A saddle search is initiated by making a local displacement of atoms from their position at the minimum of the current state. This displacement can be done using the different strategies indicated by the displace_type option, and the following parameters. If the user knows something about the local environment where reactions are likely to take place in the system, this information can be used to make saddle searches more efficient by getting them started in the right part of configuration space.
method:
default:
min_modeoptions:
min_mode: Use a min-mode following scheme to locate the saddle point.
dynamics: Experimental method that uses molecular dynamics to find new states and then runs a climbing image NEB calculation to find the saddle and a dimer calculation to estimate the eigenmode at the saddle.
min_mode_method:
max_energy: The energy at which a saddle search is considered bad and terminated.
default:
20.0
displace_radius: Atoms within this distance of the epicenter will be displaced.
default:
5.0
displace_magnitude: The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
default:
0.1
displace_random_weight: Relative probability to displace with a random epicenter.
default:
1.0, if no other weights set
displace_not_FCC_HCP_weight: Relative probabilty to displace with an epicenter that is not FCC or HCP coordinated.
default:
0.0
displace_least_coordinated_weight: Relative probability to displace with an epicenter that has a coordination number equal to the least-coordinated atom in the configuration.
default:
0.0
displace_under_coordinated_weight: Relative probability to displace with an epicenter with a coordination equal to or less than displace_max_coordination.
default:
0.0
displace_listed_atom_weight: Relative probability to displace with an epicenter listed in displace_atomlist.
default:
0.0
displace_atom_list: The individual index should be separated by a comma 10, 20,-1 would be the 10, 20 and the last atom.
default:
0
displace_listed_type_weight: Relative probability to displace with an epicenter listed in displace_typelist.
default:
0.0
displace_type_list: The atom types should be separated by a comma
default:
none
displace_all_listed: If true, each displacement will include all of the degrees of freedom of all of the listed atoms in displace_atom_list or displace_type_list. If false one of the atoms in displace_atom_list or displace_type_list will be selected at random for each displacement. In either case all atoms up to displace_radius distance away from any displaced atom will be included in the displacement. This can be disabled by setting displace_radius to 0.
default:
false
displace_max_coordination: When using under_coordinated as the displacement type, choose only atoms with a coordination equal to or less than this.
default:
11
converged_force: When the maximum force (in eV/A) on any one atom is smaller than this value, the structure is considered converged onto a saddle point.
default:
[Optimizer] converged_force
max_iterations: The maximum number of translation steps to be taken.
default:
[Optimizer] max_iterations
nonlocal_count_abort: If this is not zero, the saddle search will abort when this many atoms have moved more than nonlocal_distance_abort from the initial displacement.
default:
0(off)
nonlocal_distance_abort: If nonlocal_count_abort is not zero, the saddle search will abort when nonlocal_count_abort atoms have moved more than this distance.
default:
0.0
zero_mode_abort_curvature: The saddle search will abort when the magnitude of the minmode curvature is less than this value.
default:
0.0
confine_positive: Activates a confinement scheme when the search is within a positive region of the PES.
default:
false
bowl_breakout: When activated the search within positive regions of PES is confined to the subset of atoms (bowl_active_atoms) that are subject to the the largest forces 3 . To activate confine_positive must also be true
default:
false
bowl_active_atoms: Size of the applied confinement in the bowl breakout scheme.
default:
20
dynamics_temperature: The temperature, in Kelvin, for the molecular dynamics run. A good initial choice might be near melting temperature of the material.
default:
[Main] temperature
dynamics_state_check_interval: The time interval, in femtoseconds, to minimizing the geometry and check if the system has left the initial state.
default:
100.0
dynamics_record_interval: The time interval, in femtoseconds, between snapshots of the molecular dynamics trajectory. These snapshots are then used to locate when the system first left the initial state. A binary search is used to locate the first snapshot that minimizes to a new geometry.
default:
10.0
dynamics_linear_interpolation: If set to true, then the band connecting the initial and final states will be initialized using a linear interpolation. If set to false, then the band
is interpolated through the first snapshot that minimizes to the final state.
default:
true
References
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
Malek and N. Mousseau, “Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique,” Phys. Rev. E 62, 7723 (2000). DOI
Pedersen and M. Luiser, “Bowl breakout, escaping the positive region when searching for saddle points,” J. Chem. Phys. 141, 024109 (2014). DOI