Merge branch 'master' of https://github.com/SimTk/openmm

platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp

 
-/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -234,9 +234,8 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
    updatePart2( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
 
    ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
-   if( referenceConstraintAlgorithm ){
-      referenceConstraintAlgorithm->apply( numberOfAtoms, atomCoordinates, xPrime, inverseMasses );
-   }
+   if (referenceConstraintAlgorithm)
+      referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
 
    // copy xPrime -> atomCoordinates
 

platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp

 
-/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -278,10 +278,8 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
    updatePart2( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
 
    ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
-   if( referenceConstraintAlgorithm ){
-      referenceConstraintAlgorithm->apply( numberOfAtoms, atomCoordinates, xPrime,
-                                           inverseMasses );
-   }
+   if (referenceConstraintAlgorithm)
+      referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
 
    // copy xPrime -> atomCoordinates
 

platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp

 
-/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman, Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
     }
     ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
     if (referenceConstraintAlgorithm)
-        referenceConstraintAlgorithm->apply(numberOfAtoms, atomCoordinates, xPrime, inverseMasses);
+        referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
 
    // Update the positions and velocities.
 

platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp

 
-/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman, Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -130,8 +130,8 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
            }
    }
    ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
-   if( referenceConstraintAlgorithm )
-      referenceConstraintAlgorithm->apply( numberOfAtoms, atomCoordinates, xPrime, inverseMasses );
+   if (referenceConstraintAlgorithm)
+      referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
    
    // Update the positions and velocities.
    

platforms/reference/tests/TestReferenceBrownianIntegrator.cpp

@@ -164,6 +164,38 @@ void testConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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);
+    BrownianIntegrator 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 | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -228,6 +260,7 @@ int main() {
         testSingleBond();
         testTemperature();
         testConstraints();
+        testConstrainedMasslessParticles();
         testRandomSeed();
     }
     catch(const exception& e) {

platforms/reference/tests/TestReferenceCustomIntegrator.cpp

@@ -159,7 +159,7 @@ void testConstraints() {
  * Test an integrator that applies constraints directly to velocities.
  */
 void testVelocityConstraints() {
-    const int numParticles = 8;
+    const int numParticles = 10;
     ReferencePlatform platform;
     System system;
     CustomIntegrator integrator(0.002);
@@ -176,7 +176,21 @@ void testVelocityConstraints() {
         system.addParticle(i%2 == 0 ? 5.0 : 10.0);
         forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    for (int i = 0; i < numParticles-1; ++i)
+    
+    // Constrain the first three particles with SHAKE.
+    
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    
+    // Constrain the next three with SETTLE.
+    
+    system.addConstraint(3, 4, 1.0);
+    system.addConstraint(5, 4, 1.0);
+    system.addConstraint(3, 5, sqrt(2.0));
+    
+    // Constraint the rest with CCMA.
+    
+    for (int i = 6; i < numParticles-1; ++i)
         system.addConstraint(i, i+1, 1.0);
     system.addForce(forceField);
     Context context(system, integrator, platform);
@@ -196,6 +210,7 @@ void testVelocityConstraints() {
     
     double initialEnergy = 0.0;
     for (int i = 0; i < 1000; ++i) {
+        integrator.step(2);
         State state = context.getState(State::Positions | State::Velocities | State::Energy);
         for (int j = 0; j < system.getNumConstraints(); ++j) {
             int particle1, particle2;
@@ -213,14 +228,51 @@ void testVelocityConstraints() {
             }
         }
         double energy = state.getKineticEnergy()+state.getPotentialEnergy();
-        if (i == 1)
+        if (i == 0)
             initialEnergy = energy;
-        else if (i > 1)
+        else if (i > 0)
             ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
-        integrator.step(2);
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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.
@@ -651,6 +703,7 @@ int main() {
         testSingleBond();
         testConstraints();
         testVelocityConstraints();
+        testConstrainedMasslessParticles();
         testWithThermostat();
         testMonteCarlo();
         testSum();

