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Commit eae8def5 authored by Peter Eastman's avatar Peter Eastman
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Began CUDA implementation of parameter derivatives

parent e47cf907
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Showing with 202 additions and 16 deletions
platforms/cuda/include/CudaBondedUtilities.h
View file @ eae8def5
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Portions copyright (c) 2011-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -100,6 +100,15 @@ public:
* refer to it by this name.
*/
std::string addArgument(CUdeviceptr data, const std::string& type);
/**
* Register that the interaction kernel will be computing the derivative of the potential energy
* with respect to a parameter.
*
* @param param the name of the parameter
* @return the variable that will be used to accumulate the derivative. Any code you pass to addInteraction() should
* add its contributions to this variable.
*/
std::string addEnergyParameterDerivative(const std::string& param);
/**
* Add some Cuda code that should be included in the program, before the start of the kernel.
* This can be used, for example, to define functions that will be called by the kernel.
......@@ -129,6 +138,7 @@ private:
std::vector<std::string> argTypes;
std::vector<std::vector<CudaArray*> > atomIndices;
std::vector<std::string> prefixCode;
std::vector<std::string> energyParameterDerivatives;
std::vector<void*> kernelArgs;
int numForceBuffers, maxBonds, allGroups;
bool hasInitializedKernels, hasInteractions;
......
platforms/cuda/include/CudaContext.h
View file @ eae8def5
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -177,6 +177,12 @@ public:
CudaArray& getEnergyBuffer() {
return *energyBuffer;
}
/**
* Get the array which contains the buffer in which derivatives of the energy with respect to parameters are computed.
*/
CudaArray& getEnergyParamDerivBuffer() {
return *energyParamDerivBuffer;
}
/**
* Get a pointer to a block of pinned memory that can be used for efficient transfers between host and device.
* This is guaranteed to be at least as large as any of the arrays returned by methods of this class.
......@@ -544,6 +550,27 @@ public:
std::vector<ForcePostComputation*>& getPostComputations() {
return postComputations;
}
/**
* Get the names of all parameters with respect to which energy derivatives are computed.
*/
const std::vector<std::string>& getEnergyParamDerivNames() const {
return energyParamDerivNames;
}
/**
* Get a workspace data structure used for accumulating the values of derivatives of the energy
* with respect to parameters.
*/
std::map<std::string, double>& getEnergyParamDerivWorkspace() {
return energyParamDerivWorkspace;
}
/**
* Register that the derivative of potential energy with respect to a context parameter
* will need to be calculated. If this is called multiple times for a single parameter,
* it is only added to the list once.
*
* @param param the name of the parameter to add
*/
void addEnergyParameterDerivative(const std::string& param);
/**
* Mark that the current molecule definitions (and hence the atom order) may be invalid.
* This should be called whenever force field parameters change. It will cause the definitions
......@@ -609,7 +636,10 @@ private:
CudaArray* velm;
CudaArray* force;
CudaArray* energyBuffer;
CudaArray* energyParamDerivBuffer;
CudaArray* atomIndexDevice;
std::vector<std::string> energyParamDerivNames;
std::map<std::string, double> energyParamDerivWorkspace;
std::vector<int> atomIndex;
std::vector<CUdeviceptr> autoclearBuffers;
std::vector<int> autoclearBufferSizes;
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ eae8def5
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2013 Stanford University and the Authors. *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -88,6 +88,15 @@ public:
* Add an array (other than a per-atom parameter) that should be passed as an argument to the default interaction kernel.
*/
void addArgument(const ParameterInfo& parameter);
/**
* Register that the interaction kernel will be computing the derivative of the potential energy
* with respect to a parameter.
*
* @param param the name of the parameter
* @return the variable that will be used to accumulate the derivative. Any code you pass to addInteraction() should
* add its contributions to this variable.
*/
std::string addEnergyParameterDerivative(const std::string& param);
/**
* Specify the list of exclusions that an interaction outside the default kernel will depend on.
*
......@@ -275,6 +284,7 @@ private:
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
std::vector<ParameterInfo> arguments;
std::vector<std::string> energyParameterDerivatives;
std::map<int, double> groupCutoff;
std::map<int, std::string> groupKernelSource;
double lastCutoff;
......
platforms/cuda/src/CudaBondedUtilities.cpp
View file @ eae8def5
......@@ -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) 2011-2015 Stanford University and the Authors. *
* Portions copyright (c) 2011-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -52,12 +52,25 @@ void CudaBondedUtilities::addInteraction(const vector<vector<int> >& atoms, cons
}
}
std::string CudaBondedUtilities::addArgument(CUdeviceptr data, const string& type) {
string CudaBondedUtilities::addArgument(CUdeviceptr data, const string& type) {
arguments.push_back(data);
argTypes.push_back(type);
return "customArg"+context.intToString(arguments.size());
}
string CudaBondedUtilities::addEnergyParameterDerivative(const string& param) {
// See if the parameter has already been added.
