FreeON

Last updated
FreeON
FreeON notext logo.jpg
Stable release
1.0.8 / November 8, 2013;8 years ago (2013-11-08)
Written in Fortran, C
Operating system Linux, FreeBSD, Unix and like operating systems
Type Computational Chemistry
License GNU GPLv3
Website

In computer software, FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry, formerly known as MondoSCF. It is highly modular, and has been written from scratch for N-scaling SCF theory in Fortran95 and C. Platform independent IO is supported with HDF5. FreeON should compile with most modern Linux distributions. FreeON performs Hartree–Fock, pure density functional, and hybrid HF/DFT calculations (e.g. B3LYP) in a Cartesian-Gaussian LCAO basis. All algorithms are O(N) or O(N lg N) for non-metallic systems. [1] [2] [3] [4] [5] [6] [7] Periodic boundary conditions in 1, 2 and 3 dimensions have been implemented through the Lorentz field (-point), and an internal coordinate geometry optimizer allows full (atom+cell) relaxation using analytic derivatives. Effective core potentials for energies and forces have been implemented, but Effective Core Potential (ECP) lattice forces do not work yet. Advanced features include O(N) static and dynamic response, as well as time reversible Born Oppenheimer Molecular Dynamics (MD).

Contents

Developers

DeveloperAffiliation
Matt ChallacombeLos Alamos National Laboratory
Eric SchweglerLawrence Livermore National Laboratory
C. J. TymczakTexas Southern University
Anders M. NiklassonLos Alamos National Laboratory
Anders OdellKTH Stockholm
Nicolas BockLos Alamos National Laboratory
Karoly NemethArgonne National Laboratory
Valery WeberUniversity of Zurich
C. K. GanInstitute for High Performance Computing
Graeme HenkelmanUniversity of Texas at Austin
Robert SnavelyUniversity of Santa Cruz

See also

Related Research Articles

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References

  1. Challacombe, M.; Schwegler, E.; Almlöf, J. (1996). "Fast assembly of the Coulomb matrix: A quantum chemical tree code". The Journal of Chemical Physics. 104 (12): 4685. Bibcode:1996JChPh.104.4685C. doi:10.1063/1.471163.
  2. Schwegler, E.; Challacombe, M. (1996). "Linear scaling computation of the Hartree–Fock exchange matrix". The Journal of Chemical Physics. 105 (7): 2726. Bibcode:1996JChPh.105.2726S. doi:10.1063/1.472135.
  3. Challacombe, M.; Schwegler, E. (1997). "Linear scaling computation of the Fock matrix". The Journal of Chemical Physics. 106 (13): 5526. Bibcode:1997JChPh.106.5526C. doi:10.1063/1.473575.
  4. Schwegler, E.; Challacombe, M.; Head-Gordon, M. (1997). "Linear scaling computation of the Fock matrix. II. Rigorous bounds on exchange integrals and incremental Fock build". The Journal of Chemical Physics. 106 (23): 9708. Bibcode:1997JChPh.106.9708S. doi:10.1063/1.473833.
  5. Schwegler, E.; Challacombe, M. (1999). "Linear scaling computation of the Fock matrix. IV. Multipole accelerated formation of the exchange matrix". The Journal of Chemical Physics. 111 (14): 6223. Bibcode:1999JChPh.111.6223S. doi:10.1063/1.479926.
  6. Schwegler, E.; Challacombe, M. (2000). "Linear scaling computation of the Fock matrix. III. Formation of the exchange matrix with permutational symmetry". Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 104 (5): 344. doi:10.1007/s002140000127. S2CID   94597829.
  7. Challacombe, M. (2000). "Linear scaling computation of the Fock matrix. V. Hierarchical Cubature for numerical integration of the exchange-correlation matrix". The Journal of Chemical Physics. 113 (22): 10037–10043. Bibcode:2000JChPh.11310037C. doi:10.1063/1.1316012.