TorsionDriveInput
- pydantic model qcelemental.models.v2.TorsionDriveInput[source]
Inputs for running a torsion drive.
Show JSON schema
{ "title": "TorsionDriveInput", "description": "Inputs for running a torsion drive.", "type": "object", "properties": { "schema_name": { "const": "qcschema_torsion_drive_input", "default": "qcschema_torsion_drive_input", "title": "Schema Name", "type": "string" }, "schema_version": { "const": 2, "default": 2, "description": "The version number of ``schema_name`` to which this model conforms.", "title": "Schema Version", "type": "integer" }, "id": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Id" }, "initial_molecule": { "description": "The starting molecule(s) for the torsion drive.", "items": { "$ref": "#/$defs/Molecule" }, "minItems": 1, "title": "Initial Molecule", "type": "array" }, "specification": { "$ref": "#/$defs/TorsionDriveSpecification" }, "provenance": { "$ref": "#/$defs/Provenance", "default": { "creator": "QCElemental", "version": "0.1.dev1+g997989000", "routine": "qcelemental.models.v2.torsion_drive" } } }, "$defs": { "AtomicProtocols": { "additionalProperties": false, "description": "Protocols regarding the manipulation of computational result data.", "properties": { "schema_name": { "const": "qcschema_atomic_protocols", "default": "qcschema_atomic_protocols", "title": "Schema Name", "type": "string" }, "wavefunction": { "$ref": "#/$defs/WavefunctionProtocolEnum", "default": "none" }, "stdout": { "default": true, "description": "Primary output file to keep from the computation", "title": "Stdout", "type": "boolean" }, "error_correction": { "$ref": "#/$defs/ErrorCorrectionProtocol", "description": "Policies for error correction" }, "native_files": { "$ref": "#/$defs/NativeFilesProtocolEnum", "default": "none", "description": "Policies for keeping processed files from the computation" } }, "title": "AtomicProtocols", "type": "object" }, "AtomicSpecification": { "additionalProperties": false, "description": "Specification for a single point QC calculation", "properties": { "schema_name": { "const": "qcschema_atomic_specification", "default": "qcschema_atomic_specification", "title": "Schema Name", "type": "string" }, "keywords": { "additionalProperties": true, "default": {}, "description": "The program specific keywords to be used.", "title": "Keywords", "type": "object" }, "program": { "default": "", "description": "The program for which the Specification is intended.", "title": "Program", "type": "string" }, "driver": { "$ref": "#/$defs/DriverEnum" }, "model": { "$ref": "#/$defs/Model" }, "protocols": { "$ref": "#/$defs/AtomicProtocols", "default": {} }, "extras": { "additionalProperties": true, "default": {}, "description": "Additional information to bundle with the computation. Use for schema development and scratch space.", "title": "Extras", "type": "object" } }, "required": [ "driver", "model" ], "title": "AtomicSpecification", "type": "object" }, "BasisCenter": { "additionalProperties": false, "description": "Data for a single atom/center in a basis set.", "properties": { "electron_shells": { "description": "Electronic shells for this center.", "items": { "$ref": "#/$defs/ElectronShell" }, "minItems": 1, "title": "Electron Shells", "type": "array", "uniqueItems": true }, "ecp_electrons": { "default": 0, "description": "Number of electrons replaced by ECP, MCP, or other field potentials.", "title": "Ecp Electrons", "type": "integer" }, "ecp_potentials": { "anyOf": [ { "items": { "$ref": "#/$defs/ECPPotential" }, "minItems": 1, "type": "array" }, { "type": "null" } ], "default": null, "description": "ECPs, MCPs, or other field potentials for this center.", "title": "Ecp Potentials", "uniqueItems": true } }, "required": [ "electron_shells" ], "title": "BasisCenter", "type": "object" }, "BasisSet": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "description": "A quantum chemistry basis description.", "properties": { "schema_name": { "const": "qcschema_basis_set", "default": "qcschema_basis_set", "description": "The QCSchema specification to which this model conforms.", "title": "Schema Name", "type": "string" }, "schema_version": { "const": 2, "default": 2, "description": "The version number of :attr:`~qcelemental.models.BasisSet.schema_name` to which this model conforms.", "title": "Schema Version", "type": "integer" }, "name": { "description": "The standard basis name if available (e.g., 