Mods

platforms/brook/src/BrookBonded.cpp

@@ -35,9 +35,9 @@
 #include "BrookPlatform.h"
 #include "BrookStreamFactory.h"
 #include "OpenMMException.h"
-#include "gpu/kinvmap_gather.h"
-#include "gpu/invmap.h"
-#include "gpu/kforce.h"
+#include "kernels/kinvmap_gather.h"
+#include "kernels/invmap.h"
+#include "kernels/kforce.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp

@@ -36,8 +36,8 @@
 
 #include "BrookStreamImpl.h"
 #include "BrookCalcGBSAOBCForceKernel.h"
-#include "gpu/kgbsa.h"
-#include "gpu/kforce.h"
+#include "kernels/kgbsa.h"
+#include "kernels/kforce.h"
 #include "math.h"
 
 using namespace OpenMM;

platforms/brook/src/BrookGbsa.cpp

@@ -34,8 +34,8 @@
 #include "BrookPlatform.h"
 #include "OpenMMException.h"
 #include "BrookStreamImpl.h"
-#include "gpu/kgbsa.h"
-#include "gpu/kforce.h"
+#include "kernels/kgbsa.h"
+#include "kernels/kforce.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookLangevinDynamics.cpp

@@ -34,9 +34,9 @@
 #include "BrookPlatform.h"
 #include "OpenMMException.h"
 #include "BrookStreamImpl.h"
-#include "gpu/kshakeh.h"
-#include "gpu/kupdatesd.h"
-#include "gpu/kcommon.h"
+#include "kernels/kshakeh.h"
+#include "kernels/kupdatesd.h"
+#include "kernels/kcommon.h"
 
 // use random number generator
 
@@ -1480,7 +1480,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
 
    // diagnostics
 
-   if( (_internalStepCount % 10) == 0 ){
+   if( (_internalStepCount % 1000) == 0 ){
       FILE*	log1     = stderr;
       float  epsilon = 1.0e-01f;
 

platforms/brook/src/BrookNonBonded.cpp

@@ -34,8 +34,8 @@
 #include "BrookPlatform.h"
 #include "BrookStreamFactory.h"
 #include "OpenMMException.h"
-#include "gpu/invmap.h"
-#include "gpu/kforce.h"
+//#include "kernels/invmap.h"
+#include "kernels/kforce.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookPlatform.cpp

@@ -41,9 +41,20 @@
 #include <sstream>
 #include <cctype>
 #include <algorithm>
+//#include "/cygdrive/c/Program\ Files/Amd/AMD\ CAL\ 1.2.1_beta/include/cal.h"
 
 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
  *

platforms/brook/src/BrookRandomNumberGenerator.cpp

@@ -33,7 +33,7 @@
 #include "BrookRandomNumberGenerator.h"
 #include "../../reference/src/SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "OpenMMException.h"
-#include "gpu/kupdatesd.h"
+#include "kernels/kupdatesd.h"
 
 using namespace OpenMM;
 using namespace std;
@@ -729,12 +729,12 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
    // ---------------------------------------------------------------------------------------
 
    static const std::string methodName = "BrookRandomNumberGenerator::advanceGVCursor";
-   int printOn                         = 1;
+   int printOn                         = 0;
    FILE* log;
 
    // ---------------------------------------------------------------------------------------
 	
-setLog( stderr );
+//setLog( stderr );
    if( printOn && getLog() ){
       log = getLog();
    } else {

platforms/brook/src/BrookStreamFactory.cpp

@@ -70,7 +70,7 @@ BrookStreamFactory::BrookStreamFactory( void ){
  * 
  */
 
-BrookStreamFactory::~BrookStreamFactory( void ){
+BrookStreamFactory::~BrookStreamFactory( ){
 }
 
 /** 
@@ -291,10 +291,9 @@ StreamImpl* BrookStreamFactory::createStreamImpl( std::string name, int size, St
 
 // ---------------------------------------------------------------------------------------
 
-
    // stream width hould be based on name & value set in platform; for now only particle stream types
 
-   int streamWidth = getDefaultParticleStreamWidth();
+   int streamWidth                             = getDefaultParticleStreamWidth();
 
    BrookStreamImpl* brookStreamImpl            = new BrookStreamImpl( name, size, streamWidth, type, platform );
 

platforms/brook/src/BrookStreamInternal.cpp

@@ -41,8 +41,6 @@
 
 #endif
 
-
-
 using namespace OpenMM;
 using namespace std;
 
@@ -564,7 +562,7 @@ int BrookStreamInternal::printStreamsToFile( std::string fileName, std::vector<B
    delete[] arrays;
    delete[] widths;
    delete[] indices;
-   for( int ii = 0; ii < 4; ii++ ){
+   for( int ii = 0; ii <  streams.size(); ii++ ){
       delete[] sums[ii];
    }
    delete[] sums;

platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp

@@ -34,7 +34,7 @@
 #include "BrookPlatform.h"
 #include "OpenMMException.h"
 #include "BrookStreamImpl.h"
-#include "gpu/kcom.h"
+#include "kernels/kcom.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/brook/src/BrookVerletDynamics.cpp

