DDX solvent support (#290)

* add ddx solvent support

* make sure the correct solvent is being used

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* PR feedback extend ddx test

* fix merge

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* update notes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

devtools/conda-envs/psi4.yaml

@@ -29,6 +29,7 @@ dependencies:
   - openeye-toolkits !=2024.1.1
 
   - psi4 >=1.9.1
+  - pyddx
 
   ### Core dependencies.
 

docs/releasehistory.md

@@ -25,6 +25,7 @@ Releases are given with dates in DD-MM-YYYY format.
 * [PR #284:] Add `portal_client_manager` for using custom `PortalClient` settings
 * [PR #288:] Adds better support for property driver psi4 calculations which require the keywords to be formatted differently (see [this issue](https://github.com/psi4/psi4/issues/3129) for an example which can be run locally). This also allows for response properties to be calculated such as the dipole polarizabilities, which is included as a new property type.
 * [PR #289:] Add `workflow_components.RECAPFragmenter` to fragment molecules using the rdkit implementation of RECAP [@jthorton]
+* [PR #290:] Add support for the DDX implicit solvent interface in Psi4 [@jthorton]
 
 ## 0.51.0 / 23-04-2024
 
@@ -144,6 +145,7 @@ For more information on this release, see https://github.com/openforcefield/open
 [PR #285:]: https://github.com/openforcefield/openff-qcsubmit/pull/285
 [PR #288:]: https://github.com/openforcefield/openff-qcsubmit/pull/288
 [PR #289:]: https://github.com/openforcefield/openff-qcsubmit/pull/289
+[PR #290:]: https://github.com/openforcefield/openff-qcsubmit/pull/290
 
 [@jthorton]: https://github.com/jthorton
 [@dotsdl]: https://github.com/dotsdl

openff/qcsubmit/_tests/test_submissions.py

@@ -15,6 +15,7 @@
 
 from openff.qcsubmit import workflow_components
 from openff.qcsubmit.common_structures import (
+    DDXSettings,
     MoleculeAttributes,
     PCMSettings,
     SCFProperties,
@@ -345,7 +346,32 @@ def test_basic_submissions_multiple_spec(fulltest_client, conformer_water):
             ) == spec.dict(include={"method", "program", "basis"})
 
 
-def test_basic_submissions_single_pcm_spec(fulltest_client, water):
+@pytest.mark.parametrize(
+    "solvent_model, solvent_energy, solvent_evidence",
+    [
+        pytest.param(
+            PCMSettings(units="au", medium_Solvent="water"),
+            "pcm polarization energy",
+            "Solvent name:          Water",
+            id="PCM",
+        ),
+        pytest.param(
+            DDXSettings(ddx_solvent_epsilon=4),
+            "dd solvation energy",
+            "solvent_epsilon         = 4.0",
+            id="DDX Epsilon",
+        ),
+        pytest.param(
+            DDXSettings(ddx_solvent="1-bromooctane"),
+            "dd solvation energy",
+            "solvent_epsilon         = 5.0244",
+            id="DDX Solvent",
+        ),
+    ],
+)
+def test_basic_submissions_single_solvent_spec(
+    fulltest_client, solvent_model, solvent_energy, solvent_evidence, water
+):
     """Test submitting a basic dataset to a snowflake server with pcm water in the specification."""
 
     client = fulltest_client
@@ -361,7 +387,7 @@ def test_basic_submissions_single_pcm_spec(fulltest_client, water):
         program=program,
         spec_name="default",
         spec_description="testing the single points with pcm",
-        implicit_solvent=PCMSettings(units="au", medium_Solvent="water"),
+        implicit_solvent=solvent_model,
         overwrite=True,
     )
 
@@ -409,10 +435,12 @@ def test_basic_submissions_single_pcm_spec(fulltest_client, water):
             assert record.error is None
             assert record.return_result is not None
             # make sure the PCM result was captured
-            assert record.properties["pcm polarization energy"] < 0
+            assert record.properties[solvent_energy] < 0
+            # make sure the correct solvent was used
+            assert solvent_evidence in record.stdout
             assert record.specification.dict(
-                include={"method", "program", "basis"}
-            ) == spec.dict(include={"method", "program", "basis"})
+                include={"method", "basis", "program"}
+            ) == spec.dict(include={"method", "basis", "program"})
 
 
 @pytest.mark.parametrize(

openff/qcsubmit/common_structures.py

@@ -2,6 +2,7 @@
 This file contains common starting structures which can be mixed into datasets, results and factories.
 """
 
