kim-tools 0.2.2__tar.gz → 0.2.4__tar.gz

{kim_tools-0.2.2/kim_tools.egg-info → kim_tools-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.2.2
+Version: 0.2.4
 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-0.2.2 → kim_tools-0.2.4}/kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.2"
+__version__ = "0.2.4"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

{kim_tools-0.2.2 → kim_tools-0.2.4}/kim_tools/aflow_util/core.py

@@ -18,6 +18,7 @@ import ase
 import numpy as np
 from ase import Atoms
 from ase.cell import Cell
+from ase.neighborlist import natural_cutoffs, neighbor_list
 from numpy.typing import ArrayLike
 from sympy import Symbol, linear_eq_to_matrix, matrix2numpy, parse_expr
 
@@ -62,6 +63,8 @@ __all__ = [
     "AFLOW",
 ]
 
+AFLOW_EXECUTABLE = "aflow"
+
 
 class IncorrectSpaceGroupException(Exception):
     """
@@ -740,7 +743,10 @@ class AFLOW:
         """
 
     def __init__(
-        self, aflow_executable: str = "aflow", aflow_work_dir: str = "", np: int = 4
+        self,
+        aflow_executable: str = AFLOW_EXECUTABLE,
+        aflow_work_dir: str = "",
+        np: int = 4,
     ):
         """
         Args:
@@ -751,7 +757,7 @@ class AFLOW:
         self.aflow_executable = aflow_executable
 
         try:
-            subprocess.check_output(["aflow", "--proto=A_cF4_225_a"])
+            subprocess.check_output([aflow_executable, "--proto=A_cF4_225_a"])
         except Exception:
             raise self.AFLOWNotFoundException(
                 "Failed to run an AFLOW test command. It is likely "
@@ -1116,9 +1122,7 @@ class AFLOW:
                 misfit_min_overall = struct["misfit"]
                 library_proto_overall = struct["name"]
                 found_overall = True
-            if struct["misfit"] < misfit_min_inlist and any(
-                proto in struct["name"] for proto in shortnames
-            ):
+            if struct["misfit"] < misfit_min_inlist and struct["name"] in shortnames:
                 misfit_min_inlist = struct["misfit"]
                 library_proto_inlist = struct["name"]
                 found_inlist = True
@@ -1429,8 +1433,10 @@ class AFLOW:
         self,
         atoms: Atoms,
         prototype_label: str,
-        max_resid: float = 1e-5,
+        max_resid: Optional[float] = None,
         cell_rtol: float = 0.01,
+        rot_rtol: float = 0.01,
+        rot_atol: float = 0.01,
     ) -> List[float]:
         """
         Given an Atoms object that is a primitive cell of its Bravais lattice as
@@ -1455,8 +1461,19 @@ class AFLOW:
             max_resid:
                 Maximum residual allowed when attempting to match the fractional
                 positions of the atoms to the crystallographic equations
+                If not provided, this is automatically set to 0.01*(minimum NN distance)
             cell_rtol:
                 Relative tolerance on cell lengths and angles
+                Justification for default value: AFLOW uses 0.01*(minimum NN distance)
+                as default tolerance.
+            rot_rtol:
+                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)
+            rot_atol:
+                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)
 
         Returns:
             List of free parameters that will regenerate `atoms` (up to permutations,
@@ -1469,6 +1486,27 @@ class AFLOW:
                 if AFLOW fails to match the re-generated crystal to the input crystal
 
