Group PARSEC

Group Description
PARSEC matrices, density functional theory. Zhou, Saad, Tiago, Chelikowsky, UMN.

------------------------------------------------------------------
 Yunkai Zhou
 Dept. of Computer Science & Eng.   http://www.cs.umn.edu/~yunkai
 University of Minnesota            fax:   612-625-0572
 200 Union St. SE.                  phone: 612-203-1816 (cell)
 Minneapolis, MN 55455              email: (first name) at the domain cs.umn.edu
------------------------------------------------------------------

The matrices I am trying to submit are from symmetric eigenvalue
problems in density functional theory calculations.

The matrices are sparse, indefinite, with multiple and clustered
eigenvalues---typical character of Hamiltonian matrices from the
Kohn-Sham equations.

Sparsity structures of the matrices may be viewed at
http://www-users.cs.umn.edu/~yunkai/matrices/
One can see very nice, kind of self-similar (fractal) sparsity
structures if using higher resolution for the plots.

------------------------------------------------------------------

Contributors:
Yunkai Zhou, Yousef Saad, Murilo L. Tiago and James R. Chelikowsky.
------------------------------------------------------------------

The matrices are obtained using the PARSEC package.

PARSEC is a FORTRAN90 package in density functional theory (DFT)
calculations, it implements the real-space pseudopotential method
(e.g. [1,2]). High order centered finite difference schemes are used
for the discretization of the Laplacian in the Kohn-Sham equations.
PARSEC is developed by a research group lead by Prof. J. R.
Chelikowsky and Prof. Y. Saad.

The Hamiltonian matrices are constructed when self-consistency
in the self-consistent loop is reached.

Some of the matrices have been used in [3, 4].

[1] @Article{cts:94,
  author =	 {J. R. Chelikowsky and N. Troullier and Y. Saad},
  title =	 {Finite-difference-pseudopotential method: Electronic
                  structure calculations without a basis},
  journal =	 {Phys. Rev. Lett.},
  year =	 1994,
  volume =	 72,
  pages =	 {1240-1243}
}

[2] @Article{che-PDFM00,
  author =	 {J.R. Chelikowsky},
  title =	 {The Pseudopotential-Density Functional Method
                  Applied to Nanostructures},
  journal =	 {J. Phys. D: Appl. Phys.},
  year =	 2000,
  volume =	 33,
  pages =	 {R33--R50}
}

[3] @TechReport{chebdav,
  author =	 {Y. Zhou and Y. Saad},
  title =	 {A {Chebyshev-Davidson} Algorithm for Large
                  Symmetric Eigenvalue Problems},
  institution =	 {Minnesota Supercomputing Institute, Univ. of
                  Minnesota},
  year =	 {2005},
}

[4] @TechReport{blkchebdav,
  author =	 {Y. Zhou},
  title =	 {Block-wise Polynomial Filtered {Davidson}-type
                  Subspace Iteration},
  institution =	 {Minnesota Supercomputing Institute, Univ. of
                  Minnesota},
  year =	 {2005},
}


======================================================================
Displaying collection matrices 1 - 20 of 21 in total
Id Name Group Rows Cols Nonzeros Kind Date Download File
1348 benzene PARSEC 8,219 8,219 242,669 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1349 CO PARSEC 221,119 221,119 7,666,057 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1350 Ga10As10H30 PARSEC 113,081 113,081 6,115,633 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1351 Ga19As19H42 PARSEC 133,123 133,123 8,884,839 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1352 Ga3As3H12 PARSEC 61,349 61,349 5,970,947 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1353 Ga41As41H72 PARSEC 268,096 268,096 18,488,476 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1354 GaAsH6 PARSEC 61,349 61,349 3,381,809 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1355 Ge87H76 PARSEC 112,985 112,985 7,892,195 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1356 Ge99H100 PARSEC 112,985 112,985 8,451,395 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1357 H2O PARSEC 67,024 67,024 2,216,736 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1358 Na5 PARSEC 5,832 5,832 305,630 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1359 Si10H16 PARSEC 17,077 17,077 875,923 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1360 Si2 PARSEC 769 769 17,801 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1361 Si34H36 PARSEC 97,569 97,569 5,156,379 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1362 Si41Ge41H72 PARSEC 185,639 185,639 15,011,265 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1363 Si5H12 PARSEC 19,896 19,896 738,598 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1364 Si87H76 PARSEC 240,369 240,369 10,661,631 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1365 SiH4 PARSEC 5,041 5,041 171,903 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1366 SiNa PARSEC 5,743 5,743 198,787 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market
1368 SiO PARSEC 33,401 33,401 1,317,655 Theoretical/Quantum Chemistry Problem 2005 MATLAB Rutherford Boeing Matrix Market