core intf ManyBodyCalculator to ManyBodyCore (#28)

* move ManyBodyCalculator to ManyBodyCore

* fix up docs with Calc->Core and paper snippets

* move Core to core. make implicit deps explicit

CHANGELOG.md

@@ -0,0 +1 @@
+See [changelog in docs](docs/changelog.md).

README.md

@@ -42,7 +42,7 @@ Full documentation is available at [https://molssi.github.io/QCManyBody/](https:
 
 ## Authors
 
-* Asem Alenaizan, @alenaizan, original Psi4 implementations of vmfc Hessians, multi-level, and embedded point charges
-* Lori A. Burns, @loriab, ManyBody QCSchema and high-level interface
-* Benjamin P. Pritchard, @bennybp, core interface and QCArchive integration
-* Daniel G. A. Smith, @dgasmith, original Psi4 implementations of nocp, cp, and vmfc single-level e/g/H and distributed driver integration
+* Asem Alenaizan, [@alenaizan](https://github.com/alenaizan), original Psi4 implementations of vmfc Hessians, multi-level, and embedded point charges
+* Lori A. Burns, [@loriab](https://github.com/loriab), ManyBody QCSchema and high-level interface
+* Benjamin P. Pritchard, [@bennybp](https://github.com/bennybp), core interface and QCArchive integration
+* Daniel G. A. Smith, [@dgasmith](https://github.com/dgasmith), original Psi4 implementations of nocp, cp, and vmfc single-level e/g/H and distributed driver integration

docs/api.md

@@ -1,6 +1,6 @@
-::: qcmanybody.ManyBodyCalculator
+::: qcmanybody.ManyBodyCore
 
-::: qcmanybody.computer.ManyBodyComputer
+::: qcmanybody.ManyBodyComputer
     options:
         show_root_heading: true
         inherited_members: true

docs/changelog.md

@@ -19,6 +19,29 @@
 -->
 
 
+## v0.3.0 / 2024-MM-DD (Unreleased)
+
+#### Breaking Changes
+
+ * [\#28](https://github.com/MolSSI/QCManyBody/pull/28) Intf -- low-level "core" interface renamed from
+   `ManyBodyCalculator` to `ManyBodyCore`. The old name will continue to work for a few months. Also, its file changed
+   from `manybody.py` to `core.py` but it was already a top-level import.
+
+#### New Features
+
+#### Enhancements
+
+ * [\#28](https://github.com/MolSSI/QCManyBody/pull/28) Intf -- high-level interface is now importable from the top level module.
+
+#### Bug Fixes
+
+#### Misc.
+
+#### MUST (Unmerged)
+
+#### WIP (Unmerged)
+
+
 ## v0.2.1 / 2024-05-14
 
 #### Enhancements

docs/core-interface.md

@@ -12,34 +12,37 @@ running the calculations.
 
 ## Using the core interface
 
-The core interface is accessed through the [`ManyBodyCalculator`][qcmanybody.manybody.ManyBodyCalculator]
+The core interface is accessed through the [`ManyBodyCore`][qcmanybody.manybody.ManyBodyCore]
 class.
 
 The first step is to create a molecule. This molecule is a
 [QCElemental molecule object](https://molssi.github.io/QCElemental/model_molecule.html), and must contain fragments.
 (see also: [moleule input](keywords.md#molecule))
 
 ```python
-import qcmanybody as qcmb
-import qcelemental as qcel
+from qcelemental.models import Molecule
 
-# Create a molecule with 3 hydrogen atoms, each as its own fragment
-mol = qcel.models.Molecule(symbols=['h', 'h', 'h'],
-                           geometry=[[0,0,0],[0,0,2],[0,0,4]],
-                           fragments=[[0], [1], [2]])
+# Create a molecule with 3 neon atoms, each as its own fragment
+
+mol = Molecule(symbols=["ne", "ne", "ne"],
+               geometry=[[0,0,0], [0,0,2], [0,0,4]],
+               fragments=[[0], [1], [2]])
 ```
 
