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Backport fix from PR #107 #108

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Merged
lohedges merged 1 commit into from
Dec 11, 2025
Merged

Backport fix from PR #107 #108

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73 changes: 54 additions & 19 deletions src/somd2/runner/_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,8 @@ def __init__(self, system, config):

# Make sure the system contains perturbable molecules.
try:
self._system.molecules("property is_perturbable")
atoms = self._system["property is_perturbable"].atoms()
pert_idxs = self._system.atoms().find(atoms)
except KeyError:
msg = "No perturbable molecules in the system"
_logger.error(msg)
Expand Down Expand Up @@ -265,7 +266,18 @@ def __init__(self, system, config):
from ghostly import modify

_logger.info("Applying modifications to ghost atom bonded terms")
self._system, self._modifications = modify(self._system)
try:
self._system, self._modifications = modify(self._system)
# Angle optimisation can sometimes fail.
except Exception as e1:
try:
self._system, self._modifications = modify(
self_system, optimise_angles=False
)
except Exception as e2:
msg = f"Unable to apply modifications to ghost atom bonded terms: {e1}; {e2}"
_logger.error(msg)
raise RuntimeError(msg)

# Check for a periodic space.
self._has_space = self._check_space()
Expand Down Expand Up @@ -363,6 +375,7 @@ def __init__(self, system, config):
from math import isclose

# Set the REST2 scale factors.
is_rest2 = False
if self._config.rest2_scale is not None:
# Single value. Interpolate between 1.0 at the end states and rest2_scale
# at lambda = 0.5.
Expand Down Expand Up @@ -396,6 +409,45 @@ def __init__(self, system, config):
raise ValueError(msg)
self._rest2_scale_factors = self._config.rest2_scale

# If there are any non-zero REST2 scale factors, then log it.
if any(
not isclose(factor, 1.0, abs_tol=1e-4)
for factor in self._rest2_scale_factors
):
is_rest2 = True
_logger.info(f"REST2 scaling factors: {self._rest2_scale_factors}")

# Make sure the REST2 selection is valid.
if self._config.rest2_selection is not None:

try:
atoms = _sr.mol.selection_to_atoms(
self._system, self._config.rest2_selection
)
except:
msg = "Invalid 'rest2_selection' value."
_logger.error(msg)
raise ValueError(msg)

# Make sure the user hasn't selected all atoms.
if len(atoms) == self._system.num_atoms():
msg = "REST2 selection cannot contain all atoms in the system."
_logger.error(msg)
raise ValueError(msg)

# Get the atom indices.
idxs = self._system.atoms().find(atoms)

# If no indices are in the perturbable region, then add them.
if not any(i in pert_idxs for i in idxs):
idxs = sorted(pert_idxs + idxs)
else:
idxs = pert_idxs

# Log the atom indices in the REST2 selection.
if is_rest2:
_logger.info(f"REST2 selection contains {len(atoms)} atoms: {idxs}")

# Apply hydrogen mass repartitioning.
if self._config.hmr:
# Work out the current hydrogen mass factor.
Expand Down Expand Up @@ -444,23 +496,6 @@ def __init__(self, system, config):
self._system, self._config.h_mass_factor
)

# Make sure the REST2 selection is valid.
if self._config.rest2_selection is not None:
from sire.mol import selection_to_atoms

try:
atoms = selection_to_atoms(self._system, self._config.rest2_selection)
except:
msg = "Invalid 'rest2_selection' value."
_logger.error(msg)
raise ValueError(msg)

# Make sure the user hasn't selected all atoms.
if len(atoms) == self._system.num_atoms():
msg = "REST2 selection cannot contain all atoms in the system."
_logger.error(msg)
raise ValueError(msg)

# Flag whether this is a GPU simulation.
self._is_gpu = self._config.platform in ["cuda", "opencl", "hip"]

Expand Down