Created architecture for multiple time step integrators and completed reference implementation

openmmapi/include/openmm/internal/MonteCarloBarostatImpl.h

@@ -52,7 +52,7 @@ public:
         return owner;
     }
     void updateContextState(ContextImpl& context);
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
         // This force doesn't apply forces to particles.
         return 0.0;
     }

openmmapi/include/openmm/internal/NonbondedForceImpl.h

@@ -58,7 +58,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     std::map<std::string, double> getDefaultParameters() {
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }

openmmapi/include/openmm/internal/PeriodicTorsionForceImpl.h

@@ -56,7 +56,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     std::map<std::string, double> getDefaultParameters() {
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }

openmmapi/include/openmm/internal/RBTorsionForceImpl.h

@@ -56,7 +56,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     std::map<std::string, double> getDefaultParameters() {
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }

openmmapi/src/CMAPTorsionForceImpl.cpp

@@ -52,8 +52,9 @@ void CMAPTorsionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCMAPTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CMAPTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCMAPTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CMAPTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCMAPTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CMAPTorsionForceImpl::getKernelNames() {

openmmapi/src/ContextImpl.cpp

@@ -191,13 +191,13 @@ void ContextImpl::computeVirtualSites() {
     dynamic_cast<VirtualSitesKernel&>(virtualSitesKernel.getImpl()).computePositions(*this);
 }
 
-double ContextImpl::calcForcesAndEnergy(bool includeForces, bool includeEnergy) {
+double ContextImpl::calcForcesAndEnergy(bool includeForces, bool includeEnergy, int groups) {
     CalcForcesAndEnergyKernel& kernel = dynamic_cast<CalcForcesAndEnergyKernel&>(initializeForcesKernel.getImpl());
     double energy = 0.0;
-    kernel.beginComputation(*this, includeForces, includeEnergy);
+    kernel.beginComputation(*this, includeForces, includeEnergy, groups);
     for (int i = 0; i < (int) forceImpls.size(); ++i)
-        energy += forceImpls[i]->calcForcesAndEnergy(*this, includeForces, includeEnergy);
-    energy += kernel.finishComputation(*this, includeForces, includeEnergy);
+        energy += forceImpls[i]->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
+    energy += kernel.finishComputation(*this, includeForces, includeEnergy, groups);
     return energy;
 }
 

openmmapi/src/CustomAngleForceImpl.cpp

@@ -88,8 +88,9 @@ void CustomAngleForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomAngleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomAngleForceImpl::getKernelNames() {

openmmapi/src/CustomBondForceImpl.cpp

@@ -82,8 +82,9 @@ void CustomBondForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomBondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomBondForceImpl::getKernelNames() {

openmmapi/src/CustomExternalForceImpl.cpp

@@ -76,8 +76,9 @@ void CustomExternalForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomExternalForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomExternalForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomExternalForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomExternalForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomExternalForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomExternalForceImpl::getKernelNames() {

openmmapi/src/CustomGBForceImpl.cpp

@@ -105,8 +105,9 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomGBForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomGBForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomGBForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomGBForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomGBForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomGBForceImpl::getKernelNames() {

openmmapi/src/CustomHbondForceImpl.cpp

@@ -178,8 +178,9 @@ void CustomHbondForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomHbondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomHbondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomHbondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomHbondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomHbondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomHbondForceImpl::getKernelNames() {

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -105,8 +105,9 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomNonbondedForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomNonbondedForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomNonbondedForceImpl::getKernelNames() {

openmmapi/src/CustomTorsionForceImpl.cpp

@@ -94,8 +94,9 @@ void CustomTorsionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcCustomTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double CustomTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcCustomTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double CustomTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcCustomTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 vector<string> CustomTorsionForceImpl::getKernelNames() {

openmmapi/src/Force.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2012 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/Force.h"
+#include "openmm/OpenMMException.h"
+
+using namespace OpenMM;
+
+int Force::getForceGroup() const {
+    return forceGroup;
+}
+
+void Force::setForceGroup(int group) {
+    if (group < 0 || group > 31)
+        throw OpenMMException("Force group must be between 0 and 31");
+    forceGroup = group;
+}

openmmapi/src/GBSAOBCForceImpl.cpp

@@ -55,8 +55,9 @@ void GBSAOBCForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcGBSAOBCForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double GBSAOBCForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcGBSAOBCForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double GBSAOBCForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcGBSAOBCForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBSAOBCForceImpl::getKernelNames() {

openmmapi/src/GBVIForceImpl.cpp

@@ -239,8 +239,9 @@ void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<st
 
 }
 
-double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcGBVIForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcGBVIForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBVIForceImpl::getKernelNames() {

openmmapi/src/HarmonicAngleForceImpl.cpp

@@ -49,8 +49,9 @@ void HarmonicAngleForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcHarmonicAngleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double HarmonicAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcHarmonicAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double HarmonicAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcHarmonicAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> HarmonicAngleForceImpl::getKernelNames() {

openmmapi/src/HarmonicBondForceImpl.cpp

@@ -49,8 +49,9 @@ void HarmonicBondForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double HarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double HarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> HarmonicBondForceImpl::getKernelNames() {

openmmapi/src/NonbondedForce.cpp

@@ -47,7 +47,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), rfDielectric(78.3), ewaldErrorTol(5e-4), useDispersionCorrection(true) {
+NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), rfDielectric(78.3), ewaldErrorTol(5e-4), useDispersionCorrection(true), recipForceGroup(0) {
 }
 
 NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
@@ -196,3 +196,13 @@ void NonbondedForce::addExclusionsToSet(const vector<set<int> >& bonded12, set<i
             addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
     }
 }
+
+int NonbondedForce::getReciprocalSpaceForceGroup() const {
+    return recipForceGroup;
+}
+
+void NonbondedForce::setReciprocalSpaceForceGroup(int group) {
+    if (group < 0 || group > 31)
+        throw OpenMMException("Force group must be between 0 and 31");
+    recipForceGroup = group;
+}

openmmapi/src/NonbondedForceImpl.cpp

@@ -98,8 +98,10 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double NonbondedForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double NonbondedForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    bool includeDirect = ((groups&(1<<owner.getForceGroup())) != 0);
+    bool includeReciprocal = ((groups&(1<<owner.getReciprocalSpaceForceGroup())) != 0);
+    return dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy, includeDirect, includeReciprocal);
 }
 
 std::vector<std::string> NonbondedForceImpl::getKernelNames() {