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Commit ab8f1021 authored by peastman's avatar peastman
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Use C++11 style loops

parent 88da682c
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Showing with 597 additions and 578 deletions
platforms/cpu/src/CpuKernels.cpp
View file @ ab8f1021
......@@ -98,8 +98,8 @@ static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<
const Lepton::Operation& op = node.getOperation();
if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("Unknown variable in expression: "+op.getName());
for (int i = 0; i < (int) node.getChildren().size(); i++)
validateVariables(node.getChildren()[i], variables);
for (auto& child : node.getChildren())
validateVariables(child, variables);
}
/**
......@@ -867,8 +867,8 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
// Record information for the long range correction.
......@@ -909,11 +909,11 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
nonbonded->setPeriodic(boxVectors);
}
bool globalParamsChanged = false;
for (int i = 0; i < (int) globalParameterNames.size(); i++) {
double value = context.getParameter(globalParameterNames[i]);
if (globalParamValues[globalParameterNames[i]] != value)
for (auto& name : globalParameterNames) {
double value = context.getParameter(name);
if (globalParamValues[name] != value)
globalParamsChanged = true;
globalParamValues[globalParameterNames[i]] = value;
globalParamValues[name] = value;
}
if (useSwitchingFunction)
nonbonded->setUseSwitchingFunction(switchingDistance);
......@@ -1155,8 +1155,8 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
ixn = new CpuCustomGBForce(numParticles, exclusions, valueExpressions, valueDerivExpressions, valueGradientExpressions, valueParamDerivExpressions,
valueNames, valueTypes, energyExpressions, energyDerivExpressions, energyGradientExpressions, energyParamDerivExpressions, energyTypes,
particleParameterNames, data.threads);
......@@ -1174,8 +1174,8 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
ixn->setUseCutoff(nonbondedCutoff, *data.neighborList);
}
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
......@@ -1236,8 +1236,8 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
if (nonbondedMethod == CutoffPeriodic) {
Vec3* boxVectors = extractBoxVectors(context);
double minAllowedSize = 2*cutoffDistance;
......
platforms/cuda/src/CudaContext.cpp
View file @ ab8f1021
......@@ -385,14 +385,14 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
CudaContext::~CudaContext() {
setAsCurrent();
for (int i = 0; i < (int) forces.size(); i++)
delete forces[i];
for (int i = 0; i < (int) reorderListeners.size(); i++)
delete reorderListeners[i];
for (int i = 0; i < (int) preComputations.size(); i++)
delete preComputations[i];
for (int i = 0; i < (int) postComputations.size(); i++)
delete postComputations[i];
for (auto force : forces)
delete force;
for (auto listener : reorderListeners)
delete listener;
for (auto computation : preComputations)
delete computation;
for (auto computation : postComputations)
delete computation;
if (pinnedBuffer != NULL)
cuMemFreeHost(pinnedBuffer);
if (posq != NULL)
......@@ -498,17 +498,17 @@ string CudaContext::replaceStrings(const string& input, const std::map<std::stri
symbolChars.insert(c);
}
string result = input;
for (map<string, string>::const_iterator iter = replacements.begin(); iter != replacements.end(); iter++) {
for (auto& pair : replacements) {
int index = 0;
int size = iter->first.size();
int size = pair.first.size();
do {
index = result.find(iter->first, index);
index = result.find(pair.first, index);
if (index != result.npos) {
if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
// We have found a complete symbol, not part of a longer symbol.
result.replace(index, size, iter->second);
index += iter->second.size();
result.replace(index, size, pair.second);
index += pair.second.size();
}
else
index++;
......@@ -528,10 +528,10 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
stringstream src;
if (!options.empty())
src << "// Compilation Options: " << options << endl << endl;
for (map<string, string>::const_iterator iter = compilationDefines.begin(); iter != compilationDefines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
for (auto& pair : compilationDefines) {
src << "#define " << pair.first;
if (!pair.second.empty())
src << " " << pair.second;
src << endl;
}
if (!compilationDefines.empty())
......@@ -561,10 +561,10 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
src << "typedef float4 mixed4;\n";
}
src << "typedef unsigned int tileflags;\n";
for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
for (auto& pair : defines) {
src << "#define " << pair.first;
if (!pair.second.empty())
src << " " << pair.second;
src << endl;
}
if (!defines.empty())
......@@ -966,10 +966,10 @@ void CudaContext::findMoleculeGroups() {
atomBonds[particle1].push_back(particle2);
atomBonds[particle2].push_back(particle1);
}
for (int i = 0; i < (int) forces.size(); i++) {
for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
for (auto force : forces) {
for (int j = 0; j < force->getNumParticleGroups(); j++) {
vector<int> particles;
forces[i]->getParticlesInGroup(j, particles);
force->getParticlesInGroup(j, particles);
for (int k = 0; k < (int) particles.size(); k++)
for (int m = 0; m < (int) particles.size(); m++)
if (k != m)
......@@ -1187,8 +1187,8 @@ bool CudaContext::invalidateMolecules(CudaForceInfo* force) {
}
atomIndexDevice->upload(atomIndex);
findMoleculeGroups();
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
for (auto listener : reorderListeners)
listener->execute();
reorderAtoms();
return true;
}
......@@ -1250,10 +1250,9 @@ void CudaContext::reorderAtomsImpl() {
vector<Real4> newPosqCorrection(paddedNumAtoms);
vector<Mixed4> newVelm(paddedNumAtoms);
vector<int4> newCellOffsets(numAtoms);
for (int group = 0; group < (int) moleculeGroups.size(); group++) {
for (auto& mol : moleculeGroups) {
// Find the center of each molecule.
MoleculeGroup& mol = moleculeGroups[group];
int numMolecules = mol.offsets.size();
vector<int>& atoms = mol.atoms;
vector<Real4> molPos(numMolecules);
......@@ -1347,9 +1346,9 @@ void CudaContext::reorderAtomsImpl() {
// Reorder the atoms.
for (int i = 0; i < numMolecules; i++) {
for (int j = 0; j < (int)atoms.size(); j++) {
int oldIndex = mol.offsets[molBins[i].second]+atoms[j];
int newIndex = mol.offsets[i]+atoms[j];
for (int atom : atoms) {
int oldIndex = mol.offsets[molBins[i].second]+atom;
int newIndex = mol.offsets[i]+atom;
originalIndex[newIndex] = atomIndex[oldIndex];
newPosq[newIndex] = oldPosq[oldIndex];
if (useMixedPrecision)
......@@ -1371,8 +1370,8 @@ void CudaContext::reorderAtomsImpl() {
posqCorrection->upload(newPosqCorrection);
velm->upload(newVelm);
atomIndexDevice->upload(atomIndex);
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
for (auto listener : reorderListeners)
listener->execute();
}
void CudaContext::addReorderListener(ReorderListener* listener) {
......
platforms/cuda/src/CudaKernels.cpp
View file @ ab8f1021
This diff is collapsed.
platforms/opencl/src/OpenCLContext.cpp
View file @ ab8f1021
......@@ -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) 2009-2016 Stanford University and the Authors. *
* Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -318,8 +318,8 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
OpenCLArray valuesArray(*this, 20, sizeof(mm_float8), "values");
vector<mm_float8> values(valuesArray.getSize());
float nextValue = 1e-4f;
for (int i = 0; i < (int) values.size(); ++i) {
values[i].s0 = nextValue;
for (auto& val : values) {
val.s0 = nextValue;
nextValue *= (float) M_PI;
}
valuesArray.upload(values);
......@@ -328,14 +328,14 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
executeKernel(accuracyKernel, values.size());
valuesArray.download(values);
double maxSqrtError = 0.0, maxRsqrtError = 0.0, maxRecipError = 0.0, maxExpError = 0.0, maxLogError = 0.0;
for (int i = 0; i < (int) values.size(); ++i) {
double v = values[i].s0;
for (auto& val : values) {
double v = val.s0;
double correctSqrt = sqrt(v);
maxSqrtError = max(maxSqrtError, fabs(correctSqrt-values[i].s1)/correctSqrt);
maxRsqrtError = max(maxRsqrtError, fabs(1.0/correctSqrt-values[i].s2)*correctSqrt);
maxRecipError = max(maxRecipError, fabs(1.0/v-values[i].s3)/values[i].s3);
maxExpError = max(maxExpError, fabs(exp(v)-values[i].s4)/values[i].s4);
maxLogError = max(maxLogError, fabs(log(v)-values[i].s5)/values[i].s5);
maxSqrtError = max(maxSqrtError, fabs(correctSqrt-val.s1)/correctSqrt);
maxRsqrtError = max(maxRsqrtError, fabs(1.0/correctSqrt-val.s2)*correctSqrt);
maxRecipError = max(maxRecipError, fabs(1.0/v-val.s3)/val.s3);
maxExpError = max(maxExpError, fabs(exp(v)-val.s4)/val.s4);
maxLogError = max(maxLogError, fabs(log(v)-val.s5)/val.s5);
}
compilationDefines["SQRT"] = (maxSqrtError < 1e-6) ? "native_sqrt" : "sqrt";
compilationDefines["RSQRT"] = (maxRsqrtError < 1e-6) ? "native_rsqrt" : "rsqrt";
......@@ -412,14 +412,14 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
}
OpenCLContext::~OpenCLContext() {
for (int i = 0; i < (int) forces.size(); i++)
delete forces[i];
for (int i = 0; i < (int) reorderListeners.size(); i++)
delete reorderListeners[i];
for (int i = 0; i < (int) preComputations.size(); i++)
delete preComputations[i];
for (int i = 0; i < (int) postComputations.size(); i++)
delete postComputations[i];
for (auto force : forces)
delete force;
for (auto listener : reorderListeners)
delete listener;
for (auto computation : preComputations)
delete computation;
for (auto computation : postComputations)
delete computation;
if (pinnedBuffer != NULL)
