Latest mods -- setup for nonbonded and bonded appears to work

platforms/brook/src/BrookFloatStreamImpl.cpp

@@ -29,221 +29,480 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include <sstream>
 #include "BrookFloatStreamImpl.h"
+#include "OpenMMException.h"
 
 using namespace OpenMM;
 
-BrookFloatStreamImpl::BrookFloatStreamImpl(std::string name, int size, Stream::DataType type, int streamWidth, const Platform& platform,
-                                           float inputDefaultDangleValue) : 
-                      StreamImpl(name, size, type, platform) {
-
-   switch (type) {
-
-   case Stream::Float:
-   case Stream::Float2:
-   case Stream::Float3:
-   case Stream::Float4:
-       baseType = Stream::Float;
-       break;
-
-   case Stream::Double:
-   case Stream::Double2:
-   case Stream::Double3:
-   case Stream::Double4:
-       baseType = Stream::Float;
-       break;
-   }
-   switch (type) {
-   case Stream::Float:
-   case Stream::Double:
-       width = 1;
-       break;
-   case Stream::Float2:
-   case Stream::Double2:
-       width = 2;
-       break;
-   case Stream::Float3:
-   case Stream::Double3:
-       width = 3;
-       break;
-   case Stream::Float4:
-   case Stream::Double4:
-       width = 4;
-       break;
+/** 
+ * BrookFloatStreamImpl constructor
+ * 
+ * @param name                      stream name
+ * @param size                      stream size
+ * @param type                      stream type (float, float2, ...)
+ * @param platform                  platform
+ * @param inputStreamWidth          stream width
+ * @param inputDefaultDangleValue   default dangle value
+ *
+ */
+
+BrookFloatStreamImpl::BrookFloatStreamImpl( std::string name, int size, Stream::DataType type,
+                                            const Platform& platform, int inputStreamWidth,
+                                            double inputDefaultDangleValue = 0.0 ) : StreamImpl( name, size, type, platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookFloatStreamImpl::BrookFloatStreamImpl";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   // set base type (currently only FLOAT supported)
+
+   switch( type ){
+
+      case Stream::Float:
+      case Stream::Float2:
+      case Stream::Float3:
+      case Stream::Float4:
+   
+          _baseType = Stream::Float;
+          break;
+   
+      case Stream::Double:
+      case Stream::Double2:
+      case Stream::Double3:
+      case Stream::Double4:
+
+          _baseType = Stream::Float;
+          break;
+
+      default:
+         std::stringstream message;
+         message << methodName << " stream=" << name << " input type=" << type << " not recognized.";
+         throw OpenMMException( message.str() );
+         break;
    }
 
-   defaultDangleValue = inputDefaultDangleValue;
+   // set _width (FLOAT, FLOAT2, ... )
 
-   // set stream height based on specified stream width
+   switch( type ){
 
-   streamWidth  = inputStreamWidth;
-   streamHeight = size/streamWidth + ((size % streamWidth) ? 1 : 0);
-   streamSize   = streamHeight*streamWidth;
+      case Stream::Float:
+      case Stream::Double:
 
-   // create Brook stream handle
+          _width = 1;
+          break;
+
+      case Stream::Float2:
+      case Stream::Double2:
+
+          _width = 2;
+          break;
+
+      case Stream::Float3:
+      case Stream::Double3:
 
-   switch( width ){
+          _width = 3;
+          break;
 
-   case 1:
-      aStream      = brook::stream::create<float>( streamHeight, streamWidth );
-      break;
+      case Stream::Float4:
+      case Stream::Double4:
 
-   case 2:
-      aStream      = brook::stream::create<float2>( streamHeight, streamWidth );
-      break;
+          _width = 4;
+          break;
+   }
+
+   _defaultDangleValue = (BrookOpenMMFloat) inputDefaultDangleValue;
+
+   // set stream height based on specified stream _width
+
+   if( inputStreamWidth < 1 ){
+      std::stringstream message;
+      message << methodName << " stream=" << name << " input stream width=" << type << " is less than 1.";
+      throw OpenMMException( message.str() );
+   }
+
+   _streamWidth    = inputStreamWidth;
+   _streamHeight   = size/_streamWidth + ((size % _streamWidth) ? 1 : 0);
+   int streamSize  = getStreamSize();
+
+   // create Brook stream handle
 
-   case 3:
-      aStream      = brook::stream::create<float3>( streamHeight, streamWidth );
-      break;
+   switch( _width ){
 
-   case 4:
-      aStream      = brook::stream::create<float4>( streamHeight, streamWidth );
-      break;
+      case 1:
+         _aStream      = brook::stream::create<float>(  _streamHeight, _streamWidth );
+         break;
+   
+      case 2:
+         _aStream      = brook::stream::create<float2>( _streamHeight, _streamWidth );
+         break;
+   
+      case 3:
+         _aStream      = brook::stream::create<float3>( _streamHeight, _streamWidth );
+         break;
+   
+      case 4:
+         _aStream      = brook::stream::create<float4>( _streamHeight, _streamWidth );
+         break;
    }
 
    // allocate memory for data buffer
 
-   data = new float*[streamSize];
-   for (int i = 0; i < streamSize; ++i){
-       data[i] = new float[width];
+   _data = new float*[streamSize];
+   for( int ii = 0; ii < streamSize; ii++ ){
+       _data[ii] = new float[_width];
    }
 
+   // check if we are using float or double
+
    if( sizeof( float ) != sizeof( RealOpenMM ) ){
    
