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Commit 08e8b206 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1769 from peastman/loops 

Use C++11 style loops
parents 55ee0b9f 083bc501
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Showing with 113 additions and 184 deletions
serialization/src/CustomIntegratorProxy.cpp
View file @ 08e8b206
......@@ -74,45 +74,40 @@ void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
throw OpenMMException("Unsupported version number");
CustomIntegrator* integrator = new CustomIntegrator(node.getDoubleProperty("stepSize"));
const SerializationNode& globalVariablesNode = node.getChildNode("GlobalVariables");
const map<string, string> &globalVariableProp = globalVariablesNode.getProperties();
for(map<string, string>::const_iterator cit = globalVariableProp.begin(); cit != globalVariableProp.end(); cit++) {
integrator->addGlobalVariable(cit->first, globalVariablesNode.getDoubleProperty(cit->first));
}
for (auto& prop : globalVariablesNode.getProperties())
integrator->addGlobalVariable(prop.first, globalVariablesNode.getDoubleProperty(prop.first));
const SerializationNode& perDofVariablesNode = node.getChildNode("PerDofVariables");
const vector<SerializationNode>& perDofVariableList = perDofVariablesNode.getChildren();
int count = 0;
for(vector<SerializationNode>::const_iterator cit=perDofVariableList.begin(); cit != perDofVariableList.end(); cit++, count++) {
const vector<SerializationNode>& perDofVariableVector = cit->getChildren();
integrator->addPerDofVariable(cit->getName(),0);
for (auto& var : perDofVariablesNode.getChildren()) {
integrator->addPerDofVariable(var.getName(), 0);
vector<Vec3> perDofValues;
for(vector<SerializationNode>::const_iterator dit=perDofVariableVector.begin(); dit!=perDofVariableVector.end(); dit++) {
perDofValues.push_back(Vec3(dit->getDoubleProperty("x"),dit->getDoubleProperty("y"),dit->getDoubleProperty("z")));
}
for (auto& child : var.getChildren())
perDofValues.push_back(Vec3(child.getDoubleProperty("x"), child.getDoubleProperty("y"), child.getDoubleProperty("z")));
integrator->setPerDofVariable(count, perDofValues);
count++;
}
const SerializationNode& computationsNode = node.getChildNode("Computations");
const vector<SerializationNode>& computationsList = computationsNode.getChildren();
for(vector<SerializationNode>::const_iterator cit = computationsList.begin(); cit != computationsList.end(); cit++) {
CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(cit->getIntProperty("computationType"));
for (auto& comp : computationsNode.getChildren()) {
CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(comp.getIntProperty("computationType"));
// make sure that the int casts to a valid enum
if(computationType == CustomIntegrator::ComputeGlobal) {
integrator->addComputeGlobal(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
} else if(computationType == CustomIntegrator::ComputePerDof) {
integrator->addComputePerDof(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
} else if(computationType == CustomIntegrator::ComputeSum) {
integrator->addComputeSum(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
} else if(computationType == CustomIntegrator::ConstrainPositions) {
if (computationType == CustomIntegrator::ComputeGlobal) {
integrator->addComputeGlobal(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
} else if (computationType == CustomIntegrator::ComputePerDof) {
integrator->addComputePerDof(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
} else if (computationType == CustomIntegrator::ComputeSum) {
integrator->addComputeSum(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
} else if (computationType == CustomIntegrator::ConstrainPositions) {
integrator->addConstrainPositions();
} else if(computationType == CustomIntegrator::ConstrainVelocities) {
} else if (computationType == CustomIntegrator::ConstrainVelocities) {
integrator->addConstrainVelocities();
} else if(computationType == CustomIntegrator::UpdateContextState) {
} else if (computationType == CustomIntegrator::UpdateContextState) {
integrator->addUpdateContextState();
} else if(computationType == CustomIntegrator::IfBlockStart) {
integrator->beginIfBlock(cit->getStringProperty("computationExpression"));
} else if(computationType == CustomIntegrator::WhileBlockStart) {
integrator->beginWhileBlock(cit->getStringProperty("computationExpression"));
} else if(computationType == CustomIntegrator::BlockEnd) {
integrator->endBlock();
} else if (computationType == CustomIntegrator::IfBlockStart) {
integrator->beginIfBlock(comp.getStringProperty("computationExpression"));
} else if (computationType == CustomIntegrator::WhileBlockStart) {
integrator->beginWhileBlock(comp.getStringProperty("computationExpression"));
} else if (computationType == CustomIntegrator::BlockEnd) {
integrator->endBlock();
} else {
throw(OpenMMException("Custom Integrator Deserialization: Unknown computation type"));
}
......
