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Commit bc85b9f0 authored by Mark Friedrichs's avatar Mark Friedrichs
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Extened Free energy plugin to allow cutoffs; cleaned up code and added tests

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plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreAux.h deleted 100644 → 0
View file @ d4441c15
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifndef __Gpu_GBVI_SOFTCORE_AUX_H__
#define __Gpu_GBVI_SOFTCORE_AUX_H__
/**
* This file contains subroutines used in evaluating quantities associated w/ the GB/VI function
*/
__device__ float getGBVI_L( float r, float x, float S )
{
float rInv = 1.0f/r;
float xInv = 1.0f/x;
float xInv2 = xInv*xInv;
float diff2 = (r + S)*(r - S);
return (1.5f*xInv2)*( (0.25f*rInv) - (xInv/3.0f) + (0.125f*diff2*xInv2*rInv) );
}
__device__ float getGBVI_Volume( float r_ij, float R, float S )
{
float upperBound = r_ij + S;
float rdiffS = r_ij - S;
float lowerBound = R > rdiffS ? R : rdiffS;
float L_upper = getGBVI_L( r_ij, upperBound, S );
float L_lower = getGBVI_L( r_ij, lowerBound, S );
float mask = r_ij < (R - S) ? 0.0f : 1.0f;
float addOn = r_ij < (S - R) ? (1.0f/(R*R*R)) : 0.0f;
return (mask*( L_upper - L_lower ) + addOn);
}
__device__ float getGBVI_dL_dr( float r, float x, float S )
{
float rInv = 1.0f/r;
float rInv2 = rInv*rInv;
float xInv = 1.0f/x;
float xInv2 = xInv*xInv;
float xInv3 = xInv2*xInv;
float diff2 = (r + S)*(r - S);
return ( (-1.5f*xInv2*rInv2)*( 0.25f + 0.125f*diff2*xInv2 ) + 0.375f*xInv3*xInv );
//return 0.0f;
}
__device__ float getGBVI_dL_dx( float r, float x, float S )
{
float rInv = 1.0f/r;
float xInv = 1.0f/x;
float xInv2 = xInv*xInv;
float xInv3 = xInv2*xInv;
float diff = (r + S)*(r - S);
return ( (-1.5f*xInv3)*( (0.5f*rInv) - xInv + (0.5f*diff*xInv2*rInv) ));
}
__device__ float getGBVI_dE2( float r, float R, float S, float bornForce )
{
float diff = S - R;
float absDiff = fabsf( S - R );
float dE = getGBVI_dL_dr( r, r+S, S ) + getGBVI_dL_dx( r, r+S, S );
float mask;
float lowerBound;
if( (R > (r - S)) && (absDiff < r) ){
mask = 0.0f;
lowerBound = R;
} else {
mask = 1.0f;
lowerBound = (r - S);
}
dE -= getGBVI_dL_dr( r, lowerBound, S ) + mask*getGBVI_dL_dx( r, lowerBound, S );
dE = (absDiff >= r) && r >= diff ? 0.0f : dE;
dE *= ( (r > 1.0e-08f) ? (bornForce/r) : 0.0f);
return (-dE);
}
__device__ float getGBVIBornForce2( float bornRadius, float R, float bornForce, float gamma )
{
float ratio = (R/bornRadius);
float returnBornForce = bornForce + (3.0f*gamma*ratio*ratio*ratio)/bornRadius; // 'cavity' term
float br2 = bornRadius*bornRadius;
returnBornForce *= (1.0f/3.0f)*br2*br2;
return returnBornForce;
}
#endif // __Gpu_GBVI_SOFTCORE_AUX_H__
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreBornSum.h
View file @ bc85b9f0
...@@ -37,7 +37,22 @@ ...@@ -37,7 +37,22 @@
#include "kCalculateGBVIAux.h" #include "kCalculateGBVIAux.h"
__global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) #undef TARGET
//#define TARGET 5443
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_NONBOND_THREADS_PER_BLOCK, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(GT2XX_NONBOND_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_NONBOND_THREADS_PER_BLOCK, 1)
#endif
#ifdef DEBUG
void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit, float4* pdE1, float4* pdE2 )
#else
void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
#endif
{ {
extern __shared__ Atom sA[]; extern __shared__ Atom sA[];
...@@ -47,10 +62,8 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -47,10 +62,8 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
unsigned int pos = warp*numWorkUnits/totalWarps; unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps; unsigned int end = (warp+1)*numWorkUnits/totalWarps;
