kim-tools 0.2.0b0__py3-none-any.whl → 0.2.2__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.0b0"
+__version__ = "0.2.2"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -719,6 +719,11 @@ class AFLOW:
 
     """
 
+    class AFLOWNotFoundException(Exception):
+        """
+        Raised when the AFLOW executable is not found
+        """
+
     class ChangedSymmetryException(Exception):
         """
         Raised when an unexpected symmetry change is detected
@@ -744,6 +749,15 @@ class AFLOW:
             np: Sets :attr:`np`
         """
         self.aflow_executable = aflow_executable
+
+        try:
+            subprocess.check_output(["aflow", "--proto=A_cF4_225_a"])
+        except Exception:
+            raise self.AFLOWNotFoundException(
+                "Failed to run an AFLOW test command. It is likely "
+                "that the AFLOW executable was not found."
+            )
+
         self.np = np
         if aflow_work_dir != "" and not aflow_work_dir.endswith("/"):
             self.aflow_work_dir = aflow_work_dir + "/"
@@ -1412,7 +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
@@ -1437,6 +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,
@@ -1635,7 +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} "
@@ -1665,8 +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:
@@ -1689,12 +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"
@@ -1736,8 +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``
@@ -1761,8 +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
@@ -1778,5 +1796,4 @@ class AFLOW:
             reference_atoms,
             get_space_group_number_from_prototype(prototype_label),
             rtol,
-            atol,
         )

kim_tools/kimunits.py

@@ -24,6 +24,19 @@ _units_output_expression = re.compile(
 )
 
 
+def check_units_util():
+    """
+    Check that units util can be found
+    """
+    try:
+        subprocess.check_output(["units", "--help"])
+    except Exception:
+        raise UnitConversion(
+            "Failed to run a 'units' test command. It is likely "
+            "that the 'units' executable was not found."
+        )
+
+
 def linear_fit(x, y):
     """
     Perform a linear fit between x,y, returning the average error for each data
@@ -55,6 +68,7 @@ def islinear(unit, to_unit=None):
 
 def convert_units(from_value, from_unit, wanted_unit=None, suppress_unit=False):
     """Works with 'units' utility"""
+    check_units_util()
     from_sign = from_value < 0
     from_value = str(abs(from_value))
     from_unit = str(from_unit)

kim_tools/symmetry_util/core.py

@@ -131,6 +131,42 @@ def cartesian_to_fractional_itc_rotation_from_ase_cell(
     return np.transpose(cell_arr @ cart_rot_arr @ np.linalg.inv(cell_arr))
 
 
+def fractional_to_cartesian_itc_rotation_from_ase_cell(
+    frac_rot: ArrayLike, cell: ArrayLike
+) -> ArrayLike:
+    """
+    Convert fractional to Cartesian rotation. Read the arguments and returns carefully,
+    as there is some unfortunate mixing of row and columns because of the different
+    conventions of the ITC and ASE and other simulation packages
+
+    Args:
+        frac_rot:
+            The fractional rotation in ITC convention, i.e. for left-multiplying column
+            vectors. Here the distinction with a matrix's transpose DOES matter, because
+            the fractional coordinate system is not orthonormal.
+        cell:
+            The cell of the crystal, with each row being a cartesian vector
+            representing a lattice vector. This is consistent with most simulation
+            packages, but transposed from the ITC
+
+    Returns:
+        Cartesian rotation. It is assumed that this is for left-multiplying column
+        vectors, although in cases where we don't care if we're working with the
+        rotation or its inverse (e.g. when checking whether or not it's in the
+        point group), this doesn't matter due to orthogonality
+    """
+
+    cell_arr = np.asarray(cell)
+    frac_rot_arr = np.asarray(frac_rot)
+
+    if not ((cell_arr.shape == (3, 3)) and (frac_rot_arr.shape == (3, 3))):
+        raise IncorrectCrystallographyException(
+            "Either the rotation matrix or the cell provided were not 3x3 matrices"
+        )
+
+    return np.transpose(np.linalg.inv(cell_arr) @ frac_rot_arr @ cell_arr)
+
+
 def cartesian_rotation_is_in_point_group(
     cart_rot: ArrayLike, sgnum: Union[int, str], cell: ArrayLike
 ) -> bool:

kim_tools/test_driver/core.py

@@ -1218,7 +1218,9 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 print(f"\nNOTE: {msg}\n")
                 logger.info(msg)
 