-Next, create a `ManyBodyCalculator` object. This object is constructed using the molecule,
+Next, create a `ManyBodyCore` object. This object is constructed using the molecule,
 the desired BSSE correction, levels of MBE, and other options of the MBE.
 
 ```python
-mbc = qcmb.ManyBodyCalculator(
-    molecule=mol,
-    bsse_type=['cp'],
-    levels={1: 'mp2/aug-cc-pvtz', 2: 'b3lyp/def2-svp', 3: 'hf/sto-3g'},
-    return_total_data=True,
-    supersystem_ie_only=False
-)
+from qcmanybody import ManyBodyCore
+
+mbc = ManyBodyCore(molecule=mol,
+                   bsse_type=["cp"],
+                   levels={1: "ccsd/cc-pvtz",
+                           2: "mp2/cc-pvdz",
+                           3: "mp2/cc-pvdz"},
+                   return_total_data: True,
+                   supersystem_ie_only: False,
+                   embedding_charges: None)
 ```
 
 The `levels` option is a dictionary that specifies the n-body level as a key, then an arbitrary
@@ -52,11 +55,11 @@ map these strings to some meaningful definition of a calculation.
     nbody you would like to calculate). All levels must be present even if the model chemistry
     is the same for all levels.
 
-For a complete discussion of the other options available in the `ManyBodyCalculator` object, see the
+For a complete discussion of the other options available in the `ManyBodyCore` object, see the
 [keywords discussion](keywords.md)
-the [`ManyBodyCalculator API documentation`][qcmanybody.manybody.ManyBodyCalculator].
+the [`ManyBodyCore API documentation`][qcmanybody.manybody.ManyBodyCore].
 
-The next step is to obtain the calculations to be run from the `ManyBodyCalculator` object.
+The next step is to obtain the calculations to be run from the `ManyBodyCore` object.
 This is done with a python generator function `iterate_molecules` that returns
 a tuple. This tuple contains
 
@@ -76,7 +79,7 @@ does not provide any tools for running the calculations.
 ### Results dictionary
 
 The data returned from the calculations is expected to be stored in a nested dictionary.
-The level is the opaque label as given from the `QCManyBodyCalculator`.
+The level is the opaque label as given from the `QCManyBodyCore`.
 The second level is the name of the property.
 
 ```python
@@ -105,4 +108,4 @@ of the MBE properties.
 final_results = mbc.analyze(calculation_results)
 ```
 
-For a discussion about what the results contain, see the [results documentation](results.md).
+For a discussion about what the results contain, see the [results documentation](results.md).

docs/index.md

@@ -1,6 +1,6 @@
 # QCManyBody Documentation
 
-QCManyBody is a python package for running quantum chemistry manybody expansions and interaction calculations in a
+QCManyBody is a python package for running quantum chemistry many-body expansions and interaction calculations in a
 package-independent way.
 
