kim-tools 0.3.2__tar.gz → 0.3.3__tar.gz

{kim_tools-0.3.2/kim_tools.egg-info → kim_tools-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.2
+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-0.3.2 → kim_tools-0.3.3}/kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

{kim_tools-0.3.2 → kim_tools-0.3.3}/kim_tools/aflow_util/core.py

@@ -552,12 +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
@@ -573,13 +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
@@ -618,6 +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-0.3.2 → kim_tools-0.3.3}/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-0.3.2 → kim_tools-0.3.3/kim_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.2
+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-0.3.2 → kim_tools-0.3.3}/kim_tools.egg-info/SOURCES.txt

@@ -2026,5 +2026,6 @@ kim_tools/test_driver/core.py
 kim_tools/vc/__init__.py
 kim_tools/vc/core.py
 tests/test_aflow_util.py
+tests/test_ase.py
 tests/test_symmetry_util.py
 tests/test_test_driver.py

kim_tools-0.3.3/tests/test_ase.py

@@ -0,0 +1,22 @@
+import numpy as np
+from ase.calculators.lj import LennardJones
+from lj_fail_no_neighbors import LennardJonesFailNoNeighbors
+
+from kim_tools import get_isolated_energy_per_atom
+
+
+def test_get_isolated_energy_per_atom():
+    assert np.isclose(
+        get_isolated_energy_per_atom(
+            "LJ_ElliottAkerson_2015_Universal__MO_959249795837_003", "H"
+        ),
+        0,
+    )
+    assert np.isclose(
+        get_isolated_energy_per_atom(LennardJones(), "H"),
+        0,
+    )
+    assert np.isclose(
+        get_isolated_energy_per_atom(LennardJonesFailNoNeighbors(), "H"),
+        0,
+    )