PCMSettings

pydantic model openff.qcsubmit.common_structures.PCMSettings[source]

A class to handle PCM settings which can be used with PSi4.

Show JSON schema
{
   "title": "PCMSettings",
   "description": "A class to handle PCM settings which can be used with PSi4.",
   "type": "object",
   "properties": {
      "units": {
         "title": "Units",
         "description": "The units used in the input options atomic units are used by default.",
         "type": "string"
      },
      "codata": {
         "title": "Codata",
         "description": "The set of fundamental physical constants to be used in the module.",
         "default": 2010,
         "type": "integer"
      },
      "cavity_Type": {
         "title": "Cavity Type",
         "description": "Completely specifies type of molecular surface and its discretization.",
         "default": "GePol",
         "type": "string"
      },
      "cavity_Area": {
         "title": "Cavity Area",
         "description": "Average area (weight) of the surface partition for the GePol cavity in the specified units. By default this is in AU.",
         "default": 0.3,
         "type": "number"
      },
      "cavity_Scaling": {
         "title": "Cavity Scaling",
         "description": "If true, the radii for the spheres will be scaled by 1.2. For finer control on the scaling factor for each sphere, select explicit creation mode.",
         "default": true,
         "type": "boolean"
      },
      "cavity_RadiiSet": {
         "title": "Cavity Radiiset",
         "description": "Select set of atomic radii to be used. Currently Bondi-Mantina Bondi, UFF  and Allinger\u2019s MM3 sets available. Radii in Allinger\u2019s MM3 set are obtained by dividing the value in the original paper by 1.2, as done in the ADF COSMO implementation We advise to turn off scaling of the radii by 1.2 when using this set.",
         "default": "Bondi",
         "type": "string"
      },
      "cavity_MinRadius": {
         "title": "Cavity Minradius",
         "description": "Minimal radius for additional spheres not centered on atoms. An arbitrarily big value is equivalent to switching off the use of added spheres, which is the default in AU.",
         "default": 100,
         "type": "number"
      },
      "cavity_Mode": {
         "title": "Cavity Mode",
         "description": "How to create the list of spheres for the generation of the molecular surface.",
         "default": "Implicit",
         "type": "string"
      },
      "medium_SolverType": {
         "title": "Medium Solvertype",
         "description": "Type of solver to be used. All solvers are based on the Integral Equation Formulation of the Polarizable Continuum Model.",
         "default": "IEFPCM",
         "type": "string"
      },
      "medium_Nonequilibrium": {
         "title": "Medium Nonequilibrium",
         "description": "Initializes an additional solver using the dynamic permittivity. To be used in response calculations.",
         "default": false,
         "type": "boolean"
      },
      "medium_Solvent": {
         "title": "Medium Solvent",
         "description": "Specification of the dielectric medium outside the cavity. Note this will always be converted to the molecular formula to aid parsing via PCM.",
         "type": "string"
      },
      "medium_MatrixSymm": {
         "title": "Medium Matrixsymm",
         "description": "If True, the PCM matrix obtained by the IEFPCM collocation solver is symmetrized.",
         "default": true,
         "type": "boolean"
      },
      "medium_Correction": {
         "title": "Medium Correction",
         "description": "Correction, k for the apparent surface charge scaling factor in the CPCM solver.",
         "default": 0.0,
         "minimum": 0,
         "type": "number"
      },
      "medium_DiagonalScaling": {
         "title": "Medium Diagonalscaling",
         "description": "Scaling factor for diagonal of collocation matrices, values commonly used in the literature are 1.07 and 1.0694.",
         "default": 1.07,
         "minimum": 0,
         "type": "number"
      },
      "medium_ProbeRadius": {
         "title": "Medium Proberadius",
         "description": "Radius of the spherical probe approximating a solvent molecule. Used for generating the solvent-excluded surface (SES) or an approximation of it. Overridden by the built-in value for the chosen solvent. Default in AU.",
         "default": 1.0,
         "type": "number"
      }
   },
   "required": [
      "units",
      "medium_Solvent"
   ]
}

Config
  • allow_mutation: bool = False

  • arbitrary_types_allowed: bool = True

  • json_encoders: dict = {<class ‘numpy.ndarray’>: <function ResultsConfig.Config.<lambda> at 0x7efe99957d00>, <enum ‘Enum’>: <function ResultsConfig.Config.<lambda> at 0x7efe99957d90>}

Fields
Validators
field units: str [Required]

The units used in the input options atomic units are used by default.

Validated by
  • _check_units

field codata: int = 2010

The set of fundamental physical constants to be used in the module.

Validated by
  • _check_codata

field cavity_Type: str = 'GePol'

Completely specifies type of molecular surface and its discretization.

Validated by
  • _check_cavity_type

field cavity_Area: float = 0.3

Average area (weight) of the surface partition for the GePol cavity in the specified units. By default this is in AU.

field cavity_Scaling: bool = True

If true, the radii for the spheres will be scaled by 1.2. For finer control on the scaling factor for each sphere, select explicit creation mode.

field cavity_RadiiSet: str = 'Bondi'

Select set of atomic radii to be used. Currently Bondi-Mantina Bondi, UFF and Allinger’s MM3 sets available. Radii in Allinger’s MM3 set are obtained by dividing the value in the original paper by 1.2, as done in the ADF COSMO implementation We advise to turn off scaling of the radii by 1.2 when using this set.

Validated by
  • _check_radii_set

field cavity_MinRadius: float = 100

Minimal radius for additional spheres not centered on atoms. An arbitrarily big value is equivalent to switching off the use of added spheres, which is the default in AU.

field cavity_Mode: str = 'Implicit'

How to create the list of spheres for the generation of the molecular surface.

Validated by
  • _check_cavity_mode

field medium_SolverType: str = 'IEFPCM'

Type of solver to be used. All solvers are based on the Integral Equation Formulation of the Polarizable Continuum Model.

Validated by
  • _check_solver

field medium_Nonequilibrium: bool = False

Initializes an additional solver using the dynamic permittivity. To be used in response calculations.

field medium_Solvent: str [Required]

Specification of the dielectric medium outside the cavity. Note this will always be converted to the molecular formula to aid parsing via PCM.

Validated by
  • _check_solvent

field medium_MatrixSymm: bool = True

If True, the PCM matrix obtained by the IEFPCM collocation solver is symmetrized.

field medium_Correction: float = 0.0

Correction, k for the apparent surface charge scaling factor in the CPCM solver.

Constraints
  • minimum = 0

field medium_DiagonalScaling: float = 1.07

Scaling factor for diagonal of collocation matrices, values commonly used in the literature are 1.07 and 1.0694.

Constraints
  • minimum = 0

field medium_ProbeRadius: float = 1.0

Radius of the spherical probe approximating a solvent molecule. Used for generating the solvent-excluded surface (SES) or an approximation of it. Overridden by the built-in value for the chosen solvent. Default in AU.

to_string()[source]

Generate the formated PCM settings string which can be ingested by psi4 via the qcschema interface.

Return type

str