Saddle Search#
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 client_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.
Configuration#
[Saddle Search]
Changed in version 2.1_TBA: In TOML, this will be [Saddle_Search]
- pydantic model eon.schema.SaddleSearchConfig[source]#
Show JSON schema
{ "title": "SaddleSearchConfig", "type": "object", "properties": { "method": { "default": "min_mode", "description": "Method to locate the saddle point.", "enum": [ "min_mode", "dynamics" ], "title": "Method", "type": "string" }, "min_mode_method": { "default": "dimer", "description": "Min-mode method to use.", "enum": [ "dimer", "lanczos", "gprdimer" ], "title": "Min Mode Method", "type": "string" }, "max_energy": { "default": 20.0, "description": "The energy at which a saddle search is considered bad and terminated.", "title": "Max Energy", "type": "number" }, "displace_radius": { "default": 5.0, "description": "Atoms within this distance of the epicenter will be displaced.", "title": "Displace Radius", "type": "number" }, "displace_magnitude": { "default": 0.1, "description": "The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.", "title": "Displace Magnitude", "type": "number" }, "displace_random_weight": { "default": 1.0, "description": "Relative probability to displace with a random epicenter.", "title": "Displace Random Weight", "type": "number" }, "displace_not_FCC_HCP_weight": { "default": 0.0, "description": "Relative probability to displace with an epicenter that is not FCC or HCP coordinated.", "title": "Displace Not Fcc Hcp Weight", "type": "number" }, "displace_least_coordinated_weight": { "default": 0.0, "description": "Relative probability to displace with an epicenter that has a coordination number equal to the least-coordinated atom in the configuration.", "title": "Displace Least Coordinated Weight", "type": "number" }, "displace_under_coordinated_weight": { "default": 0.0, "description": "Relative probability to displace with an epicenter with a coordination equal to or less than displace_max_coordination.", "title": "Displace Under Coordinated Weight", "type": "number" }, "displace_listed_atom_weight": { "default": 0.0, "description": "Relative probability to displace with an epicenter listed in displace_atom_list.", "title": "Displace Listed Atom Weight", "type": "number" }, "displace_atom_list": { "default": [ -1 ], "description": "The individual index should be separated by a comma. Example: 10, 20, -1 would be the 10, 20, and the last atom.", "items": { "type": "integer" }, "title": "Displace Atom List", "type": "array" }, "displace_listed_type_weight": { "default": 0.0, "description": "Relative probability to displace with an epicenter listed in displace_type_list.", "title": "Displace Listed Type Weight", "type": "number" }, "displace_type_list": { "default": [], "description": "The atom types should be separated by a comma.", "items": { "type": "string" }, "title": "Displace Type List", "type": "array" }, "displace_all_listed": { "default": false, "description": "This can be disabled by setting `displace_radius` to 0. Otherwise:\n\n- 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`.\n- If false, one of the atoms in `displace_atom_list` or `displace_type_list` will be selected at random for each displacement.\n- In either case, all atoms up to `displace_radius` distance away from any displaced atom will be included in the displacement.", "title": "Displace All Listed", "type": "boolean" }, "displace_max_coordination": { "default": 11, "description": "When using under_coordinated as the displacement type, choose only atoms with a coordination equal to or less than this.", "title": "Displace Max Coordination", "type": "integer" }, "converged_force": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "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.", "title": "Converged Force" }, "max_iterations": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "The maximum number of translation steps to be taken.", "title": "Max Iterations" }, "nonlocal_count_abort": { "default": 0, "description": "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.", "title": "Nonlocal Count Abort", "type": "integer" }, "nonlocal_distance_abort": { "default": 0.0, "description": "If nonlocal_count_abort is not zero, the saddle search will abort when nonlocal_count_abort atoms have moved more than this distance.", "title": "Nonlocal Distance Abort", "type": "number" }, "client_displace_type": { "default": "load", "description": "Type