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

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

@@ -128,12 +128,12 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 if (copies > maxContractedCopies)
                     maxContractedCopies = copies;
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }
     if (maxContractedCopies > 0) {
@@ -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.
 
@@ -285,6 +288,14 @@ void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
         void* contractForceArgs[] = {&forces->getDevicePointer(), &contractedForces->getDevicePointer()};
         cu.executeKernel(forceContractionKernels[copies], contractForceArgs, numParticles*numCopies, workgroupSize);
     }
+    if (groupsByCopies.size() > 0) {
+        // Ensure the Context contains the positions from the last copy, since we'll assume that later.
+        
+        int i = numCopies-1;
+        void* copyToContextArgs[] = {&velocities->getDevicePointer(), &cu.getVelm().getDevicePointer(), &positions->getDevicePointer(),
+                &cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
+        cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
+    }
 }
 
 double CudaIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
@@ -374,7 +385,6 @@ void CudaIntegrateRPMDStepKernel::copyToContext(int copy, ContextImpl& context)
 
 string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable, bool forward) {
     stringstream source;
-    int unfactored = size;
     int stage = 0;
     int L = size;
     int m = 1;
@@ -390,16 +400,27 @@ string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable,
 
     // Factor size, generating an appropriate block of code for each factor.
 
-    while (unfactored > 1) {
+    while (L > 1) {
         int input = stage%2;
         int output = 1-input;
+        int radix;
+        if (L%5 == 0)
+            radix = 5;
+        else if (L%4 == 0)
+            radix = 4;
+        else if (L%3 == 0)
+            radix = 3;
+        else if (L%2 == 0)
+            radix = 2;
+        else
+            throw OpenMMException("Illegal size for FFT: "+cu.intToString(size));
         source<<"{\n";
-        if (unfactored%5 == 0) {
-            L = L/5;
-            source<<"// Pass "<<(stage+1)<<" (radix 5)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        L = L/radix;
+        source<<"// Pass "<<(stage+1)<<" (radix "<<radix<<")\n";
+        source<<"if (indexInBlock < "<<(L*m)<<") {\n";
+        source<<"int i = indexInBlock;\n";
+        source<<"int j = i/"<<m<<";\n";
+        if (radix == 5) {
             source<<"mixed3 c0r = real"<<input<<"[i];\n";
             source<<"mixed3 c0i = imag"<<input<<"[i];\n";
             source<<"mixed3 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -443,16 +464,8 @@ string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable,
             source<<"imag"<<output<<"[i+(4*j+3)*"<<m<<"] = "<<multImag<<"(w[j*"<<(3*size)<<"/"<<(5*L)<<"], d8r-d10r, d8i-d10i);\n";
             source<<"real"<<output<<"[i+(4*j+4)*"<<m<<"] = "<<multReal<<"(w[j*"<<(4*size)<<"/"<<(5*L)<<"], d7r-d9r, d7i-d9i);\n";
             source<<"imag"<<output<<"[i+(4*j+4)*"<<m<<"] = "<<multImag<<"(w[j*"<<(4*size)<<"/"<<(5*L)<<"], d7r-d9r, d7i-d9i);\n";
-            source<<"}\n";
-            m = m*5;
-            unfactored /= 5;
         }
-        else if (unfactored%4 == 0) {
-            L = L/4;
-            source<<"// Pass "<<(stage+1)<<" (radix 4)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 4) {
             source<<"mixed3 c0r = real"<<input<<"[i];\n";
             source<<"mixed3 c0i = imag"<<input<<"[i];\n";
             source<<"mixed3 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -477,16 +490,8 @@ string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable,
             source<<"imag"<<output<<"[i+(3*j+2)*"<<m<<"] = "<<multImag<<"(w[j*"<<(2*size)<<"/"<<(4*L)<<"], d0r-d2r, d0i-d2i);\n";
             source<<"real"<<output<<"[i+(3*j+3)*"<<m<<"] = "<<multReal<<"(w[j*"<<(3*size)<<"/"<<(4*L)<<"], d1r-d3r, d1i-d3i);\n";
             source<<"imag"<<output<<"[i+(3*j+3)*"<<m<<"] = "<<multImag<<"(w[j*"<<(3*size)<<"/"<<(4*L)<<"], d1r-d3r, d1i-d3i);\n";
-            source<<"}\n";
-            m = m*4;
-            unfactored /= 4;
         }
-        else if (unfactored%3 == 0) {
-            L = L/3;
-            source<<"// Pass "<<(stage+1)<<" (radix 3)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 3) {
             source<<"mixed3 c0r = real"<<input<<"[i];\n";
             source<<"mixed3 c0i = imag"<<input<<"[i];\n";
             source<<"mixed3 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -505,16 +510,8 @@ string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable,
             source<<"imag"<<output<<"[i+(2*j+1)*"<<m<<"] = "<<multImag<<"(w[j*"<<size<<"/"<<(3*L)<<"], d1r+d2r, d1i+d2i);\n";
             source<<"real"<<output<<"[i+(2*j+2)*"<<m<<"] = "<<multReal<<"(w[j*"<<(2*size)<<"/"<<(3*L)<<"], d1r-d2r, d1i-d2i);\n";
             source<<"imag"<<output<<"[i+(2*j+2)*"<<m<<"] = "<<multImag<<"(w[j*"<<(2*size)<<"/"<<(3*L)<<"], d1r-d2r, d1i-d2i);\n";
-            source<<"}\n";
-            m = m*3;
-            unfactored /= 3;
         }
-        else if (unfactored%2 == 0) {
-            L = L/2;
-            source<<"// Pass "<<(stage+1)<<" (radix 2)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 2) {
             source<<"mixed3 c0r = real"<<input<<"[i];\n";
             source<<"mixed3 c0i = imag"<<input<<"[i];\n";
             source<<"mixed3 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -523,12 +520,9 @@ string CudaIntegrateRPMDStepKernel::createFFT(int size, const string& variable,
             source<<"imag"<<output<<"[i+j*"<<m<<"] = c0i+c1i;\n";
             source<<"real"<<output<<"[i+(j+1)*"<<m<<"] = "<<multReal<<"(w[j*"<<size<<"/"<<(2*L)<<"], c0r-c1r, c0i-c1i);\n";
             source<<"imag"<<output<<"[i+(j+1)*"<<m<<"] = "<<multImag<<"(w[j*"<<size<<"/"<<(2*L)<<"], c0r-c1r, c0i-c1i);\n";
-            source<<"}\n";
-            m = m*2;
-            unfactored /= 2;
         }
-        else
-            throw OpenMMException("Illegal size for FFT: "+cu.intToString(size));
+        source<<"}\n";
+        m = m*radix;
         source<<"__syncthreads();\n";
         source<<"}\n";
         ++stage;

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

@@ -108,12 +108,12 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 if (copies > maxContractedCopies)
                     maxContractedCopies = copies;
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }
     if (maxContractedCopies > 0) {
@@ -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.
 
@@ -301,6 +304,13 @@ void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
             cl.executeKernel(forceContractionKernels[copies], numParticles*numCopies, workgroupSize);
         }
     }
+    if (groupsByCopies.size() > 0) {
+        // Ensure the Context contains the positions from the last copy, since we'll assume that later.
+        
+        copyToContextKernel.setArg<cl::Buffer>(2, positions->getDeviceBuffer());
+        copyToContextKernel.setArg<cl_int>(5, numCopies-1);
+        cl.executeKernel(copyToContextKernel, cl.getNumAtoms());
+    }
 }
 
 double OpenCLIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
@@ -380,7 +390,6 @@ void OpenCLIntegrateRPMDStepKernel::copyToContext(int copy, ContextImpl& context
 
 string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable, bool forward) {
     stringstream source;
-    int unfactored = size;
     int stage = 0;
     int L = size;
     int m = 1;
@@ -396,16 +405,27 @@ string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable
 
     // Factor size, generating an appropriate block of code for each factor.
 