'cc-pVDZ').", "title": "Name", "type": "string" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Brief description of the basis set.", "title": "Description" }, "center_data": { "additionalProperties": { "$ref": "#/$defs/BasisCenter" }, "description": "Shared basis data for all atoms/centers in the parent molecule", "title": "Center Data", "type": "object" }, "atom_map": { "description": "Mapping of all atoms/centers in the parent molecule to centers in ``center_data``.", "items": { "type": "string" }, "title": "Atom Map", "type": "array" }, "nbf": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "The number of basis functions. Use for convenience or as checksum", "title": "Nbf" } }, "required": [ "name", "center_data", "atom_map" ], "title": "BasisSet", "type": "object" }, "DriverEnum": { "description": "Allowed computation driver values.", "enum": [ "energy", "gradient", "hessian", "properties" ], "title": "DriverEnum", "type": "string" }, "ECPPotential": { "additionalProperties": false, "description": "Information for a single ECP potential.", "properties": { "ecp_type": { "$ref": "#/$defs/ECPType" }, "angular_momentum": { "description": "Angular momentum for the potential as an array of integers.", "items": { "minimum": 0, "type": "integer" }, "minItems": 1, "title": "Angular Momentum", "type": "array", "uniqueItems": true }, "r_exponents": { "description": "Exponents of the 'r' term.", "items": { "type": "integer" }, "minItems": 1, "title": "R Exponents", "type": "array" }, "gaussian_exponents": { "description": "Exponents of the 'gaussian' term.", "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "minItems": 1, "title": "Gaussian Exponents", "type": "array" }, "coefficients": { "description": "General contraction coefficients for the potential; individual list components will be the individual segment contraction coefficients.", "items": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "type": "array" }, "minItems": 1, "title": "Coefficients", "type": "array" } }, "required": [ "ecp_type", "angular_momentum", "r_exponents", "gaussian_exponents", "coefficients" ], "title": "ECPPotential", "type": "object" }, "ECPType": { "description": "The type of the ECP potential.", "enum": [ "scalar", "spinorbit" ], "title": "ECPType", "type": "string" }, "ElectronShell": { "additionalProperties": false, "description": "Information for a single electronic shell.", "properties": { "angular_momentum": { "description": "Angular momentum for the shell as an array of integers.", "items": { "minimum": 0, "type": "integer" }, "minItems": 1, "title": "Angular Momentum", "type": "array", "uniqueItems": true }, "harmonic_type": { "$ref": "#/$defs/HarmonicType" }, "exponents": { "description": "Exponents for the contracted shell.", "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "minItems": 1, "title": "Exponents", "type": "array" }, "coefficients": { "description": "General contraction coefficients for the shell; individual list components will be the individual segment contraction coefficients.", "items": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "type": "array" }, "minItems": 1, "title": "Coefficients", "type": "array" } }, "required": [ "angular_momentum", "harmonic_type", "exponents", "coefficients" ], "title": "ElectronShell", "type": "object" }, "ErrorCorrectionProtocol": { "additionalProperties": false, "description": "Configuration for how QCEngine handles error correction\n\nWARNING: These protocols are currently experimental and only supported by NWChem tasks", "properties": { "default_policy": { "default": true, "description": "Whether to allow error corrections to be used if not directly specified in `policies`", "title": "Default Policy", "type": "boolean" }, "policies": { "anyOf": [ { "additionalProperties": { "type": "boolean" }, "type": "object" }, { "type": "null" } ], "default": null, "description": "Settings that define whether specific error corrections are allowed. Keys are the name of a known error and values are whether it is allowed to be used.", "title": "Policies" } }, "title": "ErrorCorrectionProtocol", "type": "object" }, "HarmonicType": { "description": "The angular momentum representation of a shell.", "enum": [ "spherical", "cartesian" ], "title": "HarmonicType", "type": "string" }, "Identifiers": { "additionalProperties": false, "description": "Canonical chemical identifiers", "properties": { "molecule_hash": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Molecule