kim-tools 0.3.0__py3-none-any.whl → 0.3.2__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.0"
+__version__ = "0.3.2"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -6,6 +6,7 @@ import os
 import subprocess
 from curses.ascii import isalpha, isdigit
 from dataclasses import dataclass
+from itertools import permutations
 from math import acos, cos, degrees, radians, sqrt
 from os import PathLike
 from tempfile import NamedTemporaryFile
@@ -343,6 +344,30 @@ def get_stoich_reduced_list_from_prototype(prototype_label: str) -> List[int]:
     return stoich_reduced_list
 
 
+def build_abstract_formula_from_stoich_reduced_list(
+    stoich_reduced_list: List[int],
+) -> str:
+    """
+    Get abstract chemical formula from numerical list of stoichiometry
+    i.e. [1,3] -> "AB3"
+
+    Args:
+        stoich_reduced_list:
+            List of reduced stoichiometric numbers
+
+    Returns:
+        Abstract chemical formula
+    """
+    formula = ""
+    for spec_num, stoich_num in enumerate(stoich_reduced_list):
+        assert isinstance(stoich_num, int)
+        assert stoich_num > 0
+        formula += chr(65 + spec_num)
+        if stoich_num > 1:
+            formula += str(stoich_num)
+    return formula
+
+
 def get_wyckoff_lists_from_prototype(prototype_label: str) -> List[str]:
     """
     Expand the list of Wyckoff letters in the prototype to account for each individual
@@ -350,7 +375,7 @@ def get_wyckoff_lists_from_prototype(prototype_label: str) -> List[str]:
     e.g. A2B3C_mC48_15_aef_3f_2e -> ['aef','fff','ee']
     """
     expanded_wyckoff_letters = []
-    prototype_label_split = prototype_label.split("_")
+    prototype_label_split = prototype_label.split("-")[0].split("_")
     for species_wyckoff_string in prototype_label_split[3:]:
         expanded_wyckoff_letters.append("")
         curr_wyckoff_count = 0
@@ -371,14 +396,17 @@ def prototype_labels_are_equivalent(
     prototype_label_1: str,
     prototype_label_2: str,
     allow_enantiomorph: bool = False,
-    allow_species_permutation: bool = False,
+    log: bool = True,
 ) -> bool:
     """
-    Checks if two prototype labels are equivalent
+    Checks if two prototype labels are equivalent (species permutations not allowed)
+
+    Args:
+        allow_enantiomorph:
+            Whether to consider enantiomorphic pairs of space groups to be equivalent
+        log:
+            Whether to log results
     """
-    if allow_species_permutation:
-        # TODO: Possibly add this (for checking library prototype labels)
-        raise NotImplementedError("Species permutations not implemented")
 
     if prototype_label_1 == prototype_label_2:
         return True
@@ -389,20 +417,22 @@ def prototype_labels_are_equivalent(
     if not stoich_reduced_list_1 == get_stoich_reduced_list_from_prototype(
         prototype_label_2
     ):
-        logger.info(
-            "Found non-matching stoichiometry in labels "
-            f"{prototype_label_1} and {prototype_label_2}"
-        )
+        if log:
+            logger.info(
+                "Found non-matching stoichiometry in labels "
+                f"{prototype_label_1} and {prototype_label_2}"
+            )
         return False
 
     # Check Pearson symbol
     if not get_pearson_symbol_from_prototype(
         prototype_label_1
     ) == get_pearson_symbol_from_prototype(prototype_label_2):
-        logger.info(
-            "Found non-matching Pearson symbol in labels "
-            f"{prototype_label_1} and {prototype_label_2}"
-        )
+        if log:
+            logger.info(
+                "Found non-matching Pearson symbol in labels "
+                f"{prototype_label_1} and {prototype_label_2}"
+            )
         return False
 
