nwchem working

qcengine/procedures/nwchem_opt/harvester.py

@@ -75,18 +75,21 @@ def harvest_as_atomic_result(input_model: OptimizationInput, nwout: str) -> List
             provenance["module"] = module
 
         # Format them inout an output
+        input_data = input_model.input_specification.model_dump()
+        input_data["driver"] = "gradient"
+        input_data["molecule"] = out_mol
+
         output_data = {
-            "schema_version": 1,
+            "schema_version": 2,
+            "input_data": input_data,
             "molecule": out_mol,
-            "driver": "gradient",
-            "extras": input_model.extras.copy(),
-            "model": input_model.input_specification.model,
-            "keywords": input_model.input_specification.keywords,
+            "extras": {},
             "properties": atprop,
             "provenance": provenance,
             "return_result": nwgrad,
             "success": True,
         }
+        # v2: perhaps lost the OptimizationInput.extras?
 
         # got to even out who needs plump/flat/Decimal/float/ndarray/list
         # Decimal --> str preserves precision

qcengine/programs/model.py

@@ -76,8 +76,8 @@ def build_input_model(
         # Note: Someday when the multiple QCSchema versions QCEngine supports are all within the
         #  Pydantic v2 API base class, this can use discriminated unions instead of logic.
 
-        v1_model = getattr(qcelemental.models.v1, "AtomicInput")
-        v2_model = getattr(qcelemental.models.v2, "AtomicInput")
+        v1_model = qcelemental.models.v1.AtomicInput
+        v2_model = qcelemental.models.v2.AtomicInput
 
         if isinstance(data, v1_model):
             mdl = model_wrapper(data, v1_model)

qcengine/programs/nwchem/runner.py

@@ -324,9 +324,10 @@ def parse_output(
 
         # Format them inout an output
         output_data = {
-            "schema_version": 1,
+            "schema_version": 2,
+            "input_data": input_model,
             "molecule": nwmol,  # overwrites with outfile Cartesians in case fix_*=F
-            "extras": {**input_model.extras},
+            "extras": {},
             "native_files": {k: v for k, v in outfiles.items() if v is not None},
             "properties": atprop,
             "provenance": provenance,
@@ -343,4 +344,4 @@ def parse_output(
             k.upper(): str(v) if isinstance(v, Decimal) else v for k, v in qcvars.items()
         }
 
-        return AtomicResult(**{**input_model.model_dump(), **output_data})
+        return AtomicResult(**output_data)

qcengine/programs/psi4.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, ClassVar, Dict
 
-from qcelemental.models.v1 import AtomicResult as AtomicResult
+from qcelemental.models.v1 import AtomicResult
 from qcelemental.models.v2 import BasisSet
 from qcelemental.util import deserialize, parse_version, safe_version, which, which_import
 

qcengine/programs/tests/standard_suite_runner.py

@@ -204,6 +204,15 @@ def runner_asserter(inp, ref_subject, method, basis, tnm, scramble, frame, model
         ref_block = mill_qcvars(ref2out_mill, ref_block)
         ref_block_conv = mill_qcvars(ref2out_mill, ref_block_conv)
 
+    # 3b. input mol in output: `wfn.input_data.molecule` should be exactly `subject` always. If frame=free fails, check
+    #     that the harness is copying AtomicInput bodily rather than duplicating AtomicResult.molecule as convert_v(2) does
+
+    if "v2" in tnm:
+        with np.printoptions(precision=3, suppress=True):
+            assert compare_values(
+                subject.geometry, wfn.input_data.molecule.geometry, atol=5.0e-8
+            ), f"coords: atres ({wfn.input_data.molecule.geometry}) != atin ({subject.geometry})"
+
     # <<<  Comparison Tests  >>>
 
     assert wfn.success is True

qcengine/programs/tests/test_ghost.py

@@ -53,7 +53,10 @@ def test_simple_ghost(driver, program, basis, keywords, hene_data, schema_versio
     res = qcng.compute(resi, program, raise_error=True, return_dict=True, return_version=retver)
     res = checkver_and_convert(res, request.node.name, "post")
 
-    assert res["driver"] == driver
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == driver
+    else:
+        assert res["driver"] == driver
     assert "provenance" in res
     assert res["success"] is True
 

qcengine/programs/tests/test_nwchem.py

@@ -74,7 +74,10 @@ def test_b3lyp(nh2_data, schema_versions, request):
 
     # Make sure the calculation completed successfully
     assert compare_values(-55.554037, res["return_result"], atol=1e-3)
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 
@@ -194,7 +197,10 @@ def test_dipole(h20_data, schema_versions, request):
 
     # Make sure the calculation completed successfully
     assert compare_values(-75.764944, res["return_result"], atol=1e-3)
-    assert res["driver"] == "properties"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "properties"
+    else:
+        assert res["driver"] == "properties"
     assert "provenance" in res
     assert res["success"] is True
 
