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Enhance poscar_scale function (/data/gen.py)to detect Selective dynamics #1439

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Enhance poscar_scale function (/data/gen.py)to detect Selective dynamics #1439

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Enhance poscar_scale function to detect Selective dynamics
Dec 28, 2023
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pre-commit-ci[bot] Dec 28, 2023
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18 changes: 15 additions & 3 deletions dpgen/data/gen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,12 +237,24 @@
def poscar_scale(poscar_in, poscar_out, scale):
with open(poscar_in) as fin:
lines = list(fin)
if "D" == lines[7][0] or "d" == lines[7][0]:

# Determine if "Selective dynamics" is present
if lines[7].strip().lower().startswith("s"):
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coord_type_line = 8 # If present, coordinates type is on line 9

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else:
coord_type_line = 7 # If not, coordinates type is on line 8
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# Process according to the coordinate type
if "D" == lines[coord_type_line][0] or "d" == lines[coord_type_line][0]:
lines = poscar_scale_direct(lines, scale)
elif "C" == lines[7][0] or "c" == lines[7][0]:
elif "C" == lines[coord_type_line][0] or "c" == lines[coord_type_line][0]:

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lines = poscar_scale_cartesian(lines, scale)
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@QodoAI-Agent QodoAI-Agent Jan 11, 2024

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Suggestion: Use the str.startswith() method to check the starting character of a string in a case-insensitive manner, instead of checking equality with both the uppercase and lowercase versions of the character. [best practice]

Suggested change
if "D" == lines[coord_type_line][0] or "d" == lines[coord_type_line][0]:
lines = poscar_scale_direct(lines, scale)
elif "C" == lines[7][0] or "c" == lines[7][0]:
elif "C" == lines[coord_type_line][0] or "c" == lines[coord_type_line][0]:
lines = poscar_scale_cartesian(lines, scale)
if lines[coord_type_line].startswith(("D", "d")):
lines = poscar_scale_direct(lines, scale)
elif lines[coord_type_line].startswith(("C", "c")):
lines = poscar_scale_cartesian(lines, scale)

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@njzjz njzjz Jan 11, 2024

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I agree with this comment

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else:
raise RuntimeError("Unknow poscar style at line 7: %s" % lines[7])
raise RuntimeError(

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f"Unknown poscar style at line {coord_type_line + 1}: {lines[coord_type_line]}"
)
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@QodoAI-Agent QodoAI-Agent Jan 11, 2024

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Suggestion: The error message in the RuntimeError could be more informative by specifying that the unknown style is related to the coordinate type. [enhancement]

Suggested change
raise RuntimeError(
f"Unknown poscar style at line {coord_type_line + 1}: {lines[coord_type_line]}"
)
raise RuntimeError(
f"Unknown coordinate type at line {coord_type_line + 1}: {lines[coord_type_line]}"
)

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@njzjz njzjz Jan 11, 2024

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So, is it poscar style or coordinate type?


# Write scaled positions back to output file
with open(poscar_out, "w") as fout:
fout.write("".join(lines))

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