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

@@ -171,6 +171,38 @@ void testConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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 | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -235,6 +267,7 @@ int main() {
         testSingleBond();
         testTemperature();
         testConstraints();
+        testConstrainedMasslessParticles();
         testRandomSeed();
     }
     catch(const exception& e) {

platforms/reference/tests/TestReferenceNeighborList.cpp

@@ -86,7 +86,7 @@ void verifyNeighborList(NeighborList& list, int numParticles, vector<RealVec>& p
         for (int j = i+1; j < numParticles; j++)
             if (distance2(positions[i], positions[j], periodicBoxSize) <= cutoff*cutoff)
                 count++;
-    ASSERT(count == list.size());
+    ASSERT_EQUAL(count, list.size());
 }
 
 void testPeriodic() {
@@ -112,16 +112,15 @@ void testPeriodic() {
 
 int main() 
 {
-try {
-    testNeighborList();
-    testPeriodic();
-    
-    cout << "Test Passed" << endl;
+    try {
+        testNeighborList();
+        testPeriodic();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
     return 0;
 }
-catch (...) {
-    cerr << "*** ERROR: Test Failed ***" << endl;
-    return 1;
-}
-}
 

platforms/reference/tests/TestReferenceSettle.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) 2008-2009 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of the SETTLE algorithm.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "ReferencePlatform.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/LangevinIntegrator.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void testConstraints() {
+    const int numMolecules = 10;
+    const int numParticles = numMolecules*3;
+    const int numConstraints = numMolecules*3;
+    const double temp = 100.0;
+    ReferencePlatform platform;
+    System system;
+    LangevinIntegrator integrator(temp, 2.0, 0.001);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numMolecules; ++i) {
+        system.addParticle(16.0);
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        forceField->addParticle(-0.82, 0.317, 0.65);
+        forceField->addParticle(0.41, 1.0, 0.0);
+        forceField->addParticle(0.41, 1.0, 0.0);
+        system.addConstraint(i*3, i*3+1, 0.1);
+        system.addConstraint(i*3, i*3+2, 0.1);
+        system.addConstraint(i*3+1, i*3+2, 0.163);
+    }
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numMolecules; ++i) {
+        positions[i*3] = Vec3((i%4)*0.4, (i/4)*0.4, 0);
+        positions[i*3+1] = positions[i*3]+Vec3(0.1, 0, 0);
+        positions[i*3+2] = positions[i*3]+Vec3(-0.03333, 0.09428, 0);
+        velocities[i*3] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+        velocities[i*3+1] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+        velocities[i*3+2] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    for (int i = 0; i < 1000; ++i) {
+        integrator.step(1);
+        State state = context.getState(State::Positions | State::Forces);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 1e-5);
+        }
+    }
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        testConstraints();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/reference/tests/TestReferenceVariableLangevinIntegrator.cpp

@@ -173,6 +173,38 @@ void testConstraints() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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 | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
@@ -296,6 +328,7 @@ int main() {
         testSingleBond();
         testTemperature();
         testConstraints();
+        testConstrainedMasslessParticles();
         testRandomSeed();
         testArgonBox();
     }

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

@@ -210,6 +210,38 @@ void testConstrainedClusters() {
     ASSERT(context.getState(State::Positions).getTime() > 0.1);
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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);
+    VariableVerletIntegrator integrator(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 | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testArgonBox() {
     const int gridSize = 8;
     const double mass = 40.0;            // Ar atomic mass
@@ -272,6 +304,7 @@ int main() {
         testSingleBond();
         testConstraints();
         testConstrainedClusters();
+        testConstrainedMasslessParticles();
         testArgonBox();
     }
     catch(const exception& e) {

