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Parsing fixes for ORCA xTB (Fixes #43) #44

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Parsing fixes for ORCA xTB (Fixes #43) #44

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a98f79f
Parsing fixes for ORCA xTB.
TroyNSmith May 21, 2026
3bda1c5
Update tests after dropping ORCA natoms parser
avcopan May 25, 2026
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

## [unreleased]

### Fixed
- Deleted ORCA `parse_natoms` to fix parsing of xTB log files.
- Fixed gradient regex to account for arbitrary number of stars in log file.


## [0.10.1] - 2026-05-02

### Fixed
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26 changes: 7 additions & 19 deletions src/qccodec/parsers/orca.py
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Expand Up @@ -147,7 +147,9 @@ def parse_hessian(contents: str) -> list[list[float]]:
for block in blocks:
lines = block.splitlines()
if not len(lines) == dim:
raise ParserError(f"Block line count {len(lines)} does not match dimension {dim}: {block}")
raise ParserError(
f"Block line count {len(lines)} does not match dimension {dim}: {block}"
)

for i, line in enumerate(block.splitlines()):
row = list(map(float, line.split()[1:]))
Expand Down Expand Up @@ -194,9 +196,10 @@ def parse_trajectory(

# Capture the stdout for each gradient calculation
regex = (
r"GEOMETRY\s*OPTIMIZATION\s*CYCLE\s*\d+\s*\*\s*\n\s*\**\s*\n" # header
r"(.*?)" # body
r"-*\s*\n\s*ORCA\s+GEOMETRY\s+RELAXATION\s+STEP"
r"GEOMETRY\s*OPTIMIZATION\s*CYCLE\s*\d+.*?" # Match cycle line
r"\*+\n" # Match the line of stars
r"(.*?)" # Body (Captured)
r"-+\s*\n\s*ORCA\s+GEOMETRY\s+RELAXATION\s+STEP" # Footer
)
per_gradient_stdout = re.findall(regex, stdout, flags=re.DOTALL)
if not per_gradient_stdout:
Expand Down Expand Up @@ -249,21 +252,6 @@ def parse_version(contents: str) -> str:
return match.group(1)


@register(filetype=OrcaFileType.STDOUT, target="calcinfo_natoms")

@coltonbh coltonbh May 28, 2026

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Maybe just make the parser optional instead?

@register(filetype=OrcaFileType.STDOUT, target="calcinfo_natoms", required=False)

This will preserve it when the the data exists but not raise an exception if not present :)

@coltonbh coltonbh May 28, 2026

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Ideally we add a test for the xTB output logs and ensure no exception is raised. This then covers the case currently causing the error.

Thanks for this!

@coltonbh coltonbh Jun 1, 2026

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@avcopan here!

def parse_natoms(contents: str) -> int:
"""Parse number of atoms value from Orca stdout.

Returns:
The number of atoms as an integer.

Raises:
MatchNotFoundError: If the regex does not match.
"""
regex = r"Number of atoms\s*...\s*(\d+)"
match = re_search(regex, contents)
return int(match.group(1))


def parse_basename(contents: str) -> str:
"""Parse the file basename from Orca stdout."""
regex = r"NAME\s+=\s+(.*)"
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10 changes: 5 additions & 5 deletions tests/data/orca/answers/trajectory.json
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Expand Up @@ -69,7 +69,7 @@
},
"success": true,
"data": {
"calcinfo_natoms": 3,
"calcinfo_natoms": null,
"calcinfo_nalpha": null,
"calcinfo_nbeta": null,
"calcinfo_nbasis": null,
Expand Down Expand Up @@ -187,7 +187,7 @@
},
"success": true,
"data": {
"calcinfo_natoms": 3,
"calcinfo_natoms": null,
"calcinfo_nalpha": null,
"calcinfo_nbeta": null,
"calcinfo_nbasis": null,
Expand Down Expand Up @@ -305,7 +305,7 @@
},
"success": true,
"data": {
"calcinfo_natoms": 3,
"calcinfo_natoms": null,
"calcinfo_nalpha": null,
"calcinfo_nbeta": null,
"calcinfo_nbasis": null,
Expand Down Expand Up @@ -423,7 +423,7 @@
},
"success": true,
"data": {
"calcinfo_natoms": 3,
"calcinfo_natoms": null,
"calcinfo_nalpha": null,
"calcinfo_nbeta": null,
"calcinfo_nbasis": null,
Expand Down Expand Up @@ -471,4 +471,4 @@
"hostmem": null
}
}
]
]
9 changes: 0 additions & 9 deletions tests/test_orca_parsers.py
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Expand Up @@ -7,7 +7,6 @@
parse_energy,
parse_gradient,
parse_hessian,
parse_natoms,
parse_trajectory,
parse_version,
)
Expand Down Expand Up @@ -87,14 +86,6 @@
answer=hessians.water_revdsd,
extra_files=["water.numhess.hess"],
),
ParserTestCase(
name="Parse number of atoms water",
parser=parse_natoms,
stdout=Path("water.energy.out"),
calctype=CalcType.energy,
success=True,
answer=3,
),
ParserTestCase(
name="Parse trajectory",
parser=parse_trajectory,
Expand Down
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