     # Check space group number
@@ -411,16 +441,18 @@ def prototype_labels_are_equivalent(
     if allow_enantiomorph and not space_group_numbers_are_enantiomorphic(
         sg_num_2, sg_num_1
     ):
-        logger.info(
-            "Found non-matching Space group in labels "
-            f"{prototype_label_1} and {prototype_label_2}"
-        )
+        if log:
+            logger.info(
+                "Found non-matching Space group in labels "
+                f"{prototype_label_1} and {prototype_label_2}"
+            )
         return False
     elif sg_num_2 != sg_num_1:
-        logger.info(
-            "Found non-matching Space group in labels "
-            f"{prototype_label_1} and {prototype_label_2}"
-        )
+        if log:
+            logger.info(
+                "Found non-matching Space group in labels "
+                f"{prototype_label_1} and {prototype_label_2}"
+            )
         return False
 
     # OK, so far everything matches, now check the Wyckoff letters
@@ -462,16 +494,18 @@ def prototype_labels_are_equivalent(
                     wyckoff_lists_match_for_each_species = False
                     break
             if wyckoff_lists_match_for_each_species:
-                logger.warning(
-                    f"Labels {prototype_label_1} and {prototype_label_2} were found to "
-                    "be equivalent despite being non-identical. "
-                    "This indicates a failure to find the lowest Wyckoff enumeration."
-                )
+                if log:
+                    logger.warning(
+                        f"Labels {prototype_label_1} and {prototype_label_2} were found"
+                        " to be equivalent despite being non-identical. This indicates "
+                        "a failure to find the lowest Wyckoff enumeration."
+                    )
                 return True
-        logger.info(
-            f"Labels {prototype_label_1} and {prototype_label_2} were not found to be "
-            "equivalent under any permutations allowable by the normalizer."
-        )
+        if log:
+            logger.info(
+                f"Labels {prototype_label_1} and {prototype_label_2} were not found to "
+                "be equivalent under any permutations allowable by the normalizer."
+            )
         return False
     else:
         for wyckoff_list_1, wyckoff_list_2 in zip(wyckoff_lists_1, wyckoff_lists_2):
@@ -480,20 +514,77 @@ def prototype_labels_are_equivalent(
                 # need to re-sort anything.
                 # This is NOT true for all SGs (e.g. #200, Wyckoff set eh )
                 if not are_in_same_wyckoff_set(letter_1, letter_2, sg_num_1):
-                    logger.info(
-                        f"Labels {prototype_label_1} and {prototype_label_2} have "
-                        f"corresponding letters {letter_1} and {letter_2} that are not "
-                        "in the same Wyckoff set"
-                    )
+                    if log:
+                        logger.info(
+                            f"Labels {prototype_label_1} and {prototype_label_2} have "
+                            f"corresponding letters {letter_1} and {letter_2} that are "
+                            "not in the same Wyckoff set"
+                        )
                     return False
-        logger.info(
-            f"Labels {prototype_label_1} and {prototype_label_2} were found to be "
-            "equivalent despite being non-identical. This is a normal occurrence for "
-            "triclinic and monoclinic space groups such as this."
-        )
+        if log:
+            logger.info(
+                f"Labels {prototype_label_1} and {prototype_label_2} were found to be "
+                "equivalent despite being non-identical. This is a normal occurrence "
+                "for triclinic and monoclinic space groups such as this."
+            )
         return True
 
 
+def find_species_permutation_between_prototype_labels(
+    prototype_label_1: str,
+    prototype_label_2: str,
+    allow_enantiomorph: bool = False,
+    log: bool = True,
+) -> Optional[Tuple[int]]:
+    """
+    Find the permutation of species required to match two prototype labels
+
+    Args:
+        allow_enantiomorph:
+            Whether to consider enantiomorphic pairs of space groups to be equivalent
+        log:
+            Whether to log results
+
+    Returns:
+        The permutation of species of ``prototype_label_1`` required to match
+        ``prototype_label_2``, or None if no match is found
+    """
+    # Disassemble prototype_label_1
+    stoich_reduced_list_1 = get_stoich_reduced_list_from_prototype(prototype_label_1)
+    pearson_1 = get_pearson_symbol_from_prototype(prototype_label_1)
+    space_group_1 = str(get_space_group_number_from_prototype(prototype_label_1))
+    species_wyckoff_sections_1 = prototype_label_1.split("-")[0].split("_")[3:]
+
+    nspecies = len(stoich_reduced_list_1)
+    assert nspecies == len(species_wyckoff_sections_1)
+
+    permutation_candidates = permutations(tuple(range(nspecies)))
+    for permutation in permutation_candidates:
+        # Permute the species
+        stoich_reduced_list_1_permuted = [stoich_reduced_list_1[i] for i in permutation]
+        species_wyckoff_sections_1_permuted = [
+            species_wyckoff_sections_1[i] for i in permutation
+        ]
+
+        # Reassemble prototype_label_1_permuted
+        abstract_formula_1_permuted = build_abstract_formula_from_stoich_reduced_list(
+            stoich_reduced_list_1_permuted
+        )
+        prototype_label_1_permuted_list = [
+            abstract_formula_1_permuted,
+            pearson_1,
+            space_group_1,
+        ] + species_wyckoff_sections_1_permuted
+        prototype_label_1_permuted = "_".join(prototype_label_1_permuted_list)
+        if prototype_labels_are_equivalent(
+            prototype_label_1=prototype_label_1_permuted,
+            prototype_label_2=prototype_label_2,
+            allow_enantiomorph=allow_enantiomorph,
+        ):
+            return permutation
+    return None
+
+
 def get_space_group_number_from_prototype(prototype_label: str) -> int:
     return int(prototype_label.split("_")[2])
 