-      realOpenMMData = new RealOpenMM*[streamSize];
-      for (int i = 0; i < streamSize; ++i){
-         realOpenMMData[i] = new RealOpenMM[width];
+      _realOpenMMData = new RealOpenMM*[streamSize];
+      for( int ii = 0; ii < streamSize; ii++ ){
+         _realOpenMMData[ii] = new RealOpenMM[_width];
+      }
+   } else {
+      _realOpenMMData = NULL;
+   }
+}
+
+/** 
+ * BrookFloatStreamImpl destructor
+ * 
+ */
+
+BrookFloatStreamImpl::~BrookFloatStreamImpl( ){
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "BrookFloatStreamImpl::~BrookFloatStreamImpl";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   //delete _aStream;
+
+   int streamSize = getStreamSize();
+
+   for( int ii = 0; ii < streamSize; ii++ ){
+      delete[] _data[ii];
+   }
+   delete[] _data;
+
+   if( _realOpenMMData ){
+      for( int ii = 0; ii < streamSize; ii++ ){
+         delete[] _realOpenMMData[ii];
       }
+      delete[] _realOpenMMData;
+   }
+
+}
+
+/** 
+ * Load _data from input array
+ * 
+ * @param  array a pointer to the start of the array.  The array is assumed to have the same length as this stream,
+ * and to contain elements of the correct _data type for this stream.  If the stream has a compound _data type, all
+ * the values should be packed into a single array: all the values for the first element, followed by all the values
+ * for the next element, etc.
+ *
+ */
+
+void BrookFloatStreamImpl::loadFromArray( const void* array ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookFloatStreamImpl::loadFromArray";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   if( _baseType == Stream::Float ){
+      loadFromArray( array, Stream::Float );
    } else {
-      realOpenMMData = NULL;
+      loadFromArray( array, Stream::Double );
    }
+
+}
+
+/** 
+ * Get width
+ * 
+ * @return width
+ */
+
+int BrookFloatStreamImpl::getWidth( void ) const {
+   return _width;
+}
+
+/** 
+ * Get stream width
+ * 
+ * @return stream width
+ */
+
+int BrookFloatStreamImpl::getStreamWidth( void ) const {
+   return _streamWidth;
 }
 
-BrookFloatStreamImpl::~BrookFloatStreamImpl() {
-   delete aStream;
-   delete data[];
-   delete realOpenMMData[];
+/** 
+ * Get stream height
+ * 
+ * @return stream height
+ */
+
+int BrookFloatStreamImpl::getStreamHeight( void ) const {
+   return _streamHeight;
+}
+
+/** 
+ * Get Brook stream
+ * 
+ * @return Brook stream 
+ */
+
+brook::stream& BrookFloatStreamImpl::getBrookStream( void ){
+   return _aStream;
+}
+
+/** 
+ * Get stream size
+ * 
+ * @return stream size
+ */
+
+int BrookFloatStreamImpl::getStreamSize( void ) const {
+   return _streamWidth*_streamHeight;
 }
 
-void BrookFloatStreamImpl::loadFromArray(const void* array) {
+/** 
+ * Load _data from input array
+ * 
+ * @param  array a pointer to the start of the array.  The array is assumed to have the same length as this stream,
+ * and to contain elements of the correct _data type for this stream.  If the stream has a compound _data type, all
+ * the values should be packed into a single array: all the values for the first element, followed by all the values
+ * for the next element, etc.
+ *
+ * @param inputType  type of input array (Stream::Float, Stream::Double, Stream::Integer)
+ *
+ * @throw if input type not recognized, an exception is thrown
+ */
 
-   if( baseType == Stream::Float ){
-      float* arrayData = (float*) array;
-      for (int i = 0; i < getSize(); ++i){
-         for (int j = 0; j < width; ++j){
-            data[i][j] = arrayData[i*width+j];
+void BrookFloatStreamImpl::loadFromArray( const void* array, Stream::DataType inputType ){
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookFloatStreamImpl::loadFromArray";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   int index = 0;
+   if( inputType == Stream::Float ){
+
+   float* arrayData = (float*) array;
+      for( int ii = 0; ii < getSize(); ii++ ){
+         for( int jj = 0; jj < getWidth(); jj++ ){
+            _data[ii][jj] = (BrookOpenMMFloat) arrayData[index++];
          }
       }
 
-   } else {
+   } else if( inputType == Stream::Double ){
 
       double* arrayData = (double*) array;
-      for (int i = 0; i < getSize(); ++i){
-         for (int j = 0; j < width; ++j){
-            data[i][j] = (float) arrayData[i*width+j];
+      for( int ii = 0; ii < getSize(); ii++ ){
+         for( int jj = 0; jj < getWidth(); jj++ ){
+            _data[ii][jj] = (BrookOpenMMFloat) arrayData[index++];
+         }
+      }
+
+   } else if( inputType == Stream::Integer ){
+
+      int* arrayData = (int*) array;
+ 
+      for( int ii = 0; ii < getSize(); ii++ ){
+         for( int jj = 0; jj < getWidth(); jj++ ){
+            _data[ii][jj] = (BrookOpenMMFloat) arrayData[index++];
          }
       }
+
+   } else {
+      
+      std::stringstream message;
+      message << methodName << " stream=" << getName() << " input type=" << inputType << " not recognized.";
+      throw OpenMMException( message.str() );
+
    }
 
    // set dangling values
 
    _loadDanglingValues();
 
