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"""
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A model for Compute Records
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"""
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import abc
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import datetime
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from enum import Enum
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from typing import TYPE_CHECKING, Any, Dict, List, Optional, Set, Union
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import numpy as np
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import qcelemental as qcel
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from pydantic import Field, constr, validator
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from ..visualization import scatter_plot
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from .common_models import DriverEnum, ObjectId, ProtoModel, QCSpecification
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from .model_utils import hash_dictionary, prepare_basis, recursive_normalizer
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if TYPE_CHECKING: # pragma: no cover
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from qcelemental.models import OptimizationInput, ResultInput
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from .common_models import KeywordSet, Molecule
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__all__ = ["OptimizationRecord", "ResultRecord", "OptimizationRecord", "RecordBase"]
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class RecordStatusEnum(str, Enum):
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"""
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The state of a record object. The states which are available are a finite set.
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"""
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complete = "COMPLETE"
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incomplete = "INCOMPLETE"
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running = "RUNNING"
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error = "ERROR"
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class RecordBase(ProtoModel, abc.ABC):
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"""
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A BaseRecord object for Result and Procedure records. Contains all basic
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fields common to the all records.
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"""
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# Classdata
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_hash_indices: Set[str]
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# Helper data
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client: Any = Field(None, description="The client object which the records are fetched from.")
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cache: Dict[str, Any] = Field(
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{},
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description="Object cache from expensive queries. It should be very rare that this needs to be set manually "
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"by the user.",
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)
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# Base identification
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id: ObjectId = Field(
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None, description="Id of the object on the database. This is assigned automatically by the database."
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)
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hash_index: Optional[str] = Field(
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None, description="Hash of this object used to detect duplication and collisions in the database."
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)
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procedure: str = Field(..., description="Name of the procedure which this Record targets.")
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program: str = Field(
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...,
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description="The quantum chemistry program which carries out the individual quantum chemistry calculations.",
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)
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version: int = Field(..., description="The version of this record object describes.")
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protocols: Optional[Dict[str, Any]] = Field(
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None, description="Protocols that change the data stored in top level fields."
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)
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# Extra fields
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extras: Dict[str, Any] = Field({}, description="Extra information to associate with this record.")
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stdout: Optional[ObjectId] = Field(
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None,
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description="The Id of the stdout data stored in the database which was used to generate this record from the "
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"various programs which were called in the process.",
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)
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stderr: Optional[ObjectId] = Field(
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None,
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description="The Id of the stderr data stored in the database which was used to generate this record from the "
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"various programs which were called in the process.",
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)
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error: Optional[ObjectId] = Field(
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None,
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description="The Id of the error data stored in the database in the event that an error was generated in the "
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"process of carrying out the process this record targets. If no errors were raised, this field "
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"will be empty.",
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)
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# Compute status
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manager_name: Optional[str] = Field(None, description="Name of the Queue Manager which generated this record.")
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status: RecordStatusEnum = Field(RecordStatusEnum.incomplete, description=str(RecordStatusEnum.__doc__))
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modified_on: datetime.datetime = Field(None, description="Last time the data this record points to was modified.")
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created_on: datetime.datetime = Field(None, description="Time the data this record points to was first created.")
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# Carry-ons
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provenance: Optional[qcel.models.Provenance] = Field(
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None,
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description="Provenance information tied to the creation of this record. This includes things such as every "
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"program which was involved in generating the data for this record.",
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)
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class Config(ProtoModel.Config):
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build_hash_index = True
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@validator("program")
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6
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def check_program(cls, v):
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return v.lower()
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def __init__(self, **data):
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# Set datetime defaults if not automatically available
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data.setdefault("modified_on", datetime.datetime.utcnow())
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data.setdefault("created_on", datetime.datetime.utcnow())
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super().__init__(**data)
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# Set hash index if not present
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if self.Config.build_hash_index and (self.hash_index is None):
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self.__dict__["hash_index"] = self.get_hash_index()
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def __repr_args__(self):
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1
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return [("id", f"{self.id}"), ("status", f"{self.status}")]
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126
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### Serialization helpers
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@classmethod
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def get_hash_fields(cls) -> Set[str]:
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"""Provides a description of the fields to be used in the hash
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that uniquely defines this object.
