibelman, Phys. Rev. B 50, 1908 (1994).
  • “Anisotropy of the Stress on fcc(110) Surfaces”
    P.J. Feibelman, Phys. Rev. B 51, 17867 (1995).

MPQuest applications

In the early 1990’s, Mark P. Sears (eventually assisted by PAS) at Sandia wrote a new, massively parallel code, ultimately named MPQUEST, to enable large-scale DFT calculations. This code was designed to be a fully capable stand-alone production code for general purpose (not just slabs!) applications.

  • “Basis-set convergence of highly defected sites in amorphous carbon”
    J.S. Nelson, E.B. Stechel, A.F. Wright, S.J. Plimpton, P.A. Schultz and M.P. Sears, Phys. Rev. B 52, 9354 (1995).
  • “Energetics of Steps on Pt(111)”
    P.J. Feibelman, Phys. Rev. B 52, 16845 (1995).
  • “O Binding Sites on Stepped Pt(111) Surfaces”
    P.J. Feibelman, Stefanie Esch, and Thomas Michely, Phys. Rev. Lett. 77, 2257 (1996).
  • “Ab initio ammonia and CO lateral interactions on Pt(111)”
    D.R. Jennison, P.A. Schultz, and M.P. Sears, Phys. Rev. Lett. 77, 4828 (1996).
  • “First-principles calculations of stress induced by gas adsorption on Pt(111)”
    P.J. Feibelman, Phys. Rev. B 56, 2175 (1997).
  • “d-electron ‘frustration’ and the large fcc vs. hcp binding preference in O adsorption on Pt(111)”
    P.J. Feibelman, Phys. Rev. B 56, 10537 (1997).
  • “Ab initio calculations of Ru, Pd, and Ag cluster with 55, 135, and 140 atoms”
    D.R. Jennison, P.A Schultz, M.P. Sears, J. Chem. Phys. 106, 1856 (1997).
  • “DIET in the bulk: evidence for hot electron cleavage of Si-H bonds in SiO2 films”
    D.R. Jennison, J.P. Sullivan, P.A. Schultz, M.P. Sears, and E.B. Stechel, Surf. Sci. 390, 112 (1997).
  • “All-atom ab initio energy minimization of the kaolinite structure”
    J.D. Hobbs, R.T. Cygan, K.L. Nagy, P.A. Schultz, and M.P Sears, Amer. Mineralogist 82, 657-662 (1997).
  • “Ordered phases of potassium on Pt(111): Experiment and theory”
    S. Moré, W. Berndt, A.M. Bradshaw, and R. Stumpf, Phys. Rev. B 57, 9246 (1998).
  • “Effects of basis set quality on the prediction of structures, energies, and properties of amorphous tetrahedral carbon”
    P.A. Schultz and E.B. Stechel, Phys. Rev. B 57, 3295 (1998).
  • “Unusual structural relaxation for rare-earth impurities in sapphire: ab initio study of lanthanum”
    C. Verdozzi, D.R. Jennison, P.A. Schultz, M.P. Sears, J.C. Barbour, and B.G. Potter, Phys. Rev. Lett. 80, 5615 (1998).
  • “Molecular orientation with visible light: reflectance-anisotropy spectroscopy of 3-thiophene carboxylate on Cu(110) surfaces”
    B.G. Frederick, R.J. Cole, J.R. Power, C.C. Perry, Q. Chen, N.V. Richardson, P. Weightman, C. Verdozzi, D.R. Jennison, P.A. Schultz, and M.P. Sears, Phys. Rev. B 58, 10883 (1998).
  • “Valence and atomic size dependent exchange barriers in vacancy-mediated dopant diffusion”
    J.S. Nelson, P.A. Schultz, and A.F. Wright, Appl. Phys. Lett. 73, 247 (1998).
  • “The saphhire(0001) surface, clean and with d-metal overlayers”
    C. Verdozzi, D.R. Jennison, P.A. Schultz, and M.P. Sears, Phys. Rev. Lett. 82, 799 (1999).
  • “Structural and adsorption properties of ultrathin Al2O3 films”
    D.R. Jennison, C. Verdozzi, P.A. Schultz, M.P. Sears, Phys. Rev. B 59, 15605 (1999).
  • “Oxygen induced restructuring of the TiO2(110) surface: A comprehensive study”
    M. Li, W. Hebenstreit, U. Diebold, M.A. Henderson, D.R. Jennison, P.A. Schultz, and M.P. Sears, Surf. Sci. 437, 173-190 (1999).

Applications of the current production code SeqQuest

In the late 1990’s, performance issues prompted reexamining and reformulating the method in detail. New more efficient serial algorithms were designed and tuned, and a highly optimized serial code developed to implement those algorithms. The vastly improved computational efficiency of the new serial code, along with greatly expanded functionality, prompted a new line of development that has evolved into the current (not-yet-“massively”) parallel code. This generation now serves as the production version of the method.

