from __future__ import annotations
import warnings
from enum import Enum, IntEnum
from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Tuple, Union
from pydantic.v1 import Field, create_model, validator
from qcelemental.models import DriverEnum, ProtoModel, Provenance
# from .basemodels import ExtendedConfigDict, ProtoModel
with warnings.catch_warnings():
# keeping longstanding imports for compatibility with pre-next qcelemental
warnings.simplefilter("ignore")
from qcelemental.models.common_models import Model
from qcelemental.models.molecule import Molecule
from qcelemental.models.results import AtomicResultProperties, AtomicResultProtocols
from qcelemental.models.types import Array
if TYPE_CHECKING:
import qcmanybody
# ==== Misplaced & Next Models ================================================
[docs]
class AtomicSpecification(ProtoModel):
"""Specification for a single point QC calculation"""
keywords: Dict[str, Any] = Field({}, description="The program specific keywords to be used.")
program: str = Field(..., description="The program for which the Specification is intended.")
schema_name: Literal["qcschema_atomicspecification"] = "qcschema_atomicspecification"
schema_version: Literal[1] = Field(
1,
description="The version number of ``schema_name`` to which this model conforms.",
)
driver: DriverEnum = Field(..., description=DriverEnum.__doc__)
model: Model = Field(..., description=Model.__doc__)
protocols: AtomicResultProtocols = Field(
AtomicResultProtocols(),
description=AtomicResultProtocols.__doc__,
)
extras: Dict[str, Any] = Field(
{},
description="Additional information to bundle with the computation. Use for schema development and scratch space.",
)
class ResultBase(ProtoModel):
"""Base class for all result classes"""
# input_data: InputBase = Field(..., description=InputBase.__doc__)
input_data: Any
success: bool = Field(
...,
description="A boolean indicator that the operation succeeded or failed. Allows programmatic assessment of "
"all results regardless of if they failed or succeeded by checking `result.success`.",
)
stdout: Optional[str] = Field(
None,
description="The primary logging output of the program, whether natively standard output or a file. Presence vs. absence (or null-ness?) configurable by protocol.",
)
stderr: Optional[str] = Field(None, description="The standard error of the program execution.")
class SuccessfulResultBase(ResultBase):
"""Base object for any successful result"""
success: Literal[True] = Field(True, description="Always `True` for a successful result")
# ==== Protocols ==============================================================
class ComponentResultsProtocolEnum(str, Enum):
r"""Which component results to preserve in a many body result; usually AtomicResults."""
all = "all"
# max_nbody = "max_nbody"
none = "none"
[docs]
class ManyBodyProtocols(ProtoModel):
"""
Protocols regarding the manipulation of a ManyBody output data.
"""
component_results: ComponentResultsProtocolEnum = Field(
ComponentResultsProtocolEnum.none, description=str(ComponentResultsProtocolEnum.__doc__)
)
class Config:
force_skip_defaults = True
[docs]
def convert_v(
self, target_version: int, /
) -> Union["qcmanybody.models.v1.ManyBodyProtocols", "qcmanybody.models.v2.ManyBodyProtocols"]:
"""Convert to instance of particular QCSchema version."""
from qcelemental.models.v1.basemodels import check_convertible_version
import qcmanybody as qcmb
if check_convertible_version(target_version, error="ManyBodyProtocols") == "self":
return self
dself = self.dict()
if target_version == 2:
# serialization is compact, so use model to assure value
dself.pop("component_results", None)
dself["cluster_results"] = self.component_results.value
self_vN = qcmb.models.v2.ManyBodyProtocols(**dself)
else:
assert False, target_version
return self_vN
# ==== Inputs =================================================================
[docs]
class BsseEnum(str, Enum):
"""Available basis-set superposition error (BSSE) treatments."""
nocp = "nocp" # plain supramolecular interaction energy
cp = "cp" # Boys-Bernardi counterpoise correction; site-site functional counterpoise (SSFC)
vmfc = "vmfc" # Valiron-Mayer function counterpoise
ssfc = "cp"
mbe = "nocp"
none = "nocp"
[docs]
def abbr(self):
return {
"nocp": "NoCP",
"cp": "CP",
"vmfc": "VMFC",
}[self]
FragBasIndex = Tuple[Tuple[int], Tuple[int]]
[docs]
class ManyBodyKeywords(ProtoModel):
"""The many-body-specific keywords for user control."""
