Merge branch 'master' into ele_band_color

CHANGES.rst

@@ -1,4 +1,15 @@
 Change log
+==========
+
+v2023.1.20
+----------
+* Passthrough kwargs support for Structure.from_file and Structure.from_str
+* Allow the `frac_tolerance` to be specified for rounding coordinates in CifParser.
+* PR #2803 from @amkrajewski add_weightbasedfunctions
+    When working with metallic alloys, weight-fraction-based notations such as Ti64 / Ti-6V-4Al or NiTiNOL60 / Ni-40Ti are commonly employed in both industrial specifications and scientific literature. Regardless of the numerous downsides of this situation, including errors in scientific experiments or NLP-parsing when they are mistaken for atomic fractions or chemical formulas, being able to create a Composition object from them (under correct interpretation) would be a useful pymatgen feature.
+    - Composition class method to initialize it from a dictionary of weight fractions
+    - Composition property giving a dictionary of weight fractions
+    - concise tests for the two above were added
 QChem: translate DMSO name in smd_solvent
 
 v2023.1.9

README.md

@@ -30,7 +30,7 @@ Pymatgen is free to use. However, we also welcome your help to improve this libr
 - Bug reports or feature requests: Please submit a [GitHub Issue](https://github.com/materialsproject/pymatgen/issues).
 - Code contributions via [pull requests](https://github.com/materialsproject/pymatgen/pulls) are welcome.
 - For help with usage that is unrelated to bugs or feature requests, please use the `pymatgen` [MatSci page](https://discuss.matsci.org/c/pymatgen).
-- [`matgenb`](https://matgenb.materialsvirtuallab.org) provides some Jupyter notebooks demonstrating functionality.
+- [`matgenb`](https://github.com/materialsvirtuallab/matgenb#introduction) provides some Jupyter notebooks demonstrating functionality.
 - Follow us on [Twitter](https://twitter.com/pymatgen) to get news and tips.
 
 ## Why use pymatgen?

dev_scripts/chemenv/equivalent_indices.py

@@ -7,15 +7,15 @@
 
 from __future__ import annotations
 
+import numpy as np
+
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "2.0"
 __maintainer__ = "David Waroquiers"
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-import numpy as np
-
 if __name__ == "__main__":
 
     cg_symbol = "O:6"

dev_scripts/chemenv/explicit_permutations.py

@@ -8,13 +8,6 @@
 
 from __future__ import annotations
 
-__author__ = "David Waroquiers"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "2.0"
-__maintainer__ = "David Waroquiers"
-__email__ = "david.waroquiers@gmail.com"
-__date__ = "Feb 20, 2016"
-
 import itertools
 import json
 import os
@@ -30,6 +23,13 @@
     LocalGeometryFinder,
 )
 
+__author__ = "David Waroquiers"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "2.0"
+__maintainer__ = "David Waroquiers"
+__email__ = "david.waroquiers@gmail.com"
+__date__ = "Feb 20, 2016"
+
 
 class Algo:
     pass

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -40,23 +40,23 @@
         if algo.algorithm_type != "SEPARATION_PLANE":
             raise ValueError("WRONG ALGORITHM !")
 
-    newalgos = []
+    new_algos = []
 
     ialgo = 1
-    for sepplanealgo in cg._algorithms:
-        print(f"In ialgo = {ialgo:d}/{len(cg._algorithms):d}")
+    for sep_plane_algo in cg._algorithms:
+        print(f"In {ialgo = :d}/{len(cg._algorithms):d}")
         ialgo += 1
-        if sepplanealgo.algorithm_type != "SEPARATION_PLANE":
+        if sep_plane_algo.algorithm_type != "SEPARATION_PLANE":
             raise ValueError("Should all be separation plane")
 
-        permsonfile = f"Permutations on file in this algorithm ({len(sepplanealgo._permutations):d}) "
-        print(permsonfile)
-        print(sepplanealgo._permutations)
-        permutations = sepplanealgo.safe_separation_permutations(
-            ordered_plane=sepplanealgo.ordered_plane, ordered_point_groups=sepplanealgo.ordered_point_groups
+        perms_on_file = f"Permutations on file in this algorithm ({len(sep_plane_algo._permutations):d}) "
+        print(perms_on_file)
+        print(sep_plane_algo._permutations)
+        permutations = sep_plane_algo.safe_separation_permutations(
+            ordered_plane=sep_plane_algo.ordered_plane, ordered_point_groups=sep_plane_algo.ordered_point_groups
         )
 
-        sepplanealgo._permutations = permutations
+        sep_plane_algo._permutations = permutations
 
         print(f"Test permutations ({len(permutations):d}) :")
         print(permutations)
@@ -72,12 +72,14 @@
         # Setting up the plane of separation
         local_plane = None
         found = False
-        for npoints in range(sepplanealgo.minimum_number_of_points, min(sepplanealgo.maximum_number_of_points, 4) + 1):
+        for n_points in range(
+            sep_plane_algo.minimum_number_of_points, min(sep_plane_algo.maximum_number_of_points, 4) + 1
+        ):
             if found:
                 break
-            for ipoints in itertools.combinations(sepplanealgo.plane_points, npoints):
+            for ipoints in itertools.combinations(sep_plane_algo.plane_points, n_points):
                 points_combination = [lgf.local_geometry.coords[ipoint] for ipoint in ipoints]
-                if npoints == 2:
+                if n_points == 2:
                     if collinear(
                         points_combination[0], points_combination[1], lgf.local_geometry.central_site, tolerance=0.25
                     ):
@@ -87,15 +89,15 @@
                     )
                     found = True
                     break
-                elif npoints == 3:
+                elif n_points == 3:
                     if collinear(points_combination[0], points_combination[1], points_combination[2], tolerance=0.25):
                         continue
                     local_plane = Plane.from_3points(
                         points_combination[0], points_combination[1], points_combination[2]
                     )
                     found = True
                     break
-                elif npoints > 3:
+                elif n_points > 3:
                     local_plane = Plane.from_npoints(points_combination, best_fit="least_square_distance")
                     found = True
                     break
@@ -106,7 +108,7 @@
         # Actual test of the permutations
         cgsm = lgf._cg_csm_separation_plane(
             coordination_geometry=cg,
-            sepplane=sepplanealgo,
+            sepplane=sep_plane_algo,
             local_plane=local_plane,
             plane_separations=[],
             dist_tolerances=[0.05, 0.1, 0.2, 0.3],
@@ -124,7 +126,7 @@
 
         print("Continuous symmetry measures")
         print(csms)
-        csms_with_recorded_permutation = []
+        csms_with_recorded_permutation: list[float] = []
         explicit_permutations = []
         for icsm, csm in enumerate(csms):
             found = False
@@ -137,16 +139,16 @@
                 csms_with_recorded_permutation.append(csm)
                 explicit_permutations.append(sep_perms[icsm])
 
-        print(permsonfile)
+        print(perms_on_file)
         print(f"Permutations found ({len(explicit_permutations):d}) : ")
         print(explicit_permutations)
-        sepplanealgo.explicit_permutations = explicit_permutations
-        newalgos.append(sepplanealgo)
+        sep_plane_algo.explicit_permutations = explicit_permutations
+        new_algos.append(sep_plane_algo)
 
     # Write update geometry file ?
     test = input('Save it ? ("y" to confirm)')
     if test == "y":
-        cg._algorithms = newalgos
+        cg._algorithms = new_algos
         cg_dict = cg.as_dict()
         with open(f"../coordination_geometries_files_new/{cg_symbol}.json", "w") as f:
             json.dump(cg_dict, f)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -48,8 +48,15 @@ def prt2(string, printing_volume):
 
 
 # Iterator function for the random permutations
-def random_permutations_iterator(initial_permutation, npermutations):
-    for _ in range(npermutations):
+def random_permutations_iterator(initial_permutation, n_permutations):
+    """
+    It takes a list and returns an iterator that yields random permutations of that list
+
+    Args:
+        initial_permutation: the initial permutation of the data
+        n_permutations: the number of permutations to generate
+    """
+    for _ in range(n_permutations):
         shuffle(initial_permutation)
         yield initial_permutation
 
@@ -157,7 +164,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
 
         cg = all_cg[cg_symbol]
 
-        print(f'Getting explicit permutations for geometry "{cg.name}" (symbol : "{cg_symbol}")\n')
+        print(f"Getting explicit permutations for geometry {cg.name!r} (symbol : {cg_symbol!r})\n")
 
         # Setup of the local geometry finder
         lgf = LocalGeometryFinder()
@@ -274,8 +281,8 @@ def random_permutations_iterator(initial_permutation, npermutations):
 
         while True:
             test = input(
-                f'Get the explicit optimized permutations for geometry "{cg.name}" (symbol : '
-                f'"{cg_symbol}") ? ("y" to confirm, "q" to quit)\n'
+                f"Get the explicit optimized permutations for geometry {cg.name!r} (symbol : "
+                f'{cg_symbol!r}) ? ("y" to confirm, "q" to quit)\n'
             )
             if test not in ["y", "q"]:
                 print("Wrong key, try again")
@@ -285,7 +292,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
             elif test == "q":
                 exit()
         # 2. Optimization of the permutations
-        print(f'Getting explicit optimized permutations for geometry "{cg.name}" (symbol : "{cg_symbol}")\n')
+        print(f"Getting explicit optimized permutations for geometry {cg.name!r} (symbol : {cg_symbol!r})\n")
         perms_used_algos = [dict() for algo in cg.algorithms]
 
         # Loop on algorithms
@@ -424,7 +431,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
                 algo.explicit_optimized_permutations = np.array(explicit_optimized_permutations)
 
         test = input(
-            f'Save coordination geometry "{cg.name}" (symbol "{cg_symbol}") and new explicit and optimized '
+            f"Save coordination geometry {cg.name!r} (symbol {cg_symbol!r}) and new explicit and optimized "
             'permutations ? ("y" to confirm)'
         )
         if test == "y":

dev_scripts/chemenv/plane_multiplicity.py

@@ -7,17 +7,17 @@
 
 from __future__ import annotations
 
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
+
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "2.0"
 __maintainer__ = "David Waroquiers"
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
-    AllCoordinationGeometries,
-)
-
 if __name__ == "__main__":
 
     allcg = AllCoordinationGeometries()

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -7,13 +7,6 @@
 
 from __future__ import annotations
 
-__author__ = "David Waroquiers"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "2.0"
-__maintainer__ = "David Waroquiers"
-__email__ = "david.waroquiers@gmail.com"
-__date__ = "Feb 20, 2016"
-
 import copy
 import json
 from typing import Sequence
@@ -40,6 +33,14 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
+__author__ = "David Waroquiers"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "2.0"
+__maintainer__ = "David Waroquiers"
+__email__ = "david.waroquiers@gmail.com"
+__date__ = "Feb 20, 2016"
+
+
 allcg = AllCoordinationGeometries()
 
 
@@ -151,23 +152,23 @@ def figure_fractions(self, weights_options: dict, morphing_factors: Sequence[flo
 
     def get_structure(self, morphing_factor):
         lattice = Lattice.cubic(5.0)
-        myspecies = ["O"] * (self.coordination_geometry.coordination_number + 1)
-        myspecies[0] = "Cu"
+        species = ["O"] * (self.coordination_geometry.coordination_number + 1)
+        species[0] = "Cu"
 
         coords = copy.deepcopy(self.abstract_geometry.points_wcs_ctwcc())
         bare_points = self.abstract_geometry.bare_points_with_centre
 
         for morphing in self.morphing_description:
             if morphing["site_type"] == "neighbor":
-                isite = morphing["ineighbor"] + 1
+                i_site = morphing["ineighbor"] + 1
                 if morphing["expansion_origin"] == "central_site":
                     origin = bare_points[0]
-                vector = bare_points[isite] - origin
-                coords[isite] += vector * (morphing_factor - 1.0)
+                vector = bare_points[i_site] - origin
+                coords[i_site] += vector * (morphing_factor - 1.0)
             else:
                 raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
 
-        structure = Structure(lattice=lattice, species=myspecies, coords=coords, coords_are_cartesian=True)
+        structure = Structure(lattice=lattice, species=species, coords=coords, coords_are_cartesian=True)
         return structure
 
     def estimate_parameters(self, dist_factor_min, dist_factor_max, symmetry_measure_type="csm_wcs_ctwcc"):

dev_scripts/chemenv/test_algos.py

@@ -7,13 +7,6 @@
 
 from __future__ import annotations
 
-__author__ = "David Waroquiers"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "2.0"
-__maintainer__ = "David Waroquiers"
-__email__ = "david.waroquiers@gmail.com"
-__date__ = "Feb 20, 2016"
-
 import itertools
 import time
 from math import factorial
@@ -29,6 +22,13 @@
     LocalGeometryFinder,
 )
 
+__author__ = "David Waroquiers"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "2.0"
+__maintainer__ = "David Waroquiers"
+__email__ = "david.waroquiers@gmail.com"
+__date__ = "Feb 20, 2016"
+
 if __name__ == "__main__":
 
     allcg = AllCoordinationGeometries()
@@ -97,4 +97,4 @@
         print("   => ", algos_results)
         iperm += 1
     t2 = time.clock()
-    print(f'Time to test {nperms} permutations for geometry "{cg.name}" (symbol "{cg_symbol}") : {t2 - t1:.2f} seconds')
+    print(f"Time to test {nperms} permutations for geometry {cg.name!r} (symbol {cg_symbol!r}) : {t2 - t1:.2f} seconds")

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -7,13 +7,6 @@
 
 from __future__ import annotations
 
-__author__ = "David Waroquiers"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "2.0"
-__maintainer__ = "David Waroquiers"
-__email__ = "david.waroquiers@gmail.com"
-__date__ = "Feb 20, 2016"
-
 import itertools
 from math import factorial
 from random import shuffle
@@ -26,6 +19,13 @@
     LocalGeometryFinder,
 )
 
+__author__ = "David Waroquiers"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "2.0"
+__maintainer__ = "David Waroquiers"
+__email__ = "david.waroquiers@gmail.com"
+__date__ = "Feb 20, 2016"
+
 if __name__ == "__main__":
 
     allcg = AllCoordinationGeometries()