Adding BrookPlatform back in -- deleted wrong file earlier

Fixed getTime() calls in _openMMBrookInterface()
Based on Sherm's suggestions:
changed '#ifdef WIN32' to '#ifdef WIN32 _MSC_VER;
reordered include files so that system files after OpenMM files
all include files should be C++ files now (as opposed to C files (<math.h> -> <cmath>

platforms/brook/src/BrookBondParameters.cpp

@@ -246,7 +246,7 @@ std::string BrookBondParameters::_getLine( const std::string& tab,
 
    std::stringstream message;
    memset( line, ' ', MAX_LINE_CHARS );  
-#ifdef WIN32
+#ifdef _MSC_VER
    (void) sprintf_s( line, MAX_LINE_CHARS, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
 #else
    (void) sprintf( line, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
@@ -282,7 +282,7 @@ std::string BrookBondParameters::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #define LOCAL_2_SPRINTF(a,b,c,d) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d) );   
 #else
@@ -309,7 +309,7 @@ std::string BrookBondParameters::getContentsString( int level ) const {
       char buffer[1024];
       (void) LOCAL_SPRINTF( description, "%6d [", ii );
 
-#ifdef WIN32
+#ifdef _MSC_VER
 
       // particle indices
 

platforms/brook/src/BrookBonded.cpp

@@ -25,8 +25,6 @@
  * -------------------------------------------------------------------------- */
 
 
-#include <math.h>
-#include <sstream>
 #include "BrookBonded.h"
 #include "BrookPlatform.h"
 #include "BrookStreamFactory.h"
@@ -35,6 +33,9 @@
 #include "kernels/invmap.h"
 #include "kernels/kforce.h"
 
+#include <cmath>
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 
@@ -1471,7 +1472,7 @@ std::string BrookBonded::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #define LOCAL_2_SPRINTF(a,b,c,d) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d) );   
 #else

platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp

@@ -24,16 +24,16 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <limits>
 #include "openmm/OpenMMException.h"
-#include <sstream>
 
 #include "BrookStreamImpl.h"
 #include "BrookCalcGBSAOBCForceKernel.h"
 #include "kernels/kgbsa.h"
 #include "kernels/kforce.h"
-#include "math.h"
+
+#include <cmath>
+#include <limits>
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcHarmonicAngleForceKernel.cpp

@@ -25,8 +25,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/OpenMMException.h"
-#include <sstream>
 #include "BrookCalcHarmonicAngleForceKernel.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp

@@ -25,8 +25,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/OpenMMException.h"
-#include <sstream>
 #include "BrookCalcHarmonicBondForceKernel.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcKineticEnergyKernel.cpp

@@ -24,10 +24,10 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <sstream>
 #include "openmm/OpenMMException.h"
 #include "BrookCalcKineticEnergyKernel.h"
 #include "BrookStreamImpl.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcNonbondedForceKernel.cpp

@@ -24,15 +24,15 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <limits>
 #include "openmm/OpenMMException.h"
-#include <sstream>
-
 #include "BrookStreamImpl.h"
 #include "BrookCalcNonbondedForceKernel.h"
 #include "openmm/NonbondedForce.h"
 
+#include <cmath>
+#include <limits>
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 

platforms/brook/src/BrookCalcPeriodicTorsionForceKernel.cpp

@@ -25,8 +25,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/OpenMMException.h"
-#include <sstream>
 #include "BrookCalcPeriodicTorsionForceKernel.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcRBTorsionForceKernel.cpp

@@ -25,8 +25,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/OpenMMException.h"
-#include <sstream>
 #include "BrookCalcRBTorsionForceKernel.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCommon.cpp

@@ -24,16 +24,15 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdlib.h>
-
-#include <sstream>
 
 #include "BrookCommon.h"
 #include "BrookPlatform.h"
 #include "BrookStreamFactory.h"
 #include "openmm/OpenMMException.h"
 
+#include <cmath>
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 
@@ -391,7 +390,7 @@ std::string BrookCommon::_getLine( const std::string& tab, const std::string& de
 
    std::stringstream message;
    memset( line, ' ', MAX_LINE_CHARS ); 
-#ifdef WIN32
+#ifdef _MSC_VER
    (void) sprintf_s( line, MAX_LINE_CHARS, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
 #else
    (void) sprintf( line, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );

platforms/brook/src/BrookFloatStreamInternal.cpp

@@ -25,10 +25,10 @@
  * -------------------------------------------------------------------------- */
 
