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 ELLPACKR sparse matrix data types are available, each with different implementations. We show how the secondorder spectral projection (SP2) algorithm used to compute the electronic structure of a molecular system represented with a tightbinding Hamiltonian can be successfully implemented with the aid of this library.
 Authors:

 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:
 Research Org.:
 Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
 Sponsoring Org.:
 USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC22)
 OSTI Identifier:
 1470853
 Alternate Identifier(s):
 OSTI ID: 1489947
 Report Number(s):
 LAUR1729481
Journal ID: ISSN 09208542
 Grant/Contract Number:
 AC0500OR22725; 89233218CNA000001
 Resource Type:
 Accepted Manuscript
 Journal Name:
 Journal of Supercomputing
 Additional Journal Information:
 Journal Volume: 74; Journal Issue: 11; Journal ID: ISSN 09208542
 Publisher:
 Springer
 Country of Publication:
 United States
 Language:
 English
 Subject:
 97 MATHEMATICS AND COMPUTING; Computer Science
Citation Formats
Bock, Nicolas, Negre, Christian F. A., Mniszewski, Susan M., MohdYusof, Jamaludin, Aradi, Bálint, Fattebert, JeanLuc, OseiKuffuor, 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/s1122701825330.
Bock, Nicolas, Negre, Christian F. A., Mniszewski, Susan M., MohdYusof, Jamaludin, Aradi, Bálint, Fattebert, JeanLuc, OseiKuffuor, Daniel, Germann, Timothy C., & Niklasson, Anders M. N. The basic matrix library (BML) for quantum chemistry. United States. doi:10.1007/s1122701825330.
Bock, Nicolas, Negre, Christian F. A., Mniszewski, Susan M., MohdYusof, Jamaludin, Aradi, Bálint, Fattebert, JeanLuc, OseiKuffuor, Daniel, Germann, Timothy C., and Niklasson, Anders M. N. Fri .
"The basic matrix library (BML) for quantum chemistry". United States. doi:10.1007/s1122701825330. https://www.osti.gov/servlets/purl/1470853.
@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 MohdYusof, Jamaludin and Aradi, Bálint and Fattebert, JeanLuc and OseiKuffuor, 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 ELLPACKR sparse matrix data types are available, each with different implementations. We show how the secondorder spectral projection (SP2) algorithm used to compute the electronic structure of a molecular system represented with a tightbinding Hamiltonian can be successfully implemented with the aid of this library.},
doi = {10.1007/s1122701825330},
journal = {Journal of Supercomputing},
number = 11,
volume = 74,
place = {United States},
year = {2018},
month = {8}
}
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Works referenced in this record:
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
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
A general parallel sparseblocked matrix multiply for linear scaling SCF theory
journal, June 2000
 Challacombe, Matt
 Computer Physics Communications, Vol. 128, Issue 12
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
Expansion algorithm for the density matrix
journal, October 2002
 Niklasson, Anders M. N.
 Physical Review B, Vol. 66, Issue 15
DFTB+, a Sparse MatrixBased Implementation of the DFTB Method ^{†}
journal, July 2007
 Aradi, B.; Hourahine, B.; Frauenheim, Th.
 The Journal of Physical Chemistry A, Vol. 111, Issue 26
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
Best Practices for Scientific Computing
journal, January 2014
 Wilson, Greg; Aruliah, D. A.; Brown, C. Titus
 PLoS Biology, Vol. 12, Issue 1
Simplified LCAO Method for the Periodic Potential Problem
journal, June 1954
 Slater, J. C.; Koster, G. F.
 Physical Review, Vol. 94, Issue 6
A simplified density matrix minimization for linear scaling selfconsistent field theory
journal, February 1999
 Challacombe, Matt
 The Journal of Chemical Physics, Vol. 110, Issue 5
Efficient Computation of Sparse Matrix Functions for LargeScale 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
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
Recursive Factorization of the Inverse Overlap Matrix in LinearScaling 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
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
Quantum theory of cohesive properties of solids
journal, January 1956
 Löwdin, PerOlov
 Advances in Physics, Vol. 5, Issue 17
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
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
Selfconsistentcharge densityfunctional tightbinding method for simulations of complex materials properties
journal, September 1998
 Elstner, M.; Porezag, D.; Jungnickel, G.
 Physical Review B, Vol. 58, Issue 11, p. 72607268
A parallel block implementation of Level3 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