dftd3 upstream atm & xtb harness updates (#500)

loriab · Lori A. Burns · web-flow · commit 96d8b5fb6f71 · 2026-04-17T16:30:20.000-04:00
* classic dftd3

* adcc: older psi for newer qcmb

* fixes for s-dftd3 atm default change

* fix psi4 dftd3/version

* atm=False

* adapt xtb

---------

Co-authored-by: Lori A. Burns &lt;lori.burns7@gmail.com&gt;
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -134,6 +134,12 @@ jobs:
             runs-on: windows-latest
             pytest: "-k 'not (hes2 or qchem or test_config)'"
 
+          - conda-env: opt-disp-v1
+            python-version: 3.12
+            label: dftd-v1
+            runs-on: ubuntu-latest
+            pytest: ""
+
             # 3.13
           #- conda-env: disp-win
           #  python-version: 3.12
diff --git a/devtools/conda-envs/opt-disp-cf.yaml b/devtools/conda-envs/opt-disp-cf.yaml
@@ -7,16 +7,14 @@ dependencies:
   - rdkit
   # - rdkit<=2025.03.4  # Windows+psi4 error with 03.5  # sometimes fine, sometimes flaky even w/exactly same packages in env
   - mopac
-  - libint=2.9.0=*_4  # old (1.10=*_2) psi4 to release qcmb constraint to use new qcnb (0.7) with new qcel (rc4)
 
     # Mixed Tests
-  - dftd3-python
-  - dftd4-python
+  - dftd3-python>=1.3
+  - dftd4-python>=4.1
   - gcp-correction
   - geometric=1.0
   - optking
   - pymdi
-  - qcmanybody>=0.7.0
   - pyberny
   - setuptools <82.0  # for berny
 
@@ -35,3 +33,7 @@ dependencies:
   - pytest-cov
   - codecov
 
+  - pip
+  - pip:
+    - qcmanybody==0.7.0
+
diff --git a/devtools/conda-envs/opt-disp-v1.yaml b/devtools/conda-envs/opt-disp-v1.yaml
@@ -0,0 +1,36 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - psi4=1.9.1
+  - libint=2.9.0=*_4
+  - rdkit
+  - mopac
+  - pydantic-settings
+
+    # Mixed Tests
+  - dftd3-python<1.3
+  - dftd4-python<4.1
+  - gcp-correction
+  - geometric
+  - optking
+  - pymdi
+  - setuptools <82.0  # for berny
+
+    # Core
+  - python
+  - pyyaml
+  - py-cpuinfo
+  - psutil
+  - conda-forge/label/qcelemental_dev::qcelemental
+  - msgpack-python
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+
+  - pip
+  - pip:
+    - pyberny
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -32,6 +32,40 @@ Changelog
 .. - UNSOLVED (:issue:`397`) extras failed
 
 
+.. _`sec:cl0500rc4`:
+
+v0.50.0rc4 / 2026-MM-DD (Prerelease) (Unreleased)
+--------------------
+
+:docs:`v0.50.0rc4` for current. :docs:`v0.34.1` for QCSchema v1.
+
+Breaking Changes
+++++++++++++++++
+- (:pr:`500`) s-dftd3 - For simple-dftd3 >=1.3.0, 3-body is now off by default
+  (s9=0.0) through the python interface used by the QCSchema interface and by
+  QCEngine. Results will change if you're not passing ``params_tweaks`` or using
+  ``apply_qcengine_aliases=True`` (see below). Pass "atm=True" and "method" to
+  re-impose s9=1.0 as in test case ``test_dftd3_task_pbe_m02``. @loriab
+
+New Features
+++++++++++++
+
+Enhancements
+++++++++++++
+- (:pr:`500`) s-dftd3 - When ``apply_qcengine_aliases=True`` for a 3-body-including
+  dispersion correction (which includes unspecified, e.g. d3bj) the parameters are
+  now explicitly passed as params_tweaks. There is no change in results, but this
+  compensates for a change in default in the simple-dftd3 v1.3.0 project. Also,
+  for 2-body-only, the returned "info" parameters (namely, s9) will more accurately
+  match those used. @loriab
+
+Bug Fixes
++++++++++
+
+Misc.
++++++
+
+
 .. _`sec:cl0500rc3`:
 
 v0.50.0rc3 / 2026-04-02 (Prerelease)
diff --git a/qcengine/programs/dftd_ng.py b/qcengine/programs/dftd_ng.py
@@ -265,7 +265,7 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
         qcvkey = method.upper() if method is not None else None
 
         # send `from_arrays` the s-dftd3 behavior of functional specification overrides explicit parameters specification
-        # * differs from dftd3 harness behavior where parameters extend or override functional
+        # * differs from classic-dftd3 harness behavior where parameters extend or override functional
         # * stash the resolved plan in extras or, if errored, leave it for the proper dftd3 api to reject
         param_tweaks = None if method else input_model.specification.keywords.get("params_tweaks", None)
         try:
@@ -294,13 +294,16 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
                 level_hint = get_dispersion_aliases()[level_hint.lower()]
                 if level_hint.endswith("atm"):
                     level_hint = level_hint[:-3]
+                    # re-route through params_tweaks needed for >=1.3.0 where atm=False became default
+                    input_data["specification"]["keywords"]["params_tweaks"] = {**planinfo["dashparams"]}
                 if level_hint.endswith("2b"):
                     level_hint = level_hint[:-2]
                     input_data["specification"]["keywords"]["params_tweaks"] = {**planinfo["dashparams"], "s9": 0.0}
+                    input_data["specification"]["extras"]["info"]["dashparams"]["s9"] = 0.0
                 input_data["specification"]["keywords"]["level_hint"] = level_hint
 
         if parse_version(self.get_version()) < parse_version("1.3.0"):
-            # sdftd3 speaks qcsk.v1
+            # s-dftd3 speaks qcsk.v1
             input_model_v1 = qcelemental.models.v2.AtomicInput(**input_data).convert_v(1)
 
             # Run the Harness
@@ -316,7 +319,7 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
             output = output_v1.convert_v(2, external_input_data=input_data)
 
         else:
-            # sdftd3 >1.3.0??? speaks qcsk.v1 or qcsk.v2
+            # s-dftd3 >1.3.0 speaks qcsk.v1 or qcsk.v2
             input_model_v2 = qcelemental.models.v2.AtomicInput(**input_data)
 
             # Run the Harness
diff --git a/qcengine/programs/tests/test_sdftd3.py b/qcengine/programs/tests/test_sdftd3.py
@@ -17,12 +17,18 @@
 
 @uusing("s-dftd3")
 def test_dftd3_task_b97m_m01(schema_versions, request):
+    import dftd3
+
     models, retver, _ = schema_versions
 
     thr = 1.0e-8
 
     return_result = -0.05879001214961249
 
+    if qcel.util.parse_version(dftd3.__version__) >= qcel.util.parse_version("1.3.0"):
+        atm_correction = 6.48732559e-05
+        return_result -= atm_correction
+
     if from_v2(request.node.name):
         atomic_input = models.AtomicInput(
             molecule=models.Molecule(**qcng.get_molecule("mindless-01", return_dict=True)),
@@ -45,6 +51,7 @@ def test_dftd3_task_b97m_m01(schema_versions, request):
 
 
 @uusing("s-dftd3")
+@pytest.mark.parametrize("atm", ["nil", True, False])
 @pytest.mark.parametrize(
     "inp",
     [
@@ -56,29 +63,44 @@ def test_dftd3_task_b97m_m01(schema_versions, request):
     ],
     ids=["d3bj", "d3zero", "d3mbj", "d3mzero", "d3op"],
 )
-def test_dftd3_task_pbe_m02(inp, schema_versions, request):
+def test_dftd3_task_pbe_m02(inp, schema_versions, request, atm):
     models, retver, _ = schema_versions
 
     # return to 1.0e-8 after https://github.com/MolSSI/QCEngine/issues/370
     thr = 1.0e-7
 
     return_result = inp["return_result"]
 
