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Commit 95dc4dc1 authored by Peter Eastman's avatar Peter Eastman
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Fixed errors

parent 122c84d2
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Showing with 17 additions and 17 deletions
platforms/cuda/include/CudaKernels.h
View file @ 95dc4dc1
......@@ -816,6 +816,7 @@ private:
int maxTiles;
CudaContext& cu;
ForceInfo* info;
CudaArray charges;
CudaArray params;
CudaArray bornSum;
CudaArray bornRadii;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 95dc4dc1
......@@ -1610,6 +1610,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
bool useCutoff = (nonbondedMethod != NoCutoff);
bool usePeriodic = (nonbondedMethod != NoCutoff && nonbondedMethod != CutoffNonPeriodic);
doLJPME = (nonbondedMethod == LJPME && hasLJ);
if (hasCoulomb)
usePosqCharges = cu.requestPosqCharges();
map<string, string> defines;
defines["HAS_COULOMB"] = (hasCoulomb ? "1" : "0");
defines["HAS_LENNARD_JONES"] = (hasLJ ? "1" : "0");
......@@ -1933,7 +1935,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
string source = cu.replaceStrings(CudaKernelSources::coulombLennardJones, defines);
charges.initialize(cu, cu.getPaddedNumAtoms(), cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float), "charges");
if (hasCoulomb) {
usePosqCharges = cu.requestPosqCharges();
map<string, string> replacements;
if (usePosqCharges) {
cu.setCharges(chargeVec);
......@@ -1965,9 +1966,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
cu.getNonbondedUtilities().addParameter(CudaNonbondedUtilities::ParameterInfo(prefix+"sigmaEpsilon", "float", 2, sizeof(float2), sigmaEpsilon.getDevicePointer()));
}
cu.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup(), true);
if (hasLJ)
cu.getNonbondedUtilities().addParameter(CudaNonbondedUtilities::ParameterInfo("sigmaEpsilon", "float", 2,
sizeof(float2), sigmaEpsilon.getDevicePointer()));
// Initialize the exceptions.
......@@ -2873,7 +2871,7 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
string prefix = "obc"+cu.intToString(forceIndex)+"_";
CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
params.initialize<float2>(cu, cu.getPaddedNumAtoms(), "gbsaObcParams");
int elementSize = (cu.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
charges.initialize(cu, cu.getPaddedNumAtoms(), elementSize, "gbsaObcCharges");
bornRadii.initialize(cu, cu.getPaddedNumAtoms(), elementSize, "bornRadii");
obcChain.initialize(cu, cu.getPaddedNumAtoms(), elementSize, "obcChain");
......
platforms/cuda/src/kernels/gbsaObc1.cu
View file @ 95dc4dc1
......@@ -441,8 +441,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
localData[threadIdx.x].bornRadius = bornRadius1;
for (unsigned int j = 0; j < TILE_SIZE; j++) {
if (atom1 < NUM_ATOMS && y*TILE_SIZE+j < NUM_ATOMS) {
real4 pos2 = make_real3(localData[tbx+j].x, localData[tbx+j].y, localData[tbx+j].z);
real charge1 = localData[tbx+j].q;
real3 pos2 = make_real3(localData[tbx+j].x, localData[tbx+j].y, localData[tbx+j].z);
real charge2 = localData[tbx+j].q;
real3 delta = make_real3(pos2.x-posq1.x, pos2.y-posq1.y, pos2.z-posq1.z);
#ifdef USE_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
......@@ -498,8 +498,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
unsigned int tj = tgx;
for (j = 0; j < TILE_SIZE; j++) {
if (atom1 < NUM_ATOMS && y*TILE_SIZE+tj < NUM_ATOMS) {
real4 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge1 = localData[tbx+tj].q;
real3 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge2 = localData[tbx+tj].q;
real3 delta = make_real3(pos2.x-posq1.x, pos2.y-posq1.y, pos2.z-posq1.z);
#ifdef USE_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
......@@ -654,8 +654,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
for (j = 0; j < TILE_SIZE; j++) {
int atom2 = atomIndices[tbx+tj];
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
real4 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge1 = localData[tbx+tj].q;
real3 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge2 = localData[tbx+tj].q;
real3 delta = make_real3(pos2.x-posq1.x, pos2.y-posq1.y, pos2.z-posq1.z);
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
if (r2 < CUTOFF_SQUARED) {
......@@ -700,8 +700,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
for (j = 0; j < TILE_SIZE; j++) {
int atom2 = atomIndices[tbx+tj];
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
real4 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge1 = localData[tbx+tj].q;
real3 pos2 = make_real3(localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z);
real charge2 = localData[tbx+tj].q;
real3 delta = make_real3(pos2.x-posq1.x, pos2.y-posq1.y, pos2.z-posq1.z);
#ifdef USE_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
......
platforms/cuda/src/kernels/gbsaObc2.cu
View file @ 95dc4dc1
......@@ -16,8 +16,8 @@
real t2I = (l_ij2I-u_ij2I);
real term1 = (0.5f*(0.25f+OBC_PARAMS2.y*OBC_PARAMS2.y*invRSquaredOver4)*t2J + t1J*invRSquaredOver4)*invR;
real term2 = (0.5f*(0.25f+OBC_PARAMS1.y*OBC_PARAMS1.y*invRSquaredOver4)*t2I + t1I*invRSquaredOver4)*invR;
real tempdEdR = (OBC_PARAMS1.x < rScaledRadiusJ ? bornForce1*term1/0x100000000 : 0);
tempdEdR += (OBC_PARAMS2.x < rScaledRadiusI ? bornForce2*term2/0x100000000 : 0);
real tempdEdR = (OBC_PARAMS1.x < rScaledRadiusJ ? BORN_FORCE1*term1/0x100000000 : 0);
tempdEdR += (OBC_PARAMS2.x < rScaledRadiusI ? BORN_FORCE2*term2/0x100000000 : 0);
#ifdef USE_CUTOFF
unsigned int includeInteraction = (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS && atom1 != atom2 && r2 < CUTOFF_SQUARED);
#else
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 95dc4dc1
......@@ -1602,6 +1602,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
bool useCutoff = (nonbondedMethod != NoCutoff);
bool usePeriodic = (nonbondedMethod != NoCutoff && nonbondedMethod != CutoffNonPeriodic);
doLJPME = (nonbondedMethod == LJPME && hasLJ);
if (hasCoulomb)
usePosqCharges = cl.requestPosqCharges();
map<string, string> defines;
defines["HAS_COULOMB"] = (hasCoulomb ? "1" : "0");
defines["HAS_LENNARD_JONES"] = (hasLJ ? "1" : "0");
......@@ -1864,7 +1866,6 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
string source = cl.replaceStrings(OpenCLKernelSources::coulombLennardJones, defines);
charges.initialize(cl, cl.getPaddedNumAtoms(), cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float), "charges");
if (hasCoulomb) {
usePosqCharges = cl.requestPosqCharges();
map<string, string> replacements;
if (usePosqCharges) {
cl.setCharges(chargeVec);
......
tests/TestNonbondedForce.h
View file @ 95dc4dc1
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......
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