Hash" }, "molecular_formula": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Molecular Formula" }, "smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Smiles" }, "inchi": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Inchi" }, "inchikey": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Inchikey" }, "canonical_explicit_hydrogen_smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Canonical Explicit Hydrogen Smiles" }, "canonical_isomeric_explicit_hydrogen_mapped_smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Canonical Isomeric Explicit Hydrogen Mapped Smiles" }, "canonical_isomeric_explicit_hydrogen_smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Canonical Isomeric Explicit Hydrogen Smiles" }, "canonical_isomeric_smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Canonical Isomeric Smiles" }, "canonical_smiles": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Canonical Smiles" }, "pubchem_cid": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "PubChem Compound ID", "title": "Pubchem Cid" }, "pubchem_sid": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "PubChem Substance ID", "title": "Pubchem Sid" }, "pubchem_conformerid": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "PubChem Conformer ID", "title": "Pubchem Conformerid" } }, "title": "Identifiers", "type": "object" }, "Model": { "additionalProperties": true, "description": "The computational molecular sciences model to run.", "properties": { "method": { "description": "The quantum chemistry method to evaluate (e.g., B3LYP, PBE, ...). For MM, name of the force field.", "title": "Method", "type": "string" }, "basis": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/BasisSet" }, { "type": "null" } ], "default": null, "description": "The quantum chemistry basis set to evaluate (e.g., 6-31g, cc-pVDZ, ...). Can be ``None`` for methods without basis sets. For molecular mechanics, name of the atom-typer.", "title": "Basis" } }, "required": [ "method" ], "title": "Model", "type": "object" }, "Molecule": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "description": "The physical Cartesian representation of the molecular system.\n\nA QCSchema representation of a Molecule. This model contains\ndata for symbols, geometry, connectivity, charges, fragmentation, etc while also supporting a wide array of I/O and manipulation capabilities.\n\nMolecule objects geometry, masses, and charges are truncated to 8, 6, and 4 decimal places respectively to assist with duplicate detection.\n\nNotes\n-----\nAll arrays are stored flat but must be reshapable into the dimensions in attribute ``shape``, with abbreviations as follows:\n\n * nat: number of atomic = calcinfo_natom\n * nfr: number of fragments\n * <varies>: irregular dimension not systematically reshapable", "properties": { "schema_name": { "const": "qcschema_molecule", "default": "qcschema_molecule", "description": "The QCSchema specification to which this model conforms.", "title": "Schema Name", "type": "string" }, "schema_version": { "const": 3, "default": 3, "description": "The version number of :attr:`~qcelemental.models.Molecule.schema_name` to which this model conforms.", "title": "Schema Version", "type": "integer" }, "validated": { "default": false, "description": "A boolean indicator (for speed purposes) that the input Molecule data has been previously checked for schema (data layout and type) and physics (e.g., non-overlapping atoms, feasible multiplicity) compliance. This should be False in most cases. A ``True`` setting should only ever be set by the constructor for this class itself or other trusted sources such as a Fractal Server or previously serialized Molecules.", "title": "Validated", "type": "boolean" }, "symbols": { "description": "The ordered array of atomic elemental symbols in title case. This field's index sets atomic order for all other per-atom fields like :attr:`~qcelemental.models.Molecule.real` and the first dimension of :attr:`~qcelemental.models.Molecule.geometry`. Ghost/virtual atoms must have an entry here in :attr:`~qcelemental.models.Molecule.symbols`; ghostedness is indicated through the :attr:`~qcelemental.models.Molecule.real` field.", "items": { "type": "number" }, "shape": [ "nat" ], "title": "Symbols", "type": "array" }, "geometry": { "description": "The ordered array for Cartesian XYZ atomic coordinates [a0]. Atom ordering is fixed; that is, a consumer who shuffles atoms must not reattach the input (pre-shuffling) molecule schema instance to any output (post-shuffling) per-atom results (e.g., gradient). Index of the first dimension matches the 0-indexed indices of all other per-atom settings like :attr:`~qcelemental.models.Molecule.symbols` and :attr:`~qcelemental.models.Molecule.real`.