Pydantic2 and MBE procedure

.github/workflows/CI.yml

@@ -103,10 +103,11 @@ jobs:
         qcore --accept-license
 
     # note: psi4 on c-f pins to a single qcel and qcng, so this may be handy for solve-and-replace
-    #- name: Special Config - QCElemental Dep
+    - name: Special Config - QCElemental Dep
     #  if: (matrix.cfg.label == 'ADCC')
-    #  run: |
-    #    conda remove qcelemental --force
+      run: |
+        conda remove qcelemental --force
+        python -m pip install git+https://github.com/loriab/QCElemental.git@v0.29.0.dev1 --no-deps
     #    python -m pip install qcelemental>=0.26.0 --no-deps
 
       # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
@@ -122,14 +123,17 @@ jobs:
       run: |
         sed -i s/from\ pydantic\ /from\ pydantic.v1\ /g ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/*py
 
+    - name: Install QCEngine
+      run: |
+        python -m pip install . --no-deps
+
     - name: Environment Information
       run: |
         mamba info
         mamba list
-
-    - name: Install QCEngine
-      run: |
-        python -m pip install . --no-deps
+        python -c "import qcelemental as q;print(q.__file__, q.__version__)"
+        python -c "import qcengine as q;print(q.__file__, q.__version__)"
+        git describe
 
     - name: QCEngineRecords
       run: |

devtools/conda-envs/adcc.yaml

@@ -13,7 +13,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.24.0
-  - pydantic=1
+  - pydantic>=2.1
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/base.yaml

@@ -8,7 +8,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.12.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/docs-cf.yaml

@@ -5,7 +5,8 @@ channels:
 dependencies:
   - python
   - networkx
-  - pydantic=1
+  - pydantic>=2.1
+  - pydantic-settings
   - numpy
   - pint
 

devtools/conda-envs/mrchem.yaml

@@ -13,7 +13,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental>=0.24
-  - pydantic 
+  - pydantic>=2.1
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/nwchem.yaml

@@ -8,7 +8,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.24.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
   - networkx>=2.4.0
 
     # Testing

devtools/conda-envs/openmm.yaml

@@ -16,7 +16,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.11.1
-  - pydantic >=1.8.2
+  - pydantic>=2.1
+  - pydantic-settings
   - pint <0.22
 
     # Testing

devtools/conda-envs/opt-disp.yaml

@@ -25,7 +25,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.26.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/psi-nightly.yaml

@@ -12,7 +12,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.26.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/psi.yaml

@@ -16,7 +16,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental=0.24.0
-  - pydantic=1.8.2  # test minimun stated version.
+  - pydantic>=2.1  # test minimum stated version.
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/qcore.yaml

@@ -11,7 +11,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.24
-  - pydantic >=1.8.2
+  - pydantic>=2.1
+  - pydantic-settings
   - tbb<2021
 
     # Testing

devtools/conda-envs/rdkit.yaml

@@ -11,7 +11,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.12.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/torchani.yaml

@@ -11,7 +11,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.12.0
-  - pydantic>=1.0.0
+  - pydantic>=2.1
+  - pydantic-settings
 
   - pytorch
 

devtools/conda-envs/xtb.yaml

@@ -11,7 +11,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.11.1
-  - pydantic >=1.8.2
+  - pydantic>=2.1
+  - pydantic-settings
 
     # Extras
   - gcp-correction

qcengine/compute.py

@@ -13,10 +13,7 @@
 from .util import compute_wrapper, environ_context, handle_output_metadata, model_wrapper
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.main import BaseModel
-    except ImportError:
-        from pydantic.main import BaseModel
+    from pydantic.main import BaseModel
     from qcelemental.models import AtomicResult
 
 
@@ -28,7 +25,7 @@ def _process_failure_and_return(model, return_dict, raise_error):
         if raise_error:
             raise InputError(model.error.error_message)
         elif return_dict:
-            return model.dict()
+            return model.model_dump()
         else:
             return model
     else:

qcengine/config.py

@@ -9,10 +9,8 @@
 import socket
 from typing import Any, Dict, Optional, Union
 
-try:
-    import pydantic.v1 as pydantic
-except ImportError:
-    import pydantic
+from pydantic import BaseModel, ConfigDict, Field
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from .extras import get_information
 
@@ -64,7 +62,7 @@ def get_global(key: Optional[str] = None) -> Union[str, Dict[str, Any]]:
         return _global_values[key]
 
 
-class NodeDescriptor(pydantic.BaseModel):
+class NodeDescriptor(BaseModel):
     """
     Description of an individual node
     """
@@ -78,7 +76,7 @@ class NodeDescriptor(pydantic.BaseModel):
     memory_safety_factor: int = 10  # Percentage of memory as a safety factor
 
     # Specifications
-    ncores: Optional[int] = pydantic.Field(
+    ncores: Optional[int] = Field(
         None,
         description="""Number of cores accessible to each task on this node
 
@@ -88,9 +86,9 @@ class NodeDescriptor(pydantic.BaseModel):
     retries: int = 0
 
     # Cluster options
-    is_batch_node: bool = pydantic.Field(
+    is_batch_node: bool = Field(
         False,
-        help="""Whether the node running QCEngine is a batch node
+        description="""Whether the node running QCEngine is a batch node
 
     Some clusters are configured such that tasks are launched from a special "batch" or "MOM" onto the compute nodes.
     The compute nodes on such clusters often have a different CPU architecture than the batch nodes and 
@@ -103,7 +101,7 @@ class NodeDescriptor(pydantic.BaseModel):
     ``mpiexec_command`` must always be used even for serial jobs (e.g., getting the version number)
     """,
     )
-    mpiexec_command: Optional[str] = pydantic.Field(
+    mpiexec_command: Optional[str] = Field(
         None,
         description="""Invocation for launching node-parallel tasks with MPI
 
@@ -140,31 +138,29 @@ def __init__(self, **data: Dict[str, Any]):
             if "{ranks_per_node}" not in self.mpiexec_command:
                 raise ValueError("mpiexec_command must explicitly state the number of ranks per node")
 
-    class Config:
-        extra = "forbid"
+    model_config = ConfigDict(
+        extra="forbid",
+    )
 
 
-class TaskConfig(pydantic.BaseSettings):
+class TaskConfig(BaseSettings):
     """Description of the configuration used to launch a task."""
 
     # Specifications
-    ncores: int = pydantic.Field(None, description="Number cores per task on each node")
-    nnodes: int = pydantic.Field(None, description="Number of nodes per task")
-    memory: float = pydantic.Field(
-        None, description="Amount of memory in GiB (2^30 bytes; not GB = 10^9 bytes) per node."
-    )
+    ncores: int = Field(None, description="Number cores per task on each node")
+    nnodes: int = Field(None, description="Number of nodes per task")
+    memory: float = Field(None, description="Amount of memory in GiB (2^30 bytes; not GB = 10^9 bytes) per node.")
     scratch_directory: Optional[str]  # What location to use as scratch
     retries: int  # Number of retries on random failures
     mpiexec_command: Optional[str]  # Command used to launch MPI tasks, see NodeDescriptor
     use_mpiexec: bool = False  # Whether it is necessary to use MPI to run an executable
-    cores_per_rank: int = pydantic.Field(1, description="Number of cores per MPI rank")
-    scratch_messy: bool = pydantic.Field(
-        False, description="Leave scratch directory and contents on disk after completion."
-    )
+    cores_per_rank: int = Field(1, description="Number of cores per MPI rank")
+    scratch_messy: bool = Field(False, description="Leave scratch directory and contents on disk after completion.")
 