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Returns
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-------
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Set[str]
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A list of all fields that are used in the hash.
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"""
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return cls._hash_indices | {"procedure", "program"}
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def get_hash_index(self) -> str:
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"""Builds (or rebuilds) the hash of this
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object using the internally known hash fields.
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Returns
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-------
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str
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The objects unique hash index.
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"""
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data = self.dict(include=self.get_hash_fields(), encoding="json")
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return hash_dictionary(data)
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def dict(self, *args, **kwargs):
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kwargs["exclude"] = (kwargs.pop("exclude", None) or set()) | {"client", "cache"}
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# kwargs["skip_defaults"] = True
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return super().dict(*args, **kwargs)
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159
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### Checkers
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def check_client(self, noraise: bool = False) -> bool:
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"""Checks whether this object owns a FractalClient or not.
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This is often done so that objects pulled from a server using
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a FractalClient still posses a connection to the server so that
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additional data related to this object can be queried.
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Raises
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------
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ValueError
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If this object does not contain own a client.
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Parameters
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----------
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noraise : bool, optional
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Does not raise an error if this is True and instead returns
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a boolean depending if a client exists or not.
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178
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Returns
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-------
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bool
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If True, the object owns a connection to a server. False otherwise.
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"""
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6
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if self.client is None:
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0
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if noraise:
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0
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return False
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187
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0
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raise ValueError("Requested method requires a client, but client was '{}'.".format(self.client))
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189
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6
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return True
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191
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### KVStore Getters
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193
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14
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def _kvstore_getter(self, field_name):
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"""
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195
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Internal KVStore getting object
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196
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"""
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197
|
6
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self.check_client()
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199
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6
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oid = self.__dict__[field_name]
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6
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if oid is None:
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0
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return None
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202
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203
|
6
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if field_name not in self.cache:
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# Decompress here, rather than later
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# that way, it is decompressed in the cache
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206
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6
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kv = self.client.query_kvstore([oid])[oid]
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207
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208
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6
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if field_name == "error":
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6
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self.cache[field_name] = kv.get_json()
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else:
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211
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1
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self.cache[field_name] = kv.get_string()
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212
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213
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6
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return self.cache[field_name]
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214
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215
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14
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def get_stdout(self) -> Optional[str]:
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216
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"""Pulls the stdout from the denormalized KVStore and returns it to the user.
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217
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218
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Returns
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219
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-------
|
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220
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Optional[str]
|
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221
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The requested stdout, none if no stdout present.
|
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222
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"""
|
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223
|
1
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return self._kvstore_getter("stdout")
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224
|
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|
225
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14
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def get_stderr(self) -> Optional[str]:
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226
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"""Pulls the stderr from the denormalized KVStore and returns it to the user.
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227
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228
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Returns
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229
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-------
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230
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Optional[str]
|
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231
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The requested stderr, none if no stderr present.
|
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232
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"""
|
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233
|
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|
234
|
0
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return self._kvstore_getter("stderr")
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|
235
|
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236
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14
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def get_error(self) -> Optional[qcel.models.ComputeError]:
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237
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"""Pulls the stderr from the denormalized KVStore and returns it to the user.
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238
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239
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Returns
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240
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-------
|
|
241
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Optional[qcel.models.ComputeError]
|
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242
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The requested compute error, none if no error present.
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243
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"""
|
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244
|
6
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value = self._kvstore_getter("error")
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245
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6
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if value:
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246
|
6
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return qcel.models.ComputeError(**value)
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247
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else:
|
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248
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0
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return value
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249
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250
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251
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14
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class ResultRecord(RecordBase):
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252
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253
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# Classdata
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254
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14
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_hash_indices = {"driver", "method", "basis", "molecule", "keywords", "program"}
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255
|
|
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|
256
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# Version data
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257
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14
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version: int = Field(1, description="Version of the ResultRecord Model which this data was created with.")
|
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258
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14
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procedure: constr(strip_whitespace=True, regex="single") = Field(
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259
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"single", description='Procedure is fixed as "single" because this is single quantum chemistry result.'