         """
+        # If max_resid not provided, determine it from neighborlist
+        if max_resid is None:
+            nl_len = 0
+            cov_mult = 1
+            while nl_len == 0:
+                logger.info(
+                    "Attempting to find NN distance by searching "
+                    f"within covalent radii times {cov_mult}"
+                )
+                nl = neighbor_list("d", atoms, natural_cutoffs(atoms, mult=cov_mult))
+                nl_len = nl.size
+                cov_mult += 1
+            # set the maximum error to 1% of NN distance to follow AFLOW convention
+            # rescale by cube root of cell volume to get rough conversion from
+            # cartesian to fractional
+            max_resid = nl.min() * 0.01 * atoms.get_volume() ** (-1 / 3)
+            logger.info(
+                "Automatically set max fractional residual for solving position "
+                f"equations to {max_resid}"
+            )
+
         # solve for cell parameters
         cell_params = solve_for_aflow_cell_params_from_primitive_ase_cell_params(
             atoms.cell.cellpar(), prototype_label
@@ -1655,11 +1693,13 @@ 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,
-                    cell_rtol,
+                    reference_atoms=atoms,
+                    species=species,
+                    prototype_label=prototype_label,
+                    parameter_values=candidate_prototype_param_values,
+                    cell_rtol=cell_rtol,
+                    rot_rtol=rot_rtol,
+                    rot_atol=rot_atol,
                 ):
                     logger.info(
                         f"Found set of parameters for prototype {prototype_label} "
@@ -1689,7 +1729,9 @@ class AFLOW:
         test_atoms: Atoms,
         ref_atoms: Atoms,
         sgnum: Union[int, str],
-        rtol: float = 0.01,
+        cell_rtol: float = 0.01,
+        rot_rtol: float = 0.01,
+        rot_atol: float = 0.01,
     ) -> bool:
         """
         Check whether `test_atoms` and `reference_atoms` are unrotated as follows:
@@ -1711,11 +1753,21 @@ class AFLOW:
                 Primitive cell of a crystal
             sgnum:
                 Space group number
-            rtol:
+            cell_rtol:
                 Parameter to pass to :func:`numpy.allclose` for comparing cell params.
+                Justification for default value: AFLOW uses 0.01*(minimum NN distance)
+                as default tolerance.
+            rot_rtol:
+                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)
+            rot_atol:
+                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)
         """
         if not np.allclose(
-            ref_atoms.cell.cellpar(), test_atoms.cell.cellpar(), rtol=rtol
+            ref_atoms.cell.cellpar(), test_atoms.cell.cellpar(), rtol=cell_rtol
         ):
             logger.info(
                 "Cell lengths and angles do not match.\n"
@@ -1748,7 +1800,11 @@ class AFLOW:
             return False
 
         return cartesian_rotation_is_in_point_group(
-            cart_rot, sgnum, test_atoms_copy.cell
+            cart_rot=cart_rot,
+            sgnum=sgnum,
+            cell=test_atoms_copy.cell,
+            rtol=rot_rtol,
+            atol=rot_atol,
         )
 
     def confirm_unrotated_prototype_designation(
@@ -1757,7 +1813,9 @@ class AFLOW:
         species: List[str],
         prototype_label: str,
         parameter_values: List[float],
-        rtol: float = 0.01,
+        cell_rtol: float = 0.01,
+        rot_rtol: float = 0.01,
+        rot_atol: float = 0.01,
     ) -> bool:
         """
         Check whether the provided prototype designation recreates ``reference_atoms``
@@ -1779,8 +1837,18 @@ class AFLOW:
                 without specified atomic species
             parameter_values:
                 The free parameters of the AFLOW prototype designation
-            rtol:
+            cell_rtol:
                 Parameter to pass to :func:`numpy.allclose` for comparing cell params
+                Justification for default value: AFLOW uses 0.01*(minimum NN distance)
+                as default tolerance.
+            rot_rtol:
+                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)
+            rot_atol:
+                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)
 
         Returns:
             Whether or not the crystals match
@@ -1792,8 +1860,10 @@ class AFLOW:
         )
 
         return self.confirm_atoms_unrotated_when_cells_aligned(
-            test_atoms,
-            reference_atoms,
-            get_space_group_number_from_prototype(prototype_label),
-            rtol,
+            test_atoms=test_atoms,
+            ref_atoms=reference_atoms,
+            sgnum=get_space_group_number_from_prototype(prototype_label),
+            cell_rtol=cell_rtol,
+            rot_rtol=rot_rtol,
+            rot_atol=rot_atol,
         )

{kim_tools-0.2.2 → kim_tools-0.2.4}/kim_tools/symmetry_util/core.py

@@ -168,7 +168,11 @@ def fractional_to_cartesian_itc_rotation_from_ase_cell(
 
 
 def cartesian_rotation_is_in_point_group(
-    cart_rot: ArrayLike, sgnum: Union[int, str], cell: ArrayLike
+    cart_rot: ArrayLike,
+    sgnum: Union[int, str],
+    cell: ArrayLike,
+    rtol: float = 1e-2,
+    atol: float = 1e-2,
 ) -> bool:
     """
     Check that a Cartesian rotation is in the point group of a crystal given by its
@@ -184,6 +188,14 @@ def cartesian_rotation_is_in_point_group(
             http://doi.org/10.1016/j.commatsci.2017.01.017, with each row being a
             cartesian vector representing a lattice vector. This is
             consistent with most simulation packages, but transposed from the ITC
+        rtol:
+            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)
+        atol:
+            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)
     """
     # we don't care about properly transposing (i.e. worrying whether it's operating on
     # row or column vectors) the input cart_rot because that one is orthogonal, and
@@ -192,9 +204,11 @@ def cartesian_rotation_is_in_point_group(
 
     space_group_ops = get_primitive_genpos_ops(sgnum)
 
+    logger.info(f"Attempting to match fractional rotation:\n{frac_rot}")
+
     for op in space_group_ops:
-        if np.allclose(frac_rot, op["W"], atol=1e-4):
-            logger.info("Found matching rotation")
+        if np.allclose(frac_rot, op["W"], rtol=rtol, atol=atol):
+            logger.info(f"Found matching rotation with point group op:\n{op['W']}")
             return True
 
     logger.info("No matching rotation found")

{kim_tools-0.2.2 → kim_tools-0.2.4}/kim_tools/test_driver/core.py

@@ -65,6 +65,7 @@ from ..aflow_util import (
     get_space_group_number_from_prototype,
     prototype_labels_are_equivalent,
 )
+from ..aflow_util.core import AFLOW_EXECUTABLE
 from ..kimunits import convert_list, convert_units
 from ..symmetry_util import (
     cartesian_rotation_is_in_point_group,
@@ -730,6 +731,7 @@ def _add_common_crystal_genome_keys_to_current_property_instance(
     a_unit: str = "angstrom",
     cell_cauchy_stress_unit: str = "eV/angstrom^3",
     temperature_unit: str = "K",
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> str:
     """
     Write common Crystal Genome keys to the last element of ``property_instances``. See
@@ -741,6 +743,8 @@ def _add_common_crystal_genome_keys_to_current_property_instance(
         property_instances:
             An EDN-serialized list of dictionaries representing KIM Property Instances.
             The key will be added to the last dictionary in the list
+        aflow_executable:
+            Path to the AFLOW executable
 
     Returns:
         Updated EDN-serialized list of property instances
@@ -756,7 +760,7 @@ def _add_common_crystal_genome_keys_to_current_property_instance(
     )
 
     # get parameter names
-    aflow = AFLOW()
+    aflow = AFLOW(aflow_executable=aflow_executable)
     aflow_parameter_names = aflow.get_param_names_from_prototype(prototype_label)
     if parameter_values is None:
         if len(aflow_parameter_names) > 1:
@@ -833,6 +837,7 @@ def _add_property_instance_and_common_crystal_genome_keys(
     temperature_unit: str = "K",
     disclaimer: Optional[str] = None,
     property_instances: Optional[str] = None,
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> str:
     """
     Initialize a new property instance to ``property_instances`` (an empty
@@ -853,6 +858,8 @@ def _add_property_instance_and_common_crystal_genome_keys(
             "This relaxation did not reach the desired tolerance."
         property_instances:
             A pre-existing EDN-serialized list of KIM Property instances to add to
+        aflow_executable:
+            Path to the AFLOW executable
 
