Convert a random seed set to 0 into one based on the wall clock in more places.

This commit hits the CPU platform (I had previously thought it just used the
Reference generator) as well as the CustomIntegrator stream that is set
separately from the standard "integrator" stream attached to each platform for
CUDA and OpenCL platforms (it seemed to me that the Reference platform's
CustomIntegrator just used the integrator random stream).

platforms/cpu/src/CpuRandom.cpp

@@ -24,6 +24,7 @@
 
 #include "CpuRandom.h"
 #include "openmm/OpenMMException.h"
+#include "openmm/OSRngSeed.h"
 #include <cmath>
 
 using namespace std;
@@ -49,9 +50,13 @@ void CpuRandom::initialize(int seed, int numThreads) {
     nextGaussian.resize(numThreads);
     nextGaussianIsValid.resize(numThreads, false);
 
-    // Use a quick and dirty RNG to pick seeds for the real random number generator.
+    /* Use a quick and dirty RNG to pick seeds for the real random number generator.
+     * A random seed of 0 means pick a new random seed based on wall clock
+     */
 
     unsigned int r = (unsigned int) seed;
+    if (r == 0)
+        r = (unsigned int) osrngseed();
     for (int i = 0; i < numThreads; i++) {
         r = (1664525*r + 1013904223) & 0xFFFFFFFF;
         threadRandom[i] = new OpenMM_SFMT::SFMT();

platforms/cuda/src/CudaKernels.cpp

@@ -36,6 +36,7 @@
 #include "openmm/internal/CustomManyParticleForceImpl.h"
 #include "openmm/internal/CustomNonbondedForceImpl.h"
 #include "openmm/internal/NonbondedForceImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "CudaBondedUtilities.h"
 #include "CudaExpressionUtilities.h"
 #include "CudaIntegrationUtilities.h"
@@ -5967,7 +5968,11 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
         uniformRandoms = CudaArray::create<float4>(cu, maxUniformRandoms, "uniformRandoms");
         randomSeed = CudaArray::create<int4>(cu, cu.getNumThreadBlocks()*CudaContext::ThreadBlockSize, "randomSeed");
         vector<int4> seed(randomSeed->getSize());
-        unsigned int r = integrator.getRandomNumberSeed()+1;
+        int rseed = integrator.getRandomNumberSeed();
+        // A random seed of 0 means generate a new one from the wall clock
+        if (rseed == 0)
+            rseed = osrngseed();
+        unsigned int r = (unsigned int) (rseed+1);
         for (int i = 0; i < randomSeed->getSize(); i++) {
             seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
             seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;

platforms/opencl/src/OpenCLKernels.cpp

@@ -36,6 +36,7 @@
 #include "openmm/internal/CustomManyParticleForceImpl.h"
 #include "openmm/internal/CustomNonbondedForceImpl.h"
 #include "openmm/internal/NonbondedForceImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "OpenCLBondedUtilities.h"
 #include "OpenCLExpressionUtilities.h"
 #include "OpenCLIntegrationUtilities.h"
@@ -6200,7 +6201,11 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
         uniformRandoms = OpenCLArray::create<mm_float4>(cl, maxUniformRandoms, "uniformRandoms");
         randomSeed = OpenCLArray::create<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
         vector<mm_int4> seed(randomSeed->getSize());
-        unsigned int r = integrator.getRandomNumberSeed()+1;
+        int rseed = integrator.getRandomNumberSeed();
+        // A random seed of 0 means generate a new one from the wall clock
+        if (rseed == 0)
+            rseed = osrngseed();
+        unsigned int r = (unsigned int) (rseed+1);
         for (int i = 0; i < randomSeed->getSize(); i++) {
             seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
             seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;