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fix "ValueError: could not convert string to float: 'ATOMIC_POSITIONS'" #721

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fix "ValueError: could not convert string to float: 'ATOMIC_POSITIONS'" #721

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e8315d7
fix "ValueError: could not convert string to float: 'ATOMIC_POSITIONS'"
Youhaojen Sep 13, 2024
1c85312
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 13, 2024
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68 changes: 44 additions & 24 deletions dpdata/qe/scf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,47 +12,67 @@
kbar2evperang3 = 1e3 / 1.602176621e6


def get_block(lines, keyword, skip=0):
ret = []
for idx, ii in enumerate(lines):
if keyword in ii:
blk_idx = idx + 1 + skip
while len(lines[blk_idx]) == 0:
blk_idx += 1
while len(lines[blk_idx]) != 0 and blk_idx != len(lines):
ret.append(lines[blk_idx])
blk_idx += 1
def get_block(lines, start_marker):
start_idx = None
for idx, line in enumerate(lines):
if start_marker in line:
start_idx = idx + 1
break
return ret
if start_idx is None:
raise RuntimeError(f"{start_marker} not found in the input lines.")

block = []
for line in lines[start_idx:]:
if line.strip() == "" or line.strip().startswith("&"):
break
block.append(line.strip())
return block


def get_block(lines, start_marker, skip=0):
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Remove the unused get_block function.

There is a redefinition of the get_block function at line 32, which is unused in the code.

Remove the unused function definition:

-def get_block(lines, start_marker, skip=0):
-    start_idx = None
-    for idx, line in enumerate(lines):
-        if start_marker in line:
-            start_idx = idx + 1 + skip
-            break
-    if start_idx is None:
-        raise RuntimeError(f"{start_marker} not found in the input lines.")
-
-    block = []
-    for line in lines[start_idx:]:
-        if line.strip() == "" or line.strip().startswith("&"):
-            break
-        block.append(line.strip())
-    return block

Committable suggestion was skipped due to low confidence.

Tools
Ruff

32-32: Redefinition of unused get_block from line 15

(F811)

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plz avoid redefining functions.

start_idx = None
for idx, line in enumerate(lines):
if start_marker in line:
start_idx = idx + 1 + skip
break
if start_idx is None:
raise RuntimeError(f"{start_marker} not found in the input lines.")

block = []
for line in lines[start_idx:]:
if line.strip() == "" or line.strip().startswith("&"):
break
block.append(line.strip())
return block


def get_cell(lines):
ret = []
for idx, ii in enumerate(lines):
if "ibrav" in ii:
for idx, line in enumerate(lines):
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Rename the unused loop control variable idx to _idx.

The loop control variable idx is not used within the loop body.

Rename idx to _idx to indicate that it is intentionally unused:

-    for idx, line in enumerate(lines):
+    for _idx, line in enumerate(lines):
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
for idx, line in enumerate(lines):
for _idx, line in enumerate(lines):
Tools
Ruff

50-50: Loop control variable idx not used within loop body

Rename unused idx to _idx

(B007)

if "ibrav" in line:
ibrav = int(line.replace(",", "").split("=")[-1])
break
blk = lines[idx : idx + 2]
ibrav = int(blk[0].replace(",", "").split("=")[-1])
else:
raise RuntimeError("ibrav not found in the input lines.")

if ibrav == 0:
for iline in lines:
if "CELL_PARAMETERS" in iline and "angstrom" not in iline.lower():
for line in lines:
if "CELL_PARAMETERS" in line and "angstrom" not in line.lower():
raise RuntimeError(
"CELL_PARAMETERS must be written in Angstrom. Other units are not supported yet."
)
blk = get_block(lines, "CELL_PARAMETERS")
for ii in blk:
ret.append([float(jj) for jj in ii.split()[0:3]])
ret = []
for line in blk:
ret.append([float(value) for value in line.split()[0:3]])
ret = np.array(ret)
elif ibrav == 1:
a = None
for iline in lines:
line = iline.replace("=", " ").replace(",", "").split()
for line in lines:
line = line.replace("=", " ").replace(",", "").split()
Comment on lines +70 to +71
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any reason for changing the variable names?

if len(line) >= 2 and "a" == line[0]:
# print("line = ", line)
a = float(line[1])
if len(line) >= 2 and "celldm(1)" == line[0]:
a = float(line[1]) * bohr2ang
# print("a = ", a)
if not a:
raise RuntimeError("parameter 'a' or 'celldm(1)' cannot be found.")
ret = np.array([[a, 0.0, 0.0], [0.0, a, 0.0], [0.0, 0.0, a]])
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