add plain qcmanybody harness (#466)

* add plain qcmanybody hanress

* lint

* update changelog

devtools/conda-envs/nwchem-cf.yaml

@@ -12,6 +12,7 @@ dependencies:
   - qcelemental >=0.24.0
   - pydantic>=1.0.0
   - networkx>=2.4.0
+  - qcmanybody
 
     # Testing
   - pytest

devtools/conda-envs/opt-disp-cf.yaml

@@ -14,6 +14,7 @@ dependencies:
   - geometric
   - optking
   - pymdi
+  - qcmanybody
 
     # Core
   - python

docs/source/changelog.rst

@@ -36,17 +36,24 @@ Breaking Changes
 
 New Features
 ++++++++++++
+- (:pr:`466`) QCManyBody - new procedure for computing interaction energies or truncation or full
+  many-body expansions with no, counterpoise, or Valiron-Mayer function counterpoise correction
+  for basis set superposition error. @loriab
 
 Enhancements
 ++++++++++++
 - (:pr:`463`) Maint - Pin to QCElemental <0.70 since we now know QCSchema v2 release schedule.
 - (:pr:`463`) MACE - New v0.3.9 release yields a pytorch error, so recommend pymace=0.3.6 .
 - (:pr:`464`, :issue:`447`) CFOUR - Allow CC-PVDZ alias basis specification. Also fix the PwCVXZ
   basis keyword. @philipmnel
+- (:pr:`440`) TorsionDrive - Support other geometric-style constraints by not overwriting those
+  already present. @jthorton
 
 Bug Fixes
 +++++++++
-- (:pr:`451`, :issue:`450`) Psi4 - Fixes bug in Psi4 detection when command `python` not available. @susilehtola, @topazus
+- (:pr:`451`, :issue:`450`) Psi4 - Fixes bug in Psi4 detection when command `python` not available.
+  @susilehtola, @topazus
+- (:pr:`466`) CFOUR - fix error collecting molecule when it's a single atom with two-letter symbol. @loriab
 
 Misc.
 +++++

qcengine/procedures/base.py

@@ -9,6 +9,7 @@
 from .geometric import GeometricProcedure
 from .nwchem_opt import NWChemDriverProcedure
 from .optking import OptKingProcedure
+from .qcmanybody import QCManyBodyProcedure
 from .torsiondrive import TorsionDriveProcedure
 from .model import ProcedureHarness
 
@@ -69,5 +70,6 @@ def list_available_procedures() -> Set[str]:
 register_procedure(GeometricProcedure())
 register_procedure(OptKingProcedure())
 register_procedure(BernyProcedure())
+register_procedure(QCManyBodyProcedure())
 register_procedure(NWChemDriverProcedure())
 register_procedure(TorsionDriveProcedure())

qcengine/procedures/qcmanybody.py

@@ -0,0 +1,51 @@
+from typing import TYPE_CHECKING, Any, Dict, Union
+
+from qcelemental.util import safe_version, which_import
+
+from .model import ProcedureHarness
+
+if TYPE_CHECKING:
+    from ..config import TaskConfig
+    from qcmanybody.models import ManyBodyInput, ManyBodyResult
+
+
+class QCManyBodyProcedure(ProcedureHarness):
+
+    # v2: ClassVar[Dict[str, Any]]
+    _defaults: Dict[str, Any] = {"name": "QCManyBody", "procedure": "manybody"}
+
+    version_cache: Dict[str, str] = {}
+
+    class Config(ProcedureHarness.Config):
+        pass
+
+    def found(self, raise_error: bool = False) -> bool:
+        return which_import(
+            "qcmanybody",
+            return_bool=True,
+            raise_error=raise_error,
+            raise_msg="Please install via `conda install qcmanybody -c conda-forge`.",
+        )
+
+    def build_input_model(self, data: Union[Dict[str, Any], "ManyBodyInput"]) -> "ManyBodyInput":
+        from qcmanybody.models import ManyBodyInput
+
+        return self._build_model(data, ManyBodyInput)
+
+    def get_version(self) -> str:
+        self.found(raise_error=True)
+
+        which_prog = which_import("qcmanybody")
+        if which_prog not in self.version_cache:
+            import qcmanybody
+
+            self.version_cache[which_prog] = safe_version(qcmanybody.__version__)
+
+        return self.version_cache[which_prog]
+
+    def compute(self, input_model: "ManyBodyInput", config: "TaskConfig") -> "ManyBodyResult":
+        from qcmanybody import ManyBodyComputer
+
+        output_model = ManyBodyComputer.from_manybodyinput(input_model)
+
+        return output_model

