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Fix issue #265 #266

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merged 2 commits into from
Dec 13, 2024
Merged

Fix issue #265 #266

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060325a
Fix update of triclinic box vectors. [closes #265]
lohedges Dec 9, 2024
c252141
Update CHANGELOG.
lohedges Dec 9, 2024
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12 changes: 7 additions & 5 deletions corelib/src/libs/SireMove/openmmfrenergydt.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1228,9 +1228,9 @@ void OpenMMFrEnergyDT::integrate(IntegratorWorkspace &workspace, const Symbol &n

// Set Periodic Box Condition

context_openmm.setPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
}
// TriclinicBox.
else if (ptr_sys.property(space_property).isA<TriclinicBox>())
Expand All @@ -1253,9 +1253,11 @@ void OpenMMFrEnergyDT::integrate(IntegratorWorkspace &workspace, const Symbol &n
const double zy = v2.y() * OpenMM::NmPerAngstrom;
const double zz = v2.z() * OpenMM::NmPerAngstrom;

context_openmm.setPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
}

context_openmm.reinitialize();
}

if (Debug)
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7 changes: 0 additions & 7 deletions corelib/src/libs/SireMove/openmmfrenergyst.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3450,10 +3450,6 @@ void OpenMMFrEnergyST::createContext(IntegratorWorkspace &workspace, SireUnits::
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
}
// TriclinicBox.
else if (ptr_sys.property(space_property).isA<TriclinicBox>())
Expand All @@ -3478,9 +3474,6 @@ void OpenMMFrEnergyST::createContext(IntegratorWorkspace &workspace, SireUnits::

system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
}

openmm_context->reinitialize();
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11 changes: 6 additions & 5 deletions corelib/src/libs/SireMove/openmmmdintegrator.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1157,9 +1157,9 @@ void OpenMMMDIntegrator::createContext(IntegratorWorkspace &workspace, SireUnits

// Set Periodic Box Condition

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
}
// TriclinicBox.
else if (ptr_sys.property(space_property).isA<TriclinicBox>())
Expand All @@ -1182,11 +1182,12 @@ void OpenMMMDIntegrator::createContext(IntegratorWorkspace &workspace, SireUnits
const double zy = v2.y() * OpenMM::NmPerAngstrom;
const double zz = v2.z() * OpenMM::NmPerAngstrom;

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
}

is_periodic = true;
openmm_context->reinitialize();
}

double AKMAPerPs = 0.04888821;
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7 changes: 0 additions & 7 deletions corelib/src/libs/SireMove/openmmpmefep.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2954,10 +2954,6 @@ void OpenMMPMEFEP::createContext(IntegratorWorkspace &workspace, SireUnits::Dime
system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(Box_x_Edge_Length, 0, 0),
OpenMM::Vec3(0, Box_y_Edge_Length, 0),
OpenMM::Vec3(0, 0, Box_z_Edge_Length));
}
// TriclinicBox
else if (ptr_sys.property(space_property).isA<TriclinicBox>())
Expand All @@ -2983,9 +2979,6 @@ void OpenMMPMEFEP::createContext(IntegratorWorkspace &workspace, SireUnits::Dime

system_openmm->setDefaultPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));

openmm_context->setPeriodicBoxVectors(OpenMM::Vec3(xx, xy, xz), OpenMM::Vec3(yx, yy, yz),
OpenMM::Vec3(zx, zy, zz));
}

openmm_context->reinitialize();
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15 changes: 15 additions & 0 deletions doc/source/changelog.rst
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Expand Up @@ -16,17 +16,32 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
---------------------------------------------------------------------------------------------

* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.

* Fixed update of triclinic box vectors in ``SOMD`` following ``OpenMM`` bug fix.

`2024.3.1 <https://github.com/openbiosim/sire/compare/2024.3.0...2024.3.1>`__ - December 2024
--------------------------------------------------------------------------------------------

* Fixed instantiaton of ``QByteArray`` in ``Sire::Mol::Frame::toByteArray`` and count bytes with ``QByteArray::size``.

* Increase timeout before terminating ``QThread`` objects during ``PageCache`` cleanup.

* Expose missing ``timeout`` kwarg in :meth:`dynamics.minimise()` method.

* Expose missing ``include_constrained_energies`` kwarg in minimisation function.

* Make minimisation function settings consistent across API.

* Reload TorchQMForce module if OpenMM platform changes.

* Fix calculation of non-equilibrium work when starting from QM state.

* Fix stereochemistry in RDKit molecule conversion.

* Fixed :func:`sire.restraints.get_standard_state_correction` to be consistent with the definition of
the "force constanst" as ``F = 2 ** k ** x`` (rather than ``F = k ** x``). Updated docstrings and
restraints documentation to make it clear how the force constants are defined.

* Fix thread safety issue in Sire OpenMM minimiser.

`2024.3.0 <https://github.com/openbiosim/sire/compare/2024.2.0...2024.3.0>`__ - October 2024
Expand Down
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