Mods

platforms/brook/src/BrookBondParameters.cpp

@@ -48,6 +48,7 @@ using namespace std;
 
 BrookBondParameters::BrookBondParameters( std::string bondName, int numberOfParticlesInBond,
                                           int numberOfParametersInBond, int numberOfBonds, FILE* log = NULL ) :
+
  _bondName( bondName ), _numberOfParticlesInBond( numberOfParticlesInBond ),
  _numberOfParametersInBond( numberOfParametersInBond ), _numberOfBonds( numberOfBonds ), _log( log ){
 
@@ -212,21 +213,13 @@ int BrookBondParameters::setBond( int bondIndex, int* particleIndices, double* b
    // load'em up
 
    int numberOfParticlesInBond = getNumberOfParticlesInBond();
-   std::vector<int> indices;
-   _particleIndices[bondIndex] = indices; 
-   indices.resize( numberOfParticlesInBond );
-
    for( int ii = 0; ii < numberOfParticlesInBond; ii++ ){
-      indices[ii] = particleIndices[ii];
+      _particleIndices[bondIndex].push_back( particleIndices[ii] );
    }
 
    int numberOfParametersInBond = getNumberOfParametersInBond();
-
-   std::vector<double> parameters;
-   _bondParameters[bondIndex] = parameters; 
-   parameters.resize( numberOfParametersInBond );
    for( int ii = 0; ii < numberOfParametersInBond; ii++ ){
-      parameters[ii] = bondParameters[ii];
+      _bondParameters[bondIndex].push_back( bondParameters[ii] );
    }
 
    // ---------------------------------------------------------------------------------------
@@ -317,16 +310,19 @@ std::string BrookBondParameters::getContentsString( int level ) const {
    (void) LOCAL_SPRINTF( value, "%d", getNumberOfParametersInBond() );
    message << _getLine( tab, "Parameters/bond:", value ); 
 
+//(void) fprintf( getLog(), "%s %s QQQ1\n", methodName.c_str(), message.str().c_str() ); (void) fflush( getLog() );
+
    message << "Bonds:"  << std::endl; 
    for( int ii = 0; ii < getNumberOfBonds(); ii++ ){
-      const static size_t descriptionSz = 256;
-      char description[256];
-      char buffer[256];
+      const static size_t descriptionSz = 1024;
+      char description[1024];
+      char buffer[1024];
       (void) LOCAL_SPRINTF( description, "%6d [", ii );
 
+#ifdef WIN32
+
       // particle indices
 
-#ifdef WIN32
       for( int jj = 0; jj < getNumberOfParticlesInBond(); jj++ ){
          (void) LOCAL_SPRINTF( buffer, "%6d ", _particleIndices[ii][jj] );
          (void) strcat_s( description, descriptionSz, buffer );
@@ -339,8 +335,12 @@ std::string BrookBondParameters::getContentsString( int level ) const {
          (void) LOCAL_SPRINTF( buffer, "%18.10e ", _bondParameters[ii][jj] );
          (void) strcat_s( description, descriptionSz, buffer );
       }
+
       (void) strcat_s( description, descriptionSz, "]" );
 #else
+
+      // particle indices
+
       for( int jj = 0; jj < getNumberOfParticlesInBond(); jj++ ){
          (void) LOCAL_SPRINTF( buffer, "%6d ", _particleIndices[ii][jj] );
          (void) strcat( description, buffer );

platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp

@@ -131,6 +131,8 @@ void BrookCalcHarmonicBondForceKernel::initialize( const System& system, const H
 
    // ---------------------------------------------------------------------------------------
 
+//(void) fprintf( getLog(), "%s\n", methodName.c_str() ); (void) fflush( getLog() );
+
    // create _brookBondParameters object containing particle indices/parameters
 
    int numberOfBonds         = force.getNumBonds();
@@ -182,7 +184,7 @@ void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context
 
 // ---------------------------------------------------------------------------------------
 
-   //static const std::string methodName   = "BrookCalcHarmonicBondForceKernel::executeForces";
+   static const std::string methodName   = "BrookCalcHarmonicBondForceKernel::executeForces";
 
 // ---------------------------------------------------------------------------------------
 

platforms/brook/src/BrookCalcNonbondedForceKernel.cpp

@@ -251,7 +251,7 @@ void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& syst
 
       _brookBondParameters->setBond( ii, particles, parameters );
    }   
-   _openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters );
+   _openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters, 1.0, 1.0 );
 
    if( log ){
       std::string contents = _brookBondParameters->getContentsString( ); 

platforms/brook/src/BrookPlatform.cpp

@@ -345,6 +345,16 @@ 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
  *
@@ -393,7 +403,7 @@ int BrookPlatform::getStreamSize( int size, int streamWidth, int* outputHeight )
 