int index;
for (index = 0; index < energyParameterDerivatives.size(); index++)
if (param == energyParameterDerivatives[index])
break;
if (index == energyParameterDerivatives.size())
energyParameterDerivatives.push_back(param);
context.addEnergyParameterDerivative(param);
return string("energyParamDeriv")+context.intToString(index);
}
void CudaBondedUtilities::addPrefixCode(const string& source) {
for (int i = 0; i < (int) prefixCode.size(); i++)
if (prefixCode[i] == source)
......@@ -109,11 +122,21 @@ void CudaBondedUtilities::initialize(const System& system) {
}
for (int i = 0; i < (int) arguments.size(); i++)
s<<", "<<argTypes[i]<<"* customArg"<<(i+1);
if (energyParameterDerivatives.size() > 0)
s<<", mixed* __restrict__ energyParamDerivs";
s<<") {\n";
s<<"mixed energy = 0;\n";
for (int i = 0; i < energyParameterDerivatives.size(); i++)
s<<"mixed energyParamDeriv"<<i<<" = 0;\n";
for (int force = 0; force < numForces; force++)
s<<createForceSource(force, forceAtoms[force].size(), forceAtoms[force][0].size(), forceGroup[force], forceSource[force]);
s<<"energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;\n";
const vector<string>& allParamDerivNames = context.getEnergyParamDerivNames();
int numDerivs = allParamDerivNames.size();
for (int i = 0; i < energyParameterDerivatives.size(); i++)
for (int index = 0; index < numDerivs; index++)
if (allParamDerivNames[index] == energyParameterDerivatives[i])
s<<"energyParamDerivs[(blockIdx.x*blockDim.x+threadIdx.x)*"<<numDerivs<<"+"<<index<<"] += energyParamDeriv"<<i<<";\n";
s<<"}\n";
map<string, string> defines;
defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
......@@ -171,6 +194,8 @@ void CudaBondedUtilities::computeInteractions(int groups) {
kernelArgs.push_back(&atomIndices[i][j]->getDevicePointer());
for (int i = 0; i < (int) arguments.size(); i++)
kernelArgs.push_back(&arguments[i]);
if (energyParameterDerivatives.size() > 0)
kernelArgs.push_back(&context.getEnergyParamDerivBuffer().getDevicePointer());
}
if (!hasInteractions)
return;
......
platforms/cuda/src/CudaContext.cpp
View file @ eae8def5
......@@ -76,7 +76,7 @@ bool CudaContext::hasInitializedCuda = false;
CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
const string& tempDir, const std::string& hostCompiler, CudaPlatform::PlatformData& platformData) : system(system), currentStream(0),
time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), hasCompilerKernel(false),
pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
this->compiler = "\""+compiler+"\"";
if (platformData.context != NULL) {
try {
......@@ -339,6 +339,8 @@ CudaContext::~CudaContext() {
delete force;
if (energyBuffer != NULL)
delete energyBuffer;
if (energyParamDerivBuffer != NULL)
delete energyParamDerivBuffer;
if (atomIndexDevice != NULL)
delete atomIndexDevice;
if (integration != NULL)
......@@ -390,6 +392,14 @@ void CudaContext::initialize() {
force = CudaArray::create<long long>(*this, paddedNumAtoms*3, "force");
addAutoclearBuffer(force->getDevicePointer(), force->getSize()*force->getElementSize());
addAutoclearBuffer(energyBuffer->getDevicePointer(), energyBuffer->getSize()*energyBuffer->getElementSize());
int numEnergyParamDerivs = energyParamDerivNames.size();
if (numEnergyParamDerivs > 0) {
if (useDoublePrecision || useMixedPrecision)
energyParamDerivBuffer = CudaArray::create<double>(*this, numEnergyParamDerivs*numEnergyBuffers, "energyParamDerivBuffer");
else
energyParamDerivBuffer = CudaArray::create<float>(*this, numEnergyParamDerivs*numEnergyBuffers, "energyParamDerivBuffer");
addAutoclearBuffer(*energyParamDerivBuffer);
}
atomIndexDevice = CudaArray::create<int>(*this, paddedNumAtoms, "atomIndex");
atomIndex.resize(paddedNumAtoms);
for (int i = 0; i < paddedNumAtoms; ++i)
......@@ -1311,6 +1321,15 @@ void CudaContext::addPostComputation(ForcePostComputation* computation) {
postComputations.push_back(computation);
}
void CudaContext::addEnergyParameterDerivative(const string& param) {
// See if this parameter has already been registered.