@@ -244,7 +250,10 @@ def test_homo_lumo(h20v2_data, schema_versions, request):
 
     # Make sure the calculation completed successfully
     assert compare_values(-75.968095, res["return_result"], atol=1e-3)
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 

qcengine/programs/tests/test_standard_suite_ccsd(t).py

@@ -54,7 +54,10 @@ def test_sp_ccsd_t_rhf_full(program, basis, keywords, h2o_data, schema_versions,
     res = qcng.compute(resi, program, raise_error=True, return_dict=True, return_version=retver)
     res = checkver_and_convert(res, request.node.name, "post")
 
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 
@@ -122,7 +125,10 @@ def test_sp_ccsd_t_rohf_full(program, basis, keywords, nh2_data, schema_versions
     res = checkver_and_convert(res, request.node.name, "post")
     res = res.model_dump()
 
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 

qcengine/programs/tests/test_standard_suite_hf.py

@@ -65,7 +65,10 @@ def test_sp_hf_rhf(program, basis, keywords, h2o_data, schema_versions, request)
     res = qcng.compute(resi, program, raise_error=True, return_dict=True, return_version=retver)
     res = checkver_and_convert(res, request.node.name, "post")
 
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 
@@ -119,7 +122,10 @@ def test_sp_hf_uhf(program, basis, keywords, nh2_data, schema_versions, request)
 
     assert res.success is True
     res = res.model_dump()
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 
@@ -163,7 +169,10 @@ def test_sp_hf_rohf(program, basis, keywords, nh2_data, schema_versions, request
     res = qcng.compute(resi, program, raise_error=True, return_dict=True, return_version=retver)
     res = checkver_and_convert(res, request.node.name, "post")
 
-    assert res["driver"] == "energy"
+    if "v2" in request.node.name:
+        assert res["input_data"]["driver"] == "energy"
+    else:
+        assert res["driver"] == "energy"
     assert "provenance" in res
     assert res["success"] is True
 

qcengine/testing.py

@@ -262,19 +262,14 @@ def check_model_v2(m):
 
     if prepost == "pre":
         dict_in = isinstance(mdl, dict)
+        cast_smodel = cast_dict_as or "AtomicInput"
         if "as_v1" in tnm or "to_v2" in tnm or "None" in tnm:
             if dict_in:
-                if cast_dict_as:
-                    mdl = getattr(qcel.models.v1, cast_dict_as)(**mdl)
-                else:
-                    mdl = qcel.models.v1.AtomicInput(**mdl)
+                mdl = getattr(qcel.models.v1, cast_smodel)(**mdl)
             check_model_v1(mdl)
         elif "as_v2" in tnm or "to_v1" in tnm:
             if dict_in:
-                if cast_dict_as:
-                    mdl = getattr(qcel.models.v2, cast_dict_as)(**mdl)
-                else:
-                    mdl = qcel.models.v2.AtomicInput(**mdl)
+                mdl = getattr(qcel.models.v2, cast_smodel)(**mdl)
             check_model_v2(mdl)
             # NOW IN COMPUTE mdl = mdl.convert_v(1)
 
@@ -286,19 +281,14 @@ def check_model_v2(m):
         #   for now these always go to v1 in programs/model.py so as_v2 returns wrongly as v1
         # follow-up: there are too many ways this can happen, so now it's forestalled by the schema_versions fixture passing 2 to as_v2
         dict_in = isinstance(mdl, dict)
+        cast_smodel = cast_dict_as or "AtomicResult"
         if "as_v1" in tnm or "to_v1" in tnm or "None" in tnm:
             if dict_in:
-                if cast_dict_as:
-                    mdl = getattr(qcel.models.v1, cast_dict_as)(**mdl)
-                else:
-                    mdl = qcel.models.v1.AtomicResult(**mdl)
+                mdl = getattr(qcel.models.v1, cast_smodel)(**mdl)
             check_model_v1(mdl)
         elif "as_v2" in tnm or "to_v2" in tnm:
             if dict_in:
-                if cast_dict_as:
-                    mdl = getattr(qcel.models.v2, cast_dict_as)(**mdl)
-                else:
-                    mdl = qcel.models.v2.AtomicResult(**mdl)
+                mdl = getattr(qcel.models.v2, cast_smodel)(**mdl)
             # NOW IN COMPUTE mdl = mdl.convert_v(2)
             check_model_v2(mdl)
 

qcengine/tests/test_harness_canonical.py

@@ -38,6 +38,8 @@
     ("mctc-gcp", {"method": "dft/sv"}, {}),
     ("mace", {"method": "small"}, {}),
     ("aimnet2", {"method": "b973c"}, {}),
+    ("s-dftd3", {"method": "b3lyp-d3"}, {}),
+    ("dftd4", {"method": "b3lyp-d4"}, {}),
     # add as programs available
     # ("terachem", {"method": "bad"}),
 ]