preparing data from CP2K aimd output

[sli259]

I am new to the deepMD and want to prepare a dp data from my aimd simulation with CP2K. I keep get this error about list index out of range. Can anyone give me some suggestions where I made the mistake?

d_outcar = dpdata.LabeledSystem('../cp2k_out/MnS-rs-pos-1.xyz', fmt = 'cp2k/aimd_output')

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In [3], line 4
      1 # dsys = dpdata.LabeledSystem('/Users/shili/Documents/ANL/projects/packages/deepmd-kit/examples/data_conv/OUTCAR')
      2 # d_poscar = dpdata.System('../cp2k_out/H2O-64-pos-1.xyz', fmt = 'cp2k/output')
      3 # d_outcar = dpdata.System('../trajectory/rs_traj.gro', fmt = 'gromacs/gro')
----> 4 d_outcar = dpdata.LabeledSystem('../cp2k_out/MnS-rs-pos-1.xyz', fmt = 'cp2k/aimd_output')
      5 # d_outcar = dpdata.LabeledSystem('../trajectory/rs_traj.gro', fmt = 'gromacs/gro')
      6 # d_outcar = dpdata.LabeledSystem('../cp2k_out/H2O.out', fmt = 'cp2k/output')
      7 # dsys = dpdata.LabeledSystem('gro', )

File ~/miniconda3/envs/deepmd/lib/python3.8/site-packages/dpdata/system.py:265, in System.__init__(self, file_name, fmt, type_map, begin, step, data, convergence_check, **kwargs)
    263 if file_name is None :
    264     return
--> 265 self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, convergence_check=convergence_check, **kwargs)
    267 if type_map is not None:
    268     self.apply_type_map(type_map)

File ~/miniconda3/envs/deepmd/lib/python3.8/site-packages/dpdata/system.py:291, in System.from_fmt(self, file_name, fmt, **kwargs)
    289 if fmt == 'auto':
    290     fmt = os.path.basename(file_name).split('.')[-1].lower()
--> 291 return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)

File ~/miniconda3/envs/deepmd/lib/python3.8/site-packages/dpdata/system.py:1073, in LabeledSystem.from_fmt_obj(self, fmtobj, file_name, **kwargs)
   1072 def from_fmt_obj(self, fmtobj, file_name, **kwargs):
-> 1073     data = fmtobj.from_labeled_system(file_name, **kwargs)
   1074     if data:
   1075         if isinstance(data, (list, tuple)):

File ~/miniconda3/envs/deepmd/lib/python3.8/site-packages/dpdata/plugins/cp2k.py:11, in CP2KAIMDOutputFormat.from_labeled_system(self, file_name, restart, **kwargs)
      9 def from_labeled_system(self, file_name, restart=False, **kwargs):
     10    # print(glob.glob("{}/*pos*.xyz".format(file_name)))
---> 11     xyz_file = sorted(glob.glob("{}/*pos*.xyz".format(file_name)))[0]
     12     log_file = sorted(glob.glob("{}/*.log".format(file_name)))[0]
     13     return tuple(Cp2kSystems(log_file, xyz_file, restart))

IndexError: list index out of range

The file is just an xyz contains several time frames. I am not sure where is the problem. it seems like the xyz_file in cp2k.py didn't read any trajectories.

[njzjz]

It looks like the same error in #103.

[sli259]

Thanks for your suggestion, I have looked at the #103 and edited my code to read from the directory with xyz trajectory and output log file. Now there is no error of reading the files but somehow the information wasn't pass to the outcar.

Here is my xyz and log file if you can take a look and let me know what I missed. Thank you!

output.zip

d_outcar = dpdata.LabeledSystem('./cp2k_data/rs', fmt = 'cp2k/aimd_output')
print(d_outcar)

./cp2k_data/rs/pos.xyz ./cp2k_data/rs/rs.log

Data Summary
Labeled System
-------------------
Frame Numbers      : 0
Atom Numbers       : 0
Including Virials  : No
Element List       :
-------------------

[robinzyb]

Hi @sli259, the first argument of dpdata.LabeledSystem for cp2k aimd is a directory, not the name of pos files.

[sli259]

Sure, thank you for your help!

[robinzyb]

Hi, if possible, you can move the problem to the issue in cp2kdata repository. I would like to develop a more user friendly and useful python tool to quickly extract information from various cp2k outputs

[sli259]

Yes, thanks for the notice. I only run this for a short time to test if I can generate the dp data. Can you give me some suggestions what I can adjust to my input to use your parser at this moment?

[robinzyb]

YES, activate the print/trajectory print/forces section as I mentioned. set EACH/MD as 1

[sli259]

Hi, if possible, you can move the problem to the issue in cp2kdata repository. I would like to develop a more user friendly and useful python tool to quickly extract information from various cp2k outputs

Hi I am not sure how to transfer this to the issue in cp2kdata, it looks like I can only transfer the discussion to repository owned by deepmodeling.

[yetnobe]

Hi I got a similar error.
When I run the output file you provided, there are no errors. I would appreciate it if you could provide me with your "inp" file.

[robinzyb]

have you tried cp2kdata plugin?

[yetnobe]

oh thanks!! I will check with cp2k plugin.
I am a noob to cp2k.
I generate the "inp" file with "Multiwfn" and then manully modify the print conents.

inp.txt