schema_name: Literal["qcschema_manybodykeywords"] = "qcschema_manybodykeywords"
schema_version: Literal[1] = Field(
1,
description="The version number of ``schema_name`` to which this model conforms.",
)
bsse_type: List[BsseEnum] = Field(
[BsseEnum.cp],
# definitive description
description="Requested BSSE treatments. First in list determines which interaction or total "
"energy/gradient/Hessian returned.",
)
embedding_charges: Optional[Dict[int, List[float]]] = Field(
None,
description="Atom-centered point charges to be used on molecule fragments whose basis sets are not included in "
"the computation. Keys: 1-based index of fragment. Values: list of atom charges for that fragment. "
"At present, QCManyBody will only accept non-None values of this keyword if environment variable "
"QCMANYBODY_EMBEDDING_CHARGES is set.",
# TODO embedding charges should sum to fragment charge, right? enforce?
# TODO embedding charges irrelevant to CP (basis sets always present)?
json_schema_extra={
"shape": ["nfr", "<varies: nat in ifr>"],
},
)
return_total_data: Optional[bool] = Field(
None,
validate_default=True,
# definitive description
description="When True, returns the total data (energy/gradient/Hessian) of the system, otherwise returns "
"interaction data. Default is False for energies, True for gradients and Hessians. Note that the calculation "
"of counterpoise corrected total energies implies the calculation of the energies of monomers in the monomer "
"basis, hence specifying ``return_total_data = True`` may carry out more computations than "
"``return_total_data = False``. For gradients and Hessians, ``return_total_data = False`` is rarely useful.",
)
levels: Optional[Dict[Union[int, Literal["supersystem"]], str]] = Field(
None,
# definitive description. appended in Computer
description="Dictionary of different levels of theory for different levels of expansion. Note that the primary "
"method_string is not used when this keyword is given. ``supersystem`` computes all higher order n-body "
"effects up to the number of fragments; this higher-order correction uses the nocp basis, regardless of "
"bsse_type. A method fills in for any lower unlisted nbody levels. Note that if "
"both this and max_nbody are provided, they must be consistent. Examples: "
"SUPERSYSTEM definition suspect"
"* {1: 'ccsd(t)', 2: 'mp2', 'supersystem': 'scf'} "
"* {2: 'ccsd(t)/cc-pvdz', 3: 'mp2'} "
"* Now invalid: {1: 2, 2: 'ccsd(t)/cc-pvdz', 3: 'mp2'} ",
)
max_nbody: Optional[int] = Field(
None,
validate_default=True,
# definitive description
description="Maximum number of bodies to include in the many-body treatment. Possible: max_nbody <= nfragments. "
"Default: max_nbody = nfragments.",
)
supersystem_ie_only: Optional[bool] = Field(
False,
validate_default=True,
# definitive description
description="Target the supersystem total/interaction energy (IE) data over the many-body expansion (MBE) "
"analysis, thereby omitting intermediate-body calculations. When False (default), compute each n-body level "
"in the MBE up through ``max_nbody``. When True (only allowed for ``max_nbody = nfragments`` ), only compute "
"enough for the overall interaction/total energy: max_nbody-body and 1-body. When True, properties "
"``INTERACTION {driver} THROUGH {max_nbody}-BODY`` will always be available; "
"``TOTAL {driver} THROUGH {max_nbody}-BODY`` will be available depending on ``return_total_data`` ; and "
"``{max_nbody}-BODY CONTRIBUTION TO {driver}`` won't be available (except for dimers). This keyword produces "
"no savings for a two-fragment molecule. But for the interaction energy of a three-fragment molecule, for "
"example, 2-body subsystems can be skipped with ``supersystem_ie_only=True``. Do not use with ``vmfc`` in "
"``bsse_type`` as it cannot produce savings.",
)
[docs]
@validator("bsse_type", pre=True)
@classmethod
def set_bsse_type(cls, v: Any) -> List[BsseEnum]:
if not isinstance(v, list):
v = [v]
# emulate ordered set
# * bt.lower() as return (w/i `list(dict.fromkeys([bt.lower() ...`)
# works until aliases added to BsseEnum
# * BsseEnum[bt].value as return works for good vals, but passing bad
# vals through as bt lets pydantic raise a clearer error message
return list(
dict.fromkeys(
[(BsseEnum[bt.lower()].value if bt.lower() in BsseEnum.__members__ else bt.lower()) for bt in v]
)
)
[docs]
class ManyBodySpecification(ProtoModel):
"""Combining the what (ManyBodyKeywords) with the how (AtomicSpecification)."""
