kim-tools 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.3"
+__version__ = "0.3.5"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/ase/core.py

@@ -208,7 +208,7 @@ def randomize_positions(atoms, pert_amp, seed=None):
 
 
 ################################################################################
-def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol):
+def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol: str) -> float:
     """
     Construct a non-periodic cell containing a single atom and compute its energy.
 
@@ -237,23 +237,16 @@ def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol):
             f"or an ASE Calculator. Instead got an object of type {type(model)}."
         )
     single_atom.calc = calc
-    try:
-        energy_per_atom = single_atom.get_potential_energy()
-    except Exception as e:
-        msg = (
-            "Energy evaluation for isolated atom raised the following error:\n"
-            f"{repr(e)}\nAssuming zero isolated atom energy."
-        )
-        logger.warning(msg)
-        print(msg)
-        energy_per_atom = 0.0
-    finally:
+    energy_per_atom = single_atom.get_potential_energy()
+    # if we are attaching an existing LAMMPS calculator to an atoms object,
+    # we can't delete it. Only do so if we are making a new one from a KIM ID.
+    if isinstance(model, str):
         if hasattr(calc, "clean"):
             calc.clean()
         if hasattr(calc, "__del__"):
             calc.__del__()
-        del single_atom
-        return energy_per_atom
+    del single_atom
+    return energy_per_atom
 
 
 ################################################################################

kim_tools/test_driver/core.py

@@ -66,6 +66,7 @@ from ..aflow_util import (
     prototype_labels_are_equivalent,
 )
 from ..aflow_util.core import AFLOW_EXECUTABLE
+from ..ase import get_isolated_energy_per_atom
 from ..kimunits import convert_list, convert_units
 from ..symmetry_util import (
     cartesian_rotation_is_in_point_group,
@@ -490,6 +491,13 @@ class KIMTestDriver(ABC):
             the Test Driver
     """
 
+    class NonKIMModelError(Exception):
+        """
+        Raised when a KIM model name is requested but is absent. This is important
+        to handle to inform users that they are trying to run a Test Driver that
+        requires a KIM model (e.g. a LAMMPS TD) with a non-KIM Calculator
+        """
+
     def __init__(self, model: Union[str, Calculator]) -> None:
         """
         Args:
@@ -690,7 +698,13 @@ class KIMTestDriver(ABC):
         """
         Get the KIM model name, if present
         """
-        return self.__kim_model_name
+        if self.__kim_model_name is not None:
+            return self.__kim_model_name
+        else:
+            raise self.NonKIMModelError(
+                "A KIM model name is being requested, but the Test Driver "
+                "is being run with a non-KIM calculator."
+            )
 
     @property
     def property_instances(self) -> Dict:
@@ -733,6 +747,23 @@ class KIMTestDriver(ABC):
                 self.__output_property_instances, f
             )  # serialize the dictionary to string first
 
+    def get_isolated_energy_per_atom(self, symbol: str) -> float:
+        """
+        Construct a non-periodic cell containing a single atom and compute its energy.
+
+        Args
+            symbol:
+                The chemical species
+
+        Returns:
+            The isolated energy of a single atom
+        """
+        try:
+            model = self.kim_model_name
+        except self.NonKIMModelError:
+            model = self._calc
+        return get_isolated_energy_per_atom(model=model, symbol=symbol)
+
 
 def _add_common_crystal_genome_keys_to_current_property_instance(
     property_instances: str,

{kim_tools-0.3.3.dist-info → kim_tools-0.3.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.3
+Version: 0.3.5
 Summary: Base classes and helper routines for writing KIM Tests
 Author-email: ilia Nikiforov <nikif002@umn.edu>, Ellad Tadmor <tadmor@umn.edu>, Claire Waters <bwaters@umn.edu>, "Daniel S. Karls" <karl0100umn@gmail.com>, Matt Bierbaum <matt.bierbaum@gmail.com>, Eric Fuemmeler <efuemmel@umn.edu>, Philipp Hoellmer <ph2484@nyu.edu>, Guanming Zhang <gz2241@nyu.edu>, Tom Egg <tje3676@nyu.edu>
 Maintainer-email: ilia Nikiforov <nikif002@umn.edu>
@@ -32,7 +32,7 @@ Dynamic: license-file
 
 # kim-tools
 
-![testing](https://github.com/openkim/kim-tools/actions/workflows/testing.yml/badge.svg)
+[![Testing](https://github.com/openkim/kim-tools/actions/workflows/testing.yml/badge.svg)](https://github.com/openkim/kim-tools/actions/workflows/testing.yml)
 [![docs](https://app.readthedocs.org/projects/kim-tools/badge/?version=latest)](https://kim-tools.readthedocs.io/en/latest/)
 [![PyPI](https://img.shields.io/pypi/v/kim-tools.svg)](https://pypi.org/project/kim-tools/)
 

{kim_tools-0.3.3.dist-info → kim_tools-0.3.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-kim_tools/__init__.py,sha256=pnnfC__2WcTkgaE8RZU5AfDIx6PQOR9Dst7oBvYsMYI,433
+kim_tools/__init__.py,sha256=y8h76B1TbTZ5GZBpVnnyhzD06UpiOrAN5xffFW2TfLI,433
 kim_tools/kimunits.py,sha256=jOxBv9gRVhxPE6ygAIUxOzCAfPI6tT6sBaF_FNl9m-M,5387
 kim_tools/aflow_util/__init__.py,sha256=lJnQ8fZCma80QVRQeKvY4MQ87oCWu-9KATV3dKJfpDc,80
 kim_tools/aflow_util/core.py,sha256=zi69wMcgkcYBTKbc-OvKlMIzUtgphO57yBA8LB7_5wc,77484
@@ -2002,7 +2002,7 @@ kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A_tP4_129_ac-001/info.jso
 kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A_tP4_136_f-001/info.json,sha256=5_xlFGOov7VoFwzhp7JtltRnWiAFfgpwF5qc3kMSAjQ,1278
 kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A_tP50_134_a2m2n-001/info.json,sha256=K601zsKLpvPLIaK17bEiNGIQJYJDvIby1lIJ3P9Ze6E,1258
 kim_tools/ase/__init__.py,sha256=1i6ko5tNr0VZC3T7hoEzq4fnSU0DdxNpxXcSaWMcJWc,76
-kim_tools/ase/core.py,sha256=KRtcNYcJLlP-WiEMOOmR-DhYw5IN5MoOCtKWJJzRkhM,31313
+kim_tools/ase/core.py,sha256=odRuHQGZl-pcRtkdYvG31_3kW6nt3qwHdKvAOJ-ifwM,31207
 kim_tools/symmetry_util/__init__.py,sha256=uu-ZSUDUTe2P81rkAS3tXverx31s_uZ3wL4SD_dn5aI,86
 kim_tools/symmetry_util/core.py,sha256=HfDy1CwNWUZIkb4cs3ebUDgWjtt4jRSkBKgGEnlkjuI,30888
 kim_tools/symmetry_util/data/possible_primitive_shifts.json,sha256=4OVNgn3NnykgGlYiAcecERmVWiIZFrmP2LZI3ml_Sh0,25010
@@ -2012,11 +2012,11 @@ kim_tools/symmetry_util/data/wyck_pos_xform_under_normalizer.json,sha256=6g1YuYh
 kim_tools/symmetry_util/data/wyckoff_multiplicities.json,sha256=qG2RPBd_-ejDIfz-E4ZhkHyRpIboxRy7oiXkdDf5Eg8,32270
 kim_tools/symmetry_util/data/wyckoff_sets.json,sha256=f5ZpHKDHo6_JWki1b7KUGoYLlhU-44Qikw_-PtbLssw,9248
 kim_tools/test_driver/__init__.py,sha256=KOiceeZNqkfrgZ66CiRiUdniceDrCmmDXQkOw0wXaCQ,92
-kim_tools/test_driver/core.py,sha256=r4hiZcV-PkWcOo0uEqfqeP1-YGGpPepaAjmR4LJog0w,89208
+kim_tools/test_driver/core.py,sha256=8FbOhQRu38zX48CBgFgMrB2tLLSXUsbrXl9dYx5CVHw,90320
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.3.3.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.3.dist-info/METADATA,sha256=d5yobjRNvHpCLftHbue8GmC0xsvD8FSOpCksGnRoxC8,1962
-kim_tools-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.3.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.3.dist-info/RECORD,,
+kim_tools-0.3.5.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.5.dist-info/METADATA,sha256=YHR8cikv3dJ0DLWxltEXkNyDbHFJMMT5hullZnEvYvs,2032
+kim_tools-0.3.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.5.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.5.dist-info/RECORD,,