clease - npm Package Compare versions

Comparing version 1.0.1 to 1.0.2

clease.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: clease
-Version: 1.0.1
+Version: 1.0.2
 Summary: CLuster Expansion in Atomistic Simulation Environment
@@ -5,0 +5,0 @@ Home-page: https://gitlab.com/computationalmaterials/clease/

clease.egg-info/requires.txt

@@ -1,2 +0,2 @@
-ase<3.23,>=3.20
+ase>=3.22
 numpy
@@ -16,21 +16,21 @@ cython
 [all]
+sphinx
+pytest-benchmark[histogram]>=3.4.1
 pre-commit
-ipython
-pyclean>=2.0.0
-pytest-benchmark[histogram]>=3.4.1
-pylint
+black>=22.1.0
 pip
-black>=22.1.0
-twine
-sphinx_rtd_theme
-build
+pytest-cov
+cython
 clang-format>=14.0.3
-pytest-cov
+pytest-mock
 tox>=3.24.0
-cython
+build
 pytest
-pytest-mock
+pyclean>=2.0.0
+pylint
+sphinx_rtd_theme
+clease-gui
 mock
-sphinx
-clease-gui
+ipython
+twine
 
@@ -37,0 +37,0 @@ [dev]

clease/_version.txt

@@ -1,1 +0,1 @@
-1.0.1
+1.0.2

clease/calculator/clease_vol_dep.py

 from typing import Dict, Optional, Iterable, Set, List, Union, Sequence
 from ase import Atoms
-from ase.calculators.calculator import Calculator
 from clease.datastructures import SystemChange
@@ -234,15 +233,12 @@ from clease.settings import ClusterExpansionSettings
         self,
-        atoms: Atoms,
-        properties: List[str],
-        system_changes: Union[Sequence[SystemChange], None],
+        atoms: Atoms = None,
+        properties: List[str] = None,
+        system_changes: Union[Sequence[SystemChange], None] = None,
     ) -> float:
         """Calculate the energy of the passed Atoms object.
 
-        If accept=True, the most recently used atoms object is used as a
-        reference structure to calculate the energy of the passed atoms.
-        Returns energy.
-
         Parameters:
 
-        :param atoms: ASE Atoms object
+        :param atoms: ASE Atoms object, or None. If None is passed,
+            the internal one is used, if the calculator has been initialized.
 
@@ -253,3 +249,3 @@ :param system_changes:
         """
-        Calculator.calculate(self, atoms)
+        super().calculate(atoms, properties, system_changes)
         self.update_cf()
@@ -256,0 +252,0 @@ return self.get_energy_given_change([], keep_changes=True)

clease/calculator/clease.py

 """Calculator for Cluster Expansion."""
 import sys
 import contextlib
-from typing import Dict, Optional, TextIO, Union, List
+from typing import Dict, Optional, TextIO, Union, List, Sequence, Any
 import numpy as np
 from ase import Atoms
-from ase.calculators.calculator import Calculator
+from ase.calculators.calculator import PropertyNotImplementedError
 from clease_cxx import PyCEUpdater, has_parallel
@@ -27,4 +27,4 @@ from clease.datastructures import SystemChange, SystemChanges
 
-# pylint: disable=too-many-instance-attributes
-class Clease(Calculator):
+# pylint: disable=too-many-instance-attributes, too-many-public-methods
+class Clease:
     """Class for calculating energy using CLEASE.
@@ -56,3 +56,2 @@
     ) -> None:
-        Calculator.__init__(self)
 
@@ -64,3 +63,3 @@ if not isinstance(settings, ClusterExpansionSettings):
         self.updater = None
-        self.parameters["eci"] = eci
+        self.results = {}
         self.settings = settings
@@ -147,11 +146,3 @@ self.corrFunc = CorrFunction(settings)
 
-    def check_state(self, atoms: Atoms, tol: float = 1e-15):
-        res = super().check_state(atoms)
-        syst_ch = self.indices_of_changed_atoms
-
-        if syst_ch and "energy" not in res:
-            res.append("energy")
-        return res
-
-    def reset(self):
+    def reset(self) -> None:
         self.results = {}
@@ -161,2 +152,3 @@
         """Calculate correlation functions from scratch."""
+        self.require_updater()
         return self.updater.calculate_cf_from_scratch(self.atoms, self.cf_names)
@@ -172,8 +164,7 @@
 
-    # pylint: disable=signature-differs
     def calculate(
         self,
-        atoms: Atoms,
-        properties: Union[List[str], str],
-        system_changes: SystemChanges,
+        atoms: Optional[Atoms] = None,
+        properties: List[str] = None,
+        system_changes: SystemChanges = None,
     ) -> float:
@@ -189,3 +180,3 @@ """Calculate the energy of the passed Atoms object.
         :param properties: List of what needs to be calculated.
-            It can only by 'energy' at the moment.
+            It can only be ['energy'] for the basic Clease calculator.
 