// int end = workUnits / gridDim.x;
// int pos = end - (threadIdx.x >> GRIDBITS) - 1;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block]; float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block];
#endif #endif
while ( pos < end ) while ( pos < end )
...@@ -85,68 +98,93 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -85,68 +98,93 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
sA[threadIdx.x].r = ar.x; sA[threadIdx.x].r = ar.x;
sA[threadIdx.x].sr = ar.y; sA[threadIdx.x].sr = ar.y;
sA[threadIdx.x].bornRadiusScaleFactor = ar.w; sA[threadIdx.x].bornRadiusScaleFactor = ar.w;
apos.w = 0.0f; float bSum = 0.0f;
for (unsigned int j = 0; j < GRID; j++) for (unsigned int j = 0; j < GRID; j++)
{ {
dx = psA[j].x - apos.x; dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#if defined USE_PERIODIC #if defined USE_CUTOFF
if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr && j != tgx)
#elif defined USE_CUTOFF #else
if (r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && x+j < cSim.atoms && j != tgx )
#endif #endif
{ {
r = sqrt(r2); bSum += psA[j].bornRadiusScaleFactor*getGBVI_Volume( sqrt(r2), ar.x, psA[j].sr );
if ((j != tgx) )
{ #ifdef DEBUG
apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr ); int jIdx = j;
} if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = psA[jIdx].bornRadiusScaleFactor*getGBVI_Volume( sqrt(r2), ar.x, psA[jIdx].sr );
pdE1[tjj].y = psA[jIdx].bornRadiusScaleFactor;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = 1.0f;
pdE2[tjj].x = sqrt(r2);
pdE2[tjj].y = psA[jIdx].sr;
pdE2[tjj].z = ar.x;
pdE2[tjj].w = 1.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = psA[jIdx].bornRadiusScaleFactor*getGBVI_Volume( sqrt(r2), ar.x, psA[jIdx].sr );
pdE1[tjj].y = psA[jIdx].bornRadiusScaleFactor;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = -1.0f;
}
#endif
} }
} }
// Write results // Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP #ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride; unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w; cSim.pBornSum[offset] += bSum;
#else #else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride; unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w; cSim.pBornSum[offset] = bSum;
#endif #endif
}
else // 100% utilization
{ } else {
// Read fixed atom data into registers and GRF // Read fixed atom data into registers and GRF
unsigned int j = y + tgx; unsigned int j = y + tgx;
unsigned int i = x + tgx; unsigned int i = x + tgx;
float4 temp = cSim.pPosq[j]; float4 temp = cSim.pPosq[j];
float4 temp1 = cSim.pGBVIData[j]; float4 temp1 = cSim.pGBVIData[j];
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr
sA[threadIdx.x].x = temp.x; sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y; sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z; sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x; sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y; sA[threadIdx.x].sr = temp1.y;
sA[threadIdx.x].bornRadiusScaleFactor = temp1.w; sA[threadIdx.x].bornRadiusScaleFactor = temp1.w;
sA[threadIdx.x].sum = apos.w = 0.0f;
sA[threadIdx.x].sum = 0.0f;
apos.w = 0.0f;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
//unsigned int flags = cSim.pInteractionFlag[pos + (blockIdx.x*workUnits)/gridDim.x];
unsigned int flags = cSim.pInteractionFlag[pos]; unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0) if (flags == 0)
{ {
// No interactions in this block. // No interactions in this block.
} }
else if (flags == 0xFFFFFFFF) else if (flags == 0xFFFFFFFF)
//else if (flags )
#endif #endif
{ {
// Compute all interactions within this block. // Compute all interactions within this block.
