Skip to content

GitLab

Commit f4545597 authored by peastman's avatar peastman
Browse files

Merge pull request #282 from peastman/master 

Fixed a bug in CustomGBForce
parents e32e1a61 1e857c31
Show whitespace changes
Inline Side-by-side
Showing with 42 additions and 12 deletions
platforms/cuda/include/CudaKernels.h
View file @ f4545597
......@@ -738,7 +738,7 @@ private:
class CudaCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
CudaCalcCustomGBForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomGBForceKernel(name, platform),
hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), longEnergyDerivs(NULL), globals(NULL),
hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), longEnergyDerivs(NULL), globals(NULL),
valueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
}
~CudaCalcCustomGBForceKernel();
......@@ -772,6 +772,7 @@ private:
CudaParameterSet* params;
CudaParameterSet* computedValues;
CudaParameterSet* energyDerivs;
CudaParameterSet* energyDerivChain;
CudaArray* longEnergyDerivs;
CudaArray* globals;
CudaArray* valueBuffers;
......
platforms/cuda/src/CudaKernels.cpp
View file @ f4545597
......@@ -2602,6 +2602,8 @@ CudaCalcCustomGBForceKernel::~CudaCalcCustomGBForceKernel() {
delete computedValues;
if (energyDerivs != NULL)
delete energyDerivs;
if (energyDerivChain != NULL)
delete energyDerivChain;
if (longEnergyDerivs != NULL)
delete longEnergyDerivs;
if (globals != NULL)
......@@ -2745,6 +2747,7 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
}
longEnergyDerivs = CudaArray::create<long long>(cu, force.getNumComputedValues()*cu.getPaddedNumAtoms(), "customGBLongEnergyDerivatives");
energyDerivs = new CudaParameterSet(cu, force.getNumComputedValues(), cu.getPaddedNumAtoms(), "customGBEnergyDerivatives", true);
energyDerivChain = new CudaParameterSet(cu, force.getNumComputedValues(), cu.getPaddedNumAtoms(), "customGBEnergyDerivativeChain", true);
// Create the kernels.
......@@ -3011,6 +3014,11 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
extraArgs << ", " << buffer.getType() << "* __restrict__ derivBuffers" << index;
compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
}
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
string index = cu.intToString(i+1);
extraArgs << ", " << buffer.getType() << "* __restrict__ derivChain" << index;
}
extraArgs << ", const long long* __restrict__ derivBuffersIn";
for (int i = 0; i < energyDerivs->getNumParameters(); ++i)
load << "derivBuffers" << energyDerivs->getParameterSuffix(i, "[index]") <<
......@@ -3056,6 +3064,10 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
// Record values.
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
string index = cu.intToString(i+1);
compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
}
compute << "forceBuffers[index] += (long long) (force.x*0x100000000);\n";
compute << "forceBuffers[index+PADDED_NUM_ATOMS] += (long long) (force.y*0x100000000);\n";
compute << "forceBuffers[index+PADDED_NUM_ATOMS*2] += (long long) (force.z*0x100000000);\n";
......@@ -3068,7 +3080,7 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
string index = cu.intToString(i+1);
compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
compute << "derivChain" << index << "[index] = deriv" << index << ";\n";
}
map<string, string> replacements;
replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
......@@ -3206,9 +3218,9 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
parameters.push_back(CudaNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
if (needChainForValue[i]) {
CudaNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
CudaNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
string paramName = prefix+"dEdV"+cu.intToString(i+1);
parameters.push_back(CudaNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
}
......@@ -3354,6 +3366,8 @@ double CudaCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFo
perParticleEnergyArgs.push_back(&computedValues->getBuffers()[i].getMemory());
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
perParticleEnergyArgs.push_back(&energyDerivs->getBuffers()[i].getMemory());
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++)
perParticleEnergyArgs.push_back(&energyDerivChain->getBuffers()[i].getMemory());
perParticleEnergyArgs.push_back(&longEnergyDerivs->getDevicePointer());
if (tabulatedFunctionParams != NULL) {
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
......
platforms/cuda/tests/TestCudaCustomGBForce.cpp
View file @ f4545597
......@@ -248,7 +248,7 @@ void testMembrane() {
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
......
platforms/opencl/include/OpenCLKernels.h
View file @ f4545597
......@@ -741,7 +741,7 @@ private:
class OpenCLCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
OpenCLCalcCustomGBForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomGBForceKernel(name, platform),
hasInitializedKernels(false), cl(cl), params(NULL), computedValues(NULL), energyDerivs(NULL), longEnergyDerivs(NULL), globals(NULL),
hasInitializedKernels(false), cl(cl), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), longEnergyDerivs(NULL), globals(NULL),
valueBuffers(NULL), longValueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
}
~OpenCLCalcCustomGBForceKernel();
......@@ -775,6 +775,7 @@ private:
OpenCLParameterSet* params;
OpenCLParameterSet* computedValues;
OpenCLParameterSet* energyDerivs;
OpenCLParameterSet* energyDerivChain;
OpenCLArray* longEnergyDerivs;
OpenCLArray* globals;
OpenCLArray* valueBuffers;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ f4545597
......@@ -2654,6 +2654,8 @@ OpenCLCalcCustomGBForceKernel::~OpenCLCalcCustomGBForceKernel() {
delete computedValues;
if (energyDerivs != NULL)
delete energyDerivs;
if (energyDerivChain != NULL)
delete energyDerivChain;
if (longEnergyDerivs != NULL)
delete longEnergyDerivs;
if (globals != NULL)
......@@ -2804,6 +2806,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
}
else
energyDerivs = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms()*cl.getNonbondedUtilities().getNumForceBuffers(), "customGBEnergyDerivatives", true);
energyDerivChain = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "customGBEnergyDerivativeChain", true);
// Create the kernels.
......@@ -3094,6 +3097,11 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index;
compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
}
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
string index = cl.intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* restrict derivChain" << index;
}
if (useLong) {
extraArgs << ", __global const long* restrict derivBuffersIn";
for (int i = 0; i < energyDerivs->getNumParameters(); ++i)
......@@ -3145,6 +3153,10 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
// Record values.
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
string index = cl.intToString(i+1);
compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
}
compute << "forceBuffers[index] = forceBuffers[index]+force;\n";
for (int i = 1; i < force.getNumComputedValues(); i++) {
compute << "real totalDeriv"<<i<<" = dV"<<i<<"dV0";
......@@ -3155,7 +3167,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
string index = cl.intToString(i+1);
compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
compute << "derivChain" << index << "[index] = deriv" << index << ";\n";
}
map<string, string> replacements;
replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
......@@ -3292,9 +3304,9 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
if (needChainForValue[i]) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
string paramName = prefix+"dEdV"+cl.intToString(i+1);
parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
}
......@@ -3487,6 +3499,8 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
perParticleEnergyKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++)
perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivChain->getBuffers()[i].getMemory());
if (useLong)
perParticleEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
if (tabulatedFunctionParams != NULL) {
......
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ f4545597
......@@ -248,7 +248,7 @@ void testMembrane() {
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ f4545597
......@@ -251,7 +251,7 @@ void testMembrane() {
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment