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Commit b90e80ff authored by Mark Friedrichs's avatar Mark Friedrichs
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Renamed OpenMMAmoeba,h to AmoebaOpenMM for consistency w/ other plugin

parent 8928a337
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Showing with 98 additions and 57 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
View file @ b90e80ff
......@@ -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
View file @ b90e80ff
......@@ -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
View file @ b90e80ff
......@@ -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";
......@@ -576,33 +581,71 @@ 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 ){
gpu->psInteractionCount->Download();
gpu->psInteractingWorkUnit->Download();
gpu->psInteractionFlag->Download();
amoebaGpu->psWorkUnit->Download();
(void) fprintf( amoebaGpu->log, "Ixn count=%u\n", gpu->psInteractionCount->_pSysStream[0][0] );
for( unsigned int ii = 0; ii < gpu->psInteractingWorkUnit->_length; ii++ ){
unsigned int x = gpu->psInteractingWorkUnit->_pSysStream[0][ii];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
//unsigned int y = ((x >> 2) & 0x7fff);
unsigned int exclusions = (x & 0x1);
x = (x >> 17) << GRIDBITS;
// x = (x >> 17);
(void) fprintf( amoebaGpu->log, "GpuCell %8u %8u [%5u %5u %1u] %10u ", ii, gpu->psInteractingWorkUnit->_pSysStream[0][ii], x,y,exclusions, gpu->psInteractionFlag->_pSysStream[0][ii] );
x = amoebaGpu->psWorkUnit->_pSysStream[0][ii];
y = ((x >> 2) & 0x7fff) << GRIDBITS;
exclusions = (x & 0x1);
x = (x >> 17) << GRIDBITS;
(void) fprintf( amoebaGpu->log, " AmGpu %8u [%5u %5u %1u]\n", amoebaGpu->psWorkUnit->_pSysStream[0][ii], x,y,exclusions );
}
}
/*
if( 0 ){
gpu->psInteractionCount->Download();
gpu->psInteractingWorkUnit->Download();
gpu->psInteractionFlag->Download();
amoebaGpu->psWorkUnit->Download();
(void) fprintf( amoebaGpu->log, "Ixn count=%u\n", gpu->psInteractionCount->_pSysStream[0][0] );
for( unsigned int ii = 0; ii < gpu->psInteractingWorkUnit->_length; ii++ ){
unsigned int x = gpu->psInteractingWorkUnit->_pSysStream[0][ii];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
//unsigned int y = ((x >> 2) & 0x7fff);
unsigned int exclusions = (x & 0x1);
x = (x >> 17) << GRIDBITS;
// x = (x >> 17);
(void) fprintf( amoebaGpu->log, "GpuCell %8u %8u [%5u %5u %1u] %10u ", ii, gpu->psInteractingWorkUnit->_pSysStream[0][ii], x,y,exclusions, gpu->psInteractionFlag->_pSysStream[0][ii] );
x = amoebaGpu->psWorkUnit->_pSysStream[0][ii];
y = ((x >> 2) & 0x7fff) << GRIDBITS;
exclusions = (x & 0x1);
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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
......@@ -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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
/* -------------------------------------------------------------------------- *
* 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
View file @ b90e80ff
......@@ -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 *
......
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