-    def _update_nominal_parameter_values(self, atoms: Atoms) -> None:
+    def _update_nominal_parameter_values(
+        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
         provided :class:`~ase.Atoms` object. It is assumed that the crystallographic
@@ -1246,6 +1248,11 @@ class SingleCrystalTestDriver(KIMTestDriver):
 
         Args:
             atoms: Structure to analyze to get the new parameter values
+            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:
@@ -1259,8 +1266,12 @@ class SingleCrystalTestDriver(KIMTestDriver):
 
         try:
             aflow_parameter_values = AFLOW().solve_for_params_of_known_prototype(
-                atoms,
-                self.__nominal_crystal_structure_npt["prototype-label"]["source-value"],
+                atoms=atoms,
+                prototype_label=self.__nominal_crystal_structure_npt["prototype-label"][
+                    "source-value"
+                ],
+                max_resid=max_resid,
+                cell_rtol=cell_rtol,
             )
         except (AFLOW.FailedToMatchException, AFLOW.ChangedSymmetryException) as e:
             raise type(e)(

{kim_tools-0.2.0b0.dist-info → kim_tools-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.2.0b0
+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-0.2.0b0.dist-info → kim_tools-0.2.2.dist-info}/RECORD

@@ -1,12 +1,12 @@
-kim_tools/__init__.py,sha256=_IDKtgO7O3TeqoIhOaAUUqV2IEv5Suk3PPsYokbtI7Q,435
-kim_tools/kimunits.py,sha256=kR5VMTurQnbPOHcWF1XN-mjY9FXRAdWI8hA-RZHhrek,5036
+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=Xqjh2Xwf4-e-98FMJ8RfRXsTdx2NeWeZXwrPP0xkvwM,71847
+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
 kim_tools/symmetry_util/__init__.py,sha256=uu-ZSUDUTe2P81rkAS3tXverx31s_uZ3wL4SD_dn5aI,86
-kim_tools/symmetry_util/core.py,sha256=eQV6gBVlLzGz3LvbRhD1H64uOooyRWTFxU346jSUbE4,20083
+kim_tools/symmetry_util/core.py,sha256=VTYH1MRADraJVc6SBfFHZweWI_WZgCViSKM4MazF7KY,21634
 kim_tools/symmetry_util/data/possible_primitive_shifts.json,sha256=4OVNgn3NnykgGlYiAcecERmVWiIZFrmP2LZI3ml_Sh0,25010
 kim_tools/symmetry_util/data/primitive_GENPOS_ops.json,sha256=FDu4H4PosOpK9yKwOPy3SxbH7xLMOmZfKZ4ItKPMjoQ,224498
 kim_tools/symmetry_util/data/space_groups_for_each_bravais_lattice.json,sha256=wSNu6d5pH72lJ6Zj5MZ64qzwS_6Fn5WOs0ts7E9uPC4,2507
@@ -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=YFLwqV6bBAxRzoinAB3cH86z90fQqENwhMcjyzrJxPM,78225
+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-0.2.0b0.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.2.0b0.dist-info/METADATA,sha256=feOdrstYpWjnu0VzAeNU0_zTWgsSM7yBZfs0RkD7fbA,1462
-kim_tools-0.2.0b0.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-kim_tools-0.2.0b0.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.2.0b0.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,,

{kim_tools-0.2.0b0.dist-info → kim_tools-0.2.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.0.0)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any