Solid State Dimer

The dimer method of Henkelman and Jónsson with improvements by Heyden et al and Kästner and Sherwood for estimating the lowest eigenmode using only first derivatives. [1] [2] [3]

The solid state dimer module extends this method to solid state phase transitions. [4]

Usage

The SSDimer_atoms is an atoms-like class, which defines suitable set_positions(), get_positions(), get_forces() for the solid-state dimer (SSDimer) method to include cell degrees of freedom in saddle search. It becomes the regular dimer by setting “ss=False”. External stress tensor can be applied by setting “express” to find saddles on enthalpy surfaces.

class SSDimer_atoms(self, R0 = None, mode = None, maxStep = 0.2, dT = 0.1, dR = 0.001,

phi_tol = 5, rotationMax = 4, ss = False, express=np.zeros((3,3)), rotationOpt = ‘cg’, weight = 1):

R0 : an atoms object, which gives the starting point

mode : initial mode (will be randomized if one is not provided)

maxStep : longest distance dimer can move in a single iteration

dT : quickmin timestep

dR : separation distance between the two images of the dimer (the finite difference distance)

phi_tol : rotation converging tolerence, degree

rotationMax : max rotations per translational step

ss : boolean, solid-state dimer or not

express : 3*3 matrix, external stress tensor. Columns are the stress vectors. Needs to be in lower triangular form to avoid rigid rotation.

rotationOpt: the optimization method for the rotation part: choose from “sd” (steepest descent), “cg” (conjugate gradient), and “bfgs”.

weight: extra weight to put on the cell degrees of freedom

Example:

from tsase.dimer import ssdimer
d = ssdimer.SSDimer_atoms(R0 = p, rotationMax = 10, phi_tol=3, ss = True)
### Use quickmin optimizer in ssdimer
d.search(minForce = 0.0001, movie = "dimer2.movie", interval = 20 )
### Or use other first order optimizer in ase.
### Second order optimizers cannot be used when "ss = True".
#dyn = MDMin(d)
#dyn.run(fmax=0.0001)

References

[1]	Henkelman and H. Jónsson, “A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives,” J. Chem. Phys. 111, 7010-7022 (1999). DOI

[2]	Heyden, A.T. Bell, and F.J. Keil, “Efficient methods for finding transition states in chemical reactions: Comparison of improved dimer method and partitioned rational function optimization method,” J. Chem. Phys. 123, 224101 (2005). DOI

[3]	Kästner and P. Sherwood, “Superlinearly converging dimer method for transition state search,” J. Chem. Phys. 128, 014106 (2008) DOI

[4]	Xiao, D. Sheppard, J. Rogal, and G. Henkelman, “Solid-state dimer method for calculating solid-solid phase transitions”, J. Chem. Phys. 140, 174104 (2014). DOI