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|
260
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)
|
|
261
|
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|
262
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# Input data
|
|
263
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14
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driver: DriverEnum = Field(..., description=str(DriverEnum.__doc__))
|
|
264
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14
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method: str = Field(..., description="The quantum chemistry method the driver runs with.")
|
|
265
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14
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molecule: ObjectId = Field(
|
|
266
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..., description="The Id of the molecule in the Database which the result is computed on."
|
|
267
|
|
)
|
|
268
|
14
|
basis: Optional[str] = Field(
|
|
269
|
|
None,
|
|
270
|
|
description="The quantum chemistry basis set to evaluate (e.g., 6-31g, cc-pVDZ, ...). Can be ``None`` for "
|
|
271
|
|
"methods without basis sets.",
|
|
272
|
|
)
|
|
273
|
14
|
keywords: Optional[ObjectId] = Field(
|
|
274
|
|
None,
|
|
275
|
|
description="The Id of the :class:`KeywordSet` which was passed into the quantum chemistry program that "
|
|
276
|
|
"performed this calculation.",
|
|
277
|
|
)
|
|
278
|
14
|
protocols: Optional[qcel.models.results.ResultProtocols] = Field(
|
|
279
|
|
qcel.models.results.ResultProtocols(), description=""
|
|
280
|
|
)
|
|
281
|
|
|
|
282
|
|
# Output data
|
|
283
|
14
|
return_result: Union[float, qcel.models.types.Array[float], Dict[str, Any]] = Field(
|
|
284
|
|
None, description="The primary result of the calculation, output is a function of the specified ``driver``."
|
|
285
|
|
)
|
|
286
|
14
|
properties: qcel.models.ResultProperties = Field(
|
|
287
|
|
None, description="Additional data and results computed as part of the ``return_result``."
|
|
288
|
|
)
|
|
289
|
14
|
wavefunction: Optional[Dict[str, Any]] = Field(None, description="Wavefunction data generated by the Result.")
|
|
290
|
14
|
wavefunction_data_id: Optional[ObjectId] = Field(None, description="The id of the wavefunction")
|
|
291
|
|
|
|
292
|
14
|
class Config(RecordBase.Config):
|
|
293
|
|
"""A hash index is not used for ResultRecords as they can be
|
|
294
|
|
uniquely determined with queryable keys.
|
|
295
|
|
"""
|
|
296
|
|
|
|
297
|
14
|
build_hash_index = False
|
|
298
|
|
|
|
299
|
14
|
@validator("method")
|
|
300
|
6
|
def check_method(cls, v):
|
|
301
|
|
"""Methods should have a lower string to match the database."""
|
|
302
|
14
|
return v.lower()
|
|
303
|
|
|
|
304
|
14
|
@validator("basis")
|
|
305
|
6
|
def check_basis(cls, v):
|
|
306
|
14
|
return prepare_basis(v)
|
|
307
|
|
|
|
308
|
14
|
def get_wavefunction(self, key: Union[str, List[str]]) -> Any:
|
|
309
|
|
"""
|
|
310
|
|
Pulls down the Wavefunction data associated with the computation.
|
|
311
|
|
"""
|
|
312
|
|
|
|
313
|
1
|
if self.wavefunction is None:
|
|
314
|
0
|
raise AttributeError("This Record was not computed with Wavefunction data.")
