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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

parent d4441c15
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plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.h
View file @ bc85b9f0
......@@ -30,17 +30,26 @@
* different versions of the kernels.
*/
#define USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
#endif
/* Cuda compiler on Windows does not recognized "static const float" values */
#define LOCAL_HACK_PI 3.1415926535897932384626433832795
#define COULOMB_ON
#undef TARGET
//#define TARGET 0
__global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* workUnit)
__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
void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* workUnit )
{
//void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* workUnit, float4* pdE1, float4* pdE2 )
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
......@@ -53,10 +62,6 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block];
#endif
#ifdef USE_EWALD
const float TWO_OVER_SQRT_PI = 2.0f/sqrt(LOCAL_HACK_PI);
#endif
unsigned int lasty = -0xFFFFFFFF;
while (pos < end)
{
......@@ -69,30 +74,36 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int i = x + tgx;
float4 apos = cSim.pPosq[i];
float2 a = cSim.pAttr[i];
float softCoreLJLambda = feSimDev.pParticleSoftCoreLJLambda[i];
float4 a = feSimDev.pSigEps4[i];
float softCoreLJLambda = a.z;
float br = cSim.pBornRadii[i];
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
float4 af;
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
af.w = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].q = apos.w;
float q2 = cSim.preFactor * apos.w;
apos.w *= cSim.epsfac;
sA[threadIdx.x].q = a.w;
sA[threadIdx.x].sig = a.x;
sA[threadIdx.x].eps = a.y;
sA[threadIdx.x].br = br;
sA[threadIdx.x].softCoreLJLambda = softCoreLJLambda;
float q2 = cSim.preFactor*a.w;
a.w *= cSim.epsfac;
if (!bExclusionFlag)
{
for (unsigned int j = 0; j < GRID; j++)
......@@ -118,29 +129,16 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJObcGbsa_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
#ifdef COULOMB_ON
float factorX = apos.w * psA[j].q * invR;
float factorX = a.w * psA[j].q * invR;
dEdR += factorX;
CDLJObcGbsa_energy += factorX;
#endif
#endif
dEdR *= invR * invR;
......@@ -153,37 +151,57 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
if ( i >= cSim.atoms || (x+j) >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#else
if ( i >= cSim.atoms || (x+j) >= cSim.atoms)
#endif
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dGpol_dalpha2_ij = 0.0f;
}
#endif
/* E */
if (i < cSim.atoms)
{
af.w += dGpol_dalpha2_ij * psA[j].br;
/*
int jIdx = j;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = dGpol_dalpha2_ij * psA[j].br;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = (q2 * psA[j].q) / denominator;
pdE1[tjj].w = 1.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = dEdR - Gpol * (1.0f - 0.25f * expTerm);
pdE1[tjj].y = r2;
pdE1[tjj].z = CDLJObcGbsa_energy - (q2 * psA[jIdx].q) / denominator;
pdE1[tjj].w = -1.0f;
} */
energy += 0.5f*CDLJObcGbsa_energy;
}
// Add Forces
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
}
}
else // bExclusion
{
} else {
unsigned int xi = x>>GRIDBITS;
unsigned int cell = xi+xi*cSim.paddedNumberOfAtoms/GRID-xi*(xi+1)/2;
unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
for (unsigned int j = 0; j < GRID; j++)
{
float dx = psA[j].x - apos.x;
......@@ -198,60 +216,42 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float invR = 1.0f / sqrt(r2);
float sig = a.x + psA[j].sig;
float eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ
float dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[j].softCoreLJLambda, &CDLJObcGbsa_energy );
//float dEdR = getSoftCoreLJMod( (invR*sig), eps, softCoreLJLambda, psA[j].softCoreLJLambda, &CDLJObcGbsa_energy );
#else
// CDLJ part
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+j && x+tgx < cSim.atoms && y+j < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[j].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJObcGbsa_energy = -apos.w * psA[j].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#ifdef USE_CUTOFF
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJObcGbsa_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
#ifdef COULOMB_ON
float factorX = apos.w * psA[j].q * invR;
float factorX = a.w * psA[j].q * invR;
dEdR += factorX;
CDLJObcGbsa_energy += factorX;
#endif
#endif
dEdR *= invR * invR;
#ifdef USE_EWALD
if (!(excl & 0x1) && !needCorrection)
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
//float dEdRx = dEdR;
// ObcGbsaForce1 part
float alpha2_ij = br * psA[j].br;
float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij);
......@@ -259,34 +259,54 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#else
if (i >= cSim.atoms || x+j >= cSim.atoms )
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
if (i < cSim.atoms)
{
dGpol_dalpha2_ij = 0.0f;
//dEdRx = 0.0f;
}
/*
int jIdx = j;
if( i == TARGET ){
int tjj = (y+jIdx);
pdE1[tjj].x = dGpol_dalpha2_ij * psA[j].br;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = (q2 * psA[j].q) / denominator;
pdE1[tjj].x = dEdRx;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = CDLJObcGbsa_energy - (q2 * psA[jIdx].q) / denominator;
pdE1[tjj].w = 2.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = dGpol_dalpha2_ij * psA[j].br;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = (q2 * psA[j].q) / denominator;
pdE1[tjj].w = -2.0f;
} */
af.w += dGpol_dalpha2_ij * psA[j].br;
energy += 0.5f*CDLJObcGbsa_energy;
}
// Add Forces
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
excl >>= 1;
}
}
......@@ -307,32 +327,32 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
cSim.pForce4[offset] = of;
cSim.pBornForce[offset] = bf;
}
else // 100% utilization
{
} else {
// Read fixed atom data into registers and GRF
if (lasty != y)
{
unsigned int j = y + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pAttr[j];
float temp2 = feSimDev.pParticleSoftCoreLJLambda[j];
//float temp2 = 1.0f;
float4 temp1 = feSimDev.pSigEps4[j];
sA[threadIdx.x].br = cSim.pBornRadii[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].q = temp.w;
sA[threadIdx.x].q = temp1.w;
sA[threadIdx.x].sig = temp1.x;
sA[threadIdx.x].eps = temp1.y;
sA[threadIdx.x].softCoreLJLambda = temp2;
sA[threadIdx.x].softCoreLJLambda = temp1.z;
}
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
sA[threadIdx.x].fb = 0.0f;
float q2 = apos.w * cSim.preFactor;
apos.w *= cSim.epsfac;
float q2 = a.w * cSim.preFactor;
a.w *= cSim.epsfac;
if (!bExclusionFlag)
{
#ifdef USE_CUTOFF
......@@ -369,33 +389,22 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[tj].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJObcGbsa_energy += a.w * psA[tj].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
#ifdef COULOMB_ON
float factorX = apos.w * psA[tj].q * invR;
float factorX = a.w * psA[tj].q * invR;
dEdR += factorX;
CDLJObcGbsa_energy += factorX;
#endif
#endif
dEdR *= invR * invR;
//float dEdRx = dEdR;
// ObcGbsaForce1 part
float alpha2_ij = br * psA[tj].br;
float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij);
......@@ -403,38 +412,64 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
if ( i >= cSim.atoms || (y+tj) >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#else
if ( i >= cSim.atoms || (y+tj) >= cSim.atoms)
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
dGpol_dalpha2_ij = 0.0f;
//dEdRx = 0.0f;
}
#endif
if (i < cSim.atoms)
{
psA[tj].fb += dGpol_dalpha2_ij * br;
af.w += dGpol_dalpha2_ij * psA[tj].br;
energy += CDLJObcGbsa_energy;
}
/*
int jIdx = tj;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = dEdRx;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = -dEdRx*dz;
pdE1[tjj].w = 3.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = dEdRx;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = dEdRx*dz;
pdE1[tjj].w = -3.0f;
} */
// Add forces
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
tj = (tj + 1) & (GRID - 1);
}
}
#ifdef USE_CUTOFF
else
{
else {
// Compute only a subset of the interactions in this block.
for (unsigned int j = 0; j < GRID; j++)
......@@ -462,28 +497,16 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJObcGbsa_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
#ifdef COULOMB_ON
float factorX = apos.w * psA[j].q * invR;
float factorX = a.w * psA[j].q * invR;
dEdR += factorX;
CDLJObcGbsa_energy += factorX;
#endif
#endif
dEdR *= invR * invR;
......@@ -495,11 +518,21 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
#ifdef USE_CUTOFF
if ( i >= cSim.atoms || (y+j) >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#else
if ( i >= cSim.atoms || (y+j) >= cSim.atoms)
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
dGpol_dalpha2_ij = 0.0f;
}
af.w += dGpol_dalpha2_ij * psA[j].br;
// Sum the Born forces.
tempBuffer[threadIdx.x] = dGpol_dalpha2_ij * br;
......@@ -513,17 +546,28 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fb += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
if (i < cSim.atoms)
{
/*
int jIdx = j;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = dEdR;
pdE1[tjj].y = r2;
pdE1[tjj].z = CDLJObcGbsa_energy - (q2 * psA[jIdx].q) / denominator;
pdE1[tjj].w = -4.7f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = dEdR;
pdE1[tjj].y = r2;
pdE1[tjj].z = CDLJObcGbsa_energy - (q2 * psA[jIdx].q) / denominator;
pdE1[tjj].w = -4.7f;
} */
energy += CDLJObcGbsa_energy;
}
// Add forces
dx *= dEdR;
dy *= dEdR;
......@@ -568,9 +612,8 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
}
}
#endif
}
else // bExclusion
{
} else {
unsigned int xi = x>>GRIDBITS;
unsigned int yi = y>>GRIDBITS;
unsigned int cell = xi+yi*cSim.paddedNumberOfAtoms/GRID-yi*(yi+1)/2;
......@@ -599,49 +642,25 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+tj && x+tgx < cSim.atoms && y+tj < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[tj].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJObcGbsa_energy = -apos.w * psA[tj].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[tj].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJObcGbsa_energy += a.w * psA[tj].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
#ifdef COULOMB_ON
float factorX = apos.w * psA[tj].q * invR;
float factorX = a.w * psA[tj].q * invR;
dEdR += factorX;
CDLJObcGbsa_energy += factorX;
#endif
#endif
dEdR *= invR * invR;
#ifdef USE_EWALD
if (!(excl & 0x1) && !needCorrection)
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
//float dEdRx = dEdR;
// ObcGbsaForce1 part
float alpha2_ij = br * psA[tj].br;
float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij);
......@@ -649,37 +668,57 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#else
if (i >= cSim.atoms || y+tj >= cSim.atoms)
#endif
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
if (i < cSim.atoms)
{
dGpol_dalpha2_ij = 0.0f;
//dEdRx = 0.0;
}
/*
int jIdx = tj;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = dEdRx;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = dEdRx*dz;
pdE1[tjj].w = 6.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE1[tjj].x = dEdRx;
pdE1[tjj].y = sqrt(r2);
pdE1[tjj].z = dEdRx*dz;
pdE1[tjj].w = -6.0f;
} */
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
energy += CDLJObcGbsa_energy;
}
// Add forces
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
excl >>= 1;
tj = (tj + 1) & (GRID - 1);
}
......@@ -714,40 +753,6 @@ __global__ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsig
cSim.pForce4[offset] = of;
cSim.pBornForce[offset] = bf;
#if 0
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
float4 of = cSim.pForce4[offset];
of.x += af.x;
of.y += af.y;
of.z += af.z;
of.w += af.w;
cSim.pForce4[offset] = of;
cSim.pBornForce[offset] = af.w;
offset = y + tgx + warp*cSim.stride;
of = cSim.pForce4[offset];
of.x += sA[threadIdx.x].fx;
of.y += sA[threadIdx.x].fy;
of.z += sA[threadIdx.x].fz;
of.w += sA[threadIdx.x].fb;
cSim.pForce4[offset] = of;
cSim.pBornForce[offset] = af.w;
#else
unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
cSim.pForce4[offset] = af;
cSim.pBornForce[offset] = af.w;
af.x = sA[threadIdx.x].fx;
af.y = sA[threadIdx.x].fy;
af.z = sA[threadIdx.x].fz;
af.w = sA[threadIdx.x].fb;
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4[offset] = af;
cSim.pBornForce[offset] = af.w;
#endif
#endif
lasty = y;
}
pos++;
......
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.cu
View file @ bc85b9f0
......@@ -29,133 +29,120 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "GpuGBVISoftcore.h"
#include "GpuFreeEnergyCudaKernels.h"
#include "freeEnergyGpuTypes.h"
#include "openmm/OpenMMException.h"
#include <cuda.h>
#include <sstream>
struct cudaFreeEnergySimulationGBVI {
float quinticLowerLimitFactor;
float quinticUpperLimit;
float* pSwitchDerivative;
};
struct cudaFreeEnergySimulationGBVI gbviSim;
#define PARAMETER_PRINT 0
#define MAX_PARAMETER_PRINT 10
//#define DEBUG
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationGBVI gbviSimDev;
static __constant__ cudaFreeEnergyGmxSimulation gbviSimDev;
void SetCalculateGBVISoftcoreBornSumGpuSim(gpuContext gpu)
void SetCalculateGBVISoftcoreBornSumGpuSim( freeEnergyGpuContext freeEnergyGpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
status = cudaMemcpyToSymbol( cSim, &freeEnergyGpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateGBVISoftcoreBornSumGpuSim copy to cSim failed");
//(void) fprintf( stderr, "SetCalculateGBVISoftcoreBornSumGpuSim\n" );
}
void GetCalculateGBVISoftcoreBornSumSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
void SetCalculateGBVISoftcoreSupplementarySim( GpuGBVISoftcore* gpuGBVISoftcore )
{
cudaError_t status;
gbviSim.pSwitchDerivative = gpuGBVISoftcore->getGpuSwitchDerivative();
gbviSim.quinticLowerLimitFactor = gpuGBVISoftcore->getQuinticLowerLimitFactor();
gbviSim.quinticUpperLimit = gpuGBVISoftcore->getQuinticUpperLimit();
status = cudaMemcpyToSymbol(gbviSimDev, &gbviSim, sizeof(cudaFreeEnergySimulationGBVI));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateGBVISoftcoreSupplementarySim");
//(void) fprintf( stderr, "SetCalculateGBVISoftcoreSupplementarySim %14.6e %14.6e swDerv=%p\n",
// gbviSim.quinticLowerLimitFactor, gbviSim.quinticUpperLimit, gbviSim.pSwitchDerivative );
status = cudaMemcpyToSymbol( gbviSimDev, &freeEnergyGpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateGBVISoftcoreBornSumGpuSim copy to feSim failed");
}
// create, initialize and enter BornRadiusScaleFactors values (used to scale contribution of atoms to Born sum of other atoms)
// return handle to GpuGBVISoftcore object
extern "C"
GpuGBVISoftcore* gpuSetGBVISoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, const std::vector<int>& atom,
void gpuSetGBVISoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, float innerDielectric, float solventDielectric, const std::vector<int>& atom,
const std::vector<float>& radius, const std::vector<float>& gamma,
const std::vector<float>& scaledRadii, const std::vector<float>& bornRadiusScaleFactors,
const std::vector<float>& quinticSplineParameters)
{
const std::vector<float>& quinticSplineParameters ){
unsigned int numberOfParticles = radius.size();
gpuContext gpu = freeEnergyGpu->gpuContext;
static const float electricConstant = -166.02691f;
unsigned int atoms = atom.size();
double tau = ((1.0f/innerDielectric)-(1.0f/solventDielectric));
freeEnergyGpu->psSwitchDerivative = new CUDAStream<float>( numberOfParticles, 1, "SwitchDerivative");
freeEnergyGpu->freeEnergySim.pSwitchDerivative = freeEnergyGpu->psSwitchDerivative->_pDevData;
// create gpuGBVISoftcore, load parameters, and track minimum softcore value
// gpuGBVISoftcore is not really being used (it was in the initial implementation) --
// will be removed in future once confirmed not needed
GpuGBVISoftcore* gpuGBVISoftcore = new GpuGBVISoftcore();
unsigned int numberOfParticles = radius.size();
// check if quintic scaling to be applied
if( quinticSplineParameters.size() == 2 ){
gpuGBVISoftcore->setBornRadiiScalingMethod( 1 );
gpuGBVISoftcore->setQuinticLowerLimitFactor( quinticSplineParameters[0] );
gpuGBVISoftcore->setQuinticUpperLimit( quinticSplineParameters[1] );
gpuGBVISoftcore->initializeGpuSwitchDerivative( gpu->sim.paddedNumberOfAtoms );
freeEnergyGpu->freeEnergySim.bornRadiiScalingMethod = 1;
freeEnergyGpu->freeEnergySim.quinticLowerLimitFactor = quinticSplineParameters[0];
freeEnergyGpu->freeEnergySim.quinticUpperLimit = quinticSplineParameters[1];
} else {
freeEnergyGpu->freeEnergySim.bornRadiiScalingMethod = 0;
freeEnergyGpu->freeEnergySim.quinticLowerLimitFactor = 0.8f;
freeEnergyGpu->freeEnergySim.quinticUpperLimit = 5.0f;
}
for (unsigned int i = 0; i < bornRadiusScaleFactors.size(); i++)
{
(*gpu->psGBVIData)[i].x = radius[i];
(*gpu->psGBVIData)[i].y = scaledRadii[i];
(*gpu->psGBVIData)[i].z = tau*gamma[i];
(*gpu->psGBVIData)[i].w = bornRadiusScaleFactors[i];
(*gpu->psObcData)[i].x = radius[i];
(*gpu->psObcData)[i].y = 0.9f*radius[i];
for( unsigned int ii = 0; ii < bornRadiusScaleFactors.size(); ii++ ){
(*gpu->psGBVIData)[ii].x = radius[ii];
(*gpu->psGBVIData)[ii].y = scaledRadii[ii];
(*gpu->psGBVIData)[ii].z = tau*gamma[ii];
(*gpu->psGBVIData)[ii].w = bornRadiusScaleFactors[ii];
}
// Dummy out extra atom data
for (unsigned int i = atoms; i < gpu->sim.paddedNumberOfAtoms; i++)
{
(*gpu->psBornRadii)[i] = 0.2f;
(*gpu->psGBVIData)[i].x = 0.01f;
(*gpu->psGBVIData)[i].y = 0.01f;
(*gpu->psGBVIData)[i].z = 0.01f;
(*gpu->psGBVIData)[i].w = 1.00f;
for( unsigned int ii = bornRadiusScaleFactors.size(); ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(*gpu->psGBVIData)[ii].x = 0.01f;
(*gpu->psGBVIData)[ii].y = 0.01f;
(*gpu->psGBVIData)[ii].z = 0.0f;
(*gpu->psGBVIData)[ii].w = 0.0f;
}
#undef DUMP_PARAMETERS
#define DUMP_PARAMETERS 0
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr,"GBVI softcore param %u %u sclMeth=%d LwFct=%8.3f UpLmt=[%12.5e (nm) %12.5e]\nR scaledR gamma*tau= bornRadiusScaleFactor \n",
bornRadiusScaleFactors.size(), gpu->sim.paddedNumberOfAtoms,
gpuGBVISoftcore->getBornRadiiScalingMethod(), gpuGBVISoftcore->getQuinticLowerLimitFactor(),
powf( gpuGBVISoftcore->getQuinticUpperLimit(), -0.3333333f ), gpuGBVISoftcore->getQuinticUpperLimit() );
int maxPrint = 31;
for (unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++)
{
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
// diagnostics
(void) fprintf( stderr,"%6u %14.7e %14.7e %14.7e %14.7e\n",
if( freeEnergyGpu->log ){
(void) fprintf( freeEnergyGpu->log,"GBVISoftcore: part.=%u padded=%u sclMeth=%d\n",
static_cast<unsigned int>(bornRadiusScaleFactors.size()), static_cast<unsigned int>(gpu->sim.paddedNumberOfAtoms),
freeEnergyGpu->freeEnergySim.bornRadiiScalingMethod );
if( quinticSplineParameters.size() == 2 ){
(void) fprintf( freeEnergyGpu->log,"QuinticScaling: LwFct=%8.3f UpLmt=[%12.5e (nm) %12.5e]\n",
freeEnergyGpu->freeEnergySim.quinticLowerLimitFactor,
powf( freeEnergyGpu->freeEnergySim.quinticUpperLimit, -0.3333333f ), freeEnergyGpu->freeEnergySim.quinticUpperLimit );
}
(void) fprintf( freeEnergyGpu->log, "gpuSetGBVISoftcoreParameters: preFactor=%14.6e elecCnstnt=%.4f frcCnvrsnFctr=%.4f tau=%.4f.\n",
gpu->sim.preFactor, 2.0f*electricConstant, gpu->sim.forceConversionFactor, ((1.0f/innerDielectric)-(1.0f/solventDielectric)) );
#ifdef PARAMETER_PRINT
int maxPrint = MAX_PARAMETER_PRINT;
(void) fprintf( freeEnergyGpu->log, " radius scaled radius tau*gamma lambda\n" );
for( unsigned int ii = 0; ii < bornRadiusScaleFactors.size(); ii++ ){
(void) fprintf( freeEnergyGpu->log,"%6u %14.7e %14.7e %14.7e %14.7e\n",
ii, (*gpu->psGBVIData)[ii].x, (*gpu->psGBVIData)[ii].y, (*gpu->psGBVIData)[ii].z, (*gpu->psGBVIData)[ii].w );
if( ii == maxPrint ){
ii = gpu->sim.paddedNumberOfAtoms - maxPrint;
ii = bornRadiusScaleFactors.size() - maxPrint;
if( ii < maxPrint )ii = maxPrint;
}
}
unsigned int offset = gpu->sim.paddedNumberOfAtoms - MAX_PARAMETER_PRINT;
if( offset > 0 && gpu->sim.paddedNumberOfAtoms > bornRadiusScaleFactors.size() ){
for( unsigned int ii = offset; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(void) fprintf( freeEnergyGpu->log,"%6u %14.7e %14.7e %14.7e %14.7e\n",
ii, (*gpu->psGBVIData)[ii].x, (*gpu->psGBVIData)[ii].y, (*gpu->psGBVIData)[ii].z, (*gpu->psGBVIData)[ii].w );
}
}
#endif
}
gpu->psBornRadii->Upload();
gpu->psGBVIData->Upload();
gpu->psObcData->Upload();
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
gpuGBVISoftcore->upload( gpu );
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr, "gpuSetGBVISoftcoreParameters: preFactor=%14.6e elecCnstnt=%.4f frcCnvrsnFctr=%.4f tau=%.4f.\n",
gpu->sim.preFactor, 2.0f*electricConstant, gpu->sim.forceConversionFactor, ((1.0f/innerDielectric)-(1.0f/solventDielectric)) );
#endif
return gpuGBVISoftcore;
return;
}
struct Atom {
......@@ -224,7 +211,9 @@ __global__ void kReduceGBVISoftcoreBornForces_kernel()
float ratio = (gbviData.x/bornRadius);
float ratio3 = ratio*ratio*ratio;
energy -= gbviData.z*ratio3;
energy -= gbviData.z*ratio3; // gbviData.z = gamma*tau
totalForce += (3.0f*gbviData.z*ratio3)/bornRadius; // 'cavity' term
float br2 = bornRadius*bornRadius;
totalForce *= (1.0f/3.0f)*br2*br2;
......@@ -236,8 +225,9 @@ __global__ void kReduceGBVISoftcoreBornForces_kernel()
cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += energy;
}
void kReduceGBVISoftcoreBornForces(gpuContext gpu)
void kReduceGBVISoftcoreBornForces( freeEnergyGpuContext freeEnergyGpu )
{
gpuContext gpu = freeEnergyGpu->gpuContext;
kReduceGBVISoftcoreBornForces_kernel<<<gpu->sim.blocks, gpu->sim.bf_reduce_threads_per_block>>>();
LAUNCHERROR("kReduceGBVISoftcoreBornForces");
......@@ -257,7 +247,6 @@ __global__ void kReduceGBVISoftcoreBornSum_kernel()
for (int i = 0; i < cSim.nonbondOutputBuffers; i++)
{
sum += *pSt;
// printf("%4d %4d A: %9.4f\n", pos, i, *pSt);
pSt += cSim.stride;
}
......@@ -270,33 +259,10 @@ __global__ void kReduceGBVISoftcoreBornSum_kernel()
}
}
void kReduceGBVISoftcoreBornSum(gpuContext gpu)
void kReduceGBVISoftcoreBornSum( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kReduceGBVISoftcoreBornSum\n");
#define GBVISoftcore_DEBUG 0
#if ( GBVISoftcore_DEBUG == 1 )
gpu->psGBVISoftcoreData->Download();
gpu->psBornSum->Download();
gpu->psPosq4->Download();
(void) fprintf( stderr, "\nkReduceGBVISoftcoreBornSum: Post BornSum %s Born radii & params\n",
(gpu->bIncludeGBVISoftcore ? "GBVI" : "Obc") );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%d bSum=%14.6e param[%14.6e %14.6e %14.6e] x[%14.6f %14.6f %14.6f %14.6f]\n",
ii,
gpu->psBornSum->_pSysStream[0][ii],
gpu->psGBVISoftcoreData->_pSysStream[0][ii].x,
gpu->psGBVISoftcoreData->_pSysStream[0][ii].y,
gpu->psGBVISoftcoreData->_pSysStream[0][ii].z,
gpu->psPosq4->_pSysStream[0][ii].x, gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, gpu->psPosq4->_pSysStream[0][ii].w
);
}
#endif
#undef GBVISoftcore_DEBUG
gpuContext gpu = freeEnergyGpu->gpuContext;
kReduceGBVISoftcoreBornSum_kernel<<<gpu->sim.blocks, 384>>>();
gpu->bRecalculateBornRadii = false;
LAUNCHERROR("kReduceGBVISoftcoreBornSum");
}
......@@ -311,7 +277,6 @@ void kReduceGBVISoftcoreBornSum(gpuContext gpu)
// Include versions of the kernels with cutoffs.
