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Commit f38a47e4 authored by Mark Friedrichs's avatar Mark Friedrichs
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Cleaned up for Windows compilation 

Removed cubic/quartic per-atom parameters from AmoebaHarmonicBondForce
parent 7eaa5d29
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Showing with 171 additions and 160 deletions
plugins/amoeba/openmmapi/include/AmoebaHarmonicBondForce.h
View file @ f38a47e4
......@@ -94,25 +94,23 @@ public:
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param cubic k the cubic harmonic force constant for the bond
* @param quartic k the quartic harmonic force constant for the bond
* @param quadratic k the quadratic harmonic force constant for the bond
* @param k the quadratic harmonic force constant for the bond
* @return the index of the bond that was added
*/
int addBond(int particle1, int particle2, double length, double quadraticK, double cubicK = DEFAULT_GLOBAL_K, double quarticK = DEFAULT_GLOBAL_K );
int addBond(int particle1, int particle2, double length, double quadraticK );
/**
* Get the force field parameters for a bond term.
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param quadratic k the quadratic harmonic force constant for the bond
* @param cubic k the cubic harmonic force constant for the bond
* @param quartic k the quartic harmonic force constant for the bond
*/
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK, double& cubicK, double& quarticK ) const;
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
/**
* Set the force field parameters for a bond term.
......@@ -121,18 +119,15 @@ public:
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param cubic k the cubic harmonic force constant for the bond
* @param quartic k the quartic harmonic force constant for the bond
* @param quadratic k the quadratic harmonic force constant for the bond
* @param k the quadratic harmonic force constant for the bond
*/
void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK, double cubicK = DEFAULT_GLOBAL_K, double quarticK = DEFAULT_GLOBAL_K);
void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
protected:
double _globalQuarticK, _globalCubicK;
ForceImpl* createImpl();
private:
static const double DEFAULT_GLOBAL_K;
class BondInfo;
// Retarded visual studio compiler complains about being unable to
......@@ -152,14 +147,13 @@ private:
class AmoebaHarmonicBondForce::BondInfo {
public:
int particle1, particle2;
double length, quadraticK, cubicK, quarticK;
double length, quadraticK;
BondInfo() {
particle1 = particle2 = -1;
length = quadraticK = 0.0;
cubicK = quarticK = DEFAULT_GLOBAL_K;
}
BondInfo(int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK) :
particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK), cubicK(cubicK), quarticK(quarticK) {
BondInfo(int particle1, int particle2, double length, double quadraticK ) :
particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
}
};
......
plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForce.cpp
View file @ f38a47e4
......@@ -36,33 +36,27 @@
using namespace OpenMM;
const double AmoebaHarmonicBondForce::DEFAULT_GLOBAL_K = -1234.567891234;
AmoebaHarmonicBondForce::AmoebaHarmonicBondForce() {
_globalCubicK = _globalQuarticK = 0.0;
}
int AmoebaHarmonicBondForce::addBond(int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK) {
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK, cubicK, quarticK));
int AmoebaHarmonicBondForce::addBond(int particle1, int particle2, double length, double quadraticK) {
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK ));
return bonds.size()-1;
}
void AmoebaHarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK, double& cubicK, double& quarticK ) const {
void AmoebaHarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const {
particle1 = bonds[index].particle1;
particle2 = bonds[index].particle2;
length = bonds[index].length;
quadraticK = bonds[index].quadraticK;
cubicK = bonds[index].cubicK == DEFAULT_GLOBAL_K ? _globalCubicK : bonds[index].cubicK;
quarticK = bonds[index].quarticK == DEFAULT_GLOBAL_K ? _globalQuarticK : bonds[index].quarticK;
}
void AmoebaHarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK ) {
void AmoebaHarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK ) {
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].length = length;
bonds[index].quadraticK = quadraticK;
bonds[index].cubicK = cubicK;
bonds[index].quarticK = quarticK;
}
void AmoebaHarmonicBondForce::setAmoebaGlobalHarmonicBondCubic(double cubicK ) {
......
plugins/amoeba/platforms/cuda/sharedTarget/CMakeLists.txt
View file @ f38a47e4
......@@ -35,9 +35,6 @@ IF(LOG)
ENDIF(LOG)
## ----------------------------------------------------------------------------
# message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
# INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
# message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
LINK_DIRECTORIES(${CUDA_TARGET_LINK})
FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
......@@ -74,6 +71,6 @@ CUDA_ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES}
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME} )
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}Cuda_d optimized ${OPENMM_LIBRARY_NAME}Cuda )
