Csse layout 536g

docs/changelog.rst

@@ -33,40 +33,39 @@ New Features
 ++++++++++++
 * Downstream code should ``from qcelemental.models.v1 import Molecule, AtomicResult`` etc. to assure medium-term availability of existing models.
 * New pydantic v2 models available as ``from qcelemental.models.v2 import Molecule, AtomicResult`` etc.
-- (:pr:`361`) Switch from poetry to setuptools build backend. 
-
-Enhancements
-++++++++++++
-- (:pr:`364`) 
-- (:pr:`364`) 
-- (:pr:`364`) 
-- (:pr:`364`) main storage for ``v2.TorsionDriveResult`` moved from ``optimization_history`` to ``scan_results``.
-- (:pr:`364`) ``v2.TorsionDriveInput.initial_molecule`` restored from ``initial_molecules``.
-- (:pr:`364`) default of OptimizationProtocol.trajectory_results changed to "none" from "all" in v1. much info can now come from properties.
-- (:pr:`364`) v2.OptimizationProtocol renamed trajectory_results from trajectory in accordance with the protocol naming the controlled field. no default change yet.
-- (:pr:`364`) v1/v2: import ElectronShell, BasisCenter, ECPPotential from top level models
-- (:pr:`364`) molparse learns to pass through schema v3, though no new field for Mol yet.
-- (:pr:`364`) ``v2.FailedOperation`` gained schema_name and schema_version=2. unversioned in v1
-- (:pr:`364`) ``v2.BasisSet.schema_version`` is now 2, with no layout change.
-- (:pr:`364`) ``v2.Molecule.schema_version`` is now 3. convert_v of all the models learned to handle the new schema_version.
-- (:pr:`364`) v2: standardizing on In/Res get versions, Ptcl/Kw/Spec get only schema_name. At, Opt, TD
-- (:pr:`364`) v1/v2: removing the version_stamps from the models: At, Opt, TD, Fail, BAsis, Mol. so it will error rather than clobber if constructed with wrong version. convert_v now handles.
-- (:pr:`364`) convert_v functions learned to handle model.basis=BasisSet, not just str.
-- (:pr:`364`) ``Molecule`` and ``BasisSet``  and ``WavefunctionProperties`` learned to ``convert_v`` to interconvert between v1 and v2. No layout changes. 
+- (:pr:`361`) Switch from poetry to setuptools build backend.
+
+Enhancements
+++++++++++++
+- (:pr:`367`) ``v1.TorsionDriveResult.final_energies`` replaced by larger ``v2.TorsionDriveResult.scan_properties``. the former is present in the latter as ``return_energy``.
+- (:pr:`367`) ``v2.TorsionDriveProperties`` added mostly as a placeholder class (one obvious prop at present).
+- (:pr:`366`) main storage for ``v2.TorsionDriveResult`` moved from ``optimization_history`` to ``scan_results``.
+- (:pr:`366`) ``v2.TorsionDriveInput.initial_molecule`` restored from ``initial_molecules``.
+- (:pr:`366`) default of OptimizationProtocol.trajectory_results changed to "none" from "all" in v1. much info can now come from properties.
+- (:pr:`366`) v2.OptimizationProtocol renamed trajectory_results from trajectory in accordance with the protocol naming the controlled field. no default change yet.
+- (:pr:`366`) v1/v2: import ElectronShell, BasisCenter, ECPPotential from top level models
+- (:pr:`366`) molparse learns to pass through schema v3, though no new field for Mol yet.
+- (:pr:`366`) ``v2.FailedOperation`` gained schema_name and schema_version=2. unversioned in v1
+- (:pr:`366`) ``v2.BasisSet.schema_version`` is now 2, with no layout change.
+- (:pr:`366`) ``v2.Molecule.schema_version`` is now 3. convert_v of all the models learned to handle the new schema_version.
+- (:pr:`366`) v2: standardizing on In/Res get versions, Ptcl/Kw/Spec get only schema_name. At, Opt, TD
+- (:pr:`366`) v1/v2: removing the version_stamps from the models: At, Opt, TD, Fail, BAsis, Mol. so it will error rather than clobber if constructed with wrong version. convert_v now handles.
+- (:pr:`366`) convert_v functions learned to handle model.basis=BasisSet, not just str.
+- (:pr:`366`) ``Molecule`` and ``BasisSet``  and ``WavefunctionProperties`` learned to ``convert_v`` to interconvert between v1 and v2. No layout changes.
   ``BasisSet.schema_name`` standardized to ``qcschema_basis_set``.
   Both classes get their ``schema_name`` as Literal now
 - (:pr:`360`) ``Molecule`` learned new functions ``element_composition`` and ``molecular_weight``.
   The first gives a dictionary of element symbols and counts, while the second gives the weight in amu.
   Both can access the whole molecule or per-fragment like the existing ``nelectrons`` and
   ``nuclear_repulsion_energy``. All four can now select all atoms or exclude ghosts (default).
-- (:pr:`364`) separated procedures.py and renamed results.py so models are separated into atomic.py, optimization.py, torsion_drive.py, failure models moved to failed_operation.py. basis.py to basis_set.py
-- (:pr:`364`) ``schema_name`` output chanded to result ``qcschema_output`` to ``qcschema_atomic_result``. also opt
-- (:pr:`364`) ``TDKeywords`` renamed to ``TorsionDriveKeywords``
-- (:pr:`364`) ``AtomicResultProtocols`` renamed to ``AtomicProtocols`` and ``AtomicResultProperties`` to ``AtomicProperties``
-- (:pr:`364`) new ``v2.TorsionDriveProtocols`` model with field ``scan_results`` to control all/none/lowest saving of optimizationresults at each grid point. Use "all" for proper conversion to v1.
+- (:pr:`366`) separated procedures.py and renamed results.py so models are separated into atomic.py, optimization.py, torsion_drive.py, failure models moved to failed_operation.py. basis.py to basis_set.py
+- (:pr:`366`) ``schema_name`` output chanded to result ``qcschema_output`` to ``qcschema_atomic_result``. also opt
+- (:pr:`366`) ``TDKeywords`` renamed to ``TorsionDriveKeywords``
+- (:pr:`366`) ``AtomicResultProtocols`` renamed to ``AtomicProtocols`` and ``AtomicResultProperties`` to ``AtomicProperties``
+- (:pr:`366`) new ``v2.TorsionDriveProtocols`` model with field ``scan_results`` to control all/none/lowest saving of optimizationresults at each grid point. Use "all" for proper conversion to v1.
 - (:pr:`363`) ``v2.TorsionDriveResult`` no longer inherits from Input and now has indep id and extras and new native_files.
 - (:pr:`363`) ``v2.TorsionDriveInput.initial_molecule`` now ``initial_molecules`` as it's a list of >=1 molecules. keep change?
-- (:pr:`363`) ``v2. TorsionDriveSpecification`` is a new model. instead of ``v2.TorsionDriveInput`` having a ``input_specification`` and an ``optimization_spec`` fields, it has a ``specification`` field that is a ``TorsionDriveSpecification`` which in turn hold opt info and in turn gradient/atomic info. 
+- (:pr:`363`) ``v2. TorsionDriveSpecification`` is a new model. instead of ``v2.TorsionDriveInput`` having a ``input_specification`` and an ``optimization_spec`` fields, it has a ``specification`` field that is a ``TorsionDriveSpecification`` which in turn hold opt info and in turn gradient/atomic info.
 - (:pr:`363`) ``v2.TDKeywords`` got a ``schema_name`` field.
 - (:pr:`363`) ``native_files`` field added to ``v2.OptimizationResult`` and ``v2.TorsionDriveResult`` gained a ``native_files`` field, though not protocols for user control.
 - (:pr:`363`) ``v2.AtomicResult.convert_v()`` learned external_protocols option to inject that field if known from OptIn

pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project.urls]
 homepage = "https://github.com/MolSSI/QCElemental"
-changelog = "https://github.com/MolSSI/QCElemental/docs/changelog.rst"
-documentation = "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/"
+changelog = "https://github.com/MolSSI/QCElemental/blob/master/docs/changelog.rst"
+documentation = "https://molssi.github.io/QCElemental/"
 issues = "https://github.com/MolSSI/QCElemental/issues"
 
 [project]

qcelemental/models/v1/procedures.py

@@ -549,13 +549,24 @@ def convert_v(
             dtop["stdout"] = dself.pop("stdout")
             dtop["stderr"] = dself.pop("stderr")
             dtop["success"] = dself.pop("success")
-            dtop["final_energies"] = dself.pop("final_energies")
+            dtop["scan_properties"] = {
+                k: {
+                    "nuclear_repulsion_energy": mol.nuclear_repulsion_energy(),
+                    "return_energy": dself["final_energies"][k],
+                    # "optimization_iterations":
+                }
+                for k, mol in self.final_molecules.items()
+            }
+            dself.pop("final_energies")
             dself.pop("final_molecules")
             dtop["final_molecules"] = {k: m.convert_v(target_version) for k, m in self.final_molecules.items()}
             dtop["scan_results"] = {
                 k: [opthist_class(**res).convert_v(target_version) for res in lst]
                 for k, lst in dself["optimization_history"].items()
             }
+            dtop["properties"] = {
+                "calcinfo_ngrid": len(dtop["scan_results"]),
+            }
             dself.pop("optimization_history")
             dself.pop("schema_name")
             dself.pop("schema_version")

