Commit ⋅ MolSSI/QCFractal

Showing 3 of 3 files from the diff.

qcfractal/interface/models/torsiondrive.py changed.

qcfractal/services/torsiondrive_service.py changed.

...ctal/interface/collections/torsiondrive_dataset.py changed.

@@ -49,10 +49,22 @@

        "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.",
    )
    additional_keywords: Dict[str, Any] = Field(
        {}, description="Additional keywords to add to the torsiondrive's optimization runs"
    )

    def __init__(self, **kwargs):
        super().__init__(**recursive_normalizer(kwargs))

    def dict(self, *args, **kwargs):
        ret = super().dict(*args, **kwargs)

        # For hash compatibility
        if len(ret["additional_keywords"]) == 0:
            ret.pop("additional_keywords")

        return ret


_td_constr = constr(strip_whitespace=True, regex="torsiondrive")
_qcfractal_constr = constr(strip_whitespace=True, regex="qcfractal")

@@ -113,6 +113,11 @@

            "meta": {"procedure": "optimization", "qc_spec": output.qc_spec.dict(), "tag": meta.pop("tag", None)}
        }
        opt_template["meta"].update(output.optimization_spec.dict())

        # allows for injection of e.g. additional constraints for
        # optimizations created by torsiondrive service
        opt_template["meta"]["keywords"].update(service_input.keywords.additional_keywords)

        meta["optimization_template"] = json.dumps(opt_template)

        # Move around geometric data

@@ -92,6 +92,7 @@

        dihedral_ranges: Optional[List[Tuple[int, int]]] = None,
        energy_decrease_thresh: Optional[float] = None,
        energy_upper_limit: Optional[float] = None,
        additional_keywords: Optional[Dict[str, Any]] = None,
        attributes: Dict[str, Any] = None,
        save: bool = True,
    ) -> None:

@@ -112,6 +113,8 @@

            The threshold of energy decrease to trigger activating grid points
        energy_upper_limit: Optional[float]
            The upper limit of energy relative to current global minimum to trigger activating grid points
        additional_keywords : Dict[str, Any], optional
            Additional keywords to add to the torsiondrive's optimization runs
        attributes : Dict[str, Any], optional
            Additional attributes and descriptions for the entry
        save : bool, optional

@@ -124,6 +127,9 @@

        if attributes is None:
            attributes = {}

        if additional_keywords is None:
            additional_keywords = {}

        # Build new objects
        molecule_ids = self.client.add_molecules(initial_molecules)
        td_keywords = TDKeywords(

@@ -132,6 +138,7 @@

            dihedral_ranges=dihedral_ranges,
            energy_decrease_thresh=energy_decrease_thresh,
            energy_upper_limit=energy_upper_limit,
            additional_keywords=additional_keywords,
        )

        entry = TDEntry(name=name, initial_molecules=molecule_ids, td_keywords=td_keywords, attributes=attributes)

Files		•	•	•	Coverage
qcfractal	9,596	8,470	0	1,126	88.26%
Project Totals (70 files)	9,596	8,470	0	1,126	88.26%

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coverage:
  ignore:
    - */tests/*
    - qcfractal/dashboard/* # early state
    - qcfractal/alembic/* # difficult to test
    - qcfractal/_version.py
    - setup.py
  status:
    patch: false
    project:
      default:
        threshold: 80%
comment:
  layout: "header"
  require_changes: false
  branches: null
  behavior: once
  flags: null
  paths: null

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49	49		"start new optimizations, in unit of a.u. I.e. if energy_upper_limit = 0.05, current global "
50	50		"minimum energy is -9.9 , then a new task starting with energy -9.8 will be skipped.",
51	51		)
	52	+	additional_keywords: Dict[str, Any] = Field(
	53	+	{}, description="Additional keywords to add to the torsiondrive's optimization runs"
	54	+	)
52	55
53	56		def __init__(self, **kwargs):
54	57		super().__init__(**recursive_normalizer(kwargs))
55	58
	59	+	def dict(self, args, *kwargs):
	60	+	ret = super().dict(args, *kwargs)
	61	+
	62	+	# For hash compatibility
	63	+	if len(ret["additional_keywords"]) == 0:
	64	+	ret.pop("additional_keywords")
	65	+
	66	+	return ret
	67	+
56	68
57	69		_td_constr = constr(strip_whitespace=True, regex="torsiondrive")
58	70		_qcfractal_constr = constr(strip_whitespace=True, regex="qcfractal")

113	113		"meta": {"procedure": "optimization", "qc_spec": output.qc_spec.dict(), "tag": meta.pop("tag", None)}
114	114		}
115	115		opt_template["meta"].update(output.optimization_spec.dict())
	116	+
	117	+	# allows for injection of e.g. additional constraints for
	118	+	# optimizations created by torsiondrive service
	119	+	opt_template["meta"]["keywords"].update(service_input.keywords.additional_keywords)
	120	+
116	121		meta["optimization_template"] = json.dumps(opt_template)
117	122
118	123		# Move around geometric data

132	138		dihedral_ranges=dihedral_ranges,
133	139		energy_decrease_thresh=energy_decrease_thresh,
134	140		energy_upper_limit=energy_upper_limit,
	141	+	additional_keywords=additional_keywords,
135	142		)
136	143
137	144		entry = TDEntry(name=name, initial_molecules=molecule_ids, td_keywords=td_keywords, attributes=attributes)

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92	92		dihedral_ranges: Optional[List[Tuple[int, int]]] = None,
93	93		energy_decrease_thresh: Optional[float] = None,
94	94		energy_upper_limit: Optional[float] = None,
	95	+	additional_keywords: Optional[Dict[str, Any]] = None,
95	96		attributes: Dict[str, Any] = None,
96	97		save: bool = True,
97	98		) -> None:

112	113		The threshold of energy decrease to trigger activating grid points
113	114		energy_upper_limit: Optional[float]
114	115		The upper limit of energy relative to current global minimum to trigger activating grid points
	116	+	additional_keywords : Dict[str, Any], optional
	117	+	Additional keywords to add to the torsiondrive's optimization runs
115	118		attributes : Dict[str, Any], optional
116	119		Additional attributes and descriptions for the entry
117	120		save : bool, optional

124	127		if attributes is None:
125	128		attributes = {}
126	129
	130	+	if additional_keywords is None:
	131	+	additional_keywords = {}
	132	+
127	133		# Build new objects
128	134		molecule_ids = self.client.add_molecules(initial_molecules)
129	135		td_keywords = TDKeywords(

1	coverage:
2	ignore:
3	- /tests/
4	- qcfractal/dashboard/* # early state
5	- qcfractal/alembic/* # difficult to test
6	- qcfractal/_version.py
7	- setup.py
8	status:
9	patch: false
10	project:
11	default:
12	threshold: 80%
13	comment:
14	layout: "header"
15	require_changes: false
16	branches: null
17	behavior: once
18	flags: null
19	paths: null

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