-    // write to GPU
+   // write to GPU
 
-    aStream.read( data );
+   _aStream.read( _data );
 }
 
-void BrookFloatStreamImpl::saveToArray(void* array) {
+void BrookFloatStreamImpl::saveToArray( void* array ){
+
+// ---------------------------------------------------------------------------------------
 
-  // get data from GPU
+   //static const std::string methodName      = "BrookFloatStreamImpl::saveToArray";
+   // static const int debug                   = 1;
 
-  aStream.write( data );
+// ---------------------------------------------------------------------------------------
+
+  // get _data from GPU
+
+  _aStream.write( _data );
 
   // load into array
 
-  if( baseType == Stream::Float ){
+  int index = 0;
+  if( _baseType == Stream::Float ){
+
      float* arrayData = (float*) array;
-     for( int i = 0; i < getSize(); ++i ){
-        for( int j = 0; j < width; ++j ){
-           arrayData[i*width+j] = data[i][j];
+     for( int ii = 0; ii < getSize(); ii++ ){
+        for( int jj = 0; jj < getWidth(); jj++ ){
+           arrayData[index++] = (float) _data[ii][jj];
         }
      }
+
    } else {
+
       double* arrayData = (double*) array;
-      for( int i = 0; i < getSize(); ++i ){
-         for( int j = 0; j < width; ++j ){
-            arrayData[i*width+j] = data[i][j];
+      for( int ii = 0; ii < getSize(); ii++ ){
+         for( int jj = 0; jj < getWidth(); jj++ ){
+            arrayData[index++] = _data[ii][jj];
          }
       }
+
    }
 }
 
+/** 
+ * Fill stream w/ specified value
+ * 
+ * @param value                     value to fill stream w/
+ *
+ */
+
 void BrookFloatStreamImpl::fillWithValue( void* value ){
 
-   if (baseType == Stream::Float) {
-      float valueData = *((float*) value);
-      for( int i = 0; i < getSize(); i++ ){
-         for( int j = 0; j < width; j++ ){
-            data[i][j] = valueData;
-         }
-      }
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookFloatStreamImpl::fillWithValue";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   BrookOpenMMFloat valueData;
+   if( _baseType == Stream::Float) {
+      valueData = (BrookOpenMMFloat) *((float*) value);
    } else {
-      double valueData = *((double*) value);
-      for( int i = 0; i < getSize(); i++ ){
-         for (int j = 0; j < width; j++ ){
-            data[i][j] = valueData;
-         }
+      valueData = (BrookOpenMMFloat) *((double*) value);
+   }
+   for( int ii = 0; ii < getSize(); ii++ ){
+      for (int jj = 0; jj < getWidth(); jj++ ){
+         _data[ii][jj] = valueData;
       }
    }
+
    _loadDanglingValues();
-   aStream.read( data );
+   _aStream.read( _data );
 }
 
+const RealOpenMM* const * BrookFloatStreamImpl::getData() const {
+   return NULL;
+}
+
+// problem w/ const here -- _data is modified (cast away?)
+
+/*
 const RealOpenMM* const * BrookFloatStreamImpl::getData() const {
 
-   // retreive data from GPU
+   // retrieve _data from GPU
 
-   aStream.write( data );
+   _aStream.write( _data );
 
    // check if RealOpenMM is float; if not, then 
    // copy into realOpenMMData[][] array
 
    if( realOpenMMData ){
       for( int i = 0; i < getSize(); i++ ){
-         for( int j = 0; j < width; j++ ){
-            realOpenMMData[i][j] = (RealOpenMM) data[i][j];
+         for( int j = 0; j < _width; j++ ){
+            realOpenMMData[i][j] = (RealOpenMM) _data[i][j];
          }
       }
       return realOpenMMData;
    } else {
-      return data;
+      return _data;
    }
 }
+*/
 
-RealOpenMM** BrookFloatStreamImpl::getData() {
-   aStream.write( data );
-   if( realOpenMMData ){
-      for( int i = 0; i < getSize(); i++ ){
-         for( int j = 0; j < width; j++ ){
-            realOpenMMData[i][j] = (RealOpenMM) data[i][j];
+/** 
+ * Get data
+ * 
+ * @return data array
+ *
+ */
+
+RealOpenMM** BrookFloatStreamImpl::getData( void ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookFloatStreamImpl::getData";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   _aStream.write( _data );
+   if( _realOpenMMData ){
+   for( int ii = 0; ii < getSize(); ii++ ){
+      for (int jj = 0; jj < getWidth(); jj++ ){
+            _realOpenMMData[ii][jj] = (RealOpenMM) _data[ii][jj];
          }
       }
-      return realOpenMMData;
+      return _realOpenMMData;
    } else {
-      return data;
+      return _data;
    }
 }
 
+
+/** 
+ * Load dangling value into stream
+ * 
+ * @param danglingValue   dangling value to load
+ *
+ */
+
 void BrookFloatStreamImpl::_loadDanglingValues( float danglingValue ){
 
-   for( int ii =  getSize(); ii < streamSize; ii++ ){
-      for( int jj = 0; jj < width; jj++ ){
-          data[ii][jj] = danglingValue;
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookFloatStreamImpl::_loadDanglingValues";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   int streamSize = getStreamSize();
+   for( int ii = getSize(); ii < streamSize; ii++ ){
+      for (int jj = 0; jj < getWidth(); jj++ ){
+          _data[ii][jj] = danglingValue;
        }
     }
 }
 
+/** 
+ * Load default dangling value into stream
+ * 
+ */
+
 void BrookFloatStreamImpl::_loadDanglingValues( void ){
-   _loadDanglingValues( defaultDangleValue );
+   _loadDanglingValues( _defaultDangleValue );
 }

platforms/brook/src/BrookFloatStreamImpl.h

@@ -9,12 +9,12 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright ( c ) 2008 Stanford University and the Authors.           *
  * Authors: Peter Eastman, Mark Friedrichs                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
+ * copy of this software and associated documentation files ( the "Software" ), *
  * to deal in the Software without restriction, including without limitation  *
  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
  * and/or sell copies of the Software, and to permit persons to whom the      *
@@ -33,37 +33,58 @@
  * -------------------------------------------------------------------------- */
 
 #include "StreamImpl.h"
+#include "BrookPlatform.h"
 #include <brook/brook.hpp>
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 namespace OpenMM {
 
 /**
- * This is the implementation of Float and Double streams in the reference Platform.
+ * This is the implementation of Float and Double streams in the Brook Platform.
  */
 
 class BrookFloatStreamImpl : public StreamImpl {
-public:
-    BrookFloatStreamImpl(std::string name, int size, Stream::DataType type, int streamWidth, const Platform& platform, float defaultDangleValue );
-    ~BrookFloatStreamImpl();
-    void loadFromArray(const void* array);
-    void saveToArray(void* array);
-    void fillWithValue(void* value);
-    const RealOpenMM* const * getData() const;
-    RealOpenMM** getData();
-private:
-    int width;
-    int streamWidth;
-    int streamHeight;
-    int streamSize;
 
-    float defaultDangleValue;
-    Stream::DataType baseType;
-    brook::stream aStream;
-    float** data;
-    RealOpenMM** realOpenMMData;
+   public:
 
-    void _loadDanglingValues(void );
+      BrookFloatStreamImpl( std::string name, int size, Stream::DataType type, const Platform& platform, int inputStreamWidth, double defaultDangleValue );
+
+      ~BrookFloatStreamImpl(  );
+      void loadFromArray( const void* array );
+      void loadFromArray( const void* array, Stream::DataType type );
+      void saveToArray( void* array );
+      void fillWithValue( void* value );
+      const RealOpenMM* const * getData( ) const;
+      RealOpenMM** getData( void );
+
+      /** 
+       * Get width
+       * 
+       * @return width
+       */
+
+      int BrookFloatStreamImpl::getWidth( void ) const;
+    
+      int getStreamWidth( void ) const;
+      int getStreamHeight( void ) const;
+      int getStreamSize( void ) const;
+
+      brook::stream& getBrookStream( void );
+
+   private:
+
+      int _width;
+      int _streamWidth;
+      int _streamHeight;
+  
+      float _defaultDangleValue;
+      Stream::DataType _baseType;
+      brook::stream _aStream;
+      float** _data;
+      RealOpenMM** _realOpenMMData;
+  
+      void _loadDanglingValues( void  );
+      void _loadDanglingValues( float );
 };
 
 } // namespace OpenMM

platforms/brook/src/BrookIntStreamImpl.cpp

@@ -30,59 +30,162 @@
  * -------------------------------------------------------------------------- */
 
 #include "BrookIntStreamImpl.h"
+#include "OpenMMException.h"
+#include <sstream>
 
 using namespace OpenMM;
 
-BrookIntStreamImpl::BrookIntStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) : StreamImpl(name, size, type, platform) {
-    switch (type) {
-    case Stream::Integer:
-        width = 1;
-        break;
-    case Stream::Integer2:
-        width = 2;
-        break;
-    case Stream::Integer3:
-        width = 3;
-        break;
-    case Stream::Integer4:
-        width = 4;
-        break;
-    }
-    data = new int*[size];
-    for (int i = 0; i < size; ++i)
-        data[i] = new int[width];
+/** 
+ * BrookIntStreamImpl constructor
+ * 
+ * @param name                      stream name
+ * @param size                      stream size
+ * @param platform                  platform
+ *
+ */
+
+BrookIntStreamImpl::BrookIntStreamImpl( std::string name, int size, Stream::DataType type, const Platform& platform ) : StreamImpl( name, size, type, platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookIntStreamImpl::BrookIntStreamImpl";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   switch( type ){
+
+      case Stream::Integer:
+          width = 1;
+          break;
+
+      case Stream::Integer2:
+          width = 2;
+          break;
+
+      case Stream::Integer3:
+          width = 3;
+          break;
+
+      case Stream::Integer4:
+          width = 4;
+          break;
+
+      default:
+         std::stringstream message;
+         message << methodName << " type=" << type << " not recognized.";
+         throw OpenMMException( message.str() );
+   }
+
+   data = new int*[size];
+
+   for( int ii = 0; ii < size; ii++ ){
+       data[ii] = new int[width];
+   }
 }
 
+/** 
+ * BrookIntStreamImpl destructor
+ * 
+ */
+
 BrookIntStreamImpl::~BrookIntStreamImpl() {
-    delete data;
+   delete[] data;
 }
 
-void BrookIntStreamImpl::loadFromArray(const void* array) {
-    int* arrayData = (int*) array;
-    for (int i = 0; i < getSize(); ++i)
-        for (int j = 0; j < width; ++j)
-            data[i][j] = arrayData[i*width+j];
+/** 
+ * Load data from array into stream
+ * 
+ * @param array                     array to load (length=size*width)
+ *
+ */
+
+void BrookIntStreamImpl::loadFromArray( const void* array ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntStreamImpl::loadFromArray";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   int* arrayData = (int*) array;
+   int index      = 0;
+   for( int ii = 0; ii < getSize(); ii++ ){
+      for( int jj = 0; jj < width; jj++ ){
+         data[ii][jj] = arrayData[index++];
+      }
+   }
 }
 