     Returns:
             Updated EDN-serialized list of property instances
@@ -861,24 +868,29 @@ def _add_property_instance_and_common_crystal_genome_keys(
         property_name, disclaimer, property_instances
     )
     return _add_common_crystal_genome_keys_to_current_property_instance(
-        property_instances,
-        prototype_label,
-        stoichiometric_species,
-        a,
-        parameter_values,
-        library_prototype_label,
-        short_name,
-        cell_cauchy_stress,
-        temperature,
-        crystal_genome_source_structure_id,
-        a_unit,
-        cell_cauchy_stress_unit,
-        temperature_unit,
+        property_instances=property_instances,
+        prototype_label=prototype_label,
+        stoichiometric_species=stoichiometric_species,
+        a=a,
+        parameter_values=parameter_values,
+        library_prototype_label=library_prototype_label,
+        short_name=short_name,
+        cell_cauchy_stress=cell_cauchy_stress,
+        temperature=temperature,
+        crystal_genome_source_structure_id=crystal_genome_source_structure_id,
+        a_unit=a_unit,
+        cell_cauchy_stress_unit=cell_cauchy_stress_unit,
+        temperature_unit=temperature_unit,
+        aflow_executable=aflow_executable,
     )
 
 
 def get_crystal_structure_from_atoms(
-    atoms: Atoms, get_short_name: bool = True, prim: bool = True, aflow_np: int = 4
+    atoms: Atoms,
+    get_short_name: bool = True,
+    prim: bool = True,
+    aflow_np: int = 4,
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> Dict:
     """
     By performing a symmetry analysis on an :class:`~ase.Atoms` object, generate a
@@ -896,6 +908,8 @@ def get_crystal_structure_from_atoms(
             whether to compare against AFLOW prototype library to obtain short-name
         prim: whether to primitivize the atoms object first
         aflow_np: Number of processors to use with AFLOW executable
+        aflow_executable:
+            Path to the AFLOW executable
 
     Returns:
         A dictionary that has the following Property Keys (possibly optionally) defined.
@@ -912,7 +926,7 @@ def get_crystal_structure_from_atoms(
         - "short-name"
 
     """
-    aflow = AFLOW(np=aflow_np)
+    aflow = AFLOW(aflow_executable=aflow_executable, np=aflow_np)
 
     proto_des = aflow.get_prototype_designation_from_atoms(atoms, prim=prim)
     library_prototype_label, short_name = (
@@ -936,13 +950,17 @@ def get_crystal_structure_from_atoms(
         parameter_values=parameter_values,
         library_prototype_label=library_prototype_label,
         short_name=short_name,
+        aflow_executable=aflow_executable,
     )
 
     return kim_edn.loads(property_instances)[0]
 
 
 def get_poscar_from_crystal_structure(
-    crystal_structure: Dict, output_file: Optional[str] = None, flat: bool = False
+    crystal_structure: Dict,
+    output_file: Optional[str] = None,
+    flat: bool = False,
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> Optional[str]:
     """
     Write a POSCAR coordinate file (or output it as a multiline string) from the AFLOW
@@ -968,6 +986,8 @@ def get_poscar_from_crystal_structure(
             Name of the output file. If not provided, the output is returned as a string
         flat:
             whether the input dictionary is flattened
+        aflow_executable:
+            path to AFLOW executable
     Returns:
         If ``output_file`` is not provided, a string in POSCAR format containg the
         primitive unit cell of the crystal as defined in
@@ -993,7 +1013,7 @@ def get_poscar_from_crystal_structure(
             "source-value"
         ]
 
-    aflow = AFLOW()
+    aflow = AFLOW(aflow_executable=aflow_executable)
     aflow_parameter_names = aflow.get_param_names_from_prototype(prototype_label)
 
     # Atoms objects are always in angstrom
@@ -1035,7 +1055,9 @@ def get_poscar_from_crystal_structure(
 
 
 def get_atoms_from_crystal_structure(
-    crystal_structure: Dict, flat: bool = False
+    crystal_structure: Dict,
+    flat: bool = False,
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> Atoms:
     """
     Generate an :class:`~ase.Atoms` object from the AFLOW Prototype Designation obtained
@@ -1059,6 +1081,8 @@ def get_atoms_from_crystal_structure(
             Dictionary containing the required keys in KIM Property Instance format
         flat:
             whether the dictionary is flattened
+        aflow_executable:
+            path to AFLOW executable
 
     Returns:
         Primitive unit cell of the crystal as defined in the
@@ -1070,7 +1094,9 @@ def get_atoms_from_crystal_structure(
             if the symmetry of the atoms object is different from ``prototype_label``
     """
     try:
-        poscar_string = get_poscar_from_crystal_structure(crystal_structure, flat=flat)
+        poscar_string = get_poscar_from_crystal_structure(
+            crystal_structure, flat=flat, aflow_executable=aflow_executable
+        )
     except AFLOW.ChangedSymmetryException as e:
         # re-raise, just indicating that this function knows about this exception
         raise e
@@ -1094,8 +1120,23 @@ class SingleCrystalTestDriver(KIMTestDriver):
             <https://openkim.org/properties/show/crystal-structure-npt>`_
             property representing the nominal crystal structure and conditions of the
             current call to the Test Driver.
+        aflow_executable [str]:
+            Path to the AFLOW executable
     """
 
+    def __init__(
+        self, model: Union[str, Calculator], aflow_executable: str = AFLOW_EXECUTABLE
+    ) -> None:
+        """
+        Args:
+            model:
+                ASE calculator or KIM model name to use
+            aflow_executable:
+                Path to AFLOW executable
+        """
+        self.aflow_executable = aflow_executable
+        super().__init__(model)
+
     def _setup(
         self,
         material: Union[Atoms, Dict],
@@ -1156,11 +1197,14 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 simply provides recordkeeping of it. It is up to derived classes to
                 implement actually setting the temperature of the system.
         """
+
         if cell_cauchy_stress_eV_angstrom3 is None:
             cell_cauchy_stress_eV_angstrom3 = [0, 0, 0, 0, 0, 0]
 
         if isinstance(material, Atoms):
-            crystal_structure = get_crystal_structure_from_atoms(material)
+            crystal_structure = get_crystal_structure_from_atoms(
+                atoms=material, aflow_executable=self.aflow_executable
+            )
             msg = (
                 "Rebuilding atoms object in a standard setting defined by "
                 "doi.org/10.1016/j.commatsci.2017.01.017. See log file or computed "
@@ -1219,7 +1263,12 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 logger.info(msg)
 
     def _update_nominal_parameter_values(
-        self, atoms: Atoms, max_resid: float = 1e-5, cell_rtol: float = 0.01
+        self,
+        atoms: Atoms,
+        max_resid: Optional[float] = None,
+        cell_rtol: float = 0.01,
+        rot_rtol: float = 0.01,
+        rot_atol: float = 0.01,
     ) -> None:
         """
         Update the nominal parameter values of the nominal crystal structure from the
@@ -1250,9 +1299,20 @@ class SingleCrystalTestDriver(KIMTestDriver):
             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
+                positions of the atoms to the crystallographic equations.
+                If not provided, this is automatically set to 0.01*(minimum NN distance)
             cell_rtol:
-                Relative tolerance on cell lengths and angles
+                Relative tolerance on cell lengths and angles.
+                Justification for default value: AFLOW uses 0.01*(minimum NN distance)
+                as default tolerance.
+            rot_rtol:
+                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)
+            rot_atol:
+                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)
 
         Raises:
             AFLOW.FailedToMatchException:
@@ -1263,15 +1323,17 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 If a more definitive error indicating a phase transformation is
                 encountered
         """
-
+        aflow = AFLOW(aflow_executable=self.aflow_executable)
         try:
-            aflow_parameter_values = AFLOW().solve_for_params_of_known_prototype(
+            aflow_parameter_values = aflow.solve_for_params_of_known_prototype(
                 atoms=atoms,
                 prototype_label=self.__nominal_crystal_structure_npt["prototype-label"][
                     "source-value"
                 ],
                 max_resid=max_resid,
                 cell_rtol=cell_rtol,
+                rot_rtol=rot_rtol,
+                rot_atol=rot_atol,
             )
         except (AFLOW.FailedToMatchException, AFLOW.ChangedSymmetryException) as e:
             raise type(e)(
@@ -1306,10 +1368,9 @@ class SingleCrystalTestDriver(KIMTestDriver):
             Whether or not the symmetry is unchanged
 
