GeometricProcedure

pydantic model openff.qcsubmit.procedures.GeometricProcedure[source]

This is a settings class controlling the various runtime options that can be used when running geometric.

Note

The coordinate systems supported by geometric are:

  • cart Cartesian

  • prim Primitive a.k.a redundant

  • dlc Delocalised Internal Coordinates

  • hdlc Hybrid Delocalised Internal Coordinates

  • tric Translation-Rotation-Internal Coordinates, this is the default default

Important

Geometric currently accepts the following convergence criteria sets:

Set

Set Name

Energy

GRMS

GMAX

DRMS

DMAX

GAU

Gaussian default

1e-6

3e-4

4.5e-4

1.2e-3

1.8e-3

NWCHEM_LOOSE

NW-Chem loose

1e-6

3e-3

4.5e-3

3.6e-3

5.4e-3

GAU_LOOSE

Gaussian loose

1e-6

1.7e-3

2.5e-3

6.7e-3

1e-2

TURBOMOLE

Turbomole default

1e-6

5e-4

1e-3

5.0e-4

1e-3

INTERFRAG_TIGHT

Interfrag tight

1e-6

1e-5

1.5e-5

4.0e-4

6.0e-4

GAU_TIGHT

Gaussian tight

1e-6

1e-5

1.5e-5

4e-5

6e-5

GAU_VERYTIGHT

Gaussian very tight

1e-6

1e-6

2e-6

4e-6

6e-6

Show JSON schema
{
   "title": "GeometricProcedure",
   "description": "This is a settings class controlling the various runtime options that can be used when running geometric.\n\nNote:\n    The coordinate systems supported by geometric are:\n\n        - `cart` Cartesian\n        - `prim` Primitive a.k.a redundant\n        - `dlc` Delocalised Internal Coordinates\n        - `hdlc` Hybrid Delocalised Internal Coordinates\n        - `tric` Translation-Rotation-Internal Coordinates, this is the default default\n\nImportant:\n    Geometric currently accepts the following convergence criteria sets:\n\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        |  Set              | Set Name            | Energy |  GRMS   | GMAX   | DRMS   | DMAX  |\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `GAU`             | Gaussian default    | 1e-6   | 3e-4    | 4.5e-4 | 1.2e-3 | 1.8e-3|\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `NWCHEM_LOOSE`    | NW-Chem loose       | 1e-6   | 3e-3    | 4.5e-3 | 3.6e-3 | 5.4e-3|\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `GAU_LOOSE`       | Gaussian loose      | 1e-6   | 1.7e-3  | 2.5e-3 | 6.7e-3 | 1e-2  |\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `TURBOMOLE`       | Turbomole default   | 1e-6   | 5e-4    | 1e-3   | 5.0e-4 | 1e-3  |\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `INTERFRAG_TIGHT` | Interfrag tight     | 1e-6   | 1e-5    | 1.5e-5 | 4.0e-4 | 6.0e-4|\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `GAU_TIGHT`       | Gaussian tight      | 1e-6   | 1e-5    | 1.5e-5 | 4e-5   | 6e-5  |\n        +-------------------+---------------------+--------+---------+--------+--------+-------+\n        | `GAU_VERYTIGHT`   | Gaussian very tight | 1e-6   | 1e-6    | 2e-6   | 4e-6   | 6e-6  |\n        +-------------------+---------------------+--------+---------+--------+--------+-------+",
   "type": "object",
   "properties": {
      "program": {
         "title": "Program",
         "description": "The name of the program executing the procedure.",
         "default": "geometric",
         "enum": [
            "geometric"
         ],
         "type": "string"
      },
      "coordsys": {
         "title": "Coordsys",
         "description": "The type of coordinate system which should be used during the optimization. Choices are tric, prim, dlc, hdlc, and cart.",
         "default": "dlc",
         "enum": [
            "tric",
            "prim",
            "dlc",
            "hdlc",
            "cart"
         ],
         "type": "string"
      },
      "enforce": {
         "title": "Enforce",
         "description": "The threshold( in a.u / rad) to activate precise constraint satisfaction.",
         "default": 0.0,
         "type": "number"
      },
      "epsilon": {
         "title": "Epsilon",
         "description": "Small eigenvalue threshold.",
         "default": 1e-05,
         "type": "number"
      },
      "reset": {
         "title": "Reset",
         "description": "Reset the Hessian when the eigenvalues are under epsilon.",
         "default": true,
         "type": "boolean"
      },
      "qccnv": {
         "title": "Qccnv",
         "description": "Activate Q-Chem style convergence criteria(i.e.gradient and either energy or displacement).",
         "default": false,
         "type": "boolean"
      },
      "molcnv": {
         "title": "Molcnv",
         "description": "Activate Molpro style convergence criteria (i.e.gradient and either energy or displacement, with different defaults).",
         "default": false,
         "type": "boolean"
      },
      "check": {
         "title": "Check",
         "description": "The interval for checking the coordinate system for changes.",
         "default": 0,
         "type": "integer"
      },
      "trust": {
         "title": "Trust",
         "description": "Starting value of the trust radius.",
         "default": 0.1,
         "type": "number"
      },
      "tmax": {
         "title": "Tmax",
         "description": "Maximum value of trust radius.",
         "default": 0.3,
         "type": "number"
      },
      "maxiter": {
         "title": "Maxiter",
         "description": "Maximum number of optimization cycles.",
         "default": 300,
         "type": "integer"
      },
      "convergence_set": {
         "title": "Convergence Set",
         "description": "The set of convergence criteria to be used for the optimisation.",
         "default": "GAU",
         "enum": [
            "GAU",
            "NWCHEM_LOOSE",
            "GAU_LOOSE",
            "TURBOMOLE",
            "INTERFRAG_TIGHT",
            "GAU_TIGHT",
            "GAU_VERYTIGHT"
         ],
         "type": "string"
      },
      "constraints": {
         "title": "Constraints",
         "description": "The list of constraints orginsed by set and freeze that should be used in the optimization",
         "default": {},
         "type": "object"
      }
   }
}