serialization/src/CustomManyParticleForceProxy.cpp
View file @ 08e8b206
......@@ -84,10 +84,10 @@ void CustomManyParticleForceProxy::serialize(const void* object, SerializationNo
force.getTypeFilter(i, types);
stringstream list;
bool first = true;
for (set<int>::const_iterator iter = types.begin(); iter != types.end(); ++iter) {
for (int type : types) {
if (!first)
list << ",";
list << *iter;
list << type;
first = false;
}
filters.createChildNode("Filter").setIntProperty("index", i).setStringProperty("types", list.str());
......@@ -108,19 +108,14 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
force->setPermutationMode((CustomManyParticleForce::PermutationMode) node.getIntProperty("permutationMode"));
force->setCutoffDistance(node.getDoubleProperty("cutoff"));
const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
const SerializationNode& parameter = perParticleParams.getChildren()[i];
for (auto& parameter : perParticleParams.getChildren())
force->addPerParticleParameter(parameter.getStringProperty("name"));
}
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
const SerializationNode& parameter = globalParams.getChildren()[i];
for (auto& parameter : globalParams.getChildren())
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
const SerializationNode& particles = node.getChildNode("Particles");
vector<double> params(force->getNumPerParticleParameters());
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (auto& particle : particles.getChildren()) {
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
......@@ -130,13 +125,10 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
force->addParticle(params, particle.getIntProperty("type"));
}
const SerializationNode& exclusions = node.getChildNode("Exclusions");
for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
const SerializationNode& exclusion = exclusions.getChildren()[i];
for (auto& exclusion : exclusions.getChildren())
force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
}
const SerializationNode& filters = node.getChildNode("TypeFilters");
for (int i = 0; i < (int) filters.getChildren().size(); i++) {
const SerializationNode& filter = filters.getChildren()[i];
for (auto& filter : filters.getChildren()) {
string typesString = filter.getStringProperty("types");
vector<string> splitTypes;
size_t searchPos = 0, nextPos;
......@@ -146,20 +138,18 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
}
splitTypes.push_back(typesString.substr(searchPos));
set<int> types;
for (int j = 0; j < (int) splitTypes.size(); j++) {
if (splitTypes[j].size() > 0) {
for (auto& t : splitTypes) {
if (t.size() > 0) {
int type;
stringstream(splitTypes[j]) >> type;
stringstream(t) >> type;
types.insert(type);
}
}
force->setTypeFilter(filter.getIntProperty("index"), types);
}
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
for (auto& function : functions.getChildren())
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
return force;
}
catch (...) {
......
serialization/src/CustomNonbondedForceProxy.cpp
View file @ 08e8b206
......@@ -92,11 +92,11 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
std::set<int> set2;
force.getInteractionGroupParameters(i, set1, set2);
SerializationNode& set1node = interactionGroup.createChildNode("Set1");
for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
set1node.createChildNode("Particle").setIntProperty("index", *it);
for (int p : set1)
set1node.createChildNode("Particle").setIntProperty("index", p);
SerializationNode& set2node = interactionGroup.createChildNode("Set2");
for (std::set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
set2node.createChildNode("Particle").setIntProperty("index", *it);
for (int p : set2)
set2node.createChildNode("Particle").setIntProperty("index", p);
}
}
......@@ -114,26 +114,19 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
const SerializationNode& parameter = perParticleParams.getChildren()[i];
for (auto& parameter : perParticleParams.getChildren())
force->addPerParticleParameter(parameter.getStringProperty("name"));
}
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
const SerializationNode& parameter = globalParams.getChildren()[i];
for (auto& parameter : globalParams.getChildren())
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 1) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
for (auto& parameter : energyDerivs.getChildren())
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& particles = node.getChildNode("Particles");
vector<double> params(force->getNumPerParticleParameters());
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (auto& particle : particles.getChildren()) {
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
......@@ -143,13 +136,10 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
force->addParticle(params);
}
const SerializationNode& exclusions = node.getChildNode("Exclusions");
for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
const SerializationNode& exclusion = exclusions.getChildren()[i];
for (auto& exclusion : exclusions.getChildren())
force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
}
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
for (auto& function : functions.getChildren()) {
if (function.hasProperty("type")) {
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
......@@ -158,30 +148,28 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
bool hasInteractionGroups = false; // Older files will be missing this block.