+    # s-dftd3 v1.3 changed the 3-body default to False to match the executable interface.
+    #   Toggle is keywords["params_tweaks"]["atm"] which isn't handled by the harness.
+    #   Here, demonstrating pass-through to s-dftd3 1st-class QCSchema interface. Requires repeating method from model.
+    atm_correction = 8.94882569e-05
+    if atm == "nil":
+        import dftd3
+
+        xtra_kw = {}
+        if qcel.util.parse_version(dftd3.__version__) >= qcel.util.parse_version("1.3.0"):
+            return_result -= atm_correction
+    else:
+        xtra_kw = {"params_tweaks": {"method": "pbe", "atm": atm}}
+        if atm is False:
+            return_result -= atm_correction
+
+    spec = {
+        "model": {"method": "pbe"},
+        "keywords": {"level_hint": inp["level_hint"], **xtra_kw},
+        "driver": "energy",
+    }
+
     if from_v2(request.node.name):
         atomic_input = models.AtomicInput(
             molecule=models.Molecule(**qcng.get_molecule("mindless-02", return_dict=True)),
-            specification={
-                "model": {"method": "pbe"},
-                "keywords": {"level_hint": inp["level_hint"]},
-                "driver": "energy",
-            },
+            specification=spec,
         )
     else:
         atomic_input = models.AtomicInput(
             molecule=models.Molecule(**qcng.get_molecule("mindless-02", return_dict=True)),
-            model={"method": "pbe"},
-            keywords={"level_hint": inp["level_hint"]},
-            driver="energy",
+            **spec,
         )
 
     atomic_input = checkver_and_convert(atomic_input, request.node.name, "pre")
@@ -156,47 +178,81 @@ def test_dftd3_task_tpss_m02(schema_versions, request):
 
 
 @uusing("s-dftd3")
-def test_dftd3_task_r2scan_m03(schema_versions, request):
+@pytest.mark.parametrize("atm", ["nil", True, False])
+def test_dftd3_task_r2scan_m03(schema_versions, request, atm):
     models, retver, _ = schema_versions
 
     thr = 1.0e-8
 
-    return_result = np.array(
-        [
-            [-9.15721221e-06, -8.18139252e-06, -6.04628002e-05],
-            [+2.63353857e-05, -5.74347326e-05, +6.43925910e-05],
-            [-2.99422439e-05, +1.88531187e-05, +3.80203831e-05],
-            [-1.05590494e-05, -6.00459729e-05, +3.93481945e-05],
-            [+1.59600548e-05, +3.66166973e-05, -2.69939628e-05],
-            [-7.21060928e-05, +1.35991320e-05, -3.71000739e-05],
-            [-9.01933781e-06, -3.41989101e-05, -4.92317946e-05],
-            [-2.38625512e-06, -4.42678339e-05, -1.95513968e-05],
-            [-3.09663159e-05, +3.41418638e-05, +2.51926884e-05],
-            [+5.60572318e-06, -1.06356845e-05, -3.91159008e-05],
-            [+7.73090102e-05, +2.75681060e-05, +2.02933984e-05],
-            [-3.23109274e-05, +5.39319105e-05, -1.44309772e-04],
-            [-4.05785623e-05, +5.03251549e-05, +3.92193348e-05],
-            [+8.46365844e-06, -3.35282588e-05, +3.76937643e-05],
-            [+1.04861677e-04, -2.99444252e-05, +8.20822571e-05],
-            [-1.50951292e-06, +4.32012272e-05, +3.05230899e-05],
-        ]
-    )
+    return_result = {
+        # s9 = 0.0
+        False: np.array(
+            [
+                [-9.35558196e-06, -7.34067064e-06, -5.91238608e-05],
+                [2.53304403e-05, -5.73248858e-05, 6.46059022e-05],
+                [-2.85980097e-05, 1.93908141e-05, 3.67399397e-05],
+                [-7.30494324e-06, -5.48095855e-05, 3.76154049e-05],
+                [1.07471133e-05, 3.03306726e-05, -2.46209798e-05],
+                [-6.64928435e-05, 1.44200457e-05, -3.64523447e-05],
+                [-7.88327389e-06, -3.03833956e-05, -4.75808422e-05],
+                [-1.90420772e-06, -4.31459317e-05, -2.02338533e-05],
+                [-3.27860042e-05, 3.68088235e-05, 2.55372601e-05],
+                [4.41178314e-06, -1.11489999e-05, -4.32651442e-05],
+                [7.61947667e-05, 2.64655830e-05, 2.10390818e-05],
+                [-3.38080082e-05, 5.29154102e-05, -1.44995850e-04],
+                [-3.85124417e-05, 4.82248838e-05, 3.75602755e-05],
+                [1.01670679e-05, -3.64563841e-05, 4.13102437e-05],
+                [1.02281493e-04, -2.98543913e-05, 8.22232550e-05],
+                [-2.48735050e-06, 4.19080117e-05, 2.96415119e-05],
+            ]
+        ),
+        # s9 = 1.0
+        True: np.array(
+            [
+                [-9.15721221e-06, -8.18139252e-06, -6.04628002e-05],
+                [+2.63353857e-05, -5.74347326e-05, +6.43925910e-05],
+                [-2.99422439e-05, +1.88531187e-05, +3.80203831e-05],
+                [-1.05590494e-05, -6.00459729e-05, +3.93481945e-05],
+                [+1.59600548e-05, +3.66166973e-05, -2.69939628e-05],
+                [-7.21060928e-05, +1.35991320e-05, -3.71000739e-05],
+                [-9.01933781e-06, -3.41989101e-05, -4.92317946e-05],
+                [-2.38625512e-06, -4.42678339e-05, -1.95513968e-05],
+                [-3.09663159e-05, +3.41418638e-05, +2.51926884e-05],
+                [+5.60572318e-06, -1.06356845e-05, -3.91159008e-05],
+                [+7.73090102e-05, +2.75681060e-05, +2.02933984e-05],
+                [-3.23109274e-05, +5.39319105e-05, -1.44309772e-04],
+                [-4.05785623e-05, +5.03251549e-05, +3.92193348e-05],
+                [+8.46365844e-06, -3.35282588e-05, +3.76937643e-05],
+                [+1.04861677e-04, -2.99444252e-05, +8.20822571e-05],
+                [-1.50951292e-06, +4.32012272e-05, +3.05230899e-05],
+            ]
+        ),
+    }
+
+    if atm == "nil":
+        import dftd3
+
+        xtra_kw = {}
+        return_result = return_result[qcel.util.parse_version(dftd3.__version__) < qcel.util.parse_version("1.3.0")]
+    else:
+        xtra_kw = {"params_tweaks": {"method": "r2scan", "atm": atm}}
+        return_result = return_result[atm]
+
+    spec = {
+        "keywords": {"level_hint": "d3bj", **xtra_kw},
+        "driver": "gradient",
+        "model": {"method": "r2scan"},
+    }
 