 // ---------------------------------------------------------------------------------------
 
-   if( streamWidth < 1 || size < 1){
+   if( streamWidth < 1 || size < 1 ){
       return -1;
    }
 
@@ -446,7 +456,7 @@ void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const {
 
 // ---------------------------------------------------------------------------------------
 
-   context.setPlatformData( new OpenMMBrookInterface() );
+   context.setPlatformData( new OpenMMBrookInterface( getParticleStreamWidth() ) );
 }
 
 /** 

platforms/brook/src/OpenMMBrookInterface.cpp

@@ -46,7 +46,7 @@ using namespace std;
  * 
  */
 
-OpenMMBrookInterface::OpenMMBrookInterface( void ){
+OpenMMBrookInterface::OpenMMBrookInterface( int streamWidth ) : _particleStreamWidth(streamWidth){
 
 // ---------------------------------------------------------------------------------------
 
@@ -54,7 +54,7 @@ OpenMMBrookInterface::OpenMMBrookInterface( void ){
 
 // ---------------------------------------------------------------------------------------
 
-   _numberOfParticles                           = 0;
+   _numberOfParticles                       = 0;
 
    _brookBonded                             = NULL;
    _brookNonBonded                          = NULL;
@@ -76,6 +76,14 @@ OpenMMBrookInterface::OpenMMBrookInterface( void ){
    _referencePlatform                       = NULL;
    _refVerletIntegrator                     = NULL;
 
+   _lj14Scale                               = 1.0;
+   _coulomb14Scale                          = 1.0;
+
+   _particleStreamSize                      = -1;
+
+   for( int ii = 0; ii < LastBondForce; ii++ ){
+      _bondParameters[ii] = NULL;
+   }
 }   
 
 /** 
@@ -93,6 +101,10 @@ OpenMMBrookInterface::~OpenMMBrookInterface( ){
 
    delete _brookBonded;
    delete _brookNonBonded;
+   delete _brookGbsa;
+   for( int ii = 0; ii < LastBondForce; ii++ ){
+      delete _bondParameters[ii];
+   }
 
    // deleted w/ kernel delete? If activated, program crashes
 
@@ -105,6 +117,65 @@ OpenMMBrookInterface::~OpenMMBrookInterface( ){
 */
 }
 
+/** 
+ * Get number of particles
+ * 
+ * @return   number of particles
+ *
+ */
+
+int OpenMMBrookInterface::getNumberOfParticles( void ) const {
+   return _numberOfParticles;
+}
+
+/** 
+ * Get particle stream width
+ * 
+ * @return    particle stream width
+ *
+ */
+
+int OpenMMBrookInterface::getParticleStreamWidth( void ) const {
+   return _particleStreamWidth;
+}
+
+/** 
+ * Get particle stream size
+ * 
+ * @return    particle stream size
+ *
+ */
+
+int OpenMMBrookInterface::getParticleStreamSize( void ) const {
+   if( _particleStreamSize < 0 && _numberOfParticles > 0 ){
+       OpenMMBrookInterface* localThis = const_cast<OpenMMBrookInterface* const>(this);
+      localThis->_particleStreamSize = BrookPlatform::getStreamSize( _numberOfParticles, _particleStreamWidth, NULL );
+   }
+   return _particleStreamSize;
+}
+
+/** 
+ * Get LJ-14 scale factor
+ * 
+ * @return    LJ-14 scale factor
+ *
+ */
+
+double OpenMMBrookInterface::getLj14Scale( void ) const {
+   return _lj14Scale;
+}
+
+/** 
+ * Get Coulomb scale factor
+ * 
+ * @return    Coulomb scale factor
+ *
+ */
+
+double OpenMMBrookInterface::getCoulomb14Scale( void ) const {
+   return _coulomb14Scale;
+}
+
 /** 
  * Get log file reference
  * 
@@ -130,6 +201,19 @@ int OpenMMBrookInterface::setLog( FILE* log ){
    return BrookCommon::DefaultReturnValue;
 }
 
+/** 
+ * Get BrookBondParameters at specified index
+ * 
+ * @param   index
+ *
+ * @return  BrookBondParameters* object
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::_getBondParameters( BondParameterIndices index ) const {
+   return _bondParameters[index];
+}
+
 /** 
  * Set BrookBondParameters at specified index
  * 
@@ -145,6 +229,17 @@ int OpenMMBrookInterface::_setBondParameters( BondParameterIndices index, BrookB
    return BrookCommon::DefaultReturnValue;
 }
 
