an error processing AIMD data for CP2K
caojiachun opened this issue · 10 comments
Hello:
I encountered an error when running dpdata to process the cp2k_aimd task data:
'>>> ls=LabeledSystem("cp2k.log",fmt='cp2k/aimd_output')
Traceback (most recent call last):
File "", line 1, in
File "/nfs/home/2001_aozhimin/apps/deepmd-kit-cpu/lib/python3.10/site-packages/dpdata/system.py", line 226, in init
self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, **kwargs)
File "/nfs/home/2001_aozhimin/apps/deepmd-kit-cpu/lib/python3.10/site-packages/dpdata/system.py", line 252, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/nfs/home/2001_aozhimin/apps/deepmd-kit-cpu/lib/python3.10/site-packages/dpdata/system.py", line 1012, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/nfs/home/2001_aozhimin/apps/deepmd-kit-cpu/lib/python3.10/site-packages/dpdata/plugins/cp2k.py", line 10, in from_labeled_system
xyz_file = sorted(glob.glob("{}/pos.xyz".format(file_name)))[0]
IndexError: list index out of range
'
cp2k.zip
hi,
You can try the cp2kdata package.
please check out this issue:#378.
If you use cp2kdata package, make sure the -pos-1.xyz,-1.ener and -frc-1.xyz files are included in the cp2k MD directory
Hi,
Have you solved this problem? I have faced the same issue.
@njzjz @PolyuWeldingSpock The zip file doesn't contain necessary files for me to parse. and I am not longer to maintain the original MD parser because it supports limited versions and compliated the problems
Hi,
Have you solved this problem? I have faced the same issue.
I copied the key file for recalculation and did not have the problem. It seems to be an occasional error.
Hi,
Have you solved this problem? I have faced the same issue.I copied the key file for recalculation and did not have the problem. It seems to be an occasional error.
Hello,
Did you solve this by using cp2kdata or cp2k/aimd fmt?
Hi,
Have you solved this problem? I have faced the same issue.I copied the key file for recalculation and did not have the problem. It seems to be an occasional error.
Hello, Did you solve this by using cp2kdata or cp2k/aimd fmt?
I didn't change it.
I see. The code will check the xyz files under the directories you specified. It seems the problem has been solved. I will close it now
Hi,
Have you solved this problem? I have faced the same issue.I copied the key file for recalculation and did not have the problem. It seems to be an occasional error.
Hello, Did you solve this by using cp2kdata or cp2k/aimd fmt?
I didn't change it.
Hi,
which version of cp2k did you use?
Hi,
Have you solved this problem? I have faced the same issue.I copied the key file for recalculation and did not have the problem. It seems to be an occasional error.
Hello, Did you solve this by using cp2kdata or cp2k/aimd fmt?
I didn't change it.
Hi, which version of cp2k did you use?
7.10 version