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_AMOEBA_LIBRARY_NAME}_d optimized ${OPENMM_AMOEBA_LIBRARY_NAME} )
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMMCUDAAMOEBA_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMMCUDA_BUILDING_SHARED_LIBRARY -DOPENMMCUDAAMOEBA_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
plugins/amoeba/platforms/cuda/src/AmoebaCudaData.h
View file @ f38a47e4
......@@ -96,7 +96,7 @@ public:
*
* @return amoebaGpuContext
*/
amoebaGpuContext getAmoebaGpu( void ) const;
amoebaGpuContext OPENMMCUDA_EXPORT getAmoebaGpu( void ) const;
/**
* Set accessor for LocalForcesKernel
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ f38a47e4
......@@ -73,23 +73,21 @@ void CudaCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, con
std::vector<int> particle2(numBonds);
std::vector<float> length(numBonds);
std::vector<float> quadratic(numBonds);
std::vector<float> cubic(numBonds);
std::vector<float> quartic(numBonds);
for (int i = 0; i < numBonds; i++) {
int particle1Index, particle2Index;
double lengthValue, kValue, cubicValue, quarticValue;
force.getBondParameters(i, particle1Index, particle2Index, lengthValue, kValue, cubicValue, quarticValue);
double lengthValue, kValue;
force.getBondParameters(i, particle1Index, particle2Index, lengthValue, kValue );
particle1[i] = particle1Index;
particle2[i] = particle2Index;
length[i] = static_cast<float>( lengthValue );
quadratic[i] = static_cast<float>( kValue );
cubic[i] = static_cast<float>( cubicValue );
quartic[i] = static_cast<float>( quarticValue );
}
gpuSetAmoebaBondParameters( data.getAmoebaGpu(), particle1, particle2, length, quadratic, cubic, quartic);
gpuSetAmoebaBondParameters( data.getAmoebaGpu(), particle1, particle2, length, quadratic,
static_cast<float>(force.getAmoebaGlobalHarmonicBondCubic()),
static_cast<float>(force.getAmoebaGlobalHarmonicBondQuartic()) );
}
void CudaCalcAmoebaHarmonicBondForceKernel::executeForces(ContextImpl& context) {
......@@ -132,10 +130,10 @@ void CudaCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, co
k[i] = static_cast<float>( kQuadratic );
}
gpuSetAmoebaAngleParameters(data.getAmoebaGpu(), particle1, particle2, particle3, angle, k,
force.getAmoebaGlobalHarmonicAngleCubic(),
force.getAmoebaGlobalHarmonicAngleQuartic(),
force.getAmoebaGlobalHarmonicAnglePentic(),
force.getAmoebaGlobalHarmonicAngleSextic() );
static_cast<float>(force.getAmoebaGlobalHarmonicAngleCubic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAngleQuartic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAnglePentic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAngleSextic()) );
}
......@@ -182,10 +180,10 @@ void CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& sys
k[i] = static_cast<float>( kQuadratic );
}
gpuSetAmoebaInPlaneAngleParameters(data.getAmoebaGpu(), particle1, particle2, particle3, particle4, angle, k,
force.getAmoebaGlobalHarmonicInPlaneAngleCubic(),
force.getAmoebaGlobalHarmonicInPlaneAngleQuartic(),
force.getAmoebaGlobalHarmonicInPlaneAnglePentic(),
force.getAmoebaGlobalHarmonicInPlaneAngleSextic() );
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleCubic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleQuartic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAnglePentic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleSextic() ) );
}
......@@ -237,9 +235,9 @@ void CudaCalcAmoebaTorsionForceKernel::initialize(const System& system, const Am
force.getTorsionParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], torsionParameter1, torsionParameter2, torsionParameter3 );
for ( unsigned int jj = 0; jj < 3; jj++) {
torsionParameters1F[jj] = torsionParameter1[jj];
torsionParameters2F[jj] = torsionParameter2[jj];
torsionParameters3F[jj] = torsionParameter3[jj];
torsionParameters1F[jj] = static_cast<float>(torsionParameter1[jj]);
torsionParameters2F[jj] = static_cast<float>(torsionParameter2[jj]);
torsionParameters3F[jj] = static_cast<float>(torsionParameter3[jj]);
}
torsionParameters1[i] = torsionParameters1F;
torsionParameters2[i] = torsionParameters2F;
......@@ -290,7 +288,7 @@ void CudaCalcAmoebaPiTorsionForceKernel::initialize(const System& system, const
double torsionKParameter;
force.getPiTorsionParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], particle5[i], particle6[i], torsionKParameter);
torsionKParameters[i] = torsionKParameter;
torsionKParameters[i] = static_cast<float>(torsionKParameter);
}
gpuSetAmoebaPiTorsionParameters(data.getAmoebaGpu(), particle1, particle2, particle3, particle4, particle5, particle6, torsionKParameters);
}
......@@ -335,10 +333,10 @@ void CudaCalcAmoebaStretchBendForceKernel::initialize(const System& system, cons
double lengthAB, lengthCB, angle, k;
force.getStretchBendParameters(i, particle1[i], particle2[i], particle3[i], lengthAB, lengthCB, angle, k);
lengthABParameters[i] = lengthAB;
lengthCBParameters[i] = lengthCB;
angleParameters[i] = angle;
kParameters[i] = k;
lengthABParameters[i] = static_cast<float>(lengthAB);
lengthCBParameters[i] = static_cast<float>(lengthCB);
angleParameters[i] = static_cast<float>(angle);
kParameters[i] = static_cast<float>(k);
}
gpuSetAmoebaStretchBendParameters(data.getAmoebaGpu(), particle1, particle2, particle3, lengthABParameters, lengthCBParameters, angleParameters, kParameters);
......@@ -381,13 +379,13 @@ void CudaCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& system, c
double k;
force.getOutOfPlaneBendParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], k);
kParameters[i] = k;
kParameters[i] = static_cast<float>(k);
}
gpuSetAmoebaOutOfPlaneBendParameters(data.getAmoebaGpu(), particle1, particle2, particle3, particle4, kParameters,
force.getAmoebaGlobalOutOfPlaneBendCubic(),
force.getAmoebaGlobalOutOfPlaneBendQuartic(),
force.getAmoebaGlobalOutOfPlaneBendPentic(),
force.getAmoebaGlobalOutOfPlaneBendSextic() );
static_cast<float>( force.getAmoebaGlobalOutOfPlaneBendCubic()),
static_cast<float>( force.getAmoebaGlobalOutOfPlaneBendQuartic()),
static_cast<float>( force.getAmoebaGlobalOutOfPlaneBendPentic()),
static_cast<float>( force.getAmoebaGlobalOutOfPlaneBendSextic() ) );
}
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ f38a47e4
......@@ -29,16 +29,18 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
//using namespace std;
#include "cudaKernels.h"
#include "amoebaCudaKernels.h"
// for some reason, these are not being included w/ cudaKernels.h on Windows
extern void OPENMMCUDA_EXPORT SetCalculateObcGbsaForces2Sim(gpuContext gpu);
extern void OPENMMCUDA_EXPORT SetForcesSim(gpuContext gpu);
#include <sstream>
#include <limits>
#ifdef WIN32
#include <windows.h>
// #include <windows.h>
#endif
#define DUMP_PARAMETERS 0
......@@ -207,9 +209,11 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
if( amoebaGpu->psAmoebaBondParameter)(void) fprintf( log, "\n" );
gpuPrintCudaStreamInt4( amoebaGpu->psAmoebaBondID, log );
gpuPrintCudaStreamFloat4( amoebaGpu->psAmoebaBondParameter, log );
gpuPrintCudaStreamFloat2( amoebaGpu->psAmoebaBondParameter, log );
(void) fprintf( log, " amoebaBonds %u\n", amoebaGpu->amoebaSim.amoebaBonds );
(void) fprintf( log, " amoebaBond_offset %u\n", amoebaGpu->amoebaSim.amoebaBond_offset );
(void) fprintf( log, " cubic %14.7e\n", amoebaGpu->amoebaSim.amoebaBondCubicParameter);
(void) fprintf( log, " quartic %14.7e\n", amoebaGpu->amoebaSim.amoebaBondQuarticicParameter);
(void) fprintf( log, " pAmoebaBondID %p\n", amoebaGpu->amoebaSim.pAmoebaBondID );
(void) fprintf( log, " pAmoebaBondParameter %p\n", amoebaGpu->amoebaSim.pAmoebaBondParameter );
......@@ -415,18 +419,22 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
extern "C"
void gpuSetAmoebaBondParameters(amoebaGpuContext amoebaGpu, const std::vector<int>& particles1, const std::vector<int>& particles2,
const std::vector<float>& length, const std::vector<float>& k, const std::vector<float>& cubic,
const std::vector<float>& quartic)
const std::vector<float>& length, const std::vector<float>& k, float cubic, float quartic)
{
_gpuContext* gpu = amoebaGpu->gpuContext;
int bonds = particles1.size();
amoebaGpu->amoebaSim.amoebaBonds = bonds;
CUDAStream<int4>* psBondID = new CUDAStream<int4>(bonds, 1, "AmoebaBondID");
amoebaGpu->psAmoebaBondID = psBondID;
amoebaGpu->amoebaSim.pAmoebaBondID = psBondID->_pDevStream[0];
CUDAStream<float4>* psBondParameter = new CUDAStream<float4>(bonds, 1, "AmoebaBondParameter");
amoebaGpu->psAmoebaBondParameter = psBondParameter;
amoebaGpu->amoebaSim.pAmoebaBondParameter = psBondParameter->_pDevStream[0];
_gpuContext* gpu = amoebaGpu->gpuContext;
int bonds = particles1.size();
amoebaGpu->amoebaSim.amoebaBonds = bonds;
CUDAStream<int4>* psBondID = new CUDAStream<int4>(bonds, 1, "AmoebaBondID");
amoebaGpu->psAmoebaBondID = psBondID;
amoebaGpu->amoebaSim.pAmoebaBondID = psBondID->_pDevStream[0];
CUDAStream<float2>* psBondParameter = new CUDAStream<float2>(bonds, 1, "AmoebaBondParameter");
amoebaGpu->psAmoebaBondParameter = psBondParameter;
amoebaGpu->amoebaSim.pAmoebaBondParameter = psBondParameter->_pDevStream[0];
amoebaGpu->amoebaSim.amoebaBondCubicParameter = cubic;
amoebaGpu->amoebaSim.amoebaBondQuarticicParameter = quartic;
for (int i = 0; i < bonds; i++)
{
(*psBondID)[i].x = particles1[i];
......@@ -435,8 +443,6 @@ void gpuSetAmoebaBondParameters(amoebaGpuContext amoebaGpu, const std::vector<in
(*psBondID)[i].w = gpu->pOutputBufferCounter[(*psBondID)[i].y]++;
(*psBondParameter)[i].x = length[i];
(*psBondParameter)[i].y = k[i];
(*psBondParameter)[i].z = cubic[i];
(*psBondParameter)[i].w = quartic[i];
#undef DUMP_PARAMETERS
#define DUMP_PARAMETERS 5
......@@ -444,7 +450,7 @@ void gpuSetAmoebaBondParameters(amoebaGpuContext amoebaGpu, const std::vector<in
if( amoebaGpu->log && (i < DUMP_PARAMETERS || i > bonds - (DUMP_PARAMETERS + 1) ) )
fprintf( amoebaGpu->log, "Bonds: %5d [%5d %5d %5d %5d] L=%14.7e k[%14.7e %14.7e %14.7e] [%5d %5d]\n",
i, (*psBondID)[i].x, (*psBondID)[i].y, (*psBondID)[i].z, (*psBondID)[i].w,
(*psBondParameter)[i].x, (*psBondParameter)[i].y, (*psBondParameter)[i].z, (*psBondParameter)[i].w,
(*psBondParameter)[i].x, (*psBondParameter)[i].y, cubic, quartic,
gpu->pOutputBufferCounter[(*psBondID)[i].x],
gpu->pOutputBufferCounter[(*psBondID)[i].y] );
#endif
......@@ -938,7 +944,7 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vect
(void) fprintf( amoebaGpu->log, "totalGridEntries=%u totalFloat4 entries=%u\n", totalGridEntries, totalEntries );
}
int index = 0;
unsigned int index = 0;
for (unsigned int ii = 0; ii < floatGrids.size(); ii++) {
for (unsigned int jj = 0; jj < floatGrids[ii].size(); jj++) {