-    while (unfactored > 1) {
+    while (L > 1) {
         int input = stage%2;
         int output = 1-input;
+        int radix;
+        if (L%5 == 0)
+            radix = 5;
+        else if (L%4 == 0)
+            radix = 4;
+        else if (L%3 == 0)
+            radix = 3;
+        else if (L%2 == 0)
+            radix = 2;
+        else
+            throw OpenMMException("Illegal size for FFT: "+cl.intToString(size));
         source<<"{\n";
-        if (unfactored%5 == 0) {
-            L = L/5;
-            source<<"// Pass "<<(stage+1)<<" (radix 5)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        L = L/radix;
+        source<<"// Pass "<<(stage+1)<<" (radix "<<radix<<")\n";
+        source<<"if (indexInBlock < "<<(L*m)<<") {\n";
+        source<<"int i = indexInBlock;\n";
+        source<<"int j = i/"<<m<<";\n";
+        if (radix == 5) {
             source<<"mixed4 c0r = real"<<input<<"[i];\n";
             source<<"mixed4 c0i = imag"<<input<<"[i];\n";
             source<<"mixed4 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -449,16 +469,8 @@ string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable
             source<<"imag"<<output<<"[i+(4*j+3)*"<<m<<"] = "<<multImag<<"(w[j*"<<(3*size)<<"/"<<(5*L)<<"], d8r-d10r, d8i-d10i);\n";
             source<<"real"<<output<<"[i+(4*j+4)*"<<m<<"] = "<<multReal<<"(w[j*"<<(4*size)<<"/"<<(5*L)<<"], d7r-d9r, d7i-d9i);\n";
             source<<"imag"<<output<<"[i+(4*j+4)*"<<m<<"] = "<<multImag<<"(w[j*"<<(4*size)<<"/"<<(5*L)<<"], d7r-d9r, d7i-d9i);\n";
-            source<<"}\n";
-            m = m*5;
-            unfactored /= 5;
         }
-        else if (unfactored%4 == 0) {
-            L = L/4;
-            source<<"// Pass "<<(stage+1)<<" (radix 4)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 4) {
             source<<"mixed4 c0r = real"<<input<<"[i];\n";
             source<<"mixed4 c0i = imag"<<input<<"[i];\n";
             source<<"mixed4 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -483,16 +495,8 @@ string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable
             source<<"imag"<<output<<"[i+(3*j+2)*"<<m<<"] = "<<multImag<<"(w[j*"<<(2*size)<<"/"<<(4*L)<<"], d0r-d2r, d0i-d2i);\n";
             source<<"real"<<output<<"[i+(3*j+3)*"<<m<<"] = "<<multReal<<"(w[j*"<<(3*size)<<"/"<<(4*L)<<"], d1r-d3r, d1i-d3i);\n";
             source<<"imag"<<output<<"[i+(3*j+3)*"<<m<<"] = "<<multImag<<"(w[j*"<<(3*size)<<"/"<<(4*L)<<"], d1r-d3r, d1i-d3i);\n";
-            source<<"}\n";
-            m = m*4;
-            unfactored /= 4;
         }
-        else if (unfactored%3 == 0) {
-            L = L/3;
-            source<<"// Pass "<<(stage+1)<<" (radix 3)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 3) {
             source<<"mixed4 c0r = real"<<input<<"[i];\n";
             source<<"mixed4 c0i = imag"<<input<<"[i];\n";
             source<<"mixed4 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -511,16 +515,8 @@ string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable
             source<<"imag"<<output<<"[i+(2*j+1)*"<<m<<"] = "<<multImag<<"(w[j*"<<size<<"/"<<(3*L)<<"], d1r+d2r, d1i+d2i);\n";
             source<<"real"<<output<<"[i+(2*j+2)*"<<m<<"] = "<<multReal<<"(w[j*"<<(2*size)<<"/"<<(3*L)<<"], d1r-d2r, d1i-d2i);\n";
             source<<"imag"<<output<<"[i+(2*j+2)*"<<m<<"] = "<<multImag<<"(w[j*"<<(2*size)<<"/"<<(3*L)<<"], d1r-d2r, d1i-d2i);\n";
-            source<<"}\n";
-            m = m*3;
-            unfactored /= 3;
         }
-        else if (unfactored%2 == 0) {
-            L = L/2;
-            source<<"// Pass "<<(stage+1)<<" (radix 2)\n";
-            source<<"if (indexInBlock < "<<(L*m)<<") {\n";
-            source<<"int i = indexInBlock;\n";
-            source<<"int j = i/"<<m<<";\n";
+        else if (radix == 2) {
             source<<"mixed4 c0r = real"<<input<<"[i];\n";
             source<<"mixed4 c0i = imag"<<input<<"[i];\n";
             source<<"mixed4 c1r = real"<<input<<"[i+"<<(L*m)<<"];\n";
@@ -529,12 +525,9 @@ string OpenCLIntegrateRPMDStepKernel::createFFT(int size, const string& variable
             source<<"imag"<<output<<"[i+j*"<<m<<"] = c0i+c1i;\n";
             source<<"real"<<output<<"[i+(j+1)*"<<m<<"] = "<<multReal<<"(w[j*"<<size<<"/"<<(2*L)<<"], c0r-c1r, c0i-c1i);\n";
             source<<"imag"<<output<<"[i+(j+1)*"<<m<<"] = "<<multImag<<"(w[j*"<<size<<"/"<<(2*L)<<"], c0r-c1r, c0i-c1i);\n";
-            source<<"}\n";
-            m = m*2;
-            unfactored /= 2;
         }
-        else
-            throw OpenMMException("Illegal size for FFT: "+cl.intToString(size));
+        source<<"}\n";
+        m = m*radix;
         source<<"barrier(CLK_LOCAL_MEM_FENCE);\n";
         source<<"}\n";
         ++stage;

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;

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -89,7 +89,6 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 contractionFFT[copies] = NULL;
                 fftpack_init_1d(&contractionFFT[copies], copies);
                 if (copies > maxContractedCopies)
@@ -97,6 +96,7 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }
     
@@ -135,36 +135,38 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
     const RealOpenMM twown = 2.0*nkT/hbar;
     const RealOpenMM c1_0 = exp(-halfdt*integrator.getFriction());
     const RealOpenMM c2_0 = sqrt(1.0-c1_0*c1_0);
-    for (int particle = 0; particle < numParticles; particle++) {
-        if (system.getParticleMass(particle) == 0.0)
-            continue;
-        const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
-        for (int component = 0; component < 3; component++) {
-            for (int k = 0; k < numCopies; k++)
-                v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
-            fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
-            
-            // Apply a local Langevin thermostat to the centroid mode.
+    if (integrator.getApplyThermostat()) {
+        for (int particle = 0; particle < numParticles; particle++) {
+            if (system.getParticleMass(particle) == 0.0)
+                continue;
+            const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
+            for (int component = 0; component < 3; component++) {
+                for (int k = 0; k < numCopies; k++)
+                    v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
+                fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
 
-            v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+                // Apply a local Langevin thermostat to the centroid mode.
 