 
-#include <sstream>
 #include "BrookFloatStreamInternal.h"
 #include "BrookPlatform.h"
 #include "openmm/OpenMMException.h"
+#include <sstream>
 
 using namespace OpenMM;
 
@@ -495,7 +495,7 @@ const std::string BrookFloatStreamInternal::getContentsString( int level ) const
    std::stringstream message;
    std::string tab   = "   ";
  
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   
@@ -546,7 +546,7 @@ int BrookFloatStreamInternal::_bodyPrintToFile( FILE* log, int maxPrint ){
 
    void* dataArrayV = getData( 1 );
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   

platforms/brook/src/BrookGbsa.cpp

@@ -24,7 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <sstream>
 #include "BrookGbsa.h"
 #include "BrookPlatform.h"
 #include "openmm/OpenMMException.h"
@@ -32,6 +31,8 @@
 #include "kernels/kgbsa.h"
 #include "kernels/kforce.h"
 
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 
@@ -837,7 +838,7 @@ std::string BrookGbsa::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   

platforms/brook/src/BrookInitializeForcesKernel.cpp

@@ -24,14 +24,14 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
+#include "BrookStreamImpl.h"
+#include "BrookInitializeForcesKernel.h"
+#include "openmm/OpenMMException.h"
+
 #include <cmath>
 #include <limits>
-#include "openmm/OpenMMException.h"
 #include <sstream>
 
-#include "BrookStreamImpl.h"
-#include "BrookInitializeForcesKernel.h"
-
 using namespace OpenMM;
 using namespace std;
 

platforms/brook/src/BrookIntStreamInternal.cpp

@@ -309,7 +309,7 @@ const std::string BrookIntStreamInternal::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   

platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp

@@ -250,5 +250,5 @@ void BrookIntegrateLangevinStepKernel::execute( OpenMMContextImpl& context, cons
 
    _brookLangevinDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()), 
                                    *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm, *_brookRandomNumberGenerator );
-   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime(integrator.getStepSize()));
+   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime());
 }

platforms/brook/src/BrookIntegrateVerletStepKernel.cpp

@@ -202,5 +202,5 @@ void BrookIntegrateVerletStepKernel::execute( OpenMMContextImpl& context, const
 
    _brookVerletDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()),
                                  *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm );
-   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime(stepSize));
+   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime());
 }

platforms/brook/src/BrookLangevinDynamics.cpp

@@ -24,7 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <sstream>
 #include "BrookLangevinDynamics.h"
 #include "BrookPlatform.h"
 #include "openmm/OpenMMException.h"
@@ -33,6 +32,8 @@
 #include "kernels/kupdatesd.h"
 #include "kernels/kcommon.h"
 
+#include <sstream>
+
 // use random number generator
 
 #include "../../reference/src/SimTKUtilities/SimTKOpenMMUtilities.h"
@@ -996,7 +997,7 @@ std::string BrookLangevinDynamics::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   

platforms/brook/src/BrookNonBonded.cpp

@@ -24,7 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <sstream>
 #include "BrookNonBonded.h"
 #include "BrookPlatform.h"
 #include "BrookStreamFactory.h"
@@ -32,6 +31,8 @@
 //#include "kernels/invmap.h"
 #include "kernels/kforce.h"
 
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 
@@ -1181,7 +1182,7 @@ std::string BrookNonBonded::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   