delete pinnedBuffer;
if (posq != NULL)
......@@ -458,8 +458,8 @@ void OpenCLContext::initialize() {
bonded->initialize(system);
numForceBuffers = platformData.contexts.size();
numForceBuffers = std::max(numForceBuffers, bonded->getNumForceBuffers());
for (int i = 0; i < (int) forces.size(); i++)
numForceBuffers = std::max(numForceBuffers, forces[i]->getRequiredForceBuffers());
for (auto force : forces)
numForceBuffers = std::max(numForceBuffers, force->getRequiredForceBuffers());
int energyBufferSize = max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers());
if (useDoublePrecision) {
forceBuffers = OpenCLArray::create<mm_double4>(*this, paddedNumAtoms*numForceBuffers, "forceBuffers");
......@@ -525,17 +525,17 @@ string OpenCLContext::replaceStrings(const string& input, const std::map<std::st
symbolChars.insert(c);
}
string result = input;
for (map<string, string>::const_iterator iter = replacements.begin(); iter != replacements.end(); iter++) {
for (auto& pair : replacements) {
int index = 0;
int size = iter->first.size();
int size = pair.first.size();
do {
index = result.find(iter->first, index);
index = result.find(pair.first, index);
if (index != result.npos) {
if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
// We have found a complete symbol, not part of a longer symbol.
result.replace(index, size, iter->second);
index += iter->second.size();
result.replace(index, size, pair.second);
index += pair.second.size();
}
else
index++;
......@@ -554,10 +554,10 @@ cl::Program OpenCLContext::createProgram(const string source, const map<string,
stringstream src;
if (!options.empty())
src << "// Compilation Options: " << options << endl << endl;
for (map<string, string>::const_iterator iter = compilationDefines.begin(); iter != compilationDefines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
for (auto& pair : compilationDefines) {
src << "#define " << pair.first;
if (!pair.second.empty())
src << " " << pair.second;
src << endl;
}
if (!compilationDefines.empty())
......@@ -588,10 +588,10 @@ cl::Program OpenCLContext::createProgram(const string source, const map<string,
src << "typedef float3 mixed3;\n";
src << "typedef float4 mixed4;\n";
}
for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
for (auto& pair : defines) {
src << "#define " << pair.first;
if (!pair.second.empty())
src << " " << pair.second;
src << endl;
}
if (!defines.empty())
......@@ -856,10 +856,10 @@ void OpenCLContext::findMoleculeGroups() {
atomBonds[particle1].push_back(particle2);
atomBonds[particle2].push_back(particle1);
}
for (int i = 0; i < (int) forces.size(); i++) {
for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
for (auto force : forces) {
for (int j = 0; j < force->getNumParticleGroups(); j++) {
vector<int> particles;
forces[i]->getParticlesInGroup(j, particles);
force->getParticlesInGroup(j, particles);
for (int k = 0; k < (int) particles.size(); k++)
for (int m = 0; m < (int) particles.size(); m++)
if (k != m)
......@@ -1076,8 +1076,8 @@ bool OpenCLContext::invalidateMolecules(OpenCLForceInfo* force) {
}
atomIndexDevice->upload(atomIndex);
findMoleculeGroups();
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
for (auto listener : reorderListeners)
listener->execute();
reorderAtoms();
return true;
}
......@@ -1138,10 +1138,9 @@ void OpenCLContext::reorderAtomsImpl() {
vector<Real4> newPosqCorrection(paddedNumAtoms, Real4(0,0,0,0));
vector<Mixed4> newVelm(paddedNumAtoms, Mixed4(0,0,0,0));
vector<mm_int4> newCellOffsets(numAtoms);
for (int group = 0; group < (int) moleculeGroups.size(); group++) {
for (auto& mol : moleculeGroups) {
// Find the center of each molecule.
MoleculeGroup& mol = moleculeGroups[group];
int numMolecules = mol.offsets.size();
vector<int>& atoms = mol.atoms;
vector<Real4> molPos(numMolecules);
......@@ -1235,9 +1234,9 @@ void OpenCLContext::reorderAtomsImpl() {
// Reorder the atoms.
for (int i = 0; i < numMolecules; i++) {
for (int j = 0; j < (int)atoms.size(); j++) {
int oldIndex = mol.offsets[molBins[i].second]+atoms[j];
int newIndex = mol.offsets[i]+atoms[j];
for (int atom : atoms) {
int oldIndex = mol.offsets[molBins[i].second]+atom;
int newIndex = mol.offsets[i]+atom;
originalIndex[newIndex] = atomIndex[oldIndex];
newPosq[newIndex] = oldPosq[oldIndex];
if (useMixedPrecision)
......@@ -1259,8 +1258,8 @@ void OpenCLContext::reorderAtomsImpl() {
posqCorrection->upload(newPosqCorrection);
velm->upload(newVelm);
atomIndexDevice->upload(atomIndex);
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
for (auto listener : reorderListeners)
listener->execute();
}
void OpenCLContext::addReorderListener(ReorderListener* listener) {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ ab8f1021
This diff is collapsed.
platforms/reference/src/ReferenceKernels.cpp
View file @ ab8f1021
......@@ -159,8 +159,8 @@ static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<
const Lepton::Operation& op = node.getOperation();
if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("Unknown variable in expression: "+op.getName());
for (int i = 0; i < (int) node.getChildren().size(); i++)
validateVariables(node.getChildren()[i], variables);
for (auto& child : node.getChildren())
validateVariables(child, variables);
}
/**
......@@ -214,8 +214,8 @@ void ReferenceCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context,
}
else
savedForces = forceData;
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
extractEnergyParameterDerivatives(context)[iter->first] = 0;
for (auto& param : context.getParameters())
extractEnergyParameterDerivatives(context)[param.first] = 0;
}
double ReferenceCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
......@@ -466,8 +466,8 @@ double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool in
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
bond.setPeriodic(extractBoxVectors(context));
......@@ -600,8 +600,8 @@ double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool i
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
customAngle.setPeriodic(extractBoxVectors(context));
......@@ -870,8 +870,8 @@ double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
customTorsion.setPeriodic(extractBoxVectors(context));
......@@ -1165,8 +1165,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
// Record information for the long range correction.
......@@ -1208,11 +1208,11 @@ double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bo
if (interactionGroups.size() > 0)
ixn.setInteractionGroups(interactionGroups);
bool globalParamsChanged = false;
for (int i = 0; i < (int) globalParameterNames.size(); i++) {
double value = context.getParameter(globalParameterNames[i]);
if (globalParamValues[globalParameterNames[i]] != value)
for (auto& name : globalParameterNames) {
double value = context.getParameter(name);
if (globalParamValues[name] != value)
globalParamsChanged = true;
globalParamValues[globalParameterNames[i]] = value;
globalParamValues[name] = value;
}
if (useSwitchingFunction)
ixn.setUseSwitchingFunction(switchingDistance);
......@@ -1459,8 +1459,8 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
}
double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1477,8 +1477,8 @@ double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool incl
ixn.setUseCutoff(nonbondedCutoff, *neighborList);
}
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn.calculateIxn(numParticles, posData, particleParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
......@@ -1593,8 +1593,8 @@ double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, boo
boxVectors = extractBoxVectors(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
ReferenceCustomExternalIxn force(energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ, parameterNames, globalParameters);
for (int i = 0; i < numParticles; ++i)
force.calculateForce(particles[i], posData, particleParamArray[i], forceData, includeEnergy ? &energy : NULL);
......@@ -1699,8 +1699,8 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
}
double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1710,8 +1710,8 @@ double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool i
ixn->setPeriodic(extractBoxVectors(context));
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
ixn->calculatePairIxn(posData, donorParamArray, acceptorParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL);
return energy;
}
......@@ -1803,8 +1803,8 @@ void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
}
double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1812,8 +1812,8 @@ double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context,
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
......@@ -1893,8 +1893,8 @@ void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
for (auto& function : functions)
delete function.second;
}
double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1902,8 +1902,8 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
......@@ -1966,8 +1966,8 @@ double ReferenceCalcCustomManyParticleForceKernel::execute(ContextImpl& context,
vector<Vec3>& forceData = extractForces(context);
double energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
for (auto& name : globalParameterNames)
globalParameters[name] = context.getParameter(name);
if (nonbondedMethod == CutoffPeriodic) {
Vec3* boxVectors = extractBoxVectors(context);
double minAllowedSize = 2*cutoffDistance;
......@@ -2232,8 +2232,8 @@ void ReferenceIntegrateCustomStepKernel::initialize(const System& system, const
for (int i = 0; i < numParticles; ++i)
masses[i] = system.getParticleMass(i);
perDofValues.resize(integrator.getNumPerDofVariables());
for (int i = 0; i < (int) perDofValues.size(); i++)
perDofValues[i].resize(numParticles);
for (auto& values : perDofValues)
values.resize(numParticles);
// Create the computation objects.
......
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