+/** 
+ * Get BrookBondParameters for harmonic bond force
+ * 
+ * @return brookBondParameters for harmonic bond force
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::getHarmonicBondForceParameters( void ) const {
+   return _getBondParameters( HarmonicBondIndex );
+}
+
 /** 
  * Set BrookBondParameters for harmonic bond force
  * 
@@ -155,7 +250,18 @@ int OpenMMBrookInterface::_setBondParameters( BondParameterIndices index, BrookB
  */
 
 int OpenMMBrookInterface::setHarmonicBondForceParameters( BrookBondParameters* brookBondParameters ){
-   return _setBondParameters( HarmonicAngleIndex, brookBondParameters );
+   return _setBondParameters( HarmonicBondIndex, brookBondParameters );
+}
+
+/** 
+ * Get BrookBondParameters for harmonic angle force
+ * 
+ * @return brookBondParameters for harmonic angle force
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::getHarmonicAngleForceParameters( void ) const {
+   return _getBondParameters( HarmonicAngleIndex );
 }
 
 /** 
@@ -172,9 +278,20 @@ int OpenMMBrookInterface::setHarmonicAngleForceParameters( BrookBondParameters*
 }
 
 /** 
- * Set BrookBondParameters for proper dihedral force
+ * Get BrookBondParameters for periodic torsion force
+ * 
+ * @return brookBondParameters for periodic torsion force
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::getPeriodicTorsionForceParameters( void ) const {
+   return _getBondParameters( PeriodicTorsionForceIndex );
+}
+
+/** 
+ * Set BrookBondParameters for periodic torsion force
  * 
- * @param brookBondParameters brookBondParameters for proper dihedral force
+ * @param brookBondParameters brookBondParameters for periodic torsion force
  *
  * @return  DefaultReturnValue
  *
@@ -185,9 +302,20 @@ int OpenMMBrookInterface::setPeriodicTorsionForceParameters( BrookBondParameters
 }
 
 /** 
- * Set BrookBondParameters for RB dihedral force
+ * Get BrookBondParameters for rb torsion force
+ * 
+ * @return brookBondParameters for rb torsion force
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::getRBTorsionForceParameters( void ) const {
+   return _getBondParameters( RbTorsionForceIndex );
+}
+
+/** 
+ * Set BrookBondParameters for RB torsion force
  * 
- * @param brookBondParameters brookBondParameters for RB force
+ * @param brookBondParameters brookBondParameters for RB torsion force
  *
  * @return  DefaultReturnValue
  *
@@ -197,16 +325,32 @@ int OpenMMBrookInterface::setRBTorsionForceParameters( BrookBondParameters* broo
    return _setBondParameters( RbTorsionForceIndex, brookBondParameters );
 }
 
+/** 
+ * Get BrookBondParameters for LJ 14 force
+ * 
+ * @return brookBondParameters for LJ 14 force
+ *
+ */
+
+BrookBondParameters* OpenMMBrookInterface::getNonBonded14ForceParameters( void ) const {
+   return _getBondParameters( LJ14Index );
+}
+
 /** 
  * Set BrookBondParameters for LJ 14 force
  * 
  * @param brookBondParameters brookBondParameters for LJ 14 force
+ * @param lj14Scale           LJ 14 scale factor
+ * @param coulomb14Scale        Coulomb 14 scale factor
  *
  * @return  DefaultReturnValue
  *
  */
 
-int OpenMMBrookInterface::setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters ){
+int OpenMMBrookInterface::setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters, 
+                                                         double lj14Scale, double coulomb14Scale ){
+   _lj14Scale        = lj14Scale;
+   _coulomb14Scale   = coulomb14Scale;
    return _setBondParameters( LJ14Index, brookBondParameters );
 }
 
@@ -373,6 +517,8 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
 
    // static const int debug                   = 1;
 
+(void) fprintf( stderr, "%s ", methodName.c_str() ); (void) fflush( stderr );
+
 // ---------------------------------------------------------------------------------------
 
    // nonbonded forces
@@ -390,6 +536,16 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
 
    if( _brookBonded ){
 
+(void) fprintf( stderr, "%s Bonded", methodName.c_str() ); (void) fflush( stderr );
+      // perform setup first time through
+
+      if( _brookBonded->isSetupCompleted() == 0 ){
+         _brookBonded->setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
+                              getPeriodicTorsionForceParameters(), getRBTorsionForceParameters(),
+                              getNonBonded14ForceParameters(),
+                              getLj14Scale(), getCoulomb14Scale(), getParticleStreamWidth(), getParticleStreamSize() );
+      }
+
       _brookBonded->computeForces( *positions, *forces );
    
