Merge OpenMM master into dtk26.04

platforms/common/src/CommonKernels.cpp

@@ -4709,7 +4709,7 @@ void CommonCalcCustomCPPForceKernel::initialize(const ContextImpl& context, Cust
     forceGroupFlag = (1<<force.getOwner().getForceGroup());
     useWorkerThread = (cc.getNumContexts() == 1);
     for (const ForceImpl* impl : context.getForceImpls())
-        if (dynamic_cast<const CustomCPPForceImpl*>(impl) != NULL || dynamic_cast<const PythonForceImpl*>(impl) != NULL)
+        if (impl != &force && (dynamic_cast<const CustomCPPForceImpl*>(impl) != NULL || dynamic_cast<const PythonForceImpl*>(impl) != NULL))
             useWorkerThread = false;
     if (useWorkerThread) {
         cc.addPreComputation(new StartCalculationPreComputation(*this));
@@ -4871,7 +4871,7 @@ void CommonCalcPythonForceKernel::initialize(const ContextImpl& context, const P
     forceGroupFlag = (1<<force.getForceGroup());
     useWorkerThread = (cc.getNumContexts() == 1);
     for (const ForceImpl* impl : context.getForceImpls())
-        if (dynamic_cast<const CustomCPPForceImpl*>(impl) != NULL || dynamic_cast<const PythonForceImpl*>(impl) != NULL)
+        if (&impl->getOwner() != &force && (dynamic_cast<const CustomCPPForceImpl*>(impl) != NULL || dynamic_cast<const PythonForceImpl*>(impl) != NULL))
             useWorkerThread = false;
     if (useWorkerThread) {
         cc.addPreComputation(new StartCalculationPreComputation(*this));

platforms/common/src/CommonMinimizeKernel.cpp

@@ -547,7 +547,11 @@ void CommonMinimizeKernel::evaluateGpu(ContextImpl& context) {
     // Evaluate the forces and energy for the desired interactions as well as
     // harmonic restraints to emulate the constraints.
 
-    energy = context.calcForcesAndEnergy(true, true, forceGroups);
+    {
+        ContextDeselector deselector(cc);
+        energy = context.calcForcesAndEnergy(true, true, forceGroups);
+    }
+
     if (numConstraints) {
         if (mixedIsDouble) {
             getConstraintEnergyForcesKernel->setArg(8, kRestraint);
@@ -592,7 +596,11 @@ double CommonMinimizeKernel::evaluateCpu(ContextImpl& context) {
     cpuContext->setState(context.getOwner().getState(State::Parameters));
     cpuContext->setPositions(hostPositions);
     cpuContext->computeVirtualSites();
-    State state = cpuContext->getState(State::Energy | State::Forces, false, forceGroups);
+    State state;
+    {
+        ContextDeselector deselector(cc);
+        state = cpuContext->getState(State::Energy | State::Forces, false, forceGroups);
+    }
     double hostEnergy = state.getPotentialEnergy();
     const vector<Vec3>& hostForces = state.getForces();
 
@@ -676,7 +684,10 @@ bool CommonMinimizeKernel::report(ContextImpl& context, int iteration) {
     args["system energy"] = energy - restraintEnergy;
     args["restraint strength"] = kRestraint;
     args["max constraint error"] = maxError;
-    return reporter->report(iteration - 1, hostX, hostGrad, args);
+    {
+        ContextDeselector deselector(cc);
+        return reporter->report(iteration - 1, hostX, hostGrad, args);
+    }
 }
 
 void CommonMinimizeKernel::downloadReturnFlagStart() {

platforms/cuda/src/CudaContext.cpp

@@ -461,8 +461,11 @@ void CudaContext::pushAsCurrent() {
 
 void CudaContext::popAsCurrent() {
     CUcontext popped;
-    if (contextIsValid)
+    if (contextIsValid) {
         cuCtxPopCurrent(&popped);
+        if (popped != context)
+            throw OpenMMException("Called popAsCurrent() on a context that is not current");
+    }
 }
 
 CUmodule CudaContext::createModule(const string source, const char* optimizationFlags) {
@@ -886,4 +889,4 @@ void CudaContext::ensureCudaInitialized() {
         CHECK_RESULT2(cuInit(0), "Error initializing CUDA");
         hasInitializedCuda = true;
     }
-}
\ No newline at end of file
+}

platforms/reference/tests/TestReferenceMonteCarloMembraneBarostat.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2025 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,13 +34,14 @@
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/MonteCarloMembraneBarostat.h"
 #include "openmm/Context.h"
-#include "ReferencePlatform.h"
+#include "openmm/CustomIntegrator.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/VerletIntegrator.h"
+#include "ReferencePlatform.h"
 #include "sfmt/SFMT.h"
 #include "SimTKOpenMMRealType.h"
 #include <iostream>
@@ -118,6 +119,73 @@ void testIdealGas(MonteCarloMembraneBarostat::XYMode xymode, MonteCarloMembraneB
     }
 }
 
