Backport fix from PR #266. [ci skip]

OpenBioSim · Dec 13, 2024 · 28e8eba · 28e8eba
1 parent 7921fe3
commit 28e8eba
Show file tree

Hide file tree

Showing 5 changed files with 20 additions and 24 deletions.
diff --git a/corelib/src/libs/SireMove/openmmfrenergydt.cpp b/corelib/src/libs/SireMove/openmmfrenergydt.cpp
@@ -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>())
@@ -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)

diff --git a/corelib/src/libs/SireMove/openmmfrenergyst.cpp b/corelib/src/libs/SireMove/openmmfrenergyst.cpp
@@ -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>())
@@ -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();

diff --git a/corelib/src/libs/SireMove/openmmmdintegrator.cpp b/corelib/src/libs/SireMove/openmmmdintegrator.cpp
@@ -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>())
@@ -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;

diff --git a/corelib/src/libs/SireMove/openmmpmefep.cpp b/corelib/src/libs/SireMove/openmmpmefep.cpp
@@ -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>())
@@ -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();

diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -12,6 +12,13 @@ Development was migrated into the
 `OpenBioSim <https://github.com/openbiosim>`__
 organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
+`2024.4.0 <https://github.com/openbiosim/sire/compare/2024.3.1...2024.4.0>`__ - December 2024
+--------------------------------------------------------------------------------------------
+
+* 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
 ---------------------------------------------------------------------------------------------