         """
+        aflow = AFLOW(aflow_executable=self.aflow_executable)
         return prototype_labels_are_equivalent(
-            AFLOW().get_prototype_designation_from_atoms(atoms)[
-                "aflow_prototype_label"
-            ],
+            aflow.get_prototype_designation_from_atoms(atoms)["aflow_prototype_label"],
             self.__nominal_crystal_structure_npt["prototype-label"]["source-value"],
         )
 
@@ -1425,6 +1486,7 @@ class SingleCrystalTestDriver(KIMTestDriver):
                 temperature_unit=temperature_unit,
                 disclaimer=disclaimer,
                 property_instances=super()._get_serialized_property_instances(),
+                aflow_executable=self.aflow_executable,
             )
         )
 
@@ -1516,7 +1578,10 @@ class SingleCrystalTestDriver(KIMTestDriver):
     def deduplicate_property_instances(
         self,
         properties_to_deduplicate: Optional[List[str]] = None,
-        allow_rotation: bool = True,
+        allow_rotation: bool = False,
+        aflow_np: int = 4,
+        rot_rtol: float = 0.01,
+        rot_atol: float = 0.01,
     ) -> None:
         """
         In the internally stored property instances,
@@ -1537,9 +1602,27 @@ class SingleCrystalTestDriver(KIMTestDriver):
             allow_rotation:
                 Whether or not structures that are rotated by a rotation that is not in
                 the crystal's point group are considered identical
+            aflow_np:
+                Number of processors to use to run the AFLOW executable
+            rot_rtol:
+                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). Used only if
+                `allow_rotation` is False
+            rot_atol:
+                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). Used only if
+                `allow_rotation` is False
         """
         deduplicated_property_instances = get_deduplicated_property_instances(
-            self.property_instances, properties_to_deduplicate, allow_rotation
+            property_instances=self.property_instances,
+            properties_to_deduplicate=properties_to_deduplicate,
+            allow_rotation=allow_rotation,
+            aflow_np=aflow_np,
+            rot_rtol=rot_rtol,
+            rot_atol=rot_atol,
+            aflow_executable=self.aflow_executable,
         )
         logger.info(
             f"Deduplicated {len(self.property_instances)} Property Instances "
@@ -1609,7 +1692,9 @@ class SingleCrystalTestDriver(KIMTestDriver):
             Lengths are always in angstrom
         """
         crystal_structure = self.__nominal_crystal_structure_npt
-        atoms_prim = get_atoms_from_crystal_structure(crystal_structure)
+        atoms_prim = get_atoms_from_crystal_structure(
+            crystal_structure, aflow_executable=self.aflow_executable
+        )
         if isinstance(change_of_basis, str):
             if change_of_basis.lower() == "primitive":
                 change_of_basis_matrix = None
@@ -1743,8 +1828,11 @@ def query_crystal_structures(
 
 def detect_unique_crystal_structures(
     crystal_structures: Union[List[Dict], Dict],
-    allow_rotation: bool = True,
+    allow_rotation: bool = False,
     aflow_np: int = 4,
+    rot_rtol: float = 0.01,
+    rot_atol: float = 0.01,
+    aflow_executable=AFLOW_EXECUTABLE,
 ) -> Dict:
     """
     Detect which of the provided crystal structures is unique
@@ -1761,6 +1849,20 @@ def detect_unique_crystal_structures(
         allow_rotation:
             Whether or not structures that are rotated by a rotation that is not in the
             crystal's point group are considered identical
+        aflow_np:
+            Number of processors to use to run the AFLOW executable
+        rot_rtol:
+            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). Used only if
+            `allow_rotation` is False
+        rot_atol:
+            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). Used only if
+            `allow_rotation` is False
+        aflow_executable:
+            Path to AFLOW executable
     Returns:
         Dictionary with keys corresponding to indices of unique structures and values
         being lists of indices of their duplicates
@@ -1768,7 +1870,7 @@ def detect_unique_crystal_structures(
     if len(crystal_structures) == 0:
         return []
 