-            // Use critical damping white noise for the remaining modes.
-            
-            for (int k = 1; k <= numCopies/2; k++) {
-                const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
-                const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
-                const RealOpenMM c1 = exp(-2.0*wk*halfdt);
-                const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
-                const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
-                RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
-                RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
-                v[k] = v[k]*c1 + t_complex(rand1, rand2);
-                if (k < numCopies-k)
-                    v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
+                v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+
+                // Use critical damping white noise for the remaining modes.
+
+                for (int k = 1; k <= numCopies/2; k++) {
+                    const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
+                    const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
+                    const RealOpenMM c1 = exp(-2.0*wk*halfdt);
+                    const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
+                    const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
+                    RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+                    RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+                    v[k] = v[k]*c1 + t_complex(rand1, rand2);
+                    if (k < numCopies-k)
+                        v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
+                }
+                fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
+                for (int k = 0; k < numCopies; k++)
+                    velocities[k][particle][component] = scale*v[k].re;
             }
-            fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
-            for (int k = 0; k < numCopies; k++)
-                velocities[k][particle][component] = scale*v[k].re;
         }
     }
 
@@ -220,36 +222,38 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
 
     // Apply the PILE-L thermostat again.
     
-    for (int particle = 0; particle < numParticles; particle++) {
-        if (system.getParticleMass(particle) == 0.0)
-            continue;
-        const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
-        for (int component = 0; component < 3; component++) {
-            for (int k = 0; k < numCopies; k++)
-                v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
-            fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
-            
-            // Apply a local Langevin thermostat to the centroid mode.
+    if (integrator.getApplyThermostat()) {
+        for (int particle = 0; particle < numParticles; particle++) {
+            if (system.getParticleMass(particle) == 0.0)
+                continue;
+            const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
+            for (int component = 0; component < 3; component++) {
+                for (int k = 0; k < numCopies; k++)
+                    v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
+                fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
 
-            v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+                // Apply a local Langevin thermostat to the centroid mode.
 
-            // Use critical damping white noise for the remaining modes.
-            
-            for (int k = 1; k <= numCopies/2; k++) {
-                const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
-                const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
-                const RealOpenMM c1 = exp(-2.0*wk*halfdt);
-                const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
-                const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
-                RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
-                RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
-                v[k] = v[k]*c1 + t_complex(rand1, rand2);
-                if (k < numCopies-k)
-                    v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
+                v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+
+                // Use critical damping white noise for the remaining modes.
+
+                for (int k = 1; k <= numCopies/2; k++) {
+                    const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
+                    const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
+                    const RealOpenMM c1 = exp(-2.0*wk*halfdt);
+                    const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
+                    const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
+                    RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
+                    RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+                    v[k] = v[k]*c1 + t_complex(rand1, rand2);
+                    if (k < numCopies-k)
+                        v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
+                }
+                fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
+                for (int k = 0; k < numCopies; k++)
+                    velocities[k][particle][component] = scale*v[k].re;
             }
-            fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
-            for (int k = 0; k < numCopies; k++)
-                velocities[k][particle][component] = scale*v[k].re;
         }
     }
     

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -313,12 +313,78 @@ 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("Reference");
+    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() {
     try {
         testFreeParticles();
         testCMMotionRemoval();
         testVirtualSites();
         testContractions();
+        testWithoutThermostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

tests/TestParser.cpp

@@ -56,6 +56,12 @@ void verifyEvaluation(const string& expression, double expectedValue) {
     ExpressionProgram program = parsed.createProgram();
     value = program.evaluate();
     ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
+
+    // Create a CompiledExpression and see if that also gives the same result.
+
+    CompiledExpression compiled = parsed.createCompiledExpression();
+    value = compiled.evaluate();
+    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
 }
 
 /**
@@ -86,6 +92,16 @@ void verifyEvaluation(const string& expression, double x, double y, double expec
     value = program.evaluate(variables);
     ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
 
+    // Create a CompiledExpression and see if that also gives the same result.
+
+    CompiledExpression compiled = parsed.createCompiledExpression();
+    if (compiled.getVariables().find("x") != compiled.getVariables().end())
+        compiled.getVariableReference("x") = x;
+    if (compiled.getVariables().find("y") != compiled.getVariables().end())
+        compiled.getVariableReference("y") = y;
+    value = compiled.evaluate();
+    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
+
     // Make sure that variable renaming works.
 
     variables.clear();

wrappers/FortranWrapper_Header.xslt

@@ -78,6 +78,10 @@ MODULE OpenMM_Types
         integer*8 :: handle = 0
     end type
 
+    type OpenMM_IntSet
+        integer*8 :: handle = 0
+    end type
+
     ! Enumerations
 
     integer*4, parameter :: OpenMM_False = 0

wrappers/python/setup.py

@@ -85,6 +85,7 @@ version = '%(version)s'
 full_version = '%(full_version)s'
 git_revision = '%(git_revision)s'
 release = %(isrelease)s
+openmm_library_path = '%(path)s'
 
 if not release:
     version = full_version
@@ -113,7 +114,8 @@ if not release:
         a.write(cnt % {'version': version,
                        'full_version' : full_version,
                        'git_revision' : git_revision,
-                       'isrelease': str(IS_RELEASED)})
+                       'isrelease': str(IS_RELEASED),
+                       'path': os.getenv('OPENMM_LIB_PATH')})
     finally:
         a.close()
 
@@ -197,7 +199,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
             macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
             if tuple(macVersion) < (10, 6):
                 os.environ['MACOSX_DEPLOYMENT_TARGET']='10.5'
-            extra_link_args.append('-Wl,-rpath,@loader_path/OpenMM')
+            extra_link_args.append('-Wl,-rpath,'+openmm_lib_path)
 
 
     library_dirs=[openmm_lib_path]
@@ -209,6 +211,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                  include_dirs = include_dirs,
                  define_macros = define_macros,
                  library_dirs = library_dirs,
+                 runtime_library_dirs = library_dirs,
                  libraries = libraries,
                  extra_compile_args=extra_compile_args,
                  extra_link_args=extra_link_args,
@@ -238,8 +241,8 @@ def main():
         uninstall()
     except:
         pass
-    writeVersionPy()
     setupKeywords=buildKeywordDictionary()
+    writeVersionPy()
     setup(**setupKeywords)
 
 if __name__ == '__main__':

wrappers/python/simtk/openmm/__init__.py

@@ -13,7 +13,7 @@ It also tries to load any plugin modules it can find.
 
 __author__ = "Randall J. Radmer"
 
-import os, sys, glob
+import os, sys, glob, os.path
 if sys.platform == "win32":
     libPrefix=""
     libExt="dll"
@@ -34,5 +34,9 @@ else:
 
 from simtk.openmm.openmm import *
 from simtk.openmm.vec3 import Vec3
-pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
+from simtk.openmm import version
+if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
+    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+else:
+    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
 __version__ = Platform.getOpenMMVersion()

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

@@ -24,6 +24,7 @@ from dcdreporter import DCDReporter
 from modeller import Modeller
 from statedatareporter import StateDataReporter
 from element import Element
+from desmonddmsfile import DesmondDMSFile
 
 # Enumerated values
 

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

@@ -61,6 +61,11 @@ class GBn(object):
         return 'GBn'
 GBn = GBn()
 
+class GBn2(object):
+    def __repr__(self):
+        return 'GBn2'
+GBn2 = GBn2()
+
 class AmberPrmtopFile(object):
     """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
 
@@ -69,6 +74,7 @@ class AmberPrmtopFile(object):
         top = Topology()
         ## The Topology read from the prmtop file
         self.topology = top
+        self.elements = []
 
         # Load the prmtop file
 
@@ -96,21 +102,30 @@ class AmberPrmtopFile(object):
             if atomName in atomReplacements:
                 atomName = atomReplacements[atomName]
 
-            # Try to guess the element.
-
-            upper = atomName.upper()
-            if upper.startswith('CL'):
-                element = elem.chlorine
-            elif upper.startswith('NA'):
-                element = elem.sodium
-            elif upper.startswith('MG'):
-                element = elem.magnesium
-            else:
+            # Get the element from the prmtop file if available
+            if prmtop.has_atomic_number:
                 try:
-                    element = elem.get_by_symbol(atomName[0])
+                    element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
                 except KeyError:
                     element = None
+            else:
+                # Try to guess the element from the atom name.
+
+                upper = atomName.upper()
+                if upper.startswith('CL'):
+                    element = elem.chlorine
+                elif upper.startswith('NA'):
+                    element = elem.sodium
+                elif upper.startswith('MG'):
+                    element = elem.magnesium
+                else:
+                    try:
+                        element = elem.get_by_symbol(atomName[0])
+                    except KeyError:
+                        element = None
+
             top.addAtom(atomName, element, r)
+            self.elements.append(element)
 
         # Add bonds to the topology
 
@@ -127,7 +142,7 @@ class AmberPrmtopFile(object):
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True,
-                     ewaldErrorTolerance=0.0005):
+                     hydrogenMass=None, ewaldErrorTolerance=0.0005):
         """Construct an OpenMM System representing the topology described by this prmtop file.
 
         Parameters:
@@ -137,10 +152,12 @@ class AmberPrmtopFile(object):
          - constraints (object=None) Specifies which bonds angles should be implemented with constraints.
            Allowed values are None, HBonds, AllBonds, or HAngles.
          - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
-         - implicitSolvent (object=None) If not None, the implicit solvent model to use.  Allowed values are HCT, OBC1, OBC2, or GBn.
+         - implicitSolvent (object=None) If not None, the implicit solvent model to use.  Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
          - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
          - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
          - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
+         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
+           subtracted from the heavy atom to keep their total mass the same.
          - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
         Returns: the newly created System
         """
@@ -165,19 +182,30 @@ class AmberPrmtopFile(object):
             raise ValueError('Illegal value for constraints')
         if implicitSolvent is None:
             implicitString = None
-        elif implicitSolvent == HCT:
+        elif implicitSolvent is HCT:
             implicitString = 'HCT'
-        elif implicitSolvent == OBC1:
+        elif implicitSolvent is OBC1:
             implicitString = 'OBC1'
-        elif implicitSolvent == OBC2:
+        elif implicitSolvent is OBC2:
             implicitString = 'OBC2'
-        elif implicitSolvent == GBn:
+        elif implicitSolvent is GBn:
             implicitString = 'GBn'
+        elif implicitSolvent is GBn2:
+            implicitString = 'GBn2'
         else:
             raise ValueError('Illegal value for implicit solvent model')
         sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
                                                  nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
-                                                 soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater)
+                                                 soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater,
+                                                 elements=self.elements)
+        if hydrogenMass is not None:
+            for atom1, atom2 in self.topology.bonds():
+                if atom1.element == elem.hydrogen:
+                    (atom1, atom2) = (atom2, atom1)
+                if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None):
+                    transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
+                    sys.setParticleMass(atom2.index, hydrogenMass)
+                    sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
         for force in sys.getForces():
             if isinstance(force, mm.NonbondedForce):
                 force.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/data/hydrogens.xml

 <Residues>
  <Residue name="A">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2" parent="C2"/>
   <H name="H2'" parent="C2'"/>
@@ -11,9 +12,7 @@
   <H name="H62" parent="N6"/>
   <H name="H8" parent="C8"/>
   <H name="HO2'" parent="O2'"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="ACE">
   <H name="H" parent="C" terminal="C"/>
@@ -80,6 +79,7 @@
   <H name="HD2" parent="OD2" maxph="4.4" variant="ASH"/>
  </Residue>
  <Residue name="C">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
   <H name="H3'" parent="C3'"/>
@@ -91,9 +91,7 @@
   <H name="H5''" parent="C5'"/>
   <H name="H6" parent="C6"/>
   <H name="HO2'" parent="O2'"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="CYS">
   <Variant name="CYS"/>
@@ -107,6 +105,7 @@
   <H name="HG" parent="SG" maxph="8.5" variant="CYS"/>
  </Residue>
  <Residue name="DA">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2" parent="C2"/>
   <H name="H2'" parent="C2'"/>
@@ -118,11 +117,10 @@
   <H name="H61" parent="N6"/>
   <H name="H62" parent="N6"/>
   <H name="H8" parent="C8"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="DC">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
   <H name="H2''" parent="C2'"/>
@@ -134,11 +132,10 @@
   <H name="H5'" parent="C5'"/>
   <H name="H5''" parent="C5'"/>
   <H name="H6" parent="C6"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="DG">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1" parent="N1"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
@@ -150,11 +147,10 @@
   <H name="H5'" parent="C5'"/>
   <H name="H5''" parent="C5'"/>
   <H name="H8" parent="C8"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="DT">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
   <H name="H2''" parent="C2'"/>
@@ -167,15 +163,14 @@
   <H name="H71" parent="C7"/>
   <H name="H72" parent="C7"/>
   <H name="H73" parent="C7"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="FOR">
   <H name="H1" parent="C"/>
   <H name="H2" parent="C"/>
  </Residue>
  <Residue name="G">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1" parent="N1"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
@@ -187,9 +182,7 @@
   <H name="H5''" parent="C5'"/>
   <H name="H8" parent="C8"/>
   <H name="HO2'" parent="O2'"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="GLN">
   <H name="H" parent="N"/>
@@ -409,6 +402,7 @@
   <H name="HH" parent="OH"/>
  </Residue>
  <Residue name="U">
+  <H name="HO5'" parent="O5'" terminal="N"/>
   <H name="H1'" parent="C1'"/>
   <H name="H2'" parent="C2'"/>
   <H name="H3" parent="N3"/>
@@ -419,9 +413,7 @@
   <H name="H5''" parent="C5'"/>
   <H name="H6" parent="C6"/>
   <H name="HO2'" parent="O2'"/>
-  <H name="HO3'" parent="O3'"/>
-  <H name="HOP2" parent="OP2"/>
-  <H name="HOP3" parent="OP3"/>
+  <H name="HO3'" parent="O3'" terminal="C"/>
  </Residue>
  <Residue name="UNK">
   <H name="H" parent="N"/>

wrappers/python/simtk/openmm/app/data/residues.xml

@@ -718,6 +718,7 @@
   <Bond from="CG" to="HG2"/>
   <Bond from="CG" to="HG3"/>
   <Bond from="H" to="N"/>
+  <Bond from="H2" to="N"/>
   <Bond from="H3" to="N"/>
   <Bond from="HXT" to="OXT"/>
  </Residue>