for (int i = 0; i < (int) node.getChildren().size(); i++) {
if (node.getChildren()[i].getName() == "InteractionGroups")
for (auto& child : node.getChildren())
if (child.getName() == "InteractionGroups")
hasInteractionGroups = true;
}
if (hasInteractionGroups) {
const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
for (auto& interactionGroup : interactionGroups.getChildren()) {
// Get set 1.
const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
std::set<int> set1;
for (int j = 0; j < (int) set1node.getChildren().size(); j++)
set1.insert(set1node.getChildren()[j].getIntProperty("index"));
for (auto& child : set1node.getChildren())
set1.insert(child.getIntProperty("index"));
// Get set 2.
const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
std::set<int> set2;
for (int j = 0; j < (int) set2node.getChildren().size(); j++)
set2.insert(set2node.getChildren()[j].getIntProperty("index"));
for (auto& child : set2node.getChildren())
set2.insert(child.getIntProperty("index"));
force->addInteractionGroup(set1, set2);
}
}
......
serialization/src/CustomTorsionForceProxy.cpp
View file @ 08e8b206
......@@ -85,26 +85,19 @@ void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& perTorsionParams = node.getChildNode("PerTorsionParameters");
for (int i = 0; i < (int) perTorsionParams.getChildren().size(); i++) {
const SerializationNode& parameter = perTorsionParams.getChildren()[i];
for (auto& parameter : perTorsionParams.getChildren())
force->addPerTorsionParameter(parameter.getStringProperty("name"));
}
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
const SerializationNode& parameter = globalParams.getChildren()[i];
for (auto& parameter : globalParams.getChildren())
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 2) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
for (auto& parameter : energyDerivs.getChildren())
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& torsions = node.getChildNode("Torsions");
vector<double> params(force->getNumPerTorsionParameters());
for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
const SerializationNode& torsion = torsions.getChildren()[i];
for (auto& torsion : torsions.getChildren()) {
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
......
serialization/src/GBSAOBCForceProxy.cpp
View file @ 08e8b206
......@@ -72,10 +72,8 @@ void* GBSAOBCForceProxy::deserialize(const SerializationNode& node) const {
if (version > 1)
force->setSurfaceAreaEnergy(node.getDoubleProperty("surfaceAreaEnergy"));
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (auto& particle : particles.getChildren())
force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("scale"));
}
}
catch (...) {
delete force;
......
serialization/src/GayBerneForceProxy.cpp
View file @ 08e8b206
......@@ -78,17 +78,13 @@ void* GayBerneForceProxy::deserialize(const SerializationNode& node) const {
force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (auto& particle : particles.getChildren())
force->addParticle(particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"), particle.getIntProperty("xparticle"),
particle.getIntProperty("yparticle"), particle.getDoubleProperty("sx"), particle.getDoubleProperty("sy"), particle.getDoubleProperty("sz"),
particle.getDoubleProperty("ex"), particle.getDoubleProperty("ey"), particle.getDoubleProperty("ez"));
}
const SerializationNode& exceptions = node.getChildNode("Exceptions");
for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
const SerializationNode& exception = exceptions.getChildren()[i];
for (auto& exception : exceptions.getChildren())
force->addException(exception.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
}
}
catch (...) {
delete force;
......
serialization/src/HarmonicAngleForceProxy.cpp
View file @ 08e8b206
......@@ -65,10 +65,8 @@ void* HarmonicAngleForceProxy::deserialize(const SerializationNode& node) const
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& angles = node.getChildNode("Angles");
for (int i = 0; i < (int) angles.getChildren().size(); i++) {
const SerializationNode& angle = angles.getChildren()[i];
for (auto& angle : angles.getChildren())
force->addAngle(angle.getIntProperty("p1"), angle.getIntProperty("p2"), angle.getIntProperty("p3"), angle.getDoubleProperty("a"), angle.getDoubleProperty("k"));
}
}
catch (...) {
delete force;
......
serialization/src/HarmonicBondForceProxy.cpp
View file @ 08e8b206
......@@ -65,10 +65,8 @@ void* HarmonicBondForceProxy::deserialize(const SerializationNode& node) const {
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& bonds = node.getChildNode("Bonds");
for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
const SerializationNode& bond = bonds.getChildren()[i];
for (auto& bond : bonds.getChildren())
force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
}
}
catch (...) {
delete force;
......
serialization/src/NonbondedForceProxy.cpp
View file @ 08e8b206
......@@ -108,15 +108,11 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
}
force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (auto& particle : particles.getChildren())
force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"));
}
const SerializationNode& exceptions = node.getChildNode("Exceptions");
for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
const SerializationNode& exception = exceptions.getChildren()[i];
for (auto& exception : exceptions.getChildren())
force->addException(exception.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("q"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
}
}
catch (...) {
delete force;
......
serialization/src/PeriodicTorsionForceProxy.cpp
View file @ 08e8b206
......@@ -65,11 +65,9 @@ void* PeriodicTorsionForceProxy::deserialize(const SerializationNode& node) cons
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& torsions = node.getChildNode("Torsions");
for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
const SerializationNode& torsion = torsions.getChildren()[i];
for (auto& torsion : torsions.getChildren())
force->addTorsion(torsion.getIntProperty("p1"), torsion.getIntProperty("p2"), torsion.getIntProperty("p3"), torsion.getIntProperty("p4"),
torsion.getIntProperty("periodicity"), torsion.getDoubleProperty("phase"), torsion.getDoubleProperty("k"));
}
}
catch (...) {
delete force;
......
serialization/src/RBTorsionForceProxy.cpp
View file @ 08e8b206
......@@ -65,12 +65,10 @@ void* RBTorsionForceProxy::deserialize(const SerializationNode& node) const {
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& torsions = node.getChildNode("Torsions");
for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
const SerializationNode& torsion = torsions.getChildren()[i];
for (auto& torsion : torsions.getChildren())
force->addTorsion(torsion.getIntProperty("p1"), torsion.getIntProperty("p2"), torsion.getIntProperty("p3"), torsion.getIntProperty("p4"),
torsion.getDoubleProperty("c0"), torsion.getDoubleProperty("c1"), torsion.getDoubleProperty("c2"),
torsion.getDoubleProperty("c3"), torsion.getDoubleProperty("c4"), torsion.getDoubleProperty("c5"));
}
}
catch (...) {
delete force;
......
serialization/src/SerializationNode.cpp
View file @ 08e8b206
......@@ -56,16 +56,16 @@ vector<SerializationNode>& SerializationNode::getChildren() {
}
const SerializationNode& SerializationNode::getChildNode(const std::string& name) const {
for (int i = 0; i < (int) children.size(); i++)
if (children[i].name == name)
return children[i];
for (auto& child : children)
if (child.name == name)
return child;
throw OpenMMException("Unknown child '"+name+"' for node '"+getName()+"'");
}
SerializationNode& SerializationNode::getChildNode(const std::string& name) {
for (int i = 0; i < (int) children.size(); i++)
if (children[i].name == name)
return children[i];
for (auto& child : children)
if (child.name == name)
return child;
throw OpenMMException("Unknown child '"+name+"' for node '"+getName()+"'");
}
......
