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fix bug for duplicated header cp2k output #233

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Merged
wanghan-iapcm merged 2 commits into from
Dec 6, 2021
Merged

fix bug for duplicated header cp2k output #233

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8393c46
fix bug: nonconverged cp2k ouput should return None virial
robinzyb Dec 6, 2021
7b7f8ea
fix bug for duplicated header cp2k output
robinzyb Dec 6, 2021
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83 changes: 46 additions & 37 deletions dpdata/cp2k/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -238,46 +238,55 @@ def get_frames (fname) :
content = fp.read()
count = content.count('SCF run converged')
if count == 0:
return [], [], [], [], [], [], [], []
return [], [], [], [], [], [], [], None

# search duplicated header
fp.seek(0)
header_idx = []
for idx, ii in enumerate(fp) :
if ('CELL| Vector' in ii) and (cell_count < 3) :
cell.append(ii.split()[4:7])
cell_count += 1
if 'Atom Kind Element' in ii :
coord_flag = True
coord_idx = idx
coord_count += 1
# get the coord block info
if coord_flag and (coord_count == 1):
if (idx > coord_idx + 1) :
if (ii == '\n') :
coord_flag = False
else :
coord.append(ii.split()[4:7])
atom_symbol_list.append(ii.split()[2])
if 'ENERGY|' in ii :
energy = (ii.split()[8])
if ' Atom Kind ' in ii :
force_flag = True
force_idx = idx
if force_flag :
if (idx > force_idx) :
if 'SUM OF ATOMIC FORCES' in ii :
force_flag = False
else :
force.append(ii.split()[3:6])
# add reading stress tensor
if 'STRESS TENSOR [GPa' in ii :
stress_flag = True
stress_idx = idx
if stress_flag :
if (idx > stress_idx + 2):
if (ii == '\n') :
stress_flag = False
else :
stress.append(ii.split()[1:4])
if 'Multiplication driver' in ii :
header_idx.append(idx)

# parse from last header
fp.seek(0)
for idx, ii in enumerate(fp) :
if idx > header_idx[-1] :
if 'CELL| Vector' in ii:
cell.append(ii.split()[4:7])

if 'Atom Kind Element' in ii :
coord_flag = True
coord_idx = idx

# get the coord block info
if coord_flag :
if (idx > coord_idx + 1) :
if (ii == '\n') :
coord_flag = False
else :
coord.append(ii.split()[4:7])
atom_symbol_list.append(ii.split()[2])
if 'ENERGY|' in ii :
energy = (ii.split()[8])
if ' Atom Kind ' in ii :
force_flag = True
force_idx = idx
if force_flag :
if (idx > force_idx) :
if 'SUM OF ATOMIC FORCES' in ii :
force_flag = False
else :
force.append(ii.split()[3:6])
# add reading stress tensor
if 'STRESS TENSOR [GPa' in ii :
stress_flag = True
stress_idx = idx
if stress_flag :
if (idx > stress_idx + 2):
if (ii == '\n') :
stress_flag = False
else :
stress.append(ii.split()[1:4])


fp.close()
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