xyz2cif小程序分享—cp2k结构优化的xyz文件转化为cif文件

obaica

cp2k结构优化输出的默认是xyz文件，其中不包含晶格信息。为了快速将结果输出，转化为cif文件、POSCAR文件，鄙人写了个小脚本（xyz2cif），读取xyz（自动读取最后一帧）、原始结构文件，快速生成cif、POSCAR文件。———by 王非凡 (附件脚本版权归王非凡)

lcthw

之前每次使用都用CP2K的restart借助Multiwfn+VESTA才能转为POSCAR 有这个就方便多了

qiutian

./xyz2cif.sh 运行了例子，报错如下：
*.xyz Read!
NO cif file!
./xyz2cif.sh: line 44: sflow: command not found
mv: cannot stat ‘POSCAR’: No such file or directory
The POSCAR_from_cif is Failed to generate
cat: POSCAR_from_cif: No such file or directory

JohnsonCheung90

请问出现这种报错是什么原因呢？

CAREFULLY CHECK ABOVE!!!THEN WE WILL BEGAIN by typing ENTER...
*.xyz Read!
*.cif Read!
./xyz2cif.sh: line 44: sflow: command not found
mv: cannot stat ‘POSCAR’: No such file or directory
*POSCAR_from_cif Read!
Traceback (most recent call last):
  File "xyz2pos.py", line 8, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
./xyz2cif.sh: line 112: sflow: command not found
XYZ2POS_output Existed
mv: cannot stat ‘cp2k_xyz_last_frame.cif’: No such file or directory
print('Okay to Generate cp2k_xyz_last_frame.cif !