M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations

Xu, Qimen; Sharma, Abhiraj; Suryanarayana, Phanish

doi:10.1016/j.softx.2020.100423

Title: M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations

Abstract

We present M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations. It can perform pseudopotential spin-polarized and unpolarized Kohn-Sham Density Functional Theory (DFT) simulations for isolated systems such as molecules as well as extended systems such as crystals, surfaces, and nanowires. M-SPARC provides a rapid prototyping platform for the development and testing of new algorithms and methods in real-space DFT, with the potential to significantly accelerate the rate of advancements in the field. It also provides a convenient avenue for the accurate first principles study of small to moderate sized systems.

Authors:: Xu, Qimen; Sharma, Abhiraj; Suryanarayana, Phanish

Publication Date:: 2020-01-01

Research Org.:: Georgia Institute of Technology, Atlanta, GA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division; National Science Foundation (NSF)

OSTI Identifier:: 1600840

Alternate Identifier(s):: OSTI ID: 1617446

Grant/Contract Number:: SC0019410

Resource Type:: Published Article

Journal Name:: SoftwareX

Additional Journal Information:: Journal Name: SoftwareX Journal Volume: 11 Journal Issue: C; Journal ID: ISSN 2352-7110

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 42 ENGINEERING; Kohn–Sham; Density Functional Theory; Electronic structure; Real-space; Matlab

Citation Formats


                    Xu, Qimen, Sharma, Abhiraj, and Suryanarayana, Phanish. M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations.  United States: N. p., 2020. 
Web.  doi:10.1016/j.softx.2020.100423.

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                    Xu, Qimen, Sharma, Abhiraj, & Suryanarayana, Phanish. M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations.  United States.  https://doi.org/10.1016/j.softx.2020.100423

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                    Xu, Qimen, Sharma, Abhiraj, and Suryanarayana, Phanish. Wed .  
"M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations".  United States.  https://doi.org/10.1016/j.softx.2020.100423.

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@article{osti_1600840,

  title        = {M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations},

  author       = {Xu, Qimen and Sharma, Abhiraj and Suryanarayana, Phanish},

  abstractNote = {We present M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations. It can perform pseudopotential spin-polarized and unpolarized Kohn-Sham Density Functional Theory (DFT) simulations for isolated systems such as molecules as well as extended systems such as crystals, surfaces, and nanowires. M-SPARC provides a rapid prototyping platform for the development and testing of new algorithms and methods in real-space DFT, with the potential to significantly accelerate the rate of advancements in the field. It also provides a convenient avenue for the accurate first principles study of small to moderate sized systems.},

  doi          = {10.1016/j.softx.2020.100423},

  journal      = {SoftwareX},

  number       = C,

  volume       = 11,

  place        = {United States},

  year         = {2020},

  month        = {1}

}

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Title: M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations

Abstract

Citation Formats

Ab initio molecular dynamics, a simple algorithm for charge extrapolation journal, April 1999

On nearsightedness in metallic systems for O ( N ) Density Functional Theory calculations: A case study on aluminum journal, July 2017

Generalized Gradient Approximation Made Simple journal, October 1996

RESCU: A real space electronic structure method journal, February 2016

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On preconditioning the self-consistent field iteration in real-space Density Functional Theory journal, January 2020

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SPARC: Accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory: Isolated clusters journal, March 2017

Structural transitions in metal clusters journal, January 1991

Finite-difference-pseudopotential method: Electronic structure calculations without a basis journal, February 1994

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Optimized norm-conserving Vanderbilt pseudopotentials journal, August 2013

Alternating Anderson–Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems journal, January 2019

Anderson acceleration of the Jacobi iterative method: An efficient alternative to Krylov methods for large, sparse linear systems journal, February 2016

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations journal, September 2010

KSSOLV—a MATLAB toolbox for solving the Kohn-Sham equations journal, March 2009

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On the calculation of the stress tensor in real-space Kohn-Sham density functional theory journal, November 2018

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Chebyshev-filtered subspace iteration method free of sparse diagonalization for solving the Kohn–Sham equation journal, October 2014

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Accurate and Scalable O ( N ) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers journal, January 2014

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First principles methods using CASTEP journal, January 2005

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Spectral Quadrature method for accurate O ( N ) electronic structure calculations of metals and insulators journal, March 2016