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -200,11 +200,44 @@ void testConstrainedClusters() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    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);
+    VerletIntegrator integrator(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 | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 int main() {
     try {
         testSingleBond();
         testConstraints();
         testConstrainedClusters();
+        testConstrainedMasslessParticles();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -34,6 +34,7 @@
 #endif
 #include "CpuPmeKernels.h"
 #include "SimTKOpenMMRealType.h"
+#include "openmm/internal/hardware.h"
 #include <cmath>
 #include <cstring>
 #include <smmintrin.h>
@@ -48,78 +49,6 @@ int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
 
 #define EXTRACT_FLOAT(v, element) _mm_cvtss_f32(_mm_shuffle_ps(v, v, _MM_SHUFFLE(0, 0, 0, element)))
 
-// Define function to get the number of processors.
-
-#ifdef __APPLE__
-   #include <sys/sysctl.h>
-   #include <dlfcn.h>
-#else
-   #ifdef WIN32
-      #include <windows.h>
-   #else
-      #include <dlfcn.h>
-      #include <unistd.h>
-   #endif
-#endif
-
-static int getNumProcessors() {
-#ifdef __APPLE__
-    int ncpu;
-    size_t len = 4;
-    if (sysctlbyname("hw.logicalcpu", &ncpu, &len, NULL, 0) == 0)
-       return ncpu;
-    else
-       return 1;
-#else
-#ifdef WIN32
-    SYSTEM_INFO siSysInfo;
-    int ncpu;
-    GetSystemInfo(&siSysInfo);
-    ncpu = siSysInfo.dwNumberOfProcessors;
-    if (ncpu < 1)
-        ncpu = 1;
-    return ncpu;
-#else
-    long nProcessorsOnline = sysconf(_SC_NPROCESSORS_ONLN);
-    if (nProcessorsOnline == -1)
-        return 1;
-    else
-        return (int) nProcessorsOnline;
-#endif
-#endif
-}
-
-// Define a function to check the CPU's capabilities.
-
-#ifdef _WIN32
-#define cpuid __cpuid
-#else
-static void cpuid(int cpuInfo[4], int infoType){
-#ifdef __LP64__
-    __asm__ __volatile__ (
-        "cpuid":
-        "=a" (cpuInfo[0]),
-        "=b" (cpuInfo[1]),
-        "=c" (cpuInfo[2]),
-        "=d" (cpuInfo[3]) :
-        "a" (infoType)
-    );
-#else
-    __asm__ __volatile__ (
-        "pushl %%ebx\n"
-        "cpuid\n"
-        "movl %%ebx, %1\n"
-        "popl %%ebx\n" :
-        "=a" (cpuInfo[0]),
-        "=r" (cpuInfo[1]),
-        "=c" (cpuInfo[2]),
-        "=d" (cpuInfo[3]) :
-        "a" (infoType)
-    );
-#endif
-}
-#endif
-
 static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
     float temp[4];
     __m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
@@ -164,6 +93,8 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
         int gridIndexX = _mm_extract_epi32(gridIndex, 0);
         int gridIndexY = _mm_extract_epi32(gridIndex, 1);
         int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
+        if (gridIndexX < 0)
+            return; // This happens when a simulation blows up and coordinates become NaN.
         int zindex[PME_ORDER];
         for (int j = 0; j < PME_ORDER; j++) {
             zindex[j] = gridIndexZ+j;
@@ -359,6 +290,8 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
         int gridIndexX = _mm_extract_epi32(gridIndex, 0);
         int gridIndexY = _mm_extract_epi32(gridIndex, 1);
         int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
+        if (gridIndexX < 0)
+            return; // This happens when a simulation blows up and coordinates become NaN.
         int zindex[PME_ORDER];
         for (int j = 0; j < PME_ORDER; j++) {
             zindex[j] = gridIndexZ+j;

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -34,7 +34,7 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
 #include "SimTKOpenMMUtilities.h"
-#include "ReferenceCCMAAlgorithm.h"
+#include "ReferenceConstraints.h"
 #include "ReferenceVirtualSites.h"
 #include <set>
 
@@ -56,20 +56,6 @@ static vector<RealVec>& extractForces(ContextImpl& context) {
     return *((vector<RealVec>*) data->forces);
 }
 
