deepmodeling/dpdata

[BUG] fmt="cp2k/aimd_output" unable to read CP2K9.1 log file

JoesonCheung opened this issue · 1 comments

Summary
Using dpdata with fmt="cp2k/aimd_output" returns the error:
File "<stdin>", line 1, in <module> File "/home/jxzhang/deepmd-kit/lib/python3.10/site-packages/dpdata/system.py", line 136, in to return self.to_fmt_obj(load_format(fmt), *args, **kwargs) File "/home/jxzhang/deepmd-kit/lib/python3.10/site-packages/dpdata/system.py", line 903, in to_fmt_obj return fmtobj.to_labeled_system(self.data, *args, **kwargs) File "/home/jxzhang/deepmd-kit/lib/python3.10/site-packages/dpdata/format.py", line 77, in to_labeled_system return self.to_system(data, *args, **kwargs) File "/home/jxzhang/deepmd-kit/lib/python3.10/site-packages/dpdata/plugins/deepmd.py", line 52, in to_system dpdata.deepmd.comp.dump( File "/home/jxzhang/deepmd-kit/lib/python3.10/site-packages/dpdata/deepmd/comp.py", line 83, in dump nframes = data['cells'].shape[0] AttributeError: 'list' object has no attribute 'shape'

Further Information, Files, and Links
cp2k.zip

import dpdata
cp2kmd_dir = "./cp2k"
cp2kmd_output_name = "cp2k.log"
dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
print(dp)
--- You are parsing data using package Cp2kData ---
You are reading cell information from [./cp2k/cp2k.log](https://file+.vscode-resource.vscode-cdn.net/Users/robinzhuang/workdir/tmp/test/cp2k/cp2k.log)
Obtian Energies From [./cp2k/cp2k-1.ener](https://file+.vscode-resource.vscode-cdn.net/Users/robinzhuang/workdir/tmp/test/cp2k/cp2k-1.ener)
Obtian Structures From [./cp2k/cp2k-pos-1.xyz](https://file+.vscode-resource.vscode-cdn.net/Users/robinzhuang/workdir/tmp/test/cp2k/cp2k-pos-1.xyz)
Obtian Froces From [./cp2k/cp2k-frc-1.xyz](https://file+.vscode-resource.vscode-cdn.net/Users/robinzhuang/workdir/tmp/test/cp2k/cp2k-frc-1.xyz)
Atom names are fake chemical symbols as you set in cp2k input.
--- You are parsing data using package Cp2kData ---
Data Summary
Labeled System
-------------------
Frame Numbers      : 3
Atom Numbers       : 350
Including Virials  : No
Element List       :
-------------------
Si  Cl  H
50  200  100