kim-tools 0.3.11__py3-none-any.whl → 0.3.13__py3-none-any.whl

kim_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.11"
+__version__ = "0.3.13"
 
 from .aflow_util import *
 from .aflow_util import __all__ as aflow_all

kim_tools/ase/core.py

@@ -34,7 +34,6 @@ 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
@@ -208,45 +207,137 @@ def randomize_positions(atoms, pert_amp, seed=None):
 
 
 ################################################################################
-def get_isolated_energy_per_atom(model: Union[str, Calculator], symbol: str) -> float:
+def get_isolated_energy_per_atom(
+    model,
+    symbol,
+    initial_separation=1.0,
+    max_separation=15.0,
+    separation_neg_exponent=4,
+    quit_early_after_convergence=True,
+    energy_tolerance=1e-12,
+):
     """
     Construct a non-periodic cell containing a single atom and compute its energy.
+    It tries to iteratively finetune the atomic separation for a dimer up to a
+    specified precision (separation_neg_exponent). If between two successive phases
+    the energy difference is less than energy_tolerance, it stops early, i.e. if
+    4.0x and 4.00x are within energy_tolerance, it stops at 4.00x.
+    All separations are in Angstroms.
 
     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
+        model: KIM model to use for calculations
+        symbol: Chemical symbol
+        initial_separation: Initial separation for dimer calculations
+        max_separation: maximum separation for dimer calculations
+        separation_neg_exponent: Number of decimal places to refine the separation
+        quit_early_after_convergence: Whether to stop early if energy converges
+        energy_tolerance: Energy difference tolerance for convergence check
     """
-    single_atom = Atoms(
-        symbol,
-        positions=[(0.1, 0.1, 0.1)],
-        cell=(20, 20, 20),
-        pbc=(False, False, False),
-    )
-    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)}."
+    try:
+        single_atom = Atoms(
+            symbol,
+            positions=[(0.1, 0.1, 0.1)],
+            cell=(20, 20, 20),
+            pbc=(False, False, False),
         )
-    single_atom.calc = calc
-    energy_per_atom = single_atom.get_potential_energy()
-    # 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 isinstance(model, str):
+            calc = KIM(model)
+        elif isinstance(model, Calculator):
+            calc = model
+
+        single_atom.calc = calc
+        energy_per_atom = single_atom.get_potential_energy()
+
+        # Clean up
         if hasattr(calc, "clean"):
             calc.clean()
         if hasattr(calc, "__del__"):
             calc.__del__()
-    del single_atom
-    return energy_per_atom
+        del single_atom
+
+        return energy_per_atom
+
+    except Exception:
+
+        def _try_dimer_energy(separation):
+            try:
+                dimer = Atoms(
+                    [symbol, symbol],
+                    positions=[(0.1, 0.1, 0.1), (0.1 + separation, 0.1, 0.1)],
+                    cell=(max(20, separation + 10), 20, 20),
+                    pbc=(False, False, False),
+                )
+                calc = KIM(model)
+                dimer.calc = calc
+
+                total_energy = dimer.get_potential_energy()
+                energy_per_atom = total_energy / 2.0
+
+                if hasattr(calc, "clean"):
+                    calc.clean()
+                if hasattr(calc, "__del__"):
+                    calc.__del__()
+                del dimer
+
+                return energy_per_atom
+
+            except Exception:
+                try:
+                    if hasattr(calc, "clean"):
+                        calc.clean()
+                    if hasattr(calc, "__del__"):
+                        calc.__del__()
+                    if "dimer" in locals():
+                        del dimer
+                except Exception:
+                    pass
+                return None
+
+        # Start with integer separations: 1.0, 2.0, 3.0, 4.0, ...
+        last_successful_separation = None
+        last_successful_energy = None
+
+        separation = initial_separation
+        while separation <= max_separation:
+            energy = _try_dimer_energy(separation)
+            if energy is not None:
+                last_successful_separation = separation
+                last_successful_energy = energy
+                separation += 1.0
+            else:
+                break
+
+        if last_successful_separation is None:
+            raise RuntimeError(
+                f"Failed to obtain isolated energy for {symbol} - no separations worked"
+            )
+
+        # refine
+        current_separation = last_successful_separation
+        previous_phase_energy = last_successful_energy
+
+        for decimal_place in range(1, separation_neg_exponent + 1):
+
+            step_size = 10 ** (-decimal_place)
+
+            for i in range(1, 10):
+                test_sep = current_separation + step_size
+                energy = _try_dimer_energy(test_sep)
+
+                if energy is not None:
+                    current_separation = test_sep
+                    last_successful_energy = energy
+                else:
+                    break
+
+            if quit_early_after_convergence:
+                energy_diff = abs(last_successful_energy - previous_phase_energy)
+                if energy_diff <= energy_tolerance:
+                    return last_successful_energy
+
+            previous_phase_energy = last_successful_energy
+
+        return last_successful_energy
 