\nSerialized storage is always flat, (3*nat,), but QCSchema implementations will want to reshape it. QCElemental can also accept array-likes which can be mapped to (nat,3) such as a 1-D list of length 3*nat, or the serialized version of the array in (3*nat,) shape; all forms will be reshaped to (nat,3) for this attribute.", "items": { "type": "number" }, "shape": [ "nat", 3 ], "title": "Geometry", "type": "array", "units": "a0" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Common or human-readable name to assign to this molecule. This field can be arbitrary; see :attr:`~qcelemental.models.Molecule.identifiers` for well-defined labels.", "title": "Name" }, "identifiers": { "anyOf": [ { "$ref": "#/$defs/Identifiers" }, { "type": "null" } ], "default": null, "description": "An optional dictionary of additional identifiers by which this molecule can be referenced, such as INCHI, canonical SMILES, etc. See the :class:`~qcelemental.models.results.Identifiers` model for more details." }, "comment": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Additional comments for this molecule. Intended for pure human/user consumption and clarity.", "title": "Comment" }, "molecular_charge": { "default": 0.0, "description": "The net electrostatic charge of the molecule.", "title": "Molecular Charge", "type": "number" }, "molecular_multiplicity": { "default": 1, "description": "The total multiplicity of the molecule.", "title": "Molecular Multiplicity", "type": "number" }, "masses": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The ordered array of atomic masses. Index order matches the 0-indexed indices of all other per-atom fields like :attr:`~qcelemental.models.Molecule.symbols` and :attr:`~qcelemental.models.Molecule.real`. If this is not provided, the mass of each atom is inferred from its most common isotope. If this is provided, it must be the same length as :attr:`~qcelemental.models.Molecule.symbols` but can accept ``None`` entries for standard masses to infer from the same index in the :attr:`~qcelemental.models.Molecule.symbols` field.", "shape": [ "nat" ], "title": "Masses", "units": "u" }, "real": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The ordered array indicating if each atom is real (``True``) or ghost/virtual (``False``). Index matches the 0-indexed indices of all other per-atom settings like :attr:`~qcelemental.models.Molecule.symbols` and the first dimension of :attr:`~qcelemental.models.Molecule.geometry`. If this is not provided, all atoms are assumed to be real (``True``). If this is provided, the reality or ghostedness of every atom must be specified.", "shape": [ "nat" ], "title": "Real" }, "atom_labels": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Additional per-atom labels as an array of strings. Typical use is in model conversions, such as Elemental <-> Molpro and not typically something which should be user assigned. See the :attr:`~qcelemental.models.Molecule.comment` field for general human-consumable text to affix to the molecule.", "shape": [ "nat" ], "title": "Atom Labels" }, "atomic_numbers": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "An optional ordered 1-D array-like object of atomic numbers of shape (nat,). Index matches the 0-indexed indices of all other per-atom settings like :attr:`~qcelemental.models.Molecule.symbols` and :attr:`~qcelemental.models.Molecule.real`. Values are inferred from the :attr:`~qcelemental.models.Molecule.symbols` list if not explicitly set. Ghostedness should be indicated through :attr:`~qcelemental.models.Molecule.real` field, not zeros here.", "shape": [ "nat" ], "title": "Atomic Numbers" }, "mass_numbers": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "An optional ordered 1-D array-like object of atomic *mass* numbers of shape (nat). Index matches the 0-indexed indices of all other per-atom settings like :attr:`~qcelemental.models.Molecule.symbols` and :attr:`~qcelemental.models.Molecule.real`. Values are inferred from the most common isotopes of the :attr:`~qcelemental.models.Molecule.symbols` list if not explicitly set. If single isotope not (yet) known for an atom, -1 is placeholder.", "shape": [ "nat" ], "title": "Mass Numbers" }, "connectivity": { "anyOf": [ { "items": { "maxItems": 3, "minItems": 3, "prefixItems": [ { "minimum": 0, "type": "integer" }, { "minimum": 0, "type": "integer" }, { "maximum": 5, "minimum": 0, "type": "number" } ], "type": "array" }, "minItems": 1, "type": "array" }, { "type": "null" } ], "default": null, "description": "A list of bonds within the molecule. Each entry is a tuple of ``(atom_index_A, atom_index_B, bond_order)`` where the ``atom_index`` matches the 0-indexed indices of all other per-atom settings like :attr:`~qcelemental.models.Molecule.symbols` and :attr:`~qcelemental.models.Molecule.real`. Bonds may be freely reordered and inverted.", "title": "Connectivity" }, "fragments": { "anyOf": [ { "items": { "items": { "type": "number" }, "type": "array" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "List of indices grouping atoms (0-indexed) into molecular fragments within the molecule. Each entry in the outer list is a new fragment; index matches the ordering in :attr:`~qcelemental.models.Molecule.fragment_charges` and :attr:`~qcelemental.models.Molecule.fragment_multiplicities`. Inner lists are 0-indexed atoms which compose the fragment; every atom must be in exactly one inner list. Noncontiguous fragments are allowed, though no QM program is known to support them. Fragment ordering is fixed; that is, a consumer who shuffles fragments must not reattach the input (pre-shuffling) molecule schema instance to any output (post-shuffling) per-fragment results (e.g., n-body energy arrays).", "shape": [ "nfr", "<varies>" ], "title": "Fragments" }, "fragment_charges": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The total charge of each fragment in the :attr:`~qcelemental.models.Molecule.fragments` list. The index of this list matches the 0-index indices of :attr:`~qcelemental.models.Molecule.fragments` list. Will be filled in based on a set of rules if not provided (and :attr:`~qcelemental.models.Molecule.fragments` are specified).", "shape": [ "nfr" ], "title": "Fragment Charges" }, "fragment_multiplicities": { "anyOf": [ { "items": { "type": "number" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The multiplicity of each fragment in the :attr:`~qcelemental.models.Molecule.fragments` list. The index of this list matches the 0-index indices of :attr:`~qcelemental.models.Molecule.fragments` list. Will be filled in based on a set of rules if not provided (and :attr:`~qcelemental.models.Molecule.fragments` are specified).", "shape": [ "nfr" ], "title": "Fragment Multiplicities" }, "fix_com": { "default": false, "description": "Whether translation of geometry is allowed (fix F) or disallowed (fix T).When False, QCElemental will pre-process the Molecule object to translate the center of mass to (0,0,0) in Euclidean coordinate space, resulting in a different :attr:`~qcelemental.models.Molecule.geometry` than the one provided. 'Fix' is used in the sense of 'specify': that is, `fix_com=True` signals that the origin in `geometry` is a deliberate part of the Molecule spec, whereas `fix_com=False` (default) allows that the origin is happenstance and may be adjusted. guidance: A consumer who translates the geometry must not reattach the input (pre-translation) molecule schema instance to any output (post-translation) origin-sensitive results (e.g., an ordinary energy when EFP present).", "title": "Fix Com", "type": "boolean" }, "fix_orientation": { "default": false, "description": "Whether rotation of geometry is allowed (fix F) or disallowed (fix T). When False, QCElemental will pre-process the Molecule object to orient via the intertial tensor, resulting in a different :attr:`~qcelemental.models.Molecule.geometry` than the one provided. 'Fix' is used in the sense of 'specify': that is, `fix_orientation=True` signals that the frame orientation in `geometry` is a deliberate part of the Molecule spec, whereas `fix_orientation=False` (default) allows that the frame is happenstance and may be adjusted. guidance: A consumer who rotates the geometry must not reattach the input (pre-rotation) molecule schema instance to any output (post-rotation) frame-sensitive results (e.g., molecular vibrations).", "title": "Fix Orientation", "type": "boolean" }, "fix_symmetry": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Maximal point group symmetry which :attr:`~qcelemental.models.Molecule.geometry` should be treated. Lowercase.", "title": "Fix Symmetry" }, "provenance": { "$ref": "#/$defs/Provenance", "description": "The