-void BrookIntStreamImpl::saveToArray(void* array) {
-    int* arrayData = (int*) array;
-    for (int i = 0; i < getSize(); ++i)
-        for (int j = 0; j < width; ++j)
-            arrayData[i*width+j] = data[i][j];
+/** 
+ * Save data from stream to array 
+ * 
+ * @param array                     array to save data to (length=size*width)
+ *
+ */
+
+void BrookIntStreamImpl::saveToArray( void* array ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntStreamImpl::saveToArray";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   int* arrayData = (int*) array;
+   int index      = 0;
+   for( int ii = 0; ii < getSize(); ii++ ){
+      for( int jj = 0; jj < width; jj++ ){
+         arrayData[index++] = data[ii][jj];
+      }
+   }
 }
 
-void BrookIntStreamImpl::fillWithValue(void* value) {
-    int valueData = *((int*) value);
-    for (int i = 0; i < getSize(); ++i)
-        for (int j = 0; j < width; ++j)
-            data[i][j] = valueData;
+/** 
+ * Set all stream entries to input value
+ * 
+ * @param value                     value to load into stream
+ *
+ */
+
+void BrookIntStreamImpl::fillWithValue( void* value ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntStreamImpl::fillWithValue";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   int valueData = *((int*) value);
+   for( int ii = 0; ii < getSize(); ii++ ){
+      for (int jj = 0; jj < width; jj++ ){
+         data[ii][jj] = valueData;
+      }
+   }
 }
 
-const int* const * BrookIntStreamImpl::getData() const {
-    return data;
+/** 
+ * Get data
+ * 
+ * @return data ptr
+ *
+ */
+
+const int* const * BrookIntStreamImpl::getData( void ) const {
+   return data;
 }
 
-int** BrookIntStreamImpl::getData() {
-    return data;
+/** 
+ * Get data
+ * 
+ * @return data ptr
+ *
+ */
+
+int** BrookIntStreamImpl::getData( void ){
+   return data;
 }
 

platforms/brook/src/BrookIntStreamImpl.h

@@ -38,22 +38,25 @@
 namespace OpenMM {
 
 /**
- * This is the implementation of Float and Double streams in the reference Platform.
+ * Implementation of int streams for the Brook platform
  */
 
 class BrookIntStreamImpl : public StreamImpl {
+
 public:
 
-    BrookIntStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform);
-    ~BrookIntStreamImpl();
+    BrookIntStreamImpl( std::string name, int size, Stream::DataType type, const Platform& platform );
+
+    ~BrookIntStreamImpl( );
 
-    void loadFromArray(const void* array);
-    void saveToArray(void* array);
-    void fillWithValue(void* value);
-    const int* const * getData() const;
-    int** getData();
+    void loadFromArray( const void* array );
+    void saveToArray( void* array );
+    void fillWithValue( void* value );
+    const int* const * getData( void  ) const;
+    int** getData( void );
 
 private:
+
     int width;
     Stream::DataType baseType;
     int** data;

platforms/brook/src/BrookKernelFactory.cpp

@@ -36,9 +36,13 @@ using namespace OpenMM;
 
 KernelImpl* BrookKernelFactory::createKernelImpl(std::string name, const Platform& platform, OpenMMContextImpl& context) const {
     if (name == CalcStandardMMForceFieldKernel::Name())
-        return new BrookCalcStandardMMForceFieldKernel(name, platform);
+		(void) fprintf( stderr, "CalcStandardMMForceFieldKernel not set BrookKernelFactory::createKernelImpl\n" );
+        (void) fflush( stderr );
+        //return new BrookCalcStandardMMForceFieldKernel(name, platform);
     if (name == CalcGBSAOBCForceFieldKernel::Name())
-        return new BrookCalcGBSAOBCForceFieldKernel(name, platform);
+        (void) fprintf( stderr, "CalcGBSAOBCForceFieldKernel not set BrookKernelFactory::createKernelImpl\n" );
+        (void) fflush( stderr );
+        //return new BrookCalcGBSAOBCForceFieldKernel(name, platform);
     if (name == IntegrateVerletStepKernel::Name())
         return new BrookIntegrateVerletStepKernel(name, platform);
     if (name == IntegrateLangevinStepKernel::Name())

platforms/brook/src/BrookKernels.cpp

@@ -31,6 +31,7 @@
 
 #include "BrookKernels.h"
 #include "BrookFloatStreamImpl.h"
+/*
 #include "SimTKBrook/BrookAngleBondIxn.h"
 #include "SimTKBrook/BrookBondForce.h"
 #include "SimTKBrook/BrookHarmonicBondIxn.h"
@@ -40,12 +41,14 @@
 #include "SimTKBrook/BrookRbDihedralBond.h"
 #include "SimTKBrook/BrookStochasticDynamics.h"
 #include "SimTKBrook/BrookShakeAlgorithm.h"
+*/
 #include <cmath>
 #include <limits>
 
 using namespace OpenMM;
 using namespace std;
 
+/*
 int** allocateIntArray(int length, int width) {
     int** array = new int*[length];
     for (int i = 0; i < length; ++i)
@@ -95,8 +98,10 @@ void disposeRealArray(RealOpenMM** array, int size) {
         delete[] array;
     }
 }
+*/
 
