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:

‘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


def test_dimer_method(testdir):
    # 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.calc = EMT()
    atoms.get_potential_energy()

    # Set up the dimer
    with DimerControl(initial_eigenmode_method='displacement',
                      displacement_method='vector', logfile=None,
                      mask=[0, 0, 0, 0, 1]) as d_control:
        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
        with MinModeTranslate(d_atoms, trajectory='dimer_method.traj',
                              logfile=None) as dim_rlx:
            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).