@@ -34,9 +34,9 @@
 #include "BrookPlatform.h"
 #include "OpenMMException.h"
 #include "BrookStreamImpl.h"
-#include "gpu/kshakeh.h"
-#include "gpu/kupdatemd.h"
-#include "gpu/kcommon.h"
+#include "kernels/kshakeh.h"
+#include "kernels/kupdatemd.h"
+#include "kernels/kcommon.h"
 
 using namespace OpenMM;
 using namespace std;
@@ -448,6 +448,7 @@ std::string BrookVerletDynamics::getContentsString( int level ) const {
 
    return message.str();
 }
+
 /** 
  * Update
  * 
@@ -467,22 +468,25 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
 // ---------------------------------------------------------------------------------------
 
    static std::string methodName  = "\nBrookVerletDynamics::update";
-   static int printOn             = 0;
+   static int printOn             = 1;
    FILE* log;
 
 // ---------------------------------------------------------------------------------------
 
    _internalStepCount++;
 
-setLog( stderr );
-   printOn = (printOn && getLog()) ? printOn : 0; 
+//setLog( stderr );
+   if( printOn && getLog() ){
+       log    = getLog();; 
+   } else {
+      printOn = 0;
+   }
 
    BrookStreamImpl& forceStream = const_cast<BrookStreamImpl&> (forceStreamC);
 
-   if( 1 || printOn ){
+   if( printOn ){
 
       static int showAux = 1;
-      log                = getLog();
       if( showAux ){
          showAux = 0; 
 
@@ -680,7 +684,7 @@ setLog( stderr );
 
    // diagnostics
 
-   if( (_internalStepCount % 10000) == 0 ){
+   if( (_internalStepCount % 100) == 0 ){
       FILE*	log1     = stderr;
       float  epsilon = 1.0e-01f;
 
@@ -698,9 +702,12 @@ setLog( stderr );
       // Shake violations
 
       std::string violationString;
-      int constraintViolations                     = brookShakeAlgorithm.checkConstraints( brookStreamInternalPos, violationString, 0.0001f );
-
-      abort                                       += abs( constraintViolations );
+      if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
+         int constraintViolations                     = brookShakeAlgorithm.checkConstraints( brookStreamInternalPos, violationString, 0.0001f );
+         abort                                       += abs( constraintViolations );
+      } else {
+         violationString                              = "Shake not active";
+      }
 
       // force sums ~ 0?
       std::vector<float> sums;

platforms/brook/src/OpenMMBrookInterface.cpp

@@ -40,7 +40,7 @@
 
 #include "BrookStreamImpl.h"
 #include "OpenMMBrookInterface.h"
-#include "gpu/kcommon.h"
+#include "kernels/kcommon.h"
 
 using namespace OpenMM;
 using namespace std;
@@ -539,15 +539,20 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
 // ---------------------------------------------------------------------------------------
 
 //setLog( stderr );
-   printOn = (printOn && getLog()) ? printOn : 0;
+
+   if( printOn && getLog() ){
+      log     = getLog();
+   } else {
+      printOn = 0;
+   }
 
    BrookStreamImpl* positions = getParticlePositions();
    BrookStreamImpl* forces    = getParticleForces();
 
    // info
 
-   //if( printOn > 1 ){
-   if( 1 ){
+   if( printOn > 1 ){
+   //if( 1 ){
       printForcesToFile( context );
    }
 
@@ -562,7 +567,6 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
    // bonded forces
 
    if( printOn ){
-      log = getLog();
       (void) fprintf( log, "%s done nonbonded: bonded=%d completed=%d\n", methodName.c_str(),
                       _brookBonded.isActive(), _brookBonded.isSetupCompleted() ); 
       (void) fflush( log );
@@ -636,7 +640,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
 
    // first step only?
 
-   if( step > 0 ){
+   if( step > 1 ){
       return;
    }
 
@@ -695,14 +699,12 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
    if( _brookGbsa.isActive() ){
 
       forces->fillWithValue( &zero );
-
       _brookGbsa.computeForces( *positions, *forces );
 
       std::string fileName = fileNameBase + "Obc.txt";
       BrookStreamInternal::printStreamsToFile( fileName, streams );
 
    }
-   forces->fillWithValue( &zero );
 
 // ---------------------------------------------------------------------------------------
 
@@ -710,6 +712,8 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
 
    if( 1 ){
 
+      forces->fillWithValue( &zero );
+
       if( _brookNonBonded.isActive() ){
          _brookNonBonded.computeForces( *positions, *forces );
       }
@@ -726,8 +730,6 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
       BrookStreamInternal::printStreamsToFile( fileName, streams );
    }
 
-(void) fprintf( stderr, "%s done computeForces\n", methodName.c_str() );
-(void) fflush( stderr );
    forces->fillWithValue( &zero );
 
    // ---------------------------------------------------------------------------------------