-    aflow = AFLOW(np=aflow_np)
+    aflow = AFLOW(aflow_executable=aflow_executable, np=aflow_np)
 
     with TemporaryDirectory() as tmpdirname:
         # I don't know if crystal_structurs is a list or a dict with integer keys
@@ -1780,7 +1882,9 @@ def detect_unique_crystal_structures(
             structure = crystal_structures[i]
             try:
                 get_poscar_from_crystal_structure(
-                    structure, os.path.join(tmpdirname, str(i))
+                    structure,
+                    os.path.join(tmpdirname, str(i)),
+                    aflow_executable=aflow_executable,
                 )
             except AFLOW.ChangedSymmetryException:
                 logger.info(
@@ -1813,7 +1917,13 @@ def detect_unique_crystal_structures(
                     "structures_duplicate"
                 ]:
                     cart_rot = potential_rotated_duplicate["rotation"]
-                    if not cartesian_rotation_is_in_point_group(cart_rot, sgnum, cell):
+                    if not cartesian_rotation_is_in_point_group(
+                        cart_rot=cart_rot,
+                        sgnum=sgnum,
+                        cell=cell,
+                        rtol=rot_rtol,
+                        atol=rot_atol,
+                    ):
                         i_rot_dup = int(
                             potential_rotated_duplicate["name"].split("/")[-1]
                         )
@@ -1825,7 +1935,12 @@ def detect_unique_crystal_structures(
 
                 unique_materials.update(
                     detect_unique_crystal_structures(
-                        rotated_structures, False, aflow_np
+                        crystal_structures=rotated_structures,
+                        allow_rotation=False,
+                        aflow_np=aflow_np,
+                        rot_rtol=rot_rtol,
+                        rot_atol=rot_atol,
+                        aflow_executable=aflow_executable,
                     )
                 )
 
@@ -1835,7 +1950,11 @@ def detect_unique_crystal_structures(
 def get_deduplicated_property_instances(
     property_instances: List[Dict],
     properties_to_deduplicate: Optional[List[str]] = None,
-    allow_rotation: bool = True,
+    allow_rotation: bool = False,
+    aflow_np: int = 4,
+    rot_rtol: float = 0.01,
+    rot_atol: float = 0.01,
+    aflow_executable: str = AFLOW_EXECUTABLE,
 ) -> List[Dict]:
     """
     Given a list of dictionaries constituting KIM Property instances,
@@ -1858,6 +1977,20 @@ def get_deduplicated_property_instances(
         allow_rotation:
             Whether or not structures that are rotated by a rotation that is not in the
             crystal's point group are considered identical
+        aflow_np:
+            Number of processors to use to run the AFLOW executable
+        rot_rtol:
+            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). Used only if
+            `allow_rotation` is False
+        rot_atol:
+            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). Used only if
+            `allow_rotation` is False
+        aflow_executable:
+            Path to aflow executable
 
     Returns:
         The deduplicated property instances
@@ -1887,7 +2020,12 @@ def get_deduplicated_property_instances(
 
         # Get unique-duplicate dictionary
         unique_crystal_structures = detect_unique_crystal_structures(
-            property_instances_curr_name, allow_rotation
+            crystal_structures=property_instances_curr_name,
+            allow_rotation=allow_rotation,
+            aflow_np=aflow_np,
+            rot_rtol=rot_rtol,
+            rot_atol=rot_atol,
+            aflow_executable=aflow_executable,
         )
 
         # Put together the list of unique instances for the current

{kim_tools-0.2.2 → kim_tools-0.2.4/kim_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.2.2
+Version: 0.2.4
 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-0.2.2 → kim_tools-0.2.4}/tests/test_symmetry_util.py

@@ -19,7 +19,9 @@ def test_change_of_basis_atoms(
 ):
     calc = KIM("LJ_ElliottAkerson_2015_Universal__MO_959249795837_003")
     atoms_conventional.calc = calc
-    crystal_structure = get_crystal_structure_from_atoms(atoms_conventional)
+    crystal_structure = get_crystal_structure_from_atoms(
+        atoms_conventional, get_short_name=False
+    )
     prototype_label = crystal_structure["prototype-label"]["source-value"]
     sgnum = get_space_group_number_from_prototype(prototype_label)
     formal_bravais_lattice = get_formal_bravais_lattice_from_space_group(sgnum)