Direct space PME

plugins/amoeba/CMakeLists.txt

@@ -38,8 +38,7 @@ ENDIF(LOG)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-#SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
-SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi )
+SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
 
 # Collect up information about the version of the OpenMM library we're building
 # and make it available to the code so it can be built into the binaries.
@@ -103,8 +102,10 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
     INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
 
-#INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
-#INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
+INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
 
 # ----------------------------------------------------------------------------
 IF(LOG)
@@ -158,7 +159,7 @@ IF(OPENMM_BUILD_STATIC_LIB)
   TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
-#ADD_SUBDIRECTORY(platforms/reference/tests)
+ADD_SUBDIRECTORY(platforms/reference/tests)
 
 # Which hardware platforms to build
 IF(CUDA_FOUND)

plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h

@@ -113,6 +113,20 @@ public:
      */
     void setCutoffDistance(double distance);
 
+   /**		   
+     * Get the aEwald parameter		 
+     *		 
+     * @return the Ewald parameter		 
+     */		 
+    double getAEwald() const;			 
+		 
+    /**		 
+     * Set the aEwald parameter		 
+     *		 
+     * @param Ewald parameter			 
+     */		 
+    void setAEwald(double aewald);		 
+		 
     /**
      * Add multipole-related info for a particle 
      *
@@ -279,6 +293,7 @@ private:
 
     AmoebaNonbondedMethod nonbondedMethod;
     double cutoffDistance;
+    double aewald;
     MutualInducedIterationMethod mutualInducedIterationMethod;
     int mutualInducedMaxIterations;
     double mutualInducedTargetEpsilon;

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -56,6 +56,14 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
     cutoffDistance = distance;
 }
 
+double AmoebaMultipoleForce::getAEwald() const {		 
+    return aewald;		 
+}		 
+		 
+void AmoebaMultipoleForce::setAEwald(double inputAewald ) {			 
+    aewald = inputAewald;		 
+}		 
+ 
 AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const {
     return mutualInducedIterationMethod;
 }

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -589,6 +589,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
                                     static_cast<float>( force.getMutualInducedTargetEpsilon()),
                                     nonbondedMethod,
                                     static_cast<float>( force.getCutoffDistance()),
+                                    static_cast<float>( force.getAEwald()),
                                     static_cast<float>( force.getElectricConstant()) );
     if (nonbondedMethod == AmoebaMultipoleForce::PME) {
         double alpha;

plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp

@@ -350,6 +350,7 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
     (void) fprintf( log, "     pP_ScaleIndices                    %p\n",      amoebaGpu->amoebaSim.pP_ScaleIndices );
     (void) fprintf( log, "     pM_ScaleIndices                    %p\n",      amoebaGpu->amoebaSim.pM_ScaleIndices );
     (void) fprintf( log, "     sqrtPi                             %15.7e\n",  amoebaGpu->amoebaSim.sqrtPi );
+    (void) fprintf( log, "     alpha Ewald                        %15.7e\n",  gpu->sim.alphaEwald );
     (void) fprintf( log, "     cutoffDistance2                    %15.7e\n",  amoebaGpu->amoebaSim.cutoffDistance2 );
     (void) fprintf( log, "     electric                           %15.7e\n",  amoebaGpu->amoebaSim.electric );
     (void) fprintf( log, "     box                                %15.7e %15.7e %15.7e\n", gpu->sim.periodicBoxSizeX, gpu->sim.periodicBoxSizeY, gpu->sim.periodicBoxSizeZ);
@@ -1463,7 +1464,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
                                      const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
                                      const std::vector<int>& minCovalentIndices,  const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, 
                                      int mutualInducedIterativeMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
-                                     int nonbondedMethod, float cutoffDistance, float electricConstant ){
+                                     int nonbondedMethod, float cutoffDistance, float alphaEwald, float electricConstant ){
 
 // ---------------------------------------------------------------------------------------
 
@@ -1565,9 +1566,8 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
     amoebaGpu->amoebaSim.cutoffDistance2             = cutoffDistance*cutoffDistance;
     amoebaGpu->amoebaSim.sqrtPi                      = sqrt( 3.1415926535897932384626433832795 );
     amoebaGpu->amoebaSim.electric                    = electricConstant;
-
+    amoebaGpu->gpuContext->sim.alphaEwald            = alphaEwald;
     amoebaGpu->gpuContext->sim.nonbondedCutoff       = cutoffDistance;
-    tabulateErfc(amoebaGpu->gpuContext); 
 
     if( amoebaGpu->amoebaSim.dielec < 1.0e-05 ){
         amoebaGpu->amoebaSim.dielec               = 1.0f;
@@ -2766,7 +2766,7 @@ void amoebaGpuSetConstants(amoebaGpuContext amoebaGpu)
     SetCalculateAmoebaCudaPmeMutualInducedFieldSim( amoebaGpu );
     SetCalculateAmoebaCudaPmeFixedEFieldSim( amoebaGpu );
     SetCalculateAmoebaElectrostaticSim( amoebaGpu );
-    SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpu );
+    SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpu );
     SetCalculateAmoebaCudaMapTorquesSim( amoebaGpu );
     SetCalculateAmoebaKirkwoodSim( amoebaGpu );
     SetCalculateAmoebaKirkwoodEDiffSim( amoebaGpu );

plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h

@@ -106,9 +106,9 @@ extern void SetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
 extern void GetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
 extern void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu );
 
-extern void SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu );
-extern void GetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu );
-extern void cudaComputeAmoebaRealSpaceEwald( amoebaGpuContext amoebaGpu );
+extern void SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
+extern void GetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
+extern void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu );
 
 extern void SetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu);
 extern void GetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu);

plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h

@@ -307,7 +307,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
                                      const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
                                      const std::vector<int>& minCovalentIndices,  const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
                                      int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
-                                     int nonbondedMethod, float cutoffDistance, float electricConstant );
+                                     int nonbondedMethod, float cutoffDistance,  float alphaEwald, float electricConstant );
 
 
 extern "C"

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu

@@ -322,7 +322,7 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
 
    --------------------------------------------------------------------------------------- */
 
-void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
+static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
 {
   
    // ---------------------------------------------------------------------------------------
@@ -487,3 +487,9 @@ void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
 
          }
 }
+
+void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
+{
+    cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu );
+    kCalculateAmoebaPMEFixedMultipoleField( amoebaGpu );
+}

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu

@@ -616,6 +616,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
         // matrix multiply
 
         cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpu, amoebaGpu->psWorkVector[0],  amoebaGpu->psWorkVector[1] );
+        kCalculateAmoebaPMEInducedDipoleField( amoebaGpu );
         LAUNCHERROR("cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply Loop\n");  
 
 
@@ -654,7 +655,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
            gpu->natoms, amoebaGpu->psPolarizability->_pDevStream[0],
            amoebaGpu->psInducedDipole->_pDevStream[0], amoebaGpu->psInducedDipolePolar->_pDevStream[0],
            amoebaGpu->psE_Field->_pDevStream[0],       amoebaGpu->psE_FieldPolar->_pDevStream[0],
-           amoebaGpu->psWorkVector[0]->_pDevStream[0],     amoebaGpu->psWorkVector[1]->_pDevStream[0] );
+           amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0] );
         LAUNCHERROR("kSorUpdatePmeMutualInducedField");  
 
         // get total epsilon -- performing sums on gpu

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaRotateFrame.cu

@@ -390,7 +390,7 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
     if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
         cudaComputeAmoebaElectrostatic( amoebaGpu );
     } else {
-        cudaComputeAmoebaRealSpaceEwald( amoebaGpu );
+        cudaComputeAmoebaPmeElectrostatic( amoebaGpu );
     }
 
     // map torques to forces

plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp

@@ -2008,6 +2008,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
         multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
     }
     multipoleForce->setCutoffDistance( cutoffDistance );
+    multipoleForce->setAEwald( aewald );
     system.setDefaultPeriodicBoxVectors( Vec3(box[0], 0.0, 0.0), Vec3(0.0, box[1], 0.0), Vec3(0.0, 0.0, box[2]) );
     if( log ){
         (void) fprintf( log, "%s number of MultipoleParameter terms=%d usePme=%d aewald=%15.7e cutoffDistance=%12.4f\n",
@@ -2111,6 +2112,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
         double polarityConversion      = AngstromToNm*AngstromToNm*AngstromToNm;
         double dampingFactorConversion = sqrt( AngstromToNm );
       
+        multipoleForce->setAEwald(                multipoleForce->getAEwald()/AngstromToNm );
         multipoleForce->setCutoffDistance(        multipoleForce->getCutoffDistance()*AngstromToNm );
         multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
 
@@ -2165,8 +2167,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
                         (useOpenMMUnits ? "OpenMM" : "Amoeba") );
 
         std::string nonbondedMethod = multipoleForce->getNonbondedMethod( ) == AmoebaMultipoleForce::PME ? "PME" : "NoCutoff";
-        (void) fprintf( log, "NonbondedMethod=%s cutoff=%15.7e.\n", nonbondedMethod.c_str(),
-                         multipoleForce->getCutoffDistance() );
+        (void) fprintf( log, "NonbondedMethod=%s aEwald=%15.7e cutoff=%15.7e.\n", nonbondedMethod.c_str(),
+                        multipoleForce->getAEwald(), multipoleForce->getCutoffDistance() );
 
         Vec3 a,b,c;
         system.getDefaultPeriodicBoxVectors( a, b, c );