#if 0
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
......@@ -333,19 +298,6 @@ void kReduceGBVISoftcoreBornSum(gpuContext gpu)
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateGBVISoftcoreBornSum.h"
#endif
#if 0
__global__ void kClearGBVISoftcoreBornSum_kernel()
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
while (pos < cSim.stride * cSim.nonbondOutputBuffers)
{
((float*)cSim.pBornSum)[pos] = 0.0f;
pos += gridDim.x * blockDim.x;
}
}
#endif
__device__ void quinticSpline( float x, float rl, float ru, float* outValue, float* outDerivative )
{
......@@ -373,7 +325,6 @@ __global__ void kReduceGBVIBornSumQuinticScaling_kernel()
for (int i = 0; i < cSim.nonbondOutputBuffers; i++)
{
sum += *pSt;
// printf("%4d %4d A: %9.4f\n", pos, i, *pSt);
pSt += cSim.stride;
}
......@@ -382,7 +333,6 @@ __global__ void kReduceGBVIBornSumQuinticScaling_kernel()
float Rinv = 1.0f/atom.x;
float r3 = Rinv*Rinv*Rinv;
float splineL = gbviSimDev.quinticLowerLimitFactor*r3;
//float bSum = sum;
float switchDeriviative;
if( sum > splineL ){
if( sum < r3 ){
......@@ -400,47 +350,16 @@ __global__ void kReduceGBVIBornSumQuinticScaling_kernel()
}
cSim.pBornRadii[pos] = pow( sum, (-1.0f/3.0f) );
//cSim.pBornSum[pos] = bSum;
gbviSimDev.pSwitchDerivative[pos] = switchDeriviative;
pos += gridDim.x * blockDim.x;
}
}
void kReduceGBVIBornSumQuinticScaling(gpuContext gpu, GpuGBVISoftcore* gpuGBVISoftcore)
void kReduceGBVIBornSumQuinticScaling( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kReduceGBVIBornSumQuinticScaling_kernel\n");
gpuContext gpu = freeEnergyGpu->gpuContext;
kReduceGBVIBornSumQuinticScaling_kernel<<<gpu->sim.blocks, 384>>>();
gpu->bRecalculateBornRadii = false;
LAUNCHERROR("kReduceGBVIBornSumQuinticScaling_kernel");
#define GBVI_DEBUG 0
#if ( GBVI_DEBUG == 1 )
gpu->psGBVIData->Download();
gpu->psBornSum->Download();
gpu->psBornRadii->Download();
gpu->psPosq4->Download();
CUDAStream<float>* psSwitchDerivative = gpuGBVISoftcore->getSwitchDerivative();
psSwitchDerivative->Download();
(void) fprintf( stderr, "\nkReduceGBVIBornSumQuinticScaling: Post BornSum %s Born radii & params\n",
(gpu->bIncludeGBVI ? "GBVI" : "Obc") );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%6d bSum=%14.6e bR=%14.6e swDerv=%14.6e param[%14.6e %14.6e %14.6e] x[%14.6f %14.6f %14.6f %14.6f] %s\n",
ii,
gpu->psBornSum->_pSysStream[0][ii],
gpu->psBornRadii->_pSysStream[0][ii],
psSwitchDerivative->_pSysStream[0][ii],
gpu->psGBVIData->_pSysStream[0][ii].x,
gpu->psGBVIData->_pSysStream[0][ii].y,
gpu->psGBVIData->_pSysStream[0][ii].z,
gpu->psPosq4->_pSysStream[0][ii].x, gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, gpu->psPosq4->_pSysStream[0][ii].w,
(fabs( psSwitchDerivative->_pSysStream[0][ii] - 1.0 ) > 1.0e-05 ? "SWWWWW" : "")
);
}
#endif
#undef GBVI_DEBUG
}
__global__ void kReduceGBVIBornForcesQuinticScaling_kernel()
......@@ -497,53 +416,108 @@ __global__ void kReduceGBVIBornForcesQuinticScaling_kernel()
cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += energy;
}
void kReduceGBVIBornForcesQuinticScaling(gpuContext gpu)
void kReduceGBVIBornForcesQuinticScaling( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kReduceObcGbsaBornForces\n");
gpuContext gpu = freeEnergyGpu->gpuContext;
kReduceGBVIBornForcesQuinticScaling_kernel<<<gpu->sim.blocks, gpu->sim.bf_reduce_threads_per_block>>>();
LAUNCHERROR("kReduceGBVIBornForcesQuinticScaling");
}
void kPrintGBVISoftcore(gpuContext gpu, GpuGBVISoftcore* gpuGBVISoftcore, std::string callId, int call)
void kPrintGBVISoftcore( freeEnergyGpuContext freeEnergyGpu, std::string callId, int call, FILE* log)
{
int maxPrint = 20;
(void) fprintf( stderr, "kPrintGBVgSoftcore %s %d\n", callId.c_str(), call );
gpuContext gpu = freeEnergyGpu->gpuContext;
//int maxPrint = gpu->natoms;
gpu->psGBVIData->Download();
gpu->psBornRadii->Download();
gpu->psBornForce->Download();
gpu->psPosq4->Download();
CUDAStream<float>* switchDeriviative = gpuGBVISoftcore-> getSwitchDerivative( );
CUDAStream<float>* switchDeriviative = freeEnergyGpu->psSwitchDerivative;
CUDAStream<float4>* sigEps4 = freeEnergyGpu->psSigEps4;
switchDeriviative->Download();
sigEps4->Download();
(void) fprintf( stderr, "BornSum Born radii & params\n" );
(void) fprintf( log, "kPrintGBViSoftcore Cuda comp bR bF swd prm sigeps4\n" );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%6d prm[%14.6e %14.6e %14.6e] bR=%14.6e bF=%14.6e swDrv=%14.6e x[%14.6f %14.6f %14.6f %14.6f]\n",
(void) fprintf( log, "%6d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e \n",
ii,
gpu->psGBVIData->_pSysStream[0][ii].x,
gpu->psGBVIData->_pSysStream[0][ii].y,
gpu->psGBVIData->_pSysStream[0][ii].z,
gpu->psBornRadii->_pSysStream[0][ii],
gpu->psBornForce->_pSysStream[0][ii],
switchDeriviative->_pSysStream[0][ii],
gpu->psPosq4->_pSysStream[0][ii].x, gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, gpu->psPosq4->_pSysStream[0][ii].w );
if( (ii == maxPrint) && ( ii < (gpu->natoms - maxPrint)) ){
ii = gpu->natoms - maxPrint;
}
gpu->psBornRadii->_pSysData[ii],
gpu->psBornForce->_pSysData[ii],
switchDeriviative->_pSysData[ii],
gpu->psGBVIData->_pSysData[ii].x,
gpu->psGBVIData->_pSysData[ii].y,
gpu->psGBVIData->_pSysData[ii].z,
gpu->psGBVIData->_pSysData[ii].w,
sigEps4->_pSysData[ii].x,
sigEps4->_pSysData[ii].y,
sigEps4->_pSysData[ii].z,
sigEps4->_pSysData[ii].w );
}
}
void kCalculateGBVISoftcoreBornSum(gpuContext gpu)
extern __global__ void kFindBlockBoundsCutoff_kernel();
extern __global__ void kFindBlockBoundsPeriodic_kernel();
extern __global__ void kFindBlocksWithInteractionsCutoff_kernel();
extern __global__ void kFindBlocksWithInteractionsPeriodic_kernel();
extern __global__ void kFindInteractionsWithinBlocksCutoff_kernel(unsigned int*);
extern __global__ void kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int*);
void kCalculateGBVISoftcoreBornSum( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kCalculateGBVIBornSum\n");
gpuContext gpu = freeEnergyGpu->gpuContext;
#ifdef DEBUG
fprintf( stderr, "kCalculateCDLJObcGbsaSoftcoreForces1 cutoff=%15.7e\n", gpu->sim.nonbondedCutoffSqr );
int psize = gpu->sim.paddedNumberOfAtoms;
CUDAStream<float4>* pdE1 = new CUDAStream<float4>( psize, 1, "pdE");
CUDAStream<float4>* pdE2 = new CUDAStream<float4>( psize, 1, "pdE");
float bF;
float bF1;
showWorkUnitsFreeEnergy( freeEnergyGpu, 1 );
for( int ii = 0; ii < psize; ii++ ){
pdE1->_pSysData[ii].x = 0.0f;
pdE1->_pSysData[ii].y = 0.001f;
pdE1->_pSysData[ii].z = 0.001f;
pdE1->_pSysData[ii].w = 0.001f;
pdE2->_pSysData[ii].x = 0.001f;
pdE2->_pSysData[ii].y = 0.001f;
pdE2->_pSysData[ii].z = 0.001f;
pdE2->_pSysData[ii].w = 0.001f;
}
pdE1->Upload();
pdE2->Upload();
#endif
kClearGBVISoftcoreBornSum( gpu );
LAUNCHERROR("kClearGBVIBornSum from kCalculateGBVISoftcoreBornSum");
//size_t numWithInteractions;
switch (gpu->sim.nonbondedMethod)
switch (freeEnergyGpu->freeEnergySim.nonbondedMethod)
{
case NO_CUTOFF:
case FREE_ENERGY_NO_CUTOFF:
#ifdef DEBUG
if (gpu->bOutputBufferPerWarp){
kCalculateGBVISoftcoreN2ByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
} else {
kCalculateGBVISoftcoreN2BornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
}
#else
if (gpu->bOutputBufferPerWarp){
kCalculateGBVISoftcoreN2ByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
......@@ -551,25 +525,93 @@ void kCalculateGBVISoftcoreBornSum(gpuContext gpu)
kCalculateGBVISoftcoreN2BornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
}
#endif
break;
#if 0
case CUTOFF:
case FREE_ENERGY_CUTOFF:
kFindBlockBoundsCutoff_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsCutoff");
kFindBlocksWithInteractionsCutoff_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsCutoff");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksCutoff_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#ifdef DEBUG
(void) fprintf( stderr, "kCalculateGBVISoftcoreBornSum cutoff=%15.7e warp=%u GridBoundingBox.length=%u interaction_blocks=%u interaction_threads_per_block=%u nonbond_blocks=%u nonbond_threads_per_block=%u\n",
gpu->sim.nonbondedCutoffSqr, gpu->bOutputBufferPerWarp, gpu->psGridBoundingBox->_length, gpu->sim.interaction_blocks,
gpu->sim.interaction_threads_per_block, gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block ); fflush( stderr );
if (gpu->bOutputBufferPerWarp)
kCalculateGBVICutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateGBVISoftcoreCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
else
kCalculateGBVISoftcoreCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData );
#else
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcoreCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateGBVICutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateGBVISoftcoreCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
break;
case PERIODIC:
#endif
case FREE_ENERGY_PERIODIC:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#ifdef DEBUG
if (gpu->bOutputBufferPerWarp)
kCalculateGBVIPeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateGBVISoftcorePeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData );
else
kCalculateGBVISoftcorePeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData );
#else
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcorePeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
else
kCalculateGBVIPeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateGBVISoftcorePeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
break;
#endif
break;
default:
throw OpenMM::OpenMMException( "Nonbonded softcore method not recognized." );
}
LAUNCHERROR("kCalculateGBVISoftcoreBornSum");
#ifdef DEBUG
pdE1->Download();
pdE2->Download();
fprintf( stderr, "bSum Cud method=%u warp=%u\n", freeEnergyGpu->freeEnergySim.nonbondedMethod, gpu->bOutputBufferPerWarp );
bF = 0.0;
bF1 = 0.0;
for( int ii = 0; ii < gpu->natoms; ii++ ){
if( fabsf( pdE1->_pSysData[ii].w ) > 0.002 ){
bF1 += pdE1->_pSysData[ii].x;
if( fabsf( pdE1->_pSysData[ii].x ) > 0.001 ){
fprintf( stderr, "%4d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n", ii,
pdE1->_pSysData[ii].x, pdE1->_pSysData[ii].y, pdE1->_pSysData[ii].z, pdE1->_pSysData[ii].w,
pdE2->_pSysData[ii].x, pdE2->_pSysData[ii].y, pdE2->_pSysData[ii].z, pdE2->_pSysData[ii].w );
}
}
bF += pdE1->_pSysData[ii].x;
}
fprintf( stderr, "bSum Cud %6d %15.7e %15.7e\n", TARGET, bF, bF1 );
#endif
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreBornSum.h
View file @ bc85b9f0
......@@ -37,7 +37,22 @@
#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[];
......@@ -47,8 +62,6 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
// int end = workUnits / gridDim.x;
// int pos = end - (threadIdx.x >> GRIDBITS) - 1;
#ifdef USE_CUTOFF
float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block];
#endif
......@@ -85,7 +98,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
sA[threadIdx.x].r = ar.x;
sA[threadIdx.x].sr = ar.y;
sA[threadIdx.x].bornRadiusScaleFactor = ar.w;
apos.w = 0.0f;
float bSum = 0.0f;
for (unsigned int j = 0; j < GRID; j++)
{
......@@ -98,55 +111,80 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#if defined USE_PERIODIC
if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#if defined USE_CUTOFF
if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr && j != tgx)
#else
if (i < cSim.atoms && x+j < cSim.atoms && j != tgx )
#endif
{
r = sqrt(r2);
if ((j != tgx) )
{
apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr );
}
bSum += psA[j].bornRadiusScaleFactor*getGBVI_Volume( sqrt(r2), ar.x, psA[j].sr );
#ifdef DEBUG
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
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
cSim.pBornSum[offset] += bSum;
#else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
cSim.pBornSum[offset] = bSum;
#endif
}
else // 100% utilization
{
} else {
// Read fixed atom data into registers and GRF
unsigned int j = y + tgx;
unsigned int i = x + tgx;
float4 temp = cSim.pPosq[j];
float4 temp1 = cSim.pGBVIData[j];
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y;
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
//unsigned int flags = cSim.pInteractionFlag[pos + (blockIdx.x*workUnits)/gridDim.x];
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
//else if (flags )
#endif
{
// Compute all interactions within this block.
......@@ -162,10 +200,10 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
#ifdef USE_CUTOFF
if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#else
if (i < cSim.atoms && y+tj < cSim.atoms )
#endif
{
r = sqrt(r2);
......@@ -175,9 +213,37 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
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 );
#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);
}
}
#ifdef USE_CUTOFF
else
......@@ -198,14 +264,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
#ifdef USE_CUTOFF
if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#else
if (i < cSim.atoms && y+j < cSim.atoms)
#endif
{
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.
......@@ -226,6 +293,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
#endif
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
......@@ -237,6 +305,7 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = sA[threadIdx.x].sum;
#endif
}
pos++;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreForces2.cu
View file @ bc85b9f0
......@@ -57,22 +57,14 @@ struct Atom {
static __constant__ cudaGmxSimulation cSim;
void SetCalculateGBVISoftcoreForces2Sim(gpuContext gpu)
void SetCalculateGBVISoftcoreForces2Sim( freeEnergyGpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
//(void) fprintf( stderr, "SetCalculateGBVISoftcoreForces2Sim called.\n" );
status = cudaMemcpyToSymbol(cSim, &gpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateGBVISoftcoreForces2Sim copy to cSim failed");
}
void GetCalculateGBVISoftcoreForces2Sim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
#include "kCalculateGBVISoftcoreAux.h"
#include "kCalculateGBVIAux.h"
/**
* This file contains the kernel for evalauating the second stage of GBSA. It is included
......@@ -134,6 +126,8 @@ __global__ void kCalculateGBVISoftcoreForces2a_kernel()
}
#define TARGET 0
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
......@@ -167,78 +161,83 @@ __global__ void kCalculateGBVISoftcoreForces2a_kernel()
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateGBVISoftcoreForces2.h"
void kCalculateGBVISoftcoreForces2(gpuContext gpu)
void kCalculateGBVISoftcoreForces2( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kCalculateGBVISoftcoreForces2\n");
size_t numWithInteractions;
#if 0
kClearForces(gpu);
(void) fprintf( stderr, "\nkCalculateGBVISoftcoreForces2: cleared force prior loop2\n" ); (void) fflush( stderr );
kCalculateGBVISoftcoreForces2a_kernel<<<gpu->sim.blocks, 384>>>();
(void) fprintf( stderr, "\ncalled kCalculateGBVISoftcoreForces2a\n" ); (void) fflush( stderr );
return;
#endif
gpuContext gpu = freeEnergyGpu->gpuContext;
switch (gpu->sim.nonbondedMethod)
/*fprintf( stderr,"kCalculateGBVISoftcoreForces2 nonbondedMethod=%d bornForce2_blocks=%d bornForce2_threads_per_block=%d\n",
freeEnergyGpu->freeEnergySim.nonbondedMethod,
gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block, gpu->psInteractionCount->_pSysData[0] ); fflush( stderr );
*/
switch (freeEnergyGpu->freeEnergySim.nonbondedMethod)
{
case NO_CUTOFF:
case FREE_ENERGY_NO_CUTOFF:
#ifdef DEBUG
int psize = 64;
CUDAStream<float4>* pdE1 = new CUDAStream<float4>( psize, 1, "pdE");
CUDAStream<float4>* pdE2 = new CUDAStream<float4>( psize, 1, "pdE");
for( int ii = 0; ii < 32; ii++ ){
pdE1->_pSysData[ii].x = 0.0f;
pdE1->_pSysData[ii].y = 0.0f;
pdE1->_pSysData[ii].z = 0.0f;
pdE1->_pSysData[ii].w = 0.0f;
pdE2->_pSysData[ii].x = 0.0f;
pdE2->_pSysData[ii].y = 0.0f;
pdE2->_pSysData[ii].z = 0.0f;
pdE2->_pSysData[ii].w = 0.0f;
}
pdE1->Upload();
pdE2->Upload();
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit, gpu->sim.workUnits);
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit, gpu->sim.workUnits, pdE1->_pDevData, pdE2->_pDevData);
else
kCalculateGBVISoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit, gpu->sim.workUnits);
//(void) fprintf( stderr, "\nkCalculateGBVIForces2: Born radii/force forces warp=%u\n", gpu->bOutputBufferPerWarp ); (void) fflush( stderr );
#define GBVI_DEBUG 0
#if ( GBVI_DEBUG == 1 )
(void) fprintf( stderr, "\nkCalculateGBVISoftcoreForces2: Born radii/force forces:\n" ); (void) fflush( stderr );
gpu->psBornForce->Download();
gpu->psForce4->Download();
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%d bF=%14.6e Fa[%14.6e %14.6e %14.6e] Fb[%14.6e %14.6e %14.6e]\n",
ii,
gpu->psBornForce->_pSysStream[0][ii],
gpu->psForce4->_pSysStream[0][ii].x,
gpu->psForce4->_pSysStream[0][ii].y,
gpu->psForce4->_pSysStream[0][ii].z,
gpu->psForce4->_pSysStream[1][ii].x,
gpu->psForce4->_pSysStream[1][ii].y,
gpu->psForce4->_pSysStream[1][ii].z
);
}
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms*2; ii++ ){
(void) fprintf( stderr, "%d bF=%14.6e Fa[%14.6e %14.6e %14.6e %14.6e]\n",
ii,
gpu->psBornForce->_pSysStream[0][ii],
gpu->psForce4->_pSysStream[0][ii].x,
gpu->psForce4->_pSysStream[0][ii].y,
gpu->psForce4->_pSysStream[0][ii].z,
gpu->psForce4->_pSysStream[0][ii].w
);
}
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit, gpu->sim.workUnits, pdE1->_pDevData, pdE2->_pDevData);
pdE1->Download();
pdE2->Download();
fprintf( stderr, "Pde\n" );
for( int ii = 0; ii < 32; ii++ ){
fprintf( stderr, "%4d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n", ii,
pdE1->_pSysData[ii].x, pdE1->_pSysData[ii].y, pdE1->_pSysData[ii].z, pdE1->_pSysData[ii].w,
pdE2->_pSysData[ii].x, pdE2->_pSysData[ii].y, pdE2->_pSysData[ii].z, pdE2->_pSysData[ii].w );
}
break;
#endif
#undef GBVI_DEBUG
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateGBVISoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
break;
case CUTOFF:
numWithInteractions = gpu->psInteractionCount->_pSysData[0];
case FREE_ENERGY_CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcoreCutoffByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
else
kCalculateGBVISoftcoreCutoffForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
break;
case PERIODIC:
numWithInteractions = gpu->psInteractionCount->_pSysData[0];
case FREE_ENERGY_PERIODIC:
if (gpu->bOutputBufferPerWarp)
kCalculateGBVISoftcorePeriodicByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
else
kCalculateGBVISoftcorePeriodicForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit );
break;
}
LAUNCHERROR("kCalculateGBVISoftcoreForces2");
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreForces2.h
View file @ bc85b9f0
......@@ -29,19 +29,29 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "kCalculateGBVISoftcoreAux.h"
#include "kCalculateGBVIAux.h"
/**
* This file contains the kernel for evalauating the second stage of GBSA. It is included
* This file contains the kernel for evaluating the second stage of GB/VI. It is included
* several times in kCalculateGBVIForces2.cu with different #defines to generate
* different versions of the kernels.
*/
__global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit, unsigned int numWorkUnits)
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_BORNFORCE2_THREADS_PER_BLOCK, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(GT2XX_BORNFORCE2_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_BORNFORCE2_THREADS_PER_BLOCK, 1)
#endif
void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit )
{
//METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit, float4* pdE1, float4* pdE2 )
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.bornForce2_blocks*cSim.bornForce2_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
#ifdef USE_CUTOFF
......@@ -63,11 +73,17 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
float fb = cSim.pBornForce[i];
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
float3 af;
sA[threadIdx.x].fx = af.x = 0.0f;
sA[threadIdx.x].fy = af.y = 0.0f;
sA[threadIdx.x].fz = af.z = 0.0f;
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
......@@ -82,9 +98,11 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
for (unsigned int j = (tgx+1)&(GRID-1); j != tgx; j = (j+1)&(GRID-1))
{
float dx = psA[j].x - apos.x;
float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
......@@ -95,31 +113,43 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
// Atom I Born forces and sum
float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb );
#if defined USE_PERIODIC
if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#endif
#if defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
if (i >= cSim.atoms || x+j >= cSim.atoms || (i == (x+j)) || r2 > cSim.nonbondedCutoffSqr)
#else
if(i >= cSim.atoms || x+j >= cSim.atoms || (i == (x+j)) )
#endif
{
dE = 0.0f;
}
#endif
/*
if( i == TARGET ){
pdE1[x+j].x = dE;
pdE1[x+j].y = psA[j].bornRadiusScaleFactor;
pdE1[x+j].z = r;
pdE1[x+j].w = dE1;
}
if( (x+j) == TARGET ){
pdE2[i].x = dE;
pdE2[i].y = psA[j].bornRadiusScaleFactor;
pdE2[i].z = r;
pdE2[i].w = psA[j].sr-ar.x;
}*/
float d = dx * dE;
af.x -= d;
psA[j].fx += d;
d = dy * dE;
af.y -= d;
psA[j].fy += d;
d = dz * dE;
af.z -= d;
psA[j].fz += d;
}
// Write results
float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
......@@ -181,18 +211,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
float dE = psA[tj].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[tj].sr, fb );
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#else
if (i >= cSim.atoms || y+tj >= cSim.atoms )
#endif
#if defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#endif
float d = dx * dE;
af.x -= d;
......@@ -207,18 +234,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
// Atom J Born sum term
dE = ar.w*getGBVI_dE2( r, psA[tj].r, ar.y, psA[tj].fb );
#ifdef USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#else
if (i >= cSim.atoms || y+tj >= cSim.atoms )
#endif
#if defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#endif
dx *= dE;
dy *= dE;
dz *= dE;
......@@ -254,18 +278,14 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
// Interleaved Atom I and J Born Forces and sum components
float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb );
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#else
if (i >= cSim.atoms || y+j >= cSim.atoms )
#endif
#if defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#endif
float d = dx * dE;
af.x -= d;
......@@ -280,18 +300,15 @@ __global__ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int
// Atom J Born sum term
dE = ar.w*getGBVI_dE2( r, psA[j].r, ar.y, psA[j].fb );
#ifdef USE_PERIODIC
#if defined USE_CUTOFF
if (i >= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#else
if (i >= cSim.atoms || y+j >= cSim.atoms )
#endif
#if defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dE = 0.0f;
}
#endif
dx *= dE;
dy *= dE;
dz *= dE;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateLocalSoftcoreForces.cu
View file @ bc85b9f0
......@@ -24,454 +24,123 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "GpuLJ14Softcore.h"
#include "GpuFreeEnergyCudaKernels.h"
//#include <cuda.h>
#include "freeEnergyGpuTypes.h"
#include <cudatypes.h>
#include "kSoftcoreLJ.h"
#define PARAMETER_PRINT 1
#define MAX_PARAMETER_PRINT 10
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationNonbonded14 feSim;
static __constant__ cudaFreeEnergyGmxSimulation feSim;
/* Cuda compiler on Windows does not recognized "static const float" values */
#define LOCAL_HACK_PI 3.1415926535897932384626433832795
void SetCalculateLocalSoftcoreGpuSim( freeEnergyGpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreGpuSim copy to cSim failed");
#define DOT3(v1, v2) (v1.x * v2.x + v1.y * v2.y + v1.z * v2.z)
status = cudaMemcpyToSymbol(feSim, &gpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreGpuSim copy to feSim failed");
#define GETNORMEDDOTPRODUCT(v1, v2, dp) \
{ \
dp = DOT3(v1, v2); \
float norm1 = DOT3(v1, v1); \
float norm2 = DOT3(v2, v2); \
dp /= sqrt(norm1 * norm2); \
dp = min(dp, 1.0f); \
dp = max(dp, -1.0f); \
}
#define CROSS_PRODUCT(v1, v2, c) \
c.x = v1.y * v2.z - v1.z * v2.y; \
c.y = v1.z * v2.x - v1.x * v2.z; \
c.z = v1.x * v2.y - v1.y * v2.x;
extern "C"
void gpuSetLJ14SoftcoreParameters( freeEnergyGpuContext gpu, float epsfac, const std::vector<int>& atom1, const std::vector<int>& atom2,
const std::vector<float>& c6, const std::vector<float>& c12, const std::vector<float>& qProd,
const std::vector<float>& softcoreLJLambdaArray ){
#define GETPREFACTORSGIVENANGLECOSINE(cosine, param, dEdR) \
{ \
float angle = acos(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal; \
}
unsigned int LJ14s = atom1.size();
gpu->freeEnergySim.LJ14_count = LJ14s;
#define GETENERGYGIVENANGLECOSINE(cosine, param, dEdR) \
{ \
float angle = acos(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal * deltaIdeal; \
}
gpu->psLJ14ID = new CUDAStream<int4>(LJ14s, 1, "LJ14SoftcoreID");
CUDAStream<int4>* psLJ14ID = gpu->psLJ14ID;
gpu->freeEnergySim.pLJ14ID = psLJ14ID->_pDevData;
#define GETANGLEBETWEENTWOVECTORS(v1, v2, angle) \
{ \
float dp; \
GETNORMEDDOTPRODUCT(v1, v2, dp); \
angle = acos(dp); \
}
gpu->psLJ14Parameter = new CUDAStream<float4>(LJ14s, 1, "LJ14SoftcoreParameter");
CUDAStream<float4>* psLJ14Parameter = gpu->psLJ14Parameter;
gpu->freeEnergySim.pLJ14Parameter = psLJ14Parameter->_pDevData;
#define GETANGLECOSINEBETWEENTWOVECTORS(v1, v2, angle, cosine) \
{ \
GETNORMEDDOTPRODUCT(v1, v2, cosine); \
angle = acos(cosine); \
}
std::vector<int> outputBufferCounter( gpu->gpuContext->sim.atoms, 0 );
#define GETDIHEDRALANGLEBETWEENTHREEVECTORS(vector1, vector2, vector3, signVector, cp0, cp1, angle) \
{ \
CROSS_PRODUCT(vector1, vector2, cp0); \
CROSS_PRODUCT(vector2, vector3, cp1); \
GETANGLEBETWEENTWOVECTORS(cp0, cp1, angle); \
float dp = DOT3(signVector, cp1); \
angle = (dp >= 0) ? angle : -angle; \
}
for( int ii = 0; ii < LJ14s; ii++ ){
#define GETDIHEDRALANGLECOSINEBETWEENTHREEVECTORS(vector1, vector2, vector3, signVector, cp0, cp1, angle, cosine) \
{ \
CROSS_PRODUCT(vector1, vector2, cp0); \
CROSS_PRODUCT(vector2, vector3, cp1); \
GETANGLECOSINEBETWEENTWOVECTORS(cp0, cp1, angle, cosine); \
float dp = DOT3(signVector, cp1); \
angle = (dp >= 0) ? angle : -angle; \
}
(*psLJ14ID)[ii].x = atom1[ii];
(*psLJ14ID)[ii].y = atom2[ii];
(*psLJ14ID)[ii].z = outputBufferCounter[atom1[ii]]++;
(*psLJ14ID)[ii].w = outputBufferCounter[atom2[ii]]++;
void SetCalculateLocalSoftcoreGpuSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreGpuSim copy to cSim failed");
float p0, p1, p2, p3;
if( c12[ii] == 0.0f ){
p0 = 0.0f;
p1 = 1.0f;
}
} else {
p0 = c6[ii] * c6[ii] / c12[ii];
p1 = pow(c12[ii] / c6[ii], 1.0f / 6.0f);
}
void SetCalculateLocalSoftcoreSim( GpuLJ14Softcore* gpuLJ14Softcore)
{
cudaError_t status;
p2 = epsfac*qProd[ii];
p3 = softcoreLJLambdaArray[ii];
status = cudaMemcpyToSymbol(feSim, &gpuLJ14Softcore->feSim, sizeof(cudaFreeEnergySimulationNonbonded14));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreSim copy to cSim failed");
}
(*psLJ14Parameter)[ii].x = p0;
(*psLJ14Parameter)[ii].y = p1;
(*psLJ14Parameter)[ii].z = p2;
(*psLJ14Parameter)[ii].w = p3;
}
void GetCalculateLocalSoftcoreForcesSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: GetCalculateLocalSoftcoreForcesSim copy from cSim failed");
// logging info
if( gpu->log ){
(void) fprintf( gpu->log, "gpuSetLJ14SoftcoreParameters: number of 1-4 bonds=%5u\n", LJ14s );
#ifdef PARAMETER_PRINT
unsigned int maxPrint = MAX_PARAMETER_PRINT;
for( unsigned int ii = 0; ii < LJ14s; ii++ ){
(void) fprintf( gpu->log, " %5d [%5d %5d %5d %5d] %15.7e %15.7e %15.7e %15.7e\n",
ii, (*psLJ14ID)[ii].x, (*psLJ14ID)[ii].y, (*psLJ14ID)[ii].z, (*psLJ14ID)[ii].w,
(*psLJ14Parameter)[ii].x, (*psLJ14Parameter)[ii].y,
(*psLJ14Parameter)[ii].z/epsfac, (*psLJ14Parameter)[ii].w );
if( ii == maxPrint ){
(void) fprintf( gpu->log, "\n" );
ii = LJ14s - maxPrint;
if( ii < maxPrint )ii = maxPrint;
}
}
(void) fprintf( gpu->log, "\n" );
#endif
(void) fflush( gpu->log );
}
psLJ14ID->Upload();
psLJ14Parameter->Upload();
return;
}
#define USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
#endif
#define DOT3(v1, v2) (v1.x * v2.x + v1.y * v2.y + v1.z * v2.z)
__global__ void kCalculateLocalSoftcoreForces_kernel()
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
//Vectors* A = &sV[threadIdx.x];
float energy = 0.0f;
#if 0
while (pos < cSim.bond_offset)
{
if (pos < cSim.bonds)
{
int4 atom = cSim.pBondID[pos];
float4 atomA = cSim.pPosq[atom.x];
float4 atomB = cSim.pPosq[atom.y];
float2 bond = cSim.pBondParameter[pos];
float dx = atomB.x - atomA.x;
float dy = atomB.y - atomA.y;
float dz = atomB.z - atomA.z;
float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2);
float deltaIdeal = r - bond.x;
/* E */ energy += 0.5f * bond.y * deltaIdeal * deltaIdeal;
float dEdR = bond.y * deltaIdeal;
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
// printf("D: %11.4f %11.4f %11.4f %11.4f %11.4f %11.4f\n", dx, dy, dz, r, deltaIdeal, dEdR);
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
unsigned int offsetB = atom.y + atom.w * cSim.stride;
float4 forceA = cSim.pForce4[offsetA];
float4 forceB = cSim.pForce4[offsetB];
forceA.x += dx;
forceA.y += dy;
forceA.z += dz;
forceB.x -= dx;
forceB.y -= dy;
forceB.z -= dz;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
while (pos < cSim.bond_angle_offset)
if (feSim.nonbondedMethod == NO_CUTOFF)
{
unsigned int pos1 = pos - cSim.bond_offset;
if (pos1 < cSim.bond_angles)
while (pos < feSim.LJ14_count)
{
int4 atom1 = cSim.pBondAngleID1[pos1];
float2 bond_angle = cSim.pBondAngleParameter[pos1];
float4 a1 = cSim.pPosq[atom1.x];
float4 a2 = cSim.pPosq[atom1.y];
float4 a3 = cSim.pPosq[atom1.z];
A->v0.x = a2.x - a1.x;
A->v0.y = a2.y - a1.y;
A->v0.z = a2.z - a1.z;
A->v1.x = a2.x - a3.x;
A->v1.y = a2.y - a3.y;
A->v1.z = a2.z - a3.z;
float3 cp;
CROSS_PRODUCT(A->v0, A->v1, cp);
float rp = DOT3(cp, cp); //cx * cx + cy * cy + cz * cz;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = DOT3(A->v0, A->v0); // dx1 * dx1 + dy1 * dy1 + dz1 * dz1;
float r23 = DOT3(A->v1, A->v1); // dx2 * dx2 + dy2 * dy2 + dz2 * dz2;
float dot = DOT3(A->v0, A->v1); // dx1 * dx2 + dy1 * dy2 + dz1 * dz2;
float cosine = dot / sqrt(r21 * r23);
float angle_energy;
/* E */ GETENERGYGIVENANGLECOSINE(cosine, bond_angle, angle_energy);
energy += 0.5f*angle_energy;
float dEdR;
GETPREFACTORSGIVENANGLECOSINE(cosine, bond_angle, dEdR);
//printf("%11.4f %11.4f\n", cosine, dEdR);
float termA = dEdR / (r21 * rp);
float termC = -dEdR / (r23 * rp);
float3 c21;
float3 c23;
CROSS_PRODUCT(A->v0, cp, c21);
CROSS_PRODUCT(A->v1, cp, c23);
c21.x *= termA;
c21.y *= termA;
c21.z *= termA;
c23.x *= termC;
c23.y *= termC;
c23.z *= termC;
int2 atom2 = cSim.pBondAngleID2[pos1];
unsigned int offset = atom1.x + atom1.w * cSim.stride;
float4 force = cSim.pForce4[offset];
force.x += c21.x;
force.y += c21.y;
force.z += c21.z;
cSim.pForce4[offset] = force;
offset = atom1.y + atom2.x * cSim.stride;
force = cSim.pForce4[offset];
force.x -= (c21.x + c23.x);
force.y -= (c21.y + c23.y);
force.z -= (c21.z + c23.z);
cSim.pForce4[offset] = force;
offset = atom1.z + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += c23.x;
force.y += c23.y;
force.z += c23.z;
cSim.pForce4[offset] = force;
}
pos += blockDim.x * gridDim.x;
}
int4 atom = feSim.pLJ14ID[pos];
float4 LJ14 = feSim.pLJ14Parameter[pos];
while (pos < cSim.dihedral_offset)
{
unsigned int pos1 = pos - cSim.bond_angle_offset;
if (pos1 < cSim.dihedrals)
{
int4 atom1 = cSim.pDihedralID1[pos1];
float4 atomA = cSim.pPosq[atom1.x];
float4 atomB = cSim.pPosq[atom1.y];
float4 atomC = cSim.pPosq[atom1.z];
float4 atomD = cSim.pPosq[atom1.w];
A->v0.x = atomA.x - atomB.x;
A->v0.y = atomA.y - atomB.y;
A->v0.z = atomA.z - atomB.z;
A->v1.x = atomC.x - atomB.x;
A->v1.y = atomC.y - atomB.y;
A->v1.z = atomC.z - atomB.z;
A->v2.x = atomC.x - atomD.x;
A->v2.y = atomC.y - atomD.y;
A->v2.z = atomC.z - atomD.z;
float3 cp0, cp1;
float dihedralAngle;
GETDIHEDRALANGLEBETWEENTHREEVECTORS(A->v0, A->v1, A->v2, A->v0, cp0, cp1, dihedralAngle);
float4 dihedral = cSim.pDihedralParameter[pos1];
float deltaAngle = dihedral.z * dihedralAngle - (dihedral.y * PI / 180.0f);
// ATTENTION: This section leads to a divergent deltaAngle values wrt
// forces and energies. We separate the case dihedral.z = n = 0, which
// is treated by the calculation of energies via a harmonic potential
/* E */ if (dihedral.z) energy += dihedral.x * (1.0f + cos(deltaAngle));
/* E */ else
{
float deltaAngle = dihedralAngle - dihedral.y;
if (deltaAngle < -PI) deltaAngle += 2.0f * PI;
else if (deltaAngle > PI) deltaAngle -= 2.0f * PI;
energy += dihedral.x * deltaAngle * deltaAngle;
}
float sinDeltaAngle = sin(deltaAngle);
float dEdAngle = -dihedral.x * dihedral.z * sinDeltaAngle;
float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1));
float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1);
ff.w = (dEdAngle * normBC) / normCross2;
float dp = 1.0f / DOT3(A->v1, A->v1);
ff.y = DOT3(A->v0, A->v1) * dp;
ff.z = DOT3(A->v2, A->v1) * dp;
int4 atom2 = cSim.pDihedralID2[pos1];
float3 internalF0;
float3 internalF3;
float3 s;
// printf("%4d: %9.4f %9.4f %9.4f %9.4f\n", pos1, ff.x, ff.y, ff.z, ff.w);
unsigned int offset = atom1.x + atom2.x * cSim.stride;
float4 force = cSim.pForce4[offset];
internalF0.x = ff.x * cp0.x;
force.x += internalF0.x;
internalF0.y = ff.x * cp0.y;
force.y += internalF0.y;
internalF0.z = ff.x * cp0.z;
force.z += internalF0.z;
cSim.pForce4[offset] = force;
//printf("%4d - 0: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.w + atom2.w * cSim.stride;
force = cSim.pForce4[offset];
internalF3.x = ff.w * cp1.x;
force.x += internalF3.x;
internalF3.y = ff.w * cp1.y;
force.y += internalF3.y;
internalF3.z = ff.w * cp1.z;
force.z += internalF3.z;
cSim.pForce4[offset] = force;
// printf("%4d - 3: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
s.x = ff.y * internalF0.x - ff.z * internalF3.x;
s.y = ff.y * internalF0.y - ff.z * internalF3.y;
s.z = ff.y * internalF0.z - ff.z * internalF3.z;
offset = atom1.y + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF0.x + s.x;
force.y += -internalF0.y + s.y;
force.z += -internalF0.z + s.z;
cSim.pForce4[offset] = force;
//printf("%4d - 1: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.z + atom2.z * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF3.x - s.x;
force.y += -internalF3.y - s.y;
force.z += -internalF3.z - s.z;
cSim.pForce4[offset] = force;
//printf("%4d - 2: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
}
pos += blockDim.x * gridDim.x;
}
// Ryckaert Bellemans dihedrals
while (pos < cSim.rb_dihedral_offset)
{
unsigned int pos1 = pos - cSim.dihedral_offset;
if (pos1 < cSim.rb_dihedrals)
{
int4 atom1 = cSim.pRbDihedralID1[pos1];
float4 atomA = cSim.pPosq[atom1.x];
float4 atomB = cSim.pPosq[atom1.y];
float4 atomC = cSim.pPosq[atom1.z];
float4 atomD = cSim.pPosq[atom1.w];
A->v0.x = atomA.x - atomB.x;
A->v0.y = atomA.y - atomB.y;
A->v0.z = atomA.z - atomB.z;
A->v1.x = atomC.x - atomB.x;
A->v1.y = atomC.y - atomB.y;
A->v1.z = atomC.z - atomB.z;
A->v2.x = atomC.x - atomD.x;
A->v2.y = atomC.y - atomD.y;
A->v2.z = atomC.z - atomD.z;
float3 cp0, cp1;
float dihedralAngle, cosPhi;
// printf("%4d - 0 : %9.4f %9.4f %9.4f\n", pos1, A->v0.x, A->v0.y, A->v0.z);
// printf("%4d - 1 : %9.4f %9.4f %9.4f\n", pos1, A->v1.x, A->v1.y, A->v1.z);
// printf("%4d - 2 : %9.4f %9.4f %9.4f\n", pos1, A->v2.x, A->v2.y, A->v2.z);
GETDIHEDRALANGLECOSINEBETWEENTHREEVECTORS(A->v0, A->v1, A->v2, A->v0, cp0, cp1, dihedralAngle, cosPhi);
if (dihedralAngle < 0.0f )
{
dihedralAngle += PI;
}
else
{
dihedralAngle -= PI;
}
cosPhi = -cosPhi;
// printf("%4d: %9.4f %9.4f\n", pos1, dihedralAngle, cosPhi);
float4 dihedral1 = cSim.pRbDihedralParameter1[pos1];
float2 dihedral2 = cSim.pRbDihedralParameter2[pos1];
float cosFactor = cosPhi;
float dEdAngle = -dihedral1.y;
/* E */ float rb_energy = dihedral1.x;
rb_energy += dihedral1.y * cosFactor;
// printf("%4d - 1: %9.4f %9.4f\n", pos1, dEdAngle, 1.0f);
dEdAngle -= 2.0f * dihedral1.z * cosFactor;
// printf("%4d - 2: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 3.0f * dihedral1.w * cosFactor;
rb_energy += dihedral1.z * cosFactor;
// printf("%4d - 3: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 4.0f * dihedral2.x * cosFactor;
rb_energy += dihedral1.w * cosFactor;
// printf("%4d - 4: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 5.0f * dihedral2.y * cosFactor;
rb_energy += dihedral2.x * cosFactor;
rb_energy += dihedral2.y * cosFactor * cosPhi;
/* E */ energy += rb_energy;
// printf("%4d - 5: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
dEdAngle *= sin(dihedralAngle);
// printf("%4d - f: %9.4f\n", pos1, dEdAngle);
float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1));
float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1);
ff.w = (dEdAngle * normBC) / normCross2;
float dp = 1.0f / DOT3(A->v1, A->v1);
ff.y = DOT3(A->v0, A->v1) * dp;
ff.z = DOT3(A->v2, A->v1) * dp;
int4 atom2 = cSim.pRbDihedralID2[pos1];
float3 internalF0;
float3 internalF3;
float3 s;
// printf("%4d: %9.4f %9.4f %9.4f %9.4f\n", pos1, ff.x, ff.y, ff.z, ff.w);
unsigned int offset = atom1.x + atom2.x * cSim.stride;
float4 force = cSim.pForce4[offset];
internalF0.x = ff.x * cp0.x;
force.x += internalF0.x;
internalF0.y = ff.x * cp0.y;
force.y += internalF0.y;
internalF0.z = ff.x * cp0.z;
force.z += internalF0.z;
cSim.pForce4[offset] = force;
// printf("%4d - 0: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.w + atom2.w * cSim.stride;
force = cSim.pForce4[offset];
internalF3.x = ff.w * cp1.x;
force.x += internalF3.x;
internalF3.y = ff.w * cp1.y;
force.y += internalF3.y;
internalF3.z = ff.w * cp1.z;
force.z += internalF3.z;
cSim.pForce4[offset] = force;
// printf("%4d - 3: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
s.x = ff.y * internalF0.x - ff.z * internalF3.x;
s.y = ff.y * internalF0.y - ff.z * internalF3.y;
s.z = ff.y * internalF0.z - ff.z * internalF3.z;
offset = atom1.y + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF0.x + s.x;
force.y += -internalF0.y + s.y;
force.z += -internalF0.z + s.z;
cSim.pForce4[offset] = force;
// printf("%4d - 1: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.z + atom2.z * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF3.x - s.x;
force.y += -internalF3.y - s.y;
force.z += -internalF3.z - s.z;
cSim.pForce4[offset] = force;
// printf("%4d - 2: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
}
pos += blockDim.x * gridDim.x;
}
#endif
if (cSim.nonbondedMethod == NO_CUTOFF)
{
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
d.x = a1.x - a2.x;
d.y = a1.y - a2.y;
d.z = a1.z - a2.z;
float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2);
#ifdef USE_SOFTCORE_LJ
......@@ -503,21 +172,14 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
else if (cSim.nonbondedMethod == CUTOFF)
{
} else if (feSim.nonbondedMethod == CUTOFF) {
float LJ14_energy;
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
while (pos < feSim.LJ14_count ){
int4 atom = feSim.pLJ14ID[pos];
float4 LJ14 = feSim.pLJ14Parameter[pos];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
......@@ -533,19 +195,16 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = LJ14.x * (12.0f * sig6 - 6.0f) * sig6;
/* E */
LJ14_energy = LJ14.x * (sig6 - 1.0f) * sig6;
#endif
LJ14_energy += LJ14.z * (inverseR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
dEdR += LJ14.z * (inverseR - 2.0f * cSim.reactionFieldK * r2);
dEdR *= inverseR * inverseR;
if (r2 > cSim.nonbondedCutoffSqr)
if (r2 > feSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
LJ14_energy = 0.0f;
}
/* E */
energy += LJ14_energy;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
......@@ -563,21 +222,13 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
else if (cSim.nonbondedMethod == PERIODIC)
{
} else if (feSim.nonbondedMethod == PERIODIC ){
float LJ14_energy;
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
while (pos < feSim.LJ14_count ){
int4 atom = feSim.pLJ14ID[pos];
float4 LJ14 = feSim.pLJ14Parameter[pos];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
......@@ -596,20 +247,17 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = LJ14.x * (12.0f * sig6 - 6.0f) * sig6;
/* E */
LJ14_energy = LJ14.x * (sig6 - 1.0f) * sig6;
#endif
LJ14_energy += LJ14.z * (inverseR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
dEdR += LJ14.z * (inverseR - 2.0f * cSim.reactionFieldK * r2);
dEdR *= inverseR * inverseR;
if (r2 > cSim.nonbondedCutoffSqr)
if (r2 > feSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
LJ14_energy = 0.0f;
}
/* E */
energy += LJ14_energy;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
......@@ -627,87 +275,15 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += energy;
}
extern "C"
GpuLJ14Softcore* gpuSetLJ14SoftcoreParameters(gpuContext gpu, float epsfac, float fudge, const std::vector<int>& atom1, const std::vector<int>& atom2,
const std::vector<float>& c6, const std::vector<float>& c12, const std::vector<float>& q1,
const std::vector<float>& q2, const std::vector<float>& softcoreLJLambdaArray)
{
int LJ14s = atom1.size();
float scale = epsfac * fudge;
GpuLJ14Softcore* gpuLJ14Softcore = new GpuLJ14Softcore();
gpuLJ14Softcore->feSim.LJ14s = LJ14s;
CUDAStream<int4>* psLJ14ID = new CUDAStream<int4>(LJ14s, 1, "LJ14SoftcoreID");
gpuLJ14Softcore->psLJ14SoftcoreID = psLJ14ID;
gpuLJ14Softcore->feSim.pLJ14ID = psLJ14ID->_pDevStream[0];
CUDAStream<float4>* psLJ14Parameter = new CUDAStream<float4>(LJ14s, 1, "LJ14SoftcoreParameter");
gpuLJ14Softcore->psLJ14SoftcoreParameter = psLJ14Parameter;
gpuLJ14Softcore->feSim.pLJ14Parameter = psLJ14Parameter->_pDevStream[0];
gpuLJ14Softcore->feSim.LJ14_offset = LJ14s;
for (int i = 0; i < LJ14s; i++)
{
(*psLJ14ID)[i].x = atom1[i];
(*psLJ14ID)[i].y = atom2[i];
psLJ14ID->_pSysData[i].z = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].x]++;
psLJ14ID->_pSysData[i].w = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].y]++;
float p0, p1, p2, p3;
if (c12[i] == 0.0f)
{
p0 = 0.0f;
p1 = 1.0f;
}
else
{
p0 = c6[i] * c6[i] / c12[i];
p1 = pow(c12[i] / c6[i], 1.0f / 6.0f);
}
p2 = scale * q1[i] * q2[i];
p3 = softcoreLJLambdaArray[i];
(*psLJ14Parameter)[i].x = p0;
(*psLJ14Parameter)[i].y = p1;
(*psLJ14Parameter)[i].z = p2;
(*psLJ14Parameter)[i].w = p3;
}
#if (DUMP_PARAMETERS == 1)
cout <<
i << " " <<
(*psLJ14ID)[i].x << " " <<
(*psLJ14ID)[i].y << " " <<
(*psLJ14ID)[i].z << " " <<
(*psLJ14ID)[i].w << " " <<
(*psLJ14Parameter)[i].x << " " <<
(*psLJ14Parameter)[i].y << " " <<
(*psLJ14Parameter)[i].z << " " <<
(*psLJ14Parameter)[i].w << " " <<
p0 << " " <<
p1 << " " <<
p2 << " " <<
p3 << " " <<
endl;
#endif
psLJ14ID->Upload();
psLJ14Parameter->Upload();
SetCalculateLocalSoftcoreSim( gpuLJ14Softcore );
return gpuLJ14Softcore;
}
void kCalculateLocalSoftcoreForces(gpuContext gpu)
void kCalculateLocalSoftcoreForces( freeEnergyGpuContext freeEnergyGpuContext )
{
// printf("kCalculateLocalForces\n");
// fprintf( stderr, "kCalculateLocalSoftcoreForces blks=%u localForces_threads_per_block=%u szVector=%u total=%u\n", gpu->sim.blocks, gpu->sim.localForces_threads_per_block, sizeof(Vectors),
// gpu->sim.localForces_threads_per_block * sizeof(Vectors) ); fflush( stderr );
gpuContext gpu = freeEnergyGpuContext->gpuContext;
kCalculateLocalSoftcoreForces_kernel<<<gpu->sim.blocks, gpu->sim.localForces_threads_per_block, gpu->sim.localForces_threads_per_block * sizeof(Vectors)>>>();
LAUNCHERROR("kCalculateLocalSoftcoreForces");
}
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateNonbondedSoftcore.cu
View file @ bc85b9f0
......@@ -24,161 +24,171 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "GpuNonbondedSoftcore.h"
#include "freeEnergyGpuTypes.h"
#include "GpuFreeEnergyCudaKernels.h"
#include "openmm/OpenMMException.h"
#include <algorithm>
#include <sstream>
// structure containing array of softcore lambdas
struct cudaFreeEnergySimulationNonBonded {
float* pParticleSoftCoreLJLambda;
};
//struct cudaFreeEnergySimulationNonBonded feSim;
#define PARAMETER_PRINT 0
#define MAX_PARAMETER_PRINT 10
// device handles
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationNonBonded feSimDev;
static __constant__ cudaFreeEnergyGmxSimulation feSimDev;
// write address of structs to devices
void SetCalculateCDLJSoftcoreGpuSim( gpuContext gpu )
{
void SetCalculateCDLJSoftcoreGpuSim( freeEnergyGpuContext freeEnergyGpu ){
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
status = cudaMemcpyToSymbol(cSim, &freeEnergyGpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateCDLJSoftcoreGpuSim copy to cSim failed");
//(void) fprintf( stderr, "SetCalculateCDLJSoftcoreGpuSim gpu=%p cSim=%p sizeof=%u\n", gpu, &gpu->sim, sizeof(cudaGmxSimulation) ); fflush( stderr );
status = cudaMemcpyToSymbol( feSimDev, &freeEnergyGpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateCDLJSoftcoreGpuSim copy to feSimDev failed");
}
void SetCalculateCDLJSoftcoreSupplementarySim( float* gpuParticleSoftCoreLJLambda)
extern "C"
void freeEnergyGpuSetPeriodicBoxSize( freeEnergyGpuContext freeEnergyGpu, float xsize, float ysize, float zsize)
{
cudaError_t status;
struct cudaFreeEnergySimulationNonBonded feSim;
freeEnergyGpu->freeEnergySim.periodicBoxSizeX = xsize;
freeEnergyGpu->freeEnergySim.periodicBoxSizeY = ysize;
freeEnergyGpu->freeEnergySim.periodicBoxSizeZ = zsize;
feSim.pParticleSoftCoreLJLambda = gpuParticleSoftCoreLJLambda;
status = cudaMemcpyToSymbol(feSimDev, &feSim, sizeof(cudaFreeEnergySimulationNonBonded));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateCDLJSoftcoreSupplementarySim");
freeEnergyGpu->freeEnergySim.invPeriodicBoxSizeX = 1.0f/xsize;
freeEnergyGpu->freeEnergySim.invPeriodicBoxSizeY = 1.0f/ysize;
freeEnergyGpu->freeEnergySim.invPeriodicBoxSizeZ = 1.0f/zsize;
//(void) fprintf( stderr, "SetCalculateCDLJSoftcoreSupplementarySim\n" );
}
freeEnergyGpu->freeEnergySim.recipBoxSizeX = 2.0f*PI/freeEnergyGpu->freeEnergySim.periodicBoxSizeX;
freeEnergyGpu->freeEnergySim.recipBoxSizeY = 2.0f*PI/freeEnergyGpu->freeEnergySim.periodicBoxSizeY;
freeEnergyGpu->freeEnergySim.recipBoxSizeZ = 2.0f*PI/freeEnergyGpu->freeEnergySim.periodicBoxSizeZ;
void GetCalculateCDLJSoftcoreForcesSim(float* gpuParticleSoftCoreLJLambda)
{
// cudaError_t status;
// status = cudaMemcpyFromSymbol(gpuParticleSoftCoreLJLambda, particleSoftCoreLJLambdaDev, sizeof(float*));
// RTERROR(status, "cudaMemcpyFromSymbol: GetCalculateCDLJSoftcoreForcesSim failed");
}
freeEnergyGpu->freeEnergySim.cellVolume = freeEnergyGpu->freeEnergySim.periodicBoxSizeX*freeEnergyGpu->freeEnergySim.periodicBoxSizeY*freeEnergyGpu->freeEnergySim.periodicBoxSizeZ;
// create, initialize and entrt SoftCoreLJLambda values
// return handle to GpuNonbondedSoftcore object
static void setSoftcoreExclusions(gpuContext gpu, const std::vector<std::vector<int> >& exclusions) {
if (gpu->exclusions.size() > 0) {
bool ok = (exclusions.size() == gpu->exclusions.size());
for (unsigned int i = 0; i < exclusions.size() && ok; i++) {
if (exclusions[i].size() != gpu->exclusions[i].size())
ok = false;
else {
for (unsigned int j = 0; j < exclusions[i].size(); j++)
if (find(gpu->exclusions[i].begin(), gpu->exclusions[i].end(), exclusions[i][j]) == gpu->exclusions[i].end())
ok = false;
}
}
if (!ok)
throw OpenMM::OpenMMException("All nonbonded forces must have identical sets of exceptions");
}
gpu->exclusions = exclusions;
gpuSetPeriodicBoxSize( freeEnergyGpu->gpuContext, xsize, ysize, zsize );
}
extern "C"
GpuNonbondedSoftcore* gpuSetNonbondedSoftcoreParameters(gpuContext gpu, float epsfac, const std::vector<int>& atom, const std::vector<float>& c6,
void gpuSetNonbondedSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, float epsfac, const std::vector<int>& atom, const std::vector<float>& c6,
const std::vector<float>& c12, const std::vector<float>& q,
const std::vector<float>& softcoreLJLambdaArray, const std::vector<char>& symbol,
const std::vector<std::vector<int> >& exclusions, CudaNonbondedMethod method)
{
const std::vector<std::vector<int> >& exclusions, CudaFreeEnergyNonbondedMethod method,
float cutoffDistance, float solventDielectric ){
unsigned int numberOfParticles = c6.size();
gpu->sim.epsfac = epsfac;
gpu->sim.nonbondedMethod = method;
if (numberOfParticles > 0)
setSoftcoreExclusions(gpu, exclusions);
gpuContext gpu = freeEnergyGpu->gpuContext;
int paddedNumberOfAtoms = gpu->sim.paddedNumberOfAtoms;
// create gpuNonbondedSoftcore
// sanity checks
GpuNonbondedSoftcore* gpuNonbondedSoftcore = new GpuNonbondedSoftcore();
gpuNonbondedSoftcore->initializeParticleSoftCoreLJLambda( numberOfParticles );
float minSoftcore = 1.0e+10;
for (unsigned int i = 0; i < numberOfParticles; i++)
{
float p0 = q[i];
if( paddedNumberOfAtoms < 1 ){
std::stringstream msg;
msg << "gpuSetNonbondedSoftcoreParameters: number of padded atoms=" << gpu->sim.paddedNumberOfAtoms << " is less than 1.";
throw OpenMM::OpenMMException( msg.str() );
}
// track min softcore value
if( freeEnergyGpu->gpuContext->sim.atoms != numberOfParticles ){
std::stringstream msg;
msg << "gpuSetNonbondedSoftcoreParameters: number of atoms in gpuContext does not match input count: " << freeEnergyGpu->gpuContext->sim.atoms << " " << numberOfParticles << ".";
throw OpenMM::OpenMMException( msg.str() );
}
freeEnergyGpu->freeEnergySim.epsfac = epsfac;
freeEnergyGpu->freeEnergySim.nonbondedMethod = method;
freeEnergyGpu->freeEnergySim.nonbondedCutoff = cutoffDistance;
freeEnergyGpu->freeEnergySim.nonbondedCutoffSqr = cutoffDistance*cutoffDistance;
gpu->sim.nonbondedCutoff = cutoffDistance;
gpu->sim.nonbondedCutoffSqr = cutoffDistance*cutoffDistance;
float softcoreLJLambda = softcoreLJLambdaArray[i];
if( minSoftcore > softcoreLJLambda ){
minSoftcore = softcoreLJLambda;
if( cutoffDistance > 0.0f ){
freeEnergyGpu->freeEnergySim.reactionFieldK = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0f)/(2.0f*solventDielectric+1.0f);
freeEnergyGpu->freeEnergySim.reactionFieldC = (1.0f / cutoffDistance)*(3.0f*solventDielectric)/(2.0f*solventDielectric+1.0f);
gpu->sim.reactionFieldK = freeEnergyGpu->freeEnergySim.reactionFieldK;
gpu->sim.reactionFieldC = freeEnergyGpu->freeEnergySim.reactionFieldC;
} else {
freeEnergyGpu->freeEnergySim.reactionFieldK = 0.0f;
freeEnergyGpu->freeEnergySim.reactionFieldC = 0.0f;
}
gpuNonbondedSoftcore->setParticleSoftCoreLJLambda( i, softcoreLJLambda );
float p1 = 0.5f, p2 = 0.0f;
if ((c6[i] > 0.0f) && (c12[i] > 0.0f))
{
p1 = 0.5f * powf(c12[i] / c6[i], 1.0f / 6.0f);
p2 = c6[i] * sqrtf(1.0f / c12[i]);
setExclusions( gpu, exclusions );
// parameters
freeEnergyGpu->psSigEps4 = new CUDAStream<float4>( paddedNumberOfAtoms, 1, "freeEnergyGpuSigEps4");
freeEnergyGpu->freeEnergySim.pSigEps4 = freeEnergyGpu->psSigEps4->_pDevData;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
float p1 = 0.5f;
float p2 = 0.0f;
if( (c6[ii] > 0.0f) && (c12[ii] > 0.0f) ){
p1 = 0.5f * powf(c12[ii] / c6[ii], 1.0f / 6.0f);
p2 = c6[ii] * sqrtf(1.0f / c12[ii]);
}
/*
if (symbol.size() > 0)
gpu->pAtomSymbol[i] = symbol[i];
freeEnergyGpu->pAtomSymbol[ii] = symbol[ii];
*/
(*gpu->psPosq4)[i].w = p0;
(*gpu->psSigEps2)[i].x = p1;
(*gpu->psSigEps2)[i].y = p2;
(*freeEnergyGpu->psSigEps4)[ii].x = p1;
(*freeEnergyGpu->psSigEps4)[ii].y = p2;
(*freeEnergyGpu->psSigEps4)[ii].z = softcoreLJLambdaArray[ii];
(*freeEnergyGpu->psSigEps4)[ii].w = q[ii];
}
gpuNonbondedSoftcore->setSoftCoreLJLambda( minSoftcore );
// Dummy out extra atom data
for (unsigned int i = numberOfParticles; i < gpu->sim.paddedNumberOfAtoms; i++)
{
(*gpu->psPosq4)[i].x = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].y = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].z = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].w = 0.0f;
(*gpu->psSigEps2)[i].x = 0.0f;
(*gpu->psSigEps2)[i].y = 0.0f;
for( unsigned int ii = numberOfParticles; ii < paddedNumberOfAtoms; ii++ ){
(*freeEnergyGpu->psSigEps4)[ii].x = 1.0f;
(*freeEnergyGpu->psSigEps4)[ii].y = 0.0f;
(*freeEnergyGpu->psSigEps4)[ii].z = 0.0f;
(*freeEnergyGpu->psSigEps4)[ii].w = 0.0f;
(*gpu->psPosq4)[ii].x = 100000.0f + ii * 10.0f;
(*gpu->psPosq4)[ii].y = 100000.0f + ii * 10.0f;
(*gpu->psPosq4)[ii].z = 100000.0f + ii * 10.0f;
(*gpu->psPosq4)[ii].w = 0.0f;
}
#undef DUMP_PARAMETERS
#define DUMP_PARAMETERS 0
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr,"gpuSetNonbondedSoftcoreParameters: %5u epsfac=%14.7e method=%d\n", numberOfParticles, gpu->sim.paddedNumberOfAtoms, epsfac, method );
int maxPrint = 31;
for (unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++){
(void) fprintf( stderr,"%6u x[%14.7e %14.7e %14.7e %14.7e] sig[%14.7e %14.7e]\n",
ii, (*gpu->psPosq4)[ii].x, (*gpu->psPosq4)[ii].y, (*gpu->psPosq4)[ii].z, (*gpu->psPosq4)[ii].w,
(*gpu->psSigEps2)[ii].x, (*gpu->psSigEps2)[ii].y );
if( ii == maxPrint && ii < gpu->sim.paddedNumberOfAtoms - maxPrint ){
ii = gpu->sim.paddedNumberOfAtoms - maxPrint;
if( freeEnergyGpu->log ){
(void) fprintf( freeEnergyGpu->log,"freeEnergyGpuSetNonbondedSoftcoreParameters: %5u padded=%u epsfac=%14.7e method=%d cutoffDistance=%9.2f solventDielectric=%9.2f\n",
numberOfParticles, freeEnergyGpu->gpuContext->sim.paddedNumberOfAtoms, epsfac, method, cutoffDistance, solventDielectric );
#ifdef PARAMETER_PRINT
int maxPrint = MAX_PARAMETER_PRINT;
for (unsigned int ii = 0; ii < numberOfParticles; ii++){
(void) fprintf( freeEnergyGpu->log,"%6u sig[%14.7e %14.7e] lambda=%10.3f q=%10.3f\n",
ii,
(*freeEnergyGpu->psSigEps4)[ii].x, (*freeEnergyGpu->psSigEps4)[ii].y, (*freeEnergyGpu->psSigEps4)[ii].z, (*freeEnergyGpu->psSigEps4)[ii].w );
if( ii == maxPrint && ii < freeEnergyGpu->gpuContext->sim.paddedNumberOfAtoms - maxPrint ){
ii = numberOfParticles - maxPrint;
}
}
unsigned int offset = paddedNumberOfAtoms - maxPrint;
if( offset > 0 ){
if( offset > numberOfParticles ){
(void) fprintf( freeEnergyGpu->log,"Dummy padded entries\n" );
for (unsigned int ii = offset; ii < paddedNumberOfAtoms; ii++){
(void) fprintf( freeEnergyGpu->log,"%6u sig[%14.7e %14.7e] lambda=%10.3f q=%10.3f\n",
ii,
(*freeEnergyGpu->psSigEps4)[ii].x, (*freeEnergyGpu->psSigEps4)[ii].y, (*freeEnergyGpu->psSigEps4)[ii].z, (*freeEnergyGpu->psSigEps4)[ii].w );
}
}
}
#endif
(void) fflush( freeEnergyGpu->log );
}
// upload data to board
gpuNonbondedSoftcore->upload( gpu );
freeEnergyGpu->psSigEps4->Upload();
gpu->psPosq4->Upload();
gpu->psSigEps2->Upload();
return gpuNonbondedSoftcore;
}
// delete gpuNonbondedSoftcore
extern "C"
void gpuDeleteNonbondedSoftcoreParameters( void* gpuNonbondedSoftcore)
{
GpuNonbondedSoftcore* internalGNonbondedSoftcore = static_cast<GpuNonbondedSoftcore*>(gpuNonbondedSoftcore);
delete internalGNonbondedSoftcore;
return;
}
extern "C"
......@@ -202,46 +212,25 @@ struct Atom {
float fz;
};
#if 0
texture<float, 1, cudaReadModeElementType> tabulatedErfcRef;
__device__ float fastErfc(float r)
{
float normalized = cSim.tabulatedErfcScale*r;
int index = (int) normalized;
float fract2 = normalized-index;
float fract1 = 1.0f-fract2;
return fract1*tex1Dfetch(tabulatedErfcRef, index) + fract2*tex1Dfetch(tabulatedErfcRef, index+1);
}
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Include versions of the kernels for N^2 calculations with softcore LJ.
#define USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
#endif
// Include versions of the kernels for N^2 calculations with softcore LJ.
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2SoftcoreLJ##b
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_SOFTCORE_LJ
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2SoftcoreLJByWarp##b
#include "kCalculateNonbondedSoftcore.h"
#undef USE_SOFTCORE_LJ
// Include versions of the kernels with cutoffs.
#if 0
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
......@@ -266,74 +255,29 @@ __device__ float fastErfc(float r)
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Include versions of the kernels for Ewald
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define USE_EWALD
#define METHOD_NAME(a, b) a##Ewald##b
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##EwaldByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Reciprocal Space Ewald summation is in a separate kernel
#include "kCalculateCDLJEwaldFastReciprocal.h"
void kCalculatePME(gpuContext gpu);
#endif
void kCalculateCDLJSoftcoreForces(gpuContext gpu )
void kCalculateCDLJSoftcoreForces( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kCalculateCDLJCutoffForces %d\n", gpu->sim.nonbondedMethod); fflush( stdout );
switch (gpu->sim.nonbondedMethod)
gpuContext gpu = freeEnergyGpu->gpuContext;
// (void) fprintf( stderr,"kCalculateCDLJCutoffForces %d warp=%u nonbond_blocks=%u nonbond_threads_per_block=%u rfK=%15.7e rfC=%15.7e\n", freeEnergyGpu->freeEnergySim.nonbondedMethod,
// gpu->bOutputBufferPerWarp, gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.reactionFieldK, gpu->sim.reactionFieldC); fflush( stderr );
switch (freeEnergyGpu->freeEnergySim.nonbondedMethod)
{
case NO_CUTOFF:
case FREE_ENERGY_NO_CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJSoftcoreN2SoftcoreLJByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateCDLJSoftcoreN2SoftcoreLJForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit );
//(gpu->sim.pWorkUnit, gpuNonbondedSoftcore->getGpuParticleSoftCoreLJLambda());
LAUNCHERROR("kCalculateCDLJSoftcoreN2Forces");
#if 0
int maxPrint = 31;
gpu->psWorkUnit->Download();
fprintf( stderr, "kCalculateCDLJSoftcoreForces: bOutputBufferPerWarp=%u blks=%u th/blk=%u wu=%u %u shrd=%u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
gpu->psPosq4->Download();
(void) fprintf( stderr, "\nkCalculateGBVISoftcoreBornSum: pre BornSum %s Born radii & params\n",
(gpu->bIncludeGBVI ? "GBVI" : "Obc") );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%6d bSum=%14.6e param[%14.6e %14.6e %14.6e] x[%14.6f %14.6f %14.6f %14.6f]\n",
ii,
gpu->psBornSum->_pSysStream[0][ii],
gpu->psGBVIData->_pSysStream[0][ii].x,
gpu->psGBVIData->_pSysStream[0][ii].y,
gpu->psGBVIData->_pSysStream[0][ii].z,
gpu->psPosq4->_pSysStream[0][ii].x, gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, gpu->psPosq4->_pSysStream[0][ii].w
);
if( (ii == maxPrint) && ( ii < (gpu->natoms - maxPrint)) ){
ii = gpu->natoms - maxPrint;
}
}
#endif
#undef GBVI
break;
case FREE_ENERGY_CUTOFF:
break;
#if 0
case CUTOFF:
kFindBlockBoundsCutoff_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsCutoff");
kFindBlocksWithInteractionsCutoff_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
......@@ -341,44 +285,19 @@ fprintf( stderr, "kCalculateCDLJSoftcoreForces: bOutputBufferPerWarp=%u blks=%u
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksCutoff_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#if 0
static int iteration = 0;
if (iteration >= 0)
{
gpu->psInteractingWorkUnit->Download();
gpu->psInteractionCount->Download();
/*
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
*/
printf("# Post kCalculateCDLJCutoffForces %d atoms warps=%d cnt=%u bOutputBufferPerWarp=%d zC=%d\n",
gpu->natoms, ((gpu->sim.nonbond_blocks*gpu->sim.nonbond_threads_per_block)/GRID),
gpu->psInteractionCount->_pSysStream[0][0], gpu->bOutputBufferPerWarp,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block);
fflush( stdout );
for (int i = 0; i < gpu->psInteractingWorkUnit->_stride; i++)
{
printf("%5d %u\n", i, gpu->psInteractingWorkUnit->_pSysStream[0][i] );
fflush( stdout );
}
}
iteration++;
#endif
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJCutoffByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJSoftcoreCutoffByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJCutoffForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJSoftcoreCutoffForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJCutoffForces");
LAUNCHERROR("kCalculateCDLJSoftcoreCutoffForces");
break;
case PERIODIC:
case FREE_ENERGY_PERIODIC:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
......@@ -387,123 +306,17 @@ fprintf( stderr, "kCalculateCDLJSoftcoreForces: bOutputBufferPerWarp=%u blks=%u
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJPeriodicByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJSoftcorePeriodicByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJPeriodicForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJSoftcorePeriodicForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJPeriodicForces");
LAUNCHERROR("kCalculateCDLJSoftcorePeriodicForces");
break;
case EWALD:
case PARTICLE_MESH_EWALD:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
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");
cudaChannelFormatDesc channelDesc = cudaCreateChannelDesc<float>();
cudaBindTexture(NULL, &tabulatedErfcRef, gpu->psTabulatedErfc->_pDevData, &channelDesc, gpu->psTabulatedErfc->_length*sizeof(float));
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJEwaldByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJEwaldForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJEwaldForces");
if (gpu->sim.nonbondedMethod == EWALD)
{
kCalculateEwaldFastCosSinSums_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastCosSinSums");
kCalculateEwaldFastForces_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastForces");
}
else
kCalculatePME(gpu);
#endif
}
}
void kPrintForces(gpuContext gpu, std::string idString, int call )
{
// printf("kReduceForces\n");
#define GBVI_DEBUG 4
#if ( GBVI_DEBUG == 4 )
gpu->psBornRadii->Download();
gpu->psObcData->Download();
gpu->psObcChain->Download();
gpu->psBornForce->Download();
gpu->psForce4->Download();
gpu->psPosq4->Download();
int maxPrint = 30;
int nanHit = 0;
int targetIndex = -852;
float maxForce = 3.0e+04;
float maxPosition = 2.0e+02;
for( int ii = 0; ii < gpu->natoms; ii++ ){
int hit = 0;
float dist = sqrtf( gpu->psPosq4->_pSysStream[0][ii].x*gpu->psPosq4->_pSysStream[0][ii].x +
gpu->psPosq4->_pSysStream[0][ii].y*gpu->psPosq4->_pSysStream[0][ii].y +
gpu->psPosq4->_pSysStream[0][ii].z*gpu->psPosq4->_pSysStream[0][ii].z );
if( fabs( gpu->psForce4->_pSysStream[0][ii].x ) > maxForce ||
fabs( gpu->psForce4->_pSysStream[0][ii].y ) > maxForce ||
fabs( gpu->psForce4->_pSysStream[0][ii].z ) > maxForce ||
// gpu->psBornRadii->_pSysStream[0][ii] <= 0.0 ||
dist > maxPosition ||
isnan( gpu->psForce4->_pSysStream[0][ii].x ) ||
isnan( gpu->psForce4->_pSysStream[0][ii].y ) ||
isnan( gpu->psForce4->_pSysStream[0][ii].z ) ){
hit = 1;
} else {
hit = 0;
}
if( ii == targetIndex || ii == (targetIndex+1) || ii == (targetIndex+2) )hit = 1;
if( isnan( gpu->psBornForce->_pSysStream[0][ii] ) ||
isnan( gpu->psBornRadii->_pSysStream[0][ii] ) ||
isnan( gpu->psObcChain->_pSysStream[0][ii] ) ||
isnan( gpu->psForce4->_pSysStream[0][ii].x ) ||
isnan( gpu->psForce4->_pSysStream[0][ii].y ) ||
isnan( gpu->psForce4->_pSysStream[0][ii].z ) ){
hit = 1;
nanHit = 1;
}
default:
throw OpenMM::OpenMMException( "Nonbonded softcore method not recognized." );
if( hit || ii < maxPrint || ii >= (gpu->natoms - maxPrint) ){
//if( hit ){
static int firstHit = 1;
if( firstHit ){
firstHit = 0;
(void) fprintf( stderr, "\nkPrintForces: %d [r, scl q] b[r/c/f] f[] x[] Born radii/force (%p %p)\n", call,
gpu->psBornForce, gpu->psBornForce->_pDevStream[0] );
}
(void) fprintf( stderr, "%6d [%8.3f %8.3f %8.3f] b[%13.6e %13.6e %13.6e] f[%13.6e %13.6e %13.6e] x[%13.6e %13.6e %13.6e] %10.3e %s %s %d\n",
ii,
(gpu->psObcData->_pSysStream[0][ii].x + 0.009f),
(gpu->psObcData->_pSysStream[0][ii].y/gpu->psObcData->_pSysStream[0][ii].x),
gpu->psPosq4->_pSysStream[0][ii].w,
gpu->psBornRadii->_pSysStream[0][ii],
gpu->psObcChain->_pSysStream[0][ii],
gpu->psBornForce->_pSysStream[0][ii],
gpu->psForce4->_pSysStream[0][ii].x,
gpu->psForce4->_pSysStream[0][ii].y,
gpu->psForce4->_pSysStream[0][ii].z,
gpu->psPosq4->_pSysStream[0][ii].x,
gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, dist,
(hit ? "XXXXXXX" : "" ), idString.c_str(), call );
}
}
(void) fflush( stderr );
// if( nanHit )exit(0);
#endif
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateNonbondedSoftcore.h
View file @ bc85b9f0
......@@ -25,20 +25,20 @@
* -------------------------------------------------------------------------- */
/**
* This file contains the kernels for evalauating nonbonded forces. It is included
* several times in kCalculateCDLJForces.cu with different #defines to generate
* This file contains the kernels for evaluating nonbonded softcore forces. It is included
* several times in kCalculateNonbondedSoftcore.cu with different #defines to generate
* different versions of the kernels.
*/
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
__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
/* Cuda compiler on Windows does not recognized "static const float" values */
#define LOCAL_HACK_PI 3.1415926535897932384626433832795f
//__global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit, float* softCoreLJLambdaArray)
__global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
......@@ -52,10 +52,6 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
float3* tempBuffer = (float3*) &sA[cSim.nonbond_threads_per_block];
#endif
#ifdef USE_EWALD
const float TWO_OVER_SQRT_PI = 2.0f/sqrt(LOCAL_HACK_PI);
#endif
unsigned int lasty = 0xFFFFFFFF;
while (pos < end)
{
......@@ -75,16 +71,17 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
float sig;
float eps;
float dEdR;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
unsigned int i = x + tgx;
apos = cSim.pPosq[i];
float2 a = cSim.pAttr[i];
//float softCoreLJLambda = cSim.pSoftCoreLJLambda[i];
//float softCoreLJLambda = softCoreLJLambdaArray[i];
float softCoreLJLambda = feSimDev.pParticleSoftCoreLJLambda[i];
float4 a = feSimDev.pSigEps4[i];
float softCoreLJLambda = a.z;
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
......@@ -94,11 +91,11 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].q = apos.w;
sA[threadIdx.x].q = a.w;
sA[threadIdx.x].sig = a.x;
sA[threadIdx.x].eps = a.y;
sA[threadIdx.x].softCoreLJLambda = softCoreLJLambda;
apos.w *= cSim.epsfac;
sA[threadIdx.x].softCoreLJLambda = a.z;
a.w *= cSim.epsfac;
if (!bExclusionFlag)
{
for (unsigned int j = 0; j < GRID; j++)
......@@ -126,33 +123,20 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI );
/* E */
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJ_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
dEdR += a.w * psA[j].q * invR;
CDLJ_energy += a.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += 0.5f*CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
......@@ -161,12 +145,13 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
af.y -= dy;
af.z -= dz;
}
}
else // bExclusion
{
} else {
unsigned int xi = x>>GRIDBITS;
unsigned int cell = xi+xi*cSim.paddedNumberOfAtoms/GRID-xi*(xi+1)/2;
unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[j].x - apos.x;
......@@ -188,53 +173,27 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+j && x+tgx < cSim.atoms && y+j < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[j].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy = -apos.w * psA[j].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJ_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
dEdR += a.w * psA[j].q * invR;
CDLJ_energy += a.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
if ((!(excl & 0x1) && !needCorrection) || r2 > cSim.nonbondedCutoffSqr)
#else
if (!(excl & 0x1) || r2 > cSim.nonbondedCutoffSqr)
#endif
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
/* E */
energy += 0.5f*CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
......@@ -263,22 +222,23 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4[offset] = of;
#endif
}
else // 100% utilization
{
} else {
// Read fixed atom data into registers and GRF
if (lasty != y)
{
unsigned int j = y + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pAttr[j];
//float2 temp1 = cSim.pAttr[j];
float4 temp1 = feSimDev.pSigEps4[j];
//float temp3 = cSim.pSoftCoreLJLambda[j];
//float temp3 = softCoreLJLambdaArray[j];
float temp3 = feSimDev.pParticleSoftCoreLJLambda[j];
float temp3 = temp1.z;
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].q = temp.w;
sA[threadIdx.x].q = temp1.w;
sA[threadIdx.x].sig = temp1.x;
sA[threadIdx.x].eps = temp1.y;
sA[threadIdx.x].softCoreLJLambda = temp3;
......@@ -286,7 +246,7 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
apos.w *= cSim.epsfac;
a.w *= cSim.epsfac;
if (!bExclusionFlag)
{
#ifdef USE_CUTOFF
......@@ -324,33 +284,21 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[tj].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJ_energy += a.w * psA[tj].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
dEdR += apos.w * psA[tj].q * invR;
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR;
dEdR += a.w * psA[tj].q * invR;
CDLJ_energy += a.w * psA[tj].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
......@@ -392,36 +340,23 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[j].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJ_energy += a.w * psA[j].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
dEdR += a.w * psA[j].q * invR;
CDLJ_energy += a.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
......@@ -499,52 +434,27 @@ __global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int*
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+tj && x+tgx < cSim.atoms && y+tj < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[tj].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy = -apos.w * psA[tj].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
dEdR += a.w * psA[tj].q * (invR - 2.0f * feSimDev.reactionFieldK * r2);
CDLJ_energy += a.w * psA[tj].q * (invR + feSimDev.reactionFieldK * r2 - feSimDev.reactionFieldC);
#else
dEdR += apos.w * psA[tj].q * invR;
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR;
dEdR += a.w * psA[tj].q * invR;
CDLJ_energy += a.w * psA[tj].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
if ((!(excl & 0x1) && !needCorrection) || r2 > cSim.nonbondedCutoffSqr)
#else
if (!(excl & 0x1) || r2 > cSim.nonbondedCutoffSqr)
#endif
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu
View file @ bc85b9f0
......@@ -25,11 +25,16 @@
* -------------------------------------------------------------------------- */
#include "gputypes.h"
#include "freeEnergyGpuTypes.h"
#include "GpuFreeEnergyCudaKernels.h"
#include "kernels/cudaKernels.h"
#include "GpuObcGbsaSoftcore.h"
#include "openmm/OpenMMException.h"
#include <cuda.h>
#include <string>
#define PARAMETER_PRINT 0
#define MAX_PARAMETER_PRINT 10
//#define DEBUG
struct Atom {
float x;
......@@ -41,38 +46,17 @@ struct Atom {
float polarScaleData;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore {
float* pNonPolarScalingFactors;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore gbsaSim;
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimDev;
static __constant__ cudaFreeEnergyGmxSimulation gbsaSimDev;
extern "C"
void SetCalculateObcGbsaSoftcoreBornSumSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "SetCalculateObcGbsaSoftcoreBornSumSim: cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim( float* nonPolarScalingFactors )
extern "C" void SetCalculateObcGbsaSoftcoreBornSumSim( freeEnergyGpuContext freeEnergyGpu)
{
cudaError_t status;
gbsaSim.pNonPolarScalingFactors = nonPolarScalingFactors;
status = cudaMemcpyToSymbol(gbsaSimDev, &gbsaSim, sizeof(cudaFreeEnergySimulationObcGbsaSoftcore));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim");
status = cudaMemcpyToSymbol( cSim, &freeEnergyGpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreBornSumSim copy to cSim failed.");
//(void) fprintf( stderr, "In SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim\n" );
}
void GetCalculateObcGbsaSoftcoreBornSumSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "GetCalculateObcGbsaSoftcoreBornSumSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed");
status = cudaMemcpyToSymbol( gbsaSimDev, &freeEnergyGpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreBornSumSim copy to gbsaSimDev failed.");
}
__global__ void kClearObcGbsaSoftcoreBornSum_kernel()
......@@ -112,6 +96,7 @@ __global__ void kReduceObcGbsaSoftcoreBornForces_kernel()
{
unsigned int pos = (blockIdx.x * blockDim.x + threadIdx.x);
float energy = 0.0f;
while (pos < cSim.atoms)
{
float bornRadius = cSim.pBornRadii[pos];
......@@ -153,7 +138,6 @@ __global__ void kReduceObcGbsaSoftcoreBornForces_kernel()
float saTerm = nonPolarScaleData*cSim.surfaceAreaFactor * r * r * ratio6;
totalForce += saTerm / bornRadius; // 1.102 == Temp mysterious fudge factor, FIX FIX FIX
/* E */
energy += saTerm;
totalForce *= bornRadius * bornRadius * obcChain;
......@@ -162,14 +146,13 @@ __global__ void kReduceObcGbsaSoftcoreBornForces_kernel()
*pFt = totalForce;
pos += gridDim.x * blockDim.x;
}
/* E */
// correct for surface area factor of -6
cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += energy / -6.0f;
}
void kReduceObcGbsaSoftcoreBornForces(gpuContext gpu)
{
void kReduceObcGbsaSoftcoreBornForces( gpuContext gpu ){
kReduceObcGbsaSoftcoreBornForces_kernel<<<gpu->sim.blocks, gpu->sim.bsf_reduce_threads_per_block>>>();
LAUNCHERROR("kReduceObcGbsaSoftcoreBornForces");
......@@ -187,7 +170,6 @@ void kReduceObcGbsaSoftcoreBornForces(gpuContext gpu)
// Include versions of the kernels with cutoffs.
#if 0
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
......@@ -209,7 +191,6 @@ void kReduceObcGbsaSoftcoreBornForces(gpuContext gpu)
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
#endif
__global__ void kReduceObcGbsaSoftcoreBornSum_kernel()
{
......@@ -222,10 +203,8 @@ __global__ void kReduceObcGbsaSoftcoreBornSum_kernel()
float2 atom = cSim.pObcData[pos];
// Get summed Born data
for (int i = 0; i < cSim.nonbondOutputBuffers; i++)
{
for( int i = 0; i < cSim.nonbondOutputBuffers; i++ ){
sum += *pSt;
// printf("%4d %4d A: %9.4f\n", pos, i, *pSt);
pSt += cSim.stride;
}
......@@ -257,7 +236,7 @@ void kReduceObcGbsaSoftcoreBornSum(gpuContext gpu)
/**
* Initialize parameters for Cuda Obc softcore
*
* @param gpu gpu context
* @param freeEnergyGpu freeEnergyGpu context
* @param innerDielectric solute dielectric
* @param solventDielectric solvent dielectric
* @param radius intrinsic Born radii
......@@ -268,7 +247,7 @@ void kReduceObcGbsaSoftcoreBornSum(gpuContext gpu)
*/
extern "C"
GpuObcGbsaSoftcore* gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, float nonPolarPrefactor,
void gpuSetObcSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, 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)
{
......@@ -281,97 +260,252 @@ GpuObcGbsaSoftcore* gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDiele
// ---------------------------------------------------------------------------------------
unsigned int atoms = radius.size();
unsigned int numberOfParticles = radius.size();
gpuContext gpu = freeEnergyGpu->gpuContext;
// initialize parameters
// gpu->bIncludeGBSA = true;
GpuObcGbsaSoftcore* gpuObcGbsaSoftcore = new GpuObcGbsaSoftcore();
gpuObcGbsaSoftcore->initializeNonPolarScalingFactors( gpu->sim.paddedNumberOfAtoms );
freeEnergyGpu->psNonPolarScalingFactors = new CUDAStream<float>( gpu->sim.paddedNumberOfAtoms, 1, "ObcSoftcoreNonPolarScaling");
freeEnergyGpu->freeEnergySim.pNonPolarScalingFactors = freeEnergyGpu->psNonPolarScalingFactors->_pDevData;
gpu->sim.surfaceAreaFactor = -6.0f*PI*4.0f*nonPolarPrefactor;
for (unsigned int i = 0; i < atoms; i++)
{
(*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
(*gpu->psObcData)[i].y = scale[i] * (*gpu->psObcData)[i].x;
(*gpu->psPosq4)[i].w = charge[i];
gpuObcGbsaSoftcore->setNonPolarScalingFactors( i, nonPolarScalingFactors[i] );
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
(*gpu->psObcData)[ii].x = radius[ii] - dielectricOffset;
(*gpu->psObcData)[ii].y = scale[ii] * (*gpu->psObcData)[ii].x;
(*gpu->psPosq4)[ii].w = charge[ii];
(*freeEnergyGpu->psNonPolarScalingFactors)[ii] = nonPolarScalingFactors[ii];
}
// 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] );
if( freeEnergyGpu->log ){
(void) fprintf( freeEnergyGpu->log, "%s %u %u\n", methodName.c_str(), gpu->natoms, gpu->sim.paddedNumberOfAtoms );
(void) fprintf( freeEnergyGpu->log, "surfaceAreaFactor=%15.7e preFactor=%15.7e\n", gpu->sim.surfaceAreaFactor, gpu->sim.preFactor);
#ifdef PARAMETER_PRINT
int maxPrint = MAX_PARAMETER_PRINT;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( freeEnergyGpu->log, "%6u %13.6e %13.6e %8.3f %8.3f\n", ii,
(*gpu->psObcData)[ii].x, (*gpu->psObcData)[ii].y, (*gpu->psPosq4)[ii].w, (*freeEnergyGpu->psNonPolarScalingFactors)[ii] );
if( ii == maxPrint ){
ii = numberOfParticles - maxPrint;
if( ii < maxPrint )ii = maxPrint;
}
}
#endif
}
// dummy out extra atom data
for (unsigned int i = gpu->natoms; i < gpu->sim.paddedNumberOfAtoms; i++)
{
(*gpu->psBornRadii)[i] = 0.2f;
(*gpu->psObcData)[i].x = 0.01f;
(*gpu->psObcData)[i].y = 0.01f;
for (unsigned int ii = gpu->natoms; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(*gpu->psObcData)[ii].x = 0.01f;
(*gpu->psObcData)[ii].y = 0.01f;
(*freeEnergyGpu->psNonPolarScalingFactors)[ii] = 0.0f;
}
// load data to board
gpuObcGbsaSoftcore->upload( gpu );
gpu->psBornRadii->Upload();
gpu->psObcData->Upload();
gpu->psPosq4->Upload();
freeEnergyGpu->psNonPolarScalingFactors->Upload();
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
return;
}
void kPrintObcGbsaSoftcore( freeEnergyGpuContext freeEnergyGpu, std::string callId, int call, FILE* log){
gpuContext gpu = freeEnergyGpu->gpuContext;
int maxPrint = gpu->natoms;
(void) fprintf( log, "kPrintObcGbsaSoftcore %s %d\n", callId.c_str(), call );
gpu->psObcData->Download();
gpu->psBornRadii->Download();
gpu->psBornForce->Download();
gpu->psPosq4->Download();
freeEnergyGpu->psNonPolarScalingFactors->Download();
CUDAStream<float4>* sigEps4 = freeEnergyGpu->psSigEps4;
sigEps4->Download();
(void) fprintf( log, "BornSum Born radii & params\n" );
for( int ii = 0; ii < gpu->natoms; ii++ ){
//(void) fprintf( log, "%6d prm[%15.7e %15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e %15.7e] bR=%15.7e bF=%15.7e swDrv=%3.1f x[%8.3f %8.3f %8.3f %15.7f]\n",
(void) fprintf( log, "%6d prm[%15.7e %15.7e %15.7e] sig/eps4[%15.7e %15.7e %15.7e %15.7e] bR=%15.7e bF=%15.7e\n",
ii,
gpu->psObcData->_pSysData[ii].x,
gpu->psObcData->_pSysData[ii].y,
freeEnergyGpu->psNonPolarScalingFactors->_pSysData[ii],
sigEps4->_pSysData[ii].x,
sigEps4->_pSysData[ii].y,
sigEps4->_pSysData[ii].z,
sigEps4->_pSysData[ii].w,
gpu->psBornRadii->_pSysData[ii],
gpu->psBornForce->_pSysData[ii]
/*
gpu->psPosq4->_pSysData[ii].x,
gpu->psPosq4->_pSysData[ii].y,
gpu->psPosq4->_pSysData[ii].z,
gpu->psPosq4->_pSysData[ii].w );
*/
);
if( (ii == maxPrint) && ( ii < (gpu->natoms - maxPrint)) ){
ii = gpu->natoms - maxPrint;
}
}
return gpuObcGbsaSoftcore;
}
extern __global__ void kFindBlockBoundsCutoff_kernel();
extern __global__ void kFindBlockBoundsPeriodic_kernel();
extern __global__ void kFindBlocksWithInteractionsCutoff_kernel();
extern __global__ void kFindBlocksWithInteractionsPeriodic_kernel();
void kCalculateObcGbsaSoftcoreBornSum(gpuContext gpu)
extern __global__ void kFindInteractionsWithinBlocksCutoff_kernel(unsigned int*);
extern __global__ void kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int*);
void kCalculateObcGbsaSoftcoreBornSum( freeEnergyGpuContext freeEnergyGpu )
{
// printf("kCalculateObcGbsaSoftcoreBornSum\n");
gpuContext gpu = freeEnergyGpu->gpuContext;
#ifdef DEBUG
fprintf( stderr, "kCalculateObcGbsaSoftcoreBornSum cutoff=%15.7e\n", gpu->sim.nonbondedCutoffSqr );
int psize = gpu->sim.paddedNumberOfAtoms;
CUDAStream<float4>* pdE1 = new CUDAStream<float4>( psize, 1, "pdE");
CUDAStream<float4>* pdE2 = new CUDAStream<float4>( psize, 1, "pdE");
float bF;
float bF1;
showWorkUnitsFreeEnergy( freeEnergyGpu, 1 );
for( int ii = 0; ii < psize; ii++ ){
pdE1->_pSysData[ii].x = 0.0f;
pdE1->_pSysData[ii].y = 0.001f;
pdE1->_pSysData[ii].z = 0.001f;
pdE1->_pSysData[ii].w = 0.001f;
pdE2->_pSysData[ii].x = 0.001f;
pdE2->_pSysData[ii].y = 0.001f;
pdE2->_pSysData[ii].z = 0.001f;
pdE2->_pSysData[ii].w = 0.001f;
}
pdE1->Upload();
pdE2->Upload();
#endif
kClearObcGbsaSoftcoreBornSum(gpu);
LAUNCHERROR("kClearBornSum from kCalculateObcGbsaSoftcoreBornSum");
switch (gpu->sim.nonbondedMethod)
switch ( freeEnergyGpu->freeEnergySim.nonbondedMethod )
{
case NO_CUTOFF:
#define GBSA 0
#if GBSA == 1
gpu->psWorkUnit->Download();
fprintf( stderr, "kCalculateObcGbsaSoftcoreBornSum: bOutputBufferPerWarp=%u blks=%u th/blk=%u wu=%u %u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysData[0] );
#endif
#undef GBSA
case FREE_ENERGY_NO_CUTOFF:
#ifdef DEBUG
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreN2ByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
else
kCalculateObcGbsaSoftcoreN2BornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
#else
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreN2ByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateObcGbsaSoftcoreN2BornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
#endif
break;
#if 0
case CUTOFF:
case FREE_ENERGY_CUTOFF:
kFindBlockBoundsCutoff_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsCutoff");
kFindBlocksWithInteractionsCutoff_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsCutoff");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksCutoff_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#ifdef DEBUG
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
else
kCalculateObcGbsaSoftcoreCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
#else
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateObcGbsaSoftcoreCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateObcGbsaSoftcoreCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#endif
break;
case PERIODIC:
case FREE_ENERGY_PERIODIC:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#ifdef DEBUG
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaPeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateObcGbsaSoftcorePeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
else
kCalculateObcGbsaSoftcorePeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, pdE1->_pDevData, pdE2->_pDevData);
#else
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcorePeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaPeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateObcGbsaSoftcorePeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break;
#endif
break;
default:
throw OpenMM::OpenMMException( "Nonbonded softcore method not recognized." );
}
LAUNCHERROR("kCalculateObcGbsaSoftcoreBornSum");
#ifdef DEBUG
pdE1->Download();
pdE2->Download();
//gpu->psBornRadii->Download();
//gpu->psObcData->Download();
fprintf( stderr, "bL Obc Cud\n" );
bF = 0.0;
bF1 = 0.0;
for( int ii = 0; ii < gpu->natoms; ii++ ){
bF1 += pdE1->_pSysData[ii].x;
fprintf( stderr, "%4d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n", ii,
pdE1->_pSysData[ii].x, pdE1->_pSysData[ii].y, pdE1->_pSysData[ii].z, pdE1->_pSysData[ii].w,
pdE2->_pSysData[ii].x, pdE2->_pSysData[ii].y, pdE2->_pSysData[ii].z, pdE2->_pSysData[ii].w );
bF += pdE1->_pSysData[ii].x;
}
fprintf( stderr, "bS Obc Cud %6d %15.7e %15.7e\n", TARGET, bF, bF1 );
#endif
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.h
View file @ bc85b9f0
......@@ -30,7 +30,22 @@
* different versions of the kernels.
*/
__global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUnit)
#undef TARGET
//#define TARGET 1
__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(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUnit, float4* pdE1, float4* pdE2)
#else
void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUnit)
#endif
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
......@@ -51,15 +66,18 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
x = (x >> 17) << GRIDBITS;
float dx;
float dy;
float dz;
float r2;
float r;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
if (x == y) // Handle diagonals uniquely at 50% efficiency
......@@ -69,9 +87,11 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float2 ar = cSim.pObcData[i]; // Local atom vr, sr
float polarScaleData = gbsaSimDev.pNonPolarScalingFactors[i]; // scale contribution
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].r = ar.x;
sA[threadIdx.x].sr = ar.y;
sA[threadIdx.x].polarScaleData = polarScaleData;
......@@ -87,35 +107,60 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
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)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#else
if (i < cSim.atoms && x+j < cSim.atoms )
#endif
{
r = sqrt(r2);
float rInverse = 1.0f / r;
float rInverse = 1.0f/r;
float rScaledRadiusJ = r + psA[j].sr;
if ((j != tgx) && (ar.x < rScaledRadiusJ))
{
if( (j != tgx) && (ar.x < rScaledRadiusJ) ){
float l_ij = 1.0f / max(ar.x, fabs(r - psA[j].sr));
float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float sum = l_ij -
u_ij +
float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * psA[j].sr * psA[j].sr * rInverse) *
(l_ij2 - u_ij2);
float rj = psA[j].r;
if (ar.x < (rj - r))
{
sum += 2.0f * ((1.0f / ar.x) - l_ij);
float rj = psA[j].sr;
if( ar.x < (rj - r) ){
term += 2.0f * ((1.0f / ar.x) - l_ij);
}
apos.w += psA[j].polarScaleData*sum;
apos.w += psA[j].polarScaleData*term;
#ifdef DEBUG
int jIdx = j;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = term;
pdE1[tjj].y = r;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = 1.0f;
pdE2[tjj].x = r;
pdE2[tjj].y = l_ij;
pdE2[tjj].z = rj;
pdE2[tjj].w = 1.0f;
}
/*
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE2[tjj].x = sum;
pdE2[tjj].y = psA[jIdx].polarScaleData;
pdE2[tjj].z = ar.x;
pdE2[tjj].w = -1.0f;
} */
#endif
}
}
}
......@@ -128,41 +173,49 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
#endif
}
else // 100% utilization
{
} else {
// Read fixed atom data into registers and GRF
unsigned int j = y + tgx;
unsigned int i = x + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pObcData[j];
float polarScaleDataJ = gbsaSimDev.pNonPolarScalingFactors[j]; // scale contribution
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
apos.w = 0.0f;
float2 ar = cSim.pObcData[i]; // Local atom vr, sr
float polarScaleDataI = gbsaSimDev.pNonPolarScalingFactors[i]; // scale contribution
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y;
sA[threadIdx.x].polarScaleData = polarScaleDataJ;
sA[threadIdx.x].sum = apos.w = 0.0f;
sA[threadIdx.x].sum = 0.0f;
#ifdef USE_CUTOFF
//unsigned int flags = cSim.pInteractionFlag[pos + (blockIdx.x*numWorkUnits)/gridDim.x];
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
// else if (flags == 0xFFFFFFFF)
else if (flags )
#endif
{
// Compute all interactions within this block.
for (unsigned int j = 0; j < GRID; j++)
{
for( unsigned int j = 0; j < GRID; j++ ){
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
......@@ -172,10 +225,10 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
#ifdef USE_CUTOFF
if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#else
if (i < cSim.atoms && y+tj < cSim.atoms )
#endif
{
r = sqrt(r2);
......@@ -188,8 +241,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * psA[tj].sr * psA[tj].sr * rInverse) *
......@@ -200,8 +252,39 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
{
term += 2.0f * ((1.0f / ar.x) - l_ij);
}
//apos.w += term;
apos.w += (scale*term);
#ifdef DEBUG
int jIdx = tj;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = term;
pdE1[tjj].y = r;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = 2.0f;
/*
pdE2[tjj].x = r;
pdE2[tjj].y = l_ij;
pdE2[tjj].z = rj;
pdE2[tjj].w = 2.0f;
*/
}
if( (y+jIdx) == TARGET ){
int tjj = i;
/*
pdE1[tjj].x = term;
pdE1[tjj].y = r;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = -2.0f;
*/
pdE2[tjj].x = term;
pdE2[tjj].y = r;
pdE2[tjj].z = ar.x;
pdE2[tjj].w = -2.0f;
}
#endif
}
float rScaledRadiusI = r + ar.y;
if (psA[tj].r < rScaledRadiusI)
......@@ -211,18 +294,38 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * ar.y * ar.y * rInverse) *
(l_ij2 - u_ij2);
float rj = psA[tj].r;
if (rj < (ar.y - r))
{
term += 2.0f * ((1.0f / psA[tj].r) - l_ij);
}
psA[tj].sum += polarScaleDataI*term;
#ifdef DEBUG
int jIdx = tj;
if( i == TARGET ){
int tjj = y+jIdx;
pdE1[tjj].x = term;
pdE1[tjj].y = r;
pdE1[tjj].z = ar.x;
pdE1[tjj].w = 3.0f;
}
if( (y+jIdx) == TARGET ){
int tjj = i;
pdE2[tjj].x = term;
pdE2[tjj].y = r;
pdE2[tjj].z = ar.x;
pdE2[tjj].w = -3.0f;
}
#endif
}
}
tj = (tj - 1) & (GRID - 1);
......@@ -247,10 +350,10 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
#ifdef USE_CUTOFF
if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#else
if (i < cSim.atoms && y+j < cSim.atoms )
#endif
{
r = sqrt(r2);
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.cu
View file @ bc85b9f0
......@@ -34,7 +34,7 @@
using namespace std;
#include "gputypes.h"
#include "GpuObcGbsaSoftcore.h"
#include "freeEnergyGpuTypes.h"
struct Atom {
float x;
......@@ -49,38 +49,19 @@ struct Atom {
float fb;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore {
float* pNonPolarScalingFactors;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimObc2;
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimDev;
static __constant__ cudaFreeEnergyGmxSimulation feSimDev;
extern "C"
void SetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
void SetCalculateObcGbsaSoftcoreForces2Sim( freeEnergyGpuContext freeEnergyGpu )
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
status = cudaMemcpyToSymbol(cSim, &freeEnergyGpu->gpuContext->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreForces2Sim copy to cSim failed");
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim( float* nonPolarScalingFactors )
{
cudaError_t status;
gbsaSimObc2.pNonPolarScalingFactors = nonPolarScalingFactors;
status = cudaMemcpyToSymbol(gbsaSimDev, &gbsaSimObc2, sizeof(cudaFreeEnergySimulationObcGbsaSoftcore));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim");
status = cudaMemcpyToSymbol( feSimDev, &freeEnergyGpu->freeEnergySim, sizeof(cudaFreeEnergyGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreForces2Sim copy to feSimDev failed");
//(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.
......@@ -116,15 +97,14 @@ void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
void kCalculateObcGbsaSoftcoreForces2( freeEnergyGpuContext freeEnergyGpu )
{
//printf("kCalculateObcGbsaSoftcoreForces2\n");
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d warp=%d\n", gpu->sim.nonbondedMethod, gpu->bOutputBufferPerWarp);
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d calling kReduceForces\n", gpu->sim.nonbondedMethod);
//kReduceForces(gpu);
switch (gpu->sim.nonbondedMethod)
gpuContext gpu = freeEnergyGpu->gpuContext;
switch (freeEnergyGpu->freeEnergySim.nonbondedMethod)
{
case NO_CUTOFF:
case FREE_ENERGY_NO_CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
......@@ -132,7 +112,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
kCalculateObcGbsaSoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
break;
case CUTOFF:
case FREE_ENERGY_CUTOFF:
if (gpu->bOutputBufferPerWarp)
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);
......@@ -140,7 +122,9 @@ void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
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);
break;
case PERIODIC:
case FREE_ENERGY_PERIODIC:
if (gpu->bOutputBufferPerWarp)
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);
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.h
View file @ bc85b9f0
......@@ -30,7 +30,15 @@
* different versions of the kernels.
*/
__global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUnit)
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_BORNFORCE2_THREADS_PER_BLOCK, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(GT2XX_BORNFORCE2_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_BORNFORCE2_THREADS_PER_BLOCK, 1)
#endif
void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUnit)
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.bornForce2_blocks*cSim.bornForce2_threads_per_block/GRID;
......@@ -55,14 +63,19 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float4 apos = cSim.pPosq[i];
float2 a = cSim.pObcData[i];
float fb = cSim.pBornForce[i];
float nonPolarScaleDataI = gbsaSimDev.pNonPolarScalingFactors[i];
float nonPolarScaleDataI = feSimDev.pNonPolarScalingFactors[i];
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
float3 af;
sA[threadIdx.x].fx = af.x = 0.0f;
sA[threadIdx.x].fy = af.y = 0.0f;
sA[threadIdx.x].fz = af.z = 0.0f;
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
......@@ -104,28 +117,28 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
t1 *= rInverse;
// Born Forces term
float term = 0.125f *
(1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3 +
float term = 0.125f * (1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3 +
0.250f * t1 * r2Inverse;
term *= psA[j].npScale*nonPolarScaleDataI;
float dE = fb * term;
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || r2 > cSim.nonbondedCutoffSqr)
#else
if (a.x >= rScaledRadiusJ)
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || x+j >= cSim.atoms )
#endif
{
dE = 0.0f;
}
float d = dx * dE;
af.x -= d;
psA[j].fx += d;
d = dy * dE;
af.y -= d;
psA[j].fy += d;
d = dz * dE;
af.z -= d;
psA[j].fz += d;
......@@ -144,9 +157,9 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
of.z += af.z + sA[threadIdx.x].fz;
of.w = 0.0f;
cSim.pForce4[offset] = of;
}
else
{
} else {
// Read fixed atom data into registers and GRF
if (lasty != y)
{
......@@ -154,7 +167,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pObcData[j];
sA[threadIdx.x].fb = cSim.pBornForce[j];
sA[threadIdx.x].npScale = gbsaSimDev.pNonPolarScalingFactors[j];
sA[threadIdx.x].npScale = feSimDev.pNonPolarScalingFactors[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
......@@ -215,12 +228,10 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
term *= psA[tj].npScale*nonPolarScaleDataI;
float dE = fb * term;
#if defined USE_PERIODIC
#if defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || r2 > cSim.nonbondedCutoffSqr)
#else
if (a.x >= rScaledRadiusJ)
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || y+tj >= cSim.atoms)
#endif
{
dE = 0.0f;
......@@ -244,12 +255,10 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
dE = psA[tj].fb * term;
float rj = psA[tj].r;
#ifdef USE_PERIODIC
#ifdef USE_CUTOFF
if (rj >= rScaledRadiusI || i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (rj >= rScaledRadiusI || r2 > cSim.nonbondedCutoffSqr)
#else
if (rj >= rScaledRadiusI)
if (rj >= rScaledRadiusI || i >= cSim.atoms || y+tj >= cSim.atoms )
#endif
{
dE = 0.0f;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kSoftcoreLJ.h
View file @ bc85b9f0
......@@ -35,14 +35,14 @@
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;
eps *= lambda;
// (r/sig)
float sig2 = r/sig;
float sig2 = 1.0f/sig;
sig2 *= sig2;
sig2 *= r2;
float sig6 = sig2*sig2*sig2;
float softcoreLJTerm = 0.5f*( 1.0f - lambda) + sig6;
......@@ -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;
}
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
plugins/freeEnergy/platforms/cuda/tests/CMakeLists.txt
View file @ bc85b9f0
......@@ -7,18 +7,34 @@ INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src/kernels)
Set( SHARED_OPENMM_TARGET OpenMMFreeEnergy)
Set( STATIC_OPENMM_TARGET OpenMMFreeEnergy_static)
Set( SHARED_CUDA_TARGET OpenMMCuda)
Set( STATIC_CUDA_TARGET OpenMMCuda_static)
# serialize test cases for GBVI and GBSAOBC softcore runs
# if INCLUDE_SERIALIZATION is TRUE
SET( INCLUDE_SERIALIZATION FALSE )
#SET( INCLUDE_SERIALIZATION TRUE )
SET( SHARED_OPENMM_TARGET OpenMMFreeEnergy)
SET( STATIC_OPENMM_TARGET OpenMMFreeEnergy_static)
SET( SHARED_CUDA_TARGET OpenMMCuda)
SET( STATIC_CUDA_TARGET OpenMMCuda_static)
IF( INCLUDE_SERIALIZATION )
INCLUDE_DIRECTORIES(${OPENMM_DIR}/serialization/include)
SET( SHARED_OPENMM_SERIALIZATION OpenMMSerialization )
SET( SHARED_FREE_ENERGY_SERIALIZATION FreeEnergySerialization )
ENDIF( INCLUDE_SERIALIZATION )
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_CUDA_TARGET ${SHARED_CUDA_TARGET}_d)
SET(SHARED_OPENMM_TARGET ${SHARED_OPENMM_TARGET}_d)
IF( INCLUDE_SERIALIZATION )
SET(SHARED_OPENMM_SERIALIZATION ${SHARED_OPENMM_SERIALIZATION}_d)
SET(SHARED_FREE_ENERGY_SERIALIZATION ${SHARED_FREE_ENERGY_SERIALIZATION}_d)
ENDIF( INCLUDE_SERIALIZATION )
SET(STATIC_CUDA_TARGET ${STATIC_CUDA_TARGET}_d)
Set(STATIC_OPENMM_TARGET ${STATIC_OPENMM_TARGET}_d)
SET(STATIC_OPENMM_TARGET ${STATIC_OPENMM_TARGET}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
#LINK_DIRECTORIES
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
......@@ -26,45 +42,28 @@ FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# Link with shared library
CUDA_ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
IF( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET} ${SHARED_OPENMM_SERIALIZATION} ${SHARED_FREE_ENERGY_SERIALIZATION})
ELSE( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDIF( INCLUDE_SERIALIZATION )
SET(DEFINE_STRING "-DUSE_SOFTCORE")
IF( INCLUDE_SERIALIZATION )
SET(DEFINE_STRING "${DEFINE_STRING} -DOPENMM_SERIALIZE")
ENDIF( INCLUDE_SERIALIZATION )
IF( ${TEST_ROOT} STREQUAL "TestCudaOBCSoftcoreForce" )
SET(DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=1")
ENDIF( ${TEST_ROOT} STREQUAL "TestCudaOBCSoftcoreForce" )
IF( ${TEST_ROOT} STREQUAL "TestCudaGBVISoftcoreForce" )
SET(DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=2")
ENDIF( ${TEST_ROOT} STREQUAL "TestCudaGBVISoftcoreForce" )
# Link with static library
# SET(TEST_STATIC ${TEST_ROOT}Static)
# CUDA_ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_OPENMM_TARGET} ${STATIC_CUDA_TARGET})
# ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
MESSAGE( "${TEST_ROOT} ${DEFINE_STRING}" )
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES COMPILE_FLAGS ${DEFINE_STRING} )
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
# TestCudaUsingParameterFile customized w/ command-line argument (input file name used in test)
#ADD_EXECUTABLE(TestFreeEnergyCudaUsingParameterFile TstFreeEnergyCudaUsingParameterFile.cpp)
#TARGET_LINK_LIBRARIES(TestFreeEnergyCudaUsingParameterFile ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
#
#SET(TEST_ROOT TestCudaUsingParameterFile)
#SET(TEST_PROG TstCudaUsingParameterFile.cpp)
#SET(TEST_STATIC ${TEST_ROOT}Static)
#SET(INCLUDE_CUDA_STATIC 1)
#IF(INCLUDE_CUDA_STATIC)
# ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET})
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfPbcParameters.txt" " +checkEnergyForceConsistent -checkForces" )
#ENDIF(INCLUDE_CUDA_STATIC)
plugins/freeEnergy/platforms/cuda/tests/TestCudaGBVISoftcoreForce.cpp
View file @ bc85b9f0
......@@ -33,80 +33,32 @@
* This tests the reference implementation of GBVIForce.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/GBVISoftcoreForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/NonbondedForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "OpenMMFreeEnergy.h"
#include "openmm/freeEnergyKernels.h"
#include "ReferenceFreeEnergyKernelFactory.h"
#include "CudaFreeEnergyKernelFactory.h"
#include "TestCudaSoftcoreForce.h"
#include <iostream>
#include <cstdio>
#include <vector>
//#define USE_SOFTCORE
//#define IMPLICIT_SOLVENT GBVI
//#define IMPLICIT_SOLVENT OBC
using namespace OpenMM;
using namespace std;
#define OBC_FLAG 1
#define GBVI_FLAG 2
const double TOL = 1e-5;
#define PRINT_ON 0
int compareForcesOfTwoStates( int numParticles, State& state1, State& state2, double relativeTolerance, double absoluteTolerance ) {
#include "openmm/GBVIForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/NonbondedForce.h"
int error = 0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f1 = state1.getForces()[i];
Vec3 f2 = state2.getForces()[i];
double diff = (f1[0] - f2[0])*(f1[0] - f2[0]) +
(f1[1] - f2[1])*(f1[1] - f2[1]) +
(f1[2] - f2[2])*(f1[2] - f2[2]);
double denom1 = fabs( f1[0] ) + fabs( f1[1] ) +fabs( f1[2] );
double denom2 = fabs( f2[0] ) + fabs( f2[1] ) +fabs( f2[2] );
int ok = 1;
if( (denom1 > 0.0 || denom2 > 0.0) && (sqrt( diff )/(denom1+denom2)) > relativeTolerance ){
error++;
ok = 0;
}
#if PRINT_ON == 1
(void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e] [%14.6e %14.6e %14.6e] %s\n", i,
f1[0], f1[1], f1[2], f2[0], f2[1], f2[2], (ok ? "":"XXXXXX") );
#ifdef USE_SOFTCORE
#include "openmm/GBVISoftcoreForce.h"
#include "openmm/GBSAOBCSoftcoreForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#endif
}
return error;
}
void testSingleParticle() {
#if 1
CudaPlatform platform;
CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
#else
#include <iomanip>
ReferencePlatform platform;
ReferenceFreeEnergyKernelFactory* referenceFactoryT = new ReferenceFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactoryT);
#endif
void testSingleParticle( FILE* log ) {
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
VerletIntegrator integrator(0.01);
GBVISoftcoreForce* forceField = new GBVISoftcoreForce;
......@@ -121,7 +73,7 @@ void testSingleParticle() {
nonbonded->addParticle( charge, 1.0, 0.0);
system.addForce(nonbonded);
Context context(system, integrator, platform);
Context context(system, integrator, Platform::getPlatformByName( "Cuda") );
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
......@@ -132,46 +84,22 @@ void testSingleParticle() {
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -0.1*gamma*tau*std::pow( radius/bornRadius, 3.0);
double nonpolarEnergy = -gamma*tau*std::pow( radius/bornRadius, 3.0);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs( obtainedE - expectedE );
#if PRINT_ON == 1
(void) fprintf( stderr, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
if( log ){
(void) fprintf( log, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy );
#endif
}
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
void testEnergyEthaneSwitchingFunction( int useSwitchingFunction, FILE* log ) {
std::string methodName = "testEnergyEthaneSwitchingFunction";
#if 1
CudaPlatform platform;
CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
#else
ReferencePlatform platform;
ReferenceFreeEnergyKernelFactory* referenceFactoryT = new ReferenceFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactoryT);
#endif
ReferencePlatform referencePlatform;
ReferenceFreeEnergyKernelFactory* referenceFactory = new ReferenceFreeEnergyKernelFactory();
referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactory);
System system;
const int numParticles = 8;
for( int i = 0; i < numParticles; i++ ){
......@@ -215,12 +143,12 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
//double bornRadiusScaleFactorsEven = 1.0;
//double bornRadiusScaleFactorsOdd = 0.5;
double bornRadiusScaleFactorsOdd = 1.0;
#if PRINT_ON == 1
(void) fprintf( stderr, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( stderr, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
if( log ){
(void) fprintf( log, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( log, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
C_charge, C_radius, C_gamma, H_charge, H_radius, H_gamma,
bornRadiusScaleFactorsEven, bornRadiusScaleFactorsOdd);
#endif
}
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int i = 0; i < numParticles; i++ ){
......@@ -281,10 +209,10 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
system.addForce(nonbonded);
LangevinIntegrator integrator1(0, 0.1, 0.01);
LangevinIntegrator integrator2(0, 0.1, 0.01);
Context referenceContext(system, integrator1, referencePlatform);
Context context(system, integrator2, platform);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context referenceContext(system, integrator1, Platform::getPlatformByName( "Reference") );
Context context(system, integrator2, Platform::getPlatformByName( "Cuda") );
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
......@@ -315,13 +243,15 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
State state = context.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
#if PRINT_ON == 1
(void) fprintf( stderr, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
#endif
if( log ){
(void) fprintf( log, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
}
// Take a small step in the direction of the energy gradient.
if( compareForcesOfTwoStates( numParticles, state, referenceState, 0.001, 0.001 ) ){
DoubleVector stats;
if( compareForcesOfTwoStates( state, referenceState, 0.001, stats, log ) ){
ASSERT_EQUAL_TOL(0.0, 1.0, 0.01)
}
......@@ -336,9 +266,9 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
}
norm = std::sqrt(norm);
#if PRINT_ON == 1
(void) fprintf( stderr, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
#endif
if( log ){
(void) fprintf( log, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
}
const double delta = 1e-03;
double step = delta/norm;
......@@ -354,10 +284,10 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
double diff = (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta;
double off = fabs( diff - norm )/norm;
#if PRINT_ON == 1
(void) fprintf( stderr, "%2d Energies %.8e %.8e norms[%13.7e %13.7e] deltaNorms=%13.7e delta=%.2e\n",
if( log ){
(void) fprintf( log, "%2d Energies %.8e %.8e norms[%13.7e %13.7e] deltaNorms=%13.7e delta=%.2e\n",
ii, state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, off, delta );
#endif
}
// See whether the potential energy changed by the expected amount.
......@@ -372,9 +302,9 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
// positions[8][2] -= static_cast<double>(ii+1)*0.1;
// positions[8][2] -= 0.001;
#if PRINT_ON == 1
(void) fprintf( stderr, "r48=%14.6e r28=%14.6e r24=%14.6e\n", positions[8][2]-positions[4][2], positions[8][2], positions[4][2] );
#endif
if( log ){
(void) fprintf( log, "r48=%14.6e r28=%14.6e r24=%14.6e\n", positions[8][2]-positions[4][2], positions[8][2], positions[4][2] );
}
}
#if 0
int carbonIndex = 1;
......@@ -388,7 +318,7 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
for( int kk = 0; kk < 3; kk++ ){
dist += (positions[carbonIndex][kk] - positions[hydrogenIndex][kk] )*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk]);
}
(void) fprintf( stderr, "H=%d C=%d r=%14.6e\n", hydrogenIndex, carbonIndex, dist );
(void) fprintf( log, "H=%d C=%d r=%14.6e\n", hydrogenIndex, carbonIndex, dist );
hydrogenIndex++;
if( hydrogenIndex == carbonIndex ){
hydrogenIndex++;
......@@ -403,13 +333,557 @@ void testEnergyEthaneSwitchingFunction( int useSwitchingFunction ) {
}
}
static GBVISoftcoreForce* copyGbviSoftcoreForce( const GBVISoftcoreForce& gbviSoftcoreForce ){
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce(gbviSoftcoreForce);
/*
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce();
copyGbviSoftcoreForce->setNonbondedMethod( gbviSoftcoreForce.getNonbondedMethod() );
copyGbviSoftcoreForce->setCutoffDistance( gbviSoftcoreForce.getCutoffDistance() );
copyGbviSoftcoreForce->setSolventDielectric( gbviSoftcoreForce.getSolventDielectric() );
copyGbviSoftcoreForce->setSoluteDielectric( gbviSoftcoreForce.getSoluteDielectric() );
copyGbviSoftcoreForce->setBornRadiusScalingMethod( gbviSoftcoreForce.getBornRadiusScalingMethod() );
copyGbviSoftcoreForce->setQuinticLowerLimitFactor( gbviSoftcoreForce.getQuinticLowerLimitFactor() );
copyGbviSoftcoreForce->setQuinticUpperBornRadiusLimit( gbviSoftcoreForce.getQuinticUpperBornRadiusLimit() );
// particle parameters
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double gamma;
double softcoreLJLambda;
gbviSoftcoreForce.getParticleParameters(ii, charge, sigma, gamma, softcoreLJLambda);
copyGbviSoftcoreForce->addParticle( charge, sigma, gamma, softcoreLJLambda);
}
// bonds
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumBonds(); ii++ ){
int particle1, particle2;
double distance;
gbviSoftcoreForce.getBondParameters( ii, particle1, particle2, distance);
copyGbviSoftcoreForce->addBond( particle1, particle2, distance );
}
*/
return copyGbviSoftcoreForce;
}
static GBVIForce* copyGbviForce( const GBVIForce& gbviForce ){
return new GBVIForce(gbviForce);
}
static GBSAOBCSoftcoreForce* copyGBSAOBCSoftcoreForce( const GBSAOBCSoftcoreForce& gbviSoftcoreForce ){
return new GBSAOBCSoftcoreForce(gbviSoftcoreForce);
}
static GBSAOBCForce* copyGbsaObcForce( const GBSAOBCForce& gbviForce ){
return new GBSAOBCForce(gbviForce);
}
void testGbviSoftcore( MapStringToDouble& inputArgumentMap, FILE* log ){
double lambda1 = 1.0;
double lambda2 = 1.0;
int nonbondedMethod = 0;
int numMolecules = 1;
int numParticlesPerMolecule = 2;
int useQuinticSpline = 1;
int applyAssert = 1;
int positionPlacementMethod = 0;
int serialize = 0;
double boxSize = 10.0;
double relativeTolerance = 1.0e-04;
setDoubleFromMapStringToDouble( inputArgumentMap, "lambda1", lambda1 );
setDoubleFromMapStringToDouble( inputArgumentMap, "lambda2", lambda2 );
setDoubleFromMapStringToDouble( inputArgumentMap, "boxSize", boxSize );
double cutoffDistance = boxSize*0.4;;
setDoubleFromMapStringToDouble( inputArgumentMap, "cutoffDistance", cutoffDistance);
setDoubleFromMapStringToDouble( inputArgumentMap, "relativeTolerance", relativeTolerance );
setIntFromMapStringToDouble( inputArgumentMap, "positionPlacementMethod", positionPlacementMethod ) ;
setIntFromMapStringToDouble( inputArgumentMap, "nonbondedMethod", nonbondedMethod );
setIntFromMapStringToDouble( inputArgumentMap, "numMolecules", numMolecules );
setIntFromMapStringToDouble( inputArgumentMap, "numParticlesPerMolecule", numParticlesPerMolecule );
setIntFromMapStringToDouble( inputArgumentMap, "serialize", serialize );
if( nonbondedMethod == 2 && cutoffDistance > boxSize*0.5 ){
cutoffDistance = boxSize*0.5;
}
int numParticles = numMolecules*numParticlesPerMolecule;
int includeGbvi = 1;
double reactionFieldDielectric = 80.0;
if( log ){
double particleDensity = static_cast<double>(numParticles)/(boxSize*boxSize*boxSize);
double particleCube = pow( particleDensity, (-1.0/3.0) );
(void) fprintf( log, "\n--------------------------------------------------------------------------------------\n" );
(void) fprintf( log, "Input arguments\n" );
(void) fflush( log );
(void) fprintf( log, " includeGbvi %d\n", includeGbvi );
(void) fprintf( log, " nonbondedMethod %d\n", nonbondedMethod );
(void) fprintf( log, " numParticles %d\n", numParticles );
(void) fprintf( log, " numMolecules %d\n", numMolecules );
(void) fprintf( log, " numParticlesPerMolecule %d\n", numParticlesPerMolecule );
(void) fprintf( log, " useQuinticSpline %d\n", useQuinticSpline );
(void) fprintf( log, " positionPlacementMethod %d\n", positionPlacementMethod);
#ifdef USE_SOFTCORE
(void) fprintf( log, " lambda1 %8.3f\n", lambda1 );
(void) fprintf( log, " lambda2 %8.3f\n", lambda2 );
#endif
(void) fprintf( log, " boxSize %8.3f\n", boxSize );
(void) fprintf( log, " cutoffDistance %8.3f\n", cutoffDistance );
(void) fprintf( log, " reactionFieldDielectric %8.3f\n", reactionFieldDielectric );
(void) fprintf( log, " relativeTolerance %8.1e\n", relativeTolerance );
(void) fprintf( log, " particleDensity %8.2e\n", particleDensity );
(void) fprintf( log, " particleCube %8.2e\n", particleCube );
}
// Create two systems: one with GbviSoftcoreForce NonbondedSoftcoreForce forces, and one using a CustomNonbondedForce, CustomGBVI force to implement the same interaction.
System standardSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
#ifdef USE_SOFTCORE
NonbondedSoftcoreForce* nonbondedSoftcoreForce = new NonbondedSoftcoreForce();
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffPeriodic );
}
}
#else
NonbondedForce* nonbondedSoftcoreForce = new NonbondedForce();
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::CutoffPeriodic );
}
}
#endif
nonbondedSoftcoreForce->setCutoffDistance( cutoffDistance );
nonbondedSoftcoreForce->setReactionFieldDielectric( reactionFieldDielectric );
#ifdef USE_SOFTCORE
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVISoftcoreForce* gbviSoftcoreForce = new GBVISoftcoreForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::CutoffPeriodic );
}
}
#else
GBSAOBCSoftcoreForce* gbviSoftcoreForce = new GBSAOBCSoftcoreForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::CutoffPeriodic );
}
}
#endif
#else
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVIForce* gbviSoftcoreForce = new GBVIForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::CutoffPeriodic );
}
}
#else
GBSAOBCForce* gbviSoftcoreForce = new GBSAOBCForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::CutoffPeriodic );
}
}
#endif
#endif
#if IMPLICIT_SOLVENT == GBVI_FLAG
#ifdef USE_SOFTCORE
if( useQuinticSpline ){
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVISoftcoreForce::QuinticSpline );
} else {
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVISoftcoreForce::NoScaling );
}
#else
if( useQuinticSpline ){
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVIForce::QuinticSpline );
} else {
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVIForce::NoScaling );
}
#endif
#endif
gbviSoftcoreForce->setSolventDielectric( 78.3 );
//gbviSoftcoreForce->setSolventDielectric( 1.0e+10 );
//gbviSoftcoreForce->setSolventDielectric( 1.0 );
gbviSoftcoreForce->setSoluteDielectric( 1.0 );
gbviSoftcoreForce->setCutoffDistance( nonbondedSoftcoreForce->getCutoffDistance( ) );
std::vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
PositionGenerator positionGenerator( numMolecules, numParticlesPerMolecule, boxSize );
if( log ){
positionGenerator.setLog( log );
}
if( positionPlacementMethod == 1 ){
positionGenerator.setPositions( PositionGenerator::SimpleGrid, sfmt, positions );
} else {
positionGenerator.setBondDistance( 0.3 );
positionGenerator.setPositions( PositionGenerator::Random, sfmt, positions );
}
// show info on particle positions
if( log ){
Vec3 box[2];
positionGenerator.getEnclosingBox( positions, box );
(void) fprintf( log, "Enclosing Box (in A): [%15.7e %15.7e] [%15.7e %15.7e] [%15.7e %15.7e] [%15.7e %15.7e %15.7e]\n",
box[0][0], box[1][0], box[0][1], box[1][1], box[0][2], box[1][2],
(box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
int showIndex = 5;
int periodicBoundaryConditions = (nonbondedMethod == 2) ? 1 : 0;
IntVector positionIndexVector;
positionIndexVector.push_back( 0 );
positionIndexVector.push_back( static_cast<int>(positions.size())-1 );
//positionIndexVector.push_back( 542 );
for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
if( positionIndexVector[ii] < positions.size() ){
int positionIndex = positionIndexVector[ii];
IntDoublePairVector sortVector;
positionGenerator.getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
(void) fprintf( log, "Min/max distance from %6d:\n ", positionIndex );
for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( log, "[%6d %15.7e] ", pair.first, pair.second);
}
(void) fprintf( log, "\n " );
for( unsigned int jj = (sortVector.size() - showIndex); jj < sortVector.size() && jj >= 0; jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( log, "[%6d %15.7e] ", pair.first, pair.second);
}
(void) fprintf( log, "\n" );
}
}
IntIntPairVector pairs;
pairs.push_back( IntIntPair( 732, 0 ) );
pairs.push_back( IntIntPair( 732, 1 ) );
pairs.push_back( IntIntPair( 732, 2 ) );
pairs.push_back( IntIntPair( 732, 3 ) );
pairs.push_back( IntIntPair( 732, 4 ) );
for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
if( ii->first < positions.size() && ii->second < positions.size() ){
double d = positionGenerator.getDistance( ii->first, ii->second, positions );
(void) fprintf( log, "Distance %6d %6d %15.7e d2=%15.7e\n", ii->first, ii->second, d, d*d );
}
}
}
const int numberOfParameters = 5;
const int ChargeIndex = 0;
const int SigmaIndex = 1;
const int EpsIndex = 2;
const int GammaIndex = 3;
const int LambdaIndex = 4;
std::vector<double> parameterLowerBound( numberOfParameters, 0.0 );
double fixedCharge = 1.0;
parameterLowerBound[ChargeIndex] = fixedCharge; // charge
parameterLowerBound[SigmaIndex] = 0.1; // sigma
parameterLowerBound[EpsIndex] = 0.5; // eps
parameterLowerBound[GammaIndex] = 0.1; // gamma
parameterLowerBound[LambdaIndex] = lambda1; // lambda
std::vector<double> parameterUpperBound( parameterLowerBound );
parameterUpperBound[ChargeIndex] = fixedCharge; // charge
parameterUpperBound[SigmaIndex] = 0.3; // sigma
parameterUpperBound[EpsIndex] = 40.0; // eps
parameterUpperBound[GammaIndex] = 40.0; // gamma
#if IMPLICIT_SOLVENT == OBC_FLAG
parameterLowerBound[GammaIndex] = 0.1; // overlap factor
parameterUpperBound[GammaIndex] = 1.5;
#endif
std::vector<double> parameters( numberOfParameters );
double charge = fixedCharge;
for( int ii = 0; ii < numMolecules; ii++) {
charge *= -1.0;
double lambda = ii < (numMolecules/2) ? lambda1 : lambda2;
randomizeParameters( parameterLowerBound, parameterUpperBound, sfmt, parameters );
#ifdef USE_SOFTCORE
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex], lambda );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex], lambda );
#else
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex] );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex] );
#endif
int baseParticleIndex = ii*numParticlesPerMolecule;
for( int jj = 1; jj < numParticlesPerMolecule; jj++) {
// alternate charges
charge *= -1.0;
randomizeParameters( parameterLowerBound, parameterUpperBound, sfmt, parameters );
#ifdef USE_SOFTCORE
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex], lambda );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex], lambda );
#else
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex] );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex] );
#endif
nonbondedSoftcoreForce->addException( baseParticleIndex, baseParticleIndex+jj, 0.0f, 1.0, 0.0f );
#if IMPLICIT_SOLVENT == GBVI_FLAG
double bondDistance = positionGenerator.getDistance( baseParticleIndex, baseParticleIndex+jj, positions );
gbviSoftcoreForce->addBond( baseParticleIndex, baseParticleIndex+jj, bondDistance );
#endif
}
// alternate charge if numParticlesPerMolecule is odd
if( (numParticlesPerMolecule % 2) ){
charge *= -1.0;
}
}
standardSystem.addForce(nonbondedSoftcoreForce);
if( includeGbvi ){
standardSystem.addForce(gbviSoftcoreForce);
}
// copy system and forces
System* systemCopy = copySystem( standardSystem );
#ifdef USE_SOFTCORE
NonbondedSoftcoreForce* nonbondedSoftcoreForceCopy;
nonbondedSoftcoreForceCopy = copyNonbondedSoftcoreForce( *nonbondedSoftcoreForce );
#else
NonbondedForce* nonbondedSoftcoreForceCopy;
nonbondedSoftcoreForceCopy = copyNonbondedForce( *nonbondedSoftcoreForce );
#endif
systemCopy->addForce( nonbondedSoftcoreForceCopy );
std::stringstream baseFileName;
if( includeGbvi ){
#ifdef USE_SOFTCORE
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVISoftcoreForce* gBVISoftcoreForceCopy = copyGbviSoftcoreForce( *gbviSoftcoreForce );
baseFileName << "GBVISoftcore";
#endif
#if IMPLICIT_SOLVENT == OBC_FLAG
baseFileName << "GBSAObcSoftcore";
GBSAOBCSoftcoreForce* gBVISoftcoreForceCopy = copyGBSAOBCSoftcoreForce( *gbviSoftcoreForce );
#endif
baseFileName << "_lbda" << std::fixed << setprecision(2) << lambda2;
#else
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVIForce* gBVISoftcoreForceCopy = copyGbviForce( *gbviSoftcoreForce );
baseFileName << "Gbvi";
#endif
#if IMPLICIT_SOLVENT == OBC_FLAG
GBSAOBCForce* gBVISoftcoreForceCopy = copyGbsaObcForce( *gbviSoftcoreForce );
baseFileName << "GBSAOBC";
#endif
#endif
systemCopy->addForce( gBVISoftcoreForceCopy );
}
// perform comparison
std::stringstream idString;
idString << "Nb " << nonbondedMethod << " l2 " << std::fixed << setprecision(2) << lambda2;
runSystemComparisonTest( standardSystem, *systemCopy, "Cuda", "Reference", positions, inputArgumentMap, idString.str(), log );
// serialize
baseFileName << "_N" << positions.size();
baseFileName << "_Nb" << nonbondedMethod;
serializeSystemAndPositions( standardSystem, positions, baseFileName.str(), log);
delete systemCopy;
}
int main() {
try {
testSingleParticle();
testEnergyEthaneSwitchingFunction( 0 );
testEnergyEthaneSwitchingFunction( 1 );
registerFreeEnergyCudaKernelFactories( );
VectorOfMapStringToDouble vectorOfMapStringToDouble;
MapStringToDouble inputArgumentMap;
MapStringToDoubleVector generativeArgumentMaps;
//FILE* log = stderr;
FILE* log = NULL;
/*
testSingleParticle( log );
testEnergyEthaneSwitchingFunction( 0, log );
testEnergyEthaneSwitchingFunction( 1, log );
*/
inputArgumentMap["lambda2"] = 1.0;
inputArgumentMap["nonbondedMethod"] = 0;
inputArgumentMap["numMolecules"] = 10;
inputArgumentMap["boxSize"] = 5.0;
inputArgumentMap["positionPlacementMethod"] = 0;
inputArgumentMap["cutoffDistance"] = 0.3*inputArgumentMap["boxSize"];
//inputArgumentMap["cutoffDistance"] = 1.0;
inputArgumentMap["relativeTolerance"] = 5.0e-04;
inputArgumentMap["serialize"] = 1;
//inputArgumentMap["numParticlesPerMolecule"] = 2;
#ifdef USE_SOFTCORE
DoubleVector lamda2;
lamda2.push_back( 1.0 );
lamda2.push_back( 0.5 );
lamda2.push_back( 0.0 );
if( lamda2.size() > 0 ){
generativeArgumentMaps["lambda2"] = lamda2;
inputArgumentMap["lambda2"] = lamda2[0];
}
catch(const exception& e) {
#endif
DoubleVector numberOfMolecules;
numberOfMolecules.push_back( 10 );
numberOfMolecules.push_back( 100 );
numberOfMolecules.push_back( 1000 );
//numberOfMolecules.push_back( 2000 );
//numberOfMolecules.push_back( 4000 );
//numberOfMolecules.push_back( 8000 );
if( numberOfMolecules.size() > 0 ){
generativeArgumentMaps["numMolecules"] = numberOfMolecules;
inputArgumentMap["numMolecules"] = numberOfMolecules[0];
}
DoubleVector nonbondedMethod;
nonbondedMethod.push_back( 0 );
nonbondedMethod.push_back( 1 );
nonbondedMethod.push_back( 2 );
if( nonbondedMethod.size() > 0 ){
generativeArgumentMaps["nonbondedMethod"] = nonbondedMethod;
inputArgumentMap["nonbondedMethod"] = nonbondedMethod[0];
}
vectorOfMapStringToDouble.push_back( inputArgumentMap );
generateInputArgumentMapsFromStringVectors( generativeArgumentMaps, vectorOfMapStringToDouble );
// big box/many particle tests
//bool bigBox = true;
bool bigBox = false;
if( bigBox ){
MapStringToDouble inputArgumentMapBig;
VectorOfMapStringToDouble vectorOfMapStringToDoubleBig;
inputArgumentMapBig["lambda2"] = 1.0;
inputArgumentMapBig["nonbondedMethod"] = 1;
inputArgumentMapBig["numMolecules"] = 10;
inputArgumentMapBig["boxSize"] = 20.0;
inputArgumentMapBig["relativeTolerance"] = 6.0e-04;
vectorOfMapStringToDoubleBig.push_back( inputArgumentMapBig );
//MapStringToDoubleVector generativeArgumentMapsBig;
numberOfMolecules.resize( 0 );
numberOfMolecules.push_back( 4000 );
generativeArgumentMaps["numMolecules"] = numberOfMolecules;
nonbondedMethod.resize( 0 );
nonbondedMethod.push_back( 1 );
nonbondedMethod.push_back( 2 );
generativeArgumentMaps["nonbondedMethod"] = nonbondedMethod;
generateInputArgumentMapsFromStringVectors( generativeArgumentMaps, vectorOfMapStringToDoubleBig );
vectorOfMapStringToDouble.resize( 0 );
vectorOfMapStringToDouble.insert( vectorOfMapStringToDouble.end(), vectorOfMapStringToDoubleBig.begin(), vectorOfMapStringToDoubleBig.end() );
}
if( log ){
MapStringToInt exclude;
exclude["lambda1"] = 1;
exclude["numParticlesPerMolecule"] = 1;
std::stringstream outputStream;
std::sort( vectorOfMapStringToDouble.begin(), vectorOfMapStringToDouble.end(), TestMapSortPredicate);
StringVector printOrder;
printOrder.push_back( "numMolecules" );
printOrder.push_back( "nonbondedMethod" );
printOrder.push_back( "lambda2" );
printOrder.push_back( "boxSize" );
for( unsigned int kk = 0; kk < vectorOfMapStringToDouble.size(); kk++ ){
streamArgumentMapOneLine( vectorOfMapStringToDouble[kk], exclude, printOrder, kk, outputStream );
}
(void) fprintf( log, "Initial argument maps: %u\n%s", static_cast<unsigned int>(vectorOfMapStringToDouble.size()), outputStream.str().c_str() );
}
// run tests
for( unsigned int kk = 0; kk < vectorOfMapStringToDouble.size(); kk++ ){
testGbviSoftcore( vectorOfMapStringToDouble[kk], log );
sleep(2);
}
} catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
......
plugins/freeEnergy/platforms/cuda/tests/TestCudaLJSoftcoreForce.cpp 0 → 100644
View file @ bc85b9f0
/* -------------------------------------------------------------------------- *
* 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) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* 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. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the reference implementation of CustomGBForce.
*/
#include "../../../tests/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "openmm/CustomBondForce.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>
#include <algorithm>
extern "C" void registerFreeEnergyCudaKernelFactories();
using namespace OpenMM;
using namespace std;
const double TOL = 1e-4;
static const int NoCutoff = 0;
static const int CutoffNonPeriodic = 1;
static const int CutoffPeriodic = 2;
void testNonbondedSoftcore( double lambda1, double lambda2, int nonbondedMethod, FILE* log ){
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
const double reactionFieldDielectric = 80.0;
const double cutoffDistance = 0.4*boxSize;
// Create two systems: one with a NonbondedSoftcoreForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
customSystem.setDefaultPeriodicBoxVectors( Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedSoftcoreForce* nonbondedSoftcoreForce = new NonbondedSoftcoreForce();
CustomNonbondedForce* customNonbonded;
CustomBondForce* customBond;
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::NoCutoff );
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customNonbonded->setNonbondedMethod( CustomNonbondedForce::NoCutoff );
customBond = new CustomBondForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
} else {
nonbondedSoftcoreForce->setCutoffDistance( cutoffDistance );
nonbondedSoftcoreForce->setReactionFieldDielectric( reactionFieldDielectric );
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffPeriodic );
}
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf);"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customBond = new CustomBondForce("withinCutoff*(lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf));"
"withinCutoff=step(cutoff-r);"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
customNonbonded->setCutoffDistance( cutoffDistance );
if( nonbondedMethod == CutoffNonPeriodic ){
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffNonPeriodic );
} else {
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffPeriodic );
}
double eps2 = (reactionFieldDielectric - 1.0)/(2.0*reactionFieldDielectric+1.0);
double kValue = eps2/(cutoffDistance*cutoffDistance*cutoffDistance);
customNonbonded->addGlobalParameter("krf", kValue );
customBond->addGlobalParameter("krf", kValue );
double cValue = (1.0/cutoffDistance)*(3.0*reactionFieldDielectric)/(2.0*reactionFieldDielectric + 1.0);
customNonbonded->addGlobalParameter("crf", cValue );
customBond->addGlobalParameter("crf", cValue );
customBond->addGlobalParameter("cutoff", cutoffDistance );
}
customNonbonded->addPerParticleParameter("q");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
customNonbonded->addPerParticleParameter("lambda");
customBond->addPerBondParameter("q");
customBond->addPerBondParameter("sigma");
customBond->addPerBondParameter("eps");
customBond->addPerBondParameter("lambda");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(4);
// periodic boundary conditions not possible w/ CustomBond?
int includeExceptions = nonbondedMethod != NoCutoff ? 0 : 1;
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
double charge = 1.0;
double sigma1 = 0.2;
double sigma2 = 0.2;
double eps1 = 0.5;
double eps2 = 0.5;
//eps1 = eps2 = 0.0;
nonbondedSoftcoreForce->addParticle( charge, sigma1, eps1, lambda1);
nonbondedSoftcoreForce->addParticle(-charge, sigma2, eps2, lambda1);
params[0] = charge;
params[1] = sigma1;
params[2] = eps1;
params[3] = lambda1;
customNonbonded->addParticle(params);
params[0] = -charge;
params[1] = sigma2;
params[2] = eps2;
customNonbonded->addParticle(params);
if( includeExceptions && i && ((i%4) == 0) ){
vector<double> bondParams(4);
nonbondedSoftcoreForce->addException(i-4, i, charge*charge, sigma1, eps1, false, lambda1);
customNonbonded->addExclusion( i-4,i);
bondParams[0] = charge*charge;
bondParams[1] = sigma1;
bondParams[2] = eps1;
bondParams[3] = lambda1;
customBond->addBond(i-4,i, bondParams );
}
} else {
double charge = 1.0;
double sigma1 = 0.2;
double sigma2 = 0.1;
double eps1 = 0.8;
double eps2 = 0.8;
//eps1 = eps2 = 0.0;
nonbondedSoftcoreForce->addParticle( charge, sigma1, eps1, lambda2);
nonbondedSoftcoreForce->addParticle(-charge, sigma2, eps2, lambda2);
params[0] = charge;
params[1] = sigma1;
params[2] = eps1;
params[3] = lambda2;
customNonbonded->addParticle(params);
params[0] = -charge;
params[1] = sigma2;
params[2] = eps2;
customNonbonded->addParticle(params);
if( includeExceptions && i && ((i%4) == 0) ){
vector<double> bondParams(4);
nonbondedSoftcoreForce->addException(i-4, i, charge*charge, sigma1, eps1, false, lambda2);
customNonbonded->addExclusion( i-4,i);
bondParams[0] = charge*charge;
bondParams[1] = sigma1;
bondParams[2] = eps1;
bondParams[3] = lambda2;
customBond->addBond(i-4,i, bondParams );
}
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
standardSystem.addForce(nonbondedSoftcoreForce);
customSystem.addForce(customNonbonded);
customSystem.addForce(customBond);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, Platform::getPlatformByName( "Cuda"));
context1.setPositions(positions);
context1.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2(customSystem, integrator2, Platform::getPlatformByName( "Reference"));
context2.setPositions(positions);
context2.setVelocities(velocities);
State state2 = context2.getState(State::Forces | State::Energy);
double diff = 0.0;
static int previousNonbondedMethod = -1;
if( state1.getPotentialEnergy() - state2.getPotentialEnergy() != 0.0 ){
diff = fabs( state1.getPotentialEnergy() - state2.getPotentialEnergy() )/( fabs( state1.getPotentialEnergy() ) + fabs( state2.getPotentialEnergy() ) );
}
if( previousNonbondedMethod != nonbondedMethod ){
if( log ){
(void) fprintf( log, "\n" );
}
previousNonbondedMethod = nonbondedMethod;
}
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
double maxDiff = -1.0;
int maxDiffIndex = -1;
for (int i = 0; i < numParticles; i++) {
Vec3 f1 = state1.getForces()[i];
Vec3 f2 = state2.getForces()[i];
double f1N = sqrt( (f1[0]*f1[0]) + (f1[1]*f1[1]) + (f1[2]*f1[2]) );
double f2N = sqrt( (f2[0]*f2[0]) + (f2[1]*f2[1]) + (f2[2]*f2[2]) );
double diff = (f1[0]-f2[0])*(f1[0]-f2[0]) +
(f1[1]-f2[1])*(f1[1]-f2[1]) +
(f1[2]-f2[2])*(f1[2]-f2[2]);
if( f1N > 0.0 || f1N > 0.0 ){
diff = 2.0*sqrt( diff )/(f1N + f2N);
}
if( diff > maxDiff ){
maxDiff = diff;
maxDiffIndex = i;
}
/*
(void) fprintf( log, "%4d %15.7e [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e] \n", i, diff,
f1[0], f1[1],f1[2], f2[0], f2[1],f2[2] );
*/
// ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
ASSERT( diff < 1.0e-3);
}
if( log ){
(void) fprintf( log, "%d %d %10.1f %10.1f %15.7e %15.7e %15.7e maxFDiff=%15.7e %d\n",
nonbondedMethod, includeExceptions, lambda1, lambda2, diff,
state1.getPotentialEnergy(), state2.getPotentialEnergy(), maxDiff, maxDiffIndex); fflush( log );
}
}
int main() {
try {
registerFreeEnergyCudaKernelFactories( );
// test various combinations of lambdas and boundary conditions/cutoffs
FILE* log = NULL;
testNonbondedSoftcore( 1.0, 1.0 , NoCutoff, log );
testNonbondedSoftcore( 1.0, 0.0 , NoCutoff, log );
testNonbondedSoftcore( 1.0, 0.5 , NoCutoff, log );
testNonbondedSoftcore( 0.0, 0.0 , NoCutoff, log );
testNonbondedSoftcore( 1.0, 1.0 , CutoffNonPeriodic, log );
testNonbondedSoftcore( 1.0, 0.0 , CutoffNonPeriodic, log );
testNonbondedSoftcore( 1.0, 0.5 , CutoffNonPeriodic, log );
testNonbondedSoftcore( 0.0, 0.0 , CutoffNonPeriodic, log );
testNonbondedSoftcore( 1.0, 1.0 , CutoffPeriodic, log );
testNonbondedSoftcore( 1.0, 0.0 , CutoffPeriodic, log );
testNonbondedSoftcore( 1.0, 0.5 , CutoffPeriodic, log );
testNonbondedSoftcore( 0.0, 0.0 , CutoffPeriodic, log );
} catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/freeEnergy/platforms/cuda/tests/TestCudaOBCSoftcoreForce.cpp 0 → 100644
View file @ bc85b9f0
/* -------------------------------------------------------------------------- *
* 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) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* 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. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of GBVIForce.
*/
#include "TestCudaSoftcoreForce.h"
//#define USE_SOFTCORE
//#define IMPLICIT_SOLVENT GBVI
//#define IMPLICIT_SOLVENT OBC
#define OBC_FLAG 1
#define GBVI_FLAG 2
#include "openmm/GBVIForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/NonbondedForce.h"
#ifdef USE_SOFTCORE
#include "openmm/GBVISoftcoreForce.h"
#include "openmm/GBSAOBCSoftcoreForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#endif
#include <iomanip>
void testSingleParticle( FILE* log ) {
System system;
system.addParticle(2.0);
VerletIntegrator integrator(0.01);
GBVISoftcoreForce* forceField = new GBVISoftcoreForce;
double charge = 1.0;
double radius = 0.15;
double gamma = 1.0;
forceField->addParticle(charge, radius, gamma);
system.addForce(forceField);
NonbondedSoftcoreForce* nonbonded = new NonbondedSoftcoreForce();
nonbonded->setNonbondedMethod(NonbondedSoftcoreForce::NoCutoff);
nonbonded->addParticle( charge, 1.0, 0.0);
system.addForce(nonbonded);
Context context(system, integrator, Platform::getPlatformByName( "Cuda") );
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = radius;
double eps0 = EPSILON0;
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -gamma*tau*std::pow( radius/bornRadius, 3.0);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs( obtainedE - expectedE );
if( log ){
(void) fprintf( log, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy );
}
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testEnergyEthaneSwitchingFunction( int useSwitchingFunction, FILE* log ) {
std::string methodName = "testEnergyEthaneSwitchingFunction";
System system;
const int numParticles = 8;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
NonbondedSoftcoreForce* nonbonded = new NonbondedSoftcoreForce();
nonbonded->setNonbondedMethod(NonbondedSoftcoreForce::NoCutoff);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
C_radius = 0.180;
//C_radius = 0.360;
C_gamma = -0.2863;
C_gamma = 1.0;
H_radius = 0.125;
//H_radius = 0.25;
H_gamma = 0.2437;
H_gamma = 1.0;
//H_charge = C_charge = 0.0;
//H_gamma = C_gamma = 0.0;
} else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
// for ethane all Coulomb forces are excluded since all atoms 3 or
// fewer bonds away from all other atoms -- is this true for H's on
// difference carbons? -- should be computed in 14 ixn
double bornRadiusScaleFactorsEven = 0.5;
//double bornRadiusScaleFactorsEven = 1.0;
//double bornRadiusScaleFactorsOdd = 0.5;
double bornRadiusScaleFactorsOdd = 1.0;
if( log ){
(void) fprintf( log, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( log, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
C_charge, C_radius, C_gamma, H_charge, H_radius, H_gamma,
bornRadiusScaleFactorsEven, bornRadiusScaleFactorsOdd);
}
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_gamma, (i%2) ? bornRadiusScaleFactorsOdd : bornRadiusScaleFactorsEven);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters( 1, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 4, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsEven);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
// forceField->setParticleParameters( 8, C_charge, (C_radius+0.5), C_gamma, bornRadiusScaleFactorsEven);
// nonbonded->setParticleParameters( 8, C_charge, C_radius, 0.0);
if( useSwitchingFunction ){
forceField->setBornRadiusScalingMethod( GBVISoftcoreForce::QuinticSpline );
} else {
forceField->setBornRadiusScalingMethod( GBVISoftcoreForce::NoScaling );
}
forceField->addBond( 0, 1, C_HBondDistance );
forceField->addBond( 2, 1, C_HBondDistance );
forceField->addBond( 3, 1, C_HBondDistance );
forceField->addBond( 1, 4, C_CBondDistance );
forceField->addBond( 5, 4, C_HBondDistance );
forceField->addBond( 6, 4, C_HBondDistance );
forceField->addBond( 7, 4, C_HBondDistance );
std::vector<pair<int, int> > bonds;
std::vector<double> bondDistances;
bonds.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(2, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(3, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(1, 4));
bondDistances.push_back( C_CBondDistance );
bonds.push_back(pair<int, int>(5, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(6, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(7, 4));
bondDistances.push_back( C_HBondDistance );
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
system.addForce(forceField);
system.addForce(nonbonded);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context referenceContext(system, integrator1, Platform::getPlatformByName( "Reference") );
Context context(system, integrator2, Platform::getPlatformByName( "Cuda") );
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
positions[1] = Vec3(0.7286, 0.8978, 0.6468);
positions[2] = Vec3(0.4974, 0.0000, 0.0588);
positions[3] = Vec3(0.0000, 0.9459, 1.4666);
positions[4] = Vec3(2.1421, 0.8746, 1.1615);
positions[5] = Vec3(2.3239, 0.0050, 1.8065);
positions[6] = Vec3(2.8705, 0.8295, 0.3416);
positions[7] = Vec3(2.3722, 1.7711, 1.7518);
//positions[8] = Vec3(2.1421, 0.8746, 2.1615);
vector<Vec3> originalPositions(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
originalPositions[ii][0] = positions[ii][0];
originalPositions[ii][1] = positions[ii][1];
originalPositions[ii][2] = positions[ii][2];
}
int tries = 1;
double positionIncrement = 0.15;
for( int ii = 0; ii < tries; ii++ ){
context.setPositions(positions);
referenceContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
if( log ){
(void) fprintf( log, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
}
// Take a small step in the direction of the energy gradient.
DoubleVector stats;
if( compareForcesOfTwoStates( state, referenceState, 0.001, stats, log ) ){
ASSERT_EQUAL_TOL(0.0, 1.0, 0.01)
}
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
if( log ){
(void) fprintf( log, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
}
const double delta = 1e-03;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta;
double off = fabs( diff - norm )/norm;
if( log ){
(void) fprintf( log, "%2d Energies %.8e %.8e norms[%13.7e %13.7e] deltaNorms=%13.7e delta=%.2e\n",
ii, state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, off, delta );
}
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 1e-3*abs(state.getPotentialEnergy()) );
if( ii < (tries-1) ){
for( int jj = 0; jj < numParticles; jj++ ){
positions[jj][0] = originalPositions[jj][0];
positions[jj][1] = originalPositions[jj][1];
positions[jj][2] = originalPositions[jj][2];
}
// positions[8][2] -= static_cast<double>(ii+1)*0.1;
// positions[8][2] -= 0.001;
if( log ){
(void) fprintf( log, "r48=%14.6e r28=%14.6e r24=%14.6e\n", positions[8][2]-positions[4][2], positions[8][2], positions[4][2] );
}
}
#if 0
int carbonIndex = 1;
int hydrogenIndex = 0;
while( hydrogenIndex < 8 ){
Vec3 carbonDelta;
for( int kk = 0; kk < 3; kk++ ){
positions[hydrogenIndex][kk] += positionIncrement*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk] );
}
double dist = 0.0;
for( int kk = 0; kk < 3; kk++ ){
dist += (positions[carbonIndex][kk] - positions[hydrogenIndex][kk] )*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk]);
}
(void) fprintf( log, "H=%d C=%d r=%14.6e\n", hydrogenIndex, carbonIndex, dist );
hydrogenIndex++;
if( hydrogenIndex == carbonIndex ){
hydrogenIndex++;
}
if( carbonIndex == 1 && hydrogenIndex == 4 ){
carbonIndex = 4;
hydrogenIndex = 5;
}
}
#endif
}
}
static GBVISoftcoreForce* copyGbviSoftcoreForce( const GBVISoftcoreForce& gbviSoftcoreForce ){
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce(gbviSoftcoreForce);
/*
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce();
copyGbviSoftcoreForce->setNonbondedMethod( gbviSoftcoreForce.getNonbondedMethod() );
copyGbviSoftcoreForce->setCutoffDistance( gbviSoftcoreForce.getCutoffDistance() );
copyGbviSoftcoreForce->setSolventDielectric( gbviSoftcoreForce.getSolventDielectric() );
copyGbviSoftcoreForce->setSoluteDielectric( gbviSoftcoreForce.getSoluteDielectric() );
copyGbviSoftcoreForce->setBornRadiusScalingMethod( gbviSoftcoreForce.getBornRadiusScalingMethod() );
copyGbviSoftcoreForce->setQuinticLowerLimitFactor( gbviSoftcoreForce.getQuinticLowerLimitFactor() );
copyGbviSoftcoreForce->setQuinticUpperBornRadiusLimit( gbviSoftcoreForce.getQuinticUpperBornRadiusLimit() );
// particle parameters
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double gamma;
double softcoreLJLambda;
gbviSoftcoreForce.getParticleParameters(ii, charge, sigma, gamma, softcoreLJLambda);
copyGbviSoftcoreForce->addParticle( charge, sigma, gamma, softcoreLJLambda);
}
// bonds
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumBonds(); ii++ ){
int particle1, particle2;
double distance;
gbviSoftcoreForce.getBondParameters( ii, particle1, particle2, distance);
copyGbviSoftcoreForce->addBond( particle1, particle2, distance );
}
*/
return copyGbviSoftcoreForce;
}
static GBVIForce* copyGbviForce( const GBVIForce& gbviForce ){
return new GBVIForce(gbviForce);
}
static GBSAOBCSoftcoreForce* copyGBSAOBCSoftcoreForce( const GBSAOBCSoftcoreForce& gbviSoftcoreForce ){
return new GBSAOBCSoftcoreForce(gbviSoftcoreForce);
}
static GBSAOBCForce* copyGbsaObcForce( const GBSAOBCForce& gbviForce ){
return new GBSAOBCForce(gbviForce);
}
void testGbviSoftcore( MapStringToDouble& inputArgumentMap, FILE* log ){
double lambda1 = 1.0;
double lambda2 = 1.0;
int nonbondedMethod = 0;
int numMolecules = 1;
int numParticlesPerMolecule = 2;
int useQuinticSpline = 1;
int applyAssert = 1;
int positionPlacementMethod = 0;
int serialize = 0;
double boxSize = 10.0;
double relativeTolerance = 1.0e-04;
setDoubleFromMapStringToDouble( inputArgumentMap, "lambda1", lambda1 );
setDoubleFromMapStringToDouble( inputArgumentMap, "lambda2", lambda2 );
setDoubleFromMapStringToDouble( inputArgumentMap, "boxSize", boxSize );
double cutoffDistance = boxSize*0.4;;
setDoubleFromMapStringToDouble( inputArgumentMap, "cutoffDistance", cutoffDistance);
setDoubleFromMapStringToDouble( inputArgumentMap, "relativeTolerance", relativeTolerance );
setIntFromMapStringToDouble( inputArgumentMap, "positionPlacementMethod", positionPlacementMethod ) ;
setIntFromMapStringToDouble( inputArgumentMap, "nonbondedMethod", nonbondedMethod );
setIntFromMapStringToDouble( inputArgumentMap, "numMolecules", numMolecules );
setIntFromMapStringToDouble( inputArgumentMap, "numParticlesPerMolecule", numParticlesPerMolecule );
setIntFromMapStringToDouble( inputArgumentMap, "serialize", serialize );
if( nonbondedMethod == 2 && cutoffDistance > boxSize*0.5 ){
cutoffDistance = boxSize*0.5;
}
int numParticles = numMolecules*numParticlesPerMolecule;
int includeGbvi = 1;
double reactionFieldDielectric = 80.0;
if( log ){
double particleDensity = static_cast<double>(numParticles)/(boxSize*boxSize*boxSize);
double particleCube = pow( particleDensity, (-1.0/3.0) );
(void) fprintf( log, "\n--------------------------------------------------------------------------------------\n" );
(void) fprintf( log, "Input arguments\n" );
(void) fflush( log );
(void) fprintf( log, " includeGbvi %d\n", includeGbvi );
(void) fprintf( log, " nonbondedMethod %d\n", nonbondedMethod );
(void) fprintf( log, " numParticles %d\n", numParticles );
(void) fprintf( log, " numMolecules %d\n", numMolecules );
(void) fprintf( log, " numParticlesPerMolecule %d\n", numParticlesPerMolecule );
(void) fprintf( log, " useQuinticSpline %d\n", useQuinticSpline );
(void) fprintf( log, " positionPlacementMethod %d\n", positionPlacementMethod);
#ifdef USE_SOFTCORE
(void) fprintf( log, " lambda1 %8.3f\n", lambda1 );
(void) fprintf( log, " lambda2 %8.3f\n", lambda2 );
#endif
(void) fprintf( log, " boxSize %8.3f\n", boxSize );
(void) fprintf( log, " cutoffDistance %8.3f\n", cutoffDistance );
(void) fprintf( log, " reactionFieldDielectric %8.3f\n", reactionFieldDielectric );
(void) fprintf( log, " relativeTolerance %8.1e\n", relativeTolerance );
(void) fprintf( log, " particleDensity %8.2e\n", particleDensity );
(void) fprintf( log, " particleCube %8.2e\n", particleCube );
}
// Create two systems: one with GbviSoftcoreForce NonbondedSoftcoreForce forces, and one using a CustomNonbondedForce, CustomGBVI force to implement the same interaction.
System standardSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
#ifdef USE_SOFTCORE
NonbondedSoftcoreForce* nonbondedSoftcoreForce = new NonbondedSoftcoreForce();
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffPeriodic );
}
}
#else
NonbondedForce* nonbondedSoftcoreForce = new NonbondedForce();
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedForce::CutoffPeriodic );
}
}
#endif
nonbondedSoftcoreForce->setCutoffDistance( cutoffDistance );
nonbondedSoftcoreForce->setReactionFieldDielectric( reactionFieldDielectric );
#ifdef USE_SOFTCORE
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVISoftcoreForce* gbviSoftcoreForce = new GBVISoftcoreForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBVISoftcoreForce::CutoffPeriodic );
}
}
#else
GBSAOBCSoftcoreForce* gbviSoftcoreForce = new GBSAOBCSoftcoreForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCSoftcoreForce::CutoffPeriodic );
}
}
#endif
#else
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVIForce* gbviSoftcoreForce = new GBVIForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBVIForce::CutoffPeriodic );
}
}
#else
GBSAOBCForce* gbviSoftcoreForce = new GBSAOBCForce();
if( nonbondedMethod == NoCutoff ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::NoCutoff );
} else {
if( nonbondedMethod == CutoffNonPeriodic ){
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::CutoffNonPeriodic );
} else {
gbviSoftcoreForce->setNonbondedMethod( GBSAOBCForce::CutoffPeriodic );
}
}
#endif
#endif
#if IMPLICIT_SOLVENT == GBVI_FLAG
#ifdef USE_SOFTCORE
if( useQuinticSpline ){
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVISoftcoreForce::QuinticSpline );
} else {
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVISoftcoreForce::NoScaling );
}
#else
if( useQuinticSpline ){
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVIForce::QuinticSpline );
} else {
gbviSoftcoreForce->setBornRadiusScalingMethod( GBVIForce::NoScaling );
}
#endif
#endif
gbviSoftcoreForce->setSolventDielectric( 78.3 );
//gbviSoftcoreForce->setSolventDielectric( 1.0e+10 );
//gbviSoftcoreForce->setSolventDielectric( 1.0 );
gbviSoftcoreForce->setSoluteDielectric( 1.0 );
gbviSoftcoreForce->setCutoffDistance( nonbondedSoftcoreForce->getCutoffDistance( ) );
std::vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
PositionGenerator positionGenerator( numMolecules, numParticlesPerMolecule, boxSize );
if( log ){
positionGenerator.setLog( log );
}
if( positionPlacementMethod == 1 ){
positionGenerator.setPositions( PositionGenerator::SimpleGrid, sfmt, positions );
} else {
positionGenerator.setBondDistance( 0.3 );
positionGenerator.setPositions( PositionGenerator::Random, sfmt, positions );
}
// show info on particle positions
if( log ){
Vec3 box[2];
positionGenerator.getEnclosingBox( positions, box );
(void) fprintf( log, "Enclosing Box (in A): [%15.7e %15.7e] [%15.7e %15.7e] [%15.7e %15.7e] [%15.7e %15.7e %15.7e]\n",
box[0][0], box[1][0], box[0][1], box[1][1], box[0][2], box[1][2],
(box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
int showIndex = 5;
int periodicBoundaryConditions = (nonbondedMethod == 2) ? 1 : 0;
IntVector positionIndexVector;
positionIndexVector.push_back( 0 );
positionIndexVector.push_back( static_cast<int>(positions.size())-1 );
//positionIndexVector.push_back( 542 );
for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
if( positionIndexVector[ii] < positions.size() ){
int positionIndex = positionIndexVector[ii];
IntDoublePairVector sortVector;
positionGenerator.getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
(void) fprintf( log, "Min/max distance from %6d:\n ", positionIndex );
for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( log, "[%6d %15.7e] ", pair.first, pair.second);
}
(void) fprintf( log, "\n " );
for( unsigned int jj = (sortVector.size() - showIndex); jj < sortVector.size() && jj >= 0; jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( log, "[%6d %15.7e] ", pair.first, pair.second);
}
(void) fprintf( log, "\n" );
}
}
IntIntPairVector pairs;
pairs.push_back( IntIntPair( 732, 0 ) );
pairs.push_back( IntIntPair( 732, 1 ) );
pairs.push_back( IntIntPair( 732, 2 ) );
pairs.push_back( IntIntPair( 732, 3 ) );
pairs.push_back( IntIntPair( 732, 4 ) );
for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
if( ii->first < positions.size() && ii->second < positions.size() ){
double d = positionGenerator.getDistance( ii->first, ii->second, positions );
(void) fprintf( log, "Distance %6d %6d %15.7e d2=%15.7e\n", ii->first, ii->second, d, d*d );
}
}
}
const int numberOfParameters = 5;
const int ChargeIndex = 0;
const int SigmaIndex = 1;
const int EpsIndex = 2;
const int GammaIndex = 3;
const int LambdaIndex = 4;
std::vector<double> parameterLowerBound( numberOfParameters, 0.0 );
double fixedCharge = 1.0;
parameterLowerBound[ChargeIndex] = fixedCharge; // charge
parameterLowerBound[SigmaIndex] = 0.1; // sigma
parameterLowerBound[EpsIndex] = 0.5; // eps
parameterLowerBound[GammaIndex] = 0.1; // gamma
parameterLowerBound[LambdaIndex] = lambda1; // lambda
std::vector<double> parameterUpperBound( parameterLowerBound );
parameterUpperBound[ChargeIndex] = fixedCharge; // charge
parameterUpperBound[SigmaIndex] = 0.3; // sigma
parameterUpperBound[EpsIndex] = 40.0; // eps
parameterUpperBound[GammaIndex] = 40.0; // gamma
#if IMPLICIT_SOLVENT == OBC_FLAG
parameterLowerBound[GammaIndex] = 0.1; // overlap factor
parameterUpperBound[GammaIndex] = 1.5;
#endif
std::vector<double> parameters( numberOfParameters );
double charge = fixedCharge;
for( int ii = 0; ii < numMolecules; ii++) {
charge *= -1.0;
double lambda = ii < (numMolecules/2) ? lambda1 : lambda2;
randomizeParameters( parameterLowerBound, parameterUpperBound, sfmt, parameters );
#ifdef USE_SOFTCORE
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex], lambda );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex], lambda );
#else
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex] );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex] );
#endif
int baseParticleIndex = ii*numParticlesPerMolecule;
for( int jj = 1; jj < numParticlesPerMolecule; jj++) {
// alternate charges
charge *= -1.0;
randomizeParameters( parameterLowerBound, parameterUpperBound, sfmt, parameters );
#ifdef USE_SOFTCORE
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex], lambda );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex], lambda );
#else
nonbondedSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[EpsIndex] );
gbviSoftcoreForce->addParticle( charge, parameters[SigmaIndex], parameters[GammaIndex] );
#endif
nonbondedSoftcoreForce->addException( baseParticleIndex, baseParticleIndex+jj, 0.0f, 1.0, 0.0f );
#if IMPLICIT_SOLVENT == GBVI_FLAG
double bondDistance = positionGenerator.getDistance( baseParticleIndex, baseParticleIndex+jj, positions );
gbviSoftcoreForce->addBond( baseParticleIndex, baseParticleIndex+jj, bondDistance );
#endif
}
// alternate charge if numParticlesPerMolecule is odd
if( (numParticlesPerMolecule % 2) ){
charge *= -1.0;
}
}
standardSystem.addForce(nonbondedSoftcoreForce);
if( includeGbvi ){
standardSystem.addForce(gbviSoftcoreForce);
}
// copy system and forces
System* systemCopy = copySystem( standardSystem );
#ifdef USE_SOFTCORE
NonbondedSoftcoreForce* nonbondedSoftcoreForceCopy;
nonbondedSoftcoreForceCopy = copyNonbondedSoftcoreForce( *nonbondedSoftcoreForce );
#else
NonbondedForce* nonbondedSoftcoreForceCopy;
nonbondedSoftcoreForceCopy = copyNonbondedForce( *nonbondedSoftcoreForce );
#endif
systemCopy->addForce( nonbondedSoftcoreForceCopy );
std::stringstream baseFileName;
if( includeGbvi ){
#ifdef USE_SOFTCORE
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVISoftcoreForce* gBVISoftcoreForceCopy = copyGbviSoftcoreForce( *gbviSoftcoreForce );
baseFileName << "GBVISoftcore";
#endif
#if IMPLICIT_SOLVENT == OBC_FLAG
baseFileName << "GBSAObcSoftcore";
GBSAOBCSoftcoreForce* gBVISoftcoreForceCopy = copyGBSAOBCSoftcoreForce( *gbviSoftcoreForce );
#endif
baseFileName << "_lbda" << std::fixed << setprecision(2) << lambda2;
#else
#if IMPLICIT_SOLVENT == GBVI_FLAG
GBVIForce* gBVISoftcoreForceCopy = copyGbviForce( *gbviSoftcoreForce );
baseFileName << "Gbvi";
#endif
#if IMPLICIT_SOLVENT == OBC_FLAG
GBSAOBCForce* gBVISoftcoreForceCopy = copyGbsaObcForce( *gbviSoftcoreForce );
baseFileName << "GBSAOBC";
#endif
#endif
systemCopy->addForce( gBVISoftcoreForceCopy );
}
// perform comparison
std::stringstream idString;
idString << "Nb " << nonbondedMethod << " l2 " << std::fixed << setprecision(2) << lambda2;
runSystemComparisonTest( standardSystem, *systemCopy, "Cuda", "Reference", positions, inputArgumentMap, idString.str(), log );
// serialize
baseFileName << "_N" << positions.size();
baseFileName << "_Nb" << nonbondedMethod;
serializeSystemAndPositions( standardSystem, positions, baseFileName.str(), log);
delete systemCopy;
}
int main() {
try {
registerFreeEnergyCudaKernelFactories( );
VectorOfMapStringToDouble vectorOfMapStringToDouble;
MapStringToDouble inputArgumentMap;
MapStringToDoubleVector generativeArgumentMaps;
//FILE* log = stderr;
FILE* log = NULL;
/*
testSingleParticle( log );
testEnergyEthaneSwitchingFunction( 0, log );
testEnergyEthaneSwitchingFunction( 1, log );
*/
inputArgumentMap["lambda2"] = 1.0;
inputArgumentMap["nonbondedMethod"] = 0;
inputArgumentMap["numMolecules"] = 10;
inputArgumentMap["boxSize"] = 5.0;
inputArgumentMap["positionPlacementMethod"] = 0;
inputArgumentMap["cutoffDistance"] = 0.3*inputArgumentMap["boxSize"];
//inputArgumentMap["cutoffDistance"] = 1.0;
inputArgumentMap["relativeTolerance"] = 5.0e-04;
inputArgumentMap["serialize"] = 1;
//inputArgumentMap["numParticlesPerMolecule"] = 2;
#ifdef USE_SOFTCORE
DoubleVector lamda2;
lamda2.push_back( 1.0 );
lamda2.push_back( 0.5 );
lamda2.push_back( 0.0 );
if( lamda2.size() > 0 ){
generativeArgumentMaps["lambda2"] = lamda2;
inputArgumentMap["lambda2"] = lamda2[0];
}
#endif
DoubleVector numberOfMolecules;
numberOfMolecules.push_back( 10 );
numberOfMolecules.push_back( 100 );
numberOfMolecules.push_back( 1000 );
//numberOfMolecules.push_back( 2000 );
//numberOfMolecules.push_back( 4000 );
//numberOfMolecules.push_back( 8000 );
if( numberOfMolecules.size() > 0 ){
generativeArgumentMaps["numMolecules"] = numberOfMolecules;
inputArgumentMap["numMolecules"] = numberOfMolecules[0];
}
DoubleVector nonbondedMethod;
nonbondedMethod.push_back( 0 );
nonbondedMethod.push_back( 1 );
nonbondedMethod.push_back( 2 );
if( nonbondedMethod.size() > 0 ){
generativeArgumentMaps["nonbondedMethod"] = nonbondedMethod;
inputArgumentMap["nonbondedMethod"] = nonbondedMethod[0];
}
vectorOfMapStringToDouble.push_back( inputArgumentMap );
generateInputArgumentMapsFromStringVectors( generativeArgumentMaps, vectorOfMapStringToDouble );
// big box/many particle tests
//bool bigBox = true;
bool bigBox = false;
if( bigBox ){
MapStringToDouble inputArgumentMapBig;
VectorOfMapStringToDouble vectorOfMapStringToDoubleBig;
inputArgumentMapBig["lambda2"] = 1.0;
inputArgumentMapBig["nonbondedMethod"] = 1;
inputArgumentMapBig["numMolecules"] = 10;
inputArgumentMapBig["boxSize"] = 20.0;
inputArgumentMapBig["relativeTolerance"] = 6.0e-04;
vectorOfMapStringToDoubleBig.push_back( inputArgumentMapBig );
//MapStringToDoubleVector generativeArgumentMapsBig;
numberOfMolecules.resize( 0 );
numberOfMolecules.push_back( 4000 );
generativeArgumentMaps["numMolecules"] = numberOfMolecules;
nonbondedMethod.resize( 0 );
nonbondedMethod.push_back( 1 );
nonbondedMethod.push_back( 2 );
generativeArgumentMaps["nonbondedMethod"] = nonbondedMethod;
generateInputArgumentMapsFromStringVectors( generativeArgumentMaps, vectorOfMapStringToDoubleBig );
vectorOfMapStringToDouble.resize( 0 );
vectorOfMapStringToDouble.insert( vectorOfMapStringToDouble.end(), vectorOfMapStringToDoubleBig.begin(), vectorOfMapStringToDoubleBig.end() );
}
if( log ){
MapStringToInt exclude;
exclude["lambda1"] = 1;
exclude["numParticlesPerMolecule"] = 1;
std::stringstream outputStream;
std::sort( vectorOfMapStringToDouble.begin(), vectorOfMapStringToDouble.end(), TestMapSortPredicate);
StringVector printOrder;
printOrder.push_back( "numMolecules" );
printOrder.push_back( "nonbondedMethod" );
printOrder.push_back( "lambda2" );
printOrder.push_back( "boxSize" );
for( unsigned int kk = 0; kk < vectorOfMapStringToDouble.size(); kk++ ){
streamArgumentMapOneLine( vectorOfMapStringToDouble[kk], exclude, printOrder, kk, outputStream );
}
(void) fprintf( log, "Initial argument maps: %u\n%s", static_cast<unsigned int>(vectorOfMapStringToDouble.size()), outputStream.str().c_str() );
}
// run tests
for( unsigned int kk = 0; kk < vectorOfMapStringToDouble.size(); kk++ ){
testGbviSoftcore( vectorOfMapStringToDouble[kk], log );
sleep(2);
}
} catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/freeEnergy/platforms/cuda/tests/TestCudaSoftcoreForce.h 0 → 100644
View file @ bc85b9f0
#ifndef TEST_CUDA_SOFTCORE_H_
#define TEST_CUDA_SOFTCORE_H_
/* -------------------------------------------------------------------------- *
* 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) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* 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. *
* -------------------------------------------------------------------------- */
/**
* Utility methods shared across unit tests
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/System.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "OpenMM.h"
#include "OpenMMFreeEnergy.h"
#include "openmm/freeEnergyKernels.h"
#include "sfmt/SFMT.h"
#include "openmm/VerletIntegrator.h"
#ifdef OPENMM_SERIALIZE
#include "../../../../../serialization/include/openmm/serialization/SerializationProxy.h"
#include "../../../../../serialization/include/openmm/serialization/SerializationNode.h"
#include "../../../../../serialization/include/openmm/serialization/XmlSerializer.h"
//extern "C" void registerSerializationProxies();
//extern "C" void registerAmoebaSerializationProxies();
#endif
#include <iostream>
#include <vector>
#include <algorithm>
#include <iostream>
#include <cstdio>
#include <vector>
#include <typeinfo>
extern "C" void registerFreeEnergyCudaKernelFactories();
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
static const int NoCutoff = 0;
static const int CutoffNonPeriodic = 1;
static const int CutoffPeriodic = 2;
typedef std::vector<std::string> StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::vector<StringVector> StringVectorVector;
typedef std::vector<int> IntVector;
typedef IntVector::iterator IntVectorI;
typedef IntVector::const_iterator IntVectorCI;
typedef std::vector<IntVector> IntVectorVector;
typedef std::vector<double> DoubleVector;
typedef DoubleVector::iterator DoubleVectorI;
typedef DoubleVector::const_iterator DoubleVectorCI;
typedef std::vector<DoubleVector> DoubleVectorVector;
// the following are used in parsing parameter file
typedef std::vector<std::string> StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::vector<StringVector> VectorStringVector;
typedef VectorStringVector::iterator VectorStringVectorI;
typedef VectorStringVector::const_iterator VectorStringVectorCI;
typedef std::vector<std::vector<double> > VectorOfVectors;
typedef VectorOfVectors::iterator VectorOfVectorsI;
typedef VectorOfVectors::const_iterator VectorOfVectorsCI;
typedef std::map< int, int> MapIntInt;
typedef MapIntInt::iterator MapIntIntI;
typedef MapIntInt::const_iterator MapIntIntCI;
typedef std::map< double, int> MapDoubleToInt;
typedef MapDoubleToInt::iterator MapDoubleToIntI;
typedef MapDoubleToInt::const_iterator MapDoubleToIntCI;
typedef std::map< std::string, VectorOfVectors > MapStringVectorOfVectors;
typedef MapStringVectorOfVectors::iterator MapStringVectorOfVectorsI;
typedef MapStringVectorOfVectors::const_iterator MapStringVectorOfVectorsCI;
typedef std::map< std::string, StringVector > MapStringStringVector;
typedef MapStringStringVector::iterator MapStringStringVectorI;
typedef MapStringStringVector::const_iterator MapStringStringVectorCI;
typedef std::map< std::string, std::string > MapStringString;
typedef MapStringString::iterator MapStringStringI;
typedef MapStringString::const_iterator MapStringStringCI;
typedef std::map< std::string, std::string > MapStringToInt;
typedef MapStringToInt::iterator MapStringToIntI;
typedef MapStringToInt::const_iterator MapStringToIntCI;
typedef std::vector< std::map< std::string, std::string > > VectorMapStringString;
typedef VectorMapStringString::iterator VectorMapStringStringI;
typedef VectorMapStringString::const_iterator VectorMapStringStringCI;
typedef std::map< std::string, int > MapStringInt;
typedef MapStringInt::iterator MapStringIntI;
typedef MapStringInt::const_iterator MapStringIntCI;
typedef std::map< std::string, std::vector<OpenMM::Vec3> > MapStringVec3;
typedef MapStringVec3::iterator MapStringVec3I;
typedef MapStringVec3::const_iterator MapStringVec3CI;
typedef std::map< std::string, double > MapStringToDouble;
typedef MapStringToDouble::iterator MapStringToDoubleI;
typedef MapStringToDouble::const_iterator MapStringToDoubleCI;
typedef std::vector< MapStringToDouble > VectorOfMapStringToDouble;
typedef std::map< std::string, DoubleVector> MapStringToDoubleVector;
typedef MapStringToDoubleVector::iterator MapStringToDoubleVectorI;
typedef MapStringToDoubleVector::const_iterator MapStringToDoubleVectorCI;
typedef std::map< std::string, DoubleVector > MapStringToDoubleVector;
typedef std::map< std::string, Force*> MapStringForce;
typedef MapStringForce::iterator MapStringForceI;
typedef MapStringForce::const_iterator MapStringForceCI;
typedef std::map< int, IntVector> MapIntIntVector;
typedef MapIntIntVector::const_iterator MapIntIntVectorCI;
typedef std::pair<int, int> IntIntPair;
typedef std::vector<IntIntPair> IntIntPairVector;
typedef IntIntPairVector::iterator IntIntPairVectorI;
typedef IntIntPairVector::const_iterator IntIntPairVectorCI;
typedef std::pair<int, double> IntDoublePair;
typedef std::vector<IntDoublePair> IntDoublePairVector;
typedef IntDoublePairVector::iterator IntDoublePairVectorI;
typedef IntDoublePairVector::const_iterator IntDoublePairVectorCI;
class PositionGenerator {
public:
enum GenerationMethod {
/**
* Random positions
*/
Random = 0,
/**
* On grid
*/
SimpleGrid = 1,
};
PositionGenerator( int numMolecules, int numParticlesPerMolecule, double boxSize );
~PositionGenerator( );
/**
* Set logging file reference
*
* @param log log
*
*/
void setLog( FILE* log );
/**
* Set positions
*
* @param method method placement
* @param positions output vector of positions
*
* @return nonzero if error detected; 0 otherwise
*/
int setPositions( GenerationMethod method, std::vector<Vec3>& positions ) const;
/**
* Set positions
*
* @param method method placement
* @param sfmt input random number generator
* @param positions output vector of positions
*
* @return nonzero if error detected; 0 otherwise
*/
int setPositions( GenerationMethod method, OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& positions ) const;
/**
* Place particles on a grid
*
* @param origin origin
* @param boxDimensions box dimensions
* @param spacing spacing
* @param sfmt input random number generator
* @param array output vector of grid values
*
* @return -1 if particles will not fit on grid; 0 if they do
*/
int setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing,
OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& array ) const;
/**
* Set bond distance
*
* @param bondDistance bond distance
*/
void setBondDistance( double bondDistance );
/**
* Get bond distance
*
* @return bond distance
*/
double getBondDistance( void ) const;
/**
* Get distance
*
* @param index1 index of first particle
* @param index2 index of second particle
* @param positions particle positions
*
* @return distance
*/
double getDistance( int index1, int index2, const std::vector<Vec3>& positions ) const;
/**
* Get distance assumming periodic boundary conditions
*
* @param index1 index of first particle
* @param index2 index of second particle
* @param positions particle positions
*
* @return distance
*/
double getPeriodicDistance( int index1, int index2, const std::vector<Vec3>& positions ) const;
/**
* Get settings
*
* @return info string
*/
std::string getSettings( void ) const;
/**
* Get enclosing box
*
* @param positions input vector of positions
* @param enclosingBox output vector of enclosing box dimensions
*
*/
void getEnclosingBox( const std::vector<Vec3>& positions, Vec3 enclosingBox[2] ) const;
/**
* Get sorted distances from particular position
*
* @param periodicBoundaryConditions if set, apply PBC
* @param positionIndex input position index
* @param positions input vector of positions
* @param sortVector on output sorted IntDoublePairVector
*
*/
void getSortedDistances( int periodicBoundaryConditions, int positionIndex, const std::vector<Vec3>& positions, IntDoublePairVector& sortVector ) const;
private:
int _numMolecules;
int _numParticlesPerMolecule;
int _numParticles;
int _seed;
double _boxSize;
double _bondDistance;
Vec3 _origin;
Vec3 _boxDimensions;
Vec3 _spacing;
FILE* _log;
};
PositionGenerator::PositionGenerator( int numMolecules, int numParticlesPerMolecule, double boxSize ) :
_numMolecules(numMolecules),
_seed(0),
_log(NULL),
_bondDistance(0.1),
_numParticlesPerMolecule(numParticlesPerMolecule),
_numParticles(numMolecules*numParticlesPerMolecule),
_boxSize(boxSize),
_boxDimensions(Vec3(boxSize,boxSize,boxSize)),
_origin(Vec3(0.0,0.0,0.0)) {
double particlesPerDimension = pow( static_cast<double>(_numParticles), (1.0/3.0) );
int particlesPerDimensionI = static_cast<int>(particlesPerDimension+0.999999);
double spacingPerDimension = _boxSize/particlesPerDimension;
_spacing[0] = spacingPerDimension;
_spacing[1] = spacingPerDimension;
_spacing[2] = spacingPerDimension;
}
PositionGenerator::~PositionGenerator( ){};
void PositionGenerator::setBondDistance( double bondDistance ){
_bondDistance = bondDistance;
}
void PositionGenerator::setLog( FILE* log ){
_log = log;
}
double PositionGenerator::getBondDistance( void ) const {
return _bondDistance;
}
double PositionGenerator::getDistance( int index1, int index2, const std::vector<Vec3>& positions ) const {
Vec3 delta = positions[index2] - positions[index1];
return sqrt( delta.dot( delta ) );
}
double PositionGenerator::getPeriodicDistance( int index1, int index2, const std::vector<Vec3>& positions ) const {
Vec3 delta = positions[index2] - positions[index1];
if( _boxSize > 0.0 ){
delta[0] -= floor(delta[0]/_boxSize+0.5f)*_boxSize;
delta[1] -= floor(delta[1]/_boxSize+0.5f)*_boxSize;
delta[2] -= floor(delta[2]/_boxSize+0.5f)*_boxSize;
}
return sqrt( delta.dot( delta ) );
}
/**
* Get positions
*
* @param method method placement
* @param positions output vector of positions
*
* @return nonzero if error detected; 0 otherwise
*/
int PositionGenerator::setPositions( GenerationMethod method, std::vector<Vec3>& positions ) const {
OpenMM_SFMT::SFMT sfmt;
init_gen_rand( _seed, sfmt);
return setPositions( method, sfmt, positions );
}
/**
* Get settings
*
* @return info string
*/
std::string PositionGenerator::getSettings( void ) const {
std::stringstream msg;
msg << "numMolecules " << _numMolecules << std::endl;
msg << "numParticlesPerMolecule " << _numParticlesPerMolecule << std::endl;
msg << "boxSize " << _boxSize << std::endl;
msg << "spacing " << _spacing[0] << std::endl;
msg << "seed " << _seed << std::endl;
return msg.str();
}
/**
* Get positions
*
* @param method method placement
* @param sfmt input random number generator
* @param positions output vector of positions
*
* @return nonzero if error detected; 0 otherwise
*/
int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& positions ) const {
int errorFlag = 0;
positions.resize( _numParticles );
if( method == Random ){
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
positions[ii] = Vec3(_boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt));
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++) {
positions[ii+jj] = positions[ii] + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
}
}
} else if( method == SimpleGrid ){
Vec3 origin, boxDimensions, spacing;
std::stringstream msg;
if( _numParticlesPerMolecule > 1 && _bondDistance > 0.0 ){
origin = Vec3(_bondDistance, _bondDistance, _bondDistance );
double particlesPerDimension = pow( static_cast<double>(_numParticles), (1.0/3.0) );
int particlesPerDimensionI = static_cast<int>(particlesPerDimension+0.999999);
double boxSize = (_boxSize-2.0*_bondDistance);
double spacingPerDimension = boxSize/particlesPerDimension;
spacing = Vec3(spacingPerDimension, spacingPerDimension, spacingPerDimension );
boxDimensions = Vec3(boxSize, boxSize, boxSize );
msg << "Bond distance " << _bondDistance << std::endl;
msg << "particlesPerDimension " << particlesPerDimension << std::endl;
msg << "boxSize " << boxSize << std::endl;
msg << "spacingPerDimension " << spacingPerDimension << std::endl;
} else {
origin = _origin;
spacing = _spacing;
boxDimensions = _boxDimensions;
}
msg << getSettings() << std::endl;
if( _log ){
(void) fprintf( _log, "SimpleGrid %s\n", msg.str().c_str() );
}
errorFlag = setParticlesOnGrid( origin, boxDimensions, spacing, sfmt, positions );
}
return errorFlag;
}
/**
* Place particles on a grid
*
* @param origin origin
* @param boxDimensions box dimensions
* @param spacing spacing
* @param array output vector of grid values
*
* @return -1 if particles will not fit on grid; 0 if they do
*/
int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing, OpenMM_SFMT::SFMT& sfmt,
std::vector<Vec3>& array ) const {
Vec3 start(origin);
if( array.size() != _numParticles ){
std::stringstream msg;
msg << "PositionGenerator::setParticlesOnGrid position vector size=" << array.size() << " != numParticles=" << _numParticles;
msg << getSettings();
throw OpenMMException( msg.str() );
}
// place molecule centers on grid
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
array[ii] = Vec3(start);
bool done = false;
for( unsigned int jj = 0; jj < 3 && !done; jj++ ){
start[jj] += spacing[jj];
if( start[jj] > boxDimensions[jj] ){
start[jj] = origin[jj];
} else {
done = true;
}
}
if( !done ){
std::stringstream msg;
msg << "PositionGenerator::setParticlesOnGrid error in grid settings";
throw OpenMMException( msg.str() );
}
}
// add molecule atoms
Vec3 bondOffset( 0.05, 0.05, 0.05 );
for( unsigned int ii = 0; ii < _numMolecules; ii++ ){
int molecularIndex = ii*_numParticlesPerMolecule;
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++ ){
array[molecularIndex+jj] = array[molecularIndex] + bondOffset + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
}
}
return 0;
}
/**
* Get enclosing box
*
* @param positions input vector of positions
* @param enclosingBox output Vec3[2] of minimum enclosing box ranges
*
*/
void PositionGenerator::getEnclosingBox( const std::vector<Vec3>& positions, Vec3 enclosingBox[2] ) const {
enclosingBox[0][0] = enclosingBox[1][0] = positions[0][0];
enclosingBox[0][1] = enclosingBox[1][1] = positions[0][1];
enclosingBox[0][2] = enclosingBox[1][2] = positions[0][2];
for( unsigned int ii = 1; ii < positions.size(); ii++ ){
if( enclosingBox[0][0] > positions[ii][0] ){
enclosingBox[0][0] = positions[ii][0];
}
if( enclosingBox[1][0] < positions[ii][0] ){
enclosingBox[1][0] = positions[ii][0];
}
if( enclosingBox[0][1] > positions[ii][1] ){
enclosingBox[0][1] = positions[ii][1];
}
if( enclosingBox[1][1] < positions[ii][1] ){
enclosingBox[1][1] = positions[ii][1];
}
if( enclosingBox[0][2] > positions[ii][2] ){
enclosingBox[0][2] = positions[ii][2];
}
if( enclosingBox[1][2] < positions[ii][2] ){
enclosingBox[1][2] = positions[ii][2];
}
}
return;
}
/**
* Predicate for sorting <int,double> pair
*
* @param d1 first IntDoublePair to compare
* @param d2 second IntDoublePair to compare
*
*/
bool TestIntDoublePair( const IntDoublePair& d1, const IntDoublePair& d2 ){
return d1.second < d2.second;
}
/**
* Get sorted distances from particular position
*
* @param periodicBoundaryConditions if set, apply PBC
* @param positionIndex input position index
* @param positions input vector of positions
* @param sortVector on output sorted IntDoublePairVector
*
*/
void PositionGenerator::getSortedDistances( int periodicBoundaryConditions, int positionIndex, const std::vector<Vec3>& positions,
IntDoublePairVector& sortVector ) const {
sortVector.resize( 0 );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
if( ii == positionIndex )continue;
double distance = periodicBoundaryConditions ? getPeriodicDistance( positionIndex, ii, positions) : getDistance( positionIndex, ii, positions);
sortVector.push_back( IntDoublePair(ii,sqrt(distance) ) );
}
std::sort( sortVector.begin(), sortVector.end(), TestIntDoublePair );
return;
}
/**---------------------------------------------------------------------------------------
*
* Set string field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setStringFromMap( MapStringString& argumentMap, std::string fieldToCheck, std::string& fieldToSet ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "setStringFromMap";
// ---------------------------------------------------------------------------------------
MapStringStringCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = (*check).second;
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Set int field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setIntFromMap( MapStringString& argumentMap, std::string fieldToCheck, int& fieldToSet ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "setIntFromMap";
// ---------------------------------------------------------------------------------------
MapStringStringCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = atoi( (*check).second.c_str() );
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Set int field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setIntFromMapStringToDouble( MapStringToDouble& argumentMap, std::string fieldToCheck, int& fieldToSet ){
// ---------------------------------------------------------------------------------------
MapStringToDoubleCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = static_cast<int>(check->second+0.0000001);
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
* Set float field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setFloatFromMap( MapStringString& argumentMap, std::string fieldToCheck, float& fieldToSet ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "setFloatFromMap";
// ---------------------------------------------------------------------------------------
MapStringStringCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = static_cast<float>(atof( (*check).second.c_str() ));
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Set double field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setDoubleFromMap( MapStringString& argumentMap, std::string fieldToCheck, double& fieldToSet ){
