hiPhive - npm Package Compare versions

Comparing version 0.7 to 0.7.1

hiphive.egg-info/PKG-INFO

 Metadata-Version: 1.2
 Name: hiphive
-Version: 0.7
+Version: 0.7.1
 Summary: High-order force constants for the masses
@@ -98,3 +98,2 @@ Home-page: http://hiphive.materialsmodeling.org/
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
 Classifier: Programming Language :: Python :: 3.6
@@ -101,0 +100,0 @@ Classifier: Programming Language :: Python :: 3.7

hiphive/__init__.py

@@ -38,3 +38,3 @@ """
                'Paul Erhart']
-__version__ = '0.7'
+__version__ = '0.7.1'
 __all__ = ['ClusterSpace',
@@ -41,0 +41,0 @@ 'StructureContainer',

hiphive/calculators/numba_calc.py

@@ -69,4 +69,4 @@ import numba
         i = 0
-        for l in range(pos):
-            v = d[cluster[l], :]
+        for m in range(pos):
+            v = d[cluster[m], :]
             tvl(fc, v, order - i)
@@ -73,0 +73,0 @@ i += 1

hiphive/cluster_space.py

@@ -43,7 +43,7 @@ """
     config : Config object
-        config object containing information on how the cluster space should
-        be built, e.g. values for tolerances and if acoustic sum rules be
-        enforced
-
-    If not config is given then kwargs can be used to specify:
+        a configuration object that holds information on how the cluster space
+        should be built, e.g., values for tolerances and specifications
+        regarding the handling of acoustic sum rules; if ``config`` is
+        not given then the keyword arguments that follow below can be
+        used for configuration.
     acoustic_sum_rules : bool
@@ -70,7 +70,8 @@ If True the aucostic sum rules will be enforced by constraining the
     >>> from ase.build import bulk
+    >>> from hiphive import ClusterSpace
     >>> prim = bulk('W')
     >>> cs = ClusterSpace(prim, [5.0, 4.0])
+
     """
-    # TODO: This class probably need some more documentation and a reference to
-    # the thesis
+    # TODO: This class probably needs some more documentation
     # TODO: Fix doc for n-body cutoff
@@ -77,0 +78,0 @@

hiphive/core/structure_alignment.py

@@ -50,9 +50,10 @@ import itertools
 
-    Aligning reference with target can be achieved via the transformations
-    >>> R, T = relate_structures(atoms_ref, atoms_target)
-    >>> atoms_ref_rotated = rotate_atoms(atoms_ref, R)
-    >>> atoms_ref_rotated.translate(T)
-    >>> atoms_ref_rotated.wrap()
-    >>> atoms_ref_rotated == atoms_target
+    Aligning reference with target can be achieved via the transformations::
 
+        R, T = relate_structures(atoms_ref, atoms_target)
+        atoms_ref_rotated = rotate_atoms(atoms_ref, R)
+        atoms_ref_rotated.translate(T)
+        atoms_ref_rotated.wrap()
+        atoms_ref_rotated == atoms_target
+
     Parameters
@@ -59,0 +60,0 @@ ----------

hiphive/force_constant_model.py

@@ -7,4 +7,10 @@ """
 import pickle
+
+from typing import IO, Tuple, Union
+
 import numpy as np
 
+from ase import Atoms
+from scipy.sparse import coo_matrix, vstack
+
 from .cluster_space import ClusterSpace
@@ -17,7 +23,6 @@ from .core.atoms import Atom, atom_to_spos, spos_to_atom
 from .core.utilities import Progress, BiMap
-from .force_constants import SortedForceConstants
+from .force_constants import ForceConstants, SortedForceConstants
 from .input_output.logging_tools import logger
 from .calculators.numba_calc import (clusters_force_contribution,
                                      cluster_force_contribution)
-from scipy.sparse import coo_matrix, vstack
 
@@ -35,8 +40,8 @@ logger = logger.getChild('fcm')
     ----------
-    atoms : ase.Atoms
+    atoms
         configuration to which the cluster space is to be applied
-    cs : ClusterSpace
+    cs
         a cluster space compatible with the structure of the atoms
     """
-    def __init__(self, atoms, cs):
+    def __init__(self, atoms: Atoms, cs: ClusterSpace):
 
@@ -50,3 +55,3 @@ self.atoms = atoms.copy()
     # TODO: refactor
-    def _populate_orbits(self, atoms):
+    def _populate_orbits(self, atoms: Atoms):
         """Map the orbits from the underlying force constant potential onto the
@@ -176,3 +181,3 @@ supercell structure associated with this force constant model.
 
-    def get_force_constants(self):
+    def get_force_constants(self) -> SortedForceConstants:
         """Returns the force constants of the super cell.
@@ -182,3 +187,3 @@
         -------
-        force constants : ForceConstants
+        force constants
             complete set of force constants
@@ -199,3 +204,3 @@ """
     @property
-    def parameters(self):
+    def parameters(self) -> np.ndarray:
         """ list(float): parameters """
@@ -205,3 +210,3 @@ return self._parameters
     @parameters.setter
-    def parameters(self, parameters):
+    def parameters(self, parameters: np.ndarray) -> None:
         self._parameters = parameters
@@ -228,3 +233,3 @@ mapped_parameters = self.cs._map_parameters(parameters)
 
-    def get_forces(self, displacements):
+    def get_forces(self, displacements: np.ndarray) -> np.ndarray:
         """ Returns the forces in the system given displacements.
@@ -236,3 +241,3 @@
         ----------
-        displacements : numpy.ndarray
+        displacements
             displacements of each atom in the supercell (`N, 3` array)
@@ -261,3 +266,3 @@ """
 
-    def get_fit_matrix(self, displacements):
+    def get_fit_matrix(self, displacements: np.ndarray) -> np.ndarray:
         """ Returns the matrix used to fit the parameters.
@@ -269,3 +274,3 @@
         ----------
-        displacements : numpy.ndarrya
+        displacements
             displacements of each atom in the supercell (`(N, 3)` array)
@@ -303,3 +308,3 @@ """
 
-    def get_fcs_sensing(self, fcs):
+    def get_fcs_sensing(self, fcs: ForceConstants) -> Tuple[np.ndarray, np.ndarray]:
         """ Creates a fit matrix from force constants directly.
@@ -313,17 +318,14 @@
 
-        The parameters can be extracted using e.g. least squares from numpy
+        The parameters can be extracted using e.g. least squares from numpy::
 
-        >>> parameters = np.linalg.lstsq(*fcm.get_fcs_sensing(fcs))[0]
+            parameters = np.linalg.lstsq(*fcm.get_fcs_sensing(fcs))[0]
 
         Parameters
         ----------
-        fcs: ForceConstants
-            Must be compatible with the ideal structure of the model
+        fcs
+            force constants that are compatible with the ideal structure of the model
 
         Returns
         -------
-        M : np.array
-            The sensing matrix
-        F : np.array
-            The flattened, irreducible force constants
+        a tuple comprising the sensing matrix and the flattened, irreducible force constants
         """
@@ -352,3 +354,3 @@ M, F = [], []
     @staticmethod
-    def read(f):
+    def read(f: Union[str, IO]):
         """Reads a force constant model from file.
@@ -358,9 +360,8 @@
         ----------
-        f : str or file object
-            name of input file (str) or stream to load from (file object)
+        f
+            name of input file (`str`) or stream to load from (`IO`)
 
         Returns
         -------
-        ForceConstantModel
-            the original object as stored in the file
+        the force constant model object as stored in the file
         """
@@ -373,3 +374,3 @@ if isinstance(f, str):
 
-    def write(self, f):
+    def write(self, f: Union[str, IO]) -> None:
         """Writes a force constant model to file.
@@ -379,4 +380,4 @@
         ----------
-        f : str or file object
-            name of input file (str) or stream to write to (file object)
+        f
+            name of input file (`str`) or stream to write to (`IO`)
         """
@@ -383,0 +384,0 @@ if isinstance(f, str):

hiphive/force_constants.py

@@ -170,4 +170,4 @@ """
                 fc_sum_ijk = np.zeros((3, )*order)
-                for l in atomic_indices:
-                    cluster = ijk + (l, )
+                for m in atomic_indices:
+                    cluster = ijk + (m, )
                     fc_sum_ijk += self[cluster]
@@ -174,0 +174,0 @@ assert np.linalg.norm(fc_sum_ijk) < tol, assert_msg.format(order, *ijk)

hiphive/utilities.py

@@ -119,8 +119,11 @@ """
     -------
-    >>> db = connect('dft_training_structures.db')
-    >>> training_structures = [row.toatoms() for row in db.select()]
-    >>> training_structures = prepare_structures(training_structures, atoms_ideal)
-    >>> for s in training_structures:
-    >>>     sc.add_structure(s)
 
+    The following example illustrates the use of this function::
+
+        db = connect('dft_training_structures.db')
+        training_structures = [row.toatoms() for row in db.select()]
+        training_structures = prepare_structures(training_structures, atoms_ideal)
+        for s in training_structures:
+            sc.add_structure(s)
+
     Parameters
@@ -156,6 +159,3 @@ ----------
     --------
-    After obtaining the permutation via
-    ```
-    p = find_permutation(atoms1, atoms2)
-    ```
+    After obtaining the permutation via ``p = find_permutation(atoms1, atoms2)``
     the reordered structure ``atoms1[p]`` will give the closest match
@@ -162,0 +162,0 @@ to ``atoms2``.

PKG-INFO

 Metadata-Version: 1.2
 Name: hiphive
-Version: 0.7
+Version: 0.7.1
 Summary: High-order force constants for the masses
@@ -98,3 +98,2 @@ Home-page: http://hiphive.materialsmodeling.org/
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
 Classifier: Programming Language :: Python :: 3.6
@@ -101,0 +100,0 @@ Classifier: Programming Language :: Python :: 3.7

setup.py

@@ -7,4 +7,4 @@ #!/usr/bin/env python3
 
-if sys.version_info < (3, 5, 0, 'final', 0):
-    raise SystemExit('Python 3.5 or later is required!')
+if sys.version_info < (3, 6, 0, 'final', 0):
+    raise SystemExit('Python 3.6 or later is required!')
 
@@ -49,3 +49,2 @@ with open('README.rst', encoding='utf-8') as fd:
           'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.5',
           'Programming Language :: Python :: 3.6',
@@ -52,0 +51,0 @@ 'Programming Language :: Python :: 3.7',

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