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Merge pull request #43 from OpenBioSim/fix_null_bonded_terms
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Fix form of null bonded terms
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@lohedges
lohedges authored May 2, 2024
2 parents 089ddcb + 85f0c4c commit 09d276f
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Showing 2 changed files with 11 additions and 32 deletions.
2 changes: 1 addition & 1 deletion src/somd2/runner/_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -969,5 +969,5 @@ def _run(sim, is_restart=False):
filename=self._fnames[lambda_value]["energy_traj"],
)
del system
_logger.success(f"{_lam_sym} = {lambda_value} complete")
_logger.success(f"{_lam_sym} = {lambda_value} complete, speed = {speed:.2f} ns day-1")
return True
41 changes: 10 additions & 31 deletions src/somd2/runner/_somd1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
from sire.system import System as _System
from sire.legacy.System import System as _LegacySystem

import sire.legacy.CAS as _SireCAS
import sire.legacy.MM as _SireMM
import sire.legacy.Mol as _SireMol

Expand Down Expand Up @@ -244,12 +243,9 @@ def _make_compatible(system):
initial_dummy = _has_dummy(mol, [idx0, idx1, idx2])
final_dummy = _has_dummy(mol, [idx0, idx1, idx2], True)

# If both end states contain a dummy, the use null potentials.
# If both end states contain a dummy, then don't add the potentials.
if initial_dummy and final_dummy:
theta = _SireCAS.Symbol("theta")
null_angle = _SireMM.AmberAngle(0.0, theta).to_expression(theta)
new_angles0.set(idx0, idx1, idx2, null_angle)
new_angles1.set(idx0, idx1, idx2, null_angle)
continue
# If the initial state contains a dummy, then use the potential from the final state.
# This should already be the case, but we explicitly set it here.
elif initial_dummy:
Expand Down Expand Up @@ -355,34 +351,25 @@ def _make_compatible(system):
all_dummy_initial = all(_is_dummy(mol, [idx0, idx1, idx2, idx3]))
all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True))

# If both end states contain a dummy, the use null potentials.
# If both end states contain a dummy, then don't add the potentials.
if has_dummy_initial and has_dummy_final:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_dihedrals0.set(idx0, idx1, idx2, idx3, null_dihedral)
new_dihedrals1.set(idx0, idx1, idx2, idx3, null_dihedral)
continue
elif has_dummy_initial:
# If all the atoms are dummy, then use the potential from the final state.
if all_dummy_initial:
new_dihedrals0.set(idx0, idx1, idx2, idx3, p1.function())
new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function())
# Otherwise, zero the potential.
# Otherwise, remove the potential from the initial state.
else:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_dihedrals0.set(idx0, idx1, idx2, idx3, null_dihedral)
new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function())
elif has_dummy_final:
# If all the atoms are dummy, then use the potential from the initial state.
if all_dummy_final:
new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function())
new_dihedrals1.set(idx0, idx1, idx2, idx3, p0.function())
# Otherwise, zero the potential.
# Otherwise, remove the potential from the final state.
else:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function())
new_dihedrals1.set(idx0, idx1, idx2, idx3, null_dihedral)
else:
new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function())
new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function())
Expand Down Expand Up @@ -490,33 +477,25 @@ def _make_compatible(system):
all_dummy_initial = all(_is_dummy(mol, [idx0, idx1, idx2, idx3]))
all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True))

# If both end states contain a dummy, then don't add the potentials.
if has_dummy_initial and has_dummy_final:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_impropers0.set(idx0, idx1, idx2, idx3, null_dihedral)
new_impropers1.set(idx0, idx1, idx2, idx3, null_dihedral)
continue
elif has_dummy_initial:
# If all the atoms are dummy, then use the potential from the final state.
if all_dummy_initial:
new_impropers0.set(idx0, idx1, idx2, idx3, p1.function())
new_impropers1.set(idx0, idx1, idx2, idx3, p1.function())
# Otherwise, zero the potential.
# Otherwise, remove the potential from the initial state.
else:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_impropers0.set(idx0, idx1, idx2, idx3, null_dihedral)
new_impropers1.set(idx0, idx1, idx2, idx3, p1.function())
elif has_dummy_final:
# If all the atoms are dummy, then use the potential from the initial state.
if all_dummy_final:
new_impropers0.set(idx0, idx1, idx2, idx3, p0.function())
new_impropers1.set(idx0, idx1, idx2, idx3, p0.function())
# Otherwise, zero the potential.
# Otherwise, remove the potential from the final state.
else:
phi = _SireCAS.Symbol("phi")
null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi)
new_impropers0.set(idx0, idx1, idx2, idx3, p0.function())
new_impropers1.set(idx0, idx1, idx2, idx3, null_dihedral)
else:
new_impropers0.set(idx0, idx1, idx2, idx3, p0.function())
new_impropers1.set(idx0, idx1, idx2, idx3, p1.function())
Expand Down

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