for (int i = 0; i < energyParamDerivNames.size(); i++)
if (param == energyParamDerivNames[i])
return;
energyParamDerivNames.push_back(param);
}
struct CudaContext::WorkThread::ThreadData {
ThreadData(std::queue<CudaContext::WorkTask*>& tasks, bool& waiting, bool& finished,
pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :
......
platforms/cuda/src/CudaKernels.cpp
View file @ eae8def5
......@@ -43,6 +43,7 @@
#include "CudaIntegrationUtilities.h"
#include "CudaNonbondedUtilities.h"
#include "CudaKernelSources.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionTreeNode.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
......@@ -55,8 +56,7 @@
using namespace OpenMM;
using namespace std;
using Lepton::ExpressionTreeNode;
using Lepton::Operation;
using namespace Lepton;
#define CHECK_RESULT(result, prefix) \
if (result != CUDA_SUCCESS) { \
......@@ -102,6 +102,9 @@ void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool
CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
cu.setComputeForceCount(cu.getComputeForceCount()+1);
nb.prepareInteractions(groups);
map<string, double>& derivs = cu.getEnergyParamDerivWorkspace();
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
derivs[iter->first] = 0;
}
double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
......@@ -340,7 +343,30 @@ void CudaUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& fo
}
void CudaUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
const vector<string>& paramDerivNames = cu.getEnergyParamDerivNames();
int numDerivs = paramDerivNames.size();
if (numDerivs == 0)
return;
derivs = cu.getEnergyParamDerivWorkspace();
CudaArray& derivArray = cu.getEnergyParamDerivBuffer();
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
vector<double> derivBuffers;
derivArray.download(derivBuffers);
for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
for (int j = 0; j < numDerivs; j++)
derivBuffers[j] += derivBuffers[i+j];
for (int i = 0; i < numDerivs; i++)
derivs[paramDerivNames[i]] += derivBuffers[i];
}
else {
vector<float> derivBuffers;
derivArray.download(derivBuffers);
for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
for (int j = 0; j < numDerivs; j++)
derivBuffers[j] += derivBuffers[i+j];
for (int i = 0; i < numDerivs; i++)
derivs[paramDerivNames[i]] += derivBuffers[i];
}
}
void CudaUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
......@@ -653,6 +679,12 @@ void CudaCalcCustomBondForceKernel::initialize(const System& system, const Custo
variables[name] = value;
}
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string paramName = force.getEnergyParameterDerivativeName(i);
string derivVariable = cu.getBondedUtilities().addEnergyParameterDerivative(paramName);
Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
expressions[derivVariable+" += "] = derivExpression;
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
......@@ -891,6 +923,12 @@ void CudaCalcCustomAngleForceKernel::initialize(const System& system, const Cust
variables[name] = value;
}
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string paramName = force.getEnergyParameterDerivativeName(i);
string derivVariable = cu.getBondedUtilities().addEnergyParameterDerivative(paramName);
Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
expressions[derivVariable+" += "] = derivExpression;
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
......@@ -1362,6 +1400,12 @@ void CudaCalcCustomTorsionForceKernel::initialize(const System& system, const Cu
variables[name] = value;
}
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string paramName = force.getEnergyParameterDerivativeName(i);
string derivVariable = cu.getBondedUtilities().addEnergyParameterDerivative(paramName);
Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
expressions[derivVariable+" += "] = derivExpression;
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
......@@ -2247,6 +2291,12 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
string value = "globals["+cu.intToString(i)+"]";
variables.push_back(makeVariable(name, prefix+value));
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string paramName = force.getEnergyParameterDerivativeName(i);
string derivVariable = cu.getNonbondedUtilities().addEnergyParameterDerivative(paramName);
Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
forceExpressions[derivVariable+" += interactionScale*switchValue*"] = derivExpression;
}
stringstream compute;
compute << cu.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, prefix+"temp");
map<string, string> replacements;
......@@ -2572,7 +2622,11 @@ double CudaCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool in
cu.executeKernel(interactionGroupKernel, &interactionGroupArgs[0], numGroupThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
double4 boxSize = cu.getPeriodicBoxSize();
return longRangeCoefficient/(boxSize.x*boxSize.y*boxSize.z);
double volume = boxSize.x*boxSize.y*boxSize.z;
map<string, double>& derivs = cu.getEnergyParamDerivWorkspace();
for (int i = 0; i < longRangeCoefficientDerivs.size(); i++)
derivs[forceCopy->getEnergyParameterDerivativeName(i)] += longRangeCoefficientDerivs[i]/volume;
return longRangeCoefficient/volume;
}
void CudaCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ eae8def5
......@@ -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) 2009-2015 Stanford University and the Authors. *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -146,6 +146,19 @@ void CudaNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
arguments.push_back(parameter);
}
string CudaNonbondedUtilities::addEnergyParameterDerivative(const string& param) {
// See if the parameter has already been added.