+void testMoleculeScaling(bool rigid) {
+    int numMolecules = 10;
+    double initialWidth = 3.0;
+
+    // Create a system of diatomic molecules.
+
+    System system;
+    Vec3 initialBox[] = {Vec3(initialWidth, 0, 0), Vec3(0, initialWidth, 0), Vec3(0, 0, initialWidth)};
+    system.setDefaultPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    system.addForce(nonbonded);
+    MonteCarloMembraneBarostat* barostat = new MonteCarloMembraneBarostat(1.0, 0.0, 300.0, MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFree, 1, rigid);
+    system.addForce(barostat);
+    vector<Vec3> positions;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        bonds->addBond(2*i, 2*i+1, 0.2, 1000.0);
+        nonbonded->addParticle(0.0, 0.1, 1.0);
+        nonbonded->addParticle(0.0, 0.1, 1.0);
+        Vec3 pos1(initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt));
+        Vec3 delta(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+        delta /= sqrt(delta.dot(delta));
+        positions.push_back(pos1);
+        positions.push_back(pos1+delta);
+    }
+
+    // Use an integrator that applies the barostat but nothing else.
+
+    CustomIntegrator integrator(1.0);
+    integrator.addUpdateContextState();
+
+    // Let the barostat make some moves.
+
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    integrator.step(100);
+    State state = context.getState(State::Positions);
+
+    // The box size should have changed.
+
+    Vec3 finalBox[3];
+    state.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
+    for (int i = 0; i < 3; i++)
+        ASSERT(finalBox[i][i] != initialBox[i][i]);
+
+    // See if the molecules were scaled correctly.
+
+    Vec3 boxScale(finalBox[0][0]/initialBox[0][0], finalBox[1][1]/initialBox[1][1], finalBox[2][2]/initialBox[2][2]);
+    for (int i = 0; i < numMolecules; i++) {
+        Vec3 delta1 = positions[2*i+1]-positions[2*i];
+        Vec3 delta2 = state.getPositions()[2*i+1]-state.getPositions()[2*i];
+        if (rigid) {
+            ASSERT_EQUAL_VEC(delta1, delta2, 1e-5);
+        }
+        else {
+            Vec3 expected(delta1[0]*boxScale[0], delta1[1]*boxScale[1], delta1[2]*boxScale[2]);
+            ASSERT_EQUAL_VEC(expected, delta2, 1e-5);
+        }
+    }
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -256,6 +324,8 @@ int main() {
         testIdealGas(MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFree);
         testIdealGas(MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFixed);
         testIdealGas(MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ConstantVolume);
+        testMoleculeScaling(true);
+        testMoleculeScaling(false);
         testRandomSeed();
         testCrystal();
     }

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -59,9 +59,7 @@ public:
     /**
      * Get the number of particles in the system.
      */
-    int getNumParticles() const {
-        return particles.size();
-    }
+    int getNumParticles() const;
 
     /**
      * Add the  parameters for a particle.  This should be called once for each particle

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -105,9 +105,7 @@ public:
     /**
      * Get the number of particles in the potential function
      */
-    int getNumMultipoles() const {
-        return multipoles.size();
-    }
+    int getNumMultipoles() const;
 
     /**
      * Get the method used for handling long-range nonbonded interactions.

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -59,16 +59,12 @@ public:
     /**
      * Get the number of torsion-torsion terms in the potential function
      */
-    int getNumTorsionTorsions(void) const {
-        return torsionTorsions.size();
-    }
+    int getNumTorsionTorsions(void) const;
 
     /**
      * Get the number of torsion-torsion grids
      */
-    int getNumTorsionTorsionGrids(void) const {
-        return torsionTorsionGrids.size();
-    }
+    int getNumTorsionTorsionGrids(void) const;
 
     /**
      * Add a torsion-torsion term to the force field.

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -143,23 +143,17 @@ public:
     /**
      * Get the number of particles
      */
-    int getNumParticles() const {
-        return parameters.size();
-    }
+    int getNumParticles() const;
 
     /**
      * Get the number of particle types.
      */
-    int getNumParticleTypes() const {
-        return types.size();
-    }
+    int getNumParticleTypes() const;
 
     /**
      * Get the number of type pairs.
      */
-    int getNumTypePairs() const {
-        return pairs.size();
-    }
+    int getNumTypePairs() const;
 
     /**
      * Set the force field parameters for a vdw particle.

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -57,9 +57,7 @@ public:
     /**
      * Get the number of particles
      */
-    int getNumParticles() const {
-        return parameters.size();
-    }
+    int getNumParticles() const;
 
     /**
      * Set the force field parameters for a WCA dispersion particle.

plugins/amoeba/openmmapi/include/openmm/HippoNonbondedForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Mark Friedrichs                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -79,15 +79,11 @@ public:
     /**
      * Get the number of particles in the potential function.
      */
-    int getNumParticles() const {
-        return particles.size();
-    }
+    int getNumParticles() const;
     /**
      * Get the number of exceptions.
      */
-    int getNumExceptions() const {
-        return exceptions.size();
-    }
+    int getNumExceptions() const;
     /**
      * Get the method used for handling long-range nonbonded interactions.
      */

plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,6 +40,10 @@ AmoebaGeneralizedKirkwoodForce::AmoebaGeneralizedKirkwoodForce() :
      surfaceAreaFactor = -6.0* 3.1415926535*0.0216*1000.0*0.4184;
 }
 
