Reactivated dupfac dynamic setting

Made setting of RNG seed consistent w/ logic used for Cuda 

platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp

@@ -31,6 +31,7 @@
 
 #include "BrookIntegrateLangevinStepKernel.h"
 #include "BrookStreamInternal.h"
+#include <ctime>
 
 using namespace OpenMM;
 using namespace std;
@@ -201,13 +202,20 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
 
    _brookRandomNumberGenerator   = new BrookRandomNumberGenerator( );
    _brookRandomNumberGenerator->setup( (int) masses.size(), getPlatform() );
-   unsigned long int seed        = static_cast<unsigned long int>( integrator.getRandomNumberSeed() );
+
+   unsigned long int seed;
+   if( integrator.getRandomNumberSeed() <= 1 ){
+      seed        = static_cast<unsigned long int>(time(NULL) & 0x000fffff);
+   } else {
+      seed        = static_cast<unsigned long int>( integrator.getRandomNumberSeed() );
+   }
    _brookRandomNumberGenerator->setRandomNumberSeed( seed );
 
    if( printOn ){
       (void) fprintf( log, "%s done setup:\nBrookShakeAlgorithm:\n%s\nBrookRandomNumberGenerator:\n%s\n\n", methodName.c_str(),
                       _brookShakeAlgorithm->getContentsString().c_str(), 
                       _brookRandomNumberGenerator->getContentsString().c_str() );
+      (void) fprintf( log, "LangevinIntegrator seed=%d\n", integrator.getRandomNumberSeed() );
       (void) fflush( log );
    }
 

platforms/brook/src/BrookLangevinDynamics.cpp

@@ -1098,7 +1098,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
 
       static int showAux = 1;
 
-      if( printOn ){
+      if( printOn && showAux ){
          (void) fprintf( log, "%s step=%d shake=%d\n", methodName.c_str(), _internalStepCount, brookShakeAlgorithm.getNumberOfConstraints() );
          (void) fflush( log );
       }
@@ -1119,6 +1119,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
          (void) fprintf( log, "%s step=%d Shake contents\n%s", methodName.c_str(), _internalStepCount, contents.c_str() );
          (void) fflush( log );
       }
+
    }
 
    // diagnostics
@@ -1178,7 +1179,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
  
    // diagnostics
 
-   if( printOn ){
+   if( 0 && printOn ){
       (void) fprintf( log, "\n%s step=%d Post kupdate_sd1_fix1: particleStrW=%3d rngStrW=%3d rngOff=%5d "
                                 "EM=%12.5e Sd1pc[]=[%12.5e %12.5e %12.5e]", methodName.c_str(), _internalStepCount,
                                 getLangevinDynamicsParticleStreamWidth(),
@@ -1264,7 +1265,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
                     brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream(),
                     getXPrimeStream()->getBrookStream() );
 
-      if( printOn ){
+      if( 0 && printOn ){
 
          (void) fprintf( log, "\n%s Post kshakeh_update1: sw=%d ShkCnstStrW=%3d tol=%.3f maxIt=%d",
                          methodName.c_str(), getLangevinDynamicsParticleStreamWidth(),
@@ -1328,7 +1329,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
 
    // diagnostics
 
-   if( printOn ){
+   if( 0 && printOn ){
       (void) fprintf( log, "\n%s step=%d Post kupdate_sd2_fix1: particleStrW=%3d rngStrW=%3d rngOff=%5d "
                                 "Sd2pc[]=[%12.5e %12.5e]", methodName.c_str(), _internalStepCount,
                                 getLangevinDynamicsParticleStreamWidth(),
@@ -1408,7 +1409,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
    
       // diagnostics
    
-      if( printOn ){
+      if( 0 && printOn ){
          (void) fprintf( log, "\n%s step=%d Post kshakeh_update2_fix1: ShakeConstraintStreamWidth=%3d rngStrW=%3d rngOff=%5d "
                               "Sd2pc[]=[%12.5e %12.5e]\n", methodName.c_str(), _internalStepCount,
                               brookShakeAlgorithm.getShakeConstraintStreamWidth(),
@@ -1453,7 +1454,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
 
       // no constraints
 
-      if( printOn ){
+      if( 0 && printOn ){
          (void) fprintf( log, "\n%s Pre ksetStr3 (no constraints)", methodName.c_str() );
          BrookStreamInternal* brookStreamInternalPos  = positionStream.getBrookStreamInternal();
          (void) fprintf( log, "\nPositionStream\n" );

platforms/brook/src/BrookPlatform.cpp

@@ -394,12 +394,12 @@ int BrookPlatform::getDuplicationFactor( int numberOfParticles ) const {
    int duplicationFactor = 4;
    if( numberOfParticles < 65 ){
       duplicationFactor = 1;
-      (void) fprintf( stderr, "%s forcing duplicationFactor=%d since number of particles=%d < 65\n",
+      (void) fprintf( stderr, "%s forcing optimization parameter 'duplicationFactor' to %d since number of particles=%d < 65\n",
                       methodName.c_str(), duplicationFactor, numberOfParticles );
    }
 
    // set only if _minSuggestedThreads is available from board
-/*
+
    if( _minSuggestedThreads > 0 ){
       float threads   = static_cast<float>( _minSuggestedThreads );
       float numP      = static_cast<float>( numberOfParticles );
@@ -414,8 +414,9 @@ int BrookPlatform::getDuplicationFactor( int numberOfParticles ) const {
          duplicationFactor   = static_cast<int>( ceil( factor*0.25f ) ); 
          duplicationFactor  *= 4; 
       }
+      // (void) fprintf( stderr, "getDuplicationFactor %.1f numiP=%.1f factor=%.1f duplicationFactor=%d\n", threads, numP, factor, duplicationFactor );
    }
-*/
+
    return duplicationFactor;
 }