platforms/brook/src/BrookPlatform.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Authors: Mark Friedrichs, Mike Houston                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+#include "BrookPlatform.h"
+#include "BrookKernelFactory.h"
+#include "OpenMMBrookInterface.h"
+#include "openmm/internal/OpenMMContextImpl.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/kernels.h"
+#include "../../reference/src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include <brook/brook.hpp>
+#include <stdlib.h>
+#include <sstream>
+#include <cctype>
+#include <algorithm>
+
+using namespace OpenMM;
+
+extern "C" void initOpenMMPlugin() {
+/*
+   CALuint numberOfDevices = 0;
+   // validateCALRuntime()
+   if( calDeviceGetCount( &numberOfDevices ) == CAL_RESULT_OK && numberOfDevices > 0 ){
+      Platform::registerPlatform(new BrookPlatform());
+   }
+*/
+}
+
+/** 
+ * BrookPlatformData constructor
+ *
+ */
+
+BrookPlatformData::BrookPlatformData( void ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatformData::BrookPlatformData";
+
+// ---------------------------------------------------------------------------------------
+
+      //_forceKernel                 = NULL;
+
+      _removeCOM                   = 0;
+      _useOBC                      = 0;
+      _hasBonds                    = 0;
+      _hasAngles                   = 0;
+      _hasPeriodicTorsions         = 0;
+      _hasRB                       = 0;
+      _hasNonbonded                = 0;
+      _cmMotionFrequency           = 0;
+
+}
+
+/** 
+ * Get _removeCOM flag
+ * 
+ * @return  _removeCOM
+ *
+ */
+
+int BrookPlatformData::removeCOM( void ) const {
+   return _removeCOM;
+}
+
+/** 
+ * Get _useOBC flag
+ * 
+ * @return  _useOBC
+ *
+ */
+
+int BrookPlatformData::useOBC( void ) const {
+   return _useOBC;
+}
+
+/** 
+ * Get _hasBonds flag
+ * 
+ * @return  _hasBonds 
+ *
+ */
+
+int BrookPlatformData::hasBonds( void ) const {
+   return _hasBonds;
+}
+
+/** 
+ * Get _hasAngles
+ * 
+ * @return  _hasAngles
+ *
+ */
+
+int BrookPlatformData::hasAngles( void ) const {
+   return _hasAngles;
+}
+
+/** 
+ * Get _hasPeriodicTorsions
+ * 
+ * @return  _hasPeriodicTorsions
+ *
+ */
+
+int BrookPlatformData::hasPeriodicTorsions( void ) const {
+   return _hasPeriodicTorsions;
+}
+
+/** 
+ * Get _hasRB
+ * 
+ * @return  _hasRB
+ *
+ */
+
+int BrookPlatformData::hasRB( void ) const {
+   return _hasRB;
+}
+
+/** 
+ * Get _hasNonbonded
+ * 
+ * @return  _hasNonbonded
+ *
+ */
+
+int BrookPlatformData::hasNonbonded( void ) const {
+   return _hasNonbonded;
+}
+
+/** 
+ * Get _cmMotionFrequency
+ * 
+ * @return  _cmMotionFrequency
+ *
+ */
+
+int BrookPlatformData::cmMotionFrequency( void ) const {
+   return _cmMotionFrequency;
+}
+
+/** 
+ * Register BrookPlatform
+ *
+ * @return BrookPlatform instance
+ *
+ */
+
+BrookPlatform* registerBrookPlatform( void ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::registerBrookPlatform";
+
+// ---------------------------------------------------------------------------------------
+
+   BrookPlatform* platform = new BrookPlatform();
+   Platform::registerPlatform(platform);
+
+   return platform;
+}
+
+BrookPlatform* staticPlatform = registerBrookPlatform( );
+
+/** 
+ * BrookPlatform constructor
+ *
+ */
+
+BrookPlatform::BrookPlatform( ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::BrookPlatform(0)";
+
+// ---------------------------------------------------------------------------------------
+
+   _particleStreamWidth  = DefaultParticleStreamWidth;
+   _minSuggestedThreads  = -1;
+   _log                  = NULL;
+
+   // get Brook runtime
+
+#ifdef WIN32
+   char* runtime;
+   size_t numberOfEnv;
+    _dupenv_s( &runtime, &numberOfEnv, "brt_runtime" );
+#else
+   char* runtime     = getenv( "brt_runtime" );
+#endif
+
+   // if environment variable 'brt_runtime' not set, default to 'cal' settinh
+
+   if( runtime == NULL ){
+      runtime = _strdup( "cal" );
+   }
+
+   _initializeKernelFactory( );
+   _setBrookRuntime( runtime );
+
+#ifdef WIN32
+   free( runtime );
+#endif
+}
+
+/** 
+ * BrookPlatform constructor
+ *
+ * @param defaultParticleStreamWidth  stream width
+ * @param runtime                     Brook runtime (cal/cpu)
+ * @param log                         log file reference
+ *
+ */
+
+BrookPlatform::BrookPlatform( int particleStreamWidth, const std::string& runtime, FILE* log ) : _particleStreamWidth( particleStreamWidth ), _log( log ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::BrookPlatform(2)";
