kim-tools 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.4"
+__version__ = "0.3.6"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -392,6 +392,30 @@ def get_wyckoff_lists_from_prototype(prototype_label: str) -> List[str]:
     return expanded_wyckoff_letters
 
 
+def get_atom_indices_for_each_wyckoff_orb(prototype_label: str) -> List[Dict]:
+    """
+    Get a list of dictionaries containing the atom indices of each Wyckoff
+    orbit.
+
+    Returns:
+        The information is in this format:
+
+        [{"letter":"a", "indices":[0,1]}, ... ]
+    """
+    return_list = []
+    wyck_lists = get_wyckoff_lists_from_prototype(prototype_label)
+    sgnum = get_space_group_number_from_prototype(prototype_label)
+    range_start = 0
+    for letter in "".join(wyck_lists):
+        multiplicity = get_primitive_wyckoff_multiplicity(sgnum, letter)
+        range_end = range_start + multiplicity
+        return_list.append(
+            {"letter": letter, "indices": list(range(range_start, range_end))}
+        )
+        range_start = range_end
+    return return_list
+
+
 def prototype_labels_are_equivalent(
     prototype_label_1: str,
     prototype_label_2: str,
@@ -841,9 +865,8 @@ class AFLOW:
                 "that the AFLOW executable was not found."
             )
         # I am fine with allowing prereleases
-        aflow_ver_no_prerelease = Version.parse(ver_str)
-        aflow_ver_no_prerelease.replace(prerelease=None)
-        if aflow_ver_no_prerelease < Version.parse(REQUIRED_AFLOW):
+        aflow_ver = Version.parse(ver_str)
+        if aflow_ver.replace(prerelease=None) < Version.parse(REQUIRED_AFLOW):
             raise self.AFLOWNotFoundException(
                 f"Your AFLOW version {ver_str} is less "
                 f"than the required {REQUIRED_AFLOW}"

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.
 
@@ -238,10 +238,13 @@ def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol):
         )
     single_atom.calc = calc
     energy_per_atom = single_atom.get_potential_energy()
-    if hasattr(calc, "clean"):
-        calc.clean()
-    if hasattr(calc, "__del__"):
-        calc.__del__()
+    # 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
 

kim_tools/symmetry_util/core.py

@@ -14,6 +14,7 @@ import numpy as np
 import numpy.typing as npt
 from ase import Atoms
 from ase.cell import Cell
+from ase.constraints import FixSymmetry
 from ase.geometry import get_distances, get_duplicate_atoms
 from matplotlib.backends.backend_pdf import PdfPages
 from pymatgen.core.operations import SymmOp
@@ -617,6 +618,20 @@ def get_primitive_genpos_ops(sgnum: Union[int, str]) -> List[Dict]:
         return np.asarray(json.load(f)[str(sgnum)])
 
 
+def transform_atoms(atoms: Atoms, op: Dict) -> Atoms:
+    """
+    Transform atoms by an operation defined by a dictionary containing a matrix 'W' and
+    translation 'w' defined as fractional operations in the unit cell. 'W' should be
+    oriented to operate on column vectors
+    """
+    frac_pos_columns = atoms.get_scaled_positions().T
+    frac_pos_cols_xform = op["W"] @ frac_pos_columns + np.reshape(op["w"], (3, 1))
+    atoms_transformed = atoms.copy()
+    atoms_transformed.set_scaled_positions(frac_pos_cols_xform.T)
+    atoms_transformed.wrap()
+    return atoms_transformed
+
+
 def reduce_and_avg(
     atoms: Atoms, repeat: Tuple[int, int, int]
 ) -> Tuple[Atoms, npt.ArrayLike]:
@@ -832,3 +847,78 @@ def fit_voigt_tensor_to_cell_and_space_group(
     t_symmetrized = sum(t_rotated_list) / len(t_rotated_list)
 
     return t_symmetrized.voigt
+
+
+class FixProvidedSymmetry(FixSymmetry):
+    """
+    A modification of :obj:`~ase.constraints.FixSymmetry` that takes
+    a prescribed symmetry instead of analyzing the atoms object on the fly
+    """
+
+    def __init__(
+        self,
+        atoms: Atoms,
+        symmetry: Union[str, int, List[Dict]],
+        adjust_positions=True,
+        adjust_cell=True,
+    ):
+        """
+        Args:
+            symmetry:
+                Either the space group number, or a list of operations
+                as dictionaries with keys "W": (fractional rotation matrix),
+                "w": (fractional translation). The space group number input
+                will not work correctly unless this contraint is applied to
+                a primitive unit cell as defined in
+                http://doi.org/10.1016/j.commatsci.2017.01.017
+        """
+        self.atoms = atoms.copy()
+        self.symmetry = symmetry
+
+        if isinstance(symmetry, str) or isinstance(symmetry, int):
+            primitive_genpos_ops = get_primitive_genpos_ops(symmetry)
+        else:
+            try:
+                for op in symmetry:
+                    assert np.asarray(op["W"]).shape == (3, 3)
+                    assert np.asarray(op["w"]).shape == (3,)
+                primitive_genpos_ops = symmetry
+            except Exception:
+                raise RuntimeError("Incorrect input provided to FixProvidedSymmetry")
+
+        self.rotations = []
+        self.translations = []
+        for op in primitive_genpos_ops:
+            self.rotations.append(np.asarray(op["W"]))
+            self.translations.append(np.asarray(op["w"]))
+        self.prep_symm_map()
+
+        self.do_adjust_positions = adjust_positions
+        self.do_adjust_cell = adjust_cell
+
+    def prep_symm_map(self) -> None:
+        """
+        Prepare self.symm_map using provided symmetries
+        """
+        self.symm_map = []
+        scaled_pos = self.atoms.get_scaled_positions()
+        for rot, trans in zip(self.rotations, self.translations):
+            this_op_map = [-1] * len(self.atoms)
+            for i_at in range(len(self.atoms)):
+                new_p = rot @ scaled_pos[i_at, :] + trans
+                dp = scaled_pos - new_p
+                dp -= np.round(dp)
+                i_at_map = np.argmin(np.linalg.norm(dp, axis=1))
+                this_op_map[i_at] = i_at_map
+            self.symm_map.append(this_op_map)
+
+    def todict(self):
+        return {
+            "name": "FixProvidedSymmetry",
+            "kwargs": {
+                "atoms": self.atoms,
+                "symmetry": self.symmetry,
+                "adjust_positions": self.do_adjust_positions,
+                "adjust_cell": self.do_adjust_cell,
+            },
+        }

kim_tools/test_driver/core.py

@@ -65,7 +65,8 @@ from ..aflow_util import (
     get_space_group_number_from_prototype,
     prototype_labels_are_equivalent,
 )
-from ..aflow_util.core import AFLOW_EXECUTABLE
+from ..aflow_util.core import AFLOW_EXECUTABLE, get_atom_indices_for_each_wyckoff_orb
+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,
@@ -138,7 +139,7 @@ def minimize_wrapper(
     logfile: Optional[Union[str, IO]] = "kim-tools.log",
     algorithm: Optimizer = LBFGSLineSearch,
     cell_filter: UnitCellFilter = FrechetCellFilter,
-    fix_symmetry: bool = False,
+    fix_symmetry: Union[bool, FixSymmetry] = False,
     opt_kwargs: Dict = {},
     flt_kwargs: Dict = {},
 ) -> bool:
@@ -178,7 +179,8 @@ def minimize_wrapper(
         CellFilter:
             Filter to use if variable_cell is requested
         fix_symmetry:
-            Whether to fix the crystallographic symmetry
+            Whether to fix the crystallographic symmetry. Can provide
+            a FixSymmetry class here instead of detecting it on the fly
         opt_kwargs:
             Dictionary of kwargs to pass to optimizer
         flt_kwargs:
@@ -187,8 +189,11 @@ def minimize_wrapper(
     Returns:
         Whether the minimization succeeded
     """
-    if fix_symmetry:
-        symmetry = FixSymmetry(atoms)
+    if fix_symmetry is not False:
+        if fix_symmetry is True:
+            symmetry = FixSymmetry(atoms)
+        else:
+            symmetry = fix_symmetry
         atoms.set_constraint(symmetry)
     if variable_cell:
         supercell_wrapped = cell_filter(atoms, **flt_kwargs)
@@ -224,11 +229,18 @@ def minimize_wrapper(
     del atoms.constraints
 
     if minimization_stalled or iteration_limits_reached:
-        logger.info("Final forces:")
-        logger.info(atoms.get_forces())
-        logger.info("Final stress:")
-        logger.info(atoms.get_stress())
-        return False
+        try:
+            logger.info("Final forces:")
+            logger.info(atoms.get_forces())
+            logger.info("Final stress:")
+            logger.info(atoms.get_stress())
+        except Exception as e:
+            logger.info(
+                "The following exception was caught "
+                "trying to evaluate final forces and stress:"
+            )
+            logger.info(repr(e))
+            return False
     else:
         return True
 
@@ -746,6 +758,23 @@ 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,
@@ -1289,7 +1318,7 @@ class SingleCrystalTestDriver(KIMTestDriver):
             )
             print(f"\nNOTE: {msg}\n")
             logger.info(msg)
-        if cell_cauchy_stress_eV_angstrom3 != [0, 0, 0, 0, 0, 0]:
+        if cell_cauchy_stress_eV_angstrom3 == [0, 0, 0, 0, 0, 0]:
             stress_max = np.max(atoms_tmp.get_stress())
             if stress_max > FMAX_INITIAL:
                 msg = (
@@ -1838,6 +1867,23 @@ class SingleCrystalTestDriver(KIMTestDriver):
         atoms_tmp.calc = self._calc
         return atoms_tmp
 
+    def get_nominal_prototype_label(self) -> str:
+        return self._get_nominal_crystal_structure_npt()["prototype-label"][
+            "source-value"
+        ]
+
+    def get_atom_indices_for_each_wyckoff_orb(self) -> List[Dict]:
+        """
+        Get a list of dictionaries containing the atom indices of each Wyckoff
+        orbit.
+
+        Returns:
+            The information is in this format:
+
+            [{"letter":"a", "indices":[0,1]}, ... ]
+        """
+        return get_atom_indices_for_each_wyckoff_orb(self.get_nominal_prototype_label())
+
 
 def query_crystal_structures(
     stoichiometric_species: List[str],
@@ -1937,7 +1983,7 @@ def query_crystal_structures(
     logger.info(len_msg)
     logger.debug(f"Query result (length={len(query_result)}):\n{query_result}")
 
-    print(f"!!! {len_msg} !!!")
+    print(f"\n!!! {len_msg} !!!\n")
 
     return query_result
 
@@ -2190,8 +2236,3 @@ def get_deduplicated_property_instances(
     property_instances_deduplicated.sort(key=lambda a: a["instance-id"])
 
     return property_instances_deduplicated
-
-
-# If called directly, do nothing
-if __name__ == "__main__":
-    pass

{kim_tools-0.3.4.dist-info → kim_tools-0.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.4
+Version: 0.3.6
 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-0.3.4.dist-info → kim_tools-0.3.6.dist-info}/RECORD

@@ -1,7 +1,7 @@
-kim_tools/__init__.py,sha256=CIQpbBUyJLgWZum2kUjz-jAOWw54_hO5_hHgtBV2DEM,433
+kim_tools/__init__.py,sha256=kYbIfF9bmWajsk_oLkaGok3kpnHeo1rlLBUAranse8o,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
+kim_tools/aflow_util/core.py,sha256=YH1KCMQjXiKMqhT1TAuoafpsGqPlybsykRRMaa8wWqc,78219
 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
@@ -2002,9 +2002,9 @@ 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=ByiwAUBZzbhbXyfdnea5XTIbK6LSOUMCOy20_AFgbAQ,30991
+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/core.py,sha256=aDaeYmtwfkNlNDcYQ3mAkez7e9_Lk84xQxwQ24cir38,34231
 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
@@ -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=Q388GSKFVvwNIMElt4dHmLd_rJOxQeUG0QIbXmrhYHc,89763
+kim_tools/test_driver/core.py,sha256=DseMkfdb-b116rRQQR0N7HKhsMsZGq8ZxtKoCBlw8X8,91307
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.3.4.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.4.dist-info/METADATA,sha256=SHsn9LcUrsa7Yg8huy7EfOTJ1MT7c0t4z0EMGvzP9YY,2032
-kim_tools-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.4.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.4.dist-info/RECORD,,
+kim_tools-0.3.6.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.6.dist-info/METADATA,sha256=Q_aemQPU34z7rSPK04WnMP6WzUnS845Frlr3YWofcjw,2032
+kim_tools-0.3.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.6.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.6.dist-info/RECORD,,