Hyperdynamics

Hyperdynamics#

The hyperdynamics method uses a bias potential which should be zero at transition states and positive in minima in order to accelerate the rate of transitions as noted by Voter [HD_Vot97].

The hyperdynamics time step \(\delta t\) can be obtained from the molecular dynamics simulation time step \(\delta t^b\) multiplied by a boost factor \(e^{\beta \Delta V}\), where \({\Delta V}\) is the bias potential.

There are several possible forms of bias potential. In EON, we have implemented the bond-boost method of Miron and Fichthorn [HD_MF03] where the bias potential is controlled by the maximal (fractional) change in any bond length in the system. This is a good bias potential for systems in which the dynamics is governed by bond breaking and forming events.

You can run a hyperdynamics job by:

Configuration#

[Hyperdynamics]
pydantic model eon.schema.HyperdynamicsConfig[source]#

Show JSON schema
{
   "title": "HyperdynamicsConfig",
   "type": "object",
   "properties": {
      "bias_potential": {
         "default": "none",
         "description": "Type of bias potential to use.",
         "enum": [
            "none",
            "bond_boost"
         ],
         "title": "Bias Potential",
         "type": "string"
      },
      "bb_dvmax": {
         "default": 0.0,
         "description": "The magnitude of the bond-boost bias potential.",
         "title": "Bb Dvmax",
         "type": "number"
      },
      "bb_rmd_time": {
         "default": 100.0,
         "description": "Regular MD duration (in fs) to determine equilibrium bond length before adding bias potential.",
         "title": "Bb Rmd Time",
         "type": "number"
      },
      "bb_boost_atom_list": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "items": {
                  "type": "integer"
               },
               "type": "array"
            }
         ],
         "default": "ALL",
         "description": "The atoms that will be displaced in the calculation: a comma delimited list of atom indices, e.g. 0,1,2. Default is 'All'.",
         "title": "Bb Boost Atom List"
      },
      "bb_rcut": {
         "default": 3.0,
         "description": "Cutoff distance (in Angstroms) for bonds included in the bond-boost potential.",
         "title": "Bb Rcut",
         "type": "number"
      },
      "bb_stretch_threshold": {
         "default": 0.2,
         "description": "Defines the bond-boost dividing surface.",
         "title": "Bb Stretch Threshold",
         "type": "number"
      },
      "bb_ds_curvature": {
         "default": 0.95,
         "description": "Curvature near the bond-boost dividing surface.",
         "title": "Bb Ds Curvature",
         "type": "number"
      }
   }
}

Config:

  • use_attribute_docstrings: bool = True

Fields:
field bb_boost_atom_list: str | list[int] = 'ALL'#

The atoms that will be displaced in the calculation: a comma delimited list of atom indices, e.g. 0,1,2. Default is ‘All’.

field bb_ds_curvature: float = 0.95#

It should have a value <= 1. We recommend the value to be 0.9-0.98.

Curvature near the bond-boost dividing surface.

field bb_dvmax: float = 0.0#

The magnitude of the bond-boost bias potential.

field bb_rcut: float = 3.0#

Cutoff distance (in Angstroms) for bonds included in the bond-boost potential.

field bb_rmd_time: float = 100.0#

Regular MD duration (in fs) to determine equilibrium bond length before adding bias potential.

field bb_stretch_threshold: float = 0.2#

It should be smaller than the maximum fractional nearest-neighbor bond stretch or compression at any transition state.

Defines the bond-boost dividing surface.

field bias_potential: Literal['none', 'bond_boost'] = 'none'#

Options: - none: With no bias potential, run regular MD. - bond_boost: Bond boost method.

Type of bias potential to use.

References#

[HD_MF03]

Radu A. Miron and Kristen A. Fichthorn. Accelerated molecular dynamics with the bond-boost method. The Journal of Chemical Physics, 119(12):6210–6216, September 2003. doi:10.1063/1.1603722.

[HD_Vot97]

Arthur F. Voter. Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events. Physical Review Letters, 78(20):3908–3911, May 1997. doi:10.1103/PhysRevLett.78.3908.

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