Merge pull request #765 from swails/stochastic-forces

Make it so that random forces and integrators generate unique seeds each time a Context is made

openmmapi/src/VariableLangevinIntegrator.cpp

@@ -33,7 +33,6 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
 #include <limits>
 #include <string>
@@ -48,7 +47,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
     setFriction(frictionCoeff);
     setErrorTolerance(errorTol);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed(osrngseed());
+    setRandomNumberSeed(0);
     setStepSize(0.0);
 }
 

platforms/cpu/src/CpuRandom.cpp

@@ -23,6 +23,7 @@
  */
 
 #include "CpuRandom.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/OpenMMException.h"
 #include <cmath>
 
@@ -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 unique seed
+     */
 
     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/CudaIntegrationUtilities.cpp

@@ -27,6 +27,7 @@
 #include "CudaIntegrationUtilities.h"
 #include "CudaArray.h"
 #include "CudaKernelSources.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/VirtualSite.h"
 #include "quern.h"
@@ -858,6 +859,7 @@ void CudaIntegrationUtilities::initRandomNumberGenerator(unsigned int randomNumb
 
     vector<int4> seed(randomSeed->getSize());
     unsigned int r = randomNumberSeed;
+    if (r == 0) r = (unsigned int) osrngseed();
     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/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 use a unique one
+        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/OpenCLIntegrationUtilities.cpp

@@ -27,6 +27,7 @@
 #include "OpenCLIntegrationUtilities.h"
 #include "OpenCLArray.h"
 #include "OpenCLKernelSources.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/VirtualSite.h"
 #include "quern.h"
@@ -1003,6 +1004,8 @@ void OpenCLIntegrationUtilities::initRandomNumberGenerator(unsigned int randomNu
 
     vector<mm_int4> seed(randomSeed->getSize());
     unsigned int r = randomNumberSeed;
+    // A seed of 0 means use a unique one
+    if (r == 0) r = (unsigned int) osrngseed();
     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 use a unique one
+        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/reference/src/SimTKUtilities/SimTKOpenMMUtilities.cpp

@@ -24,6 +24,7 @@
 
 // class of shared, static utility methods
 
+#include "openmm/internal/OSRngSeed.h"
 #include "SimTKOpenMMUtilities.h"
 #include "SimTKOpenMMLog.h"
 #include "sfmt/SFMT.h"
@@ -361,7 +362,11 @@ void SimTKOpenMMUtilities::setRandomNumberSeed( uint32_t seed ) {
 
    // ---------------------------------------------------------------------------------------
 
-   _randomNumberSeed = seed;
+    // If the seed is 0, use a unique seed
+    if (seed == 0)
+        _randomNumberSeed = (uint32_t) osrngseed();
+    else
+        _randomNumberSeed = seed;
    _randomInitialized = false;
 }
 

plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h

@@ -142,6 +142,10 @@ public:
      * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
      * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
      * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
      */
     void setRandomNumberSeed(int seed) {
         randomNumberSeed = seed;

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp

@@ -33,7 +33,6 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "openmm/internal/OSRngSeed.h"
 #include "openmm/DrudeKernels.h"
 #include <ctime>
 #include <string>
@@ -49,7 +48,7 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
     setDrudeFriction(drudeFrictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed(osrngseed());
+    setRandomNumberSeed(0);
 }
 
 void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {

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

@@ -155,6 +155,10 @@ public:
      * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
      * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
      * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
      */
     void setRandomNumberSeed(int seed) {
         randomNumberSeed = seed;

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -33,7 +33,6 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "openmm/internal/OSRngSeed.h"
 #include "openmm/RpmdKernels.h"
 #include "SimTKOpenMMRealType.h"
 #include <cmath>
@@ -48,7 +47,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed(osrngseed());
+    setRandomNumberSeed(0);
 }
 
 RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
@@ -57,7 +56,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed(osrngseed());
+    setRandomNumberSeed(0);
 }
 
 void RPMDIntegrator::initialize(ContextImpl& contextRef) {