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Don't gen xyz when checking if a species is monoatomic #785

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Merged
alongd merged 2 commits into from
Aug 25, 2025
Merged

Don't gen xyz when checking if a species is monoatomic #785

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2078cae
Don't gen xyz when checking if a species is monoatomic
alongd Apr 11, 2025
1967e9d
In job trsh, check len rev_lines before accessing line i+300
alongd Apr 11, 2025
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13 changes: 7 additions & 6 deletions arc/job/trsh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,7 @@ def determine_ess_status(output_path: str,
return 'errored', ['NoOutput'], 'Log file could not be read', ''
forward_lines = tuple(lines)
reverse_lines = tuple(lines[::-1])
len_reversed_lines, len_forward_lines = len(reverse_lines), len(forward_lines)

if software == 'gaussian':
for line in forward_lines[-1:-20:-1]:
Expand All @@ -93,7 +94,7 @@ def determine_ess_status(output_path: str,
if 'l9999.exe' in line or 'link 9999' in line:
cycle_issue = False
neg_eigenvalues = False
for j in range(i,len(reverse_lines)):
for j in range(i, len_reversed_lines):
if 'Number of steps exceeded' in reverse_lines[j]:
keywords = ['MaxOptCycles', 'GL9999']
error = 'Maximum optimization cycles reached.'
Expand Down Expand Up @@ -132,7 +133,7 @@ def determine_ess_status(output_path: str,
# Check if Inaccurate quadrature in CalDSu
inacc_quad = False
for j in range(i + 300, i, -1):
if 'Inaccurate quadrature in CalDSu' in reverse_lines[j]:
if j < len_reversed_lines and 'Inaccurate quadrature in CalDSu' in reverse_lines[j]:
inacc_quad = True
keywords = ['InaccurateQuadrature', 'GL502']
error = 'Inaccurate quadrature in CalDSu'
Expand All @@ -158,7 +159,7 @@ def determine_ess_status(output_path: str,
elif 'l123.exe' in line:
delta_x = False
gs2_opt = False
for j in range(i + 1, len(reverse_lines)):
for j in range(i + 1, len_reversed_lines):
if 'Delta-x Convergence NOT Met' in reverse_lines[j]:
delta_x = True
keywords = ['DeltaX', 'GL123']
Expand All @@ -172,16 +173,16 @@ def determine_ess_status(output_path: str,
line = 'GS2 Optimization Failure'
break
if any([keyword in ['GL301', 'GL401'] for keyword in keywords]):
additional_info = forward_lines[len(forward_lines) - i - 2]
additional_info = forward_lines[len_forward_lines - i - 2]
if 'No data on chk file' in additional_info \
or 'Basis set data is not on the checkpoint file' in additional_info \
or 'Error in GetGes' in additional_info:
keywords = ['CheckFile']
error = additional_info.strip()
elif 'GL301' in keywords:
if 'Atomic number out of range for' in forward_lines[len(forward_lines) - i - 2]:
if 'Atomic number out of range for' in forward_lines[len_forward_lines - i - 2]:
keywords.append('BasisSet')
error = f'The basis set {forward_lines[len(forward_lines) - i - 2].split()[6]} ' \
error = f'The basis set {forward_lines[len_forward_lines - i - 2].split()[6]} ' \
f'is not appropriate for the this chemistry.'
else:
keywords.append('InputError')
Expand Down
4 changes: 3 additions & 1 deletion arc/species/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1035,7 +1035,9 @@ def is_monoatomic(self) -> Optional[bool]:
"""
if self.mol is not None and len(self.mol.atoms):
return len(self.mol.atoms) == 1
xyz = self.get_xyz()
if self.mol_list is not None and len(self.mol_list):
return len(self.mol_list[0].atoms) == 1
xyz = self.get_xyz(generate=False)
if xyz is not None:
return len(xyz['symbols']) == 1
return None
Expand Down
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