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Backport fixes from PR #97 #98

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Merged
lohedges merged 2 commits into from
Dec 2, 2025
Merged

Backport fixes from PR #97 #98

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a164cf5
Fix typos. [ci skip]
lohedges Dec 2, 2025
95c2b61
Backport API update from PR #97. [ci skip]
lohedges Dec 2, 2025
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10 changes: 5 additions & 5 deletions src/somd2/_utils/_somd1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ def apply_pert(system, pert_file):
return system


def make_compatible(system, fix_perturbable_zero_sigams=False):
def make_compatible(system, fix_perturbable_zero_sigmas=False):
"""
Makes a perturbation SOMD1 compatible.

Expand All @@ -94,7 +94,7 @@ def make_compatible(system, fix_perturbable_zero_sigams=False):
system : sire.system.System, sire.legacy.System.System
The system containing the molecules to be perturbed.

fix_perturbable_zero_sigams : bool
fix_perturbable_zero_sigmas : bool
Whether to prevent LJ sigma values being perturbed to zero.

Returns
Expand All @@ -110,8 +110,8 @@ def make_compatible(system, fix_perturbable_zero_sigams=False):
"'system' must of type 'sire.system.System' or 'sire.legacy.System.System'"
)

if not isinstance(fix_perturbable_zero_sigams, bool):
raise TypeError("'fix_perturbable_zero_sigams' must be of type 'bool'.")
if not isinstance(fix_perturbable_zero_sigmas, bool):
raise TypeError("'fix_perturbable_zero_sigmas' must be of type 'bool'.")

# Extract the legacy system.
if isinstance(system, _LegacySystem):
Expand All @@ -138,7 +138,7 @@ def make_compatible(system, fix_perturbable_zero_sigams=False):
##################################
# First fix zero LJ sigmas values.
##################################
if fix_perturbable_zero_sigams:
if fix_perturbable_zero_sigmas:
# Tolerance for zero sigma values.
null_lj_sigma = 1e-9

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2 changes: 1 addition & 1 deletion src/somd2/runner/_base.py
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Expand Up @@ -264,7 +264,7 @@ def __init__(self, system, config):
from ghostly import modify

_logger.info("Applying modifications to ghost atom bonded terms")
self._system = modify(self._system)
self._system, self._modifications = modify(self._system)

# Check for a periodic space.
self._has_space = self._check_space()
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