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fix cp2k 2023 output #533

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Merged
wanghan-iapcm merged 7 commits into from
Sep 6, 2023
Merged

fix cp2k 2023 output #533

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0166c97
fix cp2k 2023 output
link89 Sep 4, 2023
a083f17
adapt cp2k 2023 format
link89 Sep 4, 2023
8504867
Merge branch 'devel' into fix-cp2k-2023-output
link89 Sep 4, 2023
b1d834b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 4, 2023
edaa946
cp2k output: handle empty line properly
link89 Sep 4, 2023
3b3d720
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 4, 2023
ed22ca6
cp2k output: remove unnecessary state
link89 Sep 4, 2023
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26 changes: 10 additions & 16 deletions dpdata/cp2k/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -409,24 +409,18 @@ def get_frames(fname):
cell.append(ii.split()[4:7])
if "Atomic kind:" in ii:
atom_symbol_list.append(ii.split()[3])
if "Atom Kind Element" in ii:

# beginning of coords block
if "Atom Kind Element" in ii or "Atom Kind Element" in ii:
coord_flag = True
coord_idx = idx
# parse coords lines
elif coord_flag:
if ii == "\n":
coord_flag = len(coord) == 0 # skip empty line at the beginning
else:
coord.append(ii.split()[4:7])
atom_symbol_idx_list.append(ii.split()[1])

# get the coord block info
if coord_flag:
if idx == coord_idx + 1:
if ii == "\n":
pass
else:
coord.append(ii.split()[4:7])
atom_symbol_idx_list.append(ii.split()[1])
if idx > coord_idx + 1:
if ii == "\n":
coord_flag = False
else:
coord.append(ii.split()[4:7])
atom_symbol_idx_list.append(ii.split()[1])
if "ENERGY|" in ii:
energy = ii.split()[8]
if " Atom Kind " in ii:
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