Problem loading data from restarted AIMD trajectories generated using CP2K

[chemrajib]

Hello All,
I am facing a problem while using dpdata. When I start the simulation from initial structure and perform AIMD run using cp2k, I can load data without any problem. However, when I use any restart point and generate a new sets of trajectories, I am getting the following errors.

--- You are parsing data using package Cp2kData ---
Parsing Energies from ./H2O_restart-1.ener
Parsing Structures from ./H2O_restart-pos-1.xyz
Parsing Forces from ./H2O_restart-frc-1.xyz
Parsing Stresses from ./tetramer_restart.log
Parsing Cells from ./H2O_restart-1.cell
Atom names are fake chemical symbols as you set in cp2k input.
Virial Parsing using cp2kdata as plug in for dpdata
was not multiplied by volume before cp2kdata v0.6.4
please check the cp2kdata version and the virial.npy

Traceback (most recent call last):
File "/home/rajib/DEEPMD/WATER/dpgen_traj/restart_run/dpdata_read.py", line 4, in
dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
File "/apps/codes/miniforge3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 200, in init
self.from_fmt(
File "/apps/codes/miniforge3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 237, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/apps/codes/miniforge3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 1205, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/apps/codes/miniforge3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/dpdata_plugin.py", line 135, in from_labeled_system
data['virials'] = cp2kmd.stress_tensor_list*volumes/EV_ANG_m3_TO_GPa
ValueError: operands could not be broadcast together with shapes (11,3,3) (10,1,1)

I have attached the required files. I will appreciate any help in this regard.
dpdata_test.zip

Thanks!

[robinzyb]

please add restart=True

dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md", restart=True)

[robinzyb]

I have fixed it. Could you provide the restart md calculation with 2 or 3 md steps ? so that I can include your case in my code testing, then I release the new version of cp2kdata. ./dpdata_test/restart_run/

[chemrajib]

Thanks! I have uploaded the files for the restart run here.
restart_run.zip

In case you need the files for the run from the scratch and inputfiles, I attached here.
dpdata_test.zip

[chemrajib]

I have fixed it. Could you provide the restart md calculation with 2 or 3 md steps ? so that I can include your case in my code testing, then I release the new version of cp2kdata. ./dpdata_test/restart_run/

Please find the files for 3 md steps restart run.
restart_run.zip

[robinzyb]

Sorry for late reply. Github didn't notify me about your reply with email. https://github.com/robinzyb/cp2kdata/releases/tag/v0.7.1
you may install the updated version with pip install. The version number is v.0.7.1. Please check the version using pip check cp2kdata

[chemrajib]

Sorry for late reply. Github didn't notify me about your reply with email. https://github.com/robinzyb/cp2kdata/releases/tag/v0.7.1 you may install the updated version with pip install. The version number is v.0.7.1. Please check the version using pip check cp2kdata

Thanks for your support. I appreciate your help. This is working now.