       // diagnostics

platforms/brook/src/OpenMMBrookInterface.h

@@ -53,7 +53,7 @@ class OpenMMBrookInterface {
 
    public:
   
-      OpenMMBrookInterface( void );
+      OpenMMBrookInterface( int streamWidth );
   
       ~OpenMMBrookInterface();
   
@@ -90,6 +90,51 @@ class OpenMMBrookInterface {
       
       std::string getContents( int level ) const;
 
+      /** 
+       * Get number of particles
+       * 
+       * @return   number of particles
+       *
+       */
+      
+      int getNumberOfParticles( void ) const;
+      
+      /** 
+       * Get particle stream width
+       * 
+       * @return    particle stream width
+       *
+       */
+      
+      int getParticleStreamWidth( void ) const;
+      
+      /** 
+       * Get particle stream size
+       * 
+       * @return    particle stream size
+       *
+       */
+      
+      int getParticleStreamSize( void ) const;
+      
+      /** 
+       * Get LJ-14 scale factor
+       * 
+       * @return    LJ-14 scale factor
+       *
+       */
+      
+      double getLj14Scale( void ) const;
+      
+      /** 
+       * Get Coulomb scale factor
+       * 
+       * @return    Coulomb scale factor
+       *
+       */
+      
+      double getCoulomb14Scale( void ) const;
+
       /** 
        * Get log file reference
        * 
@@ -169,7 +214,7 @@ class OpenMMBrookInterface {
        *
        */
       
-      BrookBondParameters* getHarmonicBondForceParameters( void );
+      BrookBondParameters* getHarmonicBondForceParameters( void ) const;
       
       /** 
        * Set BrookBondParameters for harmonic bond force
@@ -189,7 +234,7 @@ class OpenMMBrookInterface {
        *
        */
       
-      BrookBondParameters* getHarmonicAngleForceParameters( void );
+      BrookBondParameters* getHarmonicAngleForceParameters( void ) const;
       
       /** 
        * Set BrookBondParameters for harmonic angle force
@@ -209,7 +254,7 @@ class OpenMMBrookInterface {
        *
        */
       
-      BrookBondParameters* getPeriodicTorsionForceParameters( void );
+      BrookBondParameters* getPeriodicTorsionForceParameters( void ) const;
 
       /** 
        * Set BrookBondParameters for periodic torsion force
@@ -229,7 +274,7 @@ class OpenMMBrookInterface {
        *
        */
       
-      BrookBondParameters* getRBTorsionForceParameters( void );
+      BrookBondParameters* getRBTorsionForceParameters( void ) const;
 
       /** 
        * Set BrookBondParameters for RB torsion force
@@ -249,18 +294,20 @@ class OpenMMBrookInterface {
        *
        */
       
-      BrookBondParameters* getNonBonded14ForceParameters( void );
+      BrookBondParameters* getNonBonded14ForceParameters( void ) const;
 
       /** 
        * Set BrookBondParameters for LJ 14 force
        * 
        * @param brookBondParameters brookBondParameters for LJ 14 force
+       * @param lj14Scale           LJ 14 scale factor
+       * @param coulomb14Scale        Coulomb 14 scale factor
        *
        * @return  DefaultReturnValue
        *
        */
       
-      int setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters );
+      int setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters, double lj14Scale, double coulomb14Scale );
       
       /** 
        * Get positions stream
@@ -333,10 +380,16 @@ class OpenMMBrookInterface {
 
       FILE* _log;
 
+      int _particleStreamWidth;
+      int _particleStreamSize;
+
        // number of particles
 
        int _numberOfParticles;
    
+       double _lj14Scale;
+       double _coulomb14Scale;
+
        // Brook bonded, nonbonded, Gbsa
 
        BrookBonded* _brookBonded;
@@ -374,6 +427,17 @@ class OpenMMBrookInterface {
       
       int _setBondParameters( BondParameterIndices index, BrookBondParameters* brookBondParameters );
       
+      /** 
+       * Get BrookBondParameters at specified index
+       * 
+       * @param   index
+       *
+       * @return  BrookBondParameters* object
+       *
+       */
+      
+      BrookBondParameters* _getBondParameters( BondParameterIndices index ) const;
+      
 };
 
 } // namespace OpenMM