The basic matrix library (BML) for quantum chemistry

Bock, Nicolas; Negre, Christian F.  A.; Mniszewski, Susan M.; Mohd-Yusof, Jamaludin; Aradi, Bálint; Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Germann, Timothy C.; Niklasson, Anders M.  N.

doi:10.1007/s11227-018-2533-0

Title: The basic matrix library (BML) for quantum chemistry

Abstract

The basic matrix library package (BML) provides a common application programming interface (API) for linear algebra and matrix functions in C and Fortran for quantum chemistry codes. The BML API is matrix format independent. Currently the dense, compressed sparse row, and ELLPACK-R sparse matrix data types are available, each with different implementations. We show how the second-order spectral projection (SP2) algorithm used to compute the electronic structure of a molecular system represented with a tight-binding Hamiltonian can be successfully implemented with the aid of this library.

Authors:

Bock, Nicolas ^[1];

^[2];

^[2]; Aradi, Bálint ^[3]; Fattebert, Jean-Luc ^[4]; Osei-Kuffuor, Daniel ^[5]; Germann, Timothy C. ^[2];

^[2]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); SUSE Linux GmbH, Nurnberg (Germany)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Bremen (Germany)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

Publication Date:: Fri Aug 17 00:00:00 EDT 2018

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1470853

Alternate Identifier(s):: OSTI ID: 1489947; OSTI ID: 1819031

Report Number(s):: LA-UR-17-29481; LLNL-JRNL-823445
Journal ID: ISSN 0920-8542

Grant/Contract Number:: AC05-00OR22725; AC52-07NA27344; 89233218CNA000001

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Supercomputing

Additional Journal Information:: Journal Volume: 74; Journal Issue: 11; Journal ID: ISSN 0920-8542

Publisher:: Springer

Country of Publication:: United States

Language:: English

Subject:: 97 MATHEMATICS AND COMPUTING; matrix formats; matrix-matrix operations; quantum chemistry packages; Computer Science

Citation Formats


                    Bock, Nicolas, Negre, Christian F.  A., Mniszewski, Susan M., Mohd-Yusof, Jamaludin, Aradi, Bálint, Fattebert, Jean-Luc, Osei-Kuffuor, Daniel, Germann, Timothy C., and Niklasson, Anders M.  N. The basic matrix library (BML) for quantum chemistry.  United States: N. p., 2018. 
Web.  doi:10.1007/s11227-018-2533-0.

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                    Bock, Nicolas, Negre, Christian F.  A., Mniszewski, Susan M., Mohd-Yusof, Jamaludin, Aradi, Bálint, Fattebert, Jean-Luc, Osei-Kuffuor, Daniel, Germann, Timothy C., & Niklasson, Anders M.  N. The basic matrix library (BML) for quantum chemistry.  United States.  https://doi.org/10.1007/s11227-018-2533-0

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                    Bock, Nicolas, Negre, Christian F.  A., Mniszewski, Susan M., Mohd-Yusof, Jamaludin, Aradi, Bálint, Fattebert, Jean-Luc, Osei-Kuffuor, Daniel, Germann, Timothy C., and Niklasson, Anders M.  N. Fri .  
"The basic matrix library (BML) for quantum chemistry".  United States.  https://doi.org/10.1007/s11227-018-2533-0.  https://www.osti.gov/servlets/purl/1470853.

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@article{osti_1470853,

  title        = {The basic matrix library (BML) for quantum chemistry},

  author       = {Bock, Nicolas and Negre, Christian F.  A. and Mniszewski, Susan M. and Mohd-Yusof, Jamaludin and Aradi, Bálint and Fattebert, Jean-Luc and Osei-Kuffuor, Daniel and Germann, Timothy C. and Niklasson, Anders M.  N.},

  abstractNote = {The basic matrix library package (BML) provides a common application programming interface (API) for linear algebra and matrix functions in C and Fortran for quantum chemistry codes. The BML API is matrix format independent. Currently the dense, compressed sparse row, and ELLPACK-R sparse matrix data types are available, each with different implementations. We show how the second-order spectral projection (SP2) algorithm used to compute the electronic structure of a molecular system represented with a tight-binding Hamiltonian can be successfully implemented with the aid of this library.},

  doi          = {10.1007/s11227-018-2533-0},

  journal      = {Journal of Supercomputing},

  number       = 11,

  volume       = 74,

  place        = {United States},

  year         = {Fri Aug 17 00:00:00 EDT 2018},

  month        = {Fri Aug 17 00:00:00 EDT 2018}

}

Copy to clipboard

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https://doi.org/10.1007/s11227-018-2533-0

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Works referenced in this record:

PIC, a paediatric-specific intensive care database
journal, January 2020

Zeng, Xian; Yu, Gang; Lu, Yang
Scientific Data, Vol. 7, Issue 1
DOI: 10.1038/s41597-020-0355-4

Computational science: ...Error
journal, October 2010

Merali, Zeeya
Nature, Vol. 467, Issue 7317
DOI: 10.1038/467775a

Techniques for Exploiting the Sparsity or the Network Admittance Matrix
journal, December 1963

Sato, Nobou; Tinney, W.
IEEE Transactions on Power Apparatus and Systems, Vol. 82, Issue 69
DOI: 10.1109/TPAS.1963.291477

Computation of the Density Matrix in Electronic Structure Theory in Parallel on Multiple Graphics Processing Units
journal, November 2014

Cawkwell, M. J.; Wood, M. A.; Niklasson, Anders M. N.
Journal of Chemical Theory and Computation, Vol. 10, Issue 12
DOI: 10.1021/ct5008229

Improving the Performance of the Sparse Matrix Vector Product with GPUs
conference, June 2010

Vázquez, F.; Ortega, G.; Fernández, J. J.
2010 IEEE 10th International Conference on Computer and Information Technology (CIT), 2010 10th IEEE International Conference on Computer and Information Technology
DOI: 10.1109/CIT.2010.208

A parallel block implementation of Level-3 BLAS for MIMD vector processors
journal, June 1994

Daydé, Michel J.; Duff, Iain S.; Petitet, Antoine
ACM Transactions on Mathematical Software, Vol. 20, Issue 2
DOI: 10.1145/178365.174413

Expansion algorithm for the density matrix
journal, October 2002

Niklasson, Anders M. N.
Physical Review B, Vol. 66, Issue 15
DOI: 10.1103/PhysRevB.66.155115

DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method ^†
journal, July 2007

Aradi, B.; Hourahine, B.; Frauenheim, Th.
The Journal of Physical Chemistry A, Vol. 111, Issue 26
DOI: 10.1021/jp070186p

Efficient Parallel Linear Scaling Construction of the Density Matrix for Born–Oppenheimer Molecular Dynamics
journal, September 2015

Mniszewski, S. M.; Cawkwell, M. J.; Wall, M. E.
Journal of Chemical Theory and Computation, Vol. 11, Issue 10
DOI: 10.1021/acs.jctc.5b00552

Simplified LCAO Method for the Periodic Potential Problem
journal, June 1954

Slater, J. C.; Koster, G. F.
Physical Review, Vol. 94, Issue 6
DOI: 10.1103/PhysRev.94.1498

Two Fast Algorithms for Sparse Matrices: Multiplication and Permuted Transposition
journal, September 1978

Gustavson, Fred G.
ACM Transactions on Mathematical Software, Vol. 4, Issue 3
DOI: 10.1145/355791.355796

Computing the Density Matrix in Electronic Structure Theory on Graphics Processing Units
journal, October 2012

Cawkwell, M. J.; Sanville, E. J.; Mniszewski, S. M.
Journal of Chemical Theory and Computation, Vol. 8, Issue 11
DOI: 10.1021/ct300442w

Direct solutions of sparse network equations by optimally ordered triangular factorization
journal, January 1967

Tinney, W. F.; Walker, J. W.
Proceedings of the IEEE, Vol. 55, Issue 11
DOI: 10.1109/PROC.1967.6011

Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998

Elstner, M.; Porezag, D.; Jungnickel, G.
Physical Review B, Vol. 58, Issue 11, p. 7260-7268
DOI: 10.1103/PhysRevB.58.7260

Iterative Methods for Sparse Linear Systems
book, January 2003

Saad, Yousef
DOI: 10.1137/1.9780898718003

Best Practices for Scientific Computing
journal, January 2014

Wilson, Greg; Aruliah, D. A.; Brown, C. Titus
PLoS Biology, Vol. 12, Issue 1
DOI: 10.1371/journal.pbio.1001745

A simplified density matrix minimization for linear scaling self-consistent field theory
journal, February 1999

Challacombe, Matt
The Journal of Chemical Physics, Vol. 110, Issue 5
DOI: 10.1063/1.477969

Efficient Computation of Sparse Matrix Functions for Large-Scale Electronic Structure Calculations: The CheSS Library
journal, September 2017

Mohr, Stephan; Dawson, William; Wagner, Michael
Journal of Chemical Theory and Computation, Vol. 13, Issue 10
DOI: 10.1021/acs.jctc.7b00348

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations
journal, June 2016

Negre, Christian F. A.; Mniszewski, Susan M.; Cawkwell, Marc J.
Journal of Chemical Theory and Computation, Vol. 12, Issue 7
DOI: 10.1021/acs.jctc.6b00154

An Optimized Sparse Approximate Matrix Multiply for Matrices with Decay
journal, January 2013

Bock, Nicolas; Challacombe, Matt
SIAM Journal on Scientific Computing, Vol. 35, Issue 1
DOI: 10.1137/120870761

Quantum theory of cohesive properties of solids
journal, January 1956

Löwdin, Per-Olov
Advances in Physics, Vol. 5, Issue 17
DOI: 10.1080/00018735600101155

Quantum theory of cohesive properties of solids
journal, September 2001

Löwdin, Per-Olov
Advances in Physics, Vol. 50, Issue 6
DOI: 10.1080/00018730110102196

Best Practices for Scientific Computing
text, January 2012

Wilson, Greg; Aruliah, D. A.; Brown, C. Titus
arXiv
DOI: 10.48550/arxiv.1210.0530

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Title: The basic matrix library (BML) for quantum chemistry

Abstract

Citation Formats

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Two Fast Algorithms for Sparse Matrices: Multiplication and Permuted Transposition journal, September 1978

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Direct solutions of sparse network equations by optimally ordered triangular factorization journal, January 1967

Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties journal, September 1998

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A simplified density matrix minimization for linear scaling self-consistent field theory journal, February 1999

Efficient Computation of Sparse Matrix Functions for Large-Scale Electronic Structure Calculations: The CheSS Library journal, September 2017

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations journal, June 2016

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Quantum theory of cohesive properties of solids journal, September 2001

Best Practices for Scientific Computing text, January 2012

PIC, a paediatric-specific intensive care database
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journal, October 2010

Techniques for Exploiting the Sparsity or the Network Admittance Matrix
journal, December 1963

Computation of the Density Matrix in Electronic Structure Theory in Parallel on Multiple Graphics Processing Units
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Improving the Performance of the Sparse Matrix Vector Product with GPUs
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A parallel block implementation of Level-3 BLAS for MIMD vector processors
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DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method ^†
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Efficient Parallel Linear Scaling Construction of the Density Matrix for Born–Oppenheimer Molecular Dynamics
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Simplified LCAO Method for the Periodic Potential Problem
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Two Fast Algorithms for Sparse Matrices: Multiplication and Permuted Transposition
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Direct solutions of sparse network equations by optimally ordered triangular factorization
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Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
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