qcelemental/models/v2/__init__.py

@@ -23,6 +23,7 @@
 from .torsion_drive import (
     TorsionDriveInput,
     TorsionDriveKeywords,
+    TorsionDriveProperties,
     TorsionDriveProtocols,
     TorsionDriveResult,
     TorsionDriveSpecification,

qcelemental/models/v2/torsion_drive.py

@@ -7,7 +7,7 @@
 from .basemodels import ExtendedConfigDict, ProtoModel, check_convertible_version
 from .common_models import DriverEnum, Provenance
 from .molecule import Molecule
-from .optimization import OptimizationResult, OptimizationSpecification
+from .optimization import OptimizationProperties, OptimizationResult, OptimizationSpecification
 from .types import Array
 
 if TYPE_CHECKING:
@@ -176,8 +176,27 @@ def convert_v(
 
 
 # ====  Properties  =============================================================
-# ========  Calcinfo  =======================================================
-# ========  Canonical  ======================================================
+
+# This is mostly a placeholder class until properties developed
+
+
+class TorsionDriveProperties(ProtoModel):
+    r"""
+    Named properties of torsion drive computations following the MolSSI QCSchema.
+    """
+
+    schema_name: Literal["qcschema_torsion_drive_properties"] = Field(
+        "qcschema_torsion_drive_properties",
+        description=f"The QCSchema specification to which this model conforms.",
+    )
+
+    # ========  Calcinfo  =======================================================
+
+    calcinfo_ngrid: Optional[int] = Field(None, description="The number of dihedral constraints optimized.")
+
+    # ========  Canonical  ======================================================
+
+    model_config = ProtoModel._merge_config_with(force_skip_defaults=True)
 
 
 # ====  Results  ================================================================
@@ -194,13 +213,14 @@ class TorsionDriveResult(ProtoModel):
     id: Optional[str] = Field(None, description="The optional ID for the computation.")
     input_data: TorsionDriveInput = Field(..., description=str(TorsionDriveInput.__doc__))
 
-    # final_energies, final_molecules, optimization_history I'm hoping to refactor into scan_properties and scan_results but need to talk to OpenFF folks
-    final_energies: Dict[str, float] = Field(
-        ..., description="The final energy at each angle of the TorsionDrive scan."
-    )
     final_molecules: Dict[str, Molecule] = Field(
         ..., description="The final molecule at each angle of the TorsionDrive scan."
     )
+    # Note: scan_results includes all opts at each point (best and intermediate), while
+    #   scan_properties and final_molecules include only the best opt. other choices could be made.
+    scan_properties: Dict[str, OptimizationProperties] = Field(
+        ..., description="The map of energies and other properties for each angle of the TorsionDrive scan."
+    )
     scan_results: Dict[str, List[OptimizationResult]] = Field(
         ...,
         description="The map of each angle of the TorsionDrive scan to each optimization computations.",
@@ -212,8 +232,7 @@ class TorsionDriveResult(ProtoModel):
     # native_files placeholder for when any td programs supply extra files or need an input file. no protocol at present
     native_files: Dict[str, Any] = Field({}, description="DSL files.")
 
-    # TODO add properties if a set can be collected
-    # properties: TorsionDriveProperties = Field(..., description=str(TorsionDriveProperties.__doc__))
+    properties: TorsionDriveProperties = Field(..., description=str(TorsionDriveProperties.__doc__))
 
     extras: Dict[str, Any] = Field(
         {},
@@ -278,7 +297,8 @@ def convert_v(
             input_data = self.input_data.convert_v(target_version).model_dump()
             input_data.pop("schema_name")  # prevent inheriting
 
-            dtop["final_energies"] = dself.pop("final_energies")
+            dtop["final_energies"] = {k: prop["return_energy"] for k, prop in dself["scan_properties"].items()}
+            dself.pop("scan_properties")
             dself.pop("final_molecules")
             dtop["final_molecules"] = {k: m.convert_v(target_version) for k, m in self.final_molecules.items()}
             dtop["optimization_history"] = {
@@ -288,6 +308,7 @@ def convert_v(
             dself.pop("scan_results")
 
             dself.pop("id")  # unused in v1
+            dself.pop("properties")  # new in v2
             dself.pop("native_files")  # new in v2
             dtop["provenance"] = dself.pop("provenance")
             dtop["stdout"] = dself.pop("stdout")