 ## Installation

docs/keywords.md

@@ -13,11 +13,10 @@ Examples:
 ```python
 from qcelemental.models import Molecule
 
-# Molecule with 3 hydrogen atoms, each as its own fragment
-h3 = Molecule(symbols=['h', 'h', 'h'],
-              geometry=[[0,0,0],[0,0,2],[0,0,4]],
-              fragments=[[0], [1], [2]])
-
+# Molecule with 3 neon atoms, each as its own fragment
+ne3 = Molecule(symbols=["ne", "ne", "ne"],
+               geometry=[[0,0,0],[0,0,2],[0,0,4]],
+               fragments=[[0], [1], [2]])
 
 # Water tetramer
 water4 = Molecule(symbols=['o', 'h', 'h', 'o', 'h', 'h', 'o', 'h', 'h', 'o', 'h', 'h'],

pyproject.toml

@@ -21,6 +21,8 @@ classifiers = [
     "Operating System :: MacOS",
 ]
 dependencies = [
+    "numpy",
+    "pydantic",
     "qcelemental",
     "qcengine",
 ]

qcmanybody/__init__.py

@@ -1,6 +1,8 @@
 from importlib.metadata import version
 
-from .manybody import ManyBodyCalculator
+from .core import ManyBodyCore
+from .core import ManyBodyCore as ManyBodyCalculator  # legacy alias
+from .computer import ManyBodyComputer
 from .models import BsseEnum
 from .utils import labeler, delabeler, resize_gradient, resize_hessian
 

qcmanybody/computer.py

@@ -21,7 +21,7 @@
 
 from qcelemental.models import FailedOperation, Molecule, DriverEnum, ProtoModel, AtomicResult, AtomicInput
 import qcengine as qcng
-from qcmanybody import ManyBodyCalculator
+from qcmanybody import ManyBodyCore
 from qcmanybody.utils import delabeler, provenance_stamp
 from qcmanybody.models import BsseEnum, ManyBodyKeywords, ManyBodyInput, ManyBodyResult, ManyBodyResultProperties
 
@@ -193,7 +193,7 @@ class ManyBodyComputer(BaseComputerQCNG):
         description=ManyBodyKeywords.__fields__["supersystem_ie_only"].field_info.description,
     )
     task_list: Dict[str, Any] = {}  #MBETaskComputers] = {}
-    qcmb_calculator: Optional[Any] = Field(
+    qcmb_core: Optional[Any] = Field(
         None,
         description="Low-level interface",
     )
@@ -399,7 +399,7 @@ def from_manybodyinput(cls, input_model: ManyBodyInput, build_tasks: bool = True
             specifications[mtd]["specification"]["driver"] = computer_model.driver  # overrides atomic driver with mb driver
             specifications[mtd]["specification"].pop("schema_name", None)
 
-        computer_model.qcmb_calculator = ManyBodyCalculator(
+        computer_model.qcmb_core = ManyBodyCore(
             computer_model.molecule,
             computer_model.bsse_type,
             comp_levels,
@@ -414,7 +414,7 @@ def from_manybodyinput(cls, input_model: ManyBodyInput, build_tasks: bool = True
         component_properties = {}
         component_results = {}
 
-        for chem, label, imol in computer_model.qcmb_calculator.iterate_molecules():
+        for chem, label, imol in computer_model.qcmb_core.iterate_molecules():
             inp = AtomicInput(molecule=imol, **specifications[chem]["specification"])
             # inp = AtomicInput(molecule=imol, **specifications[chem]["specification"], extras={"psiapi": True})  # faster for p4
 
@@ -450,7 +450,7 @@ def from_manybodyinput(cls, input_model: ManyBodyInput, build_tasks: bool = True
         # print("\n<<<  (ZZ 2) QCEngine harness ManyBodyComputerQCNG.from_qcschema_ben component_properties  >>>")
         # pprint.pprint(component_properties, width=200)
 
-        analyze_back = computer_model.qcmb_calculator.analyze(component_properties)
+        analyze_back = computer_model.qcmb_core.analyze(component_properties)
         analyze_back["nbody_number"] = len(component_properties)
         # print("\n<<<  (ZZ 3) QCEngine harness ManyBodyComputerQCNG.from_qcschema_ben analyze_back  >>>")
         # pprint.pprint(analyze_back, width=200)

qcmanybody/manybody.py → qcmanybody/core.py

@@ -27,7 +27,7 @@
 logger = logging.getLogger(__name__)
 
 
-class ManyBodyCalculator:
+class ManyBodyCore:
     def __init__(
         self,
         molecule: Molecule,

qcmanybody/tests/common.py

@@ -1,4 +1,4 @@
-from qcmanybody.manybody import Molecule
+from qcelemental.models import Molecule
 
 mol_ne2 = Molecule(
     symbols=["Ne", "Ne"], fragments=[[0], [1]], geometry=[0.0, 0.0, -2.834589188186742, 0.0, 0.0, 2.834589188186742]

qcmanybody/tests/test_mbe_he4_multilevel.py

@@ -896,7 +896,7 @@ def test_count_he4_multi(mbe_keywords, ref_count, he_tetramer, request):
     mbe_model = ManyBodyInput(specification={"specification": atomic_spec, "keywords": mbe_keywords, "driver": "energy"}, molecule=he_tetramer)
 
     ret = ManyBodyComputer.from_manybodyinput(mbe_model, build_tasks=False)
-    ret = ret.qcmb_calculator
+    ret = ret.qcmb_core
 
     text, dcount = ret.format_calc_plan()
     assert compare_recursive(ref_count["all"], dcount, atol=1.e-6)

qcmanybody/tests/test_mbe_he4_singlelevel.py

@@ -9,7 +9,8 @@
 from qcelemental.testing import compare_values, compare_recursive
 
 from qcmanybody.models import AtomicSpecification, ManyBodyKeywords, ManyBodyInput
-from qcmanybody.computer import ManyBodyComputer, qcvars_to_manybodyproperties
+from qcmanybody import ManyBodyComputer
+from qcmanybody.computer import qcvars_to_manybodyproperties
 
 from .addons import using
 
@@ -712,7 +713,7 @@ def test_count_he4_single(mbe_keywords, ref_count, he_tetramer):
     mbe_model = ManyBodyInput(specification={"specification": atomic_spec, "keywords": mbe_keywords, "driver": "energy"}, molecule=he_tetramer)
 
     ret = ManyBodyComputer.from_manybodyinput(mbe_model, build_tasks=False)
-    ret = ret.qcmb_calculator
+    ret = ret.qcmb_core
 
     text, dcount = ret.format_calc_plan()
     assert compare_recursive(ref_count["all"], dcount, atol=1.e-6)

qcmanybody/tests/test_mbe_keywords.py

@@ -14,7 +14,7 @@
 
 # qcng: from qcengine.procedures.manybody import ManyBodyComputer
 from qcmanybody.computer import ManyBodyComputer
-from qcmanybody import ManyBodyCalculator
+from qcmanybody import ManyBodyCalculator  # test old name still operational
 
 
 @pytest.fixture(scope="function")

qcmanybody/tests/test_multi.py

@@ -1,6 +1,6 @@
 import pytest
 
-from qcmanybody import ManyBodyCalculator
+from qcmanybody import ManyBodyCalculator  # test old name still operational
 from qcmanybody.models import BsseEnum
 from .common import mol_h2o_3
 from .utils import load_ref_data, compare_results, load_component_data

qcmanybody/tests/test_multi_ss.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from qcmanybody import ManyBodyCalculator
+from qcmanybody import ManyBodyCore
 from qcmanybody.models import BsseEnum
 from .common import mol_h2o_3
 from .utils import load_ref_data, compare_results, load_component_data
@@ -28,6 +28,6 @@ def test_h2o_trimer_multi_ss(levels, component_file, ref_file):
     component_results = load_component_data(component_file)
     ref_data = load_ref_data(ref_file)
 
-    mc = ManyBodyCalculator(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
+    mc = ManyBodyCore(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
     nbody_results = mc.analyze(component_results)
     compare_results(nbody_results, ref_data, levels)

qcmanybody/tests/test_single.py

@@ -1,6 +1,6 @@
 import pytest
 
-from qcmanybody import ManyBodyCalculator
+from qcmanybody import ManyBodyCore
 from qcmanybody.models import BsseEnum
 from .common import mol_h2o_3
 from .utils import load_ref_data, compare_results, load_component_data
@@ -25,6 +25,6 @@ def test_h2o_trimer_single(levels, component_file, ref_file):
     component_results = load_component_data(component_file)
     ref_data = load_ref_data(ref_file)
 
-    mc = ManyBodyCalculator(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
+    mc = ManyBodyCore(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
     nbody_results = mc.analyze(component_results)
     compare_results(nbody_results, ref_data, levels)

qcmanybody/tests/utils.py

@@ -8,7 +8,7 @@
 import zstandard
 from qcelemental.models import Molecule, AtomicInput
 
-from qcmanybody import ManyBodyCalculator, delabeler
+from qcmanybody import ManyBodyCore, delabeler
 from qcmanybody.models import BsseEnum
 
 _my_dir = os.path.dirname(os.path.realpath(__file__))
@@ -172,7 +172,7 @@ def run_qcengine(
     embedding_charges: Optional[Mapping[int, list]],
 ):
 
-    mc = ManyBodyCalculator(molecule, bsse_type, levels, return_total_data, supersystem_ie_only, embedding_charges)
+    mc = ManyBodyCore(molecule, bsse_type, levels, return_total_data, supersystem_ie_only, embedding_charges)
 
     component_results = {}