Created reference implementation of BrownianIntegrator

platforms/reference/src/ReferenceKernels.cpp

@@ -34,6 +34,7 @@
 #include "gbsa/CpuObc.h"
 #include "SimTKReference/ReferenceAngleBondIxn.h"
 #include "SimTKReference/ReferenceBondForce.h"
+#include "SimTKReference/ReferenceBrownianDynamics.h"
 #include "SimTKReference/ReferenceHarmonicBondIxn.h"
 #include "SimTKReference/ReferenceLJCoulomb14.h"
 #include "SimTKReference/ReferenceLJCoulombIxn.h"
@@ -258,7 +259,7 @@ void ReferenceIntegrateVerletStepKernel::initialize(const vector<double>& masses
 void ReferenceIntegrateVerletStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize) {
     
 }
-#include <iostream>
+
 ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
     if (dynamics)
         delete dynamics;
@@ -310,13 +311,54 @@ void ReferenceIntegrateLangevinStepKernel::execute(Stream& positions, Stream& ve
     dynamics->update(positions.getSize(), posData, velData, forceData, masses);
 }
 
+ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
+    if (dynamics)
+        delete dynamics;
+    if (shake)
+        delete shake;
+    if (masses)
+        delete[] masses;
+    if (constraintIndices)
+        disposeIntArray(constraintIndices, numConstraints);
+    if (shakeParameters)
+        disposeRealArray(shakeParameters, numConstraints);
+}
+
 void ReferenceIntegrateBrownianStepKernel::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];
+    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 (int i = 0; i < constraintLengths.size(); ++i)
+        shakeParameters[i][0] = constraintLengths[i];
 }
 
 void ReferenceIntegrateBrownianStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
+    RealOpenMM** posData = ((ReferenceFloatStreamImpl&) positions.getImpl()).getData();
+    RealOpenMM** velData = ((ReferenceFloatStreamImpl&) velocities.getImpl()).getData();
+    RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) forces.getImpl()).getData()); // Reference code needs to be made const correct
+    if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
+        // Recreate the computation objects with the new parameters.
         
+        if (dynamics) {
+            delete dynamics;
+            delete shake;
+        }
+        dynamics = new ReferenceBrownianDynamics(positions.getSize(), stepSize, friction, temperature);
+        shake = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, shakeParameters);
+        dynamics->setReferenceShakeAlgorithm(shake);
+        prevTemp = temperature;
+        prevFriction = friction;
+        prevStepSize = stepSize;
+    }
+    dynamics->update(positions.getSize(), posData, velData, forceData, masses);
 }
 
 void ReferenceApplyAndersenThermostatKernel::initialize(const vector<double>& masses) {

platforms/reference/src/ReferenceKernels.h

@@ -36,6 +36,7 @@
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 class CpuObc;
+class ReferenceBrownianDynamics;
 class ReferenceStochasticDynamics;
 class ReferenceShakeAlgorithm;
 
@@ -203,8 +204,10 @@ private:
  */
 class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
 public:
-    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform) {
+    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform),
+        dynamics(0), shake(0), masses(0), shakeParameters(0), constraintIndices(0) {
     }
+    ~ReferenceIntegrateBrownianStepKernel();
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
      * 
@@ -225,6 +228,14 @@ public:
      * @param stepSize           the integration step size
      */
     void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
+private:
+    ReferenceBrownianDynamics* dynamics;
+    ReferenceShakeAlgorithm* shake;
+    RealOpenMM* masses;
+    RealOpenMM** shakeParameters;
+    int** constraintIndices;
+    int numConstraints;
+    double prevTemp, prevFriction, prevStepSize;
 };
 
 /**

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp

+
+/* Portions copyright (c) 2006-2008 Stanford University and Simbios.
+ * Contributors: Peter Eastman, Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "ReferenceBrownianDynamics.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBrownianDynamics constructor
+
+   @param numberOfAtoms  number of atoms
+   @param deltaT         delta t for dynamics
+   @param friction       friction coefficient
+   @param temperature    temperature
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms,
+                                                          RealOpenMM deltaT, RealOpenMM friction,
+                                                          RealOpenMM temperature ) : 
+           ReferenceDynamics( numberOfAtoms, deltaT, temperature ), friction( friction ) {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName      = "\nReferenceBrownianDynamics::ReferenceBrownianDynamics";
+
+   static const RealOpenMM zero       =  0.0;
+   static const RealOpenMM one        =  1.0;
+
+   // ---------------------------------------------------------------------------------------
+
+   if( friction <= zero ){
+
+      std::stringstream message;
+      message << methodName;
+      message << " input frction value=" << friction << " is invalid -- setting to 1.";
+      SimTKOpenMMLog::printError( message );
+
+      this->friction = one;
+     
+   }
+   allocate2DArrays( numberOfAtoms, 3, Max2DArrays );
+   allocate1DArrays( numberOfAtoms, Max1DArrays );
+   
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBrownianDynamics destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBrownianDynamics::~ReferenceBrownianDynamics( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceBrownianDynamics::~ReferenceBrownianDynamics";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get the friction coefficient
+
+   @return friction
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceBrownianDynamics::getFriction";
+
+   // ---------------------------------------------------------------------------------------
+
+   return friction;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Print parameters
+
+   @param message             message
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceBrownianDynamics::printParameters( std::stringstream& message ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName  = "\nReferenceBrownianDynamics::printParameters";
+
+   // ---------------------------------------------------------------------------------------
+
+   // print parameters
+
+   ReferenceDynamics::printParameters( message );
+   message << " friction=" << getFriction();
+   message << " T=" << getTemperature();
+
+   return ReferenceDynamics::DefaultReturn;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Update -- driver routine for performing Brownian dynamics update of coordinates
+   and velocities
+
+   @param numberOfAtoms       number of atoms
+   @param atomCoordinates     atom coordinates
+   @param velocities          velocities
+   @param forces              forces
+   @param masses              atom masses
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                                          RealOpenMM** velocities,
+                                          RealOpenMM** forces, RealOpenMM* masses ){
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName      = "\nReferenceBrownianDynamics::update";
+
+   static const RealOpenMM zero       =  0.0;
+   static const RealOpenMM one        =  1.0;
+
+   static int debug                   =  0;
+
+   // ---------------------------------------------------------------------------------------
+
+   // get work arrays
+
+   RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
+   RealOpenMM* inverseMasses = get1DArrayAtIndex( InverseMasses );
+
+   // first-time-through initialization
+
+   if( getTimeStep() == 0 ){
+
+      std::stringstream message;
+      message << methodName;
+      int errors = 0;
+
+      // invert masses
+
+      for( int ii = 0; ii < numberOfAtoms; ii++ ){
+         if( masses[ii] <= zero ){
+            message << "mass at atom index=" << ii << " (" << masses[ii] << ") is <= 0" << std::endl;
+            errors++;
+         } else {
+            inverseMasses[ii] = one/masses[ii];
+         }
+      }
+
+      // exit if errors
+
+      if( errors ){
+         SimTKOpenMMLog::printError( message );
+      }
+   }
+   
+   // Perform the integration.
+   
+   const RealOpenMM noiseAmplitude = sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction());
+   const RealOpenMM forceScale = getDeltaT()/getFriction();
+   for (int i = 0; i < numberOfAtoms; ++i) {
+       for (int j = 0; j < 3; ++j) {
+           xPrime[i][j] = atomCoordinates[i][j] + forceScale*forces[i][j] + noiseAmplitude*getNormallyDistributedRandomNumber();
+       }
+   }
+   ReferenceShakeAlgorithm* referenceShakeAlgorithm = getReferenceShakeAlgorithm();
+   if( referenceShakeAlgorithm )
+      referenceShakeAlgorithm->applyShake( numberOfAtoms, atomCoordinates, xPrime, inverseMasses );
+   
+   // Update the positions and velocities.
+   
+   RealOpenMM velocityScale = 1.0/getDeltaT();
+   for (int i = 0; i < numberOfAtoms; ++i) {
+       for (int j = 0; j < 3; ++j) {
+           velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
+           atomCoordinates[i][j] = xPrime[i][j];
+       }
+   }
+
+   incrementTimeStep();
+
+   return ReferenceDynamics::DefaultReturn;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Write state
+
+   @param numberOfAtoms       number of atoms
+   @param atomCoordinates     atom coordinates
+   @param velocities          velocities
+   @param forces              forces
+   @param masses              atom masses
+   @param state               0 if initial state; otherwise nonzero
+   @param baseFileName        base file name
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceBrownianDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                                             RealOpenMM** velocities,
+                                             RealOpenMM** forces, RealOpenMM* masses,
+                                             int state, const std::string& baseFileName ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName      = "\nReferenceBrownianDynamics::writeState";
+
+   static const RealOpenMM zero       =  0.0;
+   static const RealOpenMM one        =  1.0;
+   static const int threeI            =  3;
+
+   // ---------------------------------------------------------------------------------------
+
+   std::stringstream stateFileName;
+
+   stateFileName << baseFileName;
+   stateFileName << "_Step" << getTimeStep();
+   // stateFileName << "_State" << state;
+   stateFileName << ".txt";
+
+   // ---------------------------------------------------------------------------------------
+
+   // open file -- return if unsuccessful
+
+   FILE* stateFile = NULL;
+#ifdef WIN32
+   fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
+#else
+   stateFile = fopen( stateFileName.str().c_str(), "w" );
+#endif
+
+   // ---------------------------------------------------------------------------------------
+
+   // diagnostics
+
+   if( stateFile != NULL ){
+      std::stringstream message;
+      message << methodName;
+      message << " Opened file=<" << stateFileName.str() << ">.\n";
+      SimTKOpenMMLog::printMessage( message );
+   } else {
+      std::stringstream message;
+      message << methodName;
+      message << " could not open file=<" << stateFileName.str() << "> -- abort output.\n";
+      SimTKOpenMMLog::printMessage( message );
+      return ReferenceDynamics::ErrorReturn;
+   }   
+
+   // ---------------------------------------------------------------------------------------
+
+   StringVector scalarNameI;
+   IntVector scalarI;
+
+   StringVector scalarNameR;
+   RealOpenMMVector scalarR;
+
+   StringVector scalarNameR1;
+   RealOpenMMPtrVector scalarR1;
+
+   StringVector scalarNameR2;
+   RealOpenMMPtrPtrVector scalarR2;
+
+   scalarI.push_back( getNumberOfAtoms() );
+   scalarNameI.push_back( "Atoms" );
+
+   scalarI.push_back( getTimeStep() );
+   scalarNameI.push_back( "Timestep" );
+
+   if( state == 0 || state == -1 ){
+
+      scalarR.push_back( getDeltaT() );
+      scalarNameR.push_back( "delta_t" );
+
+      scalarR.push_back( getTemperature() );
+      scalarNameR.push_back( "T" );
+
+      scalarR.push_back( getFriction() );
+      scalarNameR.push_back( "Friction" );
+
+      scalarR1.push_back( masses );
+      scalarNameR1.push_back( "mass" );
+
+      scalarR2.push_back( atomCoordinates );
+      scalarNameR2.push_back( "coord" );
+
+      scalarR2.push_back( velocities );
+      scalarNameR2.push_back( "velocities" );
+
+      scalarR2.push_back( forces );
+      scalarNameR2.push_back( "forces" );
+
+      if( state == -1 ){
+
+         RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
+
+         scalarR2.push_back( xPrime );
+         scalarNameR2.push_back( "xPrime" );
+      }
+      
+   } else {
+
+      scalarR2.push_back( atomCoordinates );
+      scalarNameR2.push_back( "coord" );
+
+      scalarR2.push_back( velocities );
+      scalarNameR2.push_back( "velocities" );
+
+   }
+
+   writeStateToFile( stateFile, scalarNameI, scalarI, scalarNameR, scalarR, getNumberOfAtoms(), scalarNameR1, scalarR1, threeI, scalarNameR2, scalarR2 ); 
+
+   (void) fclose( stateFile );
+
+   return ReferenceDynamics::DefaultReturn;
+
+}

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.h

+
+/* Portions copyright (c) 2006-2008 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceBrownianDynamics_H__
+#define __ReferenceBrownianDynamics_H__
+
+#include "ReferenceDynamics.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceBrownianDynamics : public ReferenceDynamics {
+
+   private:
+
+      enum TwoDArrayIndicies { xPrime2D, Max2DArrays };
+      enum OneDArrayIndicies { InverseMasses, Max1DArrays };
+
+      RealOpenMM friction;
+      
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+
+         @param numberOfAtoms  number of atoms
+         @param deltaT         delta t for dynamics
+         @param friction       friction coefficient
+         @param temperature    temperature
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceBrownianDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceBrownianDynamics( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get the friction coefficient
+      
+         @return friction
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getFriction( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Print parameters
+      
+         @param message message
+
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int printParameters( std::stringstream& message ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Update
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+     
+      int update( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                  RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Write state
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+         @param state               0 if initial state; otherwise nonzero
+         @param baseFileName        base file name
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                      RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses,
+                      int state, const std::string& baseFileName ) const;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceBrownianDynamics_H__

platforms/reference/tests/TestReferenceBrownianIntegrator.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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of BrownianIntegrator.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "OpenMMContext.h"
+#include "ReferencePlatform.h"
+#include "StandardMMForceField.h"
+#include "System.h"
+#include "BrownianIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond() {
+    ReferencePlatform platform;
+    System system(2, 0);
+    system.setAtomMass(0, 2.0);
+    system.setAtomMass(1, 2.0);
+    double dt = 0.01;
+    BrownianIntegrator integrator(0, 0.1, dt);
+    StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0);
+    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    
+    // This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
+    
+    double rate = 2*1.0/0.1;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Velocities);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::exp(-rate*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        if (i > 0) {
+            double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
+        }
+        integrator.step(1);
+    }
+}
+
+void testTemperature() {
+    const int numAtoms = 8;
+    const int numBonds = numAtoms-1;
+    const double temp = 100.0;
+    ReferencePlatform platform;
+    System system(numAtoms, 0);
+    BrownianIntegrator integrator(temp, 2.0, 0.01);
+    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, numBonds, 0, 0, 0);
+    for (int i = 0; i < numAtoms; ++i) {
+        system.setAtomMass(i, 2.0);
+//        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    for (int i = 0; i < numBonds; ++i)
+        forceField->setBondParameters(i, i, i+1, 1.0, i);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numAtoms);
+    for (int i = 0; i < numAtoms; ++i)
+        positions[i] = Vec3(i, 0, 0);
+    context.setPositions(positions);
+    
+    // Let it equilibrate.
+    
+    integrator.step(1000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double pe = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Energy);
+        pe += state.getPotentialEnergy();
+        integrator.step(1);
+    }
+    pe /= 1000;
+    double expected = 0.5*numBonds*BOLTZ*temp;
+    ASSERT_EQUAL_TOL(expected, pe, 3*expected/std::sqrt(1000.0));
+}
+
+void testConstraints() {
+    const int numAtoms = 8;
+    const double temp = 100.0;
+    ReferencePlatform platform;
+    System system(numAtoms, numAtoms-1);
+    BrownianIntegrator integrator(temp, 2.0, 0.001);
+    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
+    for (int i = 0; i < numAtoms; ++i) {
+        system.setAtomMass(i, 10.0);
+        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    for (int i = 0; i < numAtoms-1; ++i)
+        system.setConstraintParameters(i, i, i+1, 1.0);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numAtoms);
+    vector<Vec3> velocities(numAtoms);
+    init_gen_rand(0);
+    for (int i = 0; i < numAtoms; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    
+    // Simulate it and see whether the constraints remain satisfied.
+    
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions);
+        for (int j = 0; j < numAtoms-1; ++j) {
+            Vec3 p1 = state.getPositions()[j];
+            Vec3 p2 = state.getPositions()[j+1];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
+        }
+        integrator.step(1);
+    }
+}
+
+int main() {
+    try {
+        testSingleBond();
+        testTemperature();
+        testConstraints();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

@@ -157,9 +157,9 @@ void testConstraints() {
     
     for (int i = 0; i < 1000; ++i) {
         State state = context.getState(State::Positions);
-        for (int i = 0; i < numAtoms-1; ++i) {
-            Vec3 p1 = state.getPositions()[i];
-            Vec3 p2 = state.getPositions()[i+1];
+        for (int j = 0; j < numAtoms-1; ++j) {
+            Vec3 p1 = state.getPositions()[j];
+            Vec3 p2 = state.getPositions()[j+1];
             double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
             ASSERT_EQUAL_TOL(1.0, dist, 1e-4);
         }