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Commit f267c51a authored by Peter Eastman's avatar Peter Eastman
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Fixed bugs in GK force

parent c2461875
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Showing with 16 additions and 49 deletions
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.cpp
View file @ f267c51a
......@@ -1365,31 +1365,19 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
else {
cu.clearBuffer(*gkKernel->getInducedField());
cu.clearBuffer(*gkKernel->getInducedFieldPolar());
vector<float> d, dp;
gkKernel->getInducedDipoles()->download(d);
gkKernel->getInducedDipolesPolar()->download(dp);
printf("dipole\n");
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g %g %g, %g %g %g\n", i, d[3*i], d[3*i+1], d[3*i+2], dp[3*i], dp[3*i+1], dp[3*i+2]);
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices,
&gkKernel->getInducedField()->getDevicePointer(), &gkKernel->getInducedFieldPolar()->getDevicePointer(),
&gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(),
&gkKernel->getBornRadii()->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
vector<long long> f, fp;
gkKernel->getInducedField()->download(f);
gkKernel->getInducedFieldPolar()->download(fp);
printf("field\n");
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g %g %g, %g %g %g\n", i, f[i]/(double) 0xFFFFFFFF, f[i+cu.getPaddedNumAtoms()]/(double) 0xFFFFFFFF, f[i+2*cu.getPaddedNumAtoms()]/(double) 0xFFFFFFFF, fp[i]/(double) 0xFFFFFFFF, fp[i+cu.getPaddedNumAtoms()]/(double) 0xFFFFFFFF, fp[i+2*cu.getPaddedNumAtoms()]/(double) 0xFFFFFFFF);
void* updateInducedGkFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(),
&gkKernel->getField()->getDevicePointer(), &gkKernel->getFieldPolar()->getDevicePointer(), &gkKernel->getInducedField()->getDevicePointer(),
&gkKernel->getInducedFieldPolar()->getDevicePointer(), &gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(),
&polarizability->getDevicePointer(), &inducedDipoleErrors->getDevicePointer()};
&gkKernel->getField()->getDevicePointer(), &gkKernel->getInducedField()->getDevicePointer(),
&gkKernel->getInducedFieldPolar()->getDevicePointer(), &gkKernel->getInducedDipoles()->getDevicePointer(),
&gkKernel->getInducedDipolesPolar()->getDevicePointer(), &polarizability->getDevicePointer(), &inducedDipoleErrors->getDevicePointer()};
cu.executeKernel(updateInducedFieldKernel, updateInducedGkFieldArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize, cu.ThreadBlockSize, cu.ThreadBlockSize*elementSize*2);
}
void* updateInducedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &npt, &npt, &inducedField->getDevicePointer(),
void* updateInducedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &npt, &inducedField->getDevicePointer(),
&inducedFieldPolar->getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&polarizability->getDevicePointer(), &inducedDipoleErrors->getDevicePointer()};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize, cu.ThreadBlockSize, cu.ThreadBlockSize*elementSize*2);
......@@ -1517,7 +1505,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* pmeRecordInducedFieldDipolesArgs[] = {&pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.executeKernel(pmeRecordInducedFieldDipolesKernel, pmeRecordInducedFieldDipolesArgs, cu.getNumAtoms());
void* updateInducedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &npt, &npt, &inducedField->getDevicePointer(),
void* updateInducedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &npt, &inducedField->getDevicePointer(),
&inducedFieldPolar->getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&polarizability->getDevicePointer(), &inducedDipoleErrors->getDevicePointer()};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize, cu.ThreadBlockSize, cu.ThreadBlockSize*elementSize*2);
......@@ -1734,7 +1722,7 @@ private:
};
CudaCalcAmoebaGeneralizedKirkwoodForceKernel::CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaGeneralizedKirkwoodForceKernel(name, platform), cu(cu), system(system), params(NULL), bornRadii(NULL), field(NULL), fieldPolar(NULL),
CalcAmoebaGeneralizedKirkwoodForceKernel(name, platform), cu(cu), system(system), params(NULL), bornRadii(NULL), field(NULL),
inducedField(NULL), inducedFieldPolar(NULL), inducedDipoleS(NULL), inducedDipolePolarS(NULL), bornSum(NULL), bornForce(NULL) {
}
......@@ -1746,8 +1734,6 @@ CudaCalcAmoebaGeneralizedKirkwoodForceKernel::~CudaCalcAmoebaGeneralizedKirkwood
delete bornRadii;
if (field != NULL)
delete field;
if (fieldPolar != NULL)
delete fieldPolar;
if (inducedField != NULL)
delete inducedField;
if (inducedFieldPolar != NULL)
......@@ -1777,7 +1763,6 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
params = CudaArray::create<float2>(cu, paddedNumAtoms, "amoebaGkParams");
bornRadii = new CudaArray(cu, paddedNumAtoms, elementSize, "bornRadii");
field = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "gkField");
fieldPolar = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "gkFieldPolar");
bornSum = CudaArray::create<long long>(cu, paddedNumAtoms, "bornSum");
bornForce = CudaArray::create<long long>(cu, paddedNumAtoms, "bornForce");
inducedDipoleS = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "inducedDipoleS");
......@@ -1787,7 +1772,6 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
inducedFieldPolar = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "gkInducedFieldPolar");
}
cu.addAutoclearBuffer(*field);
cu.addAutoclearBuffer(*fieldPolar);
cu.addAutoclearBuffer(*bornSum);
cu.addAutoclearBuffer(*bornForce);
vector<float2> paramsVector(paddedNumAtoms);
......