qcelemental/tests/test_model_results.py

@@ -292,9 +292,10 @@ def torsiondrive_data_fixture(ethane_data_fixture, optimization_data_fixture, re
             "input_data": input_data,
             "success": True,
             "provenance": {"creator": "qcel"},
-            "final_energies": {"180": -2.3, "0": -4.5},
+            "scan_properties": {"180": {"return_energy": -2.3}, "0": {"return_energy": -4.5}},
             "final_molecules": {"180": ethane, "0": ethane},
             "scan_results": {"180": [optres, optres], "0": [optres]},
+            "properties": {"calcinfo_ngrid": 1},
         }
     else:
         ret = {
@@ -897,7 +898,9 @@ def every_model_fixture(request):
     data = request.getfixturevalue("torsiondrive_data_fixture")
     datas[smodel] = data
 
-    # smodel = "TorsionDriveProperties"  # DNE
+    smodel = "TorsionDriveProperties"
+    data = {"calcinfo_ngrid": 1}
+    datas[smodel] = data
 
     smodel = "ManyBodyInput"
     data = request.getfixturevalue("manybody_data_fixture")
@@ -955,7 +958,7 @@ def every_model_fixture(request):
     pytest.param("TDKeywords",                  "TorsionDriveKeywords",         id="TDKw"),
     pytest.param(None,                          "TorsionDriveProtocols",        id="TDPtcl"),
     pytest.param("TorsionDriveResult",          "TorsionDriveResult",           id="TDRes"), 
-    # pytest.param(None,                        "TorsionDriveProperties",       id="TDProp"),
+    pytest.param(None,                          "TorsionDriveProperties",       id="TDProp"),
     pytest.param("ManyBodyInput",               None,                           id="MBIn", marks=using_qcmb), 
     pytest.param("ManyBodySpecification",       None,                           id="MBSpec", marks=using_qcmb), 
     pytest.param("ManyBodyKeywords",            None,                           id="MBKw", marks=using_qcmb),
@@ -1166,7 +1169,7 @@ def test_model_survey_extras(smodel1, smodel2, every_model_fixture, request, sch
         "v1-TDKw"     : None,  "v2-TDKw"     : None,
         "v1-TDPtcl"   : None,  "v2-TDPtcl"   : None,  # v1 DNE 
         "v1-TDRes"    : {},    "v2-TDRes"    : {},
-        "v1-TDProp"   : None,  "v2-TDProp"   : None,  # v1/v2 DNE
+        "v1-TDProp"   : None,  "v2-TDProp"   : None,  # v1 DNE
         "v1-MBIn"     : {},    "v2-MBIn"     : None,  # v2 DNE
         "v1-MBSpec"   : {},    "v2-MBSpec"   : {},    # v2 DNE
         "v1-MBKw"     : None,  "v2-MBKw"     : None,  # v2 DNE
@@ -1272,7 +1275,7 @@ def test_model_survey_convertible(smodel1, smodel2, every_model_fixture, request
         # "v1-TDKw"     ,  "v2-TDKw"    , 
         "v1-TDPtcl"   ,  "v2-TDPtcl"  , 
         "v1-TDRes"    ,  "v2-TDRes"   , 
-        # "v1-TDProp"   ,  "v2-TDProp"  , 
+        "v1-TDProp"   ,  "v2-TDProp"  , 
         # "v1-MBIn"     ,  "v2-MBIn"    , 
         # "v1-MBSpec"   ,  "v2-MBSpec"  , 
         # "v1-MBKw"     ,  "v2-MBKw"    , 
@@ -1341,7 +1344,7 @@ def test_model_survey_schema_name(smodel1, smodel2, every_model_fixture, request
         "v1-TDKw"     : None,                                   "v2-TDKw"     : "qcschema_torsion_drive_keywords",
         "v1-TDPtcl"   : None,                                   "v2-TDPtcl"   : "qcschema_torsion_drive_protocols",  # v1 DNE
         "v1-TDRes"    : "qcschema_torsion_drive_output",        "v2-TDRes"    : "qcschema_torsion_drive_result",
-        "v1-TDProp"   : None,                                   "v2-TDProp"   : None,  # v1 DNE, v2 DNE
+        "v1-TDProp"   : None,                                   "v2-TDProp"   : "qcschema_torsion_drive_properties",  # v1 DNE
         "v1-MBIn"     : "qcschema_manybodyinput",               "v2-MBIn"     : "qcschema_many_body_input",     # v2 DNE
         "v1-MBSpec"   : "qcschema_manybodyspecification",       "v2-MBSpec"   : "qcschema_many_body_specification",  # v2 DNE
         "v1-MBKw"     : "qcschema_manybodykeywords",            "v2-MBKw"     : "qcschema_many_body_keywords",       # v2 DNE