...@@ -157,15 +195,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -157,15 +195,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
dy = psA[tj].y - apos.y; dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z; dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC #ifdef USE_CUTOFF
if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF #else
if (r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && y+tj < cSim.atoms )
#endif #endif
{ {
r = sqrt(r2); r = sqrt(r2);
...@@ -173,11 +211,39 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -173,11 +211,39 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
// psA[tj].sr = Sj // psA[tj].sr = Sj
// ar.x = Ri // ar.x = Ri
apos.w += psA[tj].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[tj].sr ); apos.w += psA[tj].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[tj].sr );
psA[tj].sum += ar.w*getGBVI_Volume( r, psA[tj].r, ar.y ); psA[tj].sum += ar.w*getGBVI_Volume( r, psA[tj].r, ar.y );
#ifdef DEBUG
int jIdx = tj;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = psA[jIdx].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[jIdx].sr );
pdE1[tjj].y = psA[jIdx].bornRadiusScaleFactor;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = 2.0f;
float R = ar.x;
float S = psA[tj].sr;
pdE2[tjj].x = getGBVI_L( r, (r + S), S );
pdE2[tjj].y = -getGBVI_L( r, (r - S), S );
pdE2[tjj].z = -getGBVI_L( r, R, S );
pdE2[tjj].w = (1.0f/(R*R*R));
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = ar.w*getGBVI_Volume( r, psA[jIdx].r, ar.y );
pdE1[tjj].y = ar.w;
pdE1[tjj].z = psA[jIdx].r;
pdE1[tjj].w = -2.0f;
}
#endif
} }
tj = (tj - 1) & (GRID - 1); tj = (tj - 1) & (GRID - 1);
} }
} }
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
else else
...@@ -193,19 +259,20 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -193,19 +259,20 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC #ifdef USE_CUTOFF
if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF #else
if (r2 < cSim.nonbondedCutoffSqr) if (i < cSim.atoms && y+j < cSim.atoms)
#endif #endif
{ {
r = sqrt(r2); r = sqrt(r2);
tempBuffer[threadIdx.x] = ar.w*getGBVI_Volume( r, psA[tj].r, ar.y ); tempBuffer[threadIdx.x] = ar.w*getGBVI_Volume( r, psA[j].r, ar.y );
apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr );
} }
// Sum the terms. // Sum the terms.
...@@ -226,6 +293,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -226,6 +293,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
#endif #endif
// Write results // Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP #ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride; unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w; cSim.pBornSum[offset] += apos.w;
...@@ -237,6 +305,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int ...@@ -237,6 +305,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
offset = y + tgx + (x >> GRIDBITS) * cSim.stride; offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = sA[threadIdx.x].sum; cSim.pBornSum[offset] = sA[threadIdx.x].sum;
#endif #endif
} }
pos++; pos++;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.cu
View file @ bc85b9f0
...@@ -34,7 +34,7 @@ ...@@ -34,7 +34,7 @@
using namespace std; using namespace std;
#include "gputypes.h" #include "gputypes.h"
#include "GpuObcGbsaSoftcore.h" #include "freeEnergyGpuTypes.h"
struct Atom { struct Atom {
float x; float x;
...@@ -49,38 +49,19 @@ struct Atom { ...@@ -49,38 +49,19 @@ struct Atom {
float fb; float fb;
}; };
struct cudaFreeEnergySimulationObcGbsaSoftcore {
float* pNonPolarScalingFactors;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimObc2;
static __constant__ cudaGmxSimulation cSim; static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimDev; static __constant__ cudaFreeEnergyGmxSimulation feSimDev;
extern "C" extern "C"
void SetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu) void SetCalculateObcGbsaSoftcoreForces2Sim( freeEnergyGpuContext freeEnergyGpu )
{ {
cudaError_t status; cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation)); status = cudaMemcpyToSymbol(cSim, &freeEnergyGpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed"); RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreForces2Sim copy to cSim failed");
}
extern "C" status = cudaMemcpyToSymbol( feSimDev, &freeEnergyGpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim( float* nonPolarScalingFactors ) RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreForces2Sim copy to feSimDev failed");
{
cudaError_t status;
gbsaSimObc2.pNonPolarScalingFactors = nonPolarScalingFactors;
status = cudaMemcpyToSymbol(gbsaSimDev, &gbsaSimObc2, sizeof(cudaFreeEnergySimulationObcGbsaSoftcore));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim");
//(void) fprintf( stderr, "In SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim\n" );
}
void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
} }
// Include versions of the kernels for N^2 calculations. // Include versions of the kernels for N^2 calculations.