  • “Generating structural models of amorphous tetrahedral carbon: basis set dependencies”
    P.A. Schultz and E.B. Stechel, in “Covalently Bonded Disordered Thin-Film Materials”, edited by M.P. Siegal, W.I. Milne, and J.E. Jaske, MRS Symposia Proc. 498, 11 (1998).
  • “Small rings and amorphous tetrahedral carbon”
    P.A. Schultz, K. Leung, and E.B. Stechel, Phys. Rev. B 59, 733 (1999).
  • “Local electrostatic moments and periodic boundary conditions”
    P.A. Schultz, Phys. Rev. B 60, 1551 (1999).
  • “Charged local defects in extended systems”
    P.A. Schultz, Phys. Rev. Lett. 84, 1942-1945 (2000).
  • “Fast through-bond diffusion of nitrogen in silicon”
    P.A. Schultz and J.S.Nelson, Appl. Phys. Lett. 78, 736-738 (2001).
  • “Unconstrained and constrained minimization, localization, and the Grassmann manifold: Theory and application to electronic structure”
    D. Raczkowski, C.Y. Fong, P.A. Schultz, R.A. Lippert, and E.B. Stechel, Phys. Rev. B 64, 155203 (2001).
  • “Layer intermixing during metal/metal oxide adsorption: Ti/sapphire(0001)” C. Verdozzi, P.A. Schultz, R.Q. Wu, A.H. Edwards, and N. Kioussis, Phys. Rev. B 66, 125408 (2002).
  • “Applicability of O(N)-like density functional study on the structural properties of nitrogen defects in SiC”
    D. Raczkowski and C.Y. Fong, Phys. Rev. B 68, 014116 (2003).
  • “Localization in an occupied-subspace-optimization approach to electronic structure: Application to yttria-stablized zirconia”
    D. Raczkowski, C.Y. Fong, and E.B. Stechel, Modelling Simul. Mater. Sci. Eng. 12, 133 (2004).
  • “Evidence for interstitial hydrogen as the dominant electronic defect in nanometer alumina films”
    D.R. Jennison, P.A. Schultz, and J.P. Sullivan, Phys. Rev. B 69, 041405 (2004).
  • “BaO/W(111) thermionic emitters and the effects of Sc, Y, La, and the density functional used in computations”
    D.R. Jennison, P.A. Schultz, D.B. King, and K.R. Zavadil, Surf. Sci. 549, 115 (2004).
  • “Spontaneous ionization of hydrogen atoms at the Si-SiO2 interface”
    A.H. Edwards, P.A. Schultz, and H.P. Hjalmarson, Phys. Rev. B 69, 125318 (2004).
  • “Density functional theory and molecular dynamics studies of the energetics and kinetics of electroactive polymers: PVDF and P(VDF-TrFE)”
    H. Su, A. Strachan, and W. A. Goddard III, Phys. Rev. B 70, 064101 (2004).
  • “First-Principles Study of the Switching Mechanism of [2]Catenane Molecular Electronic Devices”
    Y.-H. Kim, S.S. Jung, Y.H. Jang, and W.A. Goddard III, Phys. Rev. Lett. 94, 156801 (2005).
  • “Conformations and charge transport characteristics of biphenyldithiol self-assembled-monolayer molecular electronic devices: A multiscale computational study”
    Y.-H. Kim, S.S. Jang, and W.A. Goddard III, J. Chem. Phys. 122, 244703 (2005).
  • “Designing meaningful density functional calculations in material science–A primer”
    A.E. Mattsson, P.A. Schultz, M.P. Desjarlais, T.R. Mattsson, and K. Leung, Modelling Simul. Mater. Sci. Eng. 13, R1-R31 (2005).
    (Invited Topical Review article)
  • “Theory of persistent, p-type, metallic conduction in c-GeTe”
    A.H. Edwards, A.C. Pineda, P.A. Schultz, M.G. Martin, A.P. Thompson, and H.P. Hjalmarson, J. Phys. Cond. Matter 17, L329-335 (2005).
  • “Density functional theory study of the geometry, energetics and reconstruction process of Si(111) surfaces”
    S.D. Solares, S. Dasgupta, Y.-H. Kim, C.B. Musgrave, P.A. Schultz, and W.A. Goddard III, Langmuir 21, 12404-12414 (2005).
  • “Electronic structure of intrinsic defects in crystalline germanium telluride”
    A.H. Edwards, A.C. Pineda, P.A. Schultz, M.G. Martin, A.P. Thompson, H.P. Hjalmarson, and C.J. Umrigar, Phys. Rev. B 73, 045210 (2006).