for (unsigned int kk = 0; kk < floatGrids[ii][jj].size(); kk++) {
......@@ -1053,7 +1059,9 @@ void gpuSetAmoebaBondOffsets(amoebaGpuContext amoebaGpu )
amoebaGpu->amoebaSim.amoebaTorsionTorsion_offset = amoebaGpu->amoebaSim.amoebaOutOfPlaneBend_offset +
(amoebaGpu->psAmoebaTorsionTorsionID1 ? amoebaGpu->psAmoebaTorsionTorsionID1->_stride : 0);
gpu->sim.localForces_threads_per_block = (std::max(amoebaGpu->amoebaSim.amoebaTorsionTorsion_offset, gpu->sim.customBonds) / gpu->sim.blocks + 15) & 0xfffffff0;
//gpu->sim.localForces_threads_per_block = (std::max(amoebaGpu->amoebaSim.amoebaTorsionTorsion_offset, gpu->sim.customBonds) / gpu->sim.blocks + 15) & 0xfffffff0;
unsigned int maxI = (amoebaGpu->amoebaSim.amoebaTorsionTorsion_offset > gpu->sim.customBonds) ? amoebaGpu->amoebaSim.amoebaTorsionTorsion_offset : gpu->sim.customBonds;
gpu->sim.localForces_threads_per_block = (maxI/gpu->sim.blocks + 15) & 0xfffffff0;
if (gpu->sim.localForces_threads_per_block > gpu->sim.max_localForces_threads_per_block)
gpu->sim.localForces_threads_per_block = gpu->sim.max_localForces_threads_per_block;
if (gpu->sim.localForces_threads_per_block < 1)
......@@ -1495,7 +1503,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
amoebaGpu->amoebaSim.dielec = 1.0f;
}
for( unsigned int ii = 0; ii < charges.size(); ii++ ){
for( int ii = 0; ii < static_cast<int>(charges.size()); ii++ ){
// axis type & multipole particles ids
......@@ -2140,16 +2148,16 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
std::vector<int> minCellIndex( dim + 1 );
std::vector<int> maxCellIndex( dim + 1 );
for (int ii = 0; ii <= dim; ii++)
for(unsigned int ii = 0; ii <= dim; ii++)
{
minCellIndex[ii] = paddedAtoms + 1;
maxCellIndex[ii] = 0;
}
for (unsigned int atom1 = 0; atom1 < actualAtoms; atom1++)
for(unsigned int atom1 = 0; atom1 < actualAtoms; atom1++)
{
int x = atom1/grid;
for (int jj = 0; jj < exclusions[atom1].size(); jj++ )
for ( unsigned int jj = 0; jj < exclusions[atom1].size(); jj++ )
{
if( exclusions[atom1][jj] > maxCellIndex[x] )
{
......@@ -2166,7 +2174,7 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
if( debugOn && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s min/max cell indices:\n", methodName.c_str() );
for (int ii = 0; ii < dim; ii++)
for ( unsigned int ii = 0; ii < dim; ii++)
{
(void) fprintf( amoebaGpu->log, "%6d [%6d %6d]\n", ii, minCellIndex[ii], maxCellIndex[ii] );
}
......@@ -2180,14 +2188,14 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
amoebaGpu->amoebaSim.pVdwExclusionIndicesIndex = psVdwExclusionIndicesIndex->_pDevStream[0];
//memset( amoebaGpu->psVdwExclusionIndicesIndex->_pSysStream[0], 0, sizeof(cells)*sizeof(int) );
for (int ii = 0; ii < cells; ii++)
for (unsigned int ii = 0; ii < cells; ii++)
{
amoebaGpu->psVdwExclusionIndicesIndex->_pSysStream[0][ii] = -1;
}
int numWithExclusionIndices = 0;
int gridOffset = grid - 1;
int lastBlock = (paddedAtoms > amoebaGpu->gpuContext->natoms) ? (amoebaGpu->gpuContext->natoms)/grid : -1;
for (int ii = 0; ii < cells; ii++)
int lastBlock = (static_cast<int>(paddedAtoms) > amoebaGpu->gpuContext->natoms) ? (amoebaGpu->gpuContext->natoms)/grid : -1;
for (unsigned int ii = 0; ii < cells; ii++)
{
unsigned int x, y, exclusion;
decodeCell( pWorkList[ii], &x, &y, &exclusion );
......@@ -2201,7 +2209,7 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
// ii, x, y, xAtomMin, xAtomMax, minCellIndex[y], maxCellIndex[y], numWithExclusionIndices, lastBlock );
}
}
for (int ii = 0; ii < cells; ii++)
for ( unsigned int ii = 0; ii < cells; ii++)
{
if( amoebaGpu->psVdwExclusionIndicesIndex->_pSysStream[0][ii] == -1 )
{
......@@ -2213,7 +2221,7 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
if( debugOn && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s %d cells w/ exclusions\n", methodName.c_str(), numWithExclusionIndices );
for (int ii = 0; ii < cells; ii++)
for (unsigned int ii = 0; ii < cells; ii++)
{
unsigned int x, y, exclusion;
decodeCell( pWorkList[ii], &x, &y, &exclusion );
......@@ -2774,10 +2782,10 @@ static int matchMaps( std::string idString, MapIntFloat* map1, MapIntFloat* map
static void getScalingDegrees( amoebaGpuContext amoebaGpu, unsigned int particleI, unsigned int particleJ, int* covalentDegree, int* polarizationDegree )
{
int particlesOffset = particleI*amoebaGpu->maxCovalentDegreeSz;
int particlesOffset = particleI*amoebaGpu->maxCovalentDegreeSz;
int minCovalentIndex = amoebaGpu->psCovalentDegree->_pSysStream[0][particlesOffset];
int minCovalentPolarizationIndex = amoebaGpu->psPolarizationDegree->_pSysStream[0][particlesOffset];
unsigned int minCovalentIndex = static_cast<unsigned int>(amoebaGpu->psCovalentDegree->_pSysStream[0][particlesOffset]);
unsigned int minCovalentPolarizationIndex = static_cast<unsigned int>( amoebaGpu->psPolarizationDegree->_pSysStream[0][particlesOffset]);
if( particleJ < minCovalentIndex || particleJ > (minCovalentIndex + amoebaGpu->maxCovalentDegreeSz) ){
*covalentDegree = 0;
......@@ -2923,13 +2931,13 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu )
minCellIndex.resize( dim + 1 );
maxCellIndex.resize( dim + 1 );
for (int ii = 0; ii <= dim; ii++)
for ( unsigned int ii = 0; ii <= dim; ii++)
{
minCellIndex[ii] = paddedAtoms + 1;
maxCellIndex[ii] = 0;
}
for (int atom1 = 0; atom1 < paddedAtoms; atom1++)
for (unsigned int atom1 = 0; atom1 < paddedAtoms; atom1++)
{
int x = atom1/grid;
int particlesOffset = atom1*amoebaGpu->maxCovalentDegreeSz;
......@@ -2962,7 +2970,7 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu )
if( debugOn && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s min/max cell indices:\n", methodName.c_str() );
for (int ii = 0; ii < dim; ii++)
for (unsigned int ii = 0; ii < dim; ii++)
{
(void) fprintf( amoebaGpu->log, "%6d [%6d %6d]\n", ii, minCellIndex[ii], maxCellIndex[ii] );
}
......@@ -2978,8 +2986,8 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu )
memset( amoebaGpu->psScalingIndicesIndex->_pSysStream[0], 0, sizeof( cells)*sizeof( unsigned int) );
int numWithScalingIndices = 0;
int gridOffset = grid - 1;
int lastBlock = (paddedAtoms > amoebaGpu->gpuContext->natoms) ? (amoebaGpu->gpuContext->natoms)/grid : -1;
for (int ii = 0; ii < cells; ii++)
int lastBlock = (static_cast<int>(paddedAtoms) > amoebaGpu->gpuContext->natoms) ? (amoebaGpu->gpuContext->natoms)/grid : -1;
for (unsigned int ii = 0; ii < cells; ii++)
{
unsigned int x, y, exclusion;
decodeCell( pWorkList[ii], &x, &y, &exclusion );
......@@ -3019,7 +3027,7 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu )
if( debugOn && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s %d cells w/ exclusions\n",
methodName.c_str(), numWithScalingIndices );
for (int ii = 0; ii < cells; ii++)
for (unsigned int ii = 0; ii < cells; ii++)
{
unsigned int x, y, exclusion;
decodeCell( pWorkList[ii], &x, &y, &exclusion );
......@@ -3703,7 +3711,7 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId
for ( unsigned int ii = 0; ii < outputVector.size(); ii++ ){
int index = 0;
for ( unsigned int jj = 0; jj < outputVector[ii].size(); jj++ ){
values[index++] = outputVector[ii][jj];
values[index++] = static_cast<float>(outputVector[ii][jj]);
}
printValues( filePtr, static_cast<int>(ii), index, values );
}
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaTypes.h
View file @ f38a47e4
......@@ -46,7 +46,9 @@ struct cudaAmoebaGmxSimulation {
unsigned int amoebaBonds; // Number of bonds
int4* pAmoebaBondID; // Bond atom and output buffer IDs
float4* pAmoebaBondParameter; // Bond parameters
float2* pAmoebaBondParameter; // Bond parameters
float amoebaBondCubicParameter; // cubic bond parameters
float amoebaBondQuarticicParameter; // quartic bond parameters
unsigned int amoebaBond_offset; // Offset to end of bonds
unsigned int amoebaAngles; // Number of bond angles
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ f38a47e4
......@@ -88,7 +88,7 @@ struct _amoebaGpuContext {
int maxCovalentDegreeSz;
CUDAStream<int4>* psAmoebaBondID;
CUDAStream<float4>* psAmoebaBondParameter;
CUDAStream<float2>* psAmoebaBondParameter;
CUDAStream<int4>* psAmoebaAngleID1;
CUDAStream<int2>* psAmoebaAngleID2;
......@@ -254,7 +254,7 @@ void amoebaGpuBuildScalingList( amoebaGpuContext gpu );
extern "C"
void gpuSetAmoebaBondParameters(amoebaGpuContext gpu, const std::vector<int>& atom1, const std::vector<int>& atom2,
const std::vector<float>& length, const std::vector<float>& k, const std::vector<float>& cubic, const std::vector<float>& quartic);
const std::vector<float>& length, const std::vector<float>& k, float cubic, float quartic);
extern "C"
void gpuSetAmoebaAngleParameters(amoebaGpuContext gpu, const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<int>& atom3,
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaLocalForces.cu
View file @ f38a47e4
......@@ -317,7 +317,7 @@ void kCalculateAmoebaLocalForces_kernel()
int4 atom = cAmoebaSim.pAmoebaBondID[pos];
float4 atomA = cSim.pPosq[atom.x];
float4 atomB = cSim.pPosq[atom.y];
float4 bond = cAmoebaSim.pAmoebaBondParameter[pos];
float2 bond = cAmoebaSim.pAmoebaBondParameter[pos];
float dx = atomB.x - atomA.x;
float dy = atomB.y - atomA.y;
float dz = atomB.z - atomA.z;
......@@ -330,8 +330,12 @@ void kCalculateAmoebaLocalForces_kernel()
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
#else
float deltaIdeal2 = deltaIdeal*deltaIdeal;
energy += bond.y * deltaIdeal2*( 1.0f + bond.z*deltaIdeal + bond.w*deltaIdeal2 );
float dEdR = 2.0f*bond.y * deltaIdeal*( 1.0f + 1.5f*bond.z*deltaIdeal + 2.0f*bond.w*deltaIdeal2 );
energy += bond.y * deltaIdeal2*( 1.0f + cAmoebaSim.amoebaBondCubicParameter*deltaIdeal +
cAmoebaSim.amoebaBondQuarticicParameter*deltaIdeal2 );
float dEdR = 2.0f*bond.y * deltaIdeal*( 1.0f + 1.5f*cAmoebaSim.amoebaBondCubicParameter*deltaIdeal +
2.0f*cAmoebaSim.amoebaBondQuarticicParameter*deltaIdeal2 );
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
#endif
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ f38a47e4
......@@ -784,9 +784,9 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
methodName.c_str(), arraySize, bondForce->getAmoebaGlobalHarmonicBondCubic(), bondForce->getAmoebaGlobalHarmonicBondQuartic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2;
double length, k, cubic, quartic;
bondForce->getBondParameters( ii, particle1, particle2, length, k, cubic, quartic );
(void) fprintf( log, "%8d %8d %8d %14.7e %14.7e %14.7e %14.7e\n", ii, particle1, particle2, length, k, cubic, quartic);
double length, k;
bondForce->getBondParameters( ii, particle1, particle2, length, k );
(void) fprintf( log, "%8d %8d %8d %14.7e %14.7e\n", ii, particle1, particle2, length, k );
// skip to end
