Start Langevin

platforms/brook/src/BrookCalcGBSAOBCForceFieldKernel.cpp

@@ -145,7 +145,7 @@ void BrookCalcGBSAOBCForceFieldKernel::initialize( const std::vector<std::vector
    _brookGbsa              = new BrookGbsa();
    _brookGbsa->setLog( log );
     
-   _brookGbsa->setup( atomParameters, solventDielectric, soluteDielectric );
+   _brookGbsa->setup( atomParameters, solventDielectric, soluteDielectric, getPlatform() );
 
    if( log ){
       std::string contents = _brookGbsa->getContentsString( ); 

platforms/brook/src/BrookIntegrateLangevinStepKernel.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) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * 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      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "BrookIntegrateKernals.h"
+#include "BrookStreamInternal.h"
+
+using namespace OpenMM;
+using namespace std;
+
+BrookIntegrateLangevinStepKernel::BrookIntegrateLangevinStepKernel( std::string name, const Platform& platform ) :
+                                IntegrateLangevinStepKernel( name, platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntegrateLangevinStepKernel::BrookIntegrateLangevinStepKernel";
+
+// ---------------------------------------------------------------------------------------
+
+   _numberOfConstraints            = -1;
+
+   _brookStochasticDynamics        = NULL;
+   _brookShakeAlgorithm            = NULL;
+   _atomMasses                     = NULL;
+   _shakeParameters                = NULL;
+   _constraintIndices              = NULL;
+   _shakeParameters                = NULL;
+   
+}
+
+BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel( ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel";
+
+// ---------------------------------------------------------------------------------------
+   
+   delete _brookkStochasticDynamics;
+   delete _brookShakeAlgorithm;
+   delete _atomMasses;
+   delete _shakeParameters;
+   delete _constraintIndices;
+   delete _shakeParameters;
+
+}
+
+void BrookIntegrateLangevinStepKernel::initialize( const vector<double>& masses,
+                                                 const vector<vector<int> >& constraintIndices,
+                                                 const vector<double>& constraintLengths ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookIntegrateLangevinStepKernel::initialize";
+
+// ---------------------------------------------------------------------------------------
+   
+/*
+    this->masses = new RealOpenMM[masses.size()];
+    for (size_t i = 0; i < masses.size(); ++i)
+        this->masses[i] = static_cast<RealOpenMM>( masses[i] );
+    numConstraints = constraintIndices.size();
+    this->constraintIndices = allocateIntArray(numConstraints, 2); 
+    for (int i = 0; i < numConstraints; ++i) {
+        this->constraintIndices[i][0] = constraintIndices[i][0];
+        this->constraintIndices[i][1] = constraintIndices[i][1];
+    }   
+    shakeParameters = allocateRealArray(constraintLengths.size(), 1); 
+    for (size_t i = 0; i < constraintLengths.size(); ++i)
+        shakeParameters[i][0] = static_cast<RealOpenMM>( constraintLengths[i] );
+
+*/
+}
+
+/** 
+ * Execute kernel
+ * 
+ * @param positions          atom coordinates
+ * @param velocities         atom velocities
+ * @param forces             atom forces
+ * @param temperature        heat bath temperature
+ * @param friction           friction coefficient coupling the system to the heat bath
+ * @param stepSize           integration step size
+ *
+ */
+
+void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& velocities,
+                                                const Stream& forces, double temperature,
+                                                double friction, double stepSize ){
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "BrookIntegrateLangevinStepKernel::execute";
+
+// ---------------------------------------------------------------------------------------
+   
+   // first time through initialize _brookStochasticDynamics
+
+   // for each subsequent call, check if parameters need to be updated due to a change
+   // in T, gamma, or the step size
+
+   // take step
+
+   if( _brookStochasticDynamics == NULL ){
+      _brookStochasticDynamics = new BrookStochasticDynamics( getNumberOfAtoms(), static_cast<RealOpenMM>(stepSize), 
+                                                              static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(temperature) );
+   } else {
+      _brookStochasticDynamics->updateParameters( temperature, friction, stepSize );
+   } 
+   _brookStochasticDynamics->update( positions, velocities, forces );
+
+}

platforms/brook/src/BrookIntegrateLangevinStepKernel.h

+#ifndef OPENMM_BROOK_INTEGRATE_LANGEVIN_STEP_KERNEL_H_
+#define OPENMM_BROOK_INTEGRATE_LANGEVIN_STEP_KERNEL_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   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 ) 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" ), *
+ * 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      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "kernels.h"
+#include "BrookStochasticDynamics.h"
+#include "BrookShakeAlgorithm.h"
+
+namespace OpenMM {
+
+/**
+ * This is the base class of Float and Double streams in the Brook Platform.
+ */
+
+class BrookIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
+
+   public:
+
+      /**
+       * BrookIntegrateLangevinStepKernel constructor
+       * 
+       * @param name        name of the stream to create
+       * @param platform    platform
+       *
+       */
+  
+      BrookIntegrateLangevinStepKernel( std::string name, const Platform& platform );
+
+      /**
+       * BrookIntegrateLangevinStepKernel destructor
+       * 
+       */
+  
+      ~BrookIntegrateLangevinStepKernel();
+
+      /** 
+       * Initialize the kernel, setting up all parameters related to integrator.
+       * 
+       * @param masses             atom masses
+       * @param constraintIndices  each element contains the indices of two atoms whose distance should be constrained
+       * @param constraintLengths  required distance between each pair of constrained atoms
+       */
+
+      void initialize( const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
+                       const std::vector<double>& constraintLengths );
+      /** 
+       * Execute kernel
+       * 
+       * @param positions          coordinates
+       * @param velocities         velocities
+       * @param forces             forces
+       * @param temperature        heat bath temperature
+       * @param friction           friction coefficient coupling the system to the heat bath
+       * @param stepSize           step size
+       *
+       */
+
+      void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
+
+   protected:
+
+      BrookStochasticDynamics* _brookStochasticDynamics;
+      BrookShakeAlgorithm* _brookShakeAlgorithm;
+      RealOpenMM*  _atomMasses;
+      RealOpenMM** _shakeParameters;
+      int** _constraintIndices;
+      int _numberOfConstraints;
+      double prevTemp, prevFriction, prevStepSize;
+        
+  
+};
+
+} // namespace OpenMM
+
+#endif /* OPENMM_BROOK_INTEGRATE_LANGEVIN_STEP_KERNEL_H_ */

platforms/brook/src/BrookIntegrateKernals.h → platforms/brook/src/BrookIntegrateVerletStepKernel.h

@@ -85,10 +85,7 @@ class BrookIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
 
    protected:
 
-      int _width;
-      int _streamWidth;
-      int _streamHeight;
-      int _streamSize;
+  
   
 };
 

platforms/brook/src/BrookStreamImpl.cpp

@@ -267,7 +267,7 @@ void BrookStreamImpl::fillWithValue( void* value ){
  * 
  * @return data array
  */
-void* BrookStreamImpl::getData( void* value ){
+void* BrookStreamImpl::getData( void ){
    return _brookStreamInternal->getData( );
 }