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

+'''
+desmonddmsfile.py: Load Desmond dms files
+
+Portions copyright (c) 2013 Stanford University and the Authors
+Authors: Robert McGibbon
+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.
+'''
+
+import os
+import math
+
+from simtk import openmm as mm
+from simtk.openmm.app import forcefield as ff
+from simtk.openmm.app import Element, Topology, PDBFile
+from simtk.openmm.app.element import hydrogen
+from simtk.unit import (nanometer, angstrom, dalton, radian,
+                        kilocalorie_per_mole, kilojoule_per_mole,
+                        degree, elementary_charge)
+
+
+class DesmondDMSFile(object):
+    '''DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
+    constructs a topology and (optionally) an OpenMM System from it
+    '''
+
+    def __init__(self, file):
+        '''Load a DMS file
+
+        Parameters:
+        - file (string) the name of the file to load
+        '''
+
+        # sqlite3 is included in the standard lib, but at python
+        # compile time, you can disable support (I think), so it's
+        # not *guarenteed* to be available. Doing the import here
+        # means we only raise an ImportError if people try to use
+        # this class, so the module can be safely imported
+        import sqlite3
+
+        self._open = False
+        self._tables = None
+        if not  os.path.exists(str(file)):
+            raise IOError("No such file or directory: '%s'" % str(file))
+        self._conn = sqlite3.connect(file)
+        self._open = True
+        self._readSchemas()
+
+        if len(self._tables) == 0:
+            raise IOError('DMS file was not loaded sucessfully. No tables found')
+        if 'nbtype' not in self._tables['particle']:
+            raise ValueError('No nonbonded parameters associated with this '
+                             'DMS file. You can add a forcefield with the '
+                             'viparr command line tool distributed with desmond')
+
+        # build the provenance string
+        provenance = []
+        q = '''SELECT id, user, timestamp, version, workdir, cmdline, executable
+        FROM provenance'''
+        #for id, user, timestamp, version, workdir, cmdline, executable in self._conn.execute(q):
+        for row in self._conn.execute('SELECT * FROM provenance'):
+            rowdict = dict(zip(self._tables['provenance'], row))
+            provenance.append('%(id)d) %(timestamp)s: %(user)s\n  version: %(version)s\n  '
+                              'cmdline: %(cmdline)s\n  executable: %(executable)s\n' % rowdict)
+        self.provenance = ''.join(provenance)
+
+        # Build the topology
+        self.topology, self.positions = self._createTopology()
+        self._topologyAtoms = list(self.topology.atoms())
+        self._atomBonds = [{} for x in range(len(self._topologyAtoms))]
+        self._angleConstraints = [{} for x in range(len(self._topologyAtoms))]
+
+    def getPositions(self):
+        '''Get the positions of each atom in the system
+        '''
+        return self.positions
+
+    def getTopology(self):
+        '''Get the topology of the system
+        '''
+        return self.topology
+
+    def getProvenance(self):
+        '''Get the provenance string of this system
+        '''
+        return self.provenance
+
+    def _createTopology(self):
+        '''Build the topology of the system
+        '''
+        top = Topology()
+        positions = []
+
+        boxVectors = []
+        for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
+            boxVectors.append(mm.Vec3(x, y, z))
+        unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
+        top.setUnitCellDimensions(unitCellDimensions*angstrom)
+
+        atoms = {}
+        lastChain = None
+        lastResId = None
+        c = top.addChain()
+        q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
+        FROM particle'''
+        for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
+            newChain = False
+            if chain != lastChain:
+                lastChain = chain
+                c = top.addChain()
+                newChain = True
+            if resId != lastResId or newChain:
+                lastResId = resId
+                if resName in PDBFile._residueNameReplacements:
+                    resName = PDBFile._residueNameReplacements[resName]
+                r = top.addResidue(resName, c)
+                if resName in PDBFile._atomNameReplacements:
+                    atomReplacements = PDBFile._atomNameReplacements[resName]
+                else:
+                    atomReplacements = {}
+
+            if atomNumber == 0 and atomName.startswith('Vrt'):
+                elem = None
+            else:
+                elem = Element.getByAtomicNumber(atomNumber)
+
+            if atomName in atomReplacements:
+                atomName = atomReplacements[atomName]
+
+            atoms[atomId] = top.addAtom(atomName, elem, r)
+            positions.append(mm.Vec3(x, y, z))
+
+        for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
+            top.addBond(atoms[p0], atoms[p1])
+
+        positions = positions*angstrom
+        return top, positions
+
+    def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*nanometer,
+                     ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None):
+        '''Construct an OpenMM System representing the topology described by this dms file
+
+        Parameters:
+        - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions.  Allowed values are
+          NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+        - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
+        - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
+        - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
+        - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
+          subtracted from the heavy atom to keep their total mass the same.
+        '''
+        self._checkForUnsupportedTerms()
+        sys = mm.System()
+
+        # Buld the box dimensions
+        sys = mm.System()
+        boxSize = self.topology.getUnitCellDimensions()
+        if boxSize is not None:
+            sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
+        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+            raise ValueError('Illegal nonbonded method for a non-periodic system')
+
+        # Create all of the particles
+        for mass in self._conn.execute('SELECT mass from particle'):
+            sys.addParticle(mass[0]*dalton)
+
+        # Add all of the forces
+        self._addBondsToSystem(sys)
+        self._addAnglesToSystem(sys)
+        self._addConstraintsToSystem(sys)
+        self._addPeriodicTorsionsToSystem(sys)
+        self._addImproperHarmonicTorsionsToSystem(sys)
+        self._addCMAPToSystem(sys)
+        self._addVirtualSitesToSystem(sys)
+        nb = self._addNonbondedForceToSystem(sys)
+
+        # Finish configuring the NonbondedForce.
+        methodMap = {ff.NoCutoff:mm.NonbondedForce.NoCutoff,
+                     ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
+                     ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
+                     ff.Ewald:mm.NonbondedForce.Ewald,
+                     ff.PME:mm.NonbondedForce.PME}
+        nb.setNonbondedMethod(methodMap[nonbondedMethod])
+        nb.setCutoffDistance(nonbondedCutoff)
+        nb.setEwaldErrorTolerance(ewaldErrorTolerance)
+
+        # Adjust masses.
+        if hydrogenMass is not None:
+            for atom1, atom2 in self.topology.bonds():
+                if atom1.element == hydrogen:
+                    (atom1, atom2) = (atom2, atom1)
+                if atom2.element == hydrogen and atom1.element not in (hydrogen, None):
+                    transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
+                    sys.setParticleMass(atom2.index, hydrogenMass)
+                    sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
+
+        # Add a CMMotionRemover.
+        if removeCMMotion:
+            sys.addForce(mm.CMMotionRemover())
+
+        return sys
+
+    def _addBondsToSystem(self, sys):
+        '''Create the harmonic bonds
+        '''
+        bonds = mm.HarmonicBondForce()
+        sys.addForce(bonds)
+
+        q = '''SELECT p0, p1, r0, fc, constrained
+        FROM stretch_harm_term INNER JOIN stretch_harm_param
+        ON stretch_harm_term.param=stretch_harm_param.id'''
+        for p0, p1, r0, fc, constrained in self._conn.execute(q):
+            if constrained:
+                sys.addConstraint(p0, p1, r0*angstrom)
+            else:
+                # Desmond writes the harmonic bond force without 1/2
+                # so we need to to double the force constant
+                bonds.addBond(p0, p1, r0*angstrom, 2*fc*kilocalorie_per_mole/angstrom**2)
+
+            # Record information that will be needed for constraining angles.
+            self._atomBonds[p0][p1] = r0*angstrom
+            self._atomBonds[p1][p0] = r0*angstrom
+
+        return bonds
+
+    def _addAnglesToSystem(self, sys):
+        '''Create the harmonic angles
+        '''
+        angles = mm.HarmonicAngleForce()
+        sys.addForce(angles)
+        degToRad = math.pi/180
+
+        q = '''SELECT p0, p1, p2, theta0, fc, constrained
+        FROM angle_harm_term INNER JOIN angle_harm_param
+        ON angle_harm_term.param=angle_harm_param.id'''
+        for p0, p1, p2, theta0, fc, constrained in self._conn.execute(q):
+            if constrained:
+                l1 = self._atomBonds[p1][p0]
+                l2 = self._atomBonds[p1][p2]
+                length = (l1*l1 + l2*l2 - 2*l1*l2*math.cos(theta0*degToRad)).sqrt()
+                sys.addConstraint(p0, p2, length)
+                self._angleConstraints[p1][p0] = p2
+                self._angleConstraints[p1][p2] = p0
+            else:
+                # Desmond writes the harmonic angle force without 1/2
+                # so we need to to double the force constant
+                angles.addAngle(p0, p1, p2, theta0*degToRad, 2*fc*kilocalorie_per_mole/radian**2)
+
+        return angles
+
+    def _addConstraintsToSystem(self, sys):
+        '''Add constraints to system. Normally these should already be
+        added by the bonds table, but we want to make sure that there's
+        no extra information in the constraints table that we're not
+        including in the system'''
+        for term_table in [n for n in self._tables.keys() if n.startswith('constraint_a') and n.endswith('term')]:
+            param_table = term_table.replace('term', 'param')
+            q = '''SELECT p0, p1, r1
+            FROM %(term)s INNER JOIN %(param)s
+            ON %(term)s.param=%(param)s.id''' % \
+                {'term': term_table, 'param': param_table}
+            for p0, p1, r1 in self._conn.execute(q):
+                if not p1 in self._atomBonds[p0]:
+                    sys.addConstraint(p0, p1, r1*angstrom)
+                    self._atomBonds[p0][p1] = r1*angstrom
+                    self._atomBonds[p1][p0] = r1*angstrom
+
+        if 'constraint_hoh_term' in self._tables:
+            degToRad = math.pi/180
+            q = '''SELECT p0, p1, p2, r1, r2, theta
+            FROM constraint_hoh_term INNER JOIN constraint_hoh_param
+            ON constraint_hoh_term.param=constraint_hoh_param.id'''
+            for p0, p1, p2, r1, r2, theta in self._conn.execute(q):
+                # Here, p0 is the heavy atom and p1 and p2 are the H1 and H2
+                # wihth O-H1 and O-H2 distances r1 and r2
+                if not (self._angleConstraints[p0].get(p1, None) == p2):
+                    length = (r1*r1 + r2*r2 - 2*r1*r2*math.cos(theta*degToRad)).sqrt()
+                    sys.addConstraint(p1, p2, length)
+
+    def _addPeriodicTorsionsToSystem(self, sys):
+        '''Create the torsion terms
+        '''
+        periodic = mm.PeriodicTorsionForce()
+        sys.addForce(periodic)
+
+        q = '''SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
+        FROM dihedral_trig_term INNER JOIN dihedral_trig_param
+        ON dihedral_trig_term.param=dihedral_trig_param.id'''
+        for p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6 in self._conn.execute(q):
+            for order, fc in enumerate([fc0, fc1, fc2, fc3, fc4, fc5, fc6]):
+                if fc == 0:
+                    continue
+                periodic.addTorsion(p0, p1, p2, p3, order, phi0*degree, fc*kilocalorie_per_mole)
+
+
+    def _addImproperHarmonicTorsionsToSystem(self, sys):
+        '''Create the improper harmonic torsion terms
+        '''
+        if not self._hasTable('improper_harm_term'):
+            return
+
+        harmonicTorsion = mm.CustomTorsionForce('k*(theta-theta0)^2')
+        harmonicTorsion.addPerTorsionParameter('theta0')
+        harmonicTorsion.addPerTorsionParameter('k')
+        sys.addForce(harmonicTorsion)
+
+        q = '''SELECT p0, p1, p2, p3, phi0, fc
+        FROM improper_harm_term INNER JOIN improper_harm_param
+        ON improper_harm_term.param=improper_harm_param.id'''
+        for p0, p1, p2, p3, phi0, fc in self._conn.execute(q):
+            harmonicTorsion.addTorsion(p0, p1, p2, p3, [phi0*degree, fc*kilocalorie_per_mole])
+
+    def _addCMAPToSystem(self, sys):
+        '''Create the CMAP terms
+        '''
+        if not self._hasTable('torsiontorsion_cmap_term'):
+            return
+
+        # Create CMAP torsion terms
+        cmap = mm.CMAPTorsionForce()
+        sys.addForce(cmap)
+        cmap_indices = {}
+
+        for name in [k for k in self._tables.keys() if k.startswith('cmap')]:
+            size2 = self._conn.execute('SELECT COUNT(*) FROM %s' % name).fetchone()[0]
+            fsize = math.sqrt(size2)
+            if fsize != int(fsize):
+                raise ValueError('Non-square CMAPs are not supported')
+            size = int(fsize)
+
+            map = [0 for i in range(size2)]
+            for phi, psi, energy in self._conn.execute("SELECT phi, psi, energy FROM %s" % name):
+                i = int((phi % 360) / (360.0 / size))
+                j = int((psi % 360) / (360.0 / size))
+                map[i+size*j] = energy
+            index = cmap.addMap(size, map*kilocalorie_per_mole)
+            cmap_indices[name] = index
+
+        q = '''SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
+        FROM torsiontorsion_cmap_term INNER JOIN torsiontorsion_cmap_param
+        ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id'''
+        for p0, p1, p2, p3, p4, p5, p6, p7, cmapid in self._conn.execute(q):
+            cmap.addTorsion(cmap_indices[cmapid], p0, p1, p2, p3, p4, p5, p6, p7)
+
+    def _addNonbondedForceToSystem(self, sys):
+        '''Create the nonbonded force
+        '''
+        nb = mm.NonbondedForce()
+        sys.addForce(nb)
+
+        q = '''SELECT charge, sigma, epsilon
+        FROM particle INNER JOIN nonbonded_param
+        ON particle.nbtype=nonbonded_param.id'''
+        for charge, sigma, epsilon in self._conn.execute(q):
+            nb.addParticle(charge, sigma*angstrom, epsilon*kilocalorie_per_mole)
+
+        for p0, p1 in self._conn.execute('SELECT p0, p1 FROM exclusion'):
+            nb.addException(p0, p1, 0.0, 1.0, 0.0)
+
+        q = '''SELECT p0, p1, aij, bij, qij
+        FROM pair_12_6_es_term INNER JOIN pair_12_6_es_param
+        ON pair_12_6_es_term.param=pair_12_6_es_param.id;'''
+        for p0, p1, a_ij, b_ij, q_ij in self._conn.execute(q):
+            a_ij = (a_ij*kilocalorie_per_mole*(angstrom**12)).in_units_of(kilojoule_per_mole*(nanometer**12))
+            b_ij = (b_ij*kilocalorie_per_mole*(angstrom**6)).in_units_of(kilojoule_per_mole*(nanometer**6))
+            q_ij = q_ij*elementary_charge**2
+
+            if (b_ij._value == 0.0) or (a_ij._value == 0.0):
+                new_epsilon = 0
+                new_sigma = 1
+            else:
+                new_epsilon =  b_ij**2/(4*a_ij)
+                new_sigma = (a_ij / b_ij)**(1.0/6.0)
+            nb.addException(p0, p1, q_ij, new_sigma, new_epsilon, True)
+
+        n_total = self._conn.execute('''SELECT COUNT(*) FROM pair_12_6_es_term''').fetchone()
+        n_in_exclusions = self._conn.execute('''SELECT COUNT(*)
+        FROM exclusion INNER JOIN pair_12_6_es_term
+        ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1''').fetchone()
+        if not n_total == n_in_exclusions:
+            raise NotImplementedError('All pair_12_6_es_terms must have a corresponding exclusion')
+
+        return nb
+
+    def _addVirtualSitesToSystem(self, sys):
+        '''Create any virtual sites in the systempy
+        '''
+        if not any(t.startswith('virtual_') for t in self._tables.keys()):
+            return
+
+        if 'virtual_lc2_term' in self._tables:
+            q = '''SELECT p0, p1, p2, c1
+            FROM virtual_lc2_term INNER JOIN virtual_lc2_param
+            ON virtual_lc2_term.param=virtual_lc2_param.id'''
+            for p0, p1, p2, c1 in self._conn.execute(q):
+                vsite = mm.TwoParticleAverageSite(p1, p2, (1-c1), c1)
+                sys.setVirtualSite(p0, vsite)
+
+        if 'virtual_lc3_term' in self._tables:
+            q = '''SELECT p0, p1, p2, p3, c1, c2
+            FROM virtual_lc3_term INNER JOIN virtual_lc3_param
+            ON virtual_lc3_term.param=virtual_lc3_param.id'''
+            for p0, p1, p2, p3, c1, c2 in self._conn.execute(q):
+                vsite = mm.ThreeParticleAverageSite(p1, p2, p3, (1-c1-c2), c1, c2)
+                sys.setVirtualSite(p0, vsite)
+
+        if 'virtual_out3_term' in self._tables:
+            q = '''SELECT p0, p1, p2, p3, c1, c2, c3
+            FROM virtual_out3_term INNER JOIN virtual_out3_param
+            ON virtual_out3_term.param=virtual_out3_param.id'''
+            for p0, p1, p2, p3, c1, c2, c3 in self._conn.execute(q):
+                vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
+                sys.setVirtualSite(p0, vsite)
+
+        if 'virtual_fdat3_term' in self._tables:
+            raise NotImplementedError('OpenMM does not currently support '
+                                      'fdat3-style virtual sites')
+
+
+    def _hasTable(self, table_name):
+        '''Does our DMS file contain this table?
+        '''
+        return table_name in self._tables
+
+    def _readSchemas(self):
+        '''Read the schemas of each of the tables in the dms file, populating
+        the `_tables` instance attribute
+        '''
+        tables = {}
+        for table in self._conn.execute("SELECT name FROM sqlite_master WHERE type='table'"):
+            names = []
+            for e in self._conn.execute('PRAGMA table_info(%s)' % table):
+                names.append(str(e[1]))
+            tables[str(table[0])] = names
+        self._tables = tables
+
+    def _checkForUnsupportedTerms(self):
+        '''Check the file for forcefield terms that are not currenty supported,
+        raising a NotImplementedError
+        '''
+        if 'posre_harm_term' in self._tables:
+            raise NotImplementedError('Position restraints are not implemented.')
+        flat_bottom_potential_terms = ['stretch_fbhw_term', 'angle_fbhw_term',
+                                       'improper_fbhw_term', 'posre_fbhw_term']
+        if any((t in self._tables) for t in flat_bottom_potential_terms):
+            raise NotImplementedError('Flat bottom potential terms '
+                                      'are not implemeneted')
+
+        nbinfo = dict(zip(self._tables['nonbonded_info'],
+                          self._conn.execute('SELECT * FROM nonbonded_info').fetchone()))
+
+        if nbinfo['vdw_funct'] != u'vdw_12_6':
+            raise NotImplementedError('Only Leonard-Jones van der Waals '
+                                      'interactions are currently supported')
+        if nbinfo['vdw_rule'] != u'arithmetic/geometric':
+            raise NotImplementedError('Only Lorentz-Berthelot nonbonded '
+                                      'combining rules are currently supported')
+
+        if 'nonbonded_combined_param' in self._tables:
+            raise NotImplementedError('nonbonded_combined_param interactions '
+                                      'are not currently supported')
+
+        if 'alchemical_particle' in self._tables:
+            raise NotImplementedError('Alchemical particles are not supported')
+        if 'alchemical_stretch_harm' in self._tables:
+            raise NotImplementedError('Alchemical bonds are not supported')
+
+        if 'polar_term' in self._tables:
+            if self._conn.execute("SELECT COUNT(*) FROM polar_term").fetchone()[0] != 0:
+                raise NotImplementedError('Drude particles are not currently supported')
+
+    def close(self):
+        '''Close the SQL connection
+        '''
+        if self._open:
+            self._conn.close()
+
+    def __del__(self):
+        self.close()

