Wrong when run readData_cp2k.py #1129
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Michael-tech88
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Wrong when run readData_cp2k.py, as follow:
(deepmd) [gengzi@master CP2K-MD]$ python readData_cp2k.py
Traceback (most recent call last):
File "/home/gengzi/CP2K-MD/readData_cp2k.py", line 4, in
data = dpdata.LabeledSystem('Pt-ontop-CeO2-111-O-rel', fmt = 'cp2k/aimd_output')
File "/home/gengzi/.local/lib/python3.9/site-packages/dpdata/system.py", line 265, in init
self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, convergence_check=convergence_check, **kwargs)
File "/home/gengzi/.local/lib/python3.9/site-packages/dpdata/system.py", line 291, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/home/gengzi/.local/lib/python3.9/site-packages/dpdata/system.py", line 1078, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/home/gengzi/.local/lib/python3.9/site-packages/dpdata/plugins/cp2k.py", line 10, in from_labeled_system
xyz_file = sorted(glob.glob("{}/pos.xyz".format(file_name)))[0]
IndexError: list index out of range
The test for readData_cp2k.py is listed as follow:
import dpdata
import numpy as np
#data = dpdata.LabeledSystem('OUTCAR', fmt = 'vasp/outcar')
data = dpdata.LabeledSystem('Pt-ontop-CeO2-111-O-rel', fmt = 'cp2k/aimd_output')
print('# the data contains %d frames' % len(data))
random choose 40 index for validation_data
index_validation = np.random.choice(109,size=20,replace=False)
other indexes are training_data
index_training = list(set(range(200))-set(index_validation))
data_training = data.sub_system(index_training)
data_validation = data.sub_system(index_validation)
all training data put into directory:"training_data"
data_training.to_deepmd_npy('training_data')
all validation data put into directory:"validation_data"
data_validation.to_deepmd_npy('validation_data')
print('# the training data contains %d frames' % len(data_training))
print('# the validation data contains %d frames' % len(data_validation))
The same wrong when put readData_cp2k.py into the fold "Pt-ontop-CeO2-111-O-rel", and set "data = dpdata.LabeledSystem('aimd', fmt = 'cp2k/aimd_output') ", However, when run readData_vasp.py (data = dpdata.LabeledSystem('OUTCAR', fmt = 'vasp/outcar')), the result is OK.
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