Merge branch 'master' of github.com:leeping/openmm

platforms/cuda/tests/TestCudaCustomGBForce.cpp

@@ -56,6 +56,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
     const int numMolecules = 70;
     const int numParticles = numMolecules*2;
     const double boxSize = 10.0;
+    const double cutoff = 2.0;
 
     // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
 
@@ -69,8 +70,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
     customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
     GBSAOBCForce* obc = new GBSAOBCForce();
     CustomGBForce* custom = new CustomGBForce();
-    obc->setCutoffDistance(2.0);
-    custom->setCutoffDistance(2.0);
+    obc->setCutoffDistance(cutoff);
+    custom->setCutoffDistance(cutoff);
     custom->addPerParticleParameter("q");
     custom->addPerParticleParameter("radius");
     custom->addPerParticleParameter("scale");
@@ -86,7 +87,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
     custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
                                   "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
     custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
+    string invCutoffString = "";
+    if (obcMethod != GBSAOBCForce::NoCutoff) {
+        stringstream s;
+        s<<(1.0/cutoff);
+        invCutoffString = s.str();
+    }
+    custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);

platforms/cuda/tests/TestCudaCustomIntegrator.cpp

@@ -233,6 +233,43 @@ void testVelocityConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    CustomIntegrator integrator(0.002);
+    integrator.addPerDofVariable("oldx", 0);
+    integrator.addComputePerDof("v", "v+dt*f/m");
+    integrator.addComputePerDof("oldx", "x");
+    integrator.addComputePerDof("x", "x+dt*v");
+    integrator.addConstrainPositions();
+    integrator.addComputePerDof("v", "(x-oldx)/dt");
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 /**
  * Test an integrator with an AndersenThermostat to see if updateContextState()
  * is being handled correctly.
@@ -724,6 +761,7 @@ int main(int argc, char* argv[]) {
         testSingleBond();
         testConstraints();
         testVelocityConstraints();
+        testConstrainedMasslessParticles();
         testWithThermostat();
         testMonteCarlo();
         testSum();

platforms/cuda/tests/TestCudaLangevinIntegrator.cpp

@@ -177,6 +177,37 @@ void testConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    LangevinIntegrator integrator(300.0, 2.0, 0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -241,6 +272,7 @@ int main(int argc, char* argv[]) {
         testSingleBond();
         testTemperature();
         testConstraints();
+        testConstrainedMasslessParticles();
         testRandomSeed();
     }
     catch(const exception& e) {

platforms/cuda/tests/TestCudaVariableLangevinIntegrator.cpp

@@ -172,6 +172,37 @@ void testConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    VariableLangevinIntegrator integrator(300.0, 2.0, 0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -295,6 +326,7 @@ int main(int argc, char* argv[]) {
         testSingleBond();
         testTemperature();
         testConstraints();
+        testConstrainedMasslessParticles();
         testRandomSeed();
         testArgonBox();
     }

platforms/opencl/src/OpenCLKernels.cpp

@@ -5978,7 +5978,7 @@ void OpenCLRemoveCMMotionKernel::initialize(const System& system, const CMMotion
     for (int i = 0; i < numAtoms; i++)
         totalMass += system.getParticleMass(i);
     map<string, string> defines;
-    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(1.0/totalMass);
+    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
     cl::Program program = cl.createProgram(OpenCLKernelSources::removeCM, defines);
     kernel1 = cl::Kernel(program, "calcCenterOfMassMomentum");
     kernel1.setArg<cl_int>(0, numAtoms);

platforms/opencl/src/kernels/fft.cl

@@ -26,5 +26,4 @@ __kernel void execFFT(__global const real2* restrict in, __global real2* restric
         barrier(CLK_LOCAL_MEM_FENCE);
         COMPUTE_FFT
     }
-
 }