provenance information about how this Molecule (and its attributes) were generated, provided, and manipulated." }, "id": { "anyOf": [ {}, { "type": "null" } ], "default": null, "description": "A unique identifier for this Molecule object. This field exists primarily for Databases (e.g. Fractal's Server) to track and lookup this specific object and should virtually never need to be manually set.", "title": "Id" }, "extras": { "additionalProperties": true, "default": {}, "description": "Additional information to bundle with the molecule. Use for schema development and scratch space.", "title": "Extras", "type": "object" } }, "required": [ "symbols", "geometry" ], "title": "Molecule", "type": "object" }, "NativeFilesProtocolEnum": { "description": "CMS program files to keep from a computation.", "enum": [ "all", "input", "none" ], "title": "NativeFilesProtocolEnum", "type": "string" }, "OptimizationProtocols": { "additionalProperties": false, "description": "Protocols regarding the manipulation of a Optimization output data.", "properties": { "schema_name": { "const": "qcschema_optimization_protocols", "default": "qcschema_optimization_protocols", "title": "Schema Name", "type": "string" }, "trajectory_results": { "$ref": "#/$defs/TrajectoryProtocolEnum", "default": "none", "description": "\n Which gradient evaluations to keep in an optimization trajectory.\n " } }, "title": "OptimizationProtocols", "type": "object" }, "OptimizationSpecification": { "additionalProperties": false, "description": "Specification for how to run a geometry optimization.", "properties": { "schema_name": { "const": "qcschema_optimization_specification", "default": "qcschema_optimization_specification", "title": "Schema Name", "type": "string" }, "program": { "default": "", "description": "Optimizer CMS code / QCEngine procedure to run the geometry optimization with.", "title": "Program", "type": "string" }, "keywords": { "additionalProperties": true, "default": {}, "description": "The optimization specific keywords to be used.", "title": "Keywords", "type": "object" }, "protocols": { "$ref": "#/$defs/OptimizationProtocols", "default": {}, "description": "\n Protocols regarding the manipulation of a Optimization output data.\n " }, "extras": { "additionalProperties": true, "default": {}, "description": "Additional information to bundle with the computation. Use for schema development and scratch space.", "title": "Extras", "type": "object" }, "specification": { "$ref": "#/$defs/AtomicSpecification", "description": "A directive for how to compute a gradient for the optimization. Either an ordinary atomic/single-point or a many-body spec." } }, "required": [ "specification" ], "title": "OptimizationSpecification", "type": "object" }, "Provenance": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": true, "description": "Provenance information.", "properties": { "creator": { "description": "The name of the program, library, or person who created the object.", "title": "Creator", "type": "string" }, "version": { "default": "", "description": "The version of the creator, blank otherwise. This should be sortable by the very broad `PEP 440 <https://www.python.org/dev/peps/pep-0440/>`_.", "title": "Version", "type": "string" }, "routine": { "default": "", "description": "The name of the routine or function within the creator, blank otherwise.", "title": "Routine", "type": "string" } }, "required": [ "creator" ], "title": "Provenance", "type": "object" }, "ScanResultsProtocolEnum": { "description": "Which gradient evaluations to keep in an optimization trajectory.", "enum": [ "all", "lowest", "none" ], "title": "ScanResultsProtocolEnum", "type": "string" }, "TorsionDriveKeywords": { "additionalProperties": false, "description": "TorsionDriveRecord options\n\nNotes\n-----\n* This class is still provisional and may be subject to removal and re-design.", "properties": { "schema_name": { "const": "qcschema_torsion_drive_keywords", "default": "qcschema_torsion_drive_keywords", "description": "The QCSchema specification to which this model conforms.", "title": "Schema Name", "type": "string" }, "dihedrals": { "description": "The list of dihedrals to select for the TorsionDrive operation. Each entry is a tuple of integers of for particle indices.", "items": { "maxItems": 4, "minItems": 4, "prefixItems": [ { "type": "integer" }, { "type": "integer" }, { "type": "integer" }, { "type": "integer" } ], "type": "array" }, "title": "Dihedrals", "type": "array" }, "grid_spacing": { "description": "List