Closed hellozhaoming closed 1 month ago
Could you provide the input and output to me? Usually, we won't set the number of atomic kinds larger than 100.
Also if there is no way to show all atomic kinds, all I can do is raise an error for this case.
The file size is too big and cannot upload as attach files. I share it with baidu netdist: 链接:https://pan.baidu.com/s/1fF-ODhDMyKxC8O40Wu97Xw 提取码:no74
I fixed the problem by a small modification of funcitons in atomic_kind.py
ATOMIC_KINDS_RE = re.compile(
#r"""
#\s{2}\d+\.\sAtomic\skind:\s+(?P<atomic_kind>\S+)
#""",
r"""
\s{2}(\d+|\*+)\.\sAtomic\skind:\s+(?P<atomic_kind>\S+)
""",
re.VERBOSE
)
def parse_atomic_kinds(output_file):
num_atomic_kinds_list = parse_num_atomic_kinds(output_file)
atomic_kinds = []
for match in ATOMIC_KINDS_RE.finditer(output_file):
atomic_kinds.append(match["atomic_kind"].rstrip('0123456789'))
#atomic_kinds.append(match["atomic_kind"])
if atomic_kinds:
# only return the last atomic kinds
return np.array(atomic_kinds[-num_atomic_kinds_list[-1]:], dtype=str)
else:
return None
thanks. I think I still need to preserve this functionality. I can add extra choice in Cp2kOutput when you just need element symbols.
hi, I decide not to add fixed this problem. This is caused by cp2k reading cif file as input. you can try to start MD with xyz format so that only 4 types of element are counted.
if we parse the atomic kind of systems with over 100 atoms, the len of atomic_kind will be 99 while the len of atomic_kind_list will be larger than 99. in output.py
def get_chemical_symbols_fake(self): if (self.atom_kind_list is not None) and (self.atomic_kind is not None): return self.atomic_kind[self.atom_kind_list-1]
there will be an error 'index 99 is out of bounds for axis 0 with size 99'This is because the output file in cp2k unable to display the number over 99, for example,
Atomic kind: O99 Number of atoms: 1 **. Atomic kind: O100 Number of atoms: 1
version of cp2k 7.1 version of cp2kdata 0.6.9