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Merged
lohedges merged 4 commits into from
May 13, 2026
Merged

Add ring-break/make softcore force #148

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44bd395
Add ring-break and ring-make lever equations to ring-break schedules.
lohedges May 8, 2026
963eacb
Add ring_open/ring_close stages to ring-break schedules.
lohedges May 8, 2026
18b66e1
Try weighting ring-breaking schedule stages.
lohedges May 8, 2026
78a311d
Add unit test for ring-break/make forces.
lohedges May 12, 2026
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85 changes: 79 additions & 6 deletions src/somd2/_utils/_schedules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,7 @@ def ring_break_morph():
"""
Build a lambda schedule for ring-breaking perturbations.

Three stages: potential_swap → restraints_off → morph.
Four stages: potential_swap → restraints_off → ring_open → morph.

Returns
-------
Expand All @@ -162,8 +162,36 @@ def ring_break_morph():
from sire.cas import LambdaSchedule as _LambdaSchedule

s = _LambdaSchedule.standard_morph()
s.set_stage_weight("morph", 2)

# ring_open: Morse is already off; ring-break nonbonded interaction ramps
# on (alpha: 1→0, kappa: 0→1) while non-bonded terms stay at initial and
# bonded terms remain at final. The softcore interaction gently pushes the
# atoms into the open-chain geometry before the full nonbonded morph begins,
# improving HREX overlap at the ring-break boundary.
s.prepend_stage("ring_open", s.initial(), weight=1)
s.set_equation(stage="ring_open", lever="morse_hard", equation=0)
s.set_equation(stage="ring_open", lever="morse_soft", equation=0)
s.set_equation(stage="ring_open", lever="bond_k", equation=s.final())
s.set_equation(stage="ring_open", lever="bond_length", equation=s.final())
s.set_equation(stage="ring_open", lever="angle_k", equation=s.final())
s.set_equation(stage="ring_open", lever="angle_size", equation=s.final())
s.set_equation(stage="ring_open", lever="torsion_k", equation=s.final())
s.set_equation(stage="ring_open", lever="torsion_phase", equation=s.final())
s.set_equation(
stage="ring_open", force="ring-break", lever="alpha", equation=1 - s.lam()
)
s.set_equation(
stage="ring_open", force="ring-break", lever="kappa", equation=s.lam()
)
s.set_equation(
stage="ring_open", force="ring-make", lever="alpha", equation=s.lam()
)
s.set_equation(
stage="ring_open", force="ring-make", lever="kappa", equation=1 - s.lam()
)

s.prepend_stage("restraints_off", s.initial())
s.prepend_stage("restraints_off", s.initial(), weight=1)
s.set_equation(stage="restraints_off", lever="morse_soft", equation=1 - s.lam())
s.set_equation(stage="restraints_off", lever="morse_hard", equation=0)
s.set_equation(stage="restraints_off", lever="bond_k", equation=s.final())
Expand All @@ -189,7 +217,7 @@ def ring_break_morph():
equation=(1 - s.lam()) * s.initial() + s.lam() * s.final(),
)

s.prepend_stage("potential_swap", s.initial())
s.prepend_stage("potential_swap", s.initial(), weight=2)
s.set_equation(stage="potential_swap", lever="morse_hard", equation=1 - s.lam())
s.set_equation(stage="potential_swap", lever="morse_soft", equation=0 + s.lam())
s.set_equation(
Expand All @@ -207,6 +235,8 @@ def ring_break_morph():
s.set_equation(stage="potential_swap", lever="torsion_k", equation=s.initial())
s.set_equation(stage="potential_swap", lever="torsion_phase", equation=s.initial())

# morph: standard nonbonded morphing. Ring-break is fixed at fully open
# (kappa=1, alpha=0) since geometry has already relaxed in ring_open.
s.set_equation(stage="morph", lever="morse_hard", equation=0)
s.set_equation(stage="morph", lever="morse_soft", equation=0)
s.set_equation(stage="morph", lever="bond_k", equation=s.final())
Expand All @@ -215,6 +245,10 @@ def ring_break_morph():
s.set_equation(stage="morph", lever="angle_size", equation=s.final())
s.set_equation(stage="morph", lever="torsion_k", equation=s.final())
s.set_equation(stage="morph", lever="torsion_phase", equation=s.final())
s.set_equation(stage="morph", force="ring-break", lever="alpha", equation=0)
s.set_equation(stage="morph", force="ring-break", lever="kappa", equation=1)
s.set_equation(stage="morph", force="ring-make", lever="alpha", equation=1)
s.set_equation(stage="morph", force="ring-make", lever="kappa", equation=0)

return s

Expand All @@ -223,7 +257,7 @@ def reverse_ring_break_morph():
"""
Build a lambda schedule for reverse ring-breaking perturbations.

Three stages: morph → bonded_perturb → potential_swap.
Four stages: morph → ring_close → bonded_perturb → potential_swap.

