Renamed OpenMMAmoeba,h to AmoebaOpenMM for consistency w/ other plugin

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

@@ -1413,7 +1413,7 @@ void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
         zeroForce( amoebaGpu );
     }
 
-    if( 0 ){
+    if( 1 ){
         gpuContext gpu = amoebaGpu->gpuContext;
         std::vector<int> fileId;
 
@@ -1448,7 +1448,6 @@ void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
         cudaWriteVectorOfDoubleVectorsToFile( "CudaPrePmeForce", fileId, outputVector );
     }
 
-//zeroForce( amoebaGpu );
     cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpu );
     kCalculateAmoebaPMEInducedDipoleForces( amoebaGpu );
 }

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

@@ -33,8 +33,8 @@ void GetCalculateAmoebaCudaPmeMutualInducedFieldSim(amoebaGpuContext amoebaGpu)
     RTERROR(status, "GetCalculateAmoebaCudaPmeMutualInducedFieldSim: cudaMemcpyFromSymbol: SetSim copy from cAmoebaSim failed");
 }
 
-//#define AMOEBA_DEBUG
-#undef AMOEBA_DEBUG
+#define AMOEBA_DEBUG
+//#undef AMOEBA_DEBUG
 
 #undef INCLUDE_MI_FIELD_BUFFERS
 #define INCLUDE_MI_FIELD_BUFFERS 

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

@@ -547,6 +547,11 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
   
 }
 
+//#define GET_INDUCED_DIPOLE_FROM_FILE
+#ifdef GET_INDUCED_DIPOLE_FROM_FILE
+#include <stdlib.h>
+#endif
+
 void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaGeneralizedKirkwood ) 
 {
     std::string methodName = "kCalculateAmoebaMultipoleForces";
@@ -576,8 +581,8 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
             kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
                     sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
             LAUNCHERROR("kFindInteractionsWithinBlocksPeriodic");
-
-if( 0 ){ 
+/*
+            if( 0 ){ 
                 gpu->psInteractionCount->Download();
                 gpu->psInteractingWorkUnit->Download();
                 gpu->psInteractionFlag->Download();
@@ -599,10 +604,48 @@ if( 0 ){
                                  x          = (x >> 17) << GRIDBITS;
                     (void) fprintf( amoebaGpu->log, "   AmGpu %8u [%5u %5u %1u]\n", amoebaGpu->psWorkUnit->_pSysStream[0][ii], x,y,exclusions );
                 }    
-}
-
+            }
+*/
             cudaComputeAmoebaPmeFixedEField( amoebaGpu );
             cudaComputeAmoebaPmeMutualInducedField( amoebaGpu );
+
+#ifdef GET_INDUCED_DIPOLE_FROM_FILE
+            if( 0 ){
+                //std::string fileName = "waterInducedDipole.txt";
+                std::string fileName = "water_3_MI.txt";
+                StringVectorVector fileContents;
+                readFile( fileName, fileContents );
+                unsigned int offset  = 0; 
+                (void) fprintf( amoebaGpu->log, "Read file: %s %u\n", fileName.c_str(), fileContents.size() ); fflush(  amoebaGpu->log );
+                for( unsigned int ii = 1; ii < fileContents.size()-1; ii++ ){
+            
+                    StringVector lineTokens     = fileContents[ii];
+                    unsigned int lineTokenIndex = 1; 
+            
+                    (void) fprintf( amoebaGpu->log, "   %u %s [%s %s %s] [%15.7e %15.7e %15.7e]\n", ii, lineTokens[0].c_str(),
+                                    lineTokens[lineTokenIndex].c_str(), lineTokens[lineTokenIndex+1].c_str(), lineTokens[lineTokenIndex+2].c_str(),
+                                    amoebaGpu->psInducedDipole->_pSysStream[0][offset], amoebaGpu->psInducedDipole->_pSysStream[0][offset+1], amoebaGpu->psInducedDipole->_pSysStream[0][offset+2]); 
+                    amoebaGpu->psInducedDipole->_pSysStream[0][offset++]       = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                    amoebaGpu->psInducedDipole->_pSysStream[0][offset++]       = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                    amoebaGpu->psInducedDipole->_pSysStream[0][offset++]       = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                    offset                                                    -= 3;
+                    amoebaGpu->psInducedDipolePolar->_pSysStream[0][offset++]  = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                    amoebaGpu->psInducedDipolePolar->_pSysStream[0][offset++]  = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                    amoebaGpu->psInducedDipolePolar->_pSysStream[0][offset++]  = static_cast<float>(atof(lineTokens[lineTokenIndex++].c_str()));
+                }
+                (void) fflush( amoebaGpu->log );
+                float conversion = 0.1f;
+                for( int ii = 0; ii < 3*gpu->natoms; ii++ ){
+                    amoebaGpu->psInducedDipole->_pSysStream[0][ii]       *= conversion;
+                    amoebaGpu->psInducedDipolePolar->_pSysStream[0][ii]  *= conversion;
+                }    
+                //amoebaGpu->gpuContext->sim.alphaEwald = 5.4459052e+00f;
+                //SetCalculateAmoebaPmeDirectElectrostaticSim(amoebaGpu);
+                amoebaGpu->psInducedDipole->Upload();
+                amoebaGpu->psInducedDipolePolar->Upload();
+           }
+#endif
+
         }
     }
 

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -37,7 +37,7 @@
 //#include "AmoebaTinkerParameterFile.h"
 const double DegreesToRadians = 3.14159265/180.0;
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/LangevinIntegrator.h"

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -36,7 +36,7 @@
 #include "../../../tests/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>

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

 /* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
+ *                                   OpenMMAmoeba                             *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *
@@ -34,9 +34,8 @@
  */
 
 #include "../../../tests/AssertionUtilities.h"
-//#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
-#include "AmoebaOpenMM.h"
+#include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaVdwForce.h"
 #include "openmm/LangevinIntegrator.h"

plugins/amoeba/platforms/reference/include/AmoebaReferenceKernelFactory.h

@@ -2,7 +2,7 @@
 #define AMOEBA_OPENMM_REFERERENCE_KERNEL_FACTORY_H_
 
 /* -------------------------------------------------------------------------- *
- *                            AmoebaOpenMM                                    *
+ *                            OpenMMAmoeba                                    *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp

 /* -------------------------------------------------------------------------- *
- *                              AmoebaOpenMM                                  *
+ *                              OpenMMAmoeba                                  *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

 /* -------------------------------------------------------------------------- *
- *                               AmoebaOpenMM                                 *
+ *                               OpenMMAmoeba                                 *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -2,7 +2,7 @@
 #define AMOEBA_OPENMM_REFERENCE_KERNELS_H_
 
 /* -------------------------------------------------------------------------- *
- *                              AmoebaOpenMM                                  *
+ *                              OpenMMAmoeba                                  *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *