Optimize updateParametersInContext() (#4610)

* Optimize CustomNonbondedForce.updateParametersInContext()

* Optimized uploading changed values to GPU

* Optimized updateParametersInContext() for lots of bonded forces

* Optimized updateParametersInContext() for CustomExternalForce

* Optimized updateParametersInContext() for NonbondedForce

* Code changes for HIP platform

openmmapi/src/CustomAngleForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -97,7 +97,7 @@ map<string, double> CustomAngleForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-void CustomAngleForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcCustomAngleForceKernel>().copyParametersToContext(context, owner);
+void CustomAngleForceImpl::updateParametersInContext(ContextImpl& context, int firstAngle, int lastAngle) {
+    kernel.getAs<CalcCustomAngleForceKernel>().copyParametersToContext(context, owner, firstAngle, lastAngle);
     context.systemChanged();
 }

openmmapi/src/CustomBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,11 +40,9 @@
 #include <utility>
 
 using namespace OpenMM;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
-CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
+CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false), numContexts(0) {
 }
 
 const string& CustomBondForce::getEnergyFunction() const {
@@ -126,14 +124,30 @@ void CustomBondForce::setBondParameters(int index, int particle1, int particle2,
     bonds[index].parameters = parameters;
     bonds[index].particle1 = particle1;
     bonds[index].particle2 = particle2;
+    if (numContexts > 0) {
+        firstChangedBond = min(index, firstChangedBond);
+        lastChangedBond = max(index, lastChangedBond);
+    }
 }
 
 ForceImpl* CustomBondForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to bonds.
+        firstChangedBond = bonds.size();
+        lastChangedBond = -1;
+    }
+    numContexts++;
     return new CustomBondForceImpl(*this);
 }
 
 void CustomBondForce::updateParametersInContext(Context& context) {
-    dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedBond, lastChangedBond);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed bonds.
+        firstChangedBond = bonds.size();
+        lastChangedBond = -1;
+    }
 }
 
 void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {

openmmapi/src/CustomBondForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -108,7 +108,7 @@ vector<pair<int, int> > CustomBondForceImpl::getBondedParticles() const {
     return bonds;
 }
 
-void CustomBondForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcCustomBondForceKernel>().copyParametersToContext(context, owner);
+void CustomBondForceImpl::updateParametersInContext(ContextImpl& context, int firstBond, int lastBond) {
+    kernel.getAs<CalcCustomBondForceKernel>().copyParametersToContext(context, owner, firstBond, lastBond);
     context.systemChanged();
 }

openmmapi/src/CustomExternalForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,11 +40,9 @@
 #include <utility>
 
 using namespace OpenMM;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
-CustomExternalForce::CustomExternalForce(const string& energy) : energyExpression(energy) {
+CustomExternalForce::CustomExternalForce(const string& energy) : energyExpression(energy), numContexts(0) {
 }
 
 const string& CustomExternalForce::getEnergyFunction() const {
@@ -110,14 +108,29 @@ void CustomExternalForce::setParticleParameters(int index, int particle, const v
     ASSERT_VALID_INDEX(index, particles);
     particles[index].parameters = parameters;
     particles[index].particle = particle;
+    if (numContexts > 0) {
+        firstChangedParticle = min(index, firstChangedParticle);
+        lastChangedParticle = max(index, lastChangedParticle);
+    }
 }
 
 ForceImpl* CustomExternalForce::createImpl() const {
-    return new CustomExternalForceImpl(*this);
+    if (numContexts == 0) {
+        // Begin tracking changes to particles.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+    }
+    numContexts++;    return new CustomExternalForceImpl(*this);
 }
 
 void CustomExternalForce::updateParametersInContext(Context& context) {
-    dynamic_cast<CustomExternalForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<CustomExternalForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedParticle, lastChangedParticle);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed particles.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+    }
 }
 
 bool CustomExternalForce::usesPeriodicBoundaryConditions() const {

openmmapi/src/CustomExternalForceImpl.cpp

@@ -96,7 +96,7 @@ map<string, double> CustomExternalForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-void CustomExternalForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcCustomExternalForceKernel>().copyParametersToContext(context, owner);
+void CustomExternalForceImpl::updateParametersInContext(ContextImpl& context, int firstParticle, int lastParticle) {
+    kernel.getAs<CalcCustomExternalForceKernel>().copyParametersToContext(context, owner, firstParticle, lastParticle);
     context.systemChanged();
 }

openmmapi/src/CustomNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2022 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,18 +40,13 @@
 #include <utility>
 
 using namespace OpenMM;
-using std::map;
-using std::pair;
-using std::set;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
 CustomNonbondedForce::CustomNonbondedForce(const string& energy) : energyExpression(energy), nonbondedMethod(NoCutoff), cutoffDistance(1.0),
-    switchingDistance(-1.0), useSwitchingFunction(false), useLongRangeCorrection(false) {
+    switchingDistance(-1.0), useSwitchingFunction(false), useLongRangeCorrection(false), numContexts(0) {
 }
 
-CustomNonbondedForce::CustomNonbondedForce(const CustomNonbondedForce& rhs) {
+CustomNonbondedForce::CustomNonbondedForce(const CustomNonbondedForce& rhs) : numContexts(0) {
     // Copy everything and deep copy the tabulated functions
     setForceGroup(rhs.getForceGroup());
     setName(rhs.getName());
@@ -194,6 +189,10 @@ void CustomNonbondedForce::getParticleParameters(int index, std::vector<double>&
 void CustomNonbondedForce::setParticleParameters(int index, const vector<double>& parameters) {
     ASSERT_VALID_INDEX(index, particles);
     particles[index].parameters = parameters;
+    if (numContexts > 0) {
+        firstChangedParticle = min(index, firstChangedParticle);
+        lastChangedParticle = max(index, lastChangedParticle);
+    }
 }
 
 int CustomNonbondedForce::addExclusion(int particle1, int particle2) {
@@ -326,9 +325,21 @@ void CustomNonbondedForce::setInteractionGroupParameters(int index, const std::s
 }
 
 ForceImpl* CustomNonbondedForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to particles.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+    }
+    numContexts++;
     return new CustomNonbondedForceImpl(*this);
 }
 
 void CustomNonbondedForce::updateParametersInContext(Context& context) {
-    dynamic_cast<CustomNonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<CustomNonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedParticle, lastChangedParticle);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed particles.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+    }
 }

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -159,8 +159,8 @@ map<string, double> CustomNonbondedForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-void CustomNonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcCustomNonbondedForceKernel>().copyParametersToContext(context, owner);
+void CustomNonbondedForceImpl::updateParametersInContext(ContextImpl& context, int firstParticle, int lastParticle) {
+    kernel.getAs<CalcCustomNonbondedForceKernel>().copyParametersToContext(context, owner, firstParticle, lastParticle);
     context.systemChanged();
 }
 

openmmapi/src/CustomTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,11 +40,9 @@
 #include <utility>
 
 using namespace OpenMM;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
-CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
+CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false), numContexts(0) {
 }
 
 const string& CustomTorsionForce::getEnergyFunction() const {
@@ -130,14 +128,30 @@ void CustomTorsionForce::setTorsionParameters(int index, int particle1, int part
     torsions[index].particle2 = particle2;
     torsions[index].particle3 = particle3;
     torsions[index].particle4 = particle4;
+    if (numContexts > 0) {
+        firstChangedTorsion = min(index, firstChangedTorsion);
+        lastChangedTorsion = max(index, lastChangedTorsion);
+    }
 }
 
 ForceImpl* CustomTorsionForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to torsions.
+        firstChangedTorsion = torsions.size();
+        lastChangedTorsion = -1;
+    }
+    numContexts++;
     return new CustomTorsionForceImpl(*this);
 }
 
 void CustomTorsionForce::updateParametersInContext(Context& context) {
-    dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedTorsion, lastChangedTorsion);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed torsions.
+        firstChangedTorsion = torsions.size();
+        lastChangedTorsion = -1;
+    }
 }
 
 void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {

openmmapi/src/CustomTorsionForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -98,7 +98,7 @@ map<string, double> CustomTorsionForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-void CustomTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcCustomTorsionForceKernel>().copyParametersToContext(context, owner);
+void CustomTorsionForceImpl::updateParametersInContext(ContextImpl& context, int firstTorsion, int lastTorsion) {
+    kernel.getAs<CalcCustomTorsionForceKernel>().copyParametersToContext(context, owner, firstTorsion, lastTorsion);
     context.systemChanged();
 }

openmmapi/src/HarmonicAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,8 +36,9 @@
 #include "openmm/internal/HarmonicAngleForceImpl.h"
 
 using namespace OpenMM;
+using namespace std;
 
-HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
+HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false), numContexts(0) {
 }
 
 int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
@@ -61,14 +62,30 @@ void HarmonicAngleForce::setAngleParameters(int index, int particle1, int partic
     angles[index].particle3 = particle3;
     angles[index].angle = angle;
     angles[index].k = k;
+    if (numContexts > 0) {
+        firstChangedAngle = min(index, firstChangedAngle);
+        lastChangedAngle = max(index, lastChangedAngle);
+    }
 }
 
