Fixed compilation errors and warnings on Windows

openmmapi/include/openmm/System.h

@@ -124,7 +124,7 @@ public:
      * @param index  the index of the particle to check
      */
     bool isVirtualSite(int index) const {
-        return (index < virtualSites.size() && virtualSites[index] != NULL);
+        return (index < (int) virtualSites.size() && virtualSites[index] != NULL);
     }
     /**
      * Get VirtualSite object for a particle.  If the particle is not a virtual

openmmapi/include/openmm/internal/AssertionUtilities.h

@@ -57,6 +57,6 @@ void OPENMM_EXPORT throwException(const char* file, int line, const std::string&
 
 #define ASSERT_USUALLY_EQUAL_TOL(expected, found, tol) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found)<<" (This test is stochastic and may occasionally fail)"; throwException(__FILE__, __LINE__, details.str());}};
 
-#define ASSERT_VALID_INDEX(index, vector) {if (index < 0 || index >= vector.size()) throwException(__FILE__, __LINE__, "Index out of range");};
+#define ASSERT_VALID_INDEX(index, vector) {if (index < 0 || index >= (int) vector.size()) throwException(__FILE__, __LINE__, "Index out of range");};
 
 #endif /*OPENMM_ASSERTIONUTILITIES_H_*/

openmmapi/src/System.cpp

@@ -62,13 +62,13 @@ void System::setParticleMass(int index, double mass) {
 
 
 void System::setVirtualSite(int index, VirtualSite* virtualSite) {
-    if (index >= virtualSites.size())
+    if (index >= (int) virtualSites.size())
         virtualSites.resize(getNumParticles(), NULL);
     virtualSites[index] = virtualSite;
 }
 
 const VirtualSite& System::getVirtualSite(int index) const {
-    if (index >= virtualSites.size() || virtualSites[index] == NULL)
+    if (index >= (int) virtualSites.size() || virtualSites[index] == NULL)
         throw OpenMMException("This particle is not a virtual site");
     return *virtualSites[index];
 }

platforms/opencl/src/OpenCLArray.h

@@ -29,6 +29,7 @@
 
 #include "OpenCLContext.h"
 #include "openmm/OpenMMException.h"
+#include "openmm/internal/windowsExport.h"
 #include <iostream>
 #include <sstream>
 #include <vector>
@@ -40,7 +41,7 @@ namespace OpenMM {
  * and for copying data to and from the OpenCL Buffer.
  */
 
-class OpenCLArray {
+class OPENMM_EXPORT OpenCLArray {
 public:
     /**
      * Create an OpenCLArray object.  The object is allocated on the heap with the "new" operator.

platforms/opencl/src/OpenCLBondedUtilities.cpp

@@ -49,7 +49,7 @@ void OpenCLBondedUtilities::addInteraction(const vector<vector<int> >& atoms, co
         forceSource.push_back(source);
         forceGroup.push_back(group);
         int width = 1;
-        while (width < atoms[0].size())
+        while (width < (int) atoms[0].size())
             width *= 2;
         indexWidth.push_back(width);
     }
@@ -124,7 +124,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
     while (unmerged.size() > 0) {
         int sum = numBuffers[unmerged.back()];
         int i;
-        for (i = 0; i < unmerged.size()-1; i++) {
+        for (i = 0; i < (int) unmerged.size()-1; i++) {
             if (sum+numBuffers[unmerged[i]] > bufferLimit)
                 break;
             sum += numBuffers[unmerged[i]];
@@ -142,7 +142,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
     
     bufferIndices.resize(numForces);
     for (int i = 0; i < (int) forceSets.size(); i++)
-        for (int j = 0; j < forceSets[i].size(); j++) {
+        for (int j = 0; j < (int) forceSets[i].size(); j++) {
             int force = forceSets[i][j];
             int numBonds = forceAtoms[force].size();
             int numAtoms = forceAtoms[force][0].size();

platforms/opencl/src/OpenCLContext.cpp

@@ -73,7 +73,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
         contextIndex = platformData.contexts.size();
         std::vector<cl::Platform> platforms;
         cl::Platform::get(&platforms);
-        if (platformIndex < 0 || platformIndex >= platforms.size())
+        if (platformIndex < 0 || platformIndex >= (int) platforms.size())
             throw OpenMMException("Illegal value for OpenCL platform index");
         string platformVendor = platforms[platformIndex].getInfo<CL_PLATFORM_VENDOR>();
         vector<cl::Device> devices;

platforms/opencl/src/OpenCLKernels.cpp

@@ -277,7 +277,7 @@ void OpenCLUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream&
         contexts[i]->setPeriodicBoxSize(box.x, box.y, box.z);
     cl.getIntegrationUtilities().loadCheckpoint(stream);
     SimTKOpenMMUtilities::loadCheckpoint(stream);
-    for (int i = 0; i < cl.getReorderListeners().size(); i++)
+    for (int i = 0; i < (int) cl.getReorderListeners().size(); i++)
         cl.getReorderListeners()[i]->execute();
 }
 
