ruff

bindings/python/examples/msympy_example.py

@@ -3,108 +3,118 @@
 import libmsym as msym, numpy as np, argparse, random, sys
 
 
-
 def read_xyz(fin):
     length = int(fin.readline())
     comment = fin.readline()[:-1]
     elements = []
-    for i in range(0,length):
+    for i in range(0, length):
         line = fin.readline().split()
-        elements.append(msym.Element(name = line[0], coordinates = map(float, line[1:4])))
+        elements.append(msym.Element(name=line[0], coordinates=map(float, line[1:4])))
 
     return (elements, comment)
 
+
 def write_xyz(fout, elements, comment):
     fout.write("%d\n%s\n" % (len(elements), comment))
     for e in elements:
         v = e.coordinates
         fout.write("%s %.14f %.14f %.14f\n" % (e.name, *v))
 
+
 parser = argparse.ArgumentParser()
-parser.add_argument('infile', type=argparse.FileType('r'))
-parser.add_argument('outfile', type=argparse.FileType('w'))
+parser.add_argument("infile", type=argparse.FileType("r"))
+parser.add_argument("outfile", type=argparse.FileType("w"))
 args = parser.parse_args()
 
 (elements, comment) = read_xyz(args.infile)
-
+
+
 def set_basis(element):
-    basis_function = msym.RealSphericalHarmonic(element = element, name = "1s")
+    basis_function = msym.RealSphericalHarmonic(element=element, name="1s")
     element.basis_functions = [basis_function]
     return basis_function
 
+
 basis_functions = [set_basis(e) for e in elements]
 
 
-#msym.init(library_location='/path_to_libmsym_library/libmsym.dylib') # e.g. for OS X without libmsym in dload path
+# msym.init(library_location='/path_to_libmsym_library/libmsym.dylib') # e.g. for OS X without libmsym in dload path
 
-#with msym.Context() as ctx:
+# with msym.Context() as ctx:
 #    ctx.elements = elements
 #    point_group = ctx.find_symmetry()
 #    selements = ctx.symmetrize_elements()
 #    write_xyz(args.outfile, selements, comment + " symmetrized by libmsym according to point group " + point_group)
- 
-with msym.Context(elements = elements, basis_functions = basis_functions) as ctx:
+
+with msym.Context(elements=elements, basis_functions=basis_functions) as ctx:
     point_group = ctx.find_symmetry()
     selements = ctx.symmetrize_elements()
-    write_xyz(args.outfile, selements, comment + " symmetrized by libmsym according to point group " + point_group)
-    ctx.symmetry_operations #symmetry operations
-    ctx.subrepresentation_spaces # subspace
-    ctx.subrepresentation_spaces[0].symmetry_species #symmetry species of space (index into character table)
-    ctx.subrepresentation_spaces[0].salcs # salcs that span space
-    ctx.subrepresentation_spaces[0].salcs[0].basis_functions # basis functions for salc    
-    ctx.subrepresentation_spaces[0].salcs[0].partner_functions # numpy array of partner functions expressed in terms of basis_functions coefficients
-
-    ctx.character_table.table # table as numpy array
-    ctx.character_table.symmetry_operations # representative symmetry operations
-    ctx.character_table.symmetry_species # symmetry species
+    write_xyz(
+        args.outfile,
+        selements,
+        comment + " symmetrized by libmsym according to point group " + point_group,
+    )
+    ctx.symmetry_operations  # symmetry operations
+    ctx.subrepresentation_spaces  # subspace
+    ctx.subrepresentation_spaces[
+        0
+    ].symmetry_species  # symmetry species of space (index into character table)
+    ctx.subrepresentation_spaces[0].salcs  # salcs that span space
+    ctx.subrepresentation_spaces[0].salcs[0].basis_functions  # basis functions for salc
+    ctx.subrepresentation_spaces[0].salcs[
+        0
+    ].partner_functions  # numpy array of partner functions expressed in terms of basis_functions coefficients
+
+    ctx.character_table.table  # table as numpy array
+    ctx.character_table.symmetry_operations  # representative symmetry operations
+    ctx.character_table.symmetry_species  # symmetry species
     ctx.character_table.symmetry_species[0].dim  # dimensionality of symmetry species
-    ctx.character_table.symmetry_species[0].name # name of symmetry species e.g. A2g
+    ctx.character_table.symmetry_species[0].name  # name of symmetry species e.g. A2g
 
-    somefunc = np.zeros((len(basis_functions)),dtype=np.float64)
-    for i in range(0,len(somefunc)):
+    somefunc = np.zeros((len(basis_functions)), dtype=np.float64)
+    for i in range(0, len(somefunc)):
         somefunc[i] = i
 
     species_components = ctx.symmetry_species_components(somefunc)
-    
+
     species = ctx.character_table.symmetry_species
 
     print(somefunc)
     for i, c in enumerate(species_components):
         print(str(c) + species[i].name)
-    
-    #matrix version of the above, as well as wave function symmetrization
+
+    # matrix version of the above, as well as wave function symmetrization
     (matrix, species, partners) = ctx.salcs
-    (d,d) = matrix.shape
+    (d, d) = matrix.shape
     print(matrix)
     print(species)
     print([(p.index, p.dim) for p in partners])
-    indexes = [x for x in range(0,d)]
+    indexes = [x for x in range(0, d)]
     random.shuffle(indexes)
-    matrix = matrix[indexes,:]
+    matrix = matrix[indexes, :]
     matrix += 0.01
     print(matrix)
-    (_same_matrix, species,partners) = ctx.symmetrize_wavefunctions(matrix)
+    (_same_matrix, species, partners) = ctx.symmetrize_wavefunctions(matrix)
     print(matrix)
     print(species)
     print([(p.index, p.dim) for p in partners])
 
-    #generating elements
+    # generating elements
     ctx.point_group = "D6h"
-    gen_elements = [msym.Element(name = "C", coordinates = [1.443524, 0.0,0.0]), msym.Element(name = "H", coordinates = [2.568381, 0.0, 0.0])]
+    gen_elements = [
+        msym.Element(name="C", coordinates=[1.443524, 0.0, 0.0]),
+        msym.Element(name="H", coordinates=[2.568381, 0.0, 0.0]),
+    ]
     benzene = ctx.generate_elements(gen_elements)
     maxcomp = max([max(e.coordinates) for e in benzene])
-    print(len(benzene),"\nbenzene")
+    print(len(benzene), "\nbenzene")
     for e in benzene:
         vec = np.asarray(e.coordinates)
-        vec[vec < maxcomp*sys.float_info.epsilon] = 0
-        print(e.name, vec[0],vec[1],vec[2])
-
+        vec[vec < maxcomp * sys.float_info.epsilon] = 0
+        print(e.name, vec[0], vec[1], vec[2])
 
-#with msym.Context(elements = elements, point_group = "T") as ctx:
+
+# with msym.Context(elements = elements, point_group = "T") as ctx:
 #    point_group = ctx.point_group
 #    selements = ctx.symmetrize_elements()
 #    write_xyz(args.outfile, selements, comment + " symmetrized by libmsym according to point group " + point_group)
-
-
-
-

bindings/python/libmsym/__init__.py

@@ -2,10 +2,8 @@
 
 _libmsym_install_location = None
 
+
 def export(defn):
     globals()[defn.__name__] = defn
     __all__.append(defn.__name__)
     return defn
-
-from . import libmsym
-