SeqQuest Bibliography
Overview
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.

Peter Feibelman's original slab code

A massively parallel code by Mark Sears (with PAS)

The current production code
I. 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).

"Pulaytype 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 BrillouinZone 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).
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II. 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 largescale DFT calculations.
This code was designed to be a fully capable standalone production
code for general purpose (not just slabs!) applications.

"Basisset 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).

"Firstprinciples calculations of stress induced by gas adsorption
on Pt(111)"
P.J. Feibelman, Phys. Rev. B 56, 2175 (1997).

"delectron '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 SiH bonds
in SiO_{2} films"
D.R. Jennison, J.P. Sullivan, P.A. Schultz, M.P. Sears, and E.B. Stechel,
Surf. Sci. 390, 112 (1997).

"Allatom 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, 657662 (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 rareearth 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: reflectanceanisotropy
spectroscopy of 3thiophene 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 vacancymediated
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 dmetal 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
Al_{2}O_{3} films"
D.R. Jennison, C. Verdozzi, P.A. Schultz, M.P. Sears,
Phys. Rev. B 59, 15605 (1999).

"Oxygen induced restructuring of the TiO_{2}(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, 173190 (1999).
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III. 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 (notyet"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 ThinFilm 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, 19421945 (2000).

"Fast throughbond diffusion of nitrogen in silicon"
P.A. Schultz and J.S.Nelson, Appl. Phys. Lett. 78, 736738 (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 occupiedsubspaceoptimization approach to electronic
structure: Application to yttriastablized 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 SiSiO_{2}
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(VDFTrFE)"
H. Su, A. Strachan, and W. A. Goddard III,
Phys. Rev. B 70, 064101 (2004).

"FirstPrinciples 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
selfassembledmonolayer 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
scienceA primer"
A.E. Mattsson, P.A. Schultz, M.P. Desjarlais,
T.R. Mattsson, and K. Leung,
Modelling Simul. Mater. Sci. Eng. 13, R1R31 (2005).
(Invited Topical Review article)

"Theory of persistent, ptype, metallic conduction in cGeTe"
A.H. Edwards, A.C. Pineda, P.A. Schultz, M.G. Martin,
A.P. Thompson, and H.P. Hjalmarson,
J. Phys. Cond. Matter 17, L329335 (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, 1240412414 (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, 36593668 (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).

"Firstprinciples approach for the chargetransport characteristics of
monolayer molecular electronic devices:
Application to hexanedithiolate devices"
Y.H. Kim, J. TahirKheli, 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).

"Doserate dependence of radiationinduced 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).

"Radiationinduced 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:
Substratemediate 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 betaphase 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.
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or SeqQuest Home
Send questions and comments to:
Peter Schultz
at
paschul@sandia.gov
Last updated: February 23, 2014