@@ -4832,8 +4832,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
             cl.executeKernel(kernels[i][0], numAtoms);
         }
         else if (stepType[i] == CustomIntegrator::ComputeGlobal && !merged[i]) {
-            kernels[i][0].setArg<cl_float>(3, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
-            kernels[i][0].setArg<cl_float>(4, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+            kernels[i][0].setArg<cl_float>(3, (cl_float) SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
+            kernels[i][0].setArg<cl_float>(4, (cl_float) SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
             cl.executeKernel(kernels[i][0], 1, 1);
         }
         else if (stepType[i] == CustomIntegrator::ComputeSum) {

platforms/opencl/tests/TestOpenCLCustomBondForce.cpp

@@ -118,7 +118,7 @@ void testManyParameters() {
     forceField->addPerBondParameter("h");
     forceField->addPerBondParameter("i");
     vector<double> parameters(forceField->getNumPerBondParameters());
-    for (int i = 0; i < parameters.size(); i++)
+    for (int i = 0; i < (int) parameters.size(); i++)
         parameters[i] = i;
     forceField->addBond(0, 1, parameters);
     system.addForce(forceField);
@@ -179,4 +179,3 @@ int main() {
     return 0;
 }
 
-

platforms/opencl/tests/TestOpenCLFFT.cpp

@@ -60,7 +60,7 @@ void testTransform() {
     vector<mm_float2> original(xsize*ysize*zsize);
     vector<t_complex> reference(original.size());
     for (int i = 0; i < (int) original.size(); i++) {
-        mm_float2 value = mm_float2(genrand_real2(sfmt), genrand_real2(sfmt));
+        mm_float2 value = mm_float2((cl_float) genrand_real2(sfmt), (cl_float) genrand_real2(sfmt));
         original[i] = value;
         reference[i] = t_complex(value.x, value.y);
     }

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.cpp

@@ -308,7 +308,7 @@ RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergy( int numParticles,
  
         RealOpenMM sigmaI      = sigmas[ii];
         RealOpenMM epsilonI    = epsilons[ii];
-        for( std::set<int>::iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++ ){
+        for( std::set<int>::const_iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++ ){
             exclusions[*jj] = 1;
         }
 
@@ -341,7 +341,7 @@ RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergy( int numParticles,
             }
         }
 
-        for( std::set<int>::iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++ ){
+        for( std::set<int>::const_iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++ ){
             exclusions[*jj] = 0;
         }
     }

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp

@@ -544,7 +544,7 @@ void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, con
     // addParticle: ivIndex, radius, epsilon, reductionFactor
 
     int classIndex = 0;
-    for( unsigned int ii = 0; ii < numberOfParticles; ii += 3 ){
+    for( int ii = 0; ii < numberOfParticles; ii += 3 ){
 
        system.addParticle(   1.5995000e+01 );
        amoebaVdwForce->addParticle( ii, 1.7025000e-01,   4.6024000e-01,   0.0000000e+00 );
@@ -559,7 +559,7 @@ void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, con
     // exclusions
 
     std::vector< int > exclusions(3);
-    for( unsigned int ii = 0; ii < numberOfParticles; ii += 3 ){
+    for( int ii = 0; ii < numberOfParticles; ii += 3 ){
         exclusions[0] = ii;
         exclusions[1] = ii+1;
         exclusions[2] = ii+2;

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

@@ -138,15 +138,15 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
     const double dt = integrator.getStepSize();
     pileKernel.setArg<cl_uint>(5, integration.prepareRandomNumbers(numParticles*numCopies));
     pileKernel.setArg<cl::Buffer>(4, integration.getRandom().getDeviceBuffer()); // Do this *after* prepareRandomNumbers(), which might rebuild the array.
-    pileKernel.setArg<cl_float>(6, dt);
-    pileKernel.setArg<cl_float>(7, integrator.getTemperature()*BOLTZ);
-    pileKernel.setArg<cl_float>(8, integrator.getFriction());
+    pileKernel.setArg<cl_float>(6, (cl_float) dt);
+    pileKernel.setArg<cl_float>(7, (cl_float) (integrator.getTemperature()*BOLTZ));
+    pileKernel.setArg<cl_float>(8, (cl_float) integrator.getFriction());
     cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
 
     // Update positions and velocities.
     
-    stepKernel.setArg<cl_float>(7, dt);
-    stepKernel.setArg<cl_float>(8, integrator.getTemperature()*BOLTZ);
+    stepKernel.setArg<cl_float>(7, (cl_float) dt);
+    stepKernel.setArg<cl_float>(8, (cl_float) (integrator.getTemperature()*BOLTZ));
     cl.executeKernel(stepKernel, numParticles*numCopies, workgroupSize);
 
     // Calculate forces based on the updated positions.
@@ -154,7 +154,7 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
     computeForces(context);
     
     // Update velocities.
-    velocitiesKernel.setArg<cl_float>(2, dt);
+    velocitiesKernel.setArg<cl_float>(2, (cl_float) dt);
     cl.executeKernel(velocitiesKernel, numParticles*numCopies, workgroupSize);
 
