Basic papers

These are some of the basic references for PARSEC and the electronic structure problem:

J. R. Chelikowsky, N. Troullier, and Y. Saad, Finite-difference-pseudopotential method: Electronic structure calculations without a basis, Phys. Rev. Lett. 72, 1240 (1994).

J. R. Chelikowsky, The pseudopotential-density functional method applied to nanostructures, J. of Phys. D 33, R33 (2000).

M. M. G. Alemany, M. Jain, L. Kronik, and J. R. Chelikowsky, Real-space pseudopotential method for computing the electronic properties of periodic systems, Phys. Rev. B 69, 075101 (2004).

L. Kronik, A. Makmal, M.L. Tiago, M.M.G. Alemany, M. Jain, X. Huang, Y. Saad, and J.R. Chelikowsky, PARSEC-the pseudopotential algorithm for real-space electronic structure calculations: Recent Advances and novel applications to nano-structures, physica status solidi (b) 243, 1063 (2006).

Y. Saad, J.R. Chelikowsky and S.M. Shontz,
Numerical methods for electronic structure calculations of materials, SIAM Rev. 52, 3 (2010).

Algorithms and Recent Additions

These papers concern algorithm development and recent additions to PARSEC:

Y.K. Zhou, Y. Saad, M.L. Tiago, and J.R. Chelikowsky,
Parallel self-consistent-field calculations via Chebyshev-filtered subspace acceleration, Phys. Rev. E 74, 066704 (2006).
Y.K. Zhou, Y. Saad, M.L. Tiago, J.R. Chelikowsky, Self-consistent-field calculations using Chebyshev-filtered subspace iteration, J. Comp. Phys. 219, 172 (2006).

A. Sitt, L. Kronik, S. Ismail-Beigi, and J. R. Chelikowsky, Excited state forces within time-dependent density functional theory: a frequency domain approach, Phys. Rev. A, 76, 054501 (2007).

D. Naveh, L. Kronik, M. L. Tiago, and J. R. Chelikowsky,
Real-Space Pseudopotential method for Spin-Orbit Coupling within Density Functional Theory, Phys. Rev. B 76, 153407 (2007).

A. Natan, A. Benjamini, D. Naveh, L. Kronik, M. L. Tiago, S. P. Beckman, and J. R. Chelikowsky,
Real-space pseudopotential method for first principles calculations of general periodic and partially periodic systems, Phys. Rev. B 78, 075109 (2008).

D. Naveh and L. Kronik, Real-Space Pseudopotential method for Noncollinear Magnetism within Density Functional Theory, Solid State Comm. 149, 177 (2009).

G. Schofield, J.R. Chelikowsky, and Y. Saad,
A spectrum slicing method for the Kohn-Sham problem, Comp. Phys. Commun. 183, 497 (2012).

Y. Zhou, J.R. Chelikowsky and Y. Saad:
Chebyshev-filtered subspace iteration method free of sparse diagonalization for solutions of the Kohn-Sham equation, J. of Comp. Phys. 274, 770 (2014).

Y. Zhou, J.R. Chelikowsky, X. Gao and A. Zhou:
On the preconditioning'' function used in plane-wave DFT calculations and its generalization, Commun. in Comput. Phys. 18, 167 (2015).

N.S. Bobbitt, G. Schofield, C. Lena, and J.R. Chelikowsky:
High Order Forces and Nonlocal Operators in a Kohn-Sham Hamiltonian, Phys. Chem. Chem. Phys. 17, 31542 (2015).


These are references for the limited-memory BFGS algorithm:
R. H. Byrd, P. Lu and J. Nocedal, A Limited Memory Algorithm for Bound Constrained Optimization, SIAM Journal on Scientific and Statistical Computing 16, 1190 (1995).

C. Zhu, R. H. Byrd and J. Nocedal, L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale bound constrained optimization, ACM Transactions on Mathematical Software 23, 550 (1997).

Recent Publications

This is a short list of relevant papers that use this real-space method:

L. Gao, J. Souto-Casares, J.R. Chelikowsky and A.A. Demkov: "Orientation dependence of the work function: metal nanocrystals,'' J. Chem. Phys. 147, 214301 (2017).

