예제 #1
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파일: cleave.py 프로젝트: obaica/maptool-1
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')
예제 #2
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          [-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")
예제 #3
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#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)
예제 #4
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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)