int index;
for (index = 0; index < energyParameterDerivatives.size(); index++)
if (param == energyParameterDerivatives[index])
break;
if (index == energyParameterDerivatives.size())
energyParameterDerivatives.push_back(param);
context.addEnergyParameterDerivative(param);
return string("energyParamDeriv")+context.intToString(index);
}
void CudaNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
if (anyExclusions) {
bool sameExclusions = (exclusionList.size() == atomExclusions.size());
......@@ -308,6 +321,8 @@ void CudaNonbondedUtilities::initialize(const System& system) {
forceArgs.push_back(&parameters[i].getMemory());
for (int i = 0; i < (int) arguments.size(); i++)
forceArgs.push_back(&arguments[i].getMemory());
if (energyParameterDerivatives.size() > 0)
forceArgs.push_back(&context.getEnergyParamDerivBuffer().getDevicePointer());
if (useCutoff) {
findBlockBoundsArgs.push_back(&numAtoms);
findBlockBoundsArgs.push_back(context.getPeriodicBoxSizePointer());
......@@ -515,6 +530,8 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
args << "* __restrict__ ";
args << arguments[i].getName();
}
if (energyParameterDerivatives.size() > 0)
args << ", mixed* __restrict__ energyParamDerivs";
replacements["PARAMETER_ARGUMENTS"] = args.str();
stringstream load1;
......@@ -623,6 +640,18 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
}
}
replacements["LOAD_ATOM2_PARAMETERS"] = load2j.str();
stringstream initDerivs;
for (int i = 0; i < energyParameterDerivatives.size(); i++)
initDerivs<<"mixed energyParamDeriv"<<i<<" = 0;\n";
replacements["INIT_DERIVATIVES"] = initDerivs.str();
stringstream saveDerivs;
const vector<string>& allParamDerivNames = context.getEnergyParamDerivNames();
int numDerivs = allParamDerivNames.size();
for (int i = 0; i < energyParameterDerivatives.size(); i++)
for (int index = 0; index < numDerivs; index++)
if (allParamDerivNames[index] == energyParameterDerivatives[i])
saveDerivs<<"energyParamDerivs[(blockIdx.x*blockDim.x+threadIdx.x)*"<<numDerivs<<"+"<<index<<"] += energyParamDeriv"<<i<<";\n";
replacements["SAVE_DERIVATIVES"] = saveDerivs.str();
stringstream shuffleWarpData;
if(useShuffle) {
......
platforms/cuda/src/kernels/customNonbonded.cu
View file @ eae8def5
......@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
if (!isExcluded) {
#endif
real tempForce = 0;
COMPUTE_FORCE
real switchValue = 1, switchDeriv = 0;
#if USE_SWITCH
if (r > SWITCH_CUTOFF) {
real x = r-SWITCH_CUTOFF;
real switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
real switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
tempEnergy *= switchValue;
switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
}
#endif
COMPUTE_FORCE
#if USE_SWITCH
tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
tempEnergy *= switchValue;
#endif
dEdR += tempForce*invR;
}
platforms/cuda/src/kernels/nonbonded.cu
View file @ eae8def5
......@@ -113,6 +113,7 @@ extern "C" __global__ void computeNonbonded(
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1); // index within the warp
const unsigned int tbx = threadIdx.x - tgx; // block warpIndex
mixed energy = 0;
INIT_DERIVATIVES
// used shared memory if the device cannot shuffle
#ifndef ENABLE_SHUFFLE
__shared__ AtomData localData[THREAD_BLOCK_SIZE];
......@@ -175,6 +176,7 @@ extern "C" __global__ void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif
real tempEnergy = 0.0f;
const real interactionScale = 0.5f;
COMPUTE_INTERACTION
energy += 0.5f*tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -243,6 +245,7 @@ extern "C" __global__ void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif
real tempEnergy = 0.0f;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -448,6 +451,7 @@ extern "C" __global__ void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif
real tempEnergy = 0.0f;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -518,6 +522,7 @@ extern "C" __global__ void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif
real tempEnergy = 0.0f;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -586,4 +591,5 @@ extern "C" __global__ void computeNonbonded(
#ifdef INCLUDE_ENERGY
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
#endif
SAVE_DERIVATIVES
}
\ No newline at end of file
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