Closed PolyuWeldingSpock closed 11 months ago
Here is my cp2k file. Please check. cp2k_test.zip
Another error occurred as below:
>>> import dpdata
>>> dp = dpdata.LabeledSystem('.', cp2k_output_name="*", fmt="cp2kdata/md")
--- You are parsing data using package Cp2kData ---
Obtian Energies From ./xyz-1.ener
Obtian Structures From ./xyz-pos-1.xyz
Obtian Froces From ./xyz-frc-1.xyz
Missing the atomic kind informations, atom names are true chemical symbols.
No cell information, please check if your inputs are correct.
--- You are parsing data using package Cp2kData ---
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 281, in __init__
self.from_fmt(
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 318, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 1169, in from_fmt_obj
self.check_data()
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 305, in check_data
dd.check(self)
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 118, in check
raise DataError(
dpdata.system.DataError: Type of cells is NoneType, but expected ndarray
It is very strange that if I type exact name of my output (cp2k.log) but not "*", the first error occurred.
have you tried 0.4.2 in devel branch?
have you tried 0.4.2 in devel branch?
Sorry, I cloned the devel branch and it still showed 0.4.1. I cannot find the 0.4.2.
have a look at git usage. You need checkout to devel branch
have a look at git usage. You need checkout to devel branch
Hi, I tried 0.4.2 and it make new error. PRINT_LEVEL was set to MEDIUM and frc.xyz was also generated.
>>> import dpdata
>>> dp = dpdata.LabeledSystem('./xyz_2', cp2k_output_name="std.out", fmt="cp2kdata/md")
--- You are parsing data using package Cp2kData ---
You are reading cell information from ./xyz_2/std.out
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 281, in __init__
self.from_fmt(
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 318, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/dpdata/system.py", line 1162, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/cp2kdata/dpdata_plugin.py", line 73, in from_labeled_system
cp2kmd = Cp2kOutput(output_file=cp2k_output_name, run_type="MD", path_prefix=path_prefix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/cp2kdata/output.py", line 83, in __init__
parse_run_type()
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/cp2kdata/output.py", line 311, in parse_md
self.init_atomic_coordinates, self.atom_kind_list, self.chemical_symbols = parse_init_atomic_coordinates(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/polyucmp/anaconda3/envs/biantieyuan/lib/python3.11/site-packages/cp2kdata/block_parser/coordinates.py", line 33, in parse_init_atomic_coordinates
for x, y, z in zip(*match.captures("x", "y", "z")):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'captures'
I upload my file in this Onedrive link since it is too big. https://1drv.ms/u/s!AtO91yh6_pLhg7BB7OnE5Cl8p7Cwbw?e=8ILfEi
Hi, today i found that cp2kdata 0.4.2 can also not parse output of cp2k v8.1. Here is the error message:
import dpdata
dp = dpdata.LabeledSystem('./xyz_4', cp2k_output_name="std.out", fmt="cp2kdata/md")
--- You are parsing data using package Cp2kData ---
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 281, in __init__
self.from_fmt(
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 318, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 1162, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/dpdata_plugin.py", line 73, in from_labeled_system
cp2kmd = Cp2kOutput(output_file=cp2k_output_name, run_type="MD", path_prefix=path_prefix)
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 83, in __init__
parse_run_type()
File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 335, in parse_md
self.num_frames = len(self.energies_list)
AttributeError: 'Cp2kOutput' object has no attribute 'energies_list'. Did you mean: 'get_energies_list'?
xyz_4(1).zip i also upload my file. Please check.
@PolyuWeldingSpock You may try if this works for you https://github.com/link89/cp2kdata/tree/fix-2023-support
@PolyuWeldingSpock You may try if this works for you https://github.com/link89/cp2kdata/tree/fix-2023-support
Thanks for your help. I will try!
Thanks @link89 , @PolyuWeldingSpock if it works please close this issue
Hi,
I am trying to convert AIMD trajectory with cp2kdata to get datasets for deepmd. my cp2k version is 2023.1 and cp2kdata version is 0.4.1. I have put my .out, .ener,frc.xyz and pos.xyz into same dictionary but still get err:
Here is the command I used:
For now I have not figure out the reason. Hope you can help me. thanks!