def read_xyz(self,modelfile):
with open(modelfile) as f:
content = f.readlines()
self.comment = content.pop(0) # Comment line
if('-1' in content[-1] and '.' not in content[-1]): # '-1' line
content.pop(-1)
self.lx,self.ly,self.lz = tuple([float(x) for x in content.pop(0).strip().split()])
self.natoms = len(content)
content = [x.strip().split() for x in content]
for i in range(0,len(content)):
for j in range(0,len(content[i])):
try:
content[i][j] = int(content[i][j])
except:
try:
content[i][j] = float(content[i][j])
except:
pass
self.atoms = []
for i,atom in enumerate(content):
self.atoms.append(Atom(i,atom[0],atom[1],atom[2],atom[3]))
if type(self.atoms[i].z) == type('hi'):
self.atoms[i].z = znum2sym.sym2z(self.atoms[i].z)
def __init__(self, id, znum, x, y, z):
self.id = id
if(isinstance(znum,int)):
self.z = znum
elif(isinstance(znum,str)):
self.z = znum2sym.sym2z(znum)
self.coord = (x,y,z)
self.vp = VoronoiPoly()
self.neighs = None # Neighbors. List when set
self.cn = None # Coordination number. int when set
self.sym = znum2sym.z2sym(self.z) #atomic symbol
def generate_coord_numbers(self):
""" atom.neighs must be defined first for all atoms """
self.coord_numbers = {}
# Form will be:
# {'Cu-Al': 4.5}, etc.
for typea in self.atomtypes:
self.coord_numbers[znum2sym.z2sym(typea)] = 0
for typeb in self.atomtypes:
self.coord_numbers[znum2sym.z2sym(typea)+'-'+znum2sym.z2sym(typeb)] = 0
for atom in self.atoms:
for n in atom.neighs:
self.coord_numbers[znum2sym.z2sym(atom.z)] += 1
self.coord_numbers[znum2sym.z2sym(atom.z)+'-'+znum2sym.z2sym(n.z)] += 1
self.bonds = self.coord_numbers.copy()
for key in self.coord_numbers:
elem = znum2sym.sym2z(key.split('-')[0])
self.coord_numbers[key] /= float(self.atomtypes[elem])
def generate_average_coord_numbers(self):
""" atom.neighs must be defined first for all atoms
Form will be:
{'Cu-Al': 4.5, ... }
"""
coord_numbers = {}
for typea in self.atomtypes:
coord_numbers[znum2sym.z2sym(typea)] = 0
for typeb in self.atomtypes:
coord_numbers[znum2sym.z2sym(typea)+'-'+znum2sym.z2sym(typeb)] = 0
for atom in self.atoms:
for n in atom.neighs:
coord_numbers[znum2sym.z2sym(atom.z)] += 1
coord_numbers[znum2sym.z2sym(atom.z)+'-'+znum2sym.z2sym(n.z)] += 1
for key in coord_numbers:
elem = znum2sym.sym2z(key.split('-')[0])
coord_numbers[key] /= float(self.atomtypes[elem])
return coord_numbers
def generate_cutoffs(m):
outcontent = []
cutoff_types = []
types = list(m.atomtypes)
types.sort()
for L in range(1, len(types)):
# for L in range(1,len(types)+1):
for subset in itertools.combinations(types, L):
# print(subset)
s = list(subset)
xx, g = gr(m, types=s)
g = list(g)
s = [znum2sym.z2sym(y) for y in s]
# g.insert(0,'gr_{0}'.format('_'.join(s)))
outcontent.append(g)
cutoff_types.append(s)
cutoff_types = [[x[0], x[0]] if len(x) == 1 else x for x in cutoff_types]
cutoff_types = [[znum2sym.sym2z(y) for y in x] for x in cutoff_types]
cutoff_types = [[types.index(y) for y in x] for x in cutoff_types]
# print(cutoff_types)
cutoffs = np.zeros((len(m.atomtypes), len(m.atomtypes)))
xx = list(xx)
# xx.insert(0,'dr')
outcontent.insert(0, xx)
for i, arr in enumerate(outcontent[1:]):
peak1 = arr.index(max(arr))
# print('peak1',peak1,xx[peak1],arr[peak1])
# print(arr[peak1:int(round(peak1*3.5))])
min1 = peak1 + arr[peak1 : int(round(peak1 * 3.5))].index(min(arr[peak1 : int(round(peak1 * 3.5))]))
# print('min1',min1,xx[min1],arr[min1])
peak2 = min1 + arr[min1:].index(max(arr[min1:]))
# print('peak2',peak2,xx[peak2],arr[peak2])
# print('')
cutoffs[cutoff_types[i][0]][cutoff_types[i][1]] = xx[min1]
cutoffs[cutoff_types[i][1]][cutoff_types[i][0]] = xx[min1]
# print(cutoffs)
return cutoffs