serialization/src/StateProxy.cpp
View file @ 08e8b206
......@@ -56,11 +56,8 @@ void StateProxy::serialize(const void* object, SerializationNode& node) const {
if ((s.getDataTypes()&State::Parameters) != 0) {
s.getParameters();
SerializationNode& parametersNode = node.createChildNode("Parameters");
map<string, double> stateParams = s.getParameters();
map<string, double>::const_iterator it;
for (it = stateParams.begin(); it!=stateParams.end();it++) {
parametersNode.setDoubleProperty(it->first, it->second);
}
for (auto& param : s.getParameters())
parametersNode.setDoubleProperty(param.first, param.second);
}
if ((s.getDataTypes()&State::Energy) != 0) {
s.getPotentialEnergy();
......@@ -108,17 +105,11 @@ void* StateProxy::deserialize(const SerializationNode& node) const {
int types = 0;
vector<int> arraySizes;
State::StateBuilder builder(outTime);
const vector<SerializationNode>& children = node.getChildren();
for (int j = 0; j < (int) children.size(); j++) {
const SerializationNode& child = children[j];
for (auto& child : node.getChildren()) {
if (child.getName() == "Parameters") {
map<string, double> outStateParams;
// inStateParams is really a <string,double> pair, where string is the name and double is the value
// but we want to avoid casting a string to a double and instead use the built in routines,
map<string, string> inStateParams = child.getProperties();
for (map<string, string>::const_iterator pit = inStateParams.begin(); pit != inStateParams.end(); pit++) {
outStateParams[pit->first] = child.getDoubleProperty(pit->first);
}
for (auto& param : child.getProperties())
outStateParams[param.first] = child.getDoubleProperty(param.first);
builder.setParameters(outStateParams);
}
else if (child.getName() == "Energies") {
......@@ -128,28 +119,22 @@ void* StateProxy::deserialize(const SerializationNode& node) const {
}
else if (child.getName() == "Positions") {
vector<Vec3> outPositions;
for (int i = 0; i < (int) child.getChildren().size(); i++) {
const SerializationNode& particle = child.getChildren()[i];
for (auto& particle : child.getChildren())
outPositions.push_back(Vec3(particle.getDoubleProperty("x"),particle.getDoubleProperty("y"),particle.getDoubleProperty("z")));
}
builder.setPositions(outPositions);
arraySizes.push_back(outPositions.size());
}
else if (child.getName() == "Velocities") {
vector<Vec3> outVelocities;
for (int i = 0; i < (int) child.getChildren().size(); i++) {
const SerializationNode& particle = child.getChildren()[i];
for (auto& particle : child.getChildren())
outVelocities.push_back(Vec3(particle.getDoubleProperty("x"),particle.getDoubleProperty("y"),particle.getDoubleProperty("z")));
}
builder.setVelocities(outVelocities);
arraySizes.push_back(outVelocities.size());
}
else if (child.getName() == "Forces") {
vector<Vec3> outForces;
for (int i = 0; i < (int) child.getChildren().size(); i++) {
const SerializationNode& particle = child.getChildren()[i];
for (auto& particle : child.getChildren())
outForces.push_back(Vec3(particle.getDoubleProperty("x"),particle.getDoubleProperty("y"),particle.getDoubleProperty("z")));
}
builder.setForces(outForces);
arraySizes.push_back(outForces.size());
}
......
serialization/src/SystemProxy.cpp
View file @ 08e8b206
......@@ -129,14 +129,11 @@ void* SystemProxy::deserialize(const SerializationNode& node) const {
}
}
const SerializationNode& constraints = node.getChildNode("Constraints");
for (int i = 0; i < (int) constraints.getChildren().size(); i++) {
const SerializationNode& constraint = constraints.getChildren()[i];
for (auto& constraint : constraints.getChildren())
system->addConstraint(constraint.getIntProperty("p1"), constraint.getIntProperty("p2"), constraint.getDoubleProperty("d"));
}
const SerializationNode& forces = node.getChildNode("Forces");
for (int i = 0; i < (int) forces.getChildren().size(); i++) {
system->addForce(forces.getChildren()[i].decodeObject<Force>());
}
for (auto& force : forces.getChildren())
system->addForce(force.decodeObject<Force>());
}
catch (...) {
delete system;
......