N.S. Bobbitt and J.R. Chelikowsky: "First-principles study of vibrational properties and Raman spectra in Li-doped Si nanocrystals,'' Chem. Phys. Lett. 646, 136 (2016).

T.-L. Chan, A.J. Lee, and J.R. Chelikowsky: "Ionization of a P-doped Si(111) nanofilm using two dimensional periodic boundary conditions," Phys. Rev. B 91, 235445 (2015).

Y. Sakai, A.J. Lee and J.R. Chelikowsky: "First-principles non-contact atomic force microscopy image simulations with frozen density embedding theory,'' Nano Lett. 16, 3242 (2016).

T.-L. Chan, J. Souto-Casares J. R. Chelikowsky, K.-M. Ho, C.-Z. Wang, and S. Zhang: "The effect of interface on quantum confinement and electronic structure across the Pb/Si(111) junction,'' Solid State Comm. 217, 43 (2015).

T.-L. Chan, A. Lee and J.R. Chelikowsky: "An effective capacitance model for computing the electronic properties of charged defects in crystals,'' Comp. Phys. Comm. 185, 1564 (2014).

A.J. Lee, T.-L. Chan and J.R. Chelikowsky: "Dopant binding energies in P-doped Ge[110] nanowires using real-space pseudopotentials,'' Phys. Rev. B 89, 075419 (2014).

A.J. Lee, M. Kim, C. Lena and J.R. Chelikowsky: "Mechanical and electronic properties of strained Ge nanowires using ab initio real-space pseudopotentials,'' Phys. Rev. B 86, 115331 (2012).

J.R. Chelikowsky, T.-L. Chan, M.M.G Alemany and G. Dalpian: "Computational studies of doped nanostructures,'' Rep. Prog. Phys. 74, 046501 (2011).

Tortajada, L. V. Besteiro, M. L. Tiago, L. J. Gallego, J. R. Chelikowsky, and M. M. G. Alemany: "Multidimensional nanoscale materials from fused quantum dots,'' Phys. Rev. B 84, 205326 (2011).

K. H. Khoo, J. T. Arantes, J. R. Chelikowsky, and G. M. Dalpian: "First-Principles Calculations of Lattice-Strained Core-Shell Nanocrystals," Physical Review B 84, 075311 (2011).

T.-L. Chan, J. R. Chelikowsky and S. B. Zhang: " An effective one-particle theory for formation energies in doping Si nanostructures,'' Appl. Phys. Lett. 98, 133116 (2011).

J.R. Chelikowsky, T.-L. Chan, M.M.G Alemany and G. Dalpian: "Computational studies of doped nanostructures,'' Rep. Prog. Phys. 74, 046501 (2011).

J.R. Chelikowsky: "Tools for Predicting Nanomaterial Properties,'' Handbook of Nanophysics 1 , K. Sattler, editor in chief. (Taylor and Francis, Boca Raton, 2011), p.3-1.

I. Vasliev and J.R. Chelikowsky: "Real-space calculations of atomic and molecular polarizabilities using asymptotically correct exchange-correlation potentials,'' Phys. Rev. A 81, 012502 (2010).

J. Han, T.-L. Chan and J. R. Chelikowsky: "Quantum confinement, core level shifts, and dopant segregation in P-doped Si <110> nanowires," Phys. Rev. B 82, 153413 (2010).

Y.  Saad, J.R. Chelikowsky and S. Shontz:  “Numerical Methods for Electronic Structure Calculations of Materials,” SIAM Review, 52, 3 (2010).

T.-L. Chan and J.R. Chelikowsky: “Controlling diffusion in semiconductor nanostructures by size and dimensionality,” Nano Letters  10,  821 (2010).

J.-H. Eom, T.-L. Chan and J.R. Chelikowsky: “The role of vacancies on B doping in Si nanocrystals,” Solid State Commun. 150, 130 (2010).

M. Lopez del Puerto, M. Jain, and J.R. Chelikowsky:   “Time-dependent density functional theory calculation of the Stokes shift in hydrogenated silicon clusters,”  Phys. Rev. B 81, 035309 (2010).

H. Kwak and J.R. Chelikowsky: “Size-dependent Spin-polarization of Carbon-doped ZnO Nanocrystals,” Applied Phys. Lett.  95, 263108   (2009).

L. V. Besteiro, L. Tortajada, M. L. Tiago, L.J. Gallego, J.  R. Chelikowsky,  and M. M. G. Alemany: “Efficient n-type doping of zinc-blende III-V semiconductor quantum dots,” Phys. Rev.  B. 81, 121307 (2010).

M. Tiago, J. C. Idrobo, S. Ogut J. Jellinek, and J. R. Chelikowsky: “Electronic and Optical Excitations in Ag_n (n=1-8) Clusters: Comparison of Density Functional and Many-Body Theories,”Phys. Rev. B 79, 155419 (2009).

K.H. Khoo and J.R. Chelikowsky: “Theoretical Study of Electron Transport across Carbon Nanotube Junctions Decorated with Au Nanoparticles,” Phys. Rev. B 79, 205422 (2009).

T.-L. Chan, A. T. Zayak, G. M. Dalpian, and J. R. Chelikowsky: “Role of Confinement on Diffusion Barriers in Semiconductor Nanocrystals,” Phys. Rev. Lett. 102, 025901 (2009).

J.R. Chelikowsky, A. T. Zayak, T.-L. Chan, M. L. Tiago, Y. Zhou and Y. Saad: “Algorithms for the Electronic and Vibrational Properties of Nanocrystals,” J. Phys. Cond. Matter 21, 064207 (2009).

H. Kwak, M.L. Tiago, T.-L. Chan, and J.R. Chelikowsky: “The Role of Quantum Confinement and Hyperfine Splitting in Li Doped ZnO Nanocrystals,'” Phys. Rev. B 78, 195324 (2008)

M. M. G. Alemany, L. Tortajada, X. Huang, M.L. Tiago,L.J. Gallego, and J.R. Chelikowsky: “The role of dimensionality and quantum confinement in p-type semiconductor indium phosphide nanomaterials,” Phys. Rev. B 78, 233101 (2008).

H. Kwak, M. L. Tiago and J. R. Chelikowsky: “Quantum Confinement and Strong Coulombic Correlation in ZnO Nanocrystals,” Solid State Commun. 145, 227 (2008).

T.-L. Chan, M. L. Tiago, E. Kaxiras and J.R. Chelikowsky, “Size Limits on Doping Phosphorus into Silicon Nanocrystals,” Nano Letters 8, 596 (2008).

M. Lopez del Puerto, M.L. Tiago, and J.R. Chelikowsky: “Ab initio methods for the optical properties of CdSe clusters,” Phys. Rev. B 77, 045404 (2008).

L. Kong and J.R. Chelikowsky: “Transport properties of transition-metal-encapsulated Si cages,” Phys. Rev. B 77, 073401 (2008).

A.T. Zayak, S. Beckman, M. Tiago, P. Entel, and J.R. Chelikowsky: “Switchable Heusler Clusters,” J. Appl. Phys. 104, 074307 (2008).

M.M.G. Alemany, X. Huang, M. L. Tiago , L.J. Gallego, and J.R. Chelikowsky: “Ab initio calculations for p-type doped bulk indium phosphide,” Solid State Commun. 146, 245 (2008).

N. Sai, M.L. Tiago, J.R. Chelikowsky, and F. A. Reboredo: “Optical spectra and exchange-correlation effects in molecular crystals,” Phys. Rev. B 77, 161306 (2008).

A.T. Zayak, P. Entel, and J.R. Chelikowsky: “Minority spin polarization and surface magnetic enhancement in Heusler clusters,” Phys. Rev. B 77, 212401 (2008).

H. Kwak, M.L. Tiago, T.-L. Chan and J.R. Chelikowsky: “Hyperfine splitting of partially ionized Li donors in ZnO nanocrystals,” Chem. Phys. Lett. 454, 337 (2008).

A. Natan, A. Mor, D. Naveh, L. Kronik, M.L. Tiago, S.P. Beckman and J.R. Chelikowsky: “Real-space pseudopotential method for first principles calculations of general periodic and partially periodic systems,” Phys. Rev. B 78, 075109 (2008).

J. Han, M. L. Tiago, T.-L. Chan, and J. R. Chelikowsky: “Real-Space First-Principles Method for the Electronic Structure of One Dimensional Periodic Systems,” J. Chem. Phys. 129, 144109 (2008).