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SC21_DP_Tutorial
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Error from QE output to dpdata, "IndexError: index 377 is out of bounds for axis 0 with size 377" #2

Open zhouyium opened 1 year ago

zhouyium commented 1 year ago

Dear all: According to https://developer.nvidia.com/blog/accelerated-molecular-simulation-using-deep-potential-workflow-with-ngc/ this page. Here is something wrong.

  1. AIMD simulation. from this page the command line is cp.x < c.md98.cp.in but in this github resporisty, there has not c.md98.cp.in. But I can run the SC21_DP_Tutorial/AIMD/QE/run.sh to finish the AIMD simulation.
  2. Training data preparation After run python3 logtodata.py, the follwing is problem /SC21_DP_Tutorial/AIMD/QE$ python3 logtodata.py /usr/lib/python3/dist-packages/requests/__init__.py:89: RequestsDependencyWarning: urllib3 (2.0.2) or chardet (3.0.4) doesn't match a supported version! warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported " Traceback (most recent call last): File "logtodata.py", line 3, in <module> d_log = dpdata.LabeledSystem('graphene', fmt = 'qe/cp/traj') File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/system.py", line 281, in __init__ self.from_fmt( File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/system.py", line 318, in from_fmt return self.from_fmt_obj(load_format(fmt), file_name, **kwargs) File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/system.py", line 1162, in from_fmt_obj data = fmtobj.from_labeled_system(file_name, **kwargs) File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/plugins/qe.py", line 22, in from_labeled_system data, cs = dpdata.qe.traj.to_system_data( File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/qe/traj.py", line 196, in to_system_data data["coords"], csteps = load_data( File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/qe/traj.py", line 132, in load_data with open(fname) as fp: FileNotFoundError: [Errno 2] No such file or directory: 'graphene.pos' How to fix this problem.
zhouyium commented 1 year ago

Sorry Guys, I DO not run the copy.sh, after run the copy.sh. The error change to "IndexError: index 377 is out of bounds for axis 0 with size 377" `SC21_DP_Tutorial/AIMD/QE$bash ./run.sh cd out SC21_DP_Tutorial/AIMD/QE/out$ python logtodata.py Data Summary Labeled System

Frame Numbers : 377 Atom Numbers : 98 Including Virials : No Element List :

C 98 200 Traceback (most recent call last): File "logtodata.py", line 12, in print(d_log_shuffled.sub_system(np.arange(iNeach, (i+1)Neach).tolist()).get_nframes()) File "/home/yizhou/.local/lib/python3.8/site-packages/dpdata/system.py", line 505, in sub_system tmp.data[tt.name] = self.data[tt.name][tuple(new_shape)] IndexError: index 377 is out of bounds for axis 0 with size 377 ` The following is my ubuntu. Ubuntu : 20.04 Conda: 2023.03-1-Linux-x86_64 DeepMD: using coda install the cpu version with python 3.8 python: 3.8.16