Merge pull request #2701 from peastman/integrationgroups

Added Integrator.setIntegrationForceGroups()

plugins/drude/platforms/common/src/CommonDrudeKernels.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) 2013-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -516,7 +516,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
 
     // Compute the forces and energy for this configuration.
 
-    double energy = context.calcForcesAndEnergy(true, true);
+    double energy = context.calcForcesAndEnergy(true, true, context.getIntegrator().getIntegrationForceGroups());
     long long* force = (long long*) cc.getPinnedBuffer();
     cc.getLongForceBuffer().download(force);
     double forceScale = -1.0/0x100000000;

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.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) 2011-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -497,7 +497,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
     vector<Vec3>& force = extractForces(context);
     for (int i = 0; i < numDrudeParticles; i++)
         pos[drudeParticles[i]] = Vec3(x[3*i], x[3*i+1], x[3*i+2]);
-    double energy = context.calcForcesAndEnergy(true, true);
+    double energy = context.calcForcesAndEnergy(true, true, context.getIntegrator().getIntegrationForceGroups());
     for (int i = 0; i < numDrudeParticles; i++) {
         Vec3 f = force[drudeParticles[i]];
         g[3*i] = -f[0];

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.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) 2011-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -123,6 +123,7 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
             groupsNotContracted -= 1<<group;
         }
     }
+    groupsNotContracted &= integrator.getIntegrationForceGroups();
     if (maxContractedCopies > 0) {
         contractedForces.initialize<long long>(cu, maxContractedCopies*paddedParticles*3, "rpmdContractedForces");
         contractedPositions.initialize(cu, maxContractedCopies*paddedParticles, elementSize, "rpmdContractedPositions");

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.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) 2011-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -103,6 +103,7 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
             groupsNotContracted -= 1<<group;
         }
     }
+    groupsNotContracted &= integrator.getIntegrationForceGroups();
     if (maxContractedCopies > 0) {
         contractedForces.initialize(cl, maxContractedCopies*paddedParticles, forceElementSize, "rpmdContractedForces");
         contractedPositions.initialize(cl, maxContractedCopies*paddedParticles, elementSize, "rpmdContractedPositions");

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.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) 2011-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -99,6 +99,7 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
             groupsNotContracted -= 1<<group;
         }
     }
+    groupsNotContracted &= integrator.getIntegrationForceGroups();
     
     // Create workspace for doing contractions.
     

tests/TestBrownianIntegrator.h

@@ -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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -279,6 +280,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    BrownianIntegrator integrator(0, 1.0, 0.001);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -290,6 +316,7 @@ int main(int argc, char* argv[]) {
         testConstrainedMasslessParticles();
         testRandomSeed();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomIntegrator.h

@@ -597,6 +597,7 @@ void testForceGroups() {
     integrator.addComputeGlobal("oute", "energy");
     integrator.addComputeGlobal("oute1", "energy1");
     integrator.addComputeGlobal("oute2", "energy2");
+    integrator.setIntegrationForceGroups((1<<1) + (1<<2));
     HarmonicBondForce* bonds = new HarmonicBondForce();
     bonds->addBond(0, 1, 1.5, 1.1);
     bonds->setForceGroup(1);
@@ -606,6 +607,10 @@ void testForceGroups() {
     nb->addParticle(0.2, 1, 0);
     nb->setForceGroup(2);
     system.addForce(nb);
+    CustomExternalForce* external = new CustomExternalForce("x");
+    external->addParticle(0);
+    external->setForceGroup(3);
+    system.addForce(external);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(-1, 0, 0);
@@ -633,13 +638,13 @@ void testForceGroups() {
     
     // Make sure they also match the values returned by the Context.
     
-    State s = context.getState(State::Forces | State::Energy, false);
+    State s = context.getState(State::Forces | State::Energy, false, 6);
     State s1 = context.getState(State::Forces | State::Energy, false, 2);
     State s2 = context.getState(State::Forces | State::Energy, false, 4);
     vector<Vec3> c, c1, c2;
-    c = context.getState(State::Forces, false).getForces();
-    c1 = context.getState(State::Forces, false, 2).getForces();
-    c2 = context.getState(State::Forces, false, 4).getForces();
+    c = s.getForces();
+    c1 = s1.getForces();
+    c2 = s2.getForces();
     ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
     ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
     ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);

tests/TestLangevinIntegrator.h

@@ -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) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -286,6 +287,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 1.0, 0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -297,6 +323,7 @@ int main(int argc, char* argv[]) {
         testConstrainedMasslessParticles();
         testRandomSeed();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestLangevinMiddleIntegrator.h

@@ -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) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -289,6 +290,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    LangevinMiddleIntegrator integrator(0.0, 1.0, 0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -300,6 +326,7 @@ int main(int argc, char* argv[]) {
         testConstrainedMasslessParticles();
         testRandomSeed();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestLocalEnergyMinimizer.h

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -231,6 +231,34 @@ void testLargeForces() {
     ASSERT(maxdist < 10.0);
 }
 
+void testForceGroups() {
+    // Create a system with two forces, only one of which is in the standard
+    // integration force groups.
+
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    HarmonicBondForce* bonds1 = new HarmonicBondForce();
+    HarmonicBondForce* bonds2 = new HarmonicBondForce();
+    system.addForce(bonds1);
+    system.addForce(bonds2);
+    bonds1->addBond(0, 1, 2.0, 1);
+    bonds2->addBond(0, 1, 4.0, 1);
+    bonds1->setForceGroup(1);
+    bonds2->setForceGroup(2);
+
+    // Minimize it and check that the bond has the correct length.
+
+    VerletIntegrator integrator(0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    Context context(system, integrator, platform);
+    context.setPositions({Vec3(0, 0, 0), Vec3(5, 0, 0)});
+    LocalEnergyMinimizer::minimize(context, 1e-5);
+    State state = context.getState(State::Positions);
+    Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
+    ASSERT_EQUAL_TOL(2.0, sqrt(delta.dot(delta)), 1e-4);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -240,6 +268,7 @@ int main(int argc, char* argv[]) {
         testLargeSystem();
         testVirtualSites();
         testLargeForces();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestNoseHooverIntegrator.h

@@ -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) 2019 Stanford University and the Authors.           *
+ * Portions copyright (c) 2019-2020 Stanford University and the Authors.      *
  * Authors: Andreas Krämer and Andrew C. Simmonett                            *
  * Contributors:                                                              *
  *                                                                            *
@@ -510,6 +510,31 @@ void testAPIChangeNumParticles() {
 
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    NoseHooverIntegrator integrator(1, 1.0, 0.001);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -528,6 +553,7 @@ int main(int argc, char* argv[]) {
         constrain = false; testDimerBox(constrain);
         constrain = true; testDimerBox(constrain);
         testCheckpoints();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestVariableLangevinIntegrator.h

@@ -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) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -358,6 +359,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    VariableLangevinIntegrator integrator(0.0, 1.0, 1e-5);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -370,6 +396,7 @@ int main(int argc, char* argv[]) {
         testRandomSeed();
         testArgonBox();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestVariableVerletIntegrator.h

@@ -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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -337,6 +338,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    VariableVerletIntegrator integrator(0.001);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -348,6 +374,7 @@ int main(int argc, char* argv[]) {
         testConstrainedMasslessParticles();
         testArgonBox();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestVerletIntegrator.h

@@ -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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -254,6 +255,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -264,6 +290,7 @@ int main(int argc, char* argv[]) {
         testConstrainedClusters();
         testConstrainedMasslessParticles();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

wrappers/python/simtk/openmm/app/simulation.py

@@ -6,7 +6,7 @@ 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) 2012-2015 Stanford University and the Authors.
+Portions copyright (c) 2012-2020 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -250,7 +250,8 @@ class Simulation(object):
             if next[4]:
                 getEnergy = True
         state = self.context.getState(getPositions=getPositions, getVelocities=getVelocities, getForces=getForces,
-                                      getEnergy=getEnergy, getParameters=True, enforcePeriodicBox=periodic)
+                                      getEnergy=getEnergy, getParameters=True, enforcePeriodicBox=periodic,
+                                      groups=self.context.getIntegrator().getIntegrationForceGroups())
         for reporter, next in reports:
             reporter.report(self, state)
 

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -106,6 +106,33 @@ Parameters:
   }
 }
 
+%extend OpenMM::Integrator {
+  %pythoncode %{
+    def setIntegrationForceGroups(self, groups):
+        """Set which force groups to use for integration.  By default, all force groups are included.
+
+        Parameters
+        ----------
+        groups : set or int
+            a set of indices for which force groups to include when integrating the equations of motion.
+            Alternatively, the groups can be passed as a single unsigned integer interpreted as a bitmask,
+            in which case group i will be included if (groups&(1<<i)) != 0.
+        """
+        try:
+            # is the input integer-like?
+            groups_mask = int(groups)
+        except TypeError:
+            if isinstance(groups, set):
+                groups_mask = functools.reduce(operator.or_,
+                        ((1<<x) & 0xffffffff for x in groups))
+            else:
+                raise TypeError('%s is neither an int nor set' % groups)
+        if groups_mask >= 0x80000000:
+            groups_mask -= 0x100000000
+        _openmm.Integrator_setIntegrationForceGroups(self, groups_mask)
+    %}
+}
+
 %extend OpenMM::RPMDIntegrator {
   %pythoncode %{
     def getState(self,