@@ -196,8 +187,38 @@ :param system_changes: List of system changes. For example, if the
             index 26 is swapped with an Al atom occupying the atomic index 12,
-            system_change = [(26, Mg, Al), (12, Al, Mg)]
+            system_change = [(26, Mg, Al), (12, Al, Mg)].
+            Currently not supported.
         """
+        if atoms is not None:
+            if self.atoms is None:
+                # We havn't yet initialized, so initialize with the passed atoms object.
+                self.set_atoms(atoms)
+            else:
+                # Use the symbols of the passed atoms object
+                self.atoms.symbols[:] = atoms.symbols
+        self.require_updater()
+
+        _check_properties(properties, self.implemented_properties)
+
+        if system_changes is not None:
+            raise ValueError("system_changes in calculate is currently not supported.")
+
         self.update_energy()
-        self.energy = self.updater.get_energy()
         return self.energy
 
+    def get_property(self, name: str, atoms: Atoms = None, allow_calculation: bool = True):
+        """Get a property from the calculator.
+
+        Exists due to compatibility with ASE, should not be used directly.
+        """
+        _check_properties([name], self.implemented_properties)
+
+        if not allow_calculation:
+            return self.energy
+        return self.get_potential_energy(atoms=atoms)
+
+    def get_potential_energy(self, atoms: Atoms = None) -> float:
+        """Calculate the energy from scratch with an atoms object"""
+        # self.set_atoms(atoms)
+        return self.calculate(atoms=atoms)
+
     def clear_history(self) -> None:
@@ -225,2 +246,24 @@ self.updater.clear_history()
 
+    def calculation_required(self, atoms: Atoms, properties: Sequence[str] = None) -> bool:
+        """Check whether a calculation is required for a given atoms object.
+        The ``properties`` argument only exists for compatibility reasons, and has no effect.
+        Primarily for ASE compatibility.
+        """
+        _check_properties(properties, self.implemented_properties)
+        if self.updater is None:
+            return True
+        if "energy" not in self.results:
+            return True
+        changed_indices = self.get_changed_sites(atoms)
+        return bool(changed_indices)
+
+    def check_state(self, atoms: Atoms) -> List[str]:
+        """Method for checking if energy needs calculation.
+        Primarily for ASE compatibility.
+        """
+        res = []
+        if self.calculation_required(atoms):
+            res.append("energy")
+        return res
+
     @property
@@ -237,3 +280,3 @@ def energy(self):
         """Return the indices of atoms that have been changed."""
-        changed = self.updater.get_changed_sites(self.atoms)
+        changed = self.get_changed_sites(self.atoms)
         for index in changed:
@@ -246,2 +289,7 @@ if self.is_backround_index[index] and not self.settings.include_background_atoms:
 
+    def get_changed_sites(self, atoms: Atoms) -> List[int]:
+        """Return the list of indices which differ from the internal ones."""
+        self.require_updater()
+        return self.updater.get_changed_sites(atoms)
+
     def get_cf(self) -> Dict[str, float]:
@@ -353,4 +401,3 @@ """Return the correlation functions as a dict"""
         """Get the number of threads from the C++ updater."""
-        if self.updater is None:
-            raise UnitializedCEError("Updater hasn't been initialized yet.")
+        self.require_updater()
         return self.updater.get_num_threads()
@@ -369,4 +416,4 @@
             raise ValueError("Number of threads must be at least 1")
-        if self.updater is None:
-            raise UnitializedCEError("Updater hasn't been initialized yet.")
+        self.require_updater()
+
         if value != 1 and not has_parallel():
@@ -376,1 +423,30 @@ # Having a value of 1 is OK, since that's not threading.
         self.updater.set_num_threads(value)
+
+    def require_updater(self) -> None:
+        if self.updater is None:
+            raise UnitializedCEError("Updater hasn't been initialized yet.")
+
+    @property
+    def parameters(self) -> Dict[str, Any]:
+        """Return a dictionary with relevant parameters."""
+        return {"eci": self.eci}
+
+    def todict(self) -> dict:
+        """Return the parameters, i.e. the ECI values.
+        For ASE compatibility.
+        """
+        return self.parameters
+
+
+def _check_properties(properties: Optional[List[str]], implemented_properties: List[str]) -> None:
+    """Check whether the passed properties is supported. If it is None, nothing is checked.
+    Raises PropertyNotImplementedError upon finding a bad property.
+    """
+    if properties is None:
+        return
+    for prop in properties:
+        if prop not in implemented_properties:
+            allowed = ", ".join(implemented_properties)
+            raise PropertyNotImplementedError(
+                f"Property '{prop}' is unsupported. Implemented properties: {allowed}"
+            )