-    class Config(pydantic.BaseSettings.Config):
-        extra = "forbid"
-        env_prefix = "QCENGINE_"
+    model_config = SettingsConfigDict(
+        extra="forbid",
+        env_prefix="QCENGINE_",
+    )
 
 
 def _load_defaults() -> None:

qcengine/procedures/base.py

@@ -10,6 +10,7 @@
 from .nwchem_opt import NWChemDriverProcedure
 from .optking import OptKingProcedure
 from .torsiondrive import TorsionDriveProcedure
+from .manybody import ManyBodyProcedure
 from .model import ProcedureHarness
 
 __all__ = ["register_procedure", "get_procedure", "list_all_procedures", "list_available_procedures"]
@@ -71,3 +72,4 @@ def list_available_procedures() -> Set[str]:
 register_procedure(BernyProcedure())
 register_procedure(NWChemDriverProcedure())
 register_procedure(TorsionDriveProcedure())
+register_procedure(ManyBodyProcedure())

qcengine/procedures/berny.py

@@ -3,7 +3,7 @@
 import sys
 import traceback
 from io import StringIO
-from typing import Any, Dict, Union
+from typing import Any, ClassVar, Dict, Union
 
 import numpy as np
 from qcelemental.models import OptimizationInput, OptimizationResult, FailedOperation
@@ -16,7 +16,7 @@
 
 
 class BernyProcedure(ProcedureHarness):
-    _defaults = {"name": "Berny", "procedure": "optimization"}
+    _defaults: ClassVar[Dict[str, Any]] = {"name": "Berny", "procedure": "optimization"}
 
     def found(self, raise_error: bool = False) -> bool:
         return which_import(
@@ -54,11 +54,11 @@ def compute(
         log.addHandler(logging.StreamHandler(log_stream))
         log.setLevel("INFO")
 
-        input_data = input_data.dict()
+        input_data = input_data.model_dump()
         geom_qcng = input_data["initial_molecule"]
         comput = {**input_data["input_specification"], "molecule": geom_qcng}
         program = input_data["keywords"].pop("program")
-        task_config = config.dict()
+        task_config = config.model_dump()
         trajectory = []
         output_data = input_data.copy()
         try:
@@ -70,14 +70,14 @@ def compute(
                 geom_qcng["geometry"] = np.stack(geom_berny.coords * berny.angstrom)
                 ret = qcengine.compute(comput, program, task_config=task_config)
                 if ret.success:
-                    trajectory.append(ret.dict())
+                    trajectory.append(ret.model_dump())
                     opt.send((ret.properties.return_energy, ret.return_result))
                 else:
                     # qcengine.compute returned FailedOperation
                     raise UnknownError("Gradient computation failed")
 
         except UnknownError:
-            error = ret.error.dict()  # ComputeError
+            error = ret.error.model_dump()  # ComputeError
         except Exception:
             error = {"error_type": "unknown", "error_message": f"Berny error:\n{traceback.format_exc()}"}
         else:

qcengine/procedures/geometric.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, Union
+from typing import Any, ClassVar, Dict, Union
 
 from qcelemental.models import OptimizationInput, OptimizationResult
 from qcelemental.util import safe_version, which_import
@@ -8,13 +8,10 @@
 
 class GeometricProcedure(ProcedureHarness):
 
-    _defaults = {"name": "geomeTRIC", "procedure": "optimization"}
+    _defaults: ClassVar[Dict[str, Any]] = {"name": "geomeTRIC", "procedure": "optimization"}
 
     version_cache: Dict[str, str] = {}
 
-    class Config(ProcedureHarness.Config):
-        pass
-
     def found(self, raise_error: bool = False) -> bool:
         return which_import(
             "geometric",
@@ -43,13 +40,13 @@ def compute(self, input_model: "OptimizationInput", config: "TaskConfig") -> "Op
         except ModuleNotFoundError:
             raise ModuleNotFoundError("Could not find geomeTRIC in the Python path.")
 
-        input_data = input_model.dict()
+        input_data = input_model.model_dump()
 
         # Temporary patch for geomeTRIC
         input_data["initial_molecule"]["symbols"] = list(input_data["initial_molecule"]["symbols"])
 
         # Set retries to two if zero while respecting local_config
-        local_config = config.dict()
+        local_config = config.model_dump()
         local_config["retries"] = local_config.get("retries", 2) or 2
         input_data["input_specification"]["extras"]["_qcengine_local_config"] = local_config