resolved PR #2611 merge conflicts

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Mark Friedrichs                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -1782,7 +1782,7 @@ void CudaCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& cont
         }
     }
     if (!multipolesAreValid)
-        context.calcForcesAndEnergy(false, false, -1);
+        context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
 }
 
 
@@ -3650,7 +3650,7 @@ void CudaCalcHippoNonbondedForceKernel::ensureMultipolesValid(ContextImpl& conte
         }
     }
     if (!multipolesAreValid)
-        context.calcForcesAndEnergy(false, false, -1);
+        context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
 }
 
 void CudaCalcHippoNonbondedForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {

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:                                                              *
  *                                                                            *
@@ -282,7 +282,7 @@ void CommonIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
         if (cc.getUseMixedPrecision())
             kernel2->addArg(cc.getPosqCorrection());
         else
-            kernel2->addArg(NULL);
+            kernel2->addArg(nullptr);
         kernel2->addArg(integration.getPosDelta());
         kernel2->addArg(cc.getVelm());
         kernel2->addArg(integration.getStepSize());
@@ -290,7 +290,7 @@ void CommonIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
         if (cc.getUseMixedPrecision())
             hardwallKernel->addArg(cc.getPosqCorrection());
         else
-            hardwallKernel->addArg(NULL);
+            hardwallKernel->addArg(nullptr);
         hardwallKernel->addArg(cc.getVelm());
         hardwallKernel->addArg(pairParticles);
         hardwallKernel->addArg(integration.getStepSize());
@@ -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/opencl/tests/CMakeLists.txt

@@ -17,10 +17,10 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET} ${SHARED_TARGET})
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
-    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
+    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
     IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
-        ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)
-        ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double)
+        ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
+        ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
     ENDIF(OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

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/opencl/tests/CMakeLists.txt

@@ -15,10 +15,10 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
-    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
+    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
     IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
-        ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)
-        ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double)
+        ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
+        ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
     ENDIF(OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

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/CMakeLists.txt

@@ -8,7 +8,7 @@ ENABLE_TESTING()
 FILE(GLOB TEST_PROGS "*Test*.cpp")
 FOREACH(TEST_PROG ${TEST_PROGS})
     GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
-    IF ((${TEST_ROOT} MATCHES TestVectorize8) AND NOT X86)
+    IF ((${TEST_ROOT} MATCHES TestVectorizeAvx*) AND NOT X86)
         CONTINUE()
     ENDIF()
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
@@ -21,9 +21,12 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     IF((${TEST_ROOT} MATCHES TestVectorize) AND X86 AND NOT MSVC)
         SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
     ENDIF()
-    IF((${TEST_ROOT} MATCHES TestVectorize8) AND X86 AND NOT MSVC)
+    IF((${TEST_ROOT} MATCHES TestVectorizeAvx) AND X86 AND NOT MSVC)
         SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -mavx")
     ENDIF()
+    IF((${TEST_ROOT} MATCHES TestVectorizeAvx2) AND X86 AND NOT MSVC)
+        SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -mfma -mavx2")
+    ENDIF()
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_TEST_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

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/TestVectorize8.cpp → tests/TestVectorizeAvx.cpp

@@ -34,7 +34,7 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "openmm/internal/vectorize8.h"
+#include "openmm/internal/vectorizeAvx.h"
 #include <iostream>
 
 #include "TestVectorizeGeneric.h"

tests/TestVectorizeAvx2.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) 2014-2015 Stanford University and the Authors.      *
+ * Authors: Daniel Towner                                                     *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests vectorized operations.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+
+#include <iostream>
+
+#ifndef __AVX2__
+int main () {
+    std::cout << "AVX2 CPU is not supported. Exiting." << std::endl;
+    return 0;
+}
+#else
+
+#include "openmm/internal/vectorizeAvx2.h"
+#include "TestVectorizeGeneric.h"
+
+using namespace OpenMM;
+
+int main(int argc, char* argv[]) {
+    try {
+        if (!isAvx2Supported()) {
+            std::cout << "CPU is not supported. Exiting." << std::endl;
+            return 0;
+        }
+
+        TestFvec<fvecAvx2>::testAll();
+    }
+    catch(const std::exception& e) {
+        std::cout << "exception: " << e.what() << std::endl;
+        return 1;
+    }
+    std::cout << "Done" << std::endl;
+    return 0;
+}
+
+#endif
\ No newline at end of file

tests/TestVectorizeGeneric.h

@@ -338,12 +338,10 @@ void TestFvec<FVEC>::testBinaryOps() const {
     ASSERT_VEC_ALMOST_EQUAL(f / v0, applyBinaryFn(fdup, v0, std::divides<float>()));
 
     // Binary functions.
-    using std::min;
-    using std::max;
     ASSERT_VEC_EQUAL(min(v0, v1),
-                     applyBinaryFn(v0, v1, [](float x, float y) { return min(x, y); }));
+                     applyBinaryFn(v0, v1, [](float x, float y) { return std::min<float>(x, y); }));
     ASSERT_VEC_EQUAL(max(v0, v1),
-                     applyBinaryFn(v0, v1, [](float x, float y) { return max(x, y); }));
+                     applyBinaryFn(v0, v1, [](float x, float y) { return std::max<float>(x, y); }));
 }
 
 template<typename FVEC>