clease/structgen/new_struct.py

@@ -5,3 +5,3 @@ """Module for generating new structures for training."""
 from functools import reduce
-from typing import List, Dict, Optional, Union, Any
+from typing import List, Dict, Optional, Union, Any, Tuple
 import logging
@@ -715,9 +715,8 @@ from itertools import product
         warn_on_skip: bool = True,
-    ) -> Optional[int]:
+    ) -> Optional[Union[int, Tuple[int, int]]]:
         """Insert a structure to the database.
 
         Returns the ID of the initial structure which was inserted into the database.
-        If a row for the final structure is also inserted, this id can be retrieved of the
-        initial row from the ``final_struct_id`` entry. If no structure was inserted,
-        ``Ǹone`` is returned, instead.
+        If a row for the final structure is also inserted, a tuple of (initial_id, final_id)
+        is returned. If no structure was inserted, ``Ǹone`` is returned, instead.
 
@@ -727,3 +726,3 @@ :param init_struct: Unrelaxed initial structure. If a string is passed,
         :param final_struct: (Optional) final structure that contains energy.
-            It can be either ASE Atoms object or file anme ending with .traj.
+            It can be either ASE Atoms object or file name readable by ASE.
         :param name: (Optional) name of the DB entry if a custom name is to be
@@ -786,3 +785,4 @@ used. If `None`, default naming convention will be used.
         con = self.connect()
-        uid_init = db_util.new_row_with_single_table(con, init_struct, tab_name, cf, **kvp)
+        uid_init: int = db_util.new_row_with_single_table(con, init_struct, tab_name, cf, **kvp)
+        ret_val = uid_init
 
@@ -793,6 +793,7 @@ if final_struct is not None:
             kvp_final = {"struct_type": "final", "name": kvp["name"]}
-            uid = con.write(final_struct, kvp_final)
-            con.update(uid_init, converged=True, started="", queued="", final_struct_id=uid)
+            uid_final: int = con.write(final_struct, kvp_final)
+            con.update(uid_init, converged=True, started="", queued="", final_struct_id=uid_final)
+            ret_val = (uid_init, uid_final)
 
-        return uid_init
+        return ret_val
 
@@ -799,0 +800,0 @@ def _exists_in_db(self, atoms: Atoms, formula_unit: Optional[str] = None) -> bool:

doc/source/index.rst

@@ -45,3 +45,3 @@ .. CLEASE documentation master file, created by
 
-  * Use one our :ref:`pre-made observers <mc_observers>` to collect thermondynamic
+  * Use one our :ref:`pre-made observers <mc_observers>` to collect thermodynamic
     data about your system during an MC run, or
@@ -48,0 +48,0 @@ :ref:`write your own <implementing your own observer>`.

doc/source/releasenotes.rst

@@ -7,2 +7,8 @@ .. _releasenotes:
 
+1.0.2
+======
+* :py:meth:`~clease.structgen.new_struct.NewStructures.insert_structure` returns both
+  the initial and final ID if both an initial and final structure was inserted.
+* Fixes a bug with writing the Clease calculator to a DB row.
+
 1.0.1
@@ -9,0 +15,0 @@ ======

PKG-INFO

 Metadata-Version: 2.1
 Name: clease
-Version: 1.0.1
+Version: 1.0.2
 Summary: CLuster Expansion in Atomistic Simulation Environment
@@ -5,0 +5,0 @@ Home-page: https://gitlab.com/computationalmaterials/clease/

setup.cfg

@@ -34,3 +34,3 @@ [metadata]
 install_requires = 
-	ase>=3.20, <3.23  # temp restriction on ASE upper version
+	ase>=3.22
 	numpy
@@ -37,0 +37,0 @@ cython

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Improved metrics

Total package byte prevSize

1596336

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Lines of code

16739

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