  • “Density functional theory and DFT+U study of transition metal porphine adsorbed on Au(111) surfaces and effects of applied electric field”
    K. Leung, S.B. Rempe, P.A. Schultz, E.M. Spoviero, V.S. Batista, M.E. Chandross, and C.J. Medforth, J. Am. Chem. Soc. 128, 3659-3668 (2006).
  • “Nonequivalence of the generalized gradient approximations PBE and PW91”
    A.E. Mattsson, R. Armiento, P.A. Schultz, and T.R. Mattsson, Phys. Rev. B 73, 195123 (2006).
  • “Possible performance improvement in [2]catenane molecular electronic switches”
    Y.-H. Kim, S.S. Jang, and W.A. Goddard III, Appl. Phys. Lett. 88, 163112 (2006).
  • “Theory of defect levels and the ‘band gap problem’ in silicon”
    P.A. Schultz, Phys. Rev. Lett. 96, 246401 (2006).
  • “First-principles approach for the charge-transport characteristics of monolayer molecular electronic devices: Application to hexanedithiolate devices”
    Y.-H. Kim, J. Tahir-Kheli, P.A. Schultz, and W.A. Goddard III, Phys. Rev. B 73, 235419 (2006).
  • “Scanning Tunneling Microscopy of Ethylated Si(111) Surfaces Prepared by a Chlorination/ Alkylation Process Hongbin Yu, Lauren J. Webb, Santiago D. Solares, Peigen Cao, William A. Goddard III, James R. Heath, and Nathan S. Lewis, J. Phys. Chem. B 110, 23989 (2006).
  • “Dose-rate dependence of radiation-induced interface trap density in silicon bipolar transistors” H.P. Hjalmarson, R.L. Pease, C.E. Hembree, R.M. Van Ginhoven, and P.A. Schultz, Nucl. Instr. and Meth. B 250, 269 (2006).
  • “Radiation-induced hydrogen release in SiO2: source sites and release mechanisms” R.M. Van Ginhoven, H.P. Hjalmarson, A.H. Edwards, and B.R. Tuttle, Nucl. Instr. and Meth. B 250, 274 (2006).
  • “Electrical effects of transient neutron irradiation of devices”
    H.P. Hjalmarson, R.L. Pease, R.M. Van Ginhoven, P.A Schultz, and N.A. Modine, Nucl. Instr. and Meth. B 255, 114 (2007).
  • “Atomistic Simulation of Si/SiO2 Interfaces”
    R.M. Van Ginhoven and H.P. Hjalmarson. Nucl. Instr. and Meth. B 255, 183 (2007).
  • “Contact Resistance Properties between Nanotubes and Various Metals from Quantum Mechanics”
    Y. Matsuda, W.-Q. Deng, and W.A. Goddard, III, J. Phys. Chem. C 111, 11113 (2007).
  • “Bifunctional Anchors Connecting Carbon Nanotubes to Metal Electrodes for Improved Nanoelectronics”
    W.-Q. Deng, Y. Matsuda, and W.A. Goddard III, J. Am. Chem. Soc. 129, 9834 (2007).
  • “Reactivities of ultrathin alumina films exposed to intemediate pressures of H2O: Substrate-mediate mechanism for growth and loss of surface order”
    J. Kelber, N. Magtoto, C. Vamala, M. Jain, D.R. Jennison, and P.A. Schultz, Surf. Sci. 601, 3464 (2007).
  • “Structure and band gaps of Ga-(V) semiconductors: The challenge of Ga pseudopotentials”
    O. Anatole von Lilienfeld and Peter A. Schultz, Phys. Rev. B 77, 115202 (2008).
  • “First principles site occupation and migration of hydrogen, helium, and oxygen in beta-phase erbium hydride”
    R.R. Wixom, J.F. Browning, C.S. Snow, P.A. Schultz, and D.R. Jennison J. Appl. Phys. 103, 123708 (2008).
  • “Schultz replies (to Comment on Theory of Defect Levels and the ‘Band Gap Problem’ in Silicon”)
    P.A. Schultz, Phys. Rev. Lett. 103, 089702 (2008).
  • “Simple intrinsic defects in gallium arsenide”
    Peter A. Schultz and O. Anatole von Lilienfeld, Modelling Simul. Mater. Sci. Eng. 17, 084007 (2009).
  • “Efficient hybrid evolutionary optimization of interatomic potential models”
    W.M. Brown, A.P. Thompson, and P.A. Schultz, J. Chem. Phys., in press.
  • I surrender — I cannot keep up with all the publications using the code.
    This page will only get intermittently and haphazardly updated, until we figure out a better means to track and post entries.
    In the meantime, google “SeqQuest” and see PAS publications page for litany of PAS publications.