serialization/src/TabulatedFunctionProxies.cpp
View file @ 08e8b206
......@@ -49,8 +49,8 @@ void Continuous1DFunctionProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("min", min);
node.setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Continuous1DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -58,8 +58,8 @@ void* Continuous1DFunctionProxy::deserialize(const SerializationNode& node) cons
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Continuous1DFunction(values, node.getDoubleProperty("min"), node.getDoubleProperty("max"));
}
......@@ -80,8 +80,8 @@ void Continuous2DFunctionProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("ymin", ymin);
node.setDoubleProperty("ymax", ymax);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Continuous2DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -89,8 +89,8 @@ void* Continuous2DFunctionProxy::deserialize(const SerializationNode& node) cons
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Continuous2DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), values,
node.getDoubleProperty("xmin"), node.getDoubleProperty("xmax"), node.getDoubleProperty("ymin"), node.getDoubleProperty("ymax"));
}
......@@ -115,8 +115,8 @@ void Continuous3DFunctionProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("zmin", zmin);
node.setDoubleProperty("zmax", zmax);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Continuous3DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -124,8 +124,8 @@ void* Continuous3DFunctionProxy::deserialize(const SerializationNode& node) cons
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Continuous3DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), node.getIntProperty("zsize"), values,
node.getDoubleProperty("xmin"), node.getDoubleProperty("xmax"), node.getDoubleProperty("ymin"), node.getDoubleProperty("ymax"),
node.getDoubleProperty("zmin"), node.getDoubleProperty("zmax"));
......@@ -140,8 +140,8 @@ void Discrete1DFunctionProxy::serialize(const void* object, SerializationNode& n
vector<double> values;
function.getFunctionParameters(values);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Discrete1DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -149,8 +149,8 @@ void* Discrete1DFunctionProxy::deserialize(const SerializationNode& node) const
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Discrete1DFunction(values);
}
......@@ -166,8 +166,8 @@ void Discrete2DFunctionProxy::serialize(const void* object, SerializationNode& n
node.setDoubleProperty("xsize", xsize);
node.setDoubleProperty("ysize", ysize);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Discrete2DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -175,8 +175,8 @@ void* Discrete2DFunctionProxy::deserialize(const SerializationNode& node) const
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Discrete2DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), values);
}
......@@ -193,8 +193,8 @@ void Discrete3DFunctionProxy::serialize(const void* object, SerializationNode& n
node.setDoubleProperty("ysize", ysize);
node.setDoubleProperty("zsize", zsize);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
for (auto v : values)
valuesNode.createChildNode("Value").setDoubleProperty("v", v);
}
void* Discrete3DFunctionProxy::deserialize(const SerializationNode& node) const {
......@@ -202,7 +202,7 @@ void* Discrete3DFunctionProxy::deserialize(const SerializationNode& node) const
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
for (auto& child : valuesNode.getChildren())
values.push_back(child.getDoubleProperty("v"));
return new Discrete3DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), node.getIntProperty("zsize"), values);
}
serialization/src/XmlSerializer.cpp
View file @ 08e8b206
......@@ -115,11 +115,10 @@ void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stre
for (int i = 0; i < depth; i++)
stream << '\t';
stream << '<' << node.getName();
const map<string, string>& properties = node.getProperties();
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
for (auto& prop : node.getProperties()) {
string name, value;
encodeString(iter->first, &name);
encodeString(iter->second, &value);
encodeString(prop.first, &name);
encodeString(prop.second, &value);
stream << ' ' << name << "=\"" << value << '\"';
}
const vector<SerializationNode>& children = node.getChildren();
......@@ -127,8 +126,8 @@ void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stre
stream << "/>\n";
else {
stream << ">\n";
for (int i = 0; i < (int) children.size(); i++)
encodeNode(children[i], stream, depth+1);
for (auto& child : children)
encodeNode(child, stream, depth+1);
for (int i = 0; i < depth; i++)
stream << '\t';
stream << "</" << node.getName() << ">\n";
......
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