kim-tools 0.2.1__py3-none-any.whl → 0.2.2__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -1426,7 +1426,11 @@ class AFLOW:
         return equation_sets
 
     def solve_for_params_of_known_prototype(
-        self, atoms: Atoms, prototype_label: str, max_resid: float = 1e-5
+        self,
+        atoms: Atoms,
+        prototype_label: str,
+        max_resid: float = 1e-5,
+        cell_rtol: float = 0.01,
     ) -> List[float]:
         """
         Given an Atoms object that is a primitive cell of its Bravais lattice as
@@ -1451,6 +1455,8 @@ class AFLOW:
             max_resid:
                 Maximum residual allowed when attempting to match the fractional
                 positions of the atoms to the crystallographic equations
+            cell_rtol:
+                Relative tolerance on cell lengths and angles
 
         Returns:
             List of free parameters that will regenerate `atoms` (up to permutations,
@@ -1649,7 +1655,11 @@ class AFLOW:
                 # The internal shift may have taken us to an internal parameter
                 # solution that represents a rotation, so we need to check
                 if self.confirm_unrotated_prototype_designation(
-                    atoms, species, prototype_label, candidate_prototype_param_values
+                    atoms,
+                    species,
+                    prototype_label,
+                    candidate_prototype_param_values,
+                    cell_rtol,
                 ):
                     logger.info(
                         f"Found set of parameters for prototype {prototype_label} "
@@ -1679,8 +1689,7 @@ class AFLOW:
         test_atoms: Atoms,
         ref_atoms: Atoms,
         sgnum: Union[int, str],
-        rtol: float = 1.0e-4,
-        atol: float = 1.0e-8,
+        rtol: float = 0.01,
     ) -> bool:
         """
         Check whether `test_atoms` and `reference_atoms` are unrotated as follows:
@@ -1703,12 +1712,10 @@ class AFLOW:
             sgnum:
                 Space group number
             rtol:
-                Parameter to pass to :func:`numpy.allclose` for comparing cell params
-            atol:
-                Parameter to pass to :func:`numpy.allclose` for comparing cell params
+                Parameter to pass to :func:`numpy.allclose` for comparing cell params.
         """
         if not np.allclose(
-            ref_atoms.cell.cellpar(), test_atoms.cell.cellpar(), atol=atol, rtol=rtol
+            ref_atoms.cell.cellpar(), test_atoms.cell.cellpar(), rtol=rtol
         ):
             logger.info(
                 "Cell lengths and angles do not match.\n"
@@ -1750,8 +1757,7 @@ class AFLOW:
         species: List[str],
         prototype_label: str,
         parameter_values: List[float],
-        rtol: float = 1.0e-4,
-        atol: float = 1.0e-8,
+        rtol: float = 0.01,
     ) -> bool:
         """
         Check whether the provided prototype designation recreates ``reference_atoms``
@@ -1775,8 +1781,6 @@ class AFLOW:
                 The free parameters of the AFLOW prototype designation
             rtol:
                 Parameter to pass to :func:`numpy.allclose` for comparing cell params
-            atol:
-                Parameter to pass to :func:`numpy.allclose` for comparing cell params
 
         Returns:
             Whether or not the crystals match
@@ -1792,5 +1796,4 @@ class AFLOW:
             reference_atoms,
             get_space_group_number_from_prototype(prototype_label),
             rtol,
-            atol,
         )

kim_tools/test_driver/core.py

@@ -1219,7 +1219,7 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 logger.info(msg)
 
     def _update_nominal_parameter_values(
-        self, atoms: Atoms, max_resid: float = 1e-5
+        self, atoms: Atoms, max_resid: float = 1e-5, cell_rtol: float = 0.01
     ) -> None:
         """
         Update the nominal parameter values of the nominal crystal structure from the
@@ -1251,6 +1251,8 @@ class SingleCrystalTestDriver(KIMTestDriver):
             max_resid:
                 Maximum residual allowed when attempting to match the fractional
                 positions of the atoms to the crystallographic equations
+            cell_rtol:
+                Relative tolerance on cell lengths and angles
 
         Raises:
             AFLOW.FailedToMatchException:
@@ -1269,6 +1271,7 @@ class SingleCrystalTestDriver(KIMTestDriver):
                     "source-value"
                 ],
                 max_resid=max_resid,
+                cell_rtol=cell_rtol,
             )
         except (AFLOW.FailedToMatchException, AFLOW.ChangedSymmetryException) as e:
             raise type(e)(

{kim_tools-0.2.1.dist-info → kim_tools-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.2.1
+Version: 0.2.2
 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>
 Maintainer-email: ilia Nikiforov <nikif002@umn.edu>

{kim_tools-0.2.1.dist-info → kim_tools-0.2.2.dist-info}/RECORD

@@ -1,7 +1,7 @@
-kim_tools/__init__.py,sha256=-dcfQfnIcs043nxVvh5sJHOkRySpNLwUf_MxHxwH2B4,433
+kim_tools/__init__.py,sha256=gGt0sG7foY9MROLXGAYUkxV8GdwEulr_PS5wMm06mcM,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=-UOiEHHA_3Bcvl49OIwnlQCl0ddN2KWdmNEZ2M9MlW4,72271
+kim_tools/aflow_util/core.py,sha256=57K2G1jGgJhUA312RkWnhb3MOmlo9B5DdenNb_dIkzc,72206
 kim_tools/aflow_util/data/README_PROTO.TXT,sha256=bTpcd8GHOkpcQn6YUZzqKhiTytwSDpkgu4boeoogT38,447851
 kim_tools/ase/__init__.py,sha256=1i6ko5tNr0VZC3T7hoEzq4fnSU0DdxNpxXcSaWMcJWc,76
 kim_tools/ase/core.py,sha256=d6eOu_HSxVr-ae0TSEbY4HKdePxhNu3yv8NN9VDl-BA,30256
@@ -14,11 +14,11 @@ 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=7l_fnLXNYNLuROY3b1vbqIA_715acaBbQGjS3PXdXB8,78538
+kim_tools/test_driver/core.py,sha256=bA1tZPM3dES5PZSanN_xPC-SApSB1usO10EvoIq8EgY,78685
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.2.1.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.2.1.dist-info/METADATA,sha256=kQVhy8AzLH5-Oa8s0NEPdzgVnmjkfKBLMcOgKL2u02g,1460
-kim_tools-0.2.1.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-kim_tools-0.2.1.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.2.1.dist-info/RECORD,,
+kim_tools-0.2.2.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.2.2.dist-info/METADATA,sha256=3OJoiiqV0-dLI_4hq--8wWF5BcedispUTMgZ1Z4ieR8,1460
+kim_tools-0.2.2.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+kim_tools-0.2.2.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.2.2.dist-info/RECORD,,