Efficient softest mode finding in transition states calculations.

Transition states are fundamental to understanding the reaction dynamics qualitatively in chemical physics. To date various methods of first principle location of the transition states have been developed. In the absence of the knowledge of the final structure, the softest-mode following method climbs up to a transition state without calculating the Hessian matrix. One weakness of this kind of approaches is that the number of rotations to determine the softest mode is usually unpredictable. In this paper, we propose a locally optimal search direction finding algorithm, namely LOR, which is an extension of the traditional conjugate gradient method without additional calculations of the forces. We also show that the translation of forces improves the numerical stability. Experiments for the Baker test system show that the proposed algorithm is much faster than the original dimer conjugate gradient method.

[1]  Jon Baker,et al.  The location of transition states: A comparison of Cartesian, Z‐matrix, and natural internal coordinates , 1996 .

[2]  Walter Thiel,et al.  DL-FIND: an open-source geometry optimizer for atomistic simulations. , 2009, The journal of physical chemistry. A.

[3]  G. Henkelman,et al.  Comparison of methods for finding saddle points without knowledge of the final states. , 2004, The Journal of chemical physics.

[4]  G. Kresse,et al.  Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set , 1996 .

[5]  Barkema,et al.  Event-Based Relaxation of Continuous Disordered Systems. , 1996, Physical review letters.

[6]  Y. Khait,et al.  Search for stationary points on multidimensional surfaces , 1997 .

[7]  A. Chakraborty,et al.  A growing string method for determining transition states: comparison to the nudged elastic band and string methods. , 2004, The Journal of chemical physics.

[8]  G. Henkelman,et al.  Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points , 2000 .

[9]  Andrew V. Knyazev,et al.  Toward the Optimal Preconditioned Eigensolver: Locally Optimal Block Preconditioned Conjugate Gradient Method , 2001, SIAM J. Sci. Comput..

[10]  D. Wales Structural and topological consequences of anisotropic interactions in clusters , 1990 .

[11]  P. Jørgensen,et al.  Walking on potential energy surfaces , 1983 .

[12]  A. Bell,et al.  Efficient methods for finding transition states in chemical reactions: comparison of improved dimer method and partitioned rational function optimization method. , 2005, The Journal of chemical physics.

[13]  Zhipan Liu,et al.  Comprehensive mechanism and structure-sensitivity of ethanol oxidation on platinum: new transition-state searching method for resolving the complex reaction network. , 2008, Journal of the American Chemical Society.

[14]  Weinan E,et al.  Atomistic simulations of rare events using gentlest ascent dynamics. , 2011, The Journal of chemical physics.

[15]  G. Henkelman,et al.  A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives , 1999 .

[16]  Theoretical study of some small van der Waals complexes containing inert gas atoms , 1991 .

[17]  Lindsey J. Munro,et al.  DEFECT MIGRATION IN CRYSTALLINE SILICON , 1999 .

[18]  Ron Elber,et al.  A method for determining reaction paths in large molecules: application to myoglobin , 1987 .

[19]  Mills,et al.  Quantum and thermal effects in H2 dissociative adsorption: Evaluation of free energy barriers in multidimensional quantum systems. , 1994, Physical review letters.

[20]  N. Mousseau,et al.  Dynamics of lennard-jones clusters: A characterization of the activation-relaxation technique , 2000 .

[21]  David J Wales,et al.  Comparison of double-ended transition state search methods. , 2007, The Journal of chemical physics.

[22]  David J. Wales,et al.  Transition states and rearrangement mechanisms from hybrid eigenvector-following and density functional theory. Application to C10H10 and defect migration in crystalline silicon , 2001 .

[23]  Evgueni E. Ovtchinnikov,et al.  Jacobi Correction Equation, Line Search, and Conjugate Gradients in Hermitian Eigenvalue Computation I: Computing an Extreme Eigenvalue , 2008, SIAM J. Numer. Anal..

[24]  G. Henkelman,et al.  A climbing image nudged elastic band method for finding saddle points and minimum energy paths , 2000 .

[25]  G. Henkelman,et al.  Optimization methods for finding minimum energy paths. , 2008, The Journal of chemical physics.

[26]  C. Shang,et al.  Constrained Broyden Minimization Combined with the Dimer Method for Locating Transition State of Complex Reactions , 2010 .

[27]  David J. Wales,et al.  Erratum: A doubly nudged elastic band method for finding transition states [J. Chem. Phys. 120, 2082 (2004)] , 2004 .

[28]  David J Wales,et al.  Finding pathways between distant local minima. , 2005, The Journal of chemical physics.

[29]  Qiang Du,et al.  Constrained shrinking dimer dynamics for saddle point search with constraints , 2012, J. Comput. Phys..

[30]  Paul Sherwood,et al.  Superlinearly converging dimer method for transition state search. , 2008, The Journal of chemical physics.

[31]  D. Wales,et al.  A doubly nudged elastic band method for finding transition states. , 2004, The Journal of chemical physics.

[32]  W. Miller,et al.  ON FINDING TRANSITION STATES , 1981 .

[33]  E. Vanden-Eijnden,et al.  String method for the study of rare events , 2002, cond-mat/0205527.

[34]  J. Baker An algorithm for the location of transition states , 1986 .

[35]  David J Wales,et al.  Protonated water clusters described by an empirical valence bond potential. , 2005, The Journal of chemical physics.

[36]  David J. Wales,et al.  Global optimization and folding pathways of selected α-helical proteins , 2005 .

[37]  E Weinan,et al.  The gentlest ascent dynamics , 2010, 1011.0042.