...@@ -116,15 +97,14 @@ void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu) ...@@ -116,15 +97,14 @@ void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
#define METHOD_NAME(a, b) a##PeriodicByWarp##b #define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateObcGbsaSoftcoreForces2.h" #include "kCalculateObcGbsaSoftcoreForces2.h"
void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu) void kCalculateObcGbsaSoftcoreForces2( freeEnergyGpuContext freeEnergyGpu )
{ {
//printf("kCalculateObcGbsaSoftcoreForces2\n"); //printf("kCalculateObcGbsaSoftcoreForces2\n");
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d warp=%d\n", gpu->sim.nonbondedMethod, gpu->bOutputBufferPerWarp); gpuContext gpu = freeEnergyGpu->gpuContext;
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d calling kReduceForces\n", gpu->sim.nonbondedMethod); switch (freeEnergyGpu->freeEnergySim.nonbondedMethod)
//kReduceForces(gpu);
switch (gpu->sim.nonbondedMethod)
{ {
case NO_CUTOFF: case FREE_ENERGY_NO_CUTOFF:
if (gpu->bOutputBufferPerWarp) if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, kCalculateObcGbsaSoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit); sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
...@@ -132,7 +112,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu) ...@@ -132,7 +112,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
kCalculateObcGbsaSoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, kCalculateObcGbsaSoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit); sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
break; break;
case CUTOFF:
case FREE_ENERGY_CUTOFF:
if (gpu->bOutputBufferPerWarp) if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreCutoffByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, kCalculateObcGbsaSoftcoreCutoffByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit); (sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
...@@ -140,7 +122,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu) ...@@ -140,7 +122,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
kCalculateObcGbsaSoftcoreCutoffForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, kCalculateObcGbsaSoftcoreCutoffForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit); (sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break; break;
case PERIODIC:
case FREE_ENERGY_PERIODIC:
if (gpu->bOutputBufferPerWarp) if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcorePeriodicByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, kCalculateObcGbsaSoftcorePeriodicByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit); (sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
......
plugins/freeEnergy/platforms/cuda/src/kernels/kSoftcoreLJ.h
View file @ bc85b9f0
...@@ -35,14 +35,14 @@ ...@@ -35,14 +35,14 @@
static __device__ float getSoftCoreLJ( float r2, float sig, float eps, float lambdaI, float lambdaJ, float* energy) static __device__ float getSoftCoreLJ( float r2, float sig, float eps, float lambdaI, float lambdaJ, float* energy)
{ {
float r = sqrt(r2);
float lambda = lambdaI < lambdaJ ? lambdaI : lambdaJ; float lambda = lambdaI < lambdaJ ? lambdaI : lambdaJ;
eps *= lambda; eps *= lambda;
// (r/sig) // (r/sig)
float sig2 = r/sig; float sig2 = 1.0f/sig;
sig2 *= sig2; sig2 *= sig2;
sig2 *= r2;
float sig6 = sig2*sig2*sig2; float sig6 = sig2*sig2*sig2;
float softcoreLJTerm = 0.5f*( 1.0f - lambda) + sig6; float softcoreLJTerm = 0.5f*( 1.0f - lambda) + sig6;
...@@ -53,6 +53,27 @@ static __device__ float getSoftCoreLJ( float r2, float sig, float eps, float la ...@@ -53,6 +53,27 @@ static __device__ float getSoftCoreLJ( float r2, float sig, float eps, float la
return eps*softcoreLJInv2*( 12.0f*softcoreLJInv - 6.0f )*sig6; return eps*softcoreLJInv2*( 12.0f*softcoreLJInv - 6.0f )*sig6;
} }
static __device__ float getSoftCoreLJMod( float sigInvR, float eps, float lambdaI, float lambdaJ, float* energy)
{
float lambda = lambdaI < lambdaJ ? lambdaI : lambdaJ;
eps *= lambda;
// (r/sig)
float sig2 = sigInvR*sigInvR;
float sig6 = sig2*sig2*sig2;
float softcoreLJTerm = 0.5f*( 1.0f - lambda) + sig6;
float softcoreLJInv = 1.0f/softcoreLJTerm;
float softcoreLJInv2 = softcoreLJInv*softcoreLJInv;
*energy = eps*(softcoreLJInv2 - softcoreLJInv);
return eps*softcoreLJInv2*( 12.0f*softcoreLJInv - 6.0f )*sig6;
}
#endif #endif
#endif #endif
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