 ForceImpl* HarmonicAngleForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to angles.
+        firstChangedAngle = angles.size();
+        lastChangedAngle = -1;
+    }
+    numContexts++;
     return new HarmonicAngleForceImpl(*this);
 }
 
 void HarmonicAngleForce::updateParametersInContext(Context& context) {
-    dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedAngle, lastChangedAngle);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed angles.
+        firstChangedAngle = angles.size();
+        lastChangedAngle = -1;
+    }
 }
 
 void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {

openmmapi/src/HarmonicAngleForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -82,7 +82,7 @@ std::vector<std::string> HarmonicAngleForceImpl::getKernelNames() {
     return names;
 }
 
-void HarmonicAngleForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcHarmonicAngleForceKernel>().copyParametersToContext(context, owner);
+void HarmonicAngleForceImpl::updateParametersInContext(ContextImpl& context, int firstAngle, int lastAngle) {
+    kernel.getAs<CalcHarmonicAngleForceKernel>().copyParametersToContext(context, owner, firstAngle, lastAngle);
     context.systemChanged();
 }

openmmapi/src/HarmonicBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,8 +36,9 @@
 #include "openmm/internal/HarmonicBondForceImpl.h"
 
 using namespace OpenMM;
+using namespace std;
 
-HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
+HarmonicBondForce::HarmonicBondForce() : usePeriodic(false), numContexts(0) {
 }
 
 int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
@@ -59,14 +60,30 @@ void HarmonicBondForce::setBondParameters(int index, int particle1, int particle
     bonds[index].particle2 = particle2;
     bonds[index].length = length;
     bonds[index].k = k;
+    if (numContexts > 0) {
+        firstChangedBond = min(index, firstChangedBond);
+        lastChangedBond = max(index, lastChangedBond);
+    }
 }
 
 ForceImpl* HarmonicBondForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to bonds.
+        firstChangedBond = bonds.size();
+        lastChangedBond = -1;
+    }
+    numContexts++;
     return new HarmonicBondForceImpl(*this);
 }
 
 void HarmonicBondForce::updateParametersInContext(Context& context) {
-    dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedBond, lastChangedBond);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed bonds.
+        firstChangedBond = bonds.size();
+        lastChangedBond = -1;
+    }
 }
 
 void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {

openmmapi/src/HarmonicBondForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -88,7 +88,7 @@ vector<pair<int, int> > HarmonicBondForceImpl::getBondedParticles() const {
     return bonds;
 }
 
-void HarmonicBondForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcHarmonicBondForceKernel>().copyParametersToContext(context, owner);
+void HarmonicBondForceImpl::updateParametersInContext(ContextImpl& context, int firstBond, int lastBond) {
+    kernel.getAs<CalcHarmonicBondForceKernel>().copyParametersToContext(context, owner, firstBond, lastBond);
     context.systemChanged();
 }

openmmapi/src/NonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,16 +40,11 @@
 #include <utility>
 
 using namespace OpenMM;
-using std::map;
-using std::pair;
-using std::set;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
 NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
         ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), exceptionsUsePeriodic(false), recipForceGroup(-1),
-        includeDirectSpace(true), nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
+        includeDirectSpace(true), nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0), numContexts(0) {
 }
 
 NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
@@ -155,7 +150,10 @@ void NonbondedForce::setParticleParameters(int index, double charge, double sigm
     particles[index].charge = charge;
     particles[index].sigma = sigma;
     particles[index].epsilon = epsilon;
-}
+    if (numContexts > 0) {
+        firstChangedParticle = min(index, firstChangedParticle);
+        lastChangedParticle = max(index, lastChangedParticle);
+    }}
 
 int NonbondedForce::addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace) {
     map<pair<int, int>, int>::iterator iter = exceptionMap.find(pair<int, int>(particle1, particle2));
@@ -198,9 +196,20 @@ void NonbondedForce::setExceptionParameters(int index, int particle1, int partic
     exceptions[index].chargeProd = chargeProd;
     exceptions[index].sigma = sigma;
     exceptions[index].epsilon = epsilon;
-}
+    if (numContexts > 0) {
+        firstChangedException = min(index, firstChangedException);
+        lastChangedException = max(index, lastChangedException);
+    }}
 
 ForceImpl* NonbondedForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to particles and exceptions.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+        firstChangedException = exceptions.size();
+        lastChangedException = -1;
+    }
+    numContexts++;
     return new NonbondedForceImpl(*this);
 }
 
@@ -353,7 +362,16 @@ void NonbondedForce::setIncludeDirectSpace(bool include) {
 }
 
 void NonbondedForce::updateParametersInContext(Context& context) {
-    dynamic_cast<NonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<NonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context),
+            firstChangedParticle, lastChangedParticle, firstChangedException, lastChangedException);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed particles and exceptions.
+        firstChangedParticle = particles.size();
+        lastChangedParticle = -1;
+        firstChangedException = exceptions.size();
+        lastChangedException = -1;
+    }
 }
 
 bool NonbondedForce::getExceptionsUsePeriodicBoundaryConditions() const {

openmmapi/src/NonbondedForceImpl.cpp

@@ -345,8 +345,8 @@ double NonbondedForceImpl::calcDispersionCorrection(const System& system, const
     return 8*numParticles*numParticles*M_PI*(sum1/(9*pow(cutoff, 9))-sum2/(3*pow(cutoff, 3))+sum3);
 }
 
-void NonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcNonbondedForceKernel>().copyParametersToContext(context, owner);
+void NonbondedForceImpl::updateParametersInContext(ContextImpl& context, int firstParticle, int lastParticle, int firstException, int lastException) {
+    kernel.getAs<CalcNonbondedForceKernel>().copyParametersToContext(context, owner, firstParticle, lastParticle, firstException, lastException);
     context.systemChanged();
 }
 

openmmapi/src/PeriodicTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,8 +36,9 @@
 #include "openmm/internal/PeriodicTorsionForceImpl.h"
 
 using namespace OpenMM;
+using namespace std;
 
-PeriodicTorsionForce::PeriodicTorsionForce() : usePeriodic(false) {
+PeriodicTorsionForce::PeriodicTorsionForce() : usePeriodic(false), numContexts(0) {
 }
 
 int PeriodicTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
@@ -65,14 +66,30 @@ void PeriodicTorsionForce::setTorsionParameters(int index, int particle1, int pa
     periodicTorsions[index].periodicity = periodicity;
     periodicTorsions[index].phase = phase;
     periodicTorsions[index].k = k;
+    if (numContexts > 0) {
+        firstChangedTorsion = min(index, firstChangedTorsion);
+        lastChangedTorsion = max(index, lastChangedTorsion);
+    }
 }
 
 ForceImpl* PeriodicTorsionForce::createImpl() const {
+    if (numContexts == 0) {
+        // Begin tracking changes to torsions.
+        firstChangedTorsion = periodicTorsions.size();
+        lastChangedTorsion = -1;
+    }
+    numContexts++;
     return new PeriodicTorsionForceImpl(*this);
 }
 
 void PeriodicTorsionForce::updateParametersInContext(Context& context) {
-    dynamic_cast<PeriodicTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+    dynamic_cast<PeriodicTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context), firstChangedTorsion, lastChangedTorsion);
+    if (numContexts == 1) {
+        // We just updated the only existing context for this force, so we can reset
+        // the tracking of changed torsions.
+        firstChangedTorsion = periodicTorsions.size();
+        lastChangedTorsion = -1;
+    }
 }
 
 void PeriodicTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {

openmmapi/src/PeriodicTorsionForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -78,7 +78,7 @@ std::vector<std::string> PeriodicTorsionForceImpl::getKernelNames() {
     return names;
 }
 
-void PeriodicTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
-    kernel.getAs<CalcPeriodicTorsionForceKernel>().copyParametersToContext(context, owner);
+void PeriodicTorsionForceImpl::updateParametersInContext(ContextImpl& context, int firstTorsion, int lastTorsion) {
+    kernel.getAs<CalcPeriodicTorsionForceKernel>().copyParametersToContext(context, owner, firstTorsion, lastTorsion);
     context.systemChanged();
 }

platforms/common/include/openmm/common/CommonKernels.h

@@ -242,8 +242,10 @@ public:
      *
      * @param context    the context to copy parameters to
      * @param force      the HarmonicBondForce to copy the parameters from
+     * @param firstBond  the index of the first bond whose parameters might have changed
+     * @param lastBond   the index of the last bond whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
+    void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force, int firstBond, int lastBond);
 private:
     class ForceInfo;
     int numBonds;
@@ -284,8 +286,10 @@ public:
      *
      * @param context    the context to copy parameters to
      * @param force      the CustomBondForce to copy the parameters from
+     * @param firstBond  the index of the first bond whose parameters might have changed
+     * @param lastBond   the index of the last bond whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
+    void copyParametersToContext(ContextImpl& context, const CustomBondForce& force, int firstBond, int lastBond);
 private:
     class ForceInfo;
     int numBonds;
@@ -328,8 +332,10 @@ public:
      *
      * @param context    the context to copy parameters to
      * @param force      the HarmonicAngleForce to copy the parameters from
+     * @param firstAngle the index of the first bond whose parameters might have changed
+     * @param lastAngle  the index of the last bond whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
+    void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force, int firstAngle, int lastAngle);
 private:
     class ForceInfo;
     int numAngles;
@@ -370,8 +376,10 @@ public:
      *
      * @param context    the context to copy parameters to
      * @param force      the CustomAngleForce to copy the parameters from
+     * @param firstAngle the index of the first bond whose parameters might have changed
+     * @param lastAngle  the index of the last bond whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
+    void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force, int firstAngle, int lastAngle);
 private:
     class ForceInfo;
     int numAngles;
@@ -412,10 +420,12 @@ public:
     /**
      * Copy changed parameters over to a context.
      *
-     * @param context    the context to copy parameters to
-     * @param force      the PeriodicTorsionForce to copy the parameters from
+     * @param context      the context to copy parameters to
+     * @param force        the PeriodicTorsionForce to copy the parameters from
+     * @param firstTorsion the index of the first torsion whose parameters might have changed
+     * @param lastTorsion  the index of the last torsion whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
+    void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force, int firstTorsion, int lastTorsion);
 private:
     class ForceInfo;
     int numTorsions;
@@ -496,10 +506,12 @@ public:
     /**
      * Copy changed parameters over to a context.
      *
-     * @param context    the context to copy parameters to
-     * @param force      the CustomTorsionForce to copy the parameters from
+     * @param context      the context to copy parameters to
+     * @param force        the CustomTorsionForce to copy the parameters from
+     * @param firstTorsion the index of the first torsion whose parameters might have changed
+     * @param lastTorsion  the index of the last torsion whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
+    void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force, int firstTorsion, int lastTorsion);
 private:
     class ForceInfo;
     int numTorsions;
@@ -585,10 +597,12 @@ public:
     /**
      * Copy changed parameters over to a context.
      *
-     * @param context    the context to copy parameters to
-     * @param force      the CustomExternalForce to copy the parameters from
+     * @param context        the context to copy parameters to
+     * @param force          the CustomExternalForce to copy the parameters from
+     * @param firstParticle  the index of the first particle whose parameters might have changed
+     * @param lastParticle   the index of the last particle whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
+    void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force, int firstParticle, int lastParticle);
 private:
     class ForceInfo;
     int numParticles;
@@ -730,8 +744,10 @@ public:
      *
      * @param context    the context to copy parameters to
      * @param force      the CustomNonbondedForce to copy the parameters from
+     * @param firstParticle  the index of the first particle whose parameters might have changed
+     * @param lastParticle   the index of the last particle whose parameters might have changed
      */
-    void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
+    void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force, int firstParticle, int lastParticle);
 private:
     class ForceInfo;
     class LongRangePostComputation;

platforms/common/include/openmm/common/ComputeContext.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2019-2023 Stanford University and the Authors.      *
+ * Portions copyright (c) 2019-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -513,7 +513,7 @@ public:
      * may be invalid.  This should be called whenever force field parameters change.  It will cause the
      * definitions and order to be revalidated.
      */
-    bool invalidateMolecules(ComputeForceInfo* force);
+    bool invalidateMolecules(ComputeForceInfo* force, bool checkAtoms=true, bool checkGroups=true);
     /**
      * Make sure the current atom order is valid, based on the forces.  If not, perform reordering
      * to generate a new valid order.  This method is only needed in very unusual situations.

platforms/common/include/openmm/common/ComputeParameterSet.h

@@ -84,6 +84,17 @@ public:
      */
     template <class T>
     void setParameterValues(const std::vector<std::vector<T> >& values, bool convert=false);
+    /**
+     * Set the values of all parameters for a subset of objects.  They must be
+     * contained in a continuous range.
+     *
+     * @param first     the index of the first object for which to set parameter values
+     * @param values    values[i][j] contains the value of parameter j for object i+first
+     * @param convert   if true, automatic conversions between single and double
+     *                  precision will be performed as necessary
+     */
+    template <class T>
+    void setParameterValuesSubset(int first, const std::vector<std::vector<T> >& values, bool convert=false);
     /**
      * Get a vector of ComputeParameterInfo objects which describe the arrays
      * containing the data.