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.h
View file @ f267c51a
......@@ -470,9 +470,6 @@ public:
CudaArray* getField() {
return field;
}
CudaArray* getFieldPolar() {
return fieldPolar;
}
CudaArray* getInducedField() {
return inducedField;
}
......@@ -494,7 +491,6 @@ private:
CudaArray* bornRadii;
CudaArray* bornForce;
CudaArray* field;
CudaArray* fieldPolar;
CudaArray* inducedField;
CudaArray* inducedFieldPolar;
CudaArray* inducedDipoleS;
......
plugins/amoeba/platforms/cuda2/src/kernels/multipoleInducedField.cu
View file @ f267c51a
......@@ -149,32 +149,16 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, real3 de
atom2.fieldPolarS += rr3*atom1.inducedDipolePolarS + dDotDelta*deltaR;
}
real rb2 = atom1.bornRadius*atom2.bornRadius;
real expterm = EXP(-r2/(GK_C*rb2));
real expc = expterm/GK_C;
real gf2 = RECIP(r2+rb2*expterm);
real gf = SQRT(gf2);
real gf3 = gf2*gf;
real gf5 = gf3*gf2;
// reaction potential auxiliary terms
real a10 = -gf3;
// reaction potential gradient auxiliary terms
real expc1 = 1 - expc;
real a11 = expc1 * 3 * gf5;
// unweighted dipole reaction potential gradient tensor
real3 gux = GK_FD*make_real3(a10+deltaR.x*deltaR.x*a11, deltaR.x*deltaR.y*a11, deltaR.x*deltaR.z*a11);
real3 guy = make_real3(gux.y, GK_FD*(a10+deltaR.y*deltaR.y*a11), GK_FD*deltaR.y*deltaR.z*a11);
real3 guz = make_real3(gux.z, guy.z, GK_FD*(a10+deltaR.z*deltaR.z*a11));
......@@ -280,6 +264,11 @@ extern "C" __global__ void computeInducedField(
localData[threadIdx.x].inducedDipolePolar = data.inducedDipolePolar;
localData[threadIdx.x].thole = data.thole;
localData[threadIdx.x].damp = data.damp;
#ifdef USE_GK
localData[threadIdx.x].inducedDipoleS = data.inducedDipoleS;
localData[threadIdx.x].inducedDipolePolarS = data.inducedDipolePolarS;
localData[threadIdx.x].bornRadius = data.bornRadius;
#endif
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real3 delta = localData[tbx+j].pos-data.pos;
#ifdef USE_PERIODIC
......@@ -435,9 +424,8 @@ extern "C" __global__ void computeInducedField(
}
extern "C" __global__ void updateInducedFieldBySOR(const long long* __restrict__ fixedField, const long long* __restrict__ fixedFieldPolar,
const long long* __restrict__ fixedFieldS, const long long* __restrict__ fixedFieldPolarS,
const long long* __restrict__ inducedField, const long long* __restrict__ inducedFieldPolar, real* __restrict__ inducedDipole,
real* __restrict__ inducedDipolePolar, const float* __restrict__ polarizability, float2* __restrict__ errors) {
const long long* __restrict__ fixedFieldS, const long long* __restrict__ inducedField, const long long* __restrict__ inducedFieldPolar,
real* __restrict__ inducedDipole, real* __restrict__ inducedDipolePolar, const float* __restrict__ polarizability, float2* __restrict__ errors) {
extern __shared__ real2 buffer[];
const float polarSOR = 0.55f;
#ifdef USE_EWALD
......@@ -455,10 +443,9 @@ extern "C" __global__ void updateInducedFieldBySOR(const long long* __restrict__
int fieldIndex = atom+component*PADDED_NUM_ATOMS;
real previousDipole = inducedDipole[dipoleIndex];
real previousDipolePolar = inducedDipolePolar[dipoleIndex];
long long fixed = fixedField[fieldIndex] + (fixedFieldS == NULL ? (long long) 0 : fixedFieldS[fieldIndex]);
long long fixedPolar = fixedFieldPolar[fieldIndex] + (fixedFieldPolarS == NULL ? (long long) 0 : fixedFieldPolarS[fieldIndex]);
real newDipole = scale*((fixed+inducedField[fieldIndex])*fieldScale+ewaldScale*previousDipole);
real newDipolePolar = scale*((fixedPolar+inducedFieldPolar[fieldIndex])*fieldScale+ewaldScale*previousDipolePolar);
long long fixedS = (fixedFieldS == NULL ? (long long) 0 : fixedFieldS[fieldIndex]);
real newDipole = scale*((fixedField[fieldIndex]+fixedS+inducedField[fieldIndex])*fieldScale+ewaldScale*previousDipole);
real newDipolePolar = scale*((fixedFieldPolar[fieldIndex]+fixedS+inducedFieldPolar[fieldIndex])*fieldScale+ewaldScale*previousDipolePolar);
newDipole = previousDipole + polarSOR*(newDipole-previousDipole);
newDipolePolar = previousDipolePolar + polarSOR*(newDipolePolar-previousDipolePolar);
inducedDipole[dipoleIndex] = newDipole;
......
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