+int AmoebaGeneralizedKirkwoodForce::getNumParticles() const {
+    return particles.size();
+}
+
 int AmoebaGeneralizedKirkwoodForce::addParticle(double charge, double radius, double scalingFactor) {
     particles.push_back(ParticleInfo(charge, radius, scalingFactor, radius, 0.0));
     return particles.size()-1;

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,6 +46,10 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
     extrapolationCoefficients.push_back(0.474);
 }
 
+int AmoebaMultipoleForce::getNumMultipoles() const {
+    return multipoles.size();
+}
+
 AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
     return nonbondedMethod;
 }

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp

@@ -39,6 +39,13 @@ using namespace std;
 AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() : usePeriodic(false) {
 }
 
+int AmoebaTorsionTorsionForce::getNumTorsionTorsions(void) const {
+    return torsionTorsions.size();
+}
+
+int AmoebaTorsionTorsionForce::getNumTorsionTorsionGrids(void) const {
+    return torsionTorsionGrids.size();
+}
 int AmoebaTorsionTorsionForce::addTorsionTorsion(int particle1, int particle2, int particle3,
                                                  int particle4, int particle5, int chiralCheckAtomIndex,
                                                  int gridIndex) {

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,18 @@ AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), potentialFunction(
         useTypes(false), alchemicalMethod(None), n(5), alpha(0.7) {
 }
 
+int AmoebaVdwForce::getNumParticles() const {
+    return parameters.size();
+}
+
+int AmoebaVdwForce::getNumParticleTypes() const {
+    return types.size();
+}
+
+int AmoebaVdwForce::getNumTypePairs() const {
+    return pairs.size();
+}
+
 int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical, double scaleFactor) {
     if (useTypes)
         throw OpenMMException("AmoebaVdwForce: must use the same version of addParticle() for all particles");

plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -54,6 +54,10 @@ AmoebaWcaDispersionForce::AmoebaWcaDispersionForce() {
     shctd = 0.82;
 }
 
+int AmoebaWcaDispersionForce::getNumParticles() const {
+    return parameters.size();
+}
+
 int AmoebaWcaDispersionForce::addParticle(double radius, double epsilon) {
     parameters.push_back(WcaDispersionInfo(radius, epsilon));
     return parameters.size()-1;

plugins/amoeba/openmmapi/src/HippoNonbondedForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,14 @@ HippoNonbondedForce::HippoNonbondedForce() : nonbondedMethod(NoCutoff), cutoffDi
     extrapolationCoefficients = {0.042, 0.635, 0.414};
 }
 
+int HippoNonbondedForce::getNumParticles() const {
+    return particles.size();
+}
+
+int HippoNonbondedForce::getNumExceptions() const {
+    return exceptions.size();
+}
+
 HippoNonbondedForce::NonbondedMethod HippoNonbondedForce::getNonbondedMethod() const {
     return nonbondedMethod;
 }

plugins/amoeba/platforms/common/src/AmoebaCommonKernels.cpp

@@ -1399,8 +1399,10 @@ void CommonCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& co
                 }
         }
     }
-    if (!multipolesAreValid)
+    if (!multipolesAreValid) {
+        ContextDeselector deselector(cc);
         context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
+    }
 }
 
 void CommonCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
@@ -3487,8 +3489,10 @@ void CommonCalcHippoNonbondedForceKernel::ensureMultipolesValid(ContextImpl& con
                 }
         }
     }
-    if (!multipolesAreValid)
+    if (!multipolesAreValid) {
+        ContextDeselector deselector(cc);
         context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
+    }
 }
 
 void CommonCalcHippoNonbondedForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {

plugins/drude/openmmapi/include/openmm/DrudeForce.h

@@ -7,7 +7,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2013-2024 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -59,15 +59,11 @@ public:
     /**
      * Get the number of particles for which force field parameters have been defined.
      */
-    int getNumParticles() const {
-        return particles.size();
-    }
+    int getNumParticles() const;
     /**
      * Get the number of special interactions that should be calculated differently from other interactions.
      */
-    int getNumScreenedPairs() const {
-        return screenedPairs.size();
-    }
+    int getNumScreenedPairs() const;
     /**
      * Add a Drude particle to which forces should be applied.
      *

plugins/drude/openmmapi/src/DrudeForce.cpp

@@ -4,7 +4,7 @@
  * This is part of the OpenMM molecular simulation toolkit.                   *
  * See https://openmm.org/development.                                        *
  *                                                                            *
- * Portions copyright (c) 2013-2024 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2026 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,6 +39,14 @@ using namespace std;
 DrudeForce::DrudeForce() : usePeriodic(false) {
 }
 
+int DrudeForce::getNumParticles() const {
+    return particles.size();
+}
+
+int DrudeForce::getNumScreenedPairs() const {
+    return screenedPairs.size();
+}
+
 int DrudeForce::addParticle(int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34) {
     if (polarizability <= 0)
         throw OpenMMException("Polarizability must be positive");