kim-tools 0.3.1__py3-none-any.whl → 0.3.3__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.1"
+__version__ = "0.3.3"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/aflow_util/core.py

@@ -396,6 +396,7 @@ def prototype_labels_are_equivalent(
     prototype_label_1: str,
     prototype_label_2: str,
     allow_enantiomorph: bool = False,
+    log: bool = True,
 ) -> bool:
     """
     Checks if two prototype labels are equivalent (species permutations not allowed)
@@ -403,6 +404,8 @@ def prototype_labels_are_equivalent(
     Args:
         allow_enantiomorph:
             Whether to consider enantiomorphic pairs of space groups to be equivalent
+        log:
+            Whether to log results
     """
 
     if prototype_label_1 == prototype_label_2:
@@ -414,20 +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
@@ -436,16 +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
@@ -487,16 +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):
@@ -505,17 +514,19 @@ 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
 
 
@@ -523,6 +534,7 @@ 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
@@ -530,6 +542,8 @@ def find_species_permutation_between_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
@@ -538,12 +552,32 @@ def find_species_permutation_between_prototype_labels(
     # 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))
+    space_group_1 = get_space_group_number_from_prototype(prototype_label_1)
+    space_group_1_str = str(space_group_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)
 
+    # For crystals with many species, it takes forever to loop through all permutations,
+    # so do some basic checks first to reject
+    stoich_reduced_list_2 = get_stoich_reduced_list_from_prototype(prototype_label_2)
+    pearson_2 = get_pearson_symbol_from_prototype(prototype_label_2)
+    space_group_2 = get_space_group_number_from_prototype(prototype_label_2)
+    if (
+        len(stoich_reduced_list_1) != len(stoich_reduced_list_2)
+        or sum(stoich_reduced_list_1) != sum(stoich_reduced_list_2)
+        or pearson_1 != pearson_2
+    ):
+        return None
+
+    if allow_enantiomorph:
+        if not space_group_numbers_are_enantiomorphic(space_group_1, space_group_2):
+            return None
+    else:
+        if space_group_1 != space_group_2:
+            return None
+
     permutation_candidates = permutations(tuple(range(nspecies)))
     for permutation in permutation_candidates:
         # Permute the species
@@ -559,13 +593,14 @@ def find_species_permutation_between_prototype_labels(
         prototype_label_1_permuted_list = [
             abstract_formula_1_permuted,
             pearson_1,
-            space_group_1,
+            space_group_1_str,
         ] + 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,
+            log=log,
         ):
             return permutation
     return None
@@ -604,6 +639,23 @@ def read_shortnames(
         with open(info_file) as f:
             info = json.load(f)
         shortnames[libproto] = info["title"]
+
+    ##################################################
+    # CUSTOM MODIFICATIONS TO SHORTNAME DICT
+    ##################################################
+    # For some reason, CsCl is AB_cP2_221_a_b-002,
+    # while AB_cP2_221_a_b-001 is Ammonium Nitrate,
+    # where the atoms represent molecular ions
+    shortnames.pop("AB_cP2_221_a_b-001")
+
+    # I am making an executive decision to include
+    # only one identical cubic prototype with no
+    # free parameters. Here I am choosing to keep
+    # 'A7B_cF32_225_ad_b-001': 'Ca₇Ge Structure'
+    # and remove
+    # 'AB7_cF32_225_a_bd-001': '𝐿1ₐ (disputed CuPt₃ Structure)'
+    shortnames.pop("AB7_cF32_225_a_bd-001")
+
     return shortnames
 
 

kim_tools/ase/core.py

@@ -32,13 +32,20 @@ Helper routines for KIM Tests and Verification Checks
 """
 
 import itertools
+import logging
 import random
+from typing import Union
 
 import numpy as np
 from ase import Atoms
+from ase.calculators.calculator import Calculator
 from ase.calculators.kim.kim import KIM
 from ase.data import chemical_symbols
 
+logger = logging.getLogger(__name__)
+logging.basicConfig(filename="kim-tools.log", level=logging.INFO, force=True)
+
+
 __all__ = [
     "KIMASEError",
     "atom_outside_cell_along_nonperiodic_dim",
@@ -201,9 +208,18 @@ def randomize_positions(atoms, pert_amp, seed=None):
 
 
 ################################################################################
-def get_isolated_energy_per_atom(model, symbol):
+def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol):
     """
     Construct a non-periodic cell containing a single atom and compute its energy.
+
+    Args:
+        model:
+            A KIM model ID or an ASE calculator for computing the energy
+        symbol:
+            The chemical species
+
+    Returns:
+        The isolated energy of a single atom
     """
     single_atom = Atoms(
         symbol,
@@ -211,15 +227,33 @@ def get_isolated_energy_per_atom(model, symbol):
         cell=(20, 20, 20),
         pbc=(False, False, False),
     )
-    calc = KIM(model)
+    if isinstance(model, str):
+        calc = KIM(model)
+    elif isinstance(model, Calculator):
+        calc = model
+    else:
+        raise KIMASEError(
+            "`model` argument must be a string indicating a KIM model "
+            f"or an ASE Calculator. Instead got an object of type {type(model)}."
+        )
     single_atom.calc = calc
-    energy_per_atom = single_atom.get_potential_energy()
-    if hasattr(calc, "clean"):
-        calc.clean()
-    if hasattr(calc, "__del__"):
-        calc.__del__()
-    del single_atom
-    return energy_per_atom
+    try:
+        energy_per_atom = single_atom.get_potential_energy()
+    except Exception as e:
+        msg = (
+            "Energy evaluation for isolated atom raised the following error:\n"
+            f"{repr(e)}\nAssuming zero isolated atom energy."
+        )
+        logger.warning(msg)
+        print(msg)
+        energy_per_atom = 0.0
+    finally:
+        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

@@ -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-0.3.1.dist-info → kim_tools-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.1
+Version: 0.3.3
 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-0.3.1.dist-info → kim_tools-0.3.3.dist-info}/RECORD

@@ -1,7 +1,7 @@
-kim_tools/__init__.py,sha256=dOQsrWeoyK-9Fr4gPNLzdouLMm0J0hhh6qd86cPECns,433
+kim_tools/__init__.py,sha256=pnnfC__2WcTkgaE8RZU5AfDIx6PQOR9Dst7oBvYsMYI,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=NULg8zJG4B5lh4p-Q7yPsJvgzPG_BgSRjgrLpyX3UUI,75526
+kim_tools/aflow_util/core.py,sha256=zi69wMcgkcYBTKbc-OvKlMIzUtgphO57yBA8LB7_5wc,77484
 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=d6eOu_HSxVr-ae0TSEbY4HKdePxhNu3yv8NN9VDl-BA,30256
+kim_tools/ase/core.py,sha256=KRtcNYcJLlP-WiEMOOmR-DhYw5IN5MoOCtKWJJzRkhM,31313
 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-0.3.1.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.1.dist-info/METADATA,sha256=scnOzhP0hy9JNn5NS6W9lSESU6G0PS2rPoCdkwIIVSE,1962
-kim_tools-0.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.1.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.1.dist-info/RECORD,,
+kim_tools-0.3.3.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.3.dist-info/METADATA,sha256=d5yobjRNvHpCLftHbue8GmC0xsvD8FSOpCksGnRoxC8,1962
+kim_tools-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.3.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.3.dist-info/RECORD,,