Returns
-------
Expand All @@ -234,7 +268,10 @@ def reverse_ring_break_morph():
from sire.cas import LambdaSchedule as _LambdaSchedule

s = _LambdaSchedule.standard_morph()
s.set_stage_weight("morph", 2)

# morph: standard nonbonded morphing. Ring-break fixed at fully open
# (kappa=1, alpha=0); ring-make fixed at full interaction (kappa=1, alpha=0).
s.set_equation(stage="morph", lever="morse_hard", equation=0)
s.set_equation(stage="morph", lever="morse_soft", equation=0)
s.set_equation(stage="morph", lever="bond_k", equation=s.initial())
Expand All @@ -243,8 +280,36 @@ def reverse_ring_break_morph():
s.set_equation(stage="morph", lever="angle_size", equation=s.initial())
s.set_equation(stage="morph", lever="torsion_k", equation=s.initial())
s.set_equation(stage="morph", lever="torsion_phase", equation=s.initial())
s.set_equation(stage="morph", force="ring-break", lever="alpha", equation=1)
s.set_equation(stage="morph", force="ring-break", lever="kappa", equation=0)
s.set_equation(stage="morph", force="ring-make", lever="alpha", equation=0)
s.set_equation(stage="morph", force="ring-make", lever="kappa", equation=1)

# ring_close: non-bonded terms fixed at final; ring-make interaction ramps
# off (alpha: 0→1, kappa: 1→0) to allow atoms to relax into ring geometry
# before Morse is applied. Symmetric counterpart to ring_open.
s.append_stage("ring_close", s.final(), weight=1)
s.set_equation(stage="ring_close", lever="morse_hard", equation=0)
s.set_equation(stage="ring_close", lever="morse_soft", equation=0)
s.set_equation(stage="ring_close", lever="bond_k", equation=s.initial())
s.set_equation(stage="ring_close", lever="bond_length", equation=s.initial())
s.set_equation(stage="ring_close", lever="angle_k", equation=s.initial())
s.set_equation(stage="ring_close", lever="angle_size", equation=s.initial())
s.set_equation(stage="ring_close", lever="torsion_k", equation=s.initial())
s.set_equation(stage="ring_close", lever="torsion_phase", equation=s.initial())
s.set_equation(stage="ring_close", force="ring-break", lever="alpha", equation=1)
s.set_equation(stage="ring_close", force="ring-break", lever="kappa", equation=0)
s.set_equation(
stage="ring_close", force="ring-make", lever="alpha", equation=s.lam()
)
s.set_equation(
stage="ring_close", force="ring-make", lever="kappa", equation=1 - s.lam()
)

s.append_stage("bonded_perturb", s.final())
# bonded_perturb: Morse soft ramps on; ring-make already off from ring_close.
# Ring-break softcore turns on as any ring-break bond opens (alpha: 1→0,
# kappa: 0→1); ring-make stays off (kappa=0, alpha=1).
s.append_stage("bonded_perturb", s.final(), weight=1)
s.set_equation(stage="bonded_perturb", lever="morse_soft", equation=0 + s.lam())
s.set_equation(stage="bonded_perturb", lever="morse_hard", equation=0)
s.set_equation(stage="bonded_perturb", lever="bond_k", equation=s.initial())
Expand All @@ -269,8 +334,16 @@ def reverse_ring_break_morph():
lever="torsion_phase",
equation=(1 - s.lam()) * s.initial() + s.lam() * s.final(),
)
s.set_equation(
stage="bonded_perturb", force="ring-break", lever="alpha", equation=1 - s.lam()
)
s.set_equation(
stage="bonded_perturb", force="ring-break", lever="kappa", equation=s.lam()
)
s.set_equation(stage="bonded_perturb", force="ring-make", lever="alpha", equation=1)
s.set_equation(stage="bonded_perturb", force="ring-make", lever="kappa", equation=0)

s.append_stage("potential_swap", s.final())
s.append_stage("potential_swap", s.final(), weight=2)
s.set_equation(stage="potential_swap", lever="morse_hard", equation=0 + s.lam())
s.set_equation(stage="potential_swap", lever="morse_soft", equation=1 - s.lam())
s.set_equation(
Expand Down
12 changes: 12 additions & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,3 +86,15 @@ def pert_rev_mols():
mols = sr.load_test_files("somd1_backward.prm7", "somd1_backward.rst7")
pert_file = str(Path(__file__).parent / "inputs" / "backward.pert")
return apply_pert(mols, pert_file)


@pytest.fixture(scope="session")
def syk_ring_break_mols():
"""
Load the SYK 5035→5033 ring-breaking perturbation system.

Reference state (λ=0): SYK-5035 with an intact ring containing a
breaking bond. Perturbed state (λ=1): SYK-5033, the open-chain analogue.
"""
mols = sr.load_test_files("syk_5035_5033.s3")
return sr.morph.link_to_reference(mols)
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