def test_nbors():
box = [[5.493642, 0, 0], [0, 5.493642, 0], [0, 0, 5.493642]]
elements = ["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"]
coords = [
[0, 0, 0],
[0.25, 0.25, 0.25],
[0.000000, 0.500000, 0.500000],
[0.250000, 0.750000, 0.750000],
[0.500000, 0.000000, 0.500000],
[0.750000, 0.250000, 0.750000],
[0.500000, 0.500000, 0.000000],
[0.750000, 0.750000, 0.250000],
]
coords = np.array(coords)
# box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
# coords = [[0, 0, 0], [0.25, 0.25, 0.25]]
# elements = ["Si", "Si"]
Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
nbr = NeighborsAnalysis(Si)
nb = nbr.get_all_distributions
tmp = round((nb["rdf"][-3]), 2)
assert (tmp) == (4.08)
nbr.get_rdf(plot=True)
# nbr.ang_dist(nbor_info=info,plot=True)
nbr.ang_dist_first(plot=True)
nbr.ang_dist_second(plot=True)
nbr.get_ddf(plot=True)
angs = nbr.atomwise_angle_dist()
ardf = nbr.atomwise_radial_dist()
cmd = "rm *.png"
os.system(cmd)
def get_comp_descp(
self,
jcell=True,
jmean_chem=True,
jmean_chg=True,
jrdf=False,
jrdf_adf=True,
print_names=False,
):
"""
Get chemo-structural CFID decriptors.
Args:
struct: Structure object
jcell: whether to use cell-size descriptors
jmean_chem: whether to use average chemical descriptors
jmean_chg: whether to use average charge distribution descriptors
jmean_rdf: whether to use radial distribution descriptors
jrdf_adf: whether to use radial and angle distribution descriptors
print_names: whether to print names of descriptors
Returns:
cat: catenated final descriptors
"""
cat = []
s = self._atoms
cell = []
mean_chem = []
rdf = []
nn = []
mean_chg = []
adfa = []
adfb = []
ddf = []
if jmean_chem:
el_dict = s.composition._content
# print (el_dict,type(el_dict))
arr = []
for k, v in el_dict.items():
des = Specie(k).get_descrp_arr
arr.append(des)
mean_chem = np.mean(np.array(arr), axis=0)
# print ('mean_chem',len(mean_chem))
if jcell:
v_pa = round(float(s.volume) / float(s.num_atoms), 5)
logv_pa = round(log(v_pa), 5)
pf = s.packing_fraction
density = round(s.density, 5)
cell = np.array([v_pa, logv_pa, pf, density])
# print ('jcell',len(cell))
if jrdf:
Nbrs = NeighborsAnalysis(s)
_, distrdf, nn = Nbrs.get_rdf()
rdf = np.array(distrdf)
print("rdf", len(rdf))
if jrdf_adf:
try:
adfa = np.zeros(179)
adfb = np.zeros(179)
ddf = np.zeros(179)
rdf = np.zeros(100)
nn = np.zeros(100)
distributions = NeighborsAnalysis(s).get_all_distributions
rdf = distributions["rdf"]
nn = distributions["nn"]
adfa = distributions["adfa"]
adfb = distributions["adfb"]
ddf = distributions["ddf"]
except Exception:
pass
adfa = np.array(adfa)
adfb = np.array(adfb)
rdf = np.array(rdf)
ddf = np.array(ddf)
nn = np.array(nn)
# print ('adfa',len(adfa))
# print ('ddf',len(ddf))
# print ('adfb',len(adfb))
# print ('rdf',len(rdf))
# print ('nn',len(nn))
if jmean_chg:
chgarr = []
el_dict = s.composition._content
for k, v in el_dict.items():
chg = Specie(k).get_chgdescrp_arr
chgarr.append(chg)
mean_chg = np.mean(chgarr, axis=0)
# print ('mean_chg',len(mean_chg))
if print_names:
nmes = []
chem_nm = get_descrp_arr_name()
for d, nm in zip(
[mean_chem, cell, mean_chg, rdf,
adfa, adfb, ddf, nn],
["mean_chem", "cell", "mean_chg",
"rdf", "adfa", "adfb", "ddf", "nn"],
):
if len(d) != 0:
for ff, dd in enumerate(d):
cat.append(dd)
if nm == "mean_chem":
tag = chem_nm[ff]
else:
tag = str(nm) + str("_") + str(ff)
nmes.append(str(tag))
cat = np.array(cat).astype(float)
# print (nmes,len(nmes))
return nmes
else:
for d, nm in zip(
[mean_chem, cell, mean_chg, rdf,
adfa, adfb, ddf, nn],
["mean_chem", "cell", "mean_chg",
"rdf", "adfa", "adfb", "ddf", "nn"],
):
if len(d) != 0:
# if d != []:
for ff, dd in enumerate(d):
cat.append(dd)
cat = np.array(cat).astype(float)
return cat