qcengine/programs/adcc.py

@@ -56,7 +56,7 @@ def found(raise_error: bool = False) -> bool:
             "psi4",
             return_bool=True,
             raise_error=raise_error,
-            raise_msg="Please install psi4 for adcc harness via `conda install psi4 -c conda-forge/label/libint_dev -c conda-forge`.",
+            raise_msg="Please install psi4 for adcc harness via `conda install psi4 -c conda-forge`.",
         )
         return found_adcc and found_psi4
 

qcengine/programs/cfour/harvester.py

@@ -1004,7 +1004,9 @@ def harvest_outfile_pass(outtext):
     # Process atom geometry
     mobj = re.search(r"^\s+" + r"@GETXYZ-I,     1 atoms read from ZMAT." + r"\s*$", outtext, re.MULTILINE)
     mobj2 = re.search(
-        r"^([A-Z]+)#1" + r"\s+" + NUMBER + r"\s+" + NUMBER + r"\s+" + NUMBER + r"\s*$", outtext, re.MULTILINE
+        r"^\s*([A-Z]+)" + r"\s*" + r"#1" + r"\s+" + NUMBER + r"\s+" + NUMBER + r"\s+" + NUMBER + r"\s*$",
+        outtext,
+        re.MULTILINE,
     )
     if mobj and mobj2:
         logger.debug("matched atom2")  # unsavory for when atom never printed except for basis file

qcengine/programs/psi4.py

@@ -92,7 +92,7 @@ def found(raise_error: bool = False) -> bool:
             "psi4",
             return_bool=True,
             raise_error=raise_error,
-            raise_msg="Please install via `conda install psi4 -c conda-forge/label/libint_dev -c conda-forge`. Check it's in your PATH with `which psi4`."
+            raise_msg="Please install via `conda install psi4 -c conda-forge`. Check it's in your PATH with `which psi4`."
             + error_msg,
         )
 

qcengine/testing.py

@@ -57,9 +57,14 @@ def is_program_new_enough(program, version_feature_introduced):
     form is equal to or later than `version_feature_introduced`.
 
     """
-    if program not in qcng.list_available_programs():
-        return False
-    candidate_version = qcng.get_program(program).get_version()
+    if program in qcng.list_all_procedures():
+        if program not in qcng.list_available_procedures():
+            return False
+        candidate_version = qcng.get_procedure(program).get_version()
+    else:
+        if program not in qcng.list_available_programs():
+            return False
+        candidate_version = qcng.get_program(program).get_version()
 
     return parse_version(candidate_version) >= parse_version(version_feature_introduced)
 
@@ -177,6 +182,7 @@ def get_job(self):
     "psi4_derqcsk": is_program_new_enough("psi4", "1.5a1.dev117"),
     "qcdb": which_import("qcdb", return_bool=True),
     "qchem": is_program_new_enough("qchem", "5.1"),
+    "qcmanybody": which_import("qcmanybody", return_bool=True),
     "rdkit": which_import("rdkit", return_bool=True),
     "terachem": which("terachem", return_bool=True),
     "terachem_pbs": is_program_new_enough("terachem_pbs", "0.7.2"),