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Add initial ring-breaking lambda schedules #129

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Merged
lohedges merged 1 commit into from
Mar 18, 2026
Merged

Add initial ring-breaking lambda schedules #129

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281 changes: 274 additions & 7 deletions src/somd2/config/_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ class Config:
"lambda_schedule": [
"standard_morph",
"charge_scaled_morph",
"ring_break_morph",
"reverse_ring_break_morph",
],
"log_level": [level.lower() for level in _logger._core.levels],
}
Expand Down Expand Up @@ -651,14 +653,20 @@ def as_dict(self, sire_compatible=False):

# Handle the lambda schedule separately so that we can use simplified
# keyword options.
if self.lambda_schedule == _LambdaSchedule.standard_morph():
d["lambda_schedule"] = "standard_morph"
elif self.lambda_schedule == _LambdaSchedule.charge_scaled_morph(
self._charge_scale_factor
):
d["lambda_schedule"] = "charge_scaled_morph"

# A keyword exists for this lambda schedule.
if self._lambda_schedule_name is not None:
d["lambda_schedule"] = self._lambda_schedule_name
# Try to match the lambda schedule to a known schedule, if not then convert to hex.
else:
d["lambda_schedule"] = self._to_hex(self.lambda_schedule)
if self.lambda_schedule == _LambdaSchedule.standard_morph():
d["lambda_schedule"] = "standard_morph"
elif self.lambda_schedule == _LambdaSchedule.charge_scaled_morph(
self._charge_scale_factor
):
d["lambda_schedule"] = "charge_scaled_morph"
else:
d["lambda_schedule"] = self._to_hex(self.lambda_schedule)

# Serialise restraints.
if self.restraints is not None:
Expand Down Expand Up @@ -997,11 +1005,268 @@ def lambda_schedule(self, lambda_schedule):
lambda_schedule = lambda_schedule.strip().lower()
if lambda_schedule == "standard_morph":
self._lambda_schedule = _LambdaSchedule.standard_morph()
self._lambda_schedule_name = "standard_morph"
elif lambda_schedule == "charge_scaled_morph":
self._lambda_schedule = _LambdaSchedule.charge_scaled_morph(0.2)
self._lambda_schedule_name = "charge_scaled_morph"
elif lambda_schedule == "ring_break_morph":
self._lambda_schedule = _LambdaSchedule.standard_morph()
self._lambda_schedule.prepend_stage(
"restraints_off", self._lambda_schedule.initial()
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="restraint",
equation=1 - self._lambda_schedule.lam(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="bond_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="bond_length",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="angle_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="angle_size",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="torsion_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="restraints_off",
lever="torsion_phase",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)

self._lambda_schedule.prepend_stage(
"potential_swap", self._lambda_schedule.initial()
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="restraint",
equation=0 + self._lambda_schedule.lam(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="bond_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="bond_length",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="angle_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="angle_size",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="torsion_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="torsion_phase",
equation=self._lambda_schedule.initial(),
)

self._lambda_schedule.set_equation(
stage="morph", lever="restraint", equation=0
)

self._lambda_schedule.set_equation(
stage="morph",
lever="bond_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="bond_length",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="angle_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="angle_size",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="torsion_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="torsion_phase",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule_name = "ring_break_morph"
elif lambda_schedule == "reverse_ring_break_morph":
self._lambda_schedule = _LambdaSchedule.standard_morph()
self._lambda_schedule.set_equation(
stage="morph", lever="restraint", equation=0
)

self._lambda_schedule.set_equation(
stage="morph",
lever="bond_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="bond_length",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="angle_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="angle_size",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="torsion_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="morph",
lever="torsion_phase",
equation=self._lambda_schedule.initial(),
)

self._lambda_schedule.append_stage(
"bonded_perturb", self._lambda_schedule.final()
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="restraint",
equation=0 + self._lambda_schedule.lam(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="bond_k",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="bond_length",
equation=self._lambda_schedule.initial(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="angle_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="angle_size",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="torsion_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="bonded_perturb",
lever="torsion_phase",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)

self._lambda_schedule.append_stage(
"potential_swap", self._lambda_schedule.final()
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="restraint",
equation=1 - self._lambda_schedule.lam(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="bond_k",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="bond_length",
equation=(1 - self._lambda_schedule.lam())
* self._lambda_schedule.initial()
+ self._lambda_schedule.lam() * self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="angle_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="angle_size",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="torsion_k",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule.set_equation(
stage="potential_swap",
lever="torsion_phase",
equation=self._lambda_schedule.final(),
)
self._lambda_schedule_name = "reverse_ring_break_morph"
else:
try:
self._lambda_schedule = self._from_hex(lambda_schedule)
self._lambda_schedule_name = None
except Exception:
raise ValueError(
"Unable to deserialise 'lambda_schedule'. Ensure that this is a "
Expand All @@ -1010,8 +1275,10 @@ def lambda_schedule(self, lambda_schedule):
)
else:
self._lambda_schedule = lambda_schedule
self._lambda_schedule_name = None
else:
self._lambda_schedule = _LambdaSchedule.standard_morph()
self._lambda_schedule_name = "standard_morph"

@property
def charge_scale_factor(self):
Expand Down
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