of displacement method used.", "enum": [ "load", "random", "last_atom", "min_coordinated", "not_fcc_or_hcp" ], "title": "Client Displace Type", "type": "string" }, "zero_mode_abort_curvature": { "default": 0.0, "description": "The saddle search will abort when the magnitude of the minmode curvature is less than this value.", "title": "Zero Mode Abort Curvature", "type": "number" }, "confine_positive": { "default": false, "description": "Activates a confinement scheme when the search is within a positive region of the PES.", "title": "Confine Positive", "type": "boolean" }, "bowl_breakout": { "default": false, "description": "When activated, the search within positive regions of PES is confined to a subset of atoms.", "title": "Bowl Breakout", "type": "boolean" }, "bowl_active_atoms": { "default": 20, "description": "Size of the applied confinement in the bowl breakout scheme.", "title": "Bowl Active Atoms", "type": "integer" }, "dynamics_temperature": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "The temperature, in Kelvin, for the molecular dynamics run.", "title": "Dynamics Temperature" }, "dynamics_state_check_interval": { "default": 100.0, "description": "The time interval, in femtoseconds, to minimize the geometry and check if the system has left the initial state.", "title": "Dynamics State Check Interval", "type": "number" }, "dynamics_record_interval": { "default": 10.0, "description": "The time interval, in femtoseconds, between snapshots of the molecular dynamics trajectory.", "title": "Dynamics Record Interval", "type": "number" }, "dynamics_linear_interpolation": { "default": true, "description": "- If true, then the band connecting the initial and final states will be\n initialized using a linear interpolation.\n- If false, then the band is interpolated through the first snapshot that\n minimizes to the final state.", "title": "Dynamics Linear Interpolation", "type": "boolean" }, "dynamics_max_init_curvature": { "default": 0.0, "description": "The maximum initial curvature for the dynamics method in eV/\u00c5^2.", "title": "Dynamics Max Init Curvature", "type": "number" }, "nonnegative_displacement_abort": { "default": false, "description": "Abort the search if a non-negative displacement is detected.", "title": "Nonnegative Displacement Abort", "type": "boolean" }, "max_single_displace": { "default": 10.0, "description": "The maximum single displacement value.", "title": "Max Single Displace", "type": "number" }, "remove_rotation": { "default": false, "description": "Remove rotational components from the displacement.", "title": "Remove Rotation", "type": "boolean" }, "perp_force_ratio": { "default": 0.0, "description": "The ratio of perpendicular force, undocumented.", "title": "Perp Force Ratio", "type": "number" }, "confine_positive_min_force": { "default": 0.5, "description": "The minimum force for confining the positive region of the PES, undocumented.", "title": "Confine Positive Min Force", "type": "number" }, "confine_positive_scale_ratio": { "default": 0.9, "description": "The scaling ratio for confining the positive region of the PES, undocumented.", "title": "Confine Positive Scale Ratio", "type": "number" }, "confine_positive_boost": { "default": 10.0, "description": "The boost factor for confining the positive region of the PES, undocumented.", "title": "Confine Positive Boost", "type": "number" }, "confine_positive_min_active": { "default": 30, "description": "The minimum number of active atoms for confining the positive region of the PES, undocumented.", "title": "Confine Positive Min Active", "type": "integer" } } }
- Config:
use_attribute_docstrings: bool = True
- Fields:
- field bowl_breakout: bool = False#
Determines
bowl_active_atomsthat are subject to the largest forces. To activate,confine_positivemust also be true. Method of Pedersen and Luiser [SS_PL14].When activated, the search within positive regions of PES is confined to a subset of atoms.
- field client_displace_type: Literal['load', 'random', 'last_atom', 'min_coordinated', 'not_fcc_or_hcp'] = 'load'#
Type of displacement method used.
- field confine_positive: bool = False#
Activates a confinement scheme when the search is within a positive region of the PES.
- field confine_positive_boost: float = 10.0#
The boost factor for confining the positive region of the PES, undocumented.
- field confine_positive_min_active: int = 30#
The minimum number of active atoms for confining the positive region of the PES, undocumented.