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

@@ -44,6 +44,7 @@ class Element:
     look up the Element with a particular chemical symbol."""
 
     _elements_by_symbol = {}
+    _elements_by_atomic_number = {}
 
     def __init__(self, number, name, symbol, mass):
         ## The atomic number of the element
@@ -58,6 +59,16 @@ class Element:
         s = symbol.strip().upper()
         assert s not in Element._elements_by_symbol
         Element._elements_by_symbol[s] = self
+        if number in Element._elements_by_atomic_number:
+            other_element = Element._elements_by_atomic_number[number]
+            if mass < other_element.mass:
+                # If two "elements" share the same atomic number, they're
+                # probably hydrogen and deuterium, and we want to choose
+                # the lighter one to put in the table by atomic_number,
+                # since it's the "canonical" element.
+                Element._elements_by_atomic_number[number] = self
+        else:
+            Element._elements_by_atomic_number[number] = self
 
     @staticmethod
     def getBySymbol(symbol):
@@ -65,6 +76,10 @@ class Element:
         s = symbol.strip().upper()
         return Element._elements_by_symbol[s]
 
+    @staticmethod
+    def getByAtomicNumber(atomic_number):
+        return Element._elements_by_atomic_number[atomic_number]
+
 # This is for backward compatibility.
 def get_by_symbol(symbol):
     s = symbol.strip().upper()
@@ -188,3 +203,8 @@ ununtrium =      Element(113, "ununtrium",      "Uut", 284*daltons)
 ununquadium =    Element(114, "ununquadium",    "Uuq", 289*daltons)
 ununpentium =    Element(115, "ununpentium",    "Uup", 288*daltons)
 ununhexium =     Element(116, "ununhexium",     "Uuh", 292*daltons)
+
+# Aliases to recognize common alternative spellings. Both the '==' and 'is'
+# relational operators will work with any chosen name
+sulphur = sulfur
+aluminium = aluminum

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

@@ -272,7 +272,7 @@ class ForceField(object):
             self.atoms = [x-self.index for x in self.atoms]
 
     def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
-                     constraints=None, rigidWater=True, removeCMMotion=True, **args):
+                     constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, **args):
         """Construct an OpenMM System representing a Topology with this force field.
 
