prune qcng_computer (#22)

* separate schema files, move computer

* rename

* missed one

qcmanybody/models/__init__.py

@@ -1,8 +1,12 @@
-from .manybody_pydv1 import (
+from .manybody_input_pydv1 import (
+    AtomicSpecification,
     BsseEnum,
     FragBasIndex,
     ManyBodyInput,
     ManyBodyKeywords,
+)
+from .manybody_output_pydv1 import (
     ManyBodyResult,
     ManyBodyResultProperties,
+    MAX_NBODY
 )

qcmanybody/models/manybody_input_pydv1.py

@@ -0,0 +1,238 @@
+
+from __future__ import annotations
+
+from enum import Enum, IntEnum
+from typing import Any, Dict, List, Optional, Literal, Tuple, Union, TYPE_CHECKING
+
+# v2: from pydantic import create_model, Field, field_validator, FieldValidationInfo
+try:
+    from pydantic.v1 import create_model, Field, validator
+except ImportError:
+    from pydantic import create_model, Field, validator
+
+from qcelemental.models.types import Array
+#from .basemodels import ExtendedConfigDict, ProtoModel
+from qcelemental.models.common_models import Model
+from qcelemental.models.molecule import Molecule
+from qcelemental.models.results import AtomicResultProperties, AtomicResultProtocols
+from qcelemental.models import DriverEnum, ProtoModel, Provenance
+
+
+# ====  Misplaced & Next Models  ================================================
+
+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"
+    driver: DriverEnum = Field(..., description=DriverEnum.__doc__)
+    model: Model = Field(..., description=Model.__doc__)
+    protocols: AtomicResultProtocols = Field(
+        AtomicResultProtocols(),
+        description=AtomicResultProtocols.__doc__,
+    )
+
+
+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 ManyBodyProtocolEnum(str, Enum):
+    """
+    Which atomic evaluations to keep in a many body evaluation.
+    """
+
+    all = "all"
+    all_real = "all_real"
+    largest_body = "largest_body"
+    none = "none"
+
+
+class ManyBodyProtocols(ProtoModel):
+    """
+    Protocols regarding the manipulation of a ManyBody output data.
+    """
+
+    atomics: ManyBodyProtocolEnum = Field(
+        ManyBodyProtocolEnum.all,
+        description=str(ManyBodyProtocolEnum.__doc__),
+    )
+
+    # v2: model_config = ExtendedConfigDict(force_skip_defaults=True)
+    class Config:
+        force_skip_defaults = True
+
+
+# ====  Inputs  =================================================================
+
+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"
+
+    def formal(self):
+        return {
+            "nocp": "Non-Counterpoise Corrected",
+            "cp": "Counterpoise Corrected",
+            "vmfc": "Valiron-Mayer Function Counterpoise",
+        }[self]
+
+    def abbr(self):
+        return {
+            "nocp": "NoCP",
+            "cp": "CP",
+            "vmfc": "VMFC",
+        }[self]
+
+
+FragBasIndex = Tuple[Tuple[int], Tuple[int]]
+
+
+class ManyBodyKeywords(ProtoModel):
+    """The many-body-specific keywords for user control."""
+
+    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: Dict[int, List[float]] = Field(
+        {},
+        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.",
+            # 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."
+    )
+
+    # v2: @field_validator("bsse_type", mode="before")
+    @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]))
+
+
+class ManyBodySpecification(ProtoModel):
+    """Combining the what (ManyBodyKeywords) with the how (AtomicSpecification)."""
+
+    schema_name: Literal["qcschema_manybodyspecification"] = "qcschema_manybodyspecification"
+    #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.")
+    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",
+    )
+
+    # v2: @field_validator("specification", mode="before")
+    @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
+
+
+class ManyBodyInput(ProtoModel):
+    """Combining the what and how (ManyBodySpecification) with the who (Molecule)."""
+
+    schema_name: Literal["qcschema_manybodyinput"] = "qcschema_manybodyinput"
+    #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.",
+    )
+    #protocols