     if from_v2(request.node.name):
         atomic_input = models.AtomicInput(
             molecule=models.Molecule(**qcng.get_molecule("mindless-03", return_dict=True)),
-            specification={
-                "keywords": {"level_hint": "d3bj"},
-                "driver": "gradient",
-                "model": {"method": "r2scan"},
-            },
+            specification=spec,
         )
     else:
         atomic_input = models.AtomicInput(
             molecule=models.Molecule(**qcng.get_molecule("mindless-03", return_dict=True)),
-            keywords={"level_hint": "d3bj"},
-            driver="gradient",
-            model={"method": "r2scan"},
+            **spec,
         )
 
     atomic_input = checkver_and_convert(atomic_input, request.node.name, "pre")
diff --git a/qcengine/programs/xtb.py b/qcengine/programs/xtb.py
@@ -12,7 +12,7 @@
 from typing import Any, ClassVar, Dict
 
 from qcelemental.models.v2 import AtomicInput, AtomicResult, FailedOperation
-from qcelemental.util import safe_version, which_import
+from qcelemental.util import parse_version, safe_version, which_import
 
 from ..config import TaskConfig
 from .model import ProgramHarness
@@ -65,13 +65,25 @@ def compute(self, input_data: AtomicInput, config: TaskConfig) -> AtomicResult:
         import xtb
         from xtb.qcschema.harness import run_qcschema
 
-        # Run the Harness
-        input_data_v1 = input_data.convert_v(1)
-        output_v1 = run_qcschema(input_data_v1)
+        if parse_version(self.get_version()) < parse_version("26.1"):
+            # xtb-python speaks qcsk.v1
 
-        # xtb qcschema interface stores error in Result model
-        if not output_v1.success:
-            return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
+            # Run the Harness
+            input_model_v1 = input_data.convert_v(1)
+            output_v1 = run_qcschema(input_model_v1)
 
-        output = output_v1.convert_v(2, external_input_data=input_data)
-        return output
+            # xtb qcschema interface stores error in Result model
+            if not output_v1.success:
+                return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
+
+            output = output_v1.convert_v(2, external_input_data=input_data)
+            return output
+
+        else:
+            # xtb-python >26.1 speaks qcsk.v1 or qcsk.v2
+
+            # Run the Harness
+            input_model_v2 = input_data
+            output_v2 = run_qcschema(input_model_v2)
+
+            return output_v2