of grid spacing for dihedral scan in degrees. Multiple values will be mapped to each dihedral angle.", "items": { "type": "integer" }, "title": "Grid Spacing", "type": "array" }, "dihedral_ranges": { "anyOf": [ { "items": { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "A list of dihedral range limits as a pair (lower, upper). Each range corresponds to the dihedrals in input.", "title": "Dihedral Ranges" }, "energy_decrease_thresh": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "The threshold of the smallest energy decrease amount to trigger activating optimizations from grid point.", "title": "Energy Decrease Thresh" }, "energy_upper_limit": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "The threshold if the energy of a grid point that is higher than the current global minimum, to start new optimizations, in unit of a.u. I.e. if energy_upper_limit = 0.05, current global minimum energy is -9.9 , then a new task starting with energy -9.8 will be skipped.", "title": "Energy Upper Limit" } }, "required": [ "dihedrals", "grid_spacing" ], "title": "TorsionDriveKeywords", "type": "object" }, "TorsionDriveProtocols": { "additionalProperties": false, "description": "Protocols regarding the manipulation of a Torsion Drive subcalculation history.", "properties": { "schema_name": { "const": "qcschema_torsion_drive_protocols", "default": "qcschema_torsion_drive_protocols", "title": "Schema Name", "type": "string" }, "scan_results": { "$ref": "#/$defs/ScanResultsProtocolEnum", "default": "none", "description": "\n Which gradient evaluations to keep in an optimization trajectory.\n " } }, "title": "TorsionDriveProtocols", "type": "object" }, "TorsionDriveSpecification": { "additionalProperties": false, "description": "Specification for how to run a torsion drive scan.", "properties": { "schema_name": { "const": "qcschema_torsion_drive_specification", "default": "qcschema_torsion_drive_specification", "title": "Schema Name", "type": "string" }, "program": { "default": "", "description": "Torsion Drive CMS code / QCEngine procedure with which to run the torsion scan.", "title": "Program", "type": "string" }, "keywords": { "$ref": "#/$defs/TorsionDriveKeywords", "description": "The torsion drive specific keywords to be used." }, "protocols": { "$ref": "#/$defs/TorsionDriveProtocols", "default": {}, "description": "\n Protocols regarding the manipulation of a Torsion Drive subcalculation history.\n " }, "extras": { "additionalProperties": true, "default": {}, "description": "Additional information to bundle with the computation. Use for schema development and scratch space.", "title": "Extras", "type": "object" }, "specification": { "$ref": "#/$defs/OptimizationSpecification", "description": "The specification for how to run optimizations for the torsion scan (within this is spec for gradients for the optimization." } }, "required": [ "keywords", "specification" ], "title": "TorsionDriveSpecification", "type": "object" }, "TrajectoryProtocolEnum": { "description": "Which gradient evaluations to keep in an optimization trajectory.", "enum": [ "all", "initial_and_final", "final", "none" ], "title": "TrajectoryProtocolEnum", "type": "string" }, "WavefunctionProtocolEnum": { "description": "Wavefunction to keep from a computation.", "enum": [ "all", "orbitals_and_eigenvalues", "occupations_and_eigenvalues", "return_results", "none" ], "title": "WavefunctionProtocolEnum", "type": "string" } }, "additionalProperties": false, "required": [ "initial_molecule", "specification" ] }
- Fields:
- Validators:
_check_input_specification»specification
- field initial_molecule: Annotated[list[Molecule], Len(min_length=1, max_length=None)] [Required]
The starting molecule(s) for the torsion drive.
- Constraints:
min_length = 1
- field provenance: Provenance = Provenance(creator='QCElemental', version='0.1.dev1+g997989000', routine='qcelemental.models.v2.torsion_drive')
Provenance information.
- field schema_version: Literal[2] = 2
The version number of
schema_nameto which this model conforms.
- field specification: TorsionDriveSpecification [Required]
Specification for how to run a torsion drive scan.
- Validated by:
_check_input_specification
- convert_v(target_version, /)[source]
Convert to instance of particular QCSchema version.
- Parameters:
target_version (int)
- Return type:
qcelemental.models.v1.TorsionDriveInput | qcelemental.models.v2.TorsionDriveInput