Skip to content

GitLab

Commit 0d42a187 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

NonPolarPrefactor for GBSA OBC was missing for CudaPlatform

parent c9e927a5
Hide whitespace changes
Inline Side-by-side
Showing with 51 additions and 10 deletions
plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp
View file @ 0d42a187
......@@ -61,7 +61,7 @@ const std::string GBSA_OBC_SOFTCORE_FORCE = "ObcSoftcore";
const std::string GBVI_FORCE = "GBVI";
const std::string GBVI_SOFTCORE_FORCE = "GBVISoftcore";
static void getForceMap(const System& system, MapStringInt& forceMap) {
static void getForceMap(const System& system, MapStringInt& forceMap, FILE* log) {
// check forces and relevant parameters
......@@ -69,6 +69,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
int hit = 0;
const Force& force = system.getForce(i);
std::string forceName = "NA";
// bond
......@@ -77,6 +78,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const HarmonicBondForce& harmonicBondForce = dynamic_cast<const HarmonicBondForce&>(force);
forceMap[HARMONIC_BOND_FORCE] = 1;
forceName = HARMONIC_BOND_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -89,6 +91,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const HarmonicAngleForce& harmonicAngleForce = dynamic_cast<const HarmonicAngleForce&>(force);
forceMap[HARMONIC_ANGLE_FORCE] = 1;
forceName = HARMONIC_ANGLE_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -101,6 +104,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const PeriodicTorsionForce & periodicTorsionForce = dynamic_cast<const PeriodicTorsionForce&>(force);
forceMap[PERIODIC_TORSION_FORCE] = 1;
forceName = PERIODIC_TORSION_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -112,6 +116,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const RBTorsionForce& rBTorsionForce = dynamic_cast<const RBTorsionForce&>(force);
forceMap[RB_TORSION_FORCE] = 1;
forceName = RB_TORSION_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -123,6 +128,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const NonbondedForce& nbForce = dynamic_cast<const NonbondedForce&>(force);
forceMap[NB_FORCE] = 1;
forceName = NB_FORCE;
} catch( std::bad_cast ){
}
}
......@@ -133,6 +139,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const NonbondedSoftcoreForce& nbForce = dynamic_cast<const NonbondedSoftcoreForce&>(force);
forceMap[NB_SOFTCORE_FORCE] = 1;
forceName = NB_SOFTCORE_FORCE;
} catch( std::bad_cast ){
}
}
......@@ -143,6 +150,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const GBSAOBCForce& obcForce = dynamic_cast<const GBSAOBCForce&>(force);
forceMap[GBSA_OBC_FORCE] = 1;
forceName = GBSA_OBC_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -154,6 +162,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const GBSAOBCSoftcoreForce& obcForce = dynamic_cast<const GBSAOBCSoftcoreForce&>(force);
forceMap[GBSA_OBC_SOFTCORE_FORCE] = 1;
forceName = GBSA_OBC_SOFTCORE_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -164,7 +173,8 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
if( !hit ){
try {
const GBVIForce& obcForce = dynamic_cast<const GBVIForce&>(force);
forceMap[GBVI_FORCE] = 1;
forceMap[GBVI_FORCE] = 1;
forceName = GBVI_FORCE;
hit++;
} catch( std::bad_cast ){
}
......@@ -176,10 +186,15 @@ static void getForceMap(const System& system, MapStringInt& forceMap) {
try {
const GBVISoftcoreForce& gbviForce = dynamic_cast<const GBVISoftcoreForce&>(force);
forceMap[GBVI_SOFTCORE_FORCE] = 1;
forceName = GBVI_SOFTCORE_FORCE;
hit++;
} catch( std::bad_cast ){
}
}
if( log ){
(void) fprintf( stderr, "Map: Force %d %s\n", i, forceName.c_str() );
}
}
}
......@@ -208,7 +223,7 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy
// check forces and relevant parameters
MapStringInt forceMap;
getForceMap( system, forceMap);
getForceMap( system, forceMap, log);
int softcore = 0;
if( forceMap.find( GBSA_OBC_FORCE ) != forceMap.end() ){
......@@ -470,13 +485,16 @@ void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& syst
_gpuContext* gpu = data.gpu;
MapStringInt forceMap;
getForceMap( system, forceMap);
getForceMap( system, forceMap, log);
// check that nonbonded (non-softcore is not active)
if( forceMap.find( NB_FORCE ) != forceMap.end() ){
throw OpenMMException( "Mixing NonbondedForce and GBSAOBCSoftoreForce not allowed -- use NonbondedSoftcoreForce " );
}
if( forceMap.find( NB_SOFTCORE_FORCE ) == forceMap.end() ){
throw OpenMMException( "NonbondedSoftcore force must be included w/ GBSAOBCSoftcore force." );
}
int numParticles = system.getNumParticles();
......@@ -495,6 +513,7 @@ void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& syst
}
gpuObcGbsaSoftcore = gpuSetObcSoftcoreParameters(gpu, static_cast<float>( force.getSoluteDielectric()),
static_cast<float>( force.getSolventDielectric()),
static_cast<float>( force.getNonPolarPrefactor()),
radius, scale, charge, nonPolarScalingFactors );
}
......@@ -585,7 +604,7 @@ void CudaFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& system,
// check forces and relevant parameters
MapStringInt forceMap;
getForceMap( system, forceMap);
getForceMap( system, forceMap, log);
// check that nonbonded (non-softcore is not active)
......
plugins/freeEnergy/platforms/cuda/src/kernels/GpuFreeEnergyCudaKernels.h
View file @ 0d42a187
......@@ -127,7 +127,8 @@ extern void kReduceGBVIBornForcesQuinticScaling( gpuContext gpu );
*/
extern "C"
GpuObcGbsaSoftcore* gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, const std::vector<float>& radius, const std::vector<float>& scale,
GpuObcGbsaSoftcore* gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, float nonPolarPrefactor,
const std::vector<float>& radius, const std::vector<float>& scale,
const std::vector<float>& charge, const std::vector<float>& nonPolarScalingFactors);
// delete supplemtentary objects, ...
......
plugins/freeEnergy/platforms/cuda/src/kernels/GpuNonbondedSoftcore.cpp
View file @ 0d42a187
......@@ -71,7 +71,24 @@ int GpuNonbondedSoftcore::setParticleSoftCoreLJLambda( unsigned int particleInde
// upload SoftCoreLJLambda array
int GpuNonbondedSoftcore::upload( gpuContext gpu ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "GpuNonbondedSoftcore::upload";
// ---------------------------------------------------------------------------------------
_psSoftcoreLJLambda->Upload();
#define DUMP_PARAMETERS 0
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr, "%s %u %u\n", methodName.c_str(), gpu->natoms, gpu->sim.paddedNumberOfAtoms );
for (unsigned int ii = 0; ii < gpu->natoms; ii++)
{
(void) fprintf( stderr, "%6u %13.6e\n", ii, (*_psSoftcoreLJLambda)[ii] );
}
#endif
SetCalculateCDLJSoftcoreSupplementarySim( getGpuParticleSoftCoreLJLambda() );
SetCalculateCDLJObcGbsaSoftcoreSupplementary1Sim( getGpuParticleSoftCoreLJLambda() );
return 0;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.cu
View file @ 0d42a187
......@@ -121,6 +121,7 @@ __device__ float fastErfc(float r)
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateCDLJObcGbsaSoftcoreForces1.h"
#undef USE_SOFTCORE_LJ
#undef USE_OUTPUT_BUFFER_PER_WARP
// Include versions of the kernel with cutoffs.
......@@ -196,7 +197,7 @@ void kCalculateCDLJObcGbsaSoftcoreForces1(gpuContext gpu )
kCalculateCDLJObcGbsaSoftcoreN2Forces1_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
LAUNCHERROR("kCalculateCDLJObcGbsaN2Forces1");
LAUNCHERROR("kCalculateCDLJObcGbsaSoftcoreForces1");
break;
#if 0
case CUTOFF:
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu
View file @ 0d42a187
......@@ -176,9 +176,11 @@ void kReduceObcGbsaBornSum(gpuContext gpu)
*/
extern "C"
void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, const std::vector<float>& radius, const std::vector<float>& scale,
void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, float nonPolarPrefactor,
const std::vector<float>& radius, const std::vector<float>& scale,
const std::vector<float>& charge, const std::vector<float>& nonPolarScalingFactors)
{
// ---------------------------------------------------------------------------------------
static const float dielectricOffset = 0.009f;
......@@ -187,7 +189,6 @@ void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float so
// ---------------------------------------------------------------------------------------
unsigned int atoms = radius.size();
// initialize parameters
......@@ -195,6 +196,7 @@ void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float so
// gpu->bIncludeGBSA = true;
GpuObcGbsaSoftcore* gpuObcGbsaSoftcore = new GpuObcGbsaSoftcore();
gpuObcGbsaSoftcore->initializeNonPolarScalingFactors( gpu->sim.paddedNumberOfAtoms );
gpu->sim.surfaceAreaFactor = -6.0f*PI*4.0f*nonPolarPrefactor*1000.0f*0.4184f;
for (unsigned int i = 0; i < atoms; i++)
{
(*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
......@@ -205,12 +207,13 @@ void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float so
}
// diagnostics
#define DUMP_PARAMETERS 0
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr, "%s %u %u\n", methodName.c_str(), gpu->natoms, gpu->sim.paddedNumberOfAtoms );
for (unsigned int i = 0; i < atoms; i++)
{
(void) fprintf( stderr, "%6u %13.6e %13.6e %8.3f %8.3f\n", i, (*gpu->psObcData)[i].x, (*gpu->psObcData)[i].y, (*gpu->psPosq4)[i].w , nonPolarScalingFactors[i] );
}
#endif
// dummy out extra atom data
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment