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fix #359: read atom names from POTCAR if not present in OUTCAR #443

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fix #359: read atom names from POTCAR if not present in OUTCAR #443

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c396348
fix #359: read atom names from POTCAR if not present in OUTCAR
Mar 30, 2023
29ea10b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 30, 2023
457e481
don't allow duplicate atom names
Mar 31, 2023
68580d6
Merge branch 'outcar' of https://github.com/hoba87/dpdata into outcar
Mar 31, 2023
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16 changes: 10 additions & 6 deletions dpdata/vasp/outcar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,16 @@ def system_info(lines, type_idx_zero=False):
ii_word_list = ii.split()
if "TITEL" in ii:
# get atom names from POTCAR info, tested only for PAW_PBE ...
_ii = ii.split()[3]
if "_" in _ii:
# for case like : TITEL = PAW_PBE Sn_d 06Sep2000
atom_names.append(_ii.split("_")[0])
else:
atom_names.append(_ii)
# for case like : TITEL = PAW_PBE Sn_d 06Sep2000
atom_name = ii.split()[3].split("_")[0]
if atom_name not in atom_names:
atom_names.append(atom_name)
elif "POTCAR" in ii:
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my outcar reads

 INCAR:
 POTCAR:    PAW_PBE Mg 13Apr2007                  
 POTCAR:    PAW_PBE Mg 13Apr2007                  
   VRHFIN =Mg: s2p0                                                             
   LEXCH  = PE                                                                  
   EATOM  =    23.0369 eV,    1.6932 Ry                                         
                                                                                
   TITEL  = PAW_PBE Mg 13Apr2007                                                
   LULTRA =        F    use ultrasoft PP ?                                      
   IUNSCR =        1    unscreen: 0-lin 1-nonlin 2-no

Then the same atom name will be added three times.

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The new commit don't allow duplicated atom names

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The dpdata is expected to abstract atom names in an order that is exact the same as how the potcars are concatenated.
Your implementation does not work for the cases like "A" "B" "A" "B"

# get atom names from POTCAR info, tested only for PAW_PBE ...
# for case like : POTCAR: PAW_PBE Ti_sv 26Sep2005
atom_name = ii.split()[2].split("_")[0]
if atom_name not in atom_names:
atom_names.append(atom_name)
# a stricker check for "NELM"; compatible with distingct formats in different versions(6 and older, newers_expect-to-work) of vasp
elif nelm is None:
m = re.search(r"NELM\s*=\s*(\d+)", ii)
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