Dimer method

The dimer method is a means of finding a saddle point on a potential energy surface starting from a single point (as opposed to a NEB calculation, which requires an initial and final state). You can read about this method here:

  1. ‘A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives’, G. Henkelman and H. Jonsson, J. Chem. Phys. 111, 7010, 1999.

An example is shown below.

from ase.build import fcc100, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.dimer import DimerControl, MinModeAtoms, MinModeTranslate

# Set up a small "slab" with an adatoms
atoms = fcc100('Pt', size = (2, 2, 1), vacuum = 10.0)
add_adsorbate(atoms, 'Pt', 1.611, 'hollow')

# Freeze the "slab"
mask = [atom.tag > 0 for atom in atoms]
atoms.set_constraint(FixAtoms(mask = mask))

# Calculate using EMT
atoms.set_calculator(EMT())
relaxed_energy = atoms.get_potential_energy()

# Set up the dimer
d_control = DimerControl(initial_eigenmode_method = 'displacement', \
                         displacement_method = 'vector', logfile = None, \
                         mask = [0, 0, 0, 0, 1])
d_atoms = MinModeAtoms(atoms, d_control)

# Displace the atoms
displacement_vector = [[0.0]*3]*5
displacement_vector[-1][1] = -0.1
d_atoms.displace(displacement_vector = displacement_vector)

# Converge to a saddle point
dim_rlx = MinModeTranslate(d_atoms, trajectory = 'dimer_method.traj', \
                           logfile = None)
dim_rlx.run(fmax = 0.001)

The module contains several classes.

class ase.dimer.DimerControl(logfile='-', eigenmode_logfile=None, **kwargs)[source]

A class that takes care of the parameters needed for a Dimer search.

Parameters:

eigenmode_method: str

The name of the eigenmode search method.

f_rot_min: float

Size of the rotational force under which no rotation will be performed.

f_rot_max: float

Size of the rotational force under which only one rotation will be performed.

max_num_rot: int

Maximum number of rotations per optimizer step.

trial_angle: float

Trial angle for the finite difference estimate of the rotational angle in radians.

trial_trans_step: float

Trial step size for the MinModeTranslate optimizer.

maximum_translation: float

Maximum step size and forced step size when the curvature is still positive for the MinModeTranslate optimizer.

cg_translation: bool

Conjugate Gradient for the MinModeTranslate optimizer.

use_central_forces: bool

Only calculate the forces at one end of the dimer and extrapolate the forces to the other.

dimer_separation: float

Separation of the dimer’s images.

initial_eigenmode_method: str

How to construct the initial eigenmode of the dimer. If an eigenmode is given when creating the MinModeAtoms object, this will be ignored. Possible choices are: ‘gauss’ and ‘displacement’

extrapolate_forces: bool

When more than one rotation is performed, an extrapolation scheme can be used to reduce the number of force evaluations.

displacement_method: str

How to displace the atoms. Possible choices are ‘gauss’ and ‘vector’.

gauss_std: float

The standard deviation of the gauss curve used when doing random displacement.

order: int

How many lowest eigenmodes will be inverted.

mask: list of bool

Which atoms will be moved during displacement.

displacement_center: int or [float, float, float]

The center of displacement, nearby atoms will be displaced.

displacement_radius: float

When choosing which atoms to displace with the displacement_center keyword, this decides how many nearby atoms to displace.

number_of_displacement_atoms: int

The amount of atoms near displacement_center to displace.

class ase.dimer.MinModeAtoms(atoms, control=None, eigenmodes=None, random_seed=None, **kwargs)[source]

Wrapper for Atoms with information related to minimum mode searching.

Contains an Atoms object and pipes all unknown function calls to that object. Other information that is stored in this object are the estimate for the lowest eigenvalue, curvature, and its corresponding eigenmode, eigenmode. Furthermore, the original configuration of the Atoms object is stored for use in multiple minimum mode searches. The forces on the system are modified by inverting the component along the eigenmode estimate. This eventually brings the system to a saddle point.

Parameters:

atomsAtoms object

A regular Atoms object

controlMinModeControl object

Contains the parameters necessary for the eigenmode search. If no control object is supplied a default DimerControl will be created and used.

mask: list of bool

Determines which atoms will be moved when calling displace()

random_seed: int

The seed used for the random number generator. Defaults to modified version the current time.

References: 1 2 3 4

1

Henkelman and Jonsson, JCP 111, 7010 (1999)

2

Olsen, Kroes, Henkelman, Arnaldsson, and Jonsson, JCP 121, 9776 (2004).

3

Heyden, Bell, and Keil, JCP 123, 224101 (2005).

4

Kastner and Sherwood, JCP 128, 014106 (2008).

class ase.dimer.MinModeTranslate(atoms, logfile='-', trajectory=None)[source]

An Optimizer specifically tailored to minimum mode following.

Structure optimizer object.

Parameters:

atoms: Atoms object

The Atoms object to relax.

restart: str

Filename for restart file. Default value is None.

logfile: file object or str

If logfile is a string, a file with that name will be opened. Use ‘-‘ for stdout.

trajectory: Trajectory object or str

Attach trajectory object. If trajectory is a string a Trajectory will be constructed. Use None for no trajectory.

master: boolean

Defaults to None, which causes only rank 0 to save files. If set to true, this rank will save files.

append_trajectory: boolean

Appended to the trajectory file instead of overwriting it.

force_consistent: boolean or None

Use force-consistent energy calls (as opposed to the energy extrapolated to 0 K). If force_consistent=None, uses force-consistent energies if available in the calculator, but falls back to force_consistent=False if not.

class ase.dimer.DimerEigenmodeSearch(atoms, control=None, eigenmode=None, basis=None, **kwargs)[source]

An implementation of the Dimer’s minimum eigenvalue mode search.

This class implements the rotational part of the dimer saddle point searching method.

Parameters:

atoms: MinModeAtoms object

MinModeAtoms is an extension to the Atoms object, which includes information about the lowest eigenvalue mode.

control: DimerControl object

Contains the parameters necessary for the eigenmode search. If no control object is supplied a default DimerControl will be created and used.

basis: list of xyz-values

Eigenmode. Must be an ndarray of shape (n, 3). It is possible to constrain the eigenmodes to be orthogonal to this given eigenmode.

Notes:

The code is inspired, with permission, by code written by the Henkelman group, which can be found at http://theory.cm.utexas.edu/vtsttools/code/

References:

  • Henkelman and Jonsson, JCP 111, 7010 (1999)

  • Olsen, Kroes, Henkelman, Arnaldsson, and Jonsson, JCP 121, 9776 (2004).

  • Heyden, Bell, and Keil, JCP 123, 224101 (2005).

  • Kastner and Sherwood, JCP 128, 014106 (2008).