 BrookCalcStandardMMForceFieldKernel::~BrookCalcStandardMMForceFieldKernel() {
+/*
     disposeIntArray(bondIndexArray, numBonds);
     disposeRealArray(bondParamArray, numBonds);
     disposeIntArray(angleIndexArray, numAngles);
@@ -109,6 +114,7 @@ BrookCalcStandardMMForceFieldKernel::~BrookCalcStandardMMForceFieldKernel() {
     disposeIntArray(exclusionArray, numAtoms);
     disposeIntArray(bonded14IndexArray, num14);
     disposeRealArray(bonded14ParamArray, num14);
+*/
 }
 
 void BrookCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters,
@@ -117,6 +123,7 @@ void BrookCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
         const vector<vector<int> >& rbTorsionIndices, const vector<vector<double> >& rbTorsionParameters,
         const vector<vector<int> >& bonded14Indices, double lj14Scale, double coulomb14Scale,
         const vector<set<int> >& exclusions, const vector<vector<double> >& nonbondedParameters) {
+/*
     numAtoms = nonbondedParameters.size();
     numBonds = bondIndices.size();
     numAngles = angleIndices.size();
@@ -155,9 +162,11 @@ void BrookCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
         bonded14ParamArray[i][1] = lj14Scale*(atomParamArray[atom1][1]*atomParamArray[atom2][1]);
         bonded14ParamArray[i][2] = coulomb14Scale*(atomParamArray[atom1][2]*atomParamArray[atom2][2]);
     }
+*/
 }
 
 void BrookCalcStandardMMForceFieldKernel::executeForces(const Stream& positions, Stream& forces) {
+/*
     RealOpenMM** posData = const_cast<RealOpenMM**>(((BrookFloatStreamImpl&) positions.getImpl()).getData()); // Brook code needs to be made const correct
     RealOpenMM** forceData = ((BrookFloatStreamImpl&) forces.getImpl()).getData();
     BrookBondForce refBondForce;
@@ -173,14 +182,16 @@ void BrookCalcStandardMMForceFieldKernel::executeForces(const Stream& positions,
     clj.calculatePairIxn(numAtoms, posData, atomParamArray, exclusionArray, 0, forceData, 0, 0);
     BrookLJCoulomb14 nonbonded14;
     refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
+*/
 }
 
 double BrookCalcStandardMMForceFieldKernel::executeEnergy(const Stream& positions) {
+    RealOpenMM energy = 0;
+/*
     RealOpenMM** posData = const_cast<RealOpenMM**>(((BrookFloatStreamImpl&) positions.getImpl()).getData()); // Brook code needs to be made const correct
     RealOpenMM** forceData = allocateRealArray(numAtoms, 3);
     int arraySize = max(max(max(max(numAtoms, numBonds), numAngles), numPeriodicTorsions), numRBTorsions);
     RealOpenMM* energyArray = new RealOpenMM[arraySize];
-    RealOpenMM energy = 0;
     BrookBondForce refBondForce;
     BrookHarmonicBondIxn harmonicBond;
     for (int i = 0; i < arraySize; ++i)
@@ -206,6 +217,7 @@ double BrookCalcStandardMMForceFieldKernel::executeEnergy(const Stream& position
     refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
     disposeRealArray(forceData, numAtoms);
     delete[] energyArray;
+*/
     return energy;
 }
 
@@ -232,6 +244,7 @@ void BrookIntegrateVerletStepKernel::execute(Stream& positions, Stream& velociti
 }
 #include <iostream>
 BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel() {
+/*
     if (dynamics)
         delete dynamics;
     if (shake)
@@ -242,10 +255,12 @@ BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel() {
         disposeIntArray(constraintIndices, numConstraints);
     if (shakeParameters)
         disposeRealArray(shakeParameters, numConstraints);
+*/
 }
 
 void BrookIntegrateLangevinStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
         const vector<double>& constraintLengths) {
+/*
     this->masses = new RealOpenMM[masses.size()];
     for (int i = 0; i < masses.size(); ++i)
         this->masses[i] = masses[i];
@@ -258,9 +273,11 @@ void BrookIntegrateLangevinStepKernel::initialize(const vector<double>& masses,
     shakeParameters = allocateRealArray(constraintLengths.size(), 1);
     for (int i = 0; i < constraintLengths.size(); ++i)
         shakeParameters[i][0] = constraintLengths[i];
+*/
 }
 
 void BrookIntegrateLangevinStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
+/*
     RealOpenMM** posData = ((BrookFloatStreamImpl&) positions.getImpl()).getData();
     RealOpenMM** velData = ((BrookFloatStreamImpl&) velocities.getImpl()).getData();
     RealOpenMM** forceData = const_cast<RealOpenMM**>(((BrookFloatStreamImpl&) forces.getImpl()).getData()); // Brook code needs to be made const correct
@@ -280,6 +297,7 @@ void BrookIntegrateLangevinStepKernel::execute(Stream& positions, Stream& veloci
         prevStepSize = stepSize;
     }
     dynamics->update(positions.getSize(), posData, velData, forceData, masses);
+*/
 }
 
 void BrookIntegrateBrownianStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
@@ -304,9 +322,11 @@ void BrookCalcKineticEnergyKernel::initialize(const vector<double>& masses) {
 }
 