 
 ################################################################################
@@ -434,9 +525,7 @@ def check_if_atoms_interacting(
         atoms_interacting_energy = check_if_atoms_interacting_energy(
             model, symbols, etol
         )
-        atoms_interacting_force = check_if_atoms_interacting_energy(
-            model, symbols, ftol
-        )
+        atoms_interacting_force = check_if_atoms_interacting_force(model, symbols, ftol)
         return atoms_interacting_energy, atoms_interacting_force
 
 

kim_tools/test_driver/core.py

@@ -46,7 +46,9 @@ import kim_edn
 import numpy as np
 import numpy.typing as npt
 from ase import Atoms
+from ase.build import bulk
 from ase.calculators.calculator import Calculator
+from ase.calculators.kim import get_model_supported_species
 from ase.constraints import FixSymmetry
 from ase.data import atomic_masses
 from ase.filters import FrechetCellFilter, UnitCellFilter
@@ -95,6 +97,7 @@ __all__ = [
     "get_deduplicated_property_instances",
     "minimize_wrapper",
     "crystal_input_from_test_generator_line",
+    "get_supported_lammps_atom_style",
 ]
 
 # Force tolerance for the optional initial relaxation of the provided cell
@@ -108,6 +111,48 @@ PROP_SEARCH_PATHS_INFO = (
 )
 
 
+def get_supported_lammps_atom_style(model: str) -> str:
+    """
+    Get the supported LAMMPS atom_style of a KIM model
+    """
+    from lammps import lammps
+
+    candidate_atom_styles = ("atomic", "charge", "full")
+    banned_species = "electron"  # Species in KIM models not understood by ASE
+    supported_species = get_model_supported_species(model)
+    test_species = None
+    for species in supported_species:
+        if species not in banned_species:
+            test_species = species
+            break
+    if test_species is None:
+        raise RuntimeError(
+            "Model appears to only support species not understood by ASE:\n"
+            + str(supported_species)
+        )
+    atoms = bulk(test_species, "fcc", 10.0)  # Very low-density FCC lattice
+    for atom_style in candidate_atom_styles:
+        with lammps(cmdargs=["-sc", "none"]) as lmp, NamedTemporaryFile() as f:
+            lmp.command(f"kim init {model} metal unit_conversion_mode")
+            atoms.write(f.name, format="lammps-data", atom_style=atom_style)
+            try:
+                lmp.command(f"read_data {f.name}")
+                return atom_style
+            except Exception as e:
+                if str(e).startswith(
+                    "ERROR: Incorrect format in Atoms section of data file:"
+                ):
+                    continue
+                else:
+                    msg = (
+                        "The following unexpected exception was encountered when trying"
+                        " to determine atom_style:\n" + repr(e)
+                    )
+                    print(msg)
+                    raise e
+    raise RuntimeError("Unable to determine supported atom type")
+
+
 def _get_optional_source_value(property_instance: Dict, key: str) -> Any:
     """
     Function for getting an optional key's source-value, or None if the key
@@ -718,6 +763,14 @@ class KIMTestDriver(ABC):
             name, os.path.relpath(final_path, output_path)
         )
 
+    def _get_supported_lammps_atom_style(self) -> str:
+        """
+        Return the atom_style that should be used when writing LAMMPS data files.
+        This atom_style will be compatible with the KIM model this object
+        was instantiated with.
+        """
+        return get_supported_lammps_atom_style(self.kim_model_name)
+
     @property
     def kim_model_name(self) -> Optional[str]:
         """

{kim_tools-0.3.11.dist-info → kim_tools-0.3.13.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: kim-tools
-Version: 0.3.11
+Version: 0.3.13
 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>
+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>, Navaneeth Mohan <mohan227@umn.edu>
 Maintainer-email: ilia Nikiforov <nikif002@umn.edu>
 Project-URL: Homepage, https://kim-tools.readthedocs.io
 Project-URL: Issues, https://github.com/openkim/kim-tools/issues

{kim_tools-0.3.11.dist-info → kim_tools-0.3.13.dist-info}/RECORD

@@ -1,4 +1,4 @@
-kim_tools/__init__.py,sha256=YZdzUiZNlEczGQLTPVRxzz5-jGxgJTEaeAK_p-oJu4o,434
+kim_tools/__init__.py,sha256=z9M4HWOpT0qCOUbGIKeUY-Oskrw_ZG6xeXli9iLTyzo,434
 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=mMS2r9ayJJ6ApOFTAIkCZ72Dg3g1EnREbrqe2YEipMo,81273
@@ -2002,7 +2002,7 @@ 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=odRuHQGZl-pcRtkdYvG31_3kW6nt3qwHdKvAOJ-ifwM,31207
+kim_tools/ase/core.py,sha256=umJY0LV3_zrEZLOXAFoz6AFigxA69sAOBzAGoBTDzxA,34335
 kim_tools/symmetry_util/__init__.py,sha256=uu-ZSUDUTe2P81rkAS3tXverx31s_uZ3wL4SD_dn5aI,86
 kim_tools/symmetry_util/core.py,sha256=eMGgVt9MPcaLi_8jVMJ5UyQHvYbiiAFQ4HdJotnp8dk,43277
 kim_tools/symmetry_util/elasticity.py,sha256=VxJ8wUcsSOPyJ8id6OpKmVlRAbIUIWxtzYJtkvVJIVs,13328
@@ -2023,11 +2023,11 @@ 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=ZHS26S8-HxCPTDhv6h6WZ2x7pDQMTu6G1bWD4rPvoz8,99107
+kim_tools/test_driver/core.py,sha256=vHmhSWix5t95SCmJEapdpZXfJS0ZlbG-8bcmV9O9v9M,101261
 kim_tools/vc/__init__.py,sha256=zXjhxXCKVMLBMXXWYG3if7VOpBnsFrn_RjVpnohDm5c,74
 kim_tools/vc/core.py,sha256=BIjzEExnQAL2S90a_npptRm3ACqAo4fZBtvTDBMWMdw,13963
-kim_tools-0.3.11.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
-kim_tools-0.3.11.dist-info/METADATA,sha256=AdNljYaTm6fqCc8eaRcIFX0oeMcsqDTcMPdmqvBPAcs,2033
-kim_tools-0.3.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-kim_tools-0.3.11.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
-kim_tools-0.3.11.dist-info/RECORD,,
+kim_tools-0.3.13.dist-info/licenses/LICENSE.CDDL,sha256=I2luEED_SHjuZ01B4rYG-AF_135amL24JpHvZ1Jhqe8,16373
+kim_tools-0.3.13.dist-info/METADATA,sha256=7ldqSmsLFyzrEtIeV-wJacw1BEJoj55DgMOupJlycIs,2069
+kim_tools-0.3.13.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+kim_tools-0.3.13.dist-info/top_level.txt,sha256=w_YCpJ5ERigj9te74ln7k64tqj1VumOzM_s9dsalIWY,10
+kim_tools-0.3.13.dist-info/RECORD,,