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Commit d3ec1d0c authored by Peter Eastman's avatar Peter Eastman
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Bug fixes to GBSA

parent 2a465d40
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Showing with 31 additions and 15 deletions
platforms/cuda/src/kernels/kCalculateCDLJObcGbsaForces1.h
View file @ d3ec1d0c
......@@ -282,7 +282,7 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int*
of.z += af.z;
of.w += af.w;
cSim.pForce4a[offset] = of;
cSim.pBornForce[offset] = af.w;
cSim.pBornForce[offset] = of.w;
#else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = af;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ d3ec1d0c
......@@ -767,6 +767,21 @@ double OpenCLCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
// SetCustomNonbondedGlobalParams(&globalParamValues[0]);
//}
//
class OpenCLGBSAOBCForceInfo : public OpenCLForceInfo {
public:
OpenCLGBSAOBCForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, radius1, radius2, scale1, scale2;
force.getParticleParameters(particle1, charge1, radius1, scale1);
force.getParticleParameters(particle2, charge2, radius2, scale2);
return (charge1 == charge2 && radius1 == radius2 && scale1 == scale2);
}
private:
const GBSAOBCForce& force;
};
OpenCLCalcGBSAOBCForceKernel::~OpenCLCalcGBSAOBCForceKernel() {
if (params != NULL)
delete params;
......@@ -807,6 +822,7 @@ void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOB
nb.addInteraction(useCutoff, usePeriodic, false, force.getCutoffDistance(), vector<vector<int> >(), source);
nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float2", sizeof(cl_float2), params->getDeviceBuffer()));;
nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "float", sizeof(cl_float), bornForce->getDeviceBuffer()));;
cl.addForce(new OpenCLGBSAOBCForceInfo(nb.getNumForceBuffers(), force));
}
void OpenCLCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ d3ec1d0c
......@@ -109,6 +109,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
delta.z -= floor(delta.z/periodicBoxSize.z+0.5f)*periodicBoxSize.z;
#endif
float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
tempBuffer[get_local_id(0)] = 0.0f;
#ifdef USE_CUTOFF
if (atom1 < numAtoms && y+j < numAtoms && r2 < cutoffSquared) {
#else
......@@ -118,7 +119,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
float invR = 1.0f/r;
float2 params2 = local_params[tbx+j];
float rScaledRadiusJ = r+params2.y;
if ((j != tgx) && (params1.x < rScaledRadiusJ)) {
if (params1.x < rScaledRadiusJ) {
float l_ij = 1.0f/max(params1.x, fabs(r-params2.y));
float u_ij = 1.0f/rScaledRadiusJ;
float l_ij2 = l_ij*l_ij;
......@@ -130,7 +131,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
bornSum += 2.0f*(1.0f/params1.x-l_ij);
}
float rScaledRadiusI = r+params1.y;
if ((j != tgx) && (params2.x < rScaledRadiusJ)) {
if (params2.x < rScaledRadiusJ) {
float l_ij = 1.0f/max(params2.x, fabs(r-params1.y));
float u_ij = 1.0f/rScaledRadiusJ;
float l_ij2 = l_ij*l_ij;
......@@ -185,7 +186,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
float invR = 1.0f/r;
float2 params2 = local_params[tbx+tj];
float rScaledRadiusJ = r+params2.y;
if ((tj != tgx) && (params1.x < rScaledRadiusJ)) {
if (params1.x < rScaledRadiusJ) {
float l_ij = 1.0f/max(params1.x, fabs(r-params2.y));
float u_ij = 1.0f/rScaledRadiusJ;
float l_ij2 = l_ij*l_ij;
......@@ -197,7 +198,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
bornSum += 2.0f*(1.0f/params1.x-l_ij);
}
float rScaledRadiusI = r+params1.y;
if ((tj != tgx) && (params2.x < rScaledRadiusJ)) {
if (params2.x < rScaledRadiusJ) {
float l_ij = 1.0f/max(params2.x, fabs(r-params1.y));
float u_ij = 1.0f/rScaledRadiusJ;
float l_ij2 = l_ij*l_ij;
......@@ -207,7 +208,7 @@ __kernel void computeBornSum(int numAtoms, int paddedNumAtoms, __global float* g
(0.25f*params1.y*params1.y*invR)*(l_ij2-u_ij2);
if (params2.x < params1.x-r)
term += 2.0f*(1.0f/params2.x-l_ij);
local_bornSum[tbx+tj] = term;
local_bornSum[tbx+tj] += term;
}
}
tj = (tj + 1) & (TileSize - 1);
......@@ -245,7 +246,6 @@ __kernel void reduceBornSum(int numAtoms, int bufferSize, int numBuffers, float
float sum = bornSum[index];
for (int i = index+bufferSize; i < totalSize; i += bufferSize)
sum += bornSum[i];
bornSum[index] = sum;
// Now calculate Born radius and OBC term.
......@@ -254,10 +254,10 @@ __kernel void reduceBornSum(int numAtoms, int bufferSize, int numBuffers, float
float sum2 = sum*sum;
float sum3 = sum*sum2;
float tanhSum = tanh(alpha*sum - beta*sum2 + gamma*sum3);
float nonOffsetRadii = offsetRadius + dielectricOffset;
float radius = 1.0f/(1.0f/offsetRadius - tanhSum/nonOffsetRadii);
float nonOffsetRadius = offsetRadius + dielectricOffset;
float radius = 1.0f/(1.0f/offsetRadius - tanhSum/nonOffsetRadius);
float chain = offsetRadius*(alpha - 2.0f*beta*sum + 3.0f*gamma*sum2);
chain = (1.0f-tanhSum*tanhSum)*chain / nonOffsetRadii;
chain = (1.0f-tanhSum*tanhSum)*chain / nonOffsetRadius;
bornRadii[index] = radius;
obcChain[index] = chain;
index += get_global_size(0);
......@@ -347,7 +347,7 @@ __kernel void computeGBSAForce1(int numAtoms, int paddedNumAtoms, float prefacto
unsigned int offset = x + tgx + warp*paddedNumAtoms;
#endif
forceBuffers[offset].xyz += force.xyz;
global_bornForce[offset] = force.w;
global_bornForce[offset] += force.w;
}
else {
// This is an off-diagonal tile.
......@@ -401,7 +401,7 @@ __kernel void computeGBSAForce1(int numAtoms, int paddedNumAtoms, float prefacto
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
tempBuffer[get_local_id(0)] = (float4) (delta.xyz, dGpol_dalpha2_ij*bornRadius2);
tempBuffer[get_local_id(0)] = (float4) (delta.xyz, dGpol_dalpha2_ij*bornRadius1);
// Sum the forces on atom j.
......@@ -459,7 +459,7 @@ __kernel void computeGBSAForce1(int numAtoms, int paddedNumAtoms, float prefacto
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
local_force[tbx+tj].xyz += delta.xyz;
local_force[tbx+tj] += (float4) (delta.xyz, dGpol_dalpha2_ij*bornRadius1);
}
tj = (tj + 1) & (TileSize - 1);
}
......@@ -475,8 +475,8 @@ __kernel void computeGBSAForce1(int numAtoms, int paddedNumAtoms, float prefacto
#endif
forceBuffers[offset1].xyz += force.xyz;
forceBuffers[offset2].xyz += local_force[get_local_id(0)].xyz;
global_bornForce[offset1] = force.w;
global_bornForce[offset2] = local_force[get_local_id(0)].w;
global_bornForce[offset1] += force.w;
global_bornForce[offset2] += local_force[get_local_id(0)].w;
lasty = y;
}
pos++;
......
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