......@@ -799,15 +799,18 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
double cubic = bondForce->getAmoebaGlobalHarmonicBondCubic()/AngstromToNm;
double quartic = bondForce->getAmoebaGlobalHarmonicBondQuartic()/AngstromToNm*AngstromToNm;
bondForce->setAmoebaGlobalHarmonicBondCubic( cubic );
bondForce->setAmoebaGlobalHarmonicBondQuartic( quartic );
for( int ii = 0; ii < bondForce->getNumBonds(); ii++ ){
int particle1, particle2;
double length, k, cubic, quartic;
bondForce->getBondParameters( ii, particle1, particle2, length, k, cubic, quartic );
double length, k;
bondForce->getBondParameters( ii, particle1, particle2, length, k );
length *= AngstromToNm;
k *= CalToJoule/(AngstromToNm*AngstromToNm);
cubic /= AngstromToNm;
quartic /= AngstromToNm*AngstromToNm;
bondForce->setBondParameters( ii, particle1, particle2, length, k, cubic, quartic );
bondForce->setBondParameters( ii, particle1, particle2, length, k );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
......@@ -816,8 +819,8 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
methodName.c_str(), arraySize, bondForce->getAmoebaGlobalHarmonicBondCubic(), bondForce->getAmoebaGlobalHarmonicBondQuartic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2;
double length, k, cubic, quartic;
bondForce->getBondParameters( ii, particle1, particle2, length, k, cubic, quartic );
double length, k;
bondForce->getBondParameters( ii, particle1, particle2, length, k );
(void) fprintf( log, "%8d %8d %8d %14.7e %14.7e %14.7e %14.7e\n", ii, particle1, particle2, length, k, cubic, quartic);
// skip to end
......@@ -944,7 +947,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3;
double length, k, cubic, quartic, pentic, sextic;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
(void) fprintf( log, "%8d %8d %8d %8d %14.7e %14.7e\n",
ii, particle1, particle2, particle3, length, k );
......@@ -962,7 +965,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
if( useOpenMMUnits ){
for( int ii = 0; ii < angleForce->getNumAngles(); ii++ ){
int particle1, particle2, particle3;
double length, k, cubic, quartic, pentic, sextic;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
k *= CalToJoule;
angleForce->setAngleParameters( ii, particle1, particle2, particle3, length, k );
......@@ -977,7 +980,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3;
double length, k, cubic, quartic, pentic, sextic;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
(void) fprintf( log, "%8d %8d %8d %8d %14.7e %14.7e\n",
ii, particle1, particle2, particle3, length, k );
......@@ -1269,7 +1272,7 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( unsigned int ii = 0; ii < torsionForce->getNumTorsions(); ii++ ){
for( int ii = 0; ii < torsionForce->getNumTorsions(); ii++ ){
int particle1, particle2, particle3, particle4;
std::vector<double> torsion1;
std::vector<double> torsion2;
......@@ -1405,7 +1408,7 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap,
}
if( useOpenMMUnits ){
for( unsigned int ii = 0; ii < piTorsionForce->getNumPiTorsions(); ii++ ){
for( int ii = 0; ii < piTorsionForce->getNumPiTorsions(); ii++ ){
int particle1, particle2, particle3, particle4, particle5, particle6;
double torsionK;
piTorsionForce->getPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
......@@ -1535,7 +1538,7 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa
}
if( useOpenMMUnits ){
for( unsigned int ii = 0; ii < stretchBendForce->getNumStretchBends(); ii++ ){
for( int ii = 0; ii < stretchBendForce->getNumStretchBends(); ii++ ){
int particle1, particle2, particle3;
double lengthAB, lengthCB, angle, k;
stretchBendForce->getStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
......@@ -1704,7 +1707,7 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
}
if( useOpenMMUnits ){
for( unsigned int ii = 0; ii < outOfPlaneBendForce->getNumOutOfPlaneBends(); ii++ ){
for( int ii = 0; ii < outOfPlaneBendForce->getNumOutOfPlaneBends(); ii++ ){
int particle1, particle2, particle3, particle4;
double k;
outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
......@@ -1776,7 +1779,7 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors
}
grid.resize( numX );
for( unsigned int ii = 0; ii < numX; ii++ ){
for( int ii = 0; ii < numX; ii++ ){
grid[ii].resize( numY );
}
for( int ii = 0; ii < gridCount; ii++ ){
......@@ -1821,7 +1824,7 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors
// 'top' of grid
for( unsigned int ii = 0; ii < gridCount; ii++ ){
for( int ii = 0; ii < gridCount; ii++ ){
std::vector<double> values = grid[xI][yI];
(void) fprintf( log, "%4d %4d %4d ", ii, xI, yI );
for( unsigned int jj = 0; jj < values.size(); jj++ ){
......@@ -1843,7 +1846,7 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors
xI = 0;
yI = (gridCount/numX) - 3;
for( unsigned int ii = 0; ii < gridCount; ii++ ){
for( int ii = 0; ii < gridCount; ii++ ){
std::vector<double> values = grid[xI][yI];
(void) fprintf( log, "%4d %4d %4d ",
ii, xI, yI );
......@@ -2038,7 +2041,7 @@ static void readAmoebaMultipoleCovalent( FILE* filePtr, AmoebaMultipoleForce* mu
char* isNotEof = "1";
for( int ii = 0; ii < numberOfMultipoles && isNotEof; ii++ ){
for( int jj = 0; jj < numberOfCovalentTypes && isNotEof; jj++ ){
for( unsigned int jj = 0; jj < numberOfCovalentTypes && isNotEof; jj++ ){
StringVector lineTokens;
