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Error in converting cp2k v2023.1 MD trajectory #15

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PolyuWeldingSpock opened this issue Jul 17, 2023 · 10 comments
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Error in converting cp2k v2023.1 MD trajectory #15

PolyuWeldingSpock opened this issue Jul 17, 2023 · 10 comments
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@robinzyb

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@PolyuWeldingSpock
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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:

--- 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 71, 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__
    self.Cp2kInfo = parse_cp2k_info(self.filename)
  File "/home/polyucmp/anaconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/block_parser/header_info.py", line 24, in parse_cp2k_info
    return Cp2kInfo(version=cp2k_info["version"][0][0][0])
IndexError: list index out of range

Here is the command I used:

import dpdata
from dpdata import System, LabeledSystem, MultiSystems
data=LabeledSystem('./xyz_3/', cp2k_output_name='cp2k.log', fmt="cp2kdata/md")

For now I have not figure out the reason. Hope you can help me. thanks!
@PolyuWeldingSpock
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Here is my cp2k file. Please check.
cp2k_test.zip

@PolyuWeldingSpock
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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.

@robinzyb
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have you tried 0.4.2 in devel branch?

@PolyuWeldingSpock
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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.

@robinzyb
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have a look at git usage. You need checkout to devel branch

@PolyuWeldingSpock
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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

@PolyuWeldingSpock
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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 PolyuWeldingSpock mentioned this issue Jul 25, 2023
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@link89 link89 mentioned this issue Sep 7, 2023
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@link89
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link89 commented Sep 7, 2023

@PolyuWeldingSpock You may try if this works for you https://github.com/link89/cp2kdata/tree/fix-2023-support

@PolyuWeldingSpock
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@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!

@robinzyb robinzyb mentioned this issue Sep 7, 2023
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@robinzyb
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robinzyb commented Sep 7, 2023

Thanks @link89 , @PolyuWeldingSpock if it works please close this issue

@robinzyb robinzyb mentioned this issue Sep 7, 2023
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@robinzyb robinzyb self-assigned this Sep 7, 2023
@robinzyb robinzyb mentioned this issue Sep 7, 2023
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@robinzyb robinzyb closed this as completed Oct 9, 2023
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