kim-tools 0.3.9__py3-none-any.whl → 0.3.11__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.9"
+__version__ = "0.3.11"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -1642,9 +1642,21 @@ class AFLOW:
         ]
 
         if match_library_proto:
-            library_prototype_label, short_name = (
-                self.get_library_prototype_label_and_shortname_from_atoms(atoms)
-            )
+            try:
+                library_prototype_label, short_name = (
+                    self.get_library_prototype_label_and_shortname_from_atoms(atoms)
+                )
+            except subprocess.CalledProcessError:
+                library_prototype_label = None
+                short_name = None
+                msg = (
+                    "WARNING: aflow --compare2prototypes returned error, skipping "
+                    "library matching"
+                )
+                print()
+                print(msg)
+                print()
+                logger.warning(msg)
 
         # NOTE: Because of below, this only works if the provided prototype label is
         # correctly alphabetized. Change this?

kim_tools/test_driver/core.py

@@ -777,8 +777,9 @@ class KIMTestDriver(ABC):
         Args:
             filename: path to write the file
         """
-        kim_property_dump(self._get_serialized_property_instances(), filename)
         filename_parent = Path(filename).parent.resolve()
+        os.makedirs(filename_parent, exist_ok=True)
+        kim_property_dump(self._get_serialized_property_instances(), filename)
         if filename_parent != Path("output").resolve():
             for file_in_output in glob.glob("output/*"):
                 file_in_output_name = str(Path(file_in_output).name)
@@ -787,6 +788,10 @@ class KIMTestDriver(ABC):
                         if isinstance(instance[key], dict):
                             if file_in_output_name == instance[key]["source-value"]:
                                 shutil.move(file_in_output, filename_parent)
+                            elif isinstance(instance[key]["source-value"], list):
+                                for file_in_property in instance[key]["source-value"]:
+                                    if file_in_output_name == file_in_property:
+                                        shutil.move(file_in_output, filename_parent)
 
     def get_isolated_energy_per_atom(self, symbol: str) -> float:
         """
@@ -1402,6 +1407,7 @@ class SingleCrystalTestDriver(KIMTestDriver):
         cell_rtol: float = 0.01,
         rot_rtol: float = 0.01,
         rot_atol: float = 0.01,
+        match_library_proto: bool = True,
     ) -> None:
         """
         Update the nominal parameter values of the nominal crystal structure from the
@@ -1446,6 +1452,8 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 Parameter to pass to :func:`numpy.allclose` for compariong fractional
                 rotations. Default value chosen to be commensurate with AFLOW
                 default distance tolerance of 0.01*(NN distance)
+            match_library_proto:
+                Whether to match to library prototypes
 
         Raises:
             AFLOW.FailedToMatchException:
@@ -1458,16 +1466,29 @@ class SingleCrystalTestDriver(KIMTestDriver):
         """
         aflow = AFLOW(aflow_executable=self.aflow_executable)
         try:
-            (aflow_parameter_values, library_prototype_label, short_name) = (
-                aflow.solve_for_params_of_known_prototype(
+            if match_library_proto:
+                (aflow_parameter_values, library_prototype_label, short_name) = (
+                    aflow.solve_for_params_of_known_prototype(
+                        atoms=atoms,
+                        prototype_label=self.get_nominal_prototype_label(),
+                        max_resid=max_resid,
+                        cell_rtol=cell_rtol,
+                        rot_rtol=rot_rtol,
+                        rot_atol=rot_atol,
+                    )
+                )
+            else:
+                aflow_parameter_values = aflow.solve_for_params_of_known_prototype(
                     atoms=atoms,
                     prototype_label=self.get_nominal_prototype_label(),
                     max_resid=max_resid,
                     cell_rtol=cell_rtol,
                     rot_rtol=rot_rtol,
                     rot_atol=rot_atol,
+                    match_library_proto=False,
                 )
-            )
+                library_prototype_label = None
+                short_name = None
         except (AFLOW.FailedToMatchException, AFLOW.ChangedSymmetryException) as e:
             raise type(e)(
                 "Encountered an error that MAY be the result of the nominal crystal "
@@ -1946,21 +1967,38 @@ class SingleCrystalTestDriver(KIMTestDriver):
     def get_nominal_space_group_number(self) -> int:
         return get_space_group_number_from_prototype(self.get_nominal_prototype_label())
 
-    def get_stoichiometry(self) -> List[int]:
+    def get_nominal_stoichiometric_species(self) -> List[str]:
+        return self._get_nominal_crystal_structure_npt()["stoichiometric-species"][
+            "source-value"
+        ]
+
+    def get_nominal_stoichiometry(self) -> List[int]:
         return get_stoich_reduced_list_from_prototype(
             self.get_nominal_prototype_label()
         )
 
+    def get_nominal_a(self) -> float:
+        return self._get_nominal_crystal_structure_npt()["a"]["source-value"]
+
     def get_nominal_parameter_names(self) -> List[str]:
-        """
-        Get the list of parameter names besides "a". Return an
-        empty list for cubic crystals
-        """
-        crystal_structure = self._get_nominal_crystal_structure_npt()
-        if "parameter-names" in crystal_structure:
-            return crystal_structure["parameter-names"]["source-value"]
-        else:
-            return []
+        return _get_optional_source_value(
+            self._get_nominal_crystal_structure_npt(), "parameter-names"
+        )
+
+    def get_nominal_parameter_values(self) -> List[float]:
+        return _get_optional_source_value(
+            self._get_nominal_crystal_structure_npt(), "parameter-values"
+        )
+
+    def get_nominal_short_name(self) -> List[str]:
+        return _get_optional_source_value(
+            self._get_nominal_crystal_structure_npt(), "short-name"
+        )
+
+    def get_nominal_library_prototype_label(self) -> str:
+        return _get_optional_source_value(
+            self._get_nominal_crystal_structure_npt(), "library-prototype-label"
+        )
 
     def get_atom_indices_for_each_wyckoff_orb(self) -> List[Dict]:
         """

{kim_tools-0.3.9.dist-info → kim_tools-0.3.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.9
+Version: 0.3.11
 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>

{kim_tools-0.3.9.dist-info → kim_tools-0.3.11.dist-info}/RECORD

@@ -1,7 +1,7 @@
-kim_tools/__init__.py,sha256=JnYWdvQufTnlREvqTcBFv0ZQoOwdekELyzJCKwE7XTI,433
+kim_tools/__init__.py,sha256=YZdzUiZNlEczGQLTPVRxzz5-jGxgJTEaeAK_p-oJu4o,434
 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=PM-ww2zoZXksGHbyPKW54v8r1bignJvFhDByx7Qm1ac,80837
+kim_tools/aflow_util/core.py,sha256=mMS2r9ayJJ6ApOFTAIkCZ72Dg3g1EnREbrqe2YEipMo,81273
 kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A108B24C11D24_cP334_222_h4i_i_bf_i-001/info.json,sha256=IsFiO9X2Ko7yoq2QkDurUVP7k1BE4WFgblu7oxl6iZs,2013
 kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A10B11_tI84_139_dehim_eh2n-001/info.json,sha256=f1EdtouuSL2y9NNw40Rvz2J9ZZcsqQBcyEmlHj6XoW8,1186
 kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A10B2C_hP39_171_5c_c_a-001/info.json,sha256=vD1xjZKWShL0E6XNsSlmIhilGcGNefl56oQDLQlHO1M,1596
@@ -2023,11 +2023,11 @@ 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=sM0SPmNFuYVdvKbmCM3kJblFs5--k1xRm57FdUtgs34,97367
+kim_tools/test_driver/core.py,sha256=ZHS26S8-HxCPTDhv6h6WZ2x7pDQMTu6G1bWD4rPvoz8,99107
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.3.9.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.9.dist-info/METADATA,sha256=mz0naaggDlfsGZXT1jSq9MbwQIaz3r8PkfKIO2DEw94,2032
-kim_tools-0.3.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.9.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.9.dist-info/RECORD,,
+kim_tools-0.3.11.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.11.dist-info/METADATA,sha256=AdNljYaTm6fqCc8eaRcIFX0oeMcsqDTcMPdmqvBPAcs,2033
+kim_tools-0.3.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.11.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.11.dist-info/RECORD,,