isNotEof = readLine( filePtr, lineTokens, lineCount, log );
std::vector<int> intVector;
......@@ -2273,12 +2276,12 @@ scalingDistanceCutoff, thole, dampingFactor, pGamma,
double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm;
double dampingFactorConversion = sqrt( AngstromToNm );
float scalingDistanceCutoff = multipoleForce->getScalingDistanceCutoff();
scalingDistanceCutoff *= AngstromToNm;
float scalingDistanceCutoff = static_cast<float>(multipoleForce->getScalingDistanceCutoff());
scalingDistanceCutoff *= static_cast<float>(AngstromToNm);
multipoleForce->setScalingDistanceCutoff( scalingDistanceCutoff );
for( unsigned int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){
for( int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){
int axisType, zAxis, xAxis;
std::vector<double> dipole;
......@@ -2299,8 +2302,8 @@ scalingDistanceCutoff, thole, dampingFactor, pGamma,
}
} else {
float electricConstant = multipoleForce->getElectricConstant();
electricConstant /= (AngstromToNm*CalToJoule);
float electricConstant = static_cast<float>(multipoleForce->getElectricConstant());
electricConstant /= static_cast<float>(AngstromToNm*CalToJoule);
multipoleForce->setElectricConstant( electricConstant );
}
......@@ -2475,7 +2478,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
}
if( useOpenMMUnits ){
for( unsigned int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
for( int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
gbsaObcForce->getParticleParameters( ii, charge, radius, scalingFactor );
radius *= AngstromToNm;
......@@ -2683,7 +2686,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
if( log ){
//static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15;
static const int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(vdwForce->getNumParticles());
unsigned int tableSize = static_cast<unsigned int>(vdwForce->getSigEpsTableSize());
(void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters; SigEpsTableSize=%d combining rules=[sig=%s eps=%s]\n",
......@@ -2714,7 +2717,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
(void) fprintf( log, "SigWEps table not loaded\n" );
}
for( unsigned int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
for( int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
int indexIV, indexClass;
double sigma, sigma4, epsilon, epsilon4, reduction;
std::vector< int > exclusions;
......@@ -2731,7 +2734,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
if( ii == maxPrint && static_cast<int>(arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
......@@ -2791,7 +2794,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
*/
}
for( unsigned int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
for( int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
int indexIV, indexClass;
double sigma, sigma4, epsilon, epsilon4, reduction;
vdwForce->getParticleParameters( ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
......@@ -2873,7 +2876,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
double epsilon = atof( lineTokens[tokenIndex++].c_str() );
wcaDispersionForce->addParticle( radius, epsilon );
if( tokenIndex < lineTokens.size() ){
if( tokenIndex < static_cast<int>(lineTokens.size()) ){
double cdisp = atof( lineTokens[tokenIndex++].c_str() );
maxDispersionEnergyVector.push_back( cdisp );
}
......@@ -3015,7 +3018,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
wcaDispersionForce->setEpso( epso );
wcaDispersionForce->setEpsh( epsh );
for( unsigned int ii = 0; ii < wcaDispersionForce->getNumParticles(); ii++ ){
for( int ii = 0; ii < wcaDispersionForce->getNumParticles(); ii++ ){
double radius, epsilon, maxDispersionEnergy;
wcaDispersionForce->getParticleParameters( ii, radius, epsilon );
......@@ -3023,7 +3026,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
epsilon *= CalToJoule;
wcaDispersionForce->setParticleParameters( ii, radius, epsilon );
if( ii < maxDispersionEnergyVector.size() ){
if( ii < static_cast<int>(maxDispersionEnergyVector.size()) ){
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
double tinkerValue = maxDispersionEnergyVector[ii];
tinkerValue *= CalToJoule;
......@@ -3694,7 +3697,6 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
static const std::string methodName = "readAmoebaParameterFile";
int PrintOn = 1;
double unitsConversion[LastUnits];
// ---------------------------------------------------------------------------------------
......@@ -4013,7 +4015,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
int useOpenMMUnits, FILE* log ) {
// ---------------------------------------------------------------------------------------
/*
static const std::string methodName = "checkIntermediateMultipoleQuantities";
// ---------------------------------------------------------------------------------------
......@@ -4074,7 +4076,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
totalMisses += misses;
}
} catch( exception& e ){
(void) fprintf( log, "Rotation matricies not available\n" );
(void) fprintf( log, "Rotation matricies not available %s\n", e.what() );
(void) fflush( log );
}
......@@ -4122,7 +4124,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
totalMisses += misses;
}
} catch( exception& e ){
(void) fprintf( log, "Fixed-E fields not available\n" );
