def generate_shell(structs,fnames,center_atom,radius,shell=None,vacuum=15):
for struct,fname in zip(structs,fnames):
center_coord=struct[center_atom].coords
if shell is None:
sites=struct.get_neighbors_in_shell(center_coord,0,radius)
file_name="sphere_"+fname+".vasp"
else:
sites=struct.get_neighbors_in_shell(center_coord,radius,shell)
file_name="shell_"+fname+".vasp"
coords=[site[0].coords for site in sites]
species=[site[0].specie for site in sites]
mol=Molecule(coords=coords,species=species)
max_dist=np.max(mol.distance_matrix)
a=b=c=max_dist+vacuum
box_struct=mol.get_boxed_structure(a,b,c)
box_struct.to(filename=file_name,fmt='poscar')
[-0.513360, 0.889165, -0.363000]]
mol = Molecule(["C", "H", "H", "H", "H"], coords)
print("mol:", mol)
print("\n")
print("mol[0]:", mol[0])
print("mol[1]:", mol[1])
print("\n")
#断连index为0和1两个原子之间的化学键，有上面的输出可以看到这两个位c和H,但是很奇怪为何会出现如下的结果？可能与空间结构有关系？
for frag in mol.break_bond(0, 1):
print("frag:", frag)
print("\n")
print("neighbors of mol[0]:", mol.get_neighbors(mol[0], 3))
#得到分子中的共价键
print("covalent_bonds of:", mol.get_covalent_bonds())
print("\n")
#Creates a Structure from a Molecule by putting the Molecule in
#the center of a orthorhombic box. Useful for creating Structure
#for calculating molecules using periodic codes.
#通过把分子放在正交晶（orthorhombic）的盒子box里，从分子Molecule生存结构Structure。
#创建结构Structure，用于通过周期代码计算分子。
structure = mol.get_boxed_structure(10, 10, 10)
print("structure:", structure)
#xyz format是用来表示分子几何结构的文件，需要定分子中原子的坐标。
from pymatgen.io.xyz import XYZ
xyz = XYZ(mol)
xyz.write_file("methane.xyz")
#scaling fator ,default 1.0
factor=1.0
all_sts={}
for i in atom_range:
print('---------'+str(i)+'-----------------')
sts=[]
#numatom atoms
numIons=[i]
while True:
try:
st=gen_cluster(system,numIons,sg=None,dimension=0,factor=1.0)
if st is not None:
opted=opt(st)
if opted is not None:
mol=Molecule(opted.species,opted.cart_coords)
a=max(mol.cart_coords[:,0])-min(mol.cart_coords[:,0])
b=max(mol.cart_coords[:,1])-min(mol.cart_coords[:,1])
c=max(mol.cart_coords[:,2])-min(mol.cart_coords[:,2])
opted=mol.get_boxed_structure(a+vac,b+vac,c+vac)
min_dist=(np.eye(len(opted))*1000+opted.distance_matrix).min()
if min_dist <2.0:
continue
opted.to('poscar','init_clusters/N-'+str(i)+'-sg-'+str(len(sts))+'.vasp')
sts.append({'origin':st,'opted':opted})
except:
pass
if len(sts)>=sg_numb:
break
all_sts[i]=sts
dumpfn(all_sts,'all.json',indent=4)
all_sts = {}
for i in atom_range:
print('---------' + str(i) + '-----------------')
sts = []
# for j in range(sg_numb):
#numatom atoms
numIons = [i]
while True:
try:
st = gen_cluster(system, numIons, sg=None, dimension=0, factor=1.0)
if st is not None:
opted = opt(st)
if opted is not None:
mol = Molecule(opted.species, opted.cart_coords)
a = b = c = np.max(mol.distance_matrix) + 10
opted = mol.get_boxed_structure(a, b, c)
opted.to(
'poscar', 'structs/N-' + str(i) + '-sg-' +
str(len(sts)) + '.vasp')
sts.append({'origin': st, 'opted': opted})
except Exception as e:
traceback.print_exc()
info = traceback.format_exc()
print(info)
if len(sts) >= sg_numb:
break
all_sts[i] = sts
dumpfn(all_sts, 'all.json', indent=4)