|
|
315
|
|
|
|
316
|
1
|
single_return = False
|
|
317
|
1
|
if isinstance(key, str):
|
|
318
|
1
|
key = [key]
|
|
319
|
1
|
single_return = True
|
|
320
|
|
|
|
321
|
1
|
keys = [x.lower() for x in key]
|
|
322
|
|
|
|
323
|
1
|
self.cache.setdefault("wavefunction", {})
|
|
324
|
|
|
|
325
|
1
|
mapped_keys = {self.wavefunction["return_map"].get(x, x) for x in keys}
|
|
326
|
1
|
missing = mapped_keys - self.cache["wavefunction"].keys()
|
|
327
|
|
|
|
328
|
1
|
unknown = missing - set(self.wavefunction["available"] + ["basis", "restricted"])
|
|
329
|
1
|
if unknown:
|
|
330
|
0
|
raise KeyError(
|
|
331
|
|
f"Wavefunction Key(s) `{unknown}` not understood, available keys are: {self.wavefunction['available']}"
|
|
332
|
|
)
|
|
333
|
|
|
|
334
|
1
|
if missing:
|
|
335
|
|
|
|
336
|
|
# Translate a return value
|
|
337
|
1
|
proj = [self.wavefunction["return_map"].get(x, x) for x in missing]
|
|
338
|
|
|
|
339
|
1
|
self.cache["wavefunction"].update(
|
|
340
|
|
self.client.custom_query(
|
|
341
|
|
"wavefunctionstore", None, {"id": self.wavefunction_data_id}, meta={"include": proj}
|
|
342
|
|
)
|
|
343
|
|
)
|
|
344
|
|
|
|
345
|
1
|
if "basis" in missing:
|
|
346
|
1
|
self.cache["wavefunction"]["basis"] = qcel.models.BasisSet(**self.cache["wavefunction"]["basis"])
|
|
347
|
|
|
|
348
|
|
# Remap once more
|
|
349
|
1
|
ret = {}
|
|
350
|
1
|
for k in keys:
|
|
351
|
1
|
mkey = self.wavefunction["return_map"].get(k, k)
|
|
352
|
1
|
ret[k] = self.cache["wavefunction"][mkey]
|
|
353
|
|
|
|
354
|
1
|
if single_return:
|
|
355
|
1
|
return ret[keys[0]]
|
|
356
|
|
else:
|
|
357
|
1
|
return ret
|
|
358
|
|
|
|
359
|
14
|
def get_molecule(self) -> "Molecule":
|
|
360
|
|
"""
|
|
361
|
|
Pulls the Result's Molecule from the connected database.
|
|
362
|
|
|
|
363
|
|
Returns
|
|
364
|
|
-------
|
|
365
|
|
Molecule
|
|
366
|
|
The requested Molecule
|
|
367
|
|
"""
|
|
368
|
6
|
self.check_client()
|
|
369
|
|
|
|
370
|
6
|
if self.molecule is None:
|
|
371
|
0
|
return None
|
|
372
|
|
|
|
373
|
6
|
if "molecule" not in self.cache:
|
|
374
|
6
|
self.cache["molecule"] = self.client.query_molecules(id=self.molecule)[0]
|
|
375
|
|
|
|
376
|
6
|
return self.cache["molecule"]
|
|
377
|
|
|
|
378
|
|
|
|
379
|
14
|
class OptimizationRecord(RecordBase):
|
|
380
|
|
"""
|
|
381
|
|
A OptimizationRecord for all optimization procedure data.
|
|
382
|
|
"""
|
|
383
|
|
|
|
384
|
|
# Class data
|
|
385
|
14
|
_hash_indices = {"initial_molecule", "keywords", "qc_spec"}
|
|
386
|
|
|
|
387
|
|
# Version data
|
|
388
|
14
|
version: int = Field(1, description="Version of the OptimizationRecord Model which this data was created with.")
|
|
389
|
14
|
procedure: constr(strip_whitespace=True, regex="optimization") = Field(
|
|
390
|
|
"optimization", description='A fixed string indication this is a record for an "Optimization".'
|
|
391
|
|
)
|
|
392
|
14
|
schema_version: int = Field(1, description="The version number of QCSchema under which this record conforms to.")
|
|
393
|
|
|
|
394
|
|
# Input data
|
|
395
|
14
|
initial_molecule: ObjectId = Field(
|
|
396
|
|
..., description="The Id of the molecule which was passed in as the reference for this Optimization."
|
|
397
|
|
)
|
|
398
|
14
|
qc_spec: QCSpecification = Field(
|
|
399
|
|
..., description="The specification of the quantum chemistry calculation to run at each point."