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On real-space Density Functional Theory for non-orthogonal crystal systems: Kronecker product formulation of the kinetic energy operator journal, May 2018

Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory journal, February 2016

Parallel implementation of time-dependent density functional theory journal, December 2003

Ab initio molecular dynamics, a simple algorithm for charge extrapolation
journal, April 1999

On nearsightedness in metallic systems for $O (N)$ Density Functional Theory calculations: A case study on aluminum
journal, July 2017

Generalized Gradient Approximation Made Simple
journal, October 1996

RESCU: A real space electronic structure method
journal, February 2016

SQDFT: Spectral Quadrature method for large-scale parallel $O (N)$ Kohn–Sham calculations at high temperature
journal, March 2018

A massively-parallel electronic-structure calculations based on real-space density functional theory
journal, March 2010

Architecture of Qbox: A scalable first-principles molecular dynamics code
journal, January 2008

Real-space electronic-structure calculations: Combination of the finite-difference and conjugate-gradient methods
journal, May 1995

Real-space adaptive-coordinate electronic-structure calculations
journal, July 1995

On preconditioning the self-consistent field iteration in real-space Density Functional Theory
journal, January 2020

Accurate and simple density functional for the electronic exchange energy: Generalized gradient approximation
journal, June 1986

SPARC: Accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory: Isolated clusters
journal, March 2017

Structural transitions in metal clusters
journal, January 1991

Finite-difference-pseudopotential method: Electronic structure calculations without a basis
journal, February 1994

\mathcal{O}(N) methods in electronic structure calculations
journal, February 2012

Optimized norm-conserving Vanderbilt pseudopotentials
journal, August 2013

Alternating Anderson–Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems
journal, January 2019

Anderson acceleration of the Jacobi iterative method: An efficient alternative to Krylov methods for large, sparse linear systems
journal, February 2016

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
journal, September 2010

KSSOLV—a MATLAB toolbox for solving the Kohn-Sham equations
journal, March 2009

Real-space pseudopotential method for first principles calculations of general periodic and partially periodic systems
journal, August 2008

Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965

Discrete discontinuous basis projection method for large-scale electronic structure calculations
journal, September 2018

Efficient pseudopotentials for plane-wave calculations
journal, January 1991

DFT: A Theory Full of Holes?
journal, April 2015

SPARC: Accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory: Extended systems
journal, July 2017

Augmented Lagrangian formulation of orbital-free density functional theory
journal, October 2014

Self-consistent-field calculations using Chebyshev-filtered subspace iteration
journal, November 2006

First-principles computation of material properties: the ABINIT software project
journal, November 2002

Linear scaling electronic structure methods
journal, July 1999

Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
journal, October 1996

Perspective: Fifty years of density-functional theory in chemical physics
journal, May 2014

Cyclic density functional theory: A route to the first principles simulation of bending in nanostructures
journal, November 2016

Inhomogeneous Electron Gas
journal, November 1964

Symmetry-adapted real-space density functional theory for cylindrical geometries: Application to large group-IV nanotubes
journal, September 2019

On the calculation of the stress tensor in real-space Kohn-Sham density functional theory
journal, November 2018

Real-space multigrid-based approach to large-scale electronic structure calculations
journal, November 1996

Parallel self-consistent-field calculations via Chebyshev-filtered subspace acceleration
journal, December 2006

Chebyshev-filtered subspace iteration method free of sparse diagonalization for solving the Kohn–Sham equation
journal, October 2014

Coarse-graining Kohn–Sham Density Functional Theory
journal, January 2013

Accurate and Scalable $O (N)$ Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers
journal, January 2014

Self-interaction correction to density-functional approximations for many-electron systems
journal, May 1981

First principles methods using CASTEP
journal, January 2005

Periodic Pulay method for robust and efficient convergence acceleration of self-consistent field iterations
journal, March 2016

Spectral Quadrature method for accurate $O (N)$ electronic structure calculations of metals and insulators
journal, March 2016

Restarted Pulay mixing for efficient and robust acceleration of fixed-point iterations
journal, August 2015

On real-space Density Functional Theory for non-orthogonal crystal systems: Kronecker product formulation of the kinetic energy operator
journal, May 2018

Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory
journal, February 2016

Parallel implementation of time-dependent density functional theory
journal, December 2003