When i use dpdata and cp2kdata to convert cp2k MD data,I encountered an error,The content of this error is :dpdata.data_type.DataError: Shape of coords is (67, 1056, 3), but expected (68, 1056, 3).

[llllkkkkkoo]

When i use dpdata and cp2kdata to convert cp2k MD data,I encountered an error,The error message is as follows:
--- You are parsing data using package Cp2kData ---
Parsing Energies from aimd/Li-LiFSI-DME-1-2-1.ener
Parsing Structures from aimd/Li-LiFSI-DME-1-2-pos-1.xyz
Parsing Froces from aimd/Li-LiFSI-DME-1-2-frc-1.xyz
Parsing Stress from the CP2K output/log file: aimd/output
Parsing Cells Information from aimd/output
Atom names are fake chemical symbols as you set in cp2k input.
--- You are parsing data using package Cp2kData ---
Traceback (most recent call last):
File "./readdata_cp2k.py", line 6, in
data = dpdata.LabeledSystem('aimd',cp2k_output_name='output', fmt = 'cp2kdata/md')
File "/fs2/home/chengroup/.local/lib/python3.8/site-packages/dpdata/system.py", line 183, in init
self.from_fmt(
File "/fs2/home/chengroup/.local/lib/python3.8/site-packages/dpdata/system.py", line 220, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/fs2/home/chengroup/.local/lib/python3.8/site-packages/dpdata/system.py", line 1120, in from_fmt_obj
self.check_data()
File "/fs2/home/chengroup/.local/lib/python3.8/site-packages/dpdata/system.py", line 207, in check_data
dd.check(self)
File "/fs2/home/chengroup/.local/lib/python3.8/site-packages/dpdata/data_type.py", line 112, in check
raise DataError(
dpdata.data_type.DataError: Shape of coords is (67, 1056, 3), but expected (68, 1056, 3)
I hope to get your help,thank you very much.
files.zip

[robinzyb]

could you include 1-2-1.ener aimd/output in the zip as well?

[llllkkkkkoo]

yes,it is a restart md simulation,do I send you my reatart files? I use a python script for my ener files to ensure the output frequency of my ener file is same as my pos file and frc file.

[llllkkkkkoo]

this is my output files ,I hope that will be helpful for you to improve cp2kdata.
files.zip

[robinzyb]

thanks. I will fix it asap

[llllkkkkkoo]

thanks a lot.

[llllkkkkkoo]

Could you please tell me if you have updated the cp2kdata package?

[llllkkkkkoo]

Could you please tell me if you have updated the cp2kdata package?

[robinzyb]

not yet, I will update today. I am developing other codes for now

[robinzyb]

I am almost finishing the debugging. Could you update a smaller restart md outputs ,for example, a restart md with onlyt 2-3 steps, includes -pos-, -frc-, ener, and output?
That would be a great help!
I will include them into cp2kdata testsuits.

[robinzyb]

I found no restart information in your cp2k output file. I guess you directly submit the Li-LiFSI-DME-1-2-1.restart through cp2k.psmp -i Li-LiFSI-DME-1-2-1.restart , which is not recommened by cp2k.
An alternative way to submit restart is using

&EXT_RESTART
      RESTART_FILE_NAME Li-LiFSI-DME-1-2-1.restart
&END EXT_RESTART 

This will write header for restart in cp2k output

 *******************************************************************************
 *                            RESTART INFORMATION                              *
 *******************************************************************************
 *                                                                             *
 *    RESTART FILE NAME: bivo4-water-1.restart                                 *
 *                                                                             *
 * RESTARTED QUANTITIES:                                                       *
 *                       CELL                                                  *
 *                       COORDINATES                                           *
 *                       RANDOM NUMBER GENERATOR                               *
 *                       VELOCITIES                                            *
 *                       MD COUNTERS                                           *
 *                       MD AVERAGES                                           *
 *                       PARTICLE THERMOSTAT                                   *
 *                       REAL TIME PROPAGATION                                 *
 *                       PINT BEAD POSITIONS                                   *
 *                       PINT BEAD VELOCITIES                                  *
 *                       PINT NOSE THERMOSTAT                                  *
 *                       PINT GLE THERMOSTAT                                   *
 *                       HELIUM BEAD POSITIONS                                 *
 *                       HELIUM PERMUTATION STATE                              *
 *                       HELIUM FORCES ON SOLUTE                               *
 *                       HELIUM RNG STATE                                      *
 *******************************************************************************

With this header, I can let cp2kdata automatically detect whether it is a restart output file.
And I will write an extra option for telling cp2kdata if it is a restart output.

[llllkkkkkoo]

i always use restart file of cp2k to continue calculate,I really didn't notice that the output file do not include the restart information,
because it outputs a separate file called .restart file,so i do not allow the restart information to output the output file.

[llllkkkkkoo]

I guess you directly submit the Li-LiFSI-DME-1-2-1.restart through cp2k.psmp -i Li-LiFSI-DME-1-2-1.restart , which is not recommened by cp2k.
That's exactly what I did.
Thank you for your suggestion,i will test this method.

[robinzyb]

Just in case of your future calculations, please follow the recommended cp2k setups in https://github.com/robinzyb/cp2kdata/blob/main/docs/dpdata_plugin.md

[llllkkkkkoo]

i indeed reference this standard,but i do not notice this setting about restarting.

[llllkkkkkoo]

I found no restart information in your cp2k output file. I guess you directly submit the Li-LiFSI-DME-1-2-1.restart through cp2k.psmp -i Li-LiFSI-DME-1-2-1.restart , which is not recommened by cp2k. An alternative way to submit restart is using

&EXT_RESTART
      RESTART_FILE_NAME Li-LiFSI-DME-1-2-1.restart
&END EXT_RESTART 

This will write header for restart in cp2k output

 *******************************************************************************
 *                            RESTART INFORMATION                              *
 *******************************************************************************
 *                                                                             *
 *    RESTART FILE NAME: bivo4-water-1.restart                                 *
 *                                                                             *
 * RESTARTED QUANTITIES:                                                       *
 *                       CELL                                                  *
 *                       COORDINATES                                           *
 *                       RANDOM NUMBER GENERATOR                               *
 *                       VELOCITIES                                            *
 *                       MD COUNTERS                                           *
 *                       MD AVERAGES                                           *
 *                       PARTICLE THERMOSTAT                                   *
 *                       REAL TIME PROPAGATION                                 *
 *                       PINT BEAD POSITIONS                                   *
 *                       PINT BEAD VELOCITIES                                  *
 *                       PINT NOSE THERMOSTAT                                  *
 *                       PINT GLE THERMOSTAT                                   *
 *                       HELIUM BEAD POSITIONS                                 *
 *                       HELIUM PERMUTATION STATE                              *
 *                       HELIUM FORCES ON SOLUTE                               *
 *                       HELIUM RNG STATE                                      *
 *******************************************************************************

With this header, I can let cp2kdata automatically detect whether it is a restart output file. And I will write an extra option for telling cp2kdata if it is a restart output.

thank you very much,i will test cp2kdata again.

[llllkkkkkoo]

I have one more question,now if all versions of cp2kdata have updatad?

[robinzyb]

I am almost finishing the debugging. Could you update a smaller restart md outputs ,for example, a restart md with onlyt 2-3 steps, includes -pos-, -frc-, ener, and output? That would be a great help! I will include them into cp2kdata testsuits.

could you update smaller md files (with only 2-3 steps), so that I can test and update the code.

[llllkkkkkoo]

I'll send it to you as soon as possible.

[llllkkkkkoo]

I am almost finishing the debugging. Could you update a smaller restart md outputs ,for example, a restart md with onlyt 2-3 steps, includes -pos-, -frc-, ener, and output? That would be a great help! I will include them into cp2kdata testsuits.

could you update smaller md files (with only 2-3 steps), so that I can test and update the code.

these are my all output files,i hope these files are helpful to you.
cp2k.zip

[robinzyb]

New version of cp2kdata 0.6.7 is released.
you can update your cp2kdata by
pip install cp2kdata -U
Your cp2k md files are included in the testsuit of cp2kdata in
cp2kdata/tests/test_dpdata/v2024.1/aimd_npt_i_restart
The documentation for parsing restarted md is updated in
https://robinzyb.github.io/cp2kdata/docs/dpdata_plugin.html

Thank you for your help.

[llllkkkkkoo]

New version of cp2kdata 0.6.7 is released. you can update your cp2kdata by pip install cp2kdata -U Your cp2k md files are included in the testsuit of cp2kdata in cp2kdata/tests/test_dpdata/v2024.1/aimd_npt_i_restart The documentation for parsing restarted md is updated in https://robinzyb.github.io/cp2kdata/docs/dpdata_plugin.html

Thank you for your help.

thank you.