调整原子顺序

背景

使用高斯建模得到的$B_{12}{H}_{12}^{2-}$分子的结构上相邻的B-H在原子顺序上不相邻，这就导致分析轨道系数的时候不方便，因此使用pywfn写个脚本来调整原子顺序

代码

import numpy as np
from pywfn.base import Mole
from pywfn.reader import LogReader
from pywfn.writer import GjfWriter

path = r"c:\Users\11032\Desktop\gfile\碳硼烷\B12H12_21_wfn.log"
reader = LogReader(path)
mole = Mole(reader)

map_dick = {}

for i, sym in enumerate(mole.atoms.syms()):
    if sym != "B":
        continue
    old_dist = 100
    map_dick[i] = 0
    for j, sym in enumerate(mole.atoms.syms()):
        if sym != "H":
            continue
        dist = np.linalg.norm(mole.atoms.xyzs[i] - mole.atoms.xyzs[j])
        if dist < old_dist:
            map_dick[i] = j
            old_dist = dist

syms = []
xyzs = []
for key, val in map_dick.items():
    print(key, val)
    syms.append(mole.atoms.syms[key])
    xyzs.append(mole.atoms.xyzs[key])
    syms.append(mole.atoms.syms[val])
    xyzs.append(mole.atoms.xyzs[val])

writer = GjfWriter()
writer.syms = syms
writer.xyzs = xyzs
writer.job = "m062x 6-311g nosymm pop=full gfinput"
writer.charge = -2
writer.multip = 1
writer.save("test.gjf")

结果

调整之后所有的B-H的原子索引是相邻的了