schema_name: Literal["qcschema_manybodyspecification"] = "qcschema_manybodyspecification"
schema_version: Literal[1] = Field(
1,
description="The version number of ``schema_name`` to which this model conforms.",
)
# provenance: Provenance = Field(Provenance(**provenance_stamp(__name__)), description=Provenance.__doc__)
keywords: ManyBodyKeywords = Field(..., description=ManyBodyKeywords.__doc__)
# program: str = Field(..., description="The program for which the Specification is intended.") # TODO is qcmanybody
protocols: ManyBodyProtocols = Field(ManyBodyProtocols(), description=str(ManyBodyProtocols.__doc__))
driver: DriverEnum = Field(
...,
description="The computation driver; i.e., energy, gradient, hessian.",
)
# specification: Union[AtomicSpecification, Dict[str, AtomicSpecification]] = Field(
specification: Dict[str, AtomicSpecification] = Field(
...,
description="??? TODO expand to cbs, fd",
)
extras: Dict[str, Any] = Field(
{},
description="Additional information to bundle with the computation. Use for schema development and scratch space.",
)
[docs]
@validator("specification", pre=True)
@classmethod
def set_specification(cls, v: Any) -> Dict[str, AtomicSpecification]:
# print(f"hit atomicspecification validator with {type(v)=} {v}", end="")
# v could be model instance or dict
if isinstance(v, AtomicSpecification) or "model" in v:
v = {"(auto)": v}
# print(f" ... setting v={v}")
return v
[docs]
def convert_v(
self, target_version: int, /
) -> Union["qcmanybody.models.v1.ManyBodySpecification", "qcmanybody.models.v2.ManyBodySpecification"]:
"""Convert to instance of particular QCSchema version."""
from qcelemental.models.v1.basemodels import check_convertible_version
import qcmanybody as qcmb
if check_convertible_version(target_version, error="ManyBodySpecification") == "self":
return self
dself = self.dict()
if target_version == 2:
dself.pop("schema_name")
dself.pop("schema_version")
dself["keywords"].pop("schema_name")
dself["keywords"].pop("schema_version")
try:
dself["specification"].pop("schema_name")
dself["specification"].pop("schema_version")
except KeyError:
for spec in dself["specification"].values():
spec.pop("schema_name")
spec.pop("schema_version")
self_vN = qcmb.models.v2.ManyBodySpecification(**dself)
else:
assert False, target_version
return self_vN
[docs]
class ManyBodyInput(ProtoModel):
"""Combining the what and how (ManyBodySpecification) with the who (Molecule)."""
schema_name: Literal["qcschema_manybodyinput"] = "qcschema_manybodyinput"
schema_version: Literal[1] = Field(
1,
description="The version number of ``schema_name`` to which this model conforms.",
)
# provenance: Provenance = Field(Provenance(**provenance_stamp(__name__)), description=Provenance.__doc__)
specification: ManyBodySpecification = Field(
...,
description="???",
)
molecule: Molecule = Field(
...,
description="Target molecule for many-body expansion (MBE) or interaction energy (IE) analysis.",
)
extras: Dict[str, Any] = Field(
{},
description="Additional information to bundle with the computation. Use for schema development and scratch space.",
)
[docs]
def convert_v(
self, target_version: int, /
) -> Union["qcmanybody.models.v1.ManyBodyInput", "qcmanybody.models.v2.ManyBodyInput"]:
"""Convert to instance of particular QCSchema version."""
from qcelemental.models.v1.basemodels import check_convertible_version
import qcmanybody as qcmb
if check_convertible_version(target_version, error="ManyBodyInput") == "self":
return self
dself = self.dict()
if target_version == 2:
dself.pop("schema_name") # changed in v2
dself.pop("schema_version") # changed in v2
# remove harmless empty extras field that v2 won't accept. if populated, pydantic will catch it.
if not dself.get("extras", True):
dself.pop("extras")
dself["molecule"] = self.molecule.convert_v(target_version)
dself["specification"] = self.specification.convert_v(target_version)
self_vN = qcmb.models.v2.ManyBodyInput(**dself)
else:
assert False, target_version
return self_vN