- TNPACK - the Truncated-Newton optimization package for multivariate nonlinear unconstrained problems.
The link below will bring you to the TNPACK code available from the Association for Computing Machinery through their journal:
Transactions on Mathematical Software (ACM TOMS).
Please contact the author, T. Schlick at schlick@nyu.edu if you have any questions.
ACCESS TNPACK
TNPACK publications
- The idea for the method tailored to molecular applications was first reported in 1987:
 |
|
|
T. Schlick and M. Overton, "A Powerful Truncated Newton Method for Potential Energy Minimization", J. Comp. Chem., 8:1025-1039, May (1987)   |
|
- The resulting FORTRAN package was submitted to ACM TOMS with two detailed papers in 1992:
| |
|
|
T. Schlick and A. Fogelson, "TNPACK - A Truncated Newton Minimization Package for Large Scale Problems: I. Algorithm and Usage", ACM Trans. Math. Softw., 18:46-70, March (1992)   |
|
| |
|
|
"T. Schlick and A. Fogelson, "TNPACK - A Truncated Newton Minimization Package for Large Scale Problems: II. Implementation Examples", ACM Trans. Math. Softw., 18:71-111, March (1992) |
|
- Related work on modified Cholesky factorizations was published in 1993:
| |
|
|
T. Schlick, "Modified Cholesky Factorizations for Sparse Preconditioners", SIAM J. Sci. Comp., 14:424-445, March (1993) |
|
- TNPACK's incorporation into CHARMM with performance assessment was described in 1994:
| |
|
|
P. Derreumaux, G. Zhang, B. Brooks, and T. Schlick, "A Truncated-Newton Method Adapted for CHARMM and Biomolecular Applications", J. Comp. Chem., 15:532-552, April (1994)  |
|
and into a meteorology package in 1993:
| |
|
|
X. Zou, I. M. Navon, M. Berger, P. K. H. Phua, T. Schlick and F. X. Le Dimet, "Numerical Experience with Limited-Memory and Truncated Newton Methods", SIAM J. Opt., 3:582-608, August (1993) |
|
- Further mathematical/computational improvements to handle indefinite preconditioners were reported in 1999:
 |
|
|
D. Xie and T. Schlick, "Efficient Implementation of the Truncated Newton Method for Large Scale Chemistry Applications", SIAM J. Opt., 10: 132-154 October (1999)   |
|
- The updated package was subsequently submitted to ACM TOMS:
| |
|
|
D. Xie and T. Schlick, "Remark on the Updated Truncated Newton Minimization Package, Algorithm 702", ACM Trans. Math. Softw., 25, 108-122, March (1999) |
|
- More details on an improved line search were published in 2002:
| |
|
|
D. Xie and T. Schlick, "A More Lenient Stopping Rule for Line Search Algorithms", Optim. Meth. Softw., in press, (2002) |
|
- For other applications of TNPACK to chemical design, see:
| |
|
|
D. Xie, A. Tropsha and T. Schlick, "An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization", J. Chem. Inf. Comput. Sci., 40:167-177, December (1999) |
|
| |
|
|
D. Xie and T. Schlick, "Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization", Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, Volume 40, pages 267-286, C. A. Floudas and P. M. Pardalos, eds., Kluwer Academic Publishers, Dororecht/Boston/London (2000) |
|
- For other applications of TNPACK to charge optimization, see:
| |
|
|
D. A. Beard and T. Schlick, "Modeling Salt-Mediated Electrostatics of Macromolecules: The Discrete Surface Charge Optimization Algorithm and Its Application to the Nucleosome", Biopolymers, 58:106-115 , January (2001) |
|
- For other applications of TNPACK to evolutionary trees, see:
| |
|
|
T. Pinou, T. Schlick, B. Li, and H. Dowling, "Addition of Darwin's Third Dimension to Evolutionary Trees", J. Theor. Bio., 219:505-512, October (1996) |
|
- For general reviews on optimization, including TNPACK, see:
| |
|
|
| |
|
|
T. Schlick, "Optimization Methods in Computational Chemistry", in Reviews in Computational Chemistry, Volume 3 , Chapter 1, pages 1-71, K. B. Lipkowitz and D. B. Boyd, eds., VCH Publishers, New York (1992) |
|
| |
|
|
T. Schlick and G. Parks, "Mathematical Optimization'', contributed chapter to a scientific computing electronic textbook (``e-book") in DOE Computational Sciences Education Project, URL: http://csep1.phy.ornl.gov/csep.html (1994) |
|
| |
|
|
T. Schlick, "Geometry Optimization", Contributed chapter to the Encyclopedia of Computational Chemistry (5 Volumes), Volume 2, pages 1136-1157, P. von Rague Schleyer, Editor in Chief and N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, and H. F. Schaefer III, eds., John Wiley & Sons, West Sussex (1998) |
|
| |
|
|