+
+// ---------------------------------------------------------------------------------------
+
+   _initializeKernelFactory( );
+   _setBrookRuntime( runtime );
+
+}
+
+/** 
+ * BrookPlatform destructor
+ *
+ */
+
+BrookPlatform::~BrookPlatform( ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::BrookPlatform";
+
+// ---------------------------------------------------------------------------------------
+
+}
+
+/** 
+ * Initialize kernel factory
+ *
+ */
+
+void BrookPlatform::_initializeKernelFactory( void ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::_initializeKernelFactory";
+
+// ---------------------------------------------------------------------------------------
+
+   BrookKernelFactory* factory = new BrookKernelFactory();
+
+   registerKernelFactory( InitializeForcesKernel::Name(),         factory );
+   registerKernelFactory( CalcHarmonicBondForceKernel::Name(),    factory );
+   registerKernelFactory( CalcHarmonicAngleForceKernel::Name(),   factory );
+   registerKernelFactory( CalcPeriodicTorsionForceKernel::Name(), factory );
+   registerKernelFactory( CalcRBTorsionForceKernel::Name(),       factory );
+   registerKernelFactory( CalcNonbondedForceKernel::Name(),       factory );
+   registerKernelFactory( CalcGBSAOBCForceKernel::Name(),         factory );
+   registerKernelFactory( IntegrateVerletStepKernel::Name(),      factory );
+   registerKernelFactory( IntegrateLangevinStepKernel::Name(),    factory );
+   registerKernelFactory( UpdateTimeKernel::Name(),               factory );
+   // registerKernelFactory( IntegrateBrownianStepKernel::Name(),    factory );
+   //registerKernelFactory( ApplyAndersenThermostatKernel::Name(),  factory );
+   registerKernelFactory( CalcKineticEnergyKernel::Name(),        factory );
+   registerKernelFactory( RemoveCMMotionKernel::Name(),           factory );
+   
+}
+
+/** 
+ * Set & validate runtime
+ *
+ * @param runtime    Brook runtime (cal/cpu)
+ *
+ * @throws exception if runtime is invalid
+ */
+
+void BrookPlatform::_setBrookRuntime( const std::string& runtime ){
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookPlatform::_setBrookRuntime";
+
+// ---------------------------------------------------------------------------------------
+
+   // set & validate runtime
+
+   _runtime = runtime;
+
+   // lower case
+
+   std::transform( _runtime.begin(), _runtime.end(), _runtime.begin(), tolower );
+   if(  _runtime != "cal" && _runtime != "cpu" ){
+      std::stringstream message;
+      message << methodName << " Brook runtime=" << _runtime << " not recognized.";
+      throw OpenMMException( message.str() );
+   }
+
+   if( 1 ){
+
+      //When compiling with cygwin/cl combo, doesn't
+      //always work from the environment, so I'm 
+      //hardcoding it here. An alternative might be to getenv() in
+      //the gromacs code and pass it here. The cygwin getenv() hopefully
+      //will work more deterministically.
+
+      char* info_string = NULL;
+      int minSuggestedThreads;
+
+      brook::initialize(  _runtime.c_str(), NULL, &info_string, &minSuggestedThreads );
+
+      FILE* log = getLog() ? getLog() : stderr;
+      (void) fprintf( log, "Using runtime %s; initializing Brook\n", _runtime.c_str() );
+      fprintf( log, "############\n\nBrook info_string:\n%s\n############\n", info_string );
+      (void) fflush( log );
+
+      if( minSuggestedThreads > 0 ){
+         _minSuggestedThreads = minSuggestedThreads;
+      }
+   
+   } else {
+
+      FILE* log = getLog() ? getLog() : stderr;
+      (void) fprintf( log, "%s Brook initializing to runtime=<%s>\n", methodName.c_str(), _runtime.c_str() ); 
+      (void) fflush( log );
+      brook::initialize( _runtime.c_str(), NULL );
+
+   }
+
+}
+
+/** 
+ * Return platform name
+ *
+ * @return "Brook"
+ */
+    
+std::string BrookPlatform::getName() const {
+  return "Brook";
+}   
+
+/** 
+ * Get DuplicationFactor 
+ *
+ * @param numberOfParticles number of particles
+ *
+ * @return DuplicationFactor
+ */
+    
+int BrookPlatform::getDuplicationFactor( int numberOfParticles ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookPlatform::getDuplicationFactor";
+
+// ---------------------------------------------------------------------------------------
+
+   // default value
+
+   int duplicationFactor = 4;
+   if( numberOfParticles < 65 ){
+      duplicationFactor = 1;
+      (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 );
+      float iUnroll   = 4.0f;
+      float factor    = (threads*iUnroll)/numP;