Config

  • title: str = GeometricProcedure

  • validate_assignment: bool = True

Fields
Validators
field program: Literal['geometric'] = 'geometric'

The name of the program executing the procedure.

field coordsys: Literal['tric', 'prim', 'dlc', 'hdlc', 'cart'] = 'dlc'

The type of coordinate system which should be used during the optimization. Choices are tric, prim, dlc, hdlc, and cart.

Validated by

  • literal_lower

field enforce: float = 0.0

The threshold( in a.u / rad) to activate precise constraint satisfaction.

field epsilon: float = 1e-05

Small eigenvalue threshold.

field reset: bool = True

Reset the Hessian when the eigenvalues are under epsilon.

field qccnv: bool = False

Activate Q-Chem style convergence criteria(i.e.gradient and either energy or displacement).

field molcnv: bool = False

Activate Molpro style convergence criteria (i.e.gradient and either energy or displacement, with different defaults).

field check: int = 0

The interval for checking the coordinate system for changes.

field trust: float = 0.1

Starting value of the trust radius.

field tmax: float = 0.3

Maximum value of trust radius.

field maxiter: int = 300

Maximum number of optimization cycles.

field convergence_set: Literal['GAU', 'NWCHEM_LOOSE', 'GAU_LOOSE', 'TURBOMOLE', 'INTERFRAG_TIGHT', 'GAU_TIGHT', 'GAU_VERYTIGHT'] = 'GAU'

The set of convergence criteria to be used for the optimisation.

Validated by

  • literal_upper

field constraints: Dict = {}

The list of constraints orginsed by set and freeze that should be used in the optimization

get_optimzation_spec()[source]

Create the optimization specification to be used in qcarchive.

Returns

A dictionary representation of the optimization specification.

Return type

qcportal.models.common_models.OptimizationSpecification

classmethod from_opt_spec(optimization_specification)[source]

Create a geometric procedure from an Optimization spec.

Parameters

optimization_specification (qcportal.models.common_models.OptimizationSpecification) –

Return type

openff.qcsubmit.procedures.GeometricProcedure