|
|
400
|
|
)
|
|
401
|
14
|
keywords: Dict[str, Any] = Field(
|
|
402
|
|
{},
|
|
403
|
|
description="The keyword options which were passed into the Optimization program. "
|
|
404
|
|
"Note: These are a dictionary and not a :class:`KeywordSet` object.",
|
|
405
|
|
)
|
|
406
|
14
|
protocols: Optional[qcel.models.procedures.OptimizationProtocols] = Field(
|
|
407
|
|
qcel.models.procedures.OptimizationProtocols(), description=""
|
|
408
|
|
)
|
|
409
|
|
|
|
410
|
|
# Automatting issue currently
|
|
411
|
|
# description=str(qcel.models.procedures.OptimizationProtocols.__doc__))
|
|
412
|
|
|
|
413
|
|
# Results
|
|
414
|
14
|
energies: List[float] = Field(None, description="The ordered list of energies at each step of the Optimization.")
|
|
415
|
14
|
final_molecule: ObjectId = Field(
|
|
416
|
|
None, description="The ``ObjectId`` of the final, optimized Molecule the Optimization procedure converged to."
|
|
417
|
|
)
|
|
418
|
14
|
trajectory: List[ObjectId] = Field(
|
|
419
|
|
None,
|
|
420
|
|
description="The list of Molecule Id's the Optimization procedure generated at each step of the optimization."
|
|
421
|
|
"``initial_molecule`` will be the first index, and ``final_molecule`` will be the last index.",
|
|
422
|
|
)
|
|
423
|
|
|
|
424
|
14
|
class Config(RecordBase.Config):
|
|
425
|
14
|
pass
|
|
426
|
|
|
|
427
|
14
|
@validator("keywords")
|
|
428
|
6
|
def check_keywords(cls, v):
|
|
429
|
14
|
if v is not None:
|
|
430
|
14
|
v = recursive_normalizer(v)
|
|
431
|
14
|
return v
|
|
432
|
|
|
|
433
|
|
## Standard function
|
|
434
|
|
|
|
435
|
14
|
def get_final_energy(self) -> float:
|
|
436
|
|
"""The final energy of the geometry optimization.
|
|
437
|
|
|
|
438
|
|
Returns
|
|
439
|
|
-------
|
|
440
|
|
float
|
|
441
|
|
The optimization molecular energy.
|
|
442
|
|
"""
|
|
443
|
1
|
return self.energies[-1]
|
|
444
|
|
|
|
445
|
14
|
def get_trajectory(self) -> List[ResultRecord]:
|
|
446
|
|
"""Returns the Result records for each gradient evaluation in the trajectory.
|
|
447
|
|
|
|
448
|
|
Returns
|
|
449
|
|
-------
|
|
450
|
|
List['ResultRecord']
|
|
451
|
|
A ordered list of Result record gradient computations.
|
|
452
|
|
|
|
453
|
|
"""
|
|
454
|
|
|
|
455
|
1
|
if "trajectory" not in self.cache:
|
|
456
|
1
|
result = {x.id: x for x in self.client.query_results(id=self.trajectory)}
|
|
457
|
|
|
|
458
|
1
|
self.cache["trajectory"] = [result[x] for x in self.trajectory]
|
|
459
|
|
|
|
460
|
1
|
return self.cache["trajectory"]
|
|
461
|
|
|
|
462
|
14
|
def get_molecular_trajectory(self) -> List["Molecule"]:
|
|
463
|
|
"""Returns the Molecule at each gradient evaluation in the trajectory.
|
|
464
|
|
|
|
465
|
|
Returns
|
|
466
|
|
-------
|
|
467
|
|
List['Molecule']
|
|
468
|
|
A ordered list of Molecules in the trajectory.
