Merge branch 'master' into image_rfo

optking/compute_wrappers.py

@@ -60,6 +60,13 @@ def generate_schema_input(self, driver):
 
         return inp
 
+    def generate_schema_input_for_procedure(self, driver):
+        molecule = Molecule(**self.molecule)
+        mbspec = self.keywords
+        mbspec["driver"] = driver
+
+        return {"molecule": molecule, "specification": mbspec}
+
     def _compute(self, driver):
         """Abstract style method for child classes"""
         pass
@@ -149,16 +156,23 @@ def _compute(self, driver):
 
         import qcengine
 
-        inp = self.generate_schema_input(driver)
-
         local_options = {}
         if self.program == "psi4":
             import psi4
 
             local_options["memory"] = psi4.core.get_memory() / 1000000000
             local_options["ncores"] = psi4.core.get_num_threads()
 
-        ret = qcengine.compute(inp, self.program, True, local_options)
+        if self.model == "(proc_spec_in_options)":
+            logger.debug("QCEngineComputer.path: ManyBody")
+            inp = self.generate_schema_input_for_procedure(driver)
+            ret = qcengine.compute_procedure(inp, "qcmanybody", True, local_options)
+
+        else:
+            logger.debug("QCEngineComputer.path: Atomic")
+            inp = self.generate_schema_input(driver)
+            ret = qcengine.compute(inp, self.program, True, local_options)
+
         return ret
 
 

optking/optwrapper.py

@@ -201,9 +201,17 @@ def make_computer(opt_input: dict, computer_type):
 
     # This gets updated so it shouldn't be a reference
     molecule = copy.deepcopy(opt_input["initial_molecule"])
-    qc_input = opt_input["input_specification"]
-    options = qc_input["keywords"]
-    model = qc_input["model"]
+
+    # Sorting by spec_schema_name isn't foolproof b/c opt_input might not be a
+    #   constructed model at this point if it's not arriving through QCEngine.
+    spec_schema_name = opt_input["input_specification"].get("schema_name", "qcschema_input")
+    if spec_schema_name == "qcschema_manybodyspecification":
+        model = "(proc_spec_in_options)"
+        options = opt_input["input_specification"]
+    else:
+        qc_input = opt_input["input_specification"]
+        options = qc_input["keywords"]
+        model = qc_input["model"]
 
     if computer_type == "psi4":
         # Please note that program is not actually used here

optking/tests/json_lif_cp.json

@@ -0,0 +1,17 @@
+{"initial_molecule": {"fragment_charges": [1, -1], "fragments": [[0], [1]], "geometry": [0.0, 0.0, 0.0, 0.0, 0.0, 3.0], "symbols": ["Li", "F"]},
+ "input_specification": {"driver": "energy",
+                         "schema_name": "qcschema_manybodyspecification",
+                         "keywords": {"bsse_type": "cp", "supersystem_ie_only": true},
+                         "protocols": {"component_results": "all"},
+                         "specification": {"driver": "energy",
+                                           "extras": {"psiapi": true},
+                                           "keywords": {},
+                                           "model": {"basis": "6-31g", "method": "hf"},
+                                           "program": "psi4",
+                                           "protocols": {"stdout": false}}},
+ "keywords": {"g_convergence": "interfrag_tight", "program": "psi4"},
+ "protocols": {"trajectory": "final"},
+ "provenance": {"creator": "optking", "routine": "optimize_qcengine", "version": "0.2.1+14.gdc8fd03.dirty"},
+ "schema_name": "qcschema_generalizedoptimizationinput",
+ "schema_version": 1}
+

optking/tests/json_lif_nocp.json

@@ -0,0 +1,17 @@
+{"initial_molecule": {"fragment_charges": [1, -1], "fragments": [[0], [1]], "geometry": [0.0, 0.0, 0.0, 0.0, 0.0, 3.0], "symbols": ["Li", "F"]},
+ "input_specification": {"driver": "energy",
+                         "keywords": {"bsse_type": "nocp", "supersystem_ie_only": true},
+                         "protocols": {"component_results": "all"},
+                         "schema_name": "qcschema_manybodyspecification",
+                         "specification": {"driver": "energy",
+                                           "extras": {"psiapi": true},
+                                           "keywords": {},
+                                           "model": {"basis": "6-31g", "method": "hf"},
+                                           "program": "psi4",
+                                           "protocols": {"stdout": false}}},
+ "keywords": {"g_convergence": "gau_verytight", "program": "psi4"},
+ "protocols": {"trajectory": "final"},
+ "provenance": {"creator": "optking", "routine": "optimize_qcengine", "version": "0.2.1+14.gdc8fd03.dirty"},
+ "schema_name": "qcschema_generalizedoptimizationinput",
+ "schema_version": 1}
+

optking/tests/psi4_helper.py

@@ -4,6 +4,7 @@
 
 import numpy
 import pytest
+from qcelemental.util import which_import
 
 # Try to pull in Psi4
 try:
@@ -15,3 +16,7 @@
 
 # Wrap Psi4 in ifden
 using_psi4 = pytest.mark.skipif(found_psi4, reason="Psi4 not found, skipping.")
+using_qcmanybody = pytest.mark.skipif(
+    which_import("qcmanybody", return_bool=True) is False,
+    reason="cound not find qcmanybody. please install the package to enable tests",
+)

optking/tests/test_jsoninput.py

@@ -6,41 +6,63 @@
 import psi4
 
 from qcelemental.models import OptimizationInput
+from qcelemental.testing import compare_values
 from .utils import utils
+from .psi4_helper import using_qcmanybody
 
 # Varying number of repulsion energy decimals to check.
 @pytest.mark.parametrize(
     "inp,expected,num_steps",
     [
-        ("json_h2o.json", (8.9064890670, -74.965901192, 3), 5),
-        ("json_betapinene.json", (568.2219045869, -383.38105559, 1), 4),
-        ("json_hooh_frozen.json", (37.969354880, -150.786372411, 2), 6),
+        pytest.param("json_h2o.json", (8.9064890670, -74.965901192, 3), 5),
+        pytest.param("json_betapinene.json", (568.2219045869, -383.38105559, 1), 4),
+        pytest.param("json_hooh_frozen.json", (37.969354880, -150.786372411, 2), 6),
+        pytest.param("json_lif_cp.json", (8.95167, -106.8867587, 2, 3.016), 4, marks=using_qcmanybody),
+        pytest.param("json_lif_nocp.json", (9.09281, -106.9208785, 2, 2.969), 5, marks=using_qcmanybody),
     ],
 )
 def test_input_through_json(inp, expected, num_steps, check_iter):
     with open(os.path.join(os.path.dirname(__file__), inp)) as input_data:
         input_copy = json.load(input_data)
-        opt_schema = OptimizationInput(**input_copy)
+        if "lif" in inp:
+            from qcmanybody.models.generalized_optimization import GeneralizedOptimizationInput
+            opt_schema = GeneralizedOptimizationInput(**input_copy)
+        else:
+            opt_schema = OptimizationInput(**input_copy)
+
+        # Note it's important to have `input_specification.schema_name = "qcschema_manybodyspecification"`
+        #   in your json for a MBE optimization. Or you can explicitly construct a
+        #   GeneralizedOptimizationInput like above.
 
     # optking.run_json_file(os.path.join(os.path.dirname(__file__), inp))
     json_dict = optking.optimize_qcengine(input_copy)
 
+    if "lif" in inp:
+        assert inp, json_dict["trajectory"][-1]["schema_name"] == "qcschema_manybodyresult"
+    else:
+        assert inp, json_dict["trajectory"][-1]["schema_name"] == "qcschema_output"
+
     # For testing purposes. If this works, we have properly returned the output, and added the result
     # to the original file. In order to preserve the form of the test suite, we now resore the input
     # to its original state
     # with open(os.path.join(os.path.dirname(__file__), inp)) as input_data:
     #    json_dict = json.load(input_data)
-    assert psi4.compare_values(
+
+    # LAB: for the MBE optimizations, psi4.compare_values strangely segfaults python, so using compare_values from qcel
+    assert compare_values(
         expected[0],
         json_dict["trajectory"][-1]["properties"]["nuclear_repulsion_energy"],
-        expected[2],
-        "Nuclear repulsion energy",
+        atol=1.0 * 10**-expected[2],
+        label="Nuclear repulsion energy",
     )
-    assert psi4.compare_values(
-        expected[1], json_dict["trajectory"][-1]["properties"]["return_energy"], 6, "Reference energy"
+    assert compare_values(
+        expected[1], json_dict["trajectory"][-1]["properties"]["return_energy"], atol=1.e-6, label="Reference energy"
     )
     utils.compare_iterations(json_dict, num_steps, check_iter)
 
+    if len(expected) > 3:
+        assert compare_values(expected[3], json_dict["final_molecule"]["geometry"][5] - json_dict["final_molecule"]["geometry"][2], atol=1.e-3, label="bond length")
+
     # with open(os.path.join(os.path.dirname(__file__), inp), 'r+') as input_data:
     #    input_data.seek(0)
     #    input_data.truncate()