     // Apply the PILE-L thermostat again.
@@ -193,7 +193,7 @@ void OpenCLIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& p
     vector<mm_float4> posq(cl.getPaddedNumAtoms());
     cl.getPosq().download(posq);
     for (int i = 0; i < numParticles; i++)
-        posq[i] = mm_float4(pos[i][0], pos[i][1], pos[i][2], posq[i].w);
+        posq[i] = mm_float4((cl_float) pos[i][0], (cl_float) pos[i][1], (cl_float) pos[i][2], posq[i].w);
     cl.getQueue().enqueueWriteBuffer(positions->getDeviceBuffer(), CL_TRUE, copy*cl.getPaddedNumAtoms()*sizeof(mm_float4), numParticles*sizeof(mm_float4), &posq[0]);
 }
 
@@ -205,7 +205,7 @@ void OpenCLIntegrateRPMDStepKernel::setVelocities(int copy, const vector<Vec3>&
     vector<mm_float4> velm(cl.getPaddedNumAtoms());
     cl.getVelm().download(velm);
     for (int i = 0; i < numParticles; i++)
-        velm[i] = mm_float4(vel[i][0], vel[i][1], vel[i][2], velm[i].w);
+        velm[i] = mm_float4((cl_float) vel[i][0], (cl_float) vel[i][1], (cl_float) vel[i][2], velm[i].w);
     cl.getQueue().enqueueWriteBuffer(velocities->getDeviceBuffer(), CL_TRUE, copy*cl.getPaddedNumAtoms()*sizeof(mm_float4), numParticles*sizeof(mm_float4), &velm[0]);
 }
 

serialization/tests/TestSerializeCustomAngleForce.cpp

@@ -81,7 +81,7 @@ void testSerialization() {
         ASSERT_EQUAL(b2, b2);
         ASSERT_EQUAL(c2, c2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
 }

serialization/tests/TestSerializeCustomBondForce.cpp

@@ -80,7 +80,7 @@ void testSerialization() {
         ASSERT_EQUAL(a1, a2);
         ASSERT_EQUAL(b2, b2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
 }

serialization/tests/TestSerializeCustomExternalForce.cpp

@@ -79,7 +79,7 @@ void testSerialization() {
         force2.getParticleParameters(i, particle2, params2);
         ASSERT_EQUAL(particle1, particle2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
 }

serialization/tests/TestSerializeCustomGBForce.cpp

@@ -109,7 +109,7 @@ void testSerialization() {
         force.getParticleParameters(i, params1);
         force2.getParticleParameters(i, params2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
     ASSERT_EQUAL(force.getNumExclusions(), force2.getNumExclusions());
@@ -131,7 +131,7 @@ void testSerialization() {
         ASSERT_EQUAL(min1, min2);
         ASSERT_EQUAL(max1, max2);
         ASSERT_EQUAL(val1.size(), val2.size());
-        for (int j = 0; j < val1.size(); j++)
+        for (int j = 0; j < (int) val1.size(); j++)
             ASSERT_EQUAL(val1[j], val2[j]);
     }
 }

serialization/tests/TestSerializeCustomHbondForce.cpp

@@ -101,7 +101,7 @@ void testSerialization() {
         ASSERT_EQUAL(b1, b2);
         ASSERT_EQUAL(c1, c2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
     ASSERT_EQUAL(force.getNumAcceptors(), force2.getNumAcceptors());
@@ -114,7 +114,7 @@ void testSerialization() {
         ASSERT_EQUAL(b1, b2);
         ASSERT_EQUAL(c1, c2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
     ASSERT_EQUAL(force.getNumExclusions(), force2.getNumExclusions());
@@ -136,7 +136,7 @@ void testSerialization() {
         ASSERT_EQUAL(min1, min2);
         ASSERT_EQUAL(max1, max2);
         ASSERT_EQUAL(val1.size(), val2.size());
-        for (int j = 0; j < val1.size(); j++)
+        for (int j = 0; j < (int) val1.size(); j++)
             ASSERT_EQUAL(val1[j], val2[j]);
     }
 }

serialization/tests/TestSerializeCustomNonbondedForce.cpp

@@ -87,7 +87,7 @@ void testSerialization() {
         force.getParticleParameters(i, params1);
         force2.getParticleParameters(i, params2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
     ASSERT_EQUAL(force.getNumExclusions(), force2.getNumExclusions());
@@ -109,7 +109,7 @@ void testSerialization() {
         ASSERT_EQUAL(min1, min2);
         ASSERT_EQUAL(max1, max2);
         ASSERT_EQUAL(val1.size(), val2.size());
-        for (int j = 0; j < val1.size(); j++)
+        for (int j = 0; j < (int) val1.size(); j++)
             ASSERT_EQUAL(val1[j], val2[j]);
     }
 }

serialization/tests/TestSerializeMonteCarloBarostat.cpp

@@ -41,7 +41,7 @@ using namespace std;
 void testSerialization() {
     // Create a Force.
 
-    MonteCarloBarostat force(25.5, 250.0, 0.2);
+    MonteCarloBarostat force(25.5, 250.0, 14);
     force.setRandomNumberSeed(3);
 
     // Serialize and then deserialize it.