|
|
469
|
|
|
|
470
|
|
"""
|
|
471
|
|
|
|
472
|
1
|
if "molecular_trajectory" not in self.cache:
|
|
473
|
1
|
mol_ids = [x.molecule for x in self.get_trajectory()]
|
|
474
|
|
|
|
475
|
1
|
mols = {x.id: x for x in self.client.query_molecules(id=mol_ids)}
|
|
476
|
1
|
self.cache["molecular_trajectory"] = [mols[x] for x in mol_ids]
|
|
477
|
|
|
|
478
|
1
|
return self.cache["molecular_trajectory"]
|
|
479
|
|
|
|
480
|
14
|
def get_initial_molecule(self) -> "Molecule":
|
|
481
|
|
"""Returns the initial molecule
|
|
482
|
|
|
|
483
|
|
Returns
|
|
484
|
|
-------
|
|
485
|
|
Molecule
|
|
486
|
|
The initial molecule
|
|
487
|
|
"""
|
|
488
|
|
|
|
489
|
0
|
ret = self.client.query_molecules(id=[self.initial_molecule])
|
|
490
|
0
|
return ret[0]
|
|
491
|
|
|
|
492
|
14
|
def get_final_molecule(self) -> "Molecule":
|
|
493
|
|
"""Returns the optimized molecule
|
|
494
|
|
|
|
495
|
|
Returns
|
|
496
|
|
-------
|
|
497
|
|
Molecule
|
|
498
|
|
The optimized molecule
|
|
499
|
|
"""
|
|
500
|
|
|
|
501
|
1
|
ret = self.client.query_molecules(id=[self.final_molecule])
|
|
502
|
1
|
return ret[0]
|
|
503
|
|
|
|
504
|
|
## Show functions
|
|
505
|
|
|
|
506
|
14
|
def show_history(
|
|
507
|
|
self, units: str = "kcal/mol", digits: int = 3, relative: bool = True, return_figure: Optional[bool] = None
|
|
508
|
|
) -> "plotly.Figure":
|
|
509
|
|
"""Plots the energy of the trajectory the optimization took.
|
|
510
|
|
|
|
511
|
|
Parameters
|
|
512
|
|
----------
|
|
513
|
|
units : str, optional
|
|
514
|
|
Units to display the trajectory in.
|
|
515
|
|
digits : int, optional
|
|
516
|
|
The number of valid digits to show.
|
|
517
|
|
relative : bool, optional
|
|
518
|
|
If True, all energies are shifted by the lowest energy in the trajectory. Otherwise provides raw energies.
|
|
519
|
|
return_figure : Optional[bool], optional
|
|
520
|
|
If True, return the raw plotly figure. If False, returns a hosted iPlot. If None, return a iPlot display in
|
|
521
|
|
Jupyter notebook and a raw plotly figure in all other circumstances.
|
|
522
|
|
|
|
523
|
|
Returns
|
|
524
|
|
-------
|
|
525
|
|
plotly.Figure
|
|
526
|
|
The requested figure.
|
|
527
|
|
"""
|
|
528
|
0
|
cf = qcel.constants.conversion_factor("hartree", units)
|
|
529
|
|
|
|
530
|
0
|
energies = np.array(self.energies)
|
|
531
|
0
|
if relative:
|
|
532
|
0
|
energies = energies - np.min(energies)
|
|
533
|
|
|
|
534
|
0
|
trace = {"mode": "lines+markers", "x": list(range(1, len(energies) + 1)), "y": np.around(energies * cf, digits)}
|
|
535
|
|
|
|
536
|
0
|
if relative:
|
|
537
|
0
|
ylabel = f"Relative Energy [{units}]"
|
|
538
|
|
else:
|
|
539
|
0
|
ylabel = f"Absolute Energy [{units}]"
|
|
540
|
|
|
|
541
|
0
|
custom_layout = {
|
|
542
|
|
"title": "Geometry Optimization",
|
|
543
|
|
"yaxis": {"title": ylabel, "zeroline": True},
|
|
544
|
|
"xaxis": {
|
|
545
|
|
"title": "Optimization Step",
|
|
546
|
|
# "zeroline": False,
|
|
547
|
|
"range": [min(trace["x"]), max(trace["x"])],
|
|
548
|
|
},
|
|
549
|
|
}
|
|
550
|
|
|
|
551
|
0
|
return scatter_plot([trace], custom_layout=custom_layout, return_figure=return_figure)
|
bennybp