How to use the smact.distorter.build_sub_lattice function in SMACT

test_case = builder.cubic_perovskite(['Ba','Ti','O'],repetitions=[2,2,2])


print "------------------------------"
print "Original coordinates: ", test_case
print "------------------------------"


# Do the single substitution first, it is trivial as all Ba sites are equivalent we will choose the first Ba
subs_site = [0.0, 0.0, 0.0]  # Fractional coordinates of the site to substitute
single_substitution = distort.make_substitution(test_case,subs_site,"Sr")
print "Single: ", single_substitution


#Build a sub-lattice you wish to disorder [test case do the Ba sub-lattice]
sub_lattice = distort.build_sub_lattice(single_substitution,"Ba")


# Enumerate the inequivalent sites
inequivalent_sites = distort.get_inequivalent_sites(sub_lattice,single_substitution)


# Replace Ba at inequivalent sites with Sr
i = 0
for inequivalent_site in inequivalent_sites:
    print "------------------------------"
    print " Substituted coordinates" 
    #print test_case,inequivalent_site
    distorted = distort.make_substitution(single_substitution,inequivalent_site,"Sr")
    io.write('POSCAR-%s'%i,distorted,format='vasp')
    i = i + 1
#    print distorted

print "------------------------------"
print "Original coordinates: ", test_case
print "------------------------------"


# Do the single substitution first, it is trivial as all Ba 
#  sites are equivalent we will choose the first Ba
subs_site = [0.0, 0.0, 0.0]
single_substitution = distort.make_substitution(test_case,subs_site,"Sr")
print "Single: ", single_substitution


#Build a sub-lattice you wish to disorder [test case do the Ba sub-lattice]
sub_lattice = distort.build_sub_lattice(single_substitution,"Ba")


# Enumerate the inequivalent sites
inequivalent_sites = distort.get_inequivalent_sites(sub_lattice,single_substitution)


# Replace Ba at inequivalent sites with Sr
for inequivalent_site in inequivalent_sites:
    print "------------------------------"
    print " Substituted coordinates" 
    #print test_case,inequivalent_site
    distorted = distort.make_substitution(single_substitution,inequivalent_site,"Sr")
    print distorted
    

print "------------------------------"

print ('-' * hlinewidth)
print "Original coordinates: "
pretty_print_atoms(test_case)
print ('-' * hlinewidth)

# Do the single substitution first, it is trivial as all Ba
#  sites are equivalent we will choose the first Ba
subs_site = [0.0, 0.0, 0.0]
single_substitution = distort.make_substitution(test_case, subs_site, "Sr")
print "Single: "
pretty_print_atoms(single_substitution)

# Build a sub-lattice you wish to disorder [test case do the Ba sub-lattice]
sub_lattice = distort.build_sub_lattice(single_substitution, "Ba")

# Enumerate the inequivalent sites
inequivalent_sites = distort.get_inequivalent_sites(sub_lattice,
                                                    single_substitution)

# Replace Ba at inequivalent sites with Sr
for i, inequivalent_site in enumerate(inequivalent_sites):
    print ('-' * hlinewidth)
    print "Substituted coordinates {0}".format(i)
    # print test_case,inequivalent_site
    distorted = distort.make_substitution(single_substitution,
                                          inequivalent_site,
                                          "Sr")
    pretty_print_atoms(distorted)

print('='*hlinewidth)