// ---------------------------------------------------------------------------------------
MapStringStringCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = atof( (*check).second.c_str() );
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Set double field if in map
*
* @param argumentMap map to check
* @param fieldToCheck key
* @param fieldToSet field to set
*
* @return 1 if argument set, else 0
*
--------------------------------------------------------------------------------------- */
static int setDoubleFromMapStringToDouble( MapStringToDouble& argumentMap, std::string fieldToCheck, double& fieldToSet ){
// ---------------------------------------------------------------------------------------
MapStringToDoubleCI check = argumentMap.find( fieldToCheck );
if( check != argumentMap.end() ){
fieldToSet = check->second;
return 1;
}
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Compare forces from two states
*
* @param state1 state1
* @param state2 state2
* @param relativeTolerance relative tolerance
* @param log if set, output forces
*
* @return number of entries with relative difference > tolerance
*
--------------------------------------------------------------------------------------- */
int compareForcesOfTwoStates( State& state1, State& state2, double relativeTolerance,
DoubleVector& stats, FILE* log ) {
int error = 0;
vector<Vec3> force1 = state1.getForces();
vector<Vec3> force2 = state2.getForces();
double maxRelativeDifference = -1.0e+30;
double maxRelativeDifferenceIndex = -1.0;
double averageRelativeDifference = 0.0;
double count = 0.0;
DoubleVector medians1( force1.size() );
DoubleVector medians2( force1.size() );
for( unsigned int ii = 0; ii < force1.size(); ii++ ){
Vec3 f1 = force1[ii];
Vec3 f2 = force2[ii];
double diff = (f1[0] - f2[0])*(f1[0] - f2[0]) +
(f1[1] - f2[1])*(f1[1] - f2[1]) +
(f1[2] - f2[2])*(f1[2] - f2[2]);
double denom1 = sqrt( f1[0]*f1[0] + f1[1]*f1[1] + f1[2]*f1[2] );
double denom2 = sqrt( f2[0]*f2[0] + f2[1]*f2[1] + f2[2]*f2[2] );
medians1[ii] = denom1;
medians2[ii] = denom2;
double relativeDiff;
if( denom1 > 0.0 || denom2 > 0.0 ){
relativeDiff = 2.0*sqrt( diff )/(denom1+denom2);
} else {
relativeDiff = 0.0;
}
if( relativeDiff > maxRelativeDifference ){
maxRelativeDifference = relativeDiff;
maxRelativeDifferenceIndex = static_cast<double>(ii);
}
averageRelativeDifference += relativeDiff;
count += 1.0;
if( relativeDiff > relativeTolerance ){
error++;
}
if( log ){
(void) fprintf( log, "F %6u %15.7e [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e] %15.7e %15.7e %s\n", static_cast<unsigned int>(ii),
relativeDiff, f1[0], f1[1], f1[2], f2[0], f2[1], f2[2], denom1, denom2, (relativeDiff < relativeTolerance ? "":"XXXXXX") );
}
}
if( count > 0.0 ){
averageRelativeDifference /= count;
}
std::sort( medians1.begin(), medians1.end() );
std::sort( medians2.begin(), medians2.end() );
double median1 = medians1[medians1.size()/2];
double median2 = medians2[medians2.size()/2];
stats.resize( 4 );
stats[0] = averageRelativeDifference;
stats[1] = maxRelativeDifference;
stats[2] = maxRelativeDifferenceIndex;
stats[3] = median1 < median2 ? median1 : median2;
return error;
}
/**
* Get forces in system
*
* @param system system to serialize
* @param stringForceVector output stringForceVector[forceName] = force index
* @param log logging file (optional -- may be NULL)
*
*/
static void getStringForceMap( System& system, MapStringInt& stringForceVector, FILE* log ){
// print active forces and relevant parameters
for( int ii = 0; ii < system.getNumForces(); ii++ ) {
int hit = 0;
Force& force = system.getForce(ii);
if( !hit ){
try {
CMAPTorsionForce& castForce = dynamic_cast<CMAPTorsionForce&>(force);
stringForceVector["CMAPTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomAngleForce& castForce = dynamic_cast<CustomAngleForce&>(force);
stringForceVector["CustomAngle"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomBondForce& castForce = dynamic_cast<CustomBondForce&>(force);
stringForceVector["CustomBond"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomExternalForce& castForce = dynamic_cast<CustomExternalForce&>(force);
stringForceVector["CustomExternal"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomGBForce& castForce = dynamic_cast<CustomGBForce&>(force);
stringForceVector["CustomGB"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomHbondForce& castForce = dynamic_cast<CustomHbondForce&>(force);
stringForceVector["CustomHbond"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomNonbondedForce& castForce = dynamic_cast<CustomNonbondedForce&>(force);
stringForceVector["CustomNonbonded"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
CustomTorsionForce& castForce = dynamic_cast<CustomTorsionForce&>(force);
stringForceVector["CustomTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
GBSAOBCForce& castForce = dynamic_cast<GBSAOBCForce&>(force);
stringForceVector["GBSAOBC"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
GBVIForce& castForce = dynamic_cast<GBVIForce&>(force);
stringForceVector["GBVI"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
HarmonicAngleForce& castForce = dynamic_cast<HarmonicAngleForce&>(force);
stringForceVector["HarmonicAngle"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
HarmonicBondForce& castForce = dynamic_cast<HarmonicBondForce&>(force);
stringForceVector["HarmonicBond"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
NonbondedForce& castForce = dynamic_cast<NonbondedForce&>(force);
stringForceVector["Nonbonded"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
PeriodicTorsionForce& castForce = dynamic_cast<PeriodicTorsionForce&>(force);
stringForceVector["PeriodicTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
RBTorsionForce& castForce = dynamic_cast<RBTorsionForce&>(force);
stringForceVector["RBTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
MonteCarloBarostat& castForce = dynamic_cast<MonteCarloBarostat&>(force);
stringForceVector["MonteCarloBarostat"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AndersenThermostat& castForce = dynamic_cast<AndersenThermostat&>(force);
stringForceVector["AndersenThermostat"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
#ifdef USE_SOFTCORE
if( !hit ){
try {
GBSAOBCSoftcoreForce& castForce = dynamic_cast<GBSAOBCSoftcoreForce&>(force);
stringForceVector["GBSAOBCSoftcore"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
GBVISoftcoreForce& castForce = dynamic_cast<GBVISoftcoreForce&>(force);
stringForceVector["GBVISoftcore"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
NonbondedSoftcoreForce& castForce = dynamic_cast<NonbondedSoftcoreForce&>(force);
stringForceVector["NonbondedSoftcore"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
#endif
#ifdef INCLUDE_AMOEBA_FORCES
if( !hit ){
try {
AmoebaHarmonicBondForce& castForce = dynamic_cast<AmoebaHarmonicBondForce&>(force);
stringForceVector["AmoebaHarmonicBond"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaHarmonicAngleForce& castForce = dynamic_cast<AmoebaHarmonicAngleForce&>(force);
stringForceVector["AmoebaHarmonicAngle"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaHarmonicInPlaneAngleForce& castForce = dynamic_cast<AmoebaHarmonicInPlaneAngleForce&>(force);
stringForceVector["AmoebaHarmonicInPlaneAngle"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaMultipoleForce& castForce = dynamic_cast<AmoebaMultipoleForce&>(force);
stringForceVector["AmoebaMultipole"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaOutOfPlaneBendForce& castForce = dynamic_cast<AmoebaOutOfPlaneBendForce&>(force);
stringForceVector["AmoebaOutOfPlaneBend"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaPiTorsionForce& castForce = dynamic_cast<AmoebaPiTorsionForce&>(force);
stringForceVector["AmoebaPiTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaStretchBendForce& castForce = dynamic_cast<AmoebaStretchBendForce&>(force);
stringForceVector["AmoebaStretchBend"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaTorsionForce& castForce = dynamic_cast<AmoebaTorsionForce&>(force);
stringForceVector["AmoebaTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaTorsionTorsionForce& castForce = dynamic_cast<AmoebaTorsionTorsionForce&>(force);
stringForceVector["AmoebaTorsionTorsion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaUreyBradleyForce& castForce = dynamic_cast<AmoebaUreyBradleyForce&>(force);
stringForceVector["AmoebaUreyBradley"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaVdwForce& castForce = dynamic_cast<AmoebaVdwForce&>(force);
stringForceVector["AmoebaVdw"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaWcaDispersionForce& castForce = dynamic_cast<AmoebaWcaDispersionForce&>(force);
stringForceVector["AmoebaWcaDispersion"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaGeneralizedKirkwoodForce& castForce = dynamic_cast<AmoebaGeneralizedKirkwoodForce&>(force);
stringForceVector["AmoebaGeneralizedKirkwood"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
try {
AmoebaTorsionTorsionForce& castForce = dynamic_cast<AmoebaTorsionTorsionForce&>(force);
stringForceVector["AmoebaTorsionTorsionForce"] = ii;
hit++;
} catch( std::bad_cast ){
}
}
#endif
// COM
if( !hit ){
try {
CMMotionRemover& cMMotionRemover = dynamic_cast<CMMotionRemover&>(force);
hit++;
} catch( std::bad_cast ){
}
}
if( !hit && log ){
(void) fprintf( log, " entry=%2d force not recognized.\n", ii );
}
}
}
/**---------------------------------------------------------------------------------------
*
* Copy NonbondedSoftcoreForce
*
* @param nonbondedSoftcoreForce NonbondedSoftcoreForce to copy
*
* @return copy of nonbondedSoftcoreForce
*
--------------------------------------------------------------------------------------- */
static NonbondedSoftcoreForce* copyNonbondedSoftcoreForce( const NonbondedSoftcoreForce& nonbondedSoftcoreForce ){
NonbondedSoftcoreForce* copyNonbondedSoftcoreForce = new NonbondedSoftcoreForce( nonbondedSoftcoreForce );
/*
copyNonbondedSoftcoreForce->setNonbondedMethod( nonbondedSoftcoreForce.getNonbondedMethod() );
copyNonbondedSoftcoreForce->setCutoffDistance( nonbondedSoftcoreForce.getCutoffDistance() );
copyNonbondedSoftcoreForce->setReactionFieldDielectric( nonbondedSoftcoreForce.getReactionFieldDielectric() );
// particle parameters
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getParticleParameters(ii, charge, sigma, epsilon, softcoreLJLambda);
copyNonbondedSoftcoreForce->addParticle( charge, sigma, epsilon, softcoreLJLambda);
}
// exceptions
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
copyNonbondedSoftcoreForce->addException( particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
}
*/
return copyNonbondedSoftcoreForce;
}
/**---------------------------------------------------------------------------------------
*
* Copy NonbondedForce
*
* @param nonbondedForce NonbondedForce to copy
*
* @return copy of nonbondedForce
*
--------------------------------------------------------------------------------------- */
static NonbondedForce* copyNonbondedForce( const NonbondedForce& nonbondedForce ){
NonbondedForce* copyNonbondedForce = new NonbondedForce( nonbondedForce );
/*
copyNonbondedForce->setNonbondedMethod( nonbondedForce.getNonbondedMethod() );
copyNonbondedForce->setCutoffDistance( nonbondedForce.getCutoffDistance() );
copyNonbondedForce->setReactionFieldDielectric( nonbondedForce.getReactionFieldDielectric() );
// particle parameters
for( unsigned int ii = 0; ii < nonbondedForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedForce.getParticleParameters(ii, charge, sigma, epsilon, softcoreLJLambda);
copyNonbondedForce->addParticle( charge, sigma, epsilon, softcoreLJLambda);
}
// exceptions
for( unsigned int ii = 0; ii < nonbondedForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
copyNonbondedForce->addException( particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
}
*/
return copyNonbondedForce;
}
/**
* Return copy of system (but not forces)
*
* @param inputSystem system to copy
*
* @return system copy
*
*/
static System* copySystem( const System& inputSystem ){
System* systemCopy = new System();
for( unsigned int ii = 0; ii < inputSystem.getNumParticles(); ii++ ){
systemCopy->addParticle( inputSystem.getParticleMass( static_cast<int>(ii) ) );
}
Vec3 a;
Vec3 b;
Vec3 c;
inputSystem.getDefaultPeriodicBoxVectors( a, b, c );
systemCopy->setDefaultPeriodicBoxVectors( a, b, c );
for( unsigned int ii = 0; ii < inputSystem.getNumConstraints(); ii++ ){
int index;
int particle1, particle2;
double distance;
inputSystem.getConstraintParameters( ii, particle1, particle2, distance);
systemCopy->addConstraint( particle1, particle2, distance);
}
return systemCopy;
}
/**
* Randomize parameters
*
* @param parametersLowerBound vector of parameter lower bounds
* @param parametersUpperBound vector of parameter upper bounds
* @param sfmt SFMT random number generator
* @param parameters output vector of randomized parameter values
*
*/
static void randomizeParameters( const std::vector<double>& parametersLowerBound,
const std::vector<double>& parametersUpperBound,
OpenMM_SFMT::SFMT& sfmt, std::vector<double>& parameters ){
if( parametersLowerBound.size() != parametersUpperBound.size() ){
std::stringstream msg;
msg << " randomizeParameters parametersLowerBound size=" << parametersLowerBound.size() << " != parametersUpperBound size=" << parametersUpperBound.size();
throw OpenMMException( msg.str() );
}
if( parametersLowerBound.size() != parameters.size() ){
std::stringstream msg;
msg << " randomizeParameters parametersLowerBound size=" << parametersLowerBound.size() << " != parameter size=" << parameters.size();
throw OpenMMException( msg.str() );
}
for( unsigned int ii = 0; ii < parametersLowerBound.size(); ii++ ){
parameters[ii] = parametersLowerBound[ii] + (parametersUpperBound[ii] - parametersLowerBound[ii])*(genrand_real2(sfmt));
}
return;
}
/**
* Randomize Vec3 vector
*
* @param average mean value
* @param range +/- range
* @param sfmt SFMT random number generator
* @param array output vector of randomized values
*
*/
static void randomizeVec3( double average, double range,
OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& array ){
range *= 2.0;
for( unsigned int ii = 0; ii < array.size(); ii++ ){
array[ii] = Vec3( average + range*(genrand_real2(sfmt) - 0.5),
average + range*(genrand_real2(sfmt) - 0.5),
average + range*(genrand_real2(sfmt) - 0.5) );
}
return;
}
/**
* Output contents of MapStringString
*
* @param inputArgumentMap map to output
* @param outputStream output stream
*
*/
static void streamArgumentMap( const MapStringString& inputArgumentMap, std::stringstream& outputStream ){
char buffer[2048];
for( MapStringStringCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){
std::string key = ii->first;
std::string value = ii->second;
(void) sprintf( buffer, " %30s %40s\n", key.c_str(), value.c_str() );
outputStream << buffer;
}
return;
}
/**
* Format argument/value
*
* @param buffer formatted output
* @param key argument name
* @param value argument value
* @param format format string
* @param call if call > 0, skip key name
* @param type type == 0, then use int value; else double
*
*/
static void formatArgument( char* buffer, const std::string& key, double value, const char* format, int call, int type ){
// if call > 0, skip key name
unsigned int index = 0;
while( index < key.size() ){
buffer[index] = call ? ' ' : key[index];
index++;
}
// add blank
buffer[index++] = ' ';
buffer[index] = static_cast<char>(NULL);
if( type == 0 ){
int valueInt = static_cast<int>(value+0.00001);
(void) sprintf( buffer + index, format, valueInt );
} else {
(void) sprintf( buffer + index, format, value );
}
return;
}
/**
* Output contents of MapStringString w/ all argument on one line
*
* @param inputArgumentMap map to output
* @param exclude map of keys to exclude from output
* @param outputStream output stream
*
*/
static void streamArgumentMapOneLine( const MapStringToDouble& inputArgumentMap, const MapStringToInt& exclude,
const StringVector& printFirst, int callId, std::stringstream& outputStream ){
char buffer[2048];
MapStringToInt excludeAll(exclude);
for( unsigned int ii = 0; ii < printFirst.size(); ii++ ){
MapStringToDoubleCI iter = inputArgumentMap.find( printFirst[ii] );
if( iter != inputArgumentMap.end() ){
std::string key = iter->first;
if( exclude.find( key ) == exclude.end() ){
double value = iter->second;
if( key == "numMolecules" ){
formatArgument( buffer, key, value, "%6d ", callId, 0 );
} else if( key == "nonbondedMethod" ){
formatArgument( buffer, key, value, "%1d ", callId, 0 );
} else if( key == "lambda1" || key == "lambda2" ){
formatArgument( buffer, key, value, "%4.2f ", callId, 1 );
} else if( key == "boxSize" ){
formatArgument( buffer, key, value, "%6.2f ", callId, 1 );
} else {
formatArgument( buffer, key, value, "%15.7e ", callId, 1 );
}
outputStream << buffer;
excludeAll[key] = 1;
}
}
}
for( MapStringToDoubleCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){
std::string key = ii->first;
if( excludeAll.find( key ) == excludeAll.end() ){
double value = ii->second;
int valueInt = static_cast<int>(value+0.00001);
double valueDouble = static_cast<double>(valueInt);
if( key == "numMolecules" ){
(void) sprintf( buffer, "%s=%6d ", key.c_str(), valueInt );
} else if( key == "nonbondedMethod" ){
(void) sprintf( buffer, "%s=%1d ", key.c_str(), valueInt );
} else if( key == "lambda1" || key == "lambda2" ){
(void) sprintf( buffer, "%s=%4.2f ", key.c_str(), value );
} else if( key == "boxSize" ){
(void) sprintf( buffer, "%s=%6.2f ", key.c_str(), value );
} else if( valueDouble == value ){
(void) sprintf( buffer, "%s=%6d ", key.c_str(), valueInt );
} else {
(void) sprintf( buffer, "%s=%15.7e ", key.c_str(), value );
}
outputStream << buffer;
}
}
outputStream << std::endl;
return;
}
/**
* Get signature of a MapStringToDouble object
*
* @param inputArgumentMap map
* @return signature
*
*/
static double getMapStringToDoubleSignature( const MapStringToDouble& inputArgumentMap ){
double signature = 0.0;
double offset = 0.1;
for( MapStringToDoubleCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){
signature += (offset + ii->second);
offset += 0.1;
}
return signature;
}
/**
* Compare two MapStringToDouble to see if they have the same (key,value) pairs
*
* @param inputArgumentMap1 map 1
* @param inputArgumentMap2 map 2
*
* @return true if maps have same (key,value) pairs; otherwise false
*
*/
static bool compareMapStringToDoubles( const MapStringToDouble& inputArgumentMap1, const MapStringToDouble& inputArgumentMap2 ){
if( inputArgumentMap1.size() != inputArgumentMap1.size() ){
return false;
}
for( MapStringToDoubleCI ii = inputArgumentMap1.begin(); ii != inputArgumentMap1.end(); ii++ ){
MapStringToDoubleCI jj = inputArgumentMap2.find( (*ii).first );
if( jj == inputArgumentMap2.end() || jj->second != ii->second ){
return false;
}
}
return true;
}
/**
* Generate collection of inputArguments maps given
* list of DoubleVectors for each argument
*
* @param inputArguments map[argumentKey] = vector of double parameter values
* @param argumentMaps output vector of generated maps
*
*/
static void generateInputArgumentMapsFromStringVectors( const MapStringToDoubleVector& inputArguments,
VectorOfMapStringToDouble& argumentMaps ){
for( MapStringToDoubleVectorCI ii = inputArguments.begin(); ii != inputArguments.end(); ii++ ){
std::string argumentName = (*ii).first;
DoubleVector arguments = (*ii).second;
unsigned int initialArgumentMapSize = argumentMaps.size();
// generate signature map for each argument map
MapDoubleToInt signatures;
for( unsigned int kk = 0; kk < initialArgumentMapSize; kk++ ){
double signature = getMapStringToDoubleSignature( argumentMaps[kk] );
signatures[signature] = 1;
}
// for each current argumment map, add a new argument map w/ (key,value)
// check that no existing map has the same arguments before adding to the
// vector of argument maps
for( unsigned int kk = 0; kk < initialArgumentMapSize; kk++ ){
for( unsigned int jj = 0; jj < arguments.size(); jj++ ){
MapStringToDouble inputArgumentMap = MapStringToDouble(argumentMaps[kk]);
inputArgumentMap[argumentName] = arguments[jj];
double signature = getMapStringToDoubleSignature( inputArgumentMap );
if( signatures.find( signature ) == signatures.end() ){
argumentMaps.push_back( inputArgumentMap );
} else {
bool match = 0;
for( unsigned int mm = 0; mm < initialArgumentMapSize && !match; mm++ ){
match = compareMapStringToDoubles( inputArgumentMap, argumentMaps[mm] );
}
if( !match ){
argumentMaps.push_back( inputArgumentMap );
}
}
}
}
}
return;
}
/**
* Predicate for sorting map[string] = double
*
* @param d1 first MapStringToDouble to compare
* @param d2 second MapStringToDouble to compare
*
*/
bool TestMapSortPredicate( const MapStringToDouble& d1, const MapStringToDouble& d2 ){
StringVector sortOrder;
sortOrder.push_back( "numMolecules" );
sortOrder.push_back( "nonbondedMethod" );
sortOrder.push_back( "lambda2" );
sortOrder.push_back( "boxSize" );
for( unsigned int ii = 0; ii < sortOrder.size(); ii++ ){
if( d1.find( sortOrder[ii] ) != d1.end() &&
d2.find( sortOrder[ii] ) != d2.end() ){
MapStringToDoubleCI d1i = d1.find( sortOrder[ii] );
MapStringToDoubleCI d2i = d2.find( sortOrder[ii] );
if( d1i->second != d2i->second ){
return d1i->second < d2i->second;
}
}
}
return false;
}
static CustomNonbondedForce* buildCustomNonbondedSoftcoreForce( const NonbondedSoftcoreForce& nonbondedSoftcoreForce ){
CustomNonbondedForce* customNonbonded;
if( nonbondedSoftcoreForce.getNonbondedMethod() == NoCutoff ){
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customNonbonded->setNonbondedMethod( CustomNonbondedForce::NoCutoff );
} else {
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf);"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customNonbonded->setCutoffDistance( nonbondedSoftcoreForce.getCutoffDistance() );
if( nonbondedSoftcoreForce.getNonbondedMethod() == CutoffNonPeriodic ){
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffNonPeriodic );
} else {
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffPeriodic );
}
double cutoffDistance = nonbondedSoftcoreForce.getCutoffDistance();
double reactionFieldDielectric = nonbondedSoftcoreForce.getReactionFieldDielectric();
double eps2 = (reactionFieldDielectric - 1.0)/(2.0*reactionFieldDielectric+1.0);
double kValue = eps2/(cutoffDistance*cutoffDistance*cutoffDistance);
customNonbonded->addGlobalParameter("krf", kValue );
double cValue = (1.0/cutoffDistance)*(3.0*reactionFieldDielectric)/(2.0*reactionFieldDielectric + 1.0);
customNonbonded->addGlobalParameter("crf", cValue );
}
customNonbonded->addPerParticleParameter("q");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
customNonbonded->addPerParticleParameter("lambda");
vector<double> nonbondedParams(4);
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getParticleParameters(ii, charge, sigma, epsilon, softcoreLJLambda);
nonbondedParams[0] = charge;
nonbondedParams[1] = sigma;
nonbondedParams[2] = epsilon;
nonbondedParams[3] = softcoreLJLambda;
customNonbonded->addParticle( nonbondedParams );
}
return customNonbonded;
}
CustomBondForce* buildCustomBondForceForNonbondedExceptions( const NonbondedSoftcoreForce& nonbondedSoftcoreForce ){
CustomBondForce* customBond;
if( nonbondedSoftcoreForce.getNonbondedMethod() == NoCutoff ){
customBond = new CustomBondForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
} else {
customBond = new CustomBondForce("withinCutoff*(lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf));"
"withinCutoff=step(cutoff-r);"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
double cutoffDistance = nonbondedSoftcoreForce.getCutoffDistance();
double reactionFieldDielectric = nonbondedSoftcoreForce.getReactionFieldDielectric();
double eps2 = (reactionFieldDielectric - 1.0)/(2.0*reactionFieldDielectric+1.0);
double kValue = eps2/(cutoffDistance*cutoffDistance*cutoffDistance);
customBond->addGlobalParameter("krf", kValue );
double cValue = (1.0/cutoffDistance)*(3.0*reactionFieldDielectric)/(2.0*reactionFieldDielectric + 1.0);
customBond->addGlobalParameter("crf", cValue );
customBond->addGlobalParameter("cutoff", cutoffDistance );
}
customBond->addPerBondParameter("q");
customBond->addPerBondParameter("sigma");
customBond->addPerBondParameter("eps");
customBond->addPerBondParameter("lambda");
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
vector<double> bondParams(4);
bondParams[0] = chargeProd;
bondParams[1] = sigma;
bondParams[2] = epsilon;
bondParams[3] = softcoreLJLambda;
customBond->addBond( particle1, particle2, bondParams );
}
return customBond;
}
/**
* Perform comparison of energies/forces for two systems
*
* @param system1 first system
* @param system2 second system
* @param platform1 first platform name (Reference, Cuda, OpenCL)
* @param platform2 second platform name (Reference, Cuda, OpenCL)
* @param positions positions
* @param inputArgumentMap arguments/flags (relativeTolerance, applyAssert, ...)
* @param idString id string
* @param log logging file (optional -- may be NULL)
*
*/
void runSystemComparisonTest( System& system1, System& system2,
const std::string& platform1, const std::string& platform2,
const std::vector<Vec3>& positions, MapStringToDouble& inputArgumentMap,
const std::string& idString, FILE* log ){
int applyAssert = 0;
double relativeTolerance = 1.0e-04;
setDoubleFromMapStringToDouble( inputArgumentMap, "relativeTolerance", relativeTolerance );
setIntFromMapStringToDouble( inputArgumentMap, "applyAssert", applyAssert ) ;
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
if( log ){
(void) fprintf( log, "System1: particles=%d forces=%d System2: particles=%d forces=%d\n",
system1.getNumParticles(), system1.getNumForces(),
system2.getNumParticles(), system2.getNumForces() );
(void) fprintf( log, "Positions=%u\n",
static_cast<unsigned int>(positions.size()) );
MapStringInt stringForceVector1;
MapStringInt stringForceVector2;
getStringForceMap( system1, stringForceVector1, log );
(void) fprintf( log, "Forces in system 1: [" );
for( MapStringIntCI ii = stringForceVector1.begin(); ii != stringForceVector1.end(); ii++ ){
(void) fprintf( log, " %s ", ii->first.c_str() );
}
getStringForceMap( system2, stringForceVector2, log );
(void) fprintf( log, "]\nForces in system 2: [" );
for( MapStringIntCI ii = stringForceVector2.begin(); ii != stringForceVector2.end(); ii++ ){
(void) fprintf( log, " %s ", ii->first.c_str() );
}
(void) fprintf( log, "]\n" );
}
if( system1.getNumParticles() != system2.getNumParticles() ){
std::stringstream msg;
msg << "Number of particles for systems to be compared are unequal: " << system1.getNumParticles() << " != " << system2.getNumParticles();
throw OpenMMException( msg.str() );
}
if( system1.getNumParticles() != static_cast<int>(positions.size()) ){
std::stringstream msg;
msg << "Number of partciles for system des not equal size of position array: " << system1.getNumParticles() << " != " << positions.size();
throw OpenMMException( msg.str() );
}
Context context1( system1, integrator1, Platform::getPlatformByName( platform1 ));
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2( system2, integrator2, Platform::getPlatformByName( "Reference"));
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
double energyDiff = 0.0;
if( fabs( state1.getPotentialEnergy() ) > 0.0 || fabs( state2.getPotentialEnergy()) > 0.0 ){
energyDiff = fabs( state1.getPotentialEnergy() - state2.getPotentialEnergy() )/( fabs( state1.getPotentialEnergy() ) + fabs( state2.getPotentialEnergy() ) );
}
if( log ){
DoubleVector stats;
compareForcesOfTwoStates( state1, state2, relativeTolerance, stats, log );
(void) fprintf( log, "%s %6d eDff=%15.7e fMx=%15.7e fAvg=%15.7e fMed=%15.7e eCd=%15.7e eRf=%15.7e mxFIdx=%d\n",
idString.c_str(), system1.getNumParticles(), energyDiff,
stats[1], stats[0], stats[3], state1.getPotentialEnergy(), state2.getPotentialEnergy(), static_cast<int>(stats[2]+0.0001));
(void) fflush( log );
}
if( applyAssert ){
ASSERT( energyDiff < relativeTolerance );
for( int ii = 0; ii < system1.getNumParticles(); ii++ ){
Vec3 f1 = state1.getForces()[ii];
Vec3 f2 = state2.getForces()[ii];
double f1N = sqrt( (f1[0]*f1[0]) + (f1[1]*f1[1]) + (f1[2]*f1[2]) );
double f2N = sqrt( (f2[0]*f2[0]) + (f2[1]*f2[1]) + (f2[2]*f2[2]) );
double diff = (f1[0]-f2[0])*(f1[0]-f2[0]) +
(f1[1]-f2[1])*(f1[1]-f2[1]) +
(f1[2]-f2[2])*(f1[2]-f2[2]);
if( f1N > 0.0 || f1N > 0.0 ){
diff = 2.0*sqrt( diff )/(f1N + f2N);
}
ASSERT( diff < relativeTolerance );
}
}
}
/**
* Serialize system
*
* @param system system to serialize
* @param serializeFileName file name for xml output
* @param log logging file (optional -- may be NULL)
*
*/
void serializeSystem( System& system, const std::string& serializeFileName, FILE* log ){
#ifdef OPENMM_SERIALIZE
//registerAmoebaSerializationProxies();
std::stringstream buffer;
XmlSerializer::serialize<System>(&system, "System", buffer);
FILE* filePtr = fopen( serializeFileName.c_str(), "w" );
if( filePtr == NULL ){
if( log ){
(void) fprintf( log, "Unable to open xml file %s\n", serializeFileName.c_str() );
return;
}
}
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
if( log ){
(void) fprintf( log, "Wrote system to xml file %s\n", serializeFileName.c_str() );
}
#endif
return;
}
/**
* Output vector of Vec3 to file
*
* @param positions system to serialize
* @param fileName file name for output
* @param log logging file (optional -- may be NULL)
*
*/
void serializeVectorOfVec3( const std::vector<Vec3>& positions, std::string fileName, FILE* log ){
#ifdef OPENMM_SERIALIZE
FILE* filePtr = fopen( fileName.c_str(), "w" );
if( filePtr == NULL ){
if( log ){
(void) fprintf( log, "Unable to open Vec3 file %s\n", fileName.c_str() );
return;
}
}
(void) fprintf( filePtr, "Positions %u\n", static_cast<unsigned int>(positions.size()) );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( filePtr, "%9u %17.10e %17.10e %17.10e\n", ii, positions[ii][0], positions[ii][1], positions[ii][2] );
}
(void) fclose( filePtr );
if( log ){
(void) fprintf( log, "Wrote to file %s\n", fileName.c_str() );
}
#endif
return;
}
/**
* Serialize system and positions
*
* @param system system to serialize
* @param positions positions to output
* @param baseFileName base file name for xml/txt output
* @param log logging file (optional -- may be NULL)
*
*/
void serializeSystemAndPositions( System& system, const std::vector<Vec3>& positions, const std::string& baseFileName, FILE* log ){
std::stringstream xmlfileName;
xmlfileName << baseFileName << ".xml";
serializeSystem( system, xmlfileName.str(), log );
std::stringstream posfileName;
posfileName << baseFileName << ".txt";
serializeVectorOfVec3( positions, posfileName.str(), log );
return;
}
#endif // TEST_CUDA_SOFTCORE_FORCE_H_
plugins/freeEnergy/platforms/cuda/tests/TstFreeEnergyCudaUsingParameterFile.cpp deleted 100644 → 0
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