 double BrookCalcKineticEnergyKernel::execute(const Stream& velocities) {
-    RealOpenMM** velData = const_cast<RealOpenMM**>(((BrookFloatStreamImpl&) velocities.getImpl()).getData()); // Brook code needs to be made const correct
     double energy = 0.0;
+/*
+    RealOpenMM** velData = const_cast<RealOpenMM**>(((BrookFloatStreamImpl&) velocities.getImpl()).getData()); // Brook code needs to be made const correct
     for (int i = 0; i < masses.size(); ++i)
         energy += masses[i]*(velData[i][0]*velData[i][0]+velData[i][1]*velData[i][1]+velData[i][2]*velData[i][2]);
+*/
     return 0.5*energy;
 }

platforms/brook/src/BrookPlatform.cpp

@@ -31,33 +31,65 @@
 
 #include "BrookPlatform.h"
 #include "BrookKernelFactory.h"
-#include "BrookKernels.h"
+//#include "BrookKernels.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 
-BrookPlatform* registerBrookPlatform() {
-    BrookPlatform* platform = new BrookPlatform();
-    Platform::registerPlatform(platform);
+BrookPlatform* registerBrookPlatform( void ){
+   BrookPlatform* platform = new BrookPlatform();
+   Platform::registerPlatform(platform);
+   return platform;
 }
 
-BrookPlatform* staticPlatform = registerBrookPlatform();
+BrookPlatform* staticPlatform = registerBrookPlatform( );
 
-BrookPlatform::BrookPlatform() {
-    BrookKernelFactory* factory = new BrookKernelFactory();
-    registerKernelFactory(CalcStandardMMForceFieldKernel::Name(), factory);
-    registerKernelFactory(CalcGBSAOBCForceFieldKernel::Name(), factory);
-    registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
-    registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
-    registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
-    registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
-    registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
+BrookPlatform::BrookPlatform( ){
+   _defaultAtomStreamWidth  = DefaultAtomStreamWidth;
+   _initializeFactory();
 }
 
-bool BrookPlatform::supportsDoublePrecision() const {
+BrookPlatform::BrookPlatform( int defaultAtomStreamWidth ){
+   _defaultAtomStreamWidth  = defaultAtomStreamWidth;
+   _initializeFactory();
+}
+
+BrookPlatform::~BrookPlatform( ){
+}
+
+void BrookPlatform::_initializeFactory( void ){
+   //BrookKernelFactory* factory = new BrookKernelFactory();
+   /*
+   registerKernelFactory( CalcStandardMMForceFieldKernel::Name(), factory);
+   registerKernelFactory( CalcGBSAOBCForceFieldKernel::Name(),    factory);
+   registerKernelFactory( IntegrateVerletStepKernel::Name(),      factory);
+   registerKernelFactory( IntegrateLangevinStepKernel::Name(),    factory);
+   registerKernelFactory( IntegrateBrownianStepKernel::Name(),    factory);
+   registerKernelFactory( ApplyAndersenThermostatKernel::Name(),  factory);
+   registerKernelFactory( CalcKineticEnergyKernel::Name(),        factory);
+   */
+}
+
+bool BrookPlatform::supportsDoublePrecision( void ) const {
     return (sizeof(RealOpenMM) >= sizeof(double));
 }
 
-const StreamFactory& BrookPlatform::getDefaultStreamFactory() const {
+const StreamFactory& BrookPlatform::getDefaultStreamFactory( void ) const {
     return defaultStreamFactory;
 }
+
+int BrookPlatform::getStreamSize( int size, int streamWidth, int* outputHeight ) const {
+
+   if( streamWidth < 1 ){
+      return -1;
+   }
+
+   int height = size/streamWidth;
+   if( streamWidth*height < size ){
+      height++;
+   }
+   if( outputHeight ){
+      *outputHeight = height;
+   }
+   return height*streamWidth;
+}

platforms/brook/src/BrookStreamFactory.cpp

@@ -29,6 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include <sstream>
 #include "OpenMMException.h"
 #include "BrookStreamFactory.h"
 #include "BrookFloatStreamImpl.h"
@@ -36,22 +37,167 @@
 
 using namespace OpenMM;
 
-StreamImpl* BrookStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, int streamWidth, const Platform& platform, OpenMMContextImpl& context) const {
-    switch (type) {
-    case Stream::Float:
-    case Stream::Float2:
-    case Stream::Float3:
-    case Stream::Float4:
-    case Stream::Double:
-    case Stream::Double2:
-    case Stream::Double3:
-    case Stream::Double4:
-        return new BrookFloatStreamImpl(name, size, type, streamWidth, platform);
-    case Stream::Integer:
-    case Stream::Integer2:
-    case Stream::Integer3:
-    case Stream::Integer4:
-        return new BrookIntStreamImpl(name, size, type, streamWidth, platform);
-    }
-    throw OpenMMException("Tried to create a Stream with an illegal DataType.");
+const std::string BrookStreamFactory::AtomPositions              = "atomPositions";
+const std::string BrookStreamFactory::AtomVelocities             = "atomVelocities";
+const std::string BrookStreamFactory::AtomForces                 = "atomForces";
+
+// bonded streams
+                                    
+const std::string BrookStreamFactory::BondedAtomIndicesStream    = "BondedAtomIndicesStream";
+const std::string BrookStreamFactory::BondedParametersStream     = "BondedParametersStream";
+const std::string BrookStreamFactory::UnrolledForceStream        = "UnrolledForceStream";
+const std::string BrookStreamFactory::BondedChargeStream         = "BondedChargeStream";
+const std::string BrookStreamFactory::BondedInverseMapStreams    = "BondedInverseMapStreams";
+
+// non-bonded streams
+
+const std::string BrookStreamFactory::NonBondedExclusionStream   = "NonBondedExclusionStream";
+const std::string BrookStreamFactory::NonBondedVdwStream         = "NonBondedVdwStream";
+
+/** 
+ * BrookStreamFactory constructor
+ * 
+ * @return BrookStreamFactory
+ */
+
+BrookStreamFactory::BrookStreamFactory( void ){
+
+	double defaultDangleValue                       = 1.0e+38;
+	int    defaultStreamWidth                       = 32;
+
+   _streamInfoMap[AtomPositions]                   = new BrookStreamInfo( AtomPositions,             defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[AtomVelocities]                  = new BrookStreamInfo( AtomVelocities,            defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[AtomForces]                      = new BrookStreamInfo( AtomForces,                defaultStreamWidth, defaultDangleValue );
+
+   // bonded streams
+
+   _streamInfoMap[BondedAtomIndicesStream]         = new BrookStreamInfo( BondedAtomIndicesStream,   defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[BondedParametersStream]          = new BrookStreamInfo( BondedParametersStream,    defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[UnrolledForceStream]             = new BrookStreamInfo( UnrolledForceStream,       defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[BondedChargeStream]              = new BrookStreamInfo( BondedChargeStream,        defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[BondedInverseMapStreams]         = new BrookStreamInfo( BondedInverseMapStreams,   defaultStreamWidth, defaultDangleValue );
+
+   _streamInfoMap[NonBondedExclusionStream]        = new BrookStreamInfo( NonBondedExclusionStream,  defaultStreamWidth, defaultDangleValue );
+   _streamInfoMap[NonBondedVdwStream]              = new BrookStreamInfo( NonBondedVdwStream,        defaultStreamWidth, defaultDangleValue );
+}
+
+/** 
+ * BrookStreamFactory destructor
+ * 
+ */
+
+BrookStreamFactory::~BrookStreamFactory( void ){
+   //_streamInfoMap[UnrolledForceStream]      = new BrookStreamInfo( UnrolledForceStream, 32, defaultDangleValue );
+}
+
+/** 
+ * Get BrookStreamInfo reference given stream name
+ *
+ * @param name stream name
+ * 
+ * @return BrookStreamInfo  -- look up streamInfo object given name; return NULL if name not recognized
+ */
+
+BrookStreamInfo* BrookStreamFactory::getBrookStreamInfo( std::string name ) const {
+
+   if( _streamInfoMap.find( name ) == _streamInfoMap.end() ){
+      return NULL;
+   }
+   return _streamInfoMap.find( name )->second;
+}
+
+/** 
+ * Create StreamImpl
+ *
+ * @param name     stream name
+ * @param size     stream size
+ * @param type     data type (float, float2, ...)
+ * @param platform platform reference
+ * @param context  context (currently ignored)
+ * 
+ * @return StreamImpl
+ */
+
+StreamImpl* BrookStreamFactory::createStreamImpl( std::string name, int size, Stream::DataType type,
+                                                  const Platform& platform, OpenMMContextImpl& context ) const {
+
+   return BrookStreamFactory::createStreamImplCommon( name, size, type, platform );
+
+}
+
+/** 
+ * Create StreamImpl
+ *
+ * @param name     stream name
+ * @param size     stream size
+ * @param type     data type (float, float2, ...)
+ * @param platform platform reference
+ * 
+ * @return StreamImpl
+ */
+
+StreamImpl* BrookStreamFactory::createStreamImpl( std::string name, int size, Stream::DataType type,
+                                                  const Platform& platform ) const {
+
+   return BrookStreamFactory::createStreamImplCommon( name, size, type, platform );
+}
+
+/** 
+ * Create StreamImpl
+ *
+ * @param name     stream name
+ * @param size     stream size
+ * @param type     data type (float, float2, ...)
+ * @param platform platform reference
+ * 
+ * @return StreamImpl
+ */
+
+StreamImpl* BrookStreamFactory::createStreamImplCommon( std::string name, int size, Stream::DataType type,
+                                                        const Platform& platform ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookStreamFactory::createStreamImplCommon";
+   //static const int debug                   = 0;
+
+// ---------------------------------------------------------------------------------------
+
+   // get stream width & dangle value
+
+   BrookStreamInfo* streamInfo = getBrookStreamInfo( name );
+   if( streamInfo == NULL ){
+      std::stringstream message;
+      message << methodName << " stream=" << name << " not registered.";
+      throw OpenMMException( message.str() );
+   }
+
+   int streamWidth    = streamInfo->getStreamWidth();
+   double dangleValue = streamInfo->getDangleValue();
+      
+   switch ( type ){
+
+      case Stream::Float:
+      case Stream::Float2:
+      case Stream::Float3:
+      case Stream::Float4:
+      case Stream::Double:
+      case Stream::Double2:
+      case Stream::Double3:
+      case Stream::Double4:
+          return new BrookFloatStreamImpl( name, size, type, platform, streamWidth, dangleValue );
+          break;
+
+      case Stream::Integer:
+      case Stream::Integer2:
+      case Stream::Integer3:
+      case Stream::Integer4:
+          return new BrookIntStreamImpl( name, size, type, platform );
+          break;
+   }
+
+   std::stringstream message;
+   message << methodName << " type=" << type << " for stream=" << name << " is invalid.";
+   throw OpenMMException( message.str() );
+
 }