(void) fprintf( log, "Fixed-E fields not available %s\n", e.what() );
(void) fflush( log );
}
......@@ -4172,10 +4174,10 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
totalMisses += misses;
}
} catch( exception& e ){
(void) fprintf( log, "Induced dipoles not available\n" );
(void) fprintf( log, "Induced dipoles not available %s\n", e.what() );
(void) fflush( log );
}
*/
}
void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, FILE* log ) {
......@@ -4636,7 +4638,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
std::vector<Vec3> expectedForces;
expectedForces.resize( system.getNumParticles() );
for( unsigned int ii = 0; ii < system.getNumParticles(); ii++ ){
for( int ii = 0; ii < system.getNumParticles(); ii++ ){
expectedForces[ii][0] = 0.0;
expectedForces[ii][1] = 0.0;
expectedForces[ii][2] = 0.0;
......@@ -4646,7 +4648,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
for( unsigned int ii = 0; ii < forceList.size(); ii++ ){
expectedEnergy += tinkerEnergies[forceList[ii]];
std::vector<Vec3> forces = tinkerForces[forceList[ii]];
for( unsigned int jj = 0; jj < system.getNumParticles(); jj++ ){
for( int jj = 0; jj < system.getNumParticles(); jj++ ){
expectedForces[jj][0] += forces[jj][0];
expectedForces[jj][1] += forces[jj][1];
expectedForces[jj][2] += forces[jj][2];
......@@ -4757,6 +4759,10 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
}
}
int isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
/**
* Check that energy and force are consistent
*
......@@ -4825,15 +4831,15 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo
// check norm is not nan
if( isinf( forceNorm ) || isnan( forceNorm ) ){
if( isNanOrInfinity( forceNorm ) ){
if( log ){
(void) fprintf( log, "%s norm of force is nan -- aborting.\n", methodName.c_str() );
unsigned int hitNan = 0;
for( unsigned int ii = 0; (ii < forces.size()) && (hitNan < 10); ii++ ){
if( isinf( forces[ii][0] ) || isnan( forces[ii][0] ) ||
isinf( forces[ii][1] ) || isnan( forces[ii][1] ) ||
isinf( forces[ii][2] ) || isnan( forces[ii][2] ) )hitNan++;
if( isNanOrInfinity( forces[ii][0] ) ||
isNanOrInfinity( forces[ii][1] ) ||
isNanOrInfinity( forces[ii][2] ) )hitNan++;
(void) fprintf( log, "%6u x[%14.7e %14.7e %14.7e] f[%14.7e %14.7e %14.7e]\n", ii,
coordinates[ii][0], coordinates[ii][1], coordinates[ii][2],
......@@ -5121,7 +5127,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
FILE* intermediateStateFile = NULL;
if( intermediateStateFileName != "NA" ){
#ifdef _MSC_VER
fopen_s( &intermediateStateFile, intermediateStateFileName.c_str(), "w"));
fopen_s( &intermediateStateFile, intermediateStateFileName.c_str(), "w");
#else
intermediateStateFile = fopen( intermediateStateFileName.c_str(), "w" );
#endif
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.h
View file @ f38a47e4
......@@ -48,6 +48,7 @@
#include "AmoebaVdwForce.h"
#include "AmoebaWcaDispersionForce.h"
#include "AmoebaSASAForce.h"
#include "internal/windowsExport.h"
#include <ctime>
#include <vector>
......@@ -232,5 +233,6 @@ void initializeForceMap( MapStringInt& forceMap, int initialValue );
void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap,
double tolerance, FILE* summaryFile, FILE* log );
int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap );
void appendInputArgumentsToArgumentMap( int numberOfArguments, char* argv[], MapStringString& argumentMap );
int OPENMM_EXPORT runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap );
void OPENMM_EXPORT appendInputArgumentsToArgumentMap( int numberOfArguments, char* argv[], MapStringString& argumentMap );
plugins/amoeba/platforms/cuda/tests/CMakeLists.txt
View file @ f38a47e4
......@@ -5,20 +5,26 @@ ENABLE_TESTING()
# INCLUDE(${CMAKE_SOURCE_DIR}/platforms/cuda/cuda-cmake/FindCuda.cmake)
INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/openmmapi/include/openmm)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src/kernels)
SET(SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET "AmoebaTinkerParameterFile" )
SET(AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES "AmoebaTinkerParameterFile.cpp" )
SET(AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES "AmoebaTinkerParameterFile.h" )
ADD_LIBRARY(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} SHARED ${AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES} ${AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES} )
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
Set( SHARED_OPENMM__AMOEBA_TARGET OpenMMAmoeba)
Set( STATIC_OPENMM_TARGET OpenMMAmoeba_static)
Set( SHARED_CUDA_TARGET OpenMMAmoebaCuda )
Set( STATIC_CUDA_TARGET OpenMMCuda_static OpenMMAmoebaCuda_static)
ADD_LIBRARY(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} SHARED ${AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES} ${AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES} )
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME})
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_OPENMM__AMOEBA_TARGET}_d optimized ${SHARED_OPENMM__AMOEBA_TARGET})
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_CUDA_TARGET}_d optimized ${SHARED_CUDA_TARGET})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_CUDA_TARGET ${SHARED_CUDA_TARGET}_d)
SET(SHARED_OPENMM__AMOEBA_TARGET ${SHARED_OPENMM__AMOEBA_TARGET}_d)
......
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