         Parameters:
@@ -284,6 +284,8 @@ class ForceField(object):
            Allowed values are None, HBonds, AllBonds, or HAngles.
          - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
          - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
+         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
+           subtracted from the heavy atom to keep their total mass the same.
          - args Arbitrary additional keyword arguments may also be specified.  This allows extra parameters to be specified that are specific to
            particular force fields.
         Returns: the newly created System
@@ -335,6 +337,17 @@ class ForceField(object):
         sys = mm.System()
         for atom in topology.atoms():
             sys.addParticle(self._atomTypes[data.atomType[atom]][1])
+        
+        # Adjust masses.
+        
+        if hydrogenMass is not None:
+            for atom1, atom2 in topology.bonds():
+                if atom1.element == elem.hydrogen:
+                    (atom1, atom2) = (atom2, atom1)
+                if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None):
+                    transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
+                    sys.setParticleMass(atom2.index, hydrogenMass)
+                    sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
 
         # Set periodic boundary conditions.
 
@@ -516,6 +529,27 @@ def _matchResidue(res, template, bondedToAtom):
         bonds = [renumberAtoms[x] for x in bondedToAtom[atom.index] if x in renumberAtoms]
         bondedTo.append(bonds)
         externalBonds.append(len([x for x in bondedToAtom[atom.index] if x not in renumberAtoms]))
+
+    # For each unique combination of element and number of bonds, make sure the residue and
+    # template have the same number of atoms.
+
+    residueTypeCount = {}
+    for i, atom in enumerate(atoms):
+        key = (atom.element, len(bondedTo[i]), externalBonds[i])
+        if key not in residueTypeCount:
+            residueTypeCount[key] = 1
+        residueTypeCount[key] += 1
+    templateTypeCount = {}
+    for i, atom in enumerate(template.atoms):
+        key = (atom.element, len(atom.bondedTo), atom.externalBonds)
+        if key not in templateTypeCount:
+            templateTypeCount[key] = 1
+        templateTypeCount[key] += 1
+    if residueTypeCount != templateTypeCount:
+        return None
+
+    # Recursively match atoms.
+
     if _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch, 0):
         return matches
     return None
@@ -590,8 +624,8 @@ def _findMatchErrors(forcefield, res):
     # Return an appropriate error message.
     
     if numBestMatchAtoms == numResidueAtoms:
-        chainLength = len(list(res.chain.residues()))
-        if chainLength > 1 and (res.index == 0 or res.index == chainLength-1):
+        chainResidues = list(res.chain.residues())
+        if len(chainResidues) > 1 and (res == chainResidues[0] or res == chainResidues[-1]):
             return 'The set of atoms matches %s, but the bonds are different.  Perhaps the chain is missing a terminal group?' % bestMatchName
         return 'The set of atoms matches %s, but the bonds are different.' % bestMatchName
     if bestMatchName is not None:

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

@@ -40,6 +40,7 @@ import simtk.unit as unit
 import simtk.openmm as mm
 import math
 import os
+import distutils.spawn
 
 HBonds = ff.HBonds
 AllBonds = ff.AllBonds
@@ -90,6 +91,9 @@ class GromacsTopFile(object):
             # A preprocessor command.
             fields = stripped.split()
             command = fields[0]
+            if len(self._ifStack) != len(self._elseStack):
+                raise RuntimeError('#if/#else stack out of sync')
+
             if command == '#include' and not ignore:
                 # Locate the file to include
                 name = stripped[len(command):].strip(' \t"<>')
@@ -116,17 +120,29 @@ class GromacsTopFile(object):
                     raise ValueError('Illegal line in .top file: '+line)
                 name = fields[1]
                 self._ifStack.append(name in self._defines)
+                self._elseStack.append(False)
             elif command == '#ifndef':
                 # See whether this block should be ignored.
                 if len(fields) < 2:
                     raise ValueError('Illegal line in .top file: '+line)
                 name = fields[1]
                 self._ifStack.append(name not in self._defines)
+                self._elseStack.append(False)
             elif command == '#endif':
                 # Pop an entry off the if stack.
                 if len(self._ifStack) == 0:
                     raise ValueError('Unexpected line in .top file: '+line)
                 del(self._ifStack[-1])
+                del(self._elseStack[-1])
+            elif command == '#else':
+                # Reverse the last entry on the if stack
+                if len(self._ifStack) == 0:
+                    raise ValueError('Unexpected line in .top file: '+line)
+                if self._elseStack[-1]:
+                    raise ValueError('Unexpected line in .top file: '
+                                     '#else has already been used ' + line)
+                self._ifStack[-1] = (not self._ifStack[-1])
+                self._elseStack[-1] = True
 
         elif not ignore:
             # A line of data for the current category
@@ -342,23 +358,34 @@ class GromacsTopFile(object):
             raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
         self._cmapTypes[tuple(fields[:5])] = fields
 
-    def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}):
+    def __init__(self, file, unitCellDimensions=None, includeDir=None, defines=None):
         """Load a top file.
 
         Parameters:
          - file (string) the name of the file to load
          - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
-         - includeDir (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files
-           included from the top file
-         - defines (map={}) preprocessor definitions that should be predefined when parsing the file
+         - includeDir (string=None) A directory in which to look for other files
+           included from the top file. If not specified, we will attempt to locate a gromacs
+           installation on your system. When gromacs is installed in /usr/local, this will resolve
+           to  /usr/local/gromacs/share/gromacs/top
+         - defines (dict={}) preprocessor definitions that should be predefined when parsing the file
          """
+        if includeDir is None:
+            includeDir = _defaultGromacsIncludeDir()
         self._includeDirs = (os.path.dirname(file), includeDir)
-        self._defines = defines
+        # Most of the gromacs water itp files for different forcefields,
+        # unless the preprocessor #define FLEXIBLE is given, don't define
+        # bonds between the water hydrogen and oxygens, but only give the
+        # constraint distances and exclusions.
+        self._defines = {'FLEXIBLE': True}
+        if defines is not None:
+            self._defines.update(defines)
 
         # Parse the file.
 
         self._currentCategory = None
         self._ifStack = []
+        self._elseStack = []
         self._moleculeTypes = {}
         self._molecules = []
         self._currentMoleculeType = None
@@ -427,7 +454,7 @@ class GromacsTopFile(object):
                     top.addBond(atoms[int(fields[0])-1], atoms[int(fields[1])-1])
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
-                     constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, ewaldErrorTolerance=0.0005, removeCMMotion=True):
+                     constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None):
         """Construct an OpenMM System representing the topology described by this prmtop file.
 
         Parameters:
@@ -442,6 +469,8 @@ class GromacsTopFile(object):
          - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
          - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
          - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
+         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
+           subtracted from the heavy atom to keep their total mass the same.
         Returns: the newly created System
         """
         # Create the System.
@@ -733,9 +762,36 @@ class GromacsTopFile(object):
         nb.setNonbondedMethod(methodMap[nonbondedMethod])
         nb.setCutoffDistance(nonbondedCutoff)
         nb.setEwaldErrorTolerance(ewaldErrorTolerance)
+        
+        # Adjust masses.
+        
+        if hydrogenMass is not None:
+            for atom1, atom2 in self.topology.bonds():
+                if atom1.element == elem.hydrogen:
+                    (atom1, atom2) = (atom2, atom1)
+                if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None):
+                    transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
+                    sys.setParticleMass(atom2.index, hydrogenMass)
+                    sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
 
         # Add a CMMotionRemover.
 
         if removeCMMotion:
             sys.addForce(mm.CMMotionRemover())
         return sys
+
+def _defaultGromacsIncludeDir():
+    """Find the location where gromacs #include files are referenced from, by
+    searching for (1) gromacs environment variables, (2) for the gromacs binary
+    'pdb2gmx' in the PATH, or (3) just using the default gromacs install
+    location, /usr/local/gromacs/share/gromacs/top """
+    if 'GMXDATA' in os.environ:
+        return os.path.join(os.environ['GMXDATA'], 'top')
+    if 'GMXBIN' in os.environ:
+        return os.path.abspath(os.path.join(os.environ['GMXBIN'], '..', 'share', 'gromacs', 'top'))
+
+    pdb2gmx_path = distutils.spawn.find_executable('pdb2gmx')
+    if pdb2gmx_path is not None:
+        return os.path.abspath(os.path.join(os.path.dirname(pdb2gmx_path), '..', 'share', 'gromacs', 'top'))
+
+    return '/usr/local/gromacs/share/gromacs/top'