+import abc
 import copy
 import getpass
 import re
@@ -14,6 +15,7 @@
     ClassVar,
     Dict,
     List,
+    Literal,
     Mapping,
     Optional,
     Set,
@@ -40,6 +42,7 @@
         BaseModel,
         Field,
         HttpUrl,
+        PositiveFloat,
         PositiveInt,
         StrictBool,
         StrictFloat,
@@ -53,6 +56,7 @@
         BaseModel,
         Field,
         HttpUrl,
+        PositiveFloat,
         PositiveInt,
         StrictBool,
         StrictFloat,
@@ -189,7 +193,18 @@ class TDSettings(DatasetConfig):
     )
 
 
-class PCMSettings(ResultsConfig):
+class _BaseSolvent(ResultsConfig, abc.ABC):
+    """
+    A base class to add new implicit solvent models
+    """
+
+    @abc.abstractmethod
+    def add_keywords(self, keyword_data: dict) -> dict:
+        """Add the keywords of this solvent model to the keyword data dict."""
+        ...
+
+
+class PCMSettings(_BaseSolvent):
     """
     A class to handle PCM settings which can be used with PSi4.
     """
@@ -401,6 +416,46 @@ def to_string(self) -> str:
         Cavity {{{cavity_str}}}"""
         return pcm_string
 
+    def add_keywords(self, keyword_data: dict) -> dict:
+        keyword_data["pcm"] = True
+        keyword_data["pcm__input"] = self.to_string()
+        return keyword_data
+
+
+class DDXSettings(_BaseSolvent):
+    """
+    A simple settings class for the ddx solvent model to be used with Psi4
+    """
+
+    ddx_model: Literal["pcm", "cosmo"] = Field(
+        "pcm", description="The solvation model to use."
+    )
+    ddx_radii_scaling: PositiveFloat = Field(
+        1.1,
+        description="The scaling factor for the cavity spheres. This also depends on the radii set chosen.",
+    )
+    ddx_radii_set: Literal["uff", "bondi"] = Field(
+        "uff", description="The atomic radii set to use."
+    )
+    ddx_solvent_epsilon: Optional[float] = Field(
+        None,
+        description="The dielectric constant of the solvent, if not specified the solvent type should be set.",
+    )
+    ddx_solvent: str = Field(
+        "water",
+        description="The name of the ddx supported solvent which should be used, the epsilon value will be determined "
+        "from `pyddx.data.solvent_epsilon`. Note that this value is ignored if the `ddx_solvent_epsilon` "
+        "is provided.",
+    )
+
+    def add_keywords(self, keyword_data: dict) -> dict:
+        keyword_data["ddx"] = True
+        ddx_data = self.dict()
+        if self.ddx_solvent_epsilon is None:
+            del ddx_data["ddx_solvent_epsilon"]
+        keyword_data.update(ddx_data)
+        return keyword_data
+
 
 class QCSpec(ResultsConfig):
     method: constr(strip_whitespace=True) = Field(
@@ -427,9 +482,9 @@ class QCSpec(ResultsConfig):
         WavefunctionProtocolEnum.none,
         description="The level of wavefunction detail that should be saved in QCArchive. Note that this is done for every calculation and should not be used with optimizations.",
     )
-    implicit_solvent: Optional[PCMSettings] = Field(
+    implicit_solvent: Optional[Union[PCMSettings, DDXSettings]] = Field(
         None,
-        description="If PCM is to be used with psi4 this is the full description of the settings that should be used.",
+        description="If PCM or DDX is to be used with psi4 this is the full description of the settings that should be used.",
     )
     maxiter: PositiveInt = Field(
         200,
@@ -526,7 +581,7 @@ def __init__(
             # make sure PCM is not set
             if implicit_solvent is not None:
                 raise QCSpecificationError(
-                    "PCM can only be used with PSI4 please set implicit solvent to None."
+                    "PCM and DDX can only be used with PSI4 please set implicit solvent to None."
                 )
             # we need to make sure it is valid in the above list
             program_settings = settings.get(program.lower(), None)
@@ -612,10 +667,9 @@ def qc_keywords(self, properties: bool = False) -> Dict[str, Any]:
         if self.implicit_solvent is not None:
             if self.program.lower() != "psi4":
                 raise QCSpecificationError(
-                    "PCM can only be used with PSI4 please set implicit solvent to None."
+                    "PCM and DDX can only be used with PSI4 please set implicit solvent to None."
                 )
-            data["pcm"] = True
-            data["pcm__input"] = self.implicit_solvent.to_string()
+            data = self.implicit_solvent.add_keywords(keyword_data=data)
         return data
 
 
@@ -670,7 +724,7 @@ def add_qc_spec(
         spec_description: str,
         store_wavefunction: str = "none",
         overwrite: bool = False,
-        implicit_solvent: Optional[PCMSettings] = None,
+        implicit_solvent: Optional[Union[PCMSettings, DDXSettings]] = None,
         maxiter: PositiveInt = 200,
         scf_properties: Optional[List[SCFProperties]] = None,
         keywords: Optional[