- field confine_positive_min_force: float = 0.5#
The minimum force for confining the positive region of the PES, undocumented.
- field confine_positive_scale_ratio: float = 0.9#
The scaling ratio for confining the positive region of the PES, undocumented.
- field converged_force: float | None = None#
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.
- field displace_all_listed: bool = False#
This can be disabled by setting displace_radius to 0. Otherwise:
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. Otherwise:
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.
- field displace_atom_list: list[int] = [-1]#
The individual index should be separated by a comma. Example: 10, 20, -1 would be the 10, 20, and the last atom.
- field displace_least_coordinated_weight: float = 0.0#
Relative probability to displace with an epicenter that has a coordination number equal to the least-coordinated atom in the configuration.
- field displace_listed_atom_weight: float = 0.0#
Relative probability to displace with an epicenter listed in displace_atom_list.
- field displace_listed_type_weight: float = 0.0#
Relative probability to displace with an epicenter listed in displace_type_list.
- field displace_magnitude: float = 0.1#
The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
- field displace_max_coordination: int = 11#
When using under_coordinated as the displacement type, choose only atoms with a coordination equal to or less than this.
- field displace_not_FCC_HCP_weight: float = 0.0#
Relative probability to displace with an epicenter that is not FCC or HCP coordinated.
- field displace_random_weight: float = 1.0#
Relative probability to displace with a random epicenter.
- field displace_under_coordinated_weight: float = 0.0#
Relative probability to displace with an epicenter with a coordination equal to or less than displace_max_coordination.
- field dynamics_linear_interpolation: bool = True#
If true, then the band connecting the initial and final states will be initialized using a linear interpolation.
If false, then the band is interpolated through the first snapshot that minimizes to the final state.
If true, then the band connecting the initial and final states will be initialized using a linear interpolation.
If false, then the band is interpolated through the first snapshot that minimizes to the final state.
- field dynamics_max_init_curvature: float = 0.0#
The maximum initial curvature for the dynamics method in eV/Å^2.
- field dynamics_record_interval: float = 10.0#
Snapshots of MD trajectories are 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.
The time interval, in femtoseconds, between snapshots of the molecular dynamics trajectory.
- field dynamics_state_check_interval: float = 100.0#
The time interval, in femtoseconds, to minimize the geometry and check if the system has left the initial state.
- field dynamics_temperature: float | None = None#
A good initial choice might be near the melting temperature of the material.
The temperature, in Kelvin, for the molecular dynamics run.
- field max_energy: float = 20.0#
The energy at which a saddle search is considered bad and terminated.
- field method: Literal['min_mode', 'dynamics'] = 'min_mode'#
- Options:
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.
Method to locate the saddle point.
- field min_mode_method: Literal['dimer', 'lanczos', 'gprdimer'] = 'dimer'#
- Options:
dimer: Use the dimer min-mode method from Henkelman and Jónsson [SS_HJonsson99]lanczos: Use the Lanczos min-mode method from Malek and Mousseau [SS_MM00]gprdimer: Use the GP accelerated dimer method.
Min-mode method to use.
- field nonlocal_count_abort: int = 0#
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.
- field nonlocal_distance_abort: float = 0.0#
If nonlocal_count_abort is not zero, the saddle search will abort when nonlocal_count_abort atoms have moved more than this distance.
- field nonnegative_displacement_abort: bool = False#
Abort the search if a non-negative displacement is detected.
References#
Graeme Henkelman and Hannes Jónsson. A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. The Journal of Chemical Physics, 111(15):7010–7022, October 1999. doi:10.1063/1.480097.
Rachid Malek and Normand Mousseau. Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique. Physical Review E, 62(6):7723–7728, December 2000. doi:10.1103/PhysRevE.62.7723.
Andreas Pedersen and Mathieu Luiser. Bowl breakout: Escaping the positive region when searching for saddle points. The Journal of Chemical Physics, 141(2):024109, July 2014. doi:10.1063/1.4885852.