kim_tools/symmetry_util/core.py

@@ -289,8 +289,11 @@ def space_group_numbers_are_enantiomorphic(sg_1: int, sg_2: int) -> bool:
         }
         enantiomorph_conversion_2 = {v: k for k, v in enantiomorph_conversion.items()}
         enantiomorph_conversion.update(enantiomorph_conversion_2)
-        if enantiomorph_conversion[sg_1] == sg_2:
-            return True
+        if sg_1 in enantiomorph_conversion:
+            if enantiomorph_conversion[sg_1] == sg_2:
+                return True
+            else:
+                return False
         else:
             return False
 

{kim_tools-0.3.0.dist-info → kim_tools-0.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.0
+Version: 0.3.2
 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>, Philipp Hoellmer <ph2484@nyu.edu>, Guanming Zhang <gz2241@nyu.edu>, Tom Egg <tje3676@nyu.edu>
 Maintainer-email: ilia Nikiforov <nikif002@umn.edu>

{kim_tools-0.3.0.dist-info → kim_tools-0.3.2.dist-info}/RECORD

@@ -1,7 +1,7 @@
-kim_tools/__init__.py,sha256=1_-Nx2m2jdCABSg3wVEK_v139McyduMthh8VNWZSsd0,433
+kim_tools/__init__.py,sha256=AhAW6unNWB_4jaiwxb0_XxUKtCv1rwG3CNqLk4aqqso,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=1Rv9LSoOgr_9-XFSK4UnHZ2XXQF0MUreMrRh7WWDTQw,72854
+kim_tools/aflow_util/core.py,sha256=CsqN6MNVXE4QFrM0SxWhahTwu_gTeUXITk7ZMXLXfv0,75954
 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
@@ -2004,7 +2004,7 @@ kim_tools/aflow_util/aflow_prototype_encyclopedia/data/A_tP50_134_a2m2n-001/info
 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=RVvKisrNxHKq36ceIorc06cnX3la3WoWNPVV0hKnptM,30789
+kim_tools/symmetry_util/core.py,sha256=HfDy1CwNWUZIkb4cs3ebUDgWjtt4jRSkBKgGEnlkjuI,30888
 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
@@ -2015,8 +2015,8 @@ kim_tools/test_driver/__init__.py,sha256=KOiceeZNqkfrgZ66CiRiUdniceDrCmmDXQkOw0w
 kim_tools/test_driver/core.py,sha256=r4hiZcV-PkWcOo0uEqfqeP1-YGGpPepaAjmR4LJog0w,89208
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.3.0.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.0.dist-info/METADATA,sha256=MAODKb510nvTCelHGq9-IHuosDJSGjTEdl1DPnP19mA,1962
-kim_tools-0.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.0.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.0.dist-info/RECORD,,
+kim_tools-0.3.2.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.2.dist-info/METADATA,sha256=EAQFkPk6S0svLhGMBstoSj4Kk9vdzbIDATWefRyb8zE,1962
+kim_tools-0.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.2.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.2.dist-info/RECORD,,