-static void findAnglesForCCMA(const System& system, vector<ReferenceCCMAAlgorithm::AngleInfo>& angles) {
-    for (int i = 0; i < system.getNumForces(); i++) {
-        const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
-        if (force != NULL) {
-            for (int j = 0; j < force->getNumAngles(); j++) {
-                int atom1, atom2, atom3;
-                double angle, k;
-                force->getAngleParameters(j, atom1, atom2, atom3, angle, k);
-                angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, (RealOpenMM)angle));
-            }
-        }
-    }
-}
-
 static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift, ReferenceConstraintAlgorithm* constraints) {
     const System& system = context.getSystem();
     int numParticles = system.getNumParticles();
@@ -91,7 +77,7 @@ static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>&
     
     if (constraints != NULL) {
         constraints->setTolerance(1e-4);
-        constraints->applyToVelocities(numParticles, posData, shiftedVel, inverseMasses);
+        constraints->applyToVelocities(posData, shiftedVel, inverseMasses);
     }
     
     // Compute the kinetic energy.
@@ -271,21 +257,19 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
     
     // Prepare constraints.
     
-    int numConstraints = system.getNumConstraints();
-    if (numConstraints > 0) {
-        vector<pair<int, int> > constraintIndices(numConstraints);
-        vector<RealOpenMM> constraintDistances(numConstraints);
-        for (int i = 0; i < numConstraints; ++i) {
+    if (system.getNumConstraints() > 0) {
+        vector<pair<int, int> > constraintIndices;
+        vector<RealOpenMM> constraintDistances;
+        for (int i = 0; i < system.getNumConstraints(); ++i) {
             int particle1, particle2;
             double distance;
             system.getConstraintParameters(i, particle1, particle2, distance);
-            constraintIndices[i].first = particle1;
-            constraintIndices[i].second = particle2;
-            constraintDistances[i] = static_cast<RealOpenMM>(distance);
+            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
+                constraintIndices.push_back(make_pair(particle1, particle2));
+                constraintDistances.push_back(distance);
+            }
         }
-        vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
-        findAnglesForCCMA(system, angles);
-        constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
+        constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
     }
 }
 
@@ -347,7 +331,7 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
     // Apply constraints.
     
     if (constraints != NULL)
-        constraints->apply(numParticles, pos, xPrime, particleInvMass);
+        constraints->apply(pos, xPrime, particleInvMass);
     
     // Record the constrained positions and velocities.
     
@@ -395,21 +379,19 @@ void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, cons
     
     // Prepare constraints.
     
-    int numConstraints = system.getNumConstraints();
-    if (numConstraints > 0) {
-        vector<pair<int, int> > constraintIndices(numConstraints);
-        vector<RealOpenMM> constraintDistances(numConstraints);
-        for (int i = 0; i < numConstraints; ++i) {
+    if (system.getNumConstraints() > 0) {
+        vector<pair<int, int> > constraintIndices;
+        vector<RealOpenMM> constraintDistances;
+        for (int i = 0; i < system.getNumConstraints(); ++i) {
             int particle1, particle2;
             double distance;
             system.getConstraintParameters(i, particle1, particle2, distance);
-            constraintIndices[i].first = particle1;
-            constraintIndices[i].second = particle2;
-            constraintDistances[i] = static_cast<RealOpenMM>(distance);
+            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
+                constraintIndices.push_back(make_pair(particle1, particle2));
+                constraintDistances.push_back(distance);
+            }
         }
-        vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
-        findAnglesForCCMA(system, angles);
-        constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
+        constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
     }
     
     // Initialize the energy minimizer.
@@ -443,7 +425,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
     // Apply constraints.
     
     if (constraints != NULL)
-        constraints->apply(numParticles, pos, xPrime, particleInvMass);
+        constraints->apply(pos, xPrime, particleInvMass);
     
     // Record the constrained positions and velocities.
     

plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h

@@ -47,6 +47,9 @@ namespace OpenMM {
  * springs to form a ring.  This allows certain quantum mechanical effects to be efficiently
  * simulated.
  * 
+ * By default this Integrator applies a PILE thermostat to the system to simulate constant
+ * temperature dynamics.  You can disable the thermostat by calling setApplyThermostat(false).
+ * 
  * Because this Integrator simulates many copies of the System at once, it must be used
  * differently from other Integrators.  Instead of setting positions and velocities by
  * calling methods of the Context, you should use the corresponding methods of the Integrator
@@ -127,6 +130,18 @@ public:
     void setFriction(double coeff) {
         friction = coeff;
     }
+    /**
+     * Get whether a thermostat is applied to the system.
+     */
+    bool getApplyThermostat() const {
+        return applyThermostat;
+    }
+    /**
+     * Set whether a thermostat is applied to the system.
+     */
+    void setApplyThermostat(bool apply) {
+        applyThermostat = apply;
+    }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */
@@ -213,6 +228,7 @@ protected:
 private:
     double temperature, friction;
     int numCopies, randomNumberSeed;
+    bool applyThermostat;
     std::map<int, int> contractions;
     bool forcesAreValid, hasSetPosition, hasSetVelocity, isFirstStep;
     Kernel kernel;

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -42,7 +42,7 @@ using namespace OpenMM;
 using namespace std;
 
 RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize, const map<int, int>& contractions) :
-        numCopies(numCopies), contractions(contractions), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
+        numCopies(numCopies), applyThermostat(true), contractions(contractions), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
     setTemperature(temperature);
     setFriction(frictionCoeff);
     setStepSize(stepSize);
@@ -51,7 +51,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
 }
 
 RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
-        numCopies(numCopies), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
+        numCopies(numCopies), applyThermostat(true), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
     setTemperature(temperature);
     setFriction(frictionCoeff);
     setStepSize(stepSize);

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -205,7 +205,8 @@ void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegr
     void* frictionPtr = (useDoublePrecision ? (void*) &friction : (void*) &frictionFloat);
     int randomIndex = integration.prepareRandomNumbers(numParticles*numCopies);
     void* pileArgs[] = {&velocities->getDevicePointer(), &integration.getRandom().getDevicePointer(), &randomIndex, dtPtr, kTPtr, frictionPtr};
-    cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
+    if (integrator.getApplyThermostat())
+        cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
 
     // Update positions and velocities.
     
@@ -223,8 +224,10 @@ void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegr
 
     // Apply the PILE-L thermostat again.
 
-    randomIndex = integration.prepareRandomNumbers(numParticles*numCopies);
-    cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
+    if (integrator.getApplyThermostat()) {
+        randomIndex = integration.prepareRandomNumbers(numParticles*numCopies);
+        cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
+    }
 
     // Update the time and step count.
 

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -431,6 +431,71 @@ void testContractions() {
     ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
 }
 
+void testWithoutThermostat() {
+    const int numParticles = 20;
+    const int numCopies = 10;
+    const double temperature = 300.0;
+    const double mass = 2.0;
+    
+    // Create a chain of particles.
+    
+    System system;
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(mass);
+        if (i > 0)
+            bonds->addBond(i-1, i, 1.0, 1000.0);
+    }
+    RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
+    integ.setApplyThermostat(false);
+    Platform& platform = Platform::getPlatformByName("CUDA");
+    Context context(system, integ, platform);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<vector<Vec3> > positions(numCopies);
+    for (int i = 0; i < numCopies; i++) {
+        positions[i].resize(numParticles);
+        for (int j = 0; j < numParticles; j++)
+            positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
+        integ.setPositions(i, positions[i]);
+    }
+    
+    // Simulate it and see if the energy remains constant.
+    
+    double initialEnergy;
+    int numSteps = 100;
+    const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
+    const double wn = numCopies*BOLTZ*temperature/hbar;
+    const double springConstant = mass*wn*wn;
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        
+        // Sum the energies of all the copies.
+        
+        double energy = 0.0;
+        for (int j = 0; j < numCopies; j++) {
+            State state = integ.getState(j, State::Positions | State::Energy);
+            positions[j] = state.getPositions();
+            energy += state.getPotentialEnergy()+state.getKineticEnergy();
+        }
+        
+        // Add the energy from the springs connecting copies.
+        
+        for (int j = 0; j < numCopies; j++) {
+            int previous = (j == 0 ? numCopies-1 : j-1);
+            for (int k = 0; k < numParticles; k++) {
+                Vec3 delta = positions[j][k]-positions[previous][k];
+                energy += 0.5*springConstant*delta.dot(delta);
+            }
+        }
+        if (i == 0)
+            initialEnergy = energy;
+        else
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         registerRPMDCudaKernelFactories();
@@ -441,6 +506,7 @@ int main(int argc, char* argv[]) {
         testCMMotionRemoval();
         testVirtualSites();
         testContractions();
+        testWithoutThermostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -223,7 +223,8 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
         stepKernel.setArg<cl_float>(4, (cl_float) (integrator.getTemperature()*BOLTZ));
         velocitiesKernel.setArg<cl_float>(2, (cl_float) dt);
     }
-    cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
+    if (integrator.getApplyThermostat())
+        cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
 
     // Update positions and velocities.
     
@@ -238,8 +239,10 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
 
     // Apply the PILE-L thermostat again.
 
-    pileKernel.setArg<cl_uint>(2, integration.prepareRandomNumbers(numParticles*numCopies));
-    cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
+    if (integrator.getApplyThermostat()) {
+        pileKernel.setArg<cl_uint>(2, integration.prepareRandomNumbers(numParticles*numCopies));
+        cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
+    }
 
     // Update the time and step count.
 

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -432,6 +432,71 @@ void testContractions() {
     ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
 }
 
+void testWithoutThermostat() {
+    const int numParticles = 20;
+    const int numCopies = 10;
+    const double temperature = 300.0;
+    const double mass = 2.0;
+    
+    // Create a chain of particles.
+    
+    System system;
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(mass);
+        if (i > 0)
+            bonds->addBond(i-1, i, 1.0, 1000.0);
+    }
+    RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
+    integ.setApplyThermostat(false);
+    Platform& platform = Platform::getPlatformByName("OpenCL");
+    Context context(system, integ, platform);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<vector<Vec3> > positions(numCopies);
+    for (int i = 0; i < numCopies; i++) {
+        positions[i].resize(numParticles);
+        for (int j = 0; j < numParticles; j++)
+            positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
+        integ.setPositions(i, positions[i]);
+    }
+    
+    // Simulate it and see if the energy remains constant.
+    
+    double initialEnergy;
+    int numSteps = 100;
+    const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
+    const double wn = numCopies*BOLTZ*temperature/hbar;
+    const double springConstant = mass*wn*wn;
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        
+        // Sum the energies of all the copies.
+        
+        double energy = 0.0;
+        for (int j = 0; j < numCopies; j++) {
+            State state = integ.getState(j, State::Positions | State::Energy);
+            positions[j] = state.getPositions();
+            energy += state.getPotentialEnergy()+state.getKineticEnergy();
+        }
+        
+        // Add the energy from the springs connecting copies.
+        
+        for (int j = 0; j < numCopies; j++) {
+            int previous = (j == 0 ? numCopies-1 : j-1);
+            for (int k = 0; k < numParticles; k++) {
+                Vec3 delta = positions[j][k]-positions[previous][k];
+                energy += 0.5*springConstant*delta.dot(delta);
+            }
+        }
+        if (i == 0)
+            initialEnergy = energy;
+        else
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         registerRPMDOpenCLKernelFactories();
@@ -442,6 +507,7 @@ int main(int argc, char* argv[]) {
         testCMMotionRemoval();
         testVirtualSites();
         testContractions();
+        testWithoutThermostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;