+      if( (factor*numP) < (threads*iUnroll) ){
+         factor += 1.0f;
+      }
+      if( factor <= 1.0f ){
+         duplicationFactor   = 1;
+      } else {
+         duplicationFactor   = static_cast<int>( ceil( factor*0.25f ) ); 
+         duplicationFactor  *= 4; 
+      }
+duplicationFactor = 4;
+      // (void) fprintf( stderr, "getDuplicationFactor %.1f numiP=%.1f factor=%.1f duplicationFactor=%d\n", threads, numP, factor, duplicationFactor );
+   }
+
+   return duplicationFactor;
+}   
+
+/** 
+ * Return platform speed
+ *
+ * @return speed
+ */
+    
+double BrookPlatform::getSpeed() const {
+  return 10.0;
+}   
+
+/** 
+ * Return particle stream width
+ *
+ * @return particle stream width
+ */
+    
+int BrookPlatform::getParticleStreamWidth() const {
+  return _particleStreamWidth;
+}   
+
+/** 
+ * Return true if BrookPlatform supports double precison
+ *
+ * @return true if BrookPlatform supports double precison
+ */
+
+bool BrookPlatform::supportsDoublePrecision( void ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::supportsDoublePrecision";
+
+// ---------------------------------------------------------------------------------------
+
+    return (sizeof(RealOpenMM) >= sizeof(double));
+}
+
+/** 
+ * Return Stream factory
+ *
+ */
+
+const StreamFactory& BrookPlatform::getDefaultStreamFactory( void ) const {
+    return _defaultStreamFactory;
+}
+
+/** 
+ *
+ * Static method
+ *
+ * Return stream size and height given size of array and stream width
+ *
+ * @param size           size of array
+ * @param streamWidth    stream width
+ * @param outputHeight   output stream height
+ *
+ * @return stream size; -1 if streamWidth < 1 || size < 1
+ *
+ */
+
+int BrookPlatform::getStreamSize( int size, int streamWidth, int* outputHeight ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::getStreamSize";
+
+// ---------------------------------------------------------------------------------------
+
+   if( streamWidth < 1 || size < 1 ){
+      return -1;
+   }
+
+   int height = size/streamWidth;
+   if( streamWidth*height < size ){
+      height++;
+   }
+   if( outputHeight ){
+      *outputHeight = height;
+   }
+   return height*streamWidth;
+}
+
+/** 
+ * Get log file reference
+ * 
+ * @return  log file reference
+ *
+ */
+
+FILE* BrookPlatform::getLog( void ) const {
+   return _log;
+}
+
+/** 
+ * Set log file reference
+ * 
+ * @param  log file reference
+ *
+ * @return  DefaultReturnValue
+ *
+ */
+
+int BrookPlatform::setLog( FILE* log ){
+   _log = log;
+   return BrookPlatform::DefaultErrorValue;
+}
+
+/** 
+ *
+ * This is called whenever a new OpenMMContext is created.  It gives the Platform a chance to initialize
+ * the context and store platform-specific data in it.
+ *
+ */
+void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::contextCreated";
+
+// ---------------------------------------------------------------------------------------
+
+   int particles = context.getSystem().getNumParticles();
+   OpenMMBrookInterface* openMMBrookInterface = new OpenMMBrookInterface( getParticleStreamWidth(), getDuplicationFactor( particles ) );
+   //openMMBrookInterface->setLog( stderr );
+ 
+   context.setPlatformData( openMMBrookInterface );
+}
+
+/** 
+ *
+ * This is called whenever an OpenMMContext is deleted.  It gives the Platform a chance to clean up
+ * any platform-specific data that was stored in it.
+ *
+ */
+
+void BrookPlatform::contextDestroyed( OpenMMContextImpl& context ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookPlatform::contextDestroyed";
+
+// ---------------------------------------------------------------------------------------
+
+}

platforms/brook/src/BrookRandomNumberGenerator.cpp

@@ -24,12 +24,13 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include <sstream>
 #include "BrookRandomNumberGenerator.h"
 #include "../../reference/src/SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "openmm/OpenMMException.h"
 #include "kernels/kupdatesd.h"
 
+#include <sstream>
+
 using namespace OpenMM;
 using namespace std;
 
@@ -1064,7 +1065,7 @@ std::string BrookRandomNumberGenerator::getContentsString( int level ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );   
@@ -1159,7 +1160,7 @@ std::string BrookRandomNumberGenerator::getStatisticsString( void ) const {
    std::stringstream message;
    std::string